The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

Phosphorylation-dependent WRN-RPA interaction promotes recovery of stalled forks at secondary DNA structure

The WRN protein is vital for managing perturbed replication forks. Replication Protein A strongly enhances WRN helicase activity in specific in vitro assays. However, the in vivo significance of RPA binding to WRN has largely remained unexplored. We identify several conserved phosphorylation sites in the acidic domain of WRN targeted by Casein Kinase 2. These phosphorylation sites are crucial for WRN-RPA interaction. Using an unphosphorylable WRN mutant, which lacks the ability to bind RPA, we determine that the WRN-RPA complex plays a critical role in fork recovery after replication stress countering the persistence of G4 structures after fork stalling. However, the interaction between WRN and RPA is not necessary for the processing of replication forks when they collapse. The absence of WRN-RPA binding hampers fork recovery, causing single-strand DNA gaps, enlarged by MRE11, and triggering MUS81-dependent double-strand breaks, which require repair by RAD51 to prevent excessive DNA damage.

The ABC transporter A7 modulates neuroinflammation via NLRP3 inflammasome in Alzheimer's disease mice

BACKGROUND

Specific genetic variants in the ATP-binding cassette transporter A7 locus (ABCA7) are associated with an increased risk of Alzheimer's disease (AD). ABCA7 transports lipids from/across cell membranes, regulates Aβ peptide processing and clearance, and modulates microglial and T-cell functions to maintain immune homeostasis in the brain. During AD pathogenesis, neuroinflammation is one of the key mechanisms involved. Therefore, we wanted to investigate the specific role of ABCA7 in microglial activation via the NLRP3 inflammasome.

METHODS

We developed the first humanized, Cre-inducible ABCA7flx knock-in mouse model, crossbred it with the APPPS1-21 β-amyloidosis model, and generated constitutive ABCA7ko and microglia Cx3cr1-specific conditional ABCA7ko AD mice. The role of ABCA7 was analyzed using histological, biochemical, molecular and mass spectrometry methods.

RESULTS

Constitutive knockout of the Abca7 gene in APPPS1 mice increased the levels of Aβ42 and the number of IBA1+ (microglia) and GFAP+ (astrocytes) cells. Changes in the levels of astrocytes and microglia are associated with the activation of the NLRP3 inflammasome and increased levels of proinflammatory cytokines, such as IL1β and TNFα. Interestingly, microglia-specific ABCA7ko restored Aβ42 peptide levels and IBA1+ and GFAP+ and NLRP3-related gene expression to the original APPPS1 mouse levels. In primary glial cell cultures of APPPS1-hA7ko microglia and APPPS1 astrocytes from newborn pups, we observed that conditioned media from LPS-stimulated microglia was able to induce NLRP3 inflammasome expression and proinflammatory cytokine release in astrocytes.

CONCLUSIONS

Our data suggest that ABCA7 transporters regulate the communication between microglia and astrocytes through the NLRP3 inflammasome and the release of proinflammatory cytokines. This regulation implicates ABCA7 as a key driver ultimately involved in the persistence of the inflammatory response observed in AD.

Longitudinal omics data and preclinical treatment suggest the proteasome inhibitor carfilzomib as therapy for ibrutinib-resistant CLL

Chronic lymphocytic leukemia is a malignant lymphoproliferative disorder for which primary or acquired drug resistance represents a major challenge. To investigate the underlying molecular mechanisms, we generate a mouse model of ibrutinib resistance, in which, after initial treatment response, relapse under therapy occurrs with an aggressive outgrowth of malignant cells, resembling observations in patients. A comparative analysis of exome, transcriptome and proteome of sorted leukemic murine cells during treatment and after relapse suggests alterations in the proteasome activity as a driver of ibrutinib resistance. Preclinical treatment with the irreversible proteasome inhibitor carfilzomib administered upon ibrutinib resistance prolongs survival of mice. Longitudinal proteomic analysis of ibrutinib-resistant patients identifies deregulation in protein post-translational modifications. Additionally, cells from ibrutinib-resistant patients effectively respond to several proteasome inhibitors in co-culture assays. Altogether, our results from orthogonal omics approaches identify proteasome inhibition as potentially attractive treatment for chronic lymphocytic leukemia patients resistant or refractory to ibrutinib.

Synaptic phosphoproteome modifications and cortical circuit dysfunction are linked to the early-stage progression of alpha-synuclein aggregation

Cortical dysfunction is increasingly recognized as a major contributor to the non-motor symptoms associated with Parkinson's disease (PD) and other synucleinopathies. Although functional alterations in cortical circuits have been observed in preclinical PD models, the underlying molecular mechanisms are unclear. To bridge this knowledge gap, we investigated tissue-level changes in the cortices of rats and mice treated with alpha-synuclein (aSyn) seeds using a multi-omics approach. Our study revealed significant phosphoproteomic changes, but not global proteomic or lipid profiling changes, in the rat sensorimotor cortex 3 months after intrastriatal injection with aSyn preformed fibrils (PFFs). Gene ontology analysis of the phosphoproteomic data indicated that PFF administration impacted pathways related to synaptic transmission and cytoskeletal organization. Similar phosphoproteomic perturbations were observed in the sensorimotor cortex of mice injected intrastriatally or intracortically with aSyn PFFs. Functional analyses demonstrated increased neuronal firing rates and enhanced spike-spike coherence in the sensorimotor cortices of PFF-treated mice, indicating seed-dependent cortical circuit dysfunction. Bioinformatic analysis of the altered phosphosites suggested the involvement of several kinases, including casein kinase-2 (CK2), which has been previously implicated in PD pathology. Collectively, these findings highlight the importance of phosphorylation-mediated signaling pathways in the cortical response to aSyn pathology spread in PD and related synucleinopathies, setting the stage for developing new therapeutic strategies.

Microbial magnetite oxidation via MtoAB porin-multiheme cytochrome complex in Sideroxydans lithotrophicus ES-1

Most of Earth's iron is mineral-bound, but it is unclear how and to what extent iron-oxidizing microbes can use solid minerals as electron donors. A prime candidate for studying mineral-oxidizing growth and pathways is Sideroxydans lithotrophicus ES-1, a robust, facultative iron oxidizer with multiple possible iron oxidation mechanisms. These include Cyc2 and Mto pathways plus other multiheme cytochromes and cupredoxins, and so we posit that the mechanisms may correspond to different Fe(II) sources. Here, S. lithotrophicus ES-1 was grown on dissolved Fe(II)-citrate and magnetite. S. lithotrophicus ES-1 oxidized all dissolved Fe2+ released from magnetite, and continued to build biomass when only solid Fe(II) remained, suggesting it can utilize magnetite as a solid electron donor. Quantitative proteomic analyses of S. lithotrophicus ES-1 grown on these substrates revealed global proteome remodeling in response to electron donor and growth state and uncovered potential proteins and metabolic pathways involved in the oxidation of solid magnetite. While the Cyc2 iron oxidases were highly expressed on both dissolved and solid substrates, MtoA was only detected during growth on solid magnetite, suggesting this protein helps catalyze oxidation of solid minerals in S. lithotrophicus ES-1. A set of cupredoxin domain-containing proteins were also specifically expressed during solid iron oxidation. This work demonstrated the iron oxidizer S. lithotrophicus ES-1 utilized additional extracellular electron transfer pathways when growing on solid mineral electron donors compared to dissolved Fe(II).

Triple-negative breast cancer modifies the systemic immune landscape and alters neutrophil functionality

Cancer disrupts intratumoral innate-adaptive immune crosstalk, but how the systemic immune landscape evolves during breast cancer progression remains unclear. We profiled circulating immune cells in stage I-III and stage IV triple-negative breast cancer (TNBC) patients and healthy donors (HDs). Metastatic TNBC (mTNBC) patients had reduced T cells, dendritic cells, and differentiated B cells compared to non-metastatic TNBC patients and HDs, partly linked to prior chemotherapy. Vδ1 γδ T cells from mTNBC patients produced more IL17 than those from HDs. Chemotherapy-naïve mTNBC patients showed increased classical monocytes and neutrophils. Transcriptional, proteomic, and functional analyses revealed that neutrophils in mTNBC exhibited enhanced migratory capacity, elevated granule proteins, and higher ROS production. Some immune changes, such as reduced non-switched B cells and heightened neutrophil migration, were evident in earlier TNBC stages. This study comprehensively maps systemic immunity in TNBC, guiding future research on patient stratification and immunomodulation strategies.

Perinatal dysfunction of innate immunity in cystic fibrosis

In patients with cystic fibrosis (CF), repeated cycles of infection and inflammation eventually lead to fatal lung damage. Although diminished mucus clearance can be restored by highly effective CFTR modulator therapy, inflammation and infection often persist. To elucidate the role of the innate immune system in CF etiology, we investigated a CF pig model and compared these results with those for preschool children with CF. In newborn CF pigs, we observed changes in lung immune cell composition before the onset of infection that were dominated by increased monocyte infiltration, whereas neutrophil numbers remained constant. Flow cytometric and transcriptomic profiling revealed that the infiltrating myeloid cells displayed a more immature status. Cells with comparably immature transcriptomic profiles were enriched in the blood of CF pigs at birth as well as in preschool children with CF. This pattern coincided with decreased CD16 expression in the myeloid cells of both pigs and humans, which translated into lower phagocytic activity and reduced production of reactive oxygen species in both species. These results were indicative of a congenital, translationally conserved, and functionally relevant aberration of the immune system in CF. In newborn wild-type pigs, CFTR transcription in immune cells, including lung-derived and circulating monocytes, isolated from the bone marrow, thymus, spleen, and blood was below the detection limits of highly sensitive assays, suggesting an indirect etiology of the observed effects. Our findings highlight the need for additional immunological treatments to target innate immune deficits in patients with CF.

Pupylation-based proximity labeling reveals regulatory factors in cellulose biosynthesis in Arabidopsis

Knowledge about how and where proteins interact provides a pillar for cell biology. Protein proximity-labeling has emerged as an important tool to detect protein interactions. Biotin-related proximity labeling approaches are by far the most commonly used but may have labeling-related drawbacks. Here, we use pupylation-based proximity labeling (PUP-IT) as a tool for protein interaction detection in plants. We show that PUP-IT readily confirmed protein interactions for several known protein complexes across different types of plant hosts and that the approach increased detection of specific interactions as compared to biotin-based proximity labeling systems. To further demonstrate the power of PUP-IT, we used the system to identify protein interactions of the protein complex that underpin cellulose synthesis in plants. Apart from known complex components, we identified the ARF-GEF BEN1 (BFA-VISUALIZED ENDOCYTIC TRAFFICKING DEFECTIVE1). We show that BEN1 contributes to cellulose synthesis by regulating both clathrin-dependent and -independent endocytosis of the cellulose synthesis protein complex from the plasma membrane. Our results highlight PUP-IT as a powerful proximity labeling system to identify protein interactions in plant cells.

Dengue virus and Zika virus alter endoplasmic reticulum-mitochondria contact sites to regulate respiration and apoptosis

During infection, dengue virus (DENV) and Zika virus (ZIKV), two (ortho)flaviviruses of public health concern worldwide, induce alterations of mitochondria morphology to favor viral replication, suggesting a viral co-opting of mitochondria functions. Here, we performed an extensive transmission electron microscopy-based quantitative analysis to demonstrate that both DENV and ZIKV alter endoplasmic reticulum-mitochondria contact sites (ERMC). This correlated at the molecular level with an impairment of ERMC tethering protein complexes located at the surface of both organelles. Furthermore, virus infection modulated the mitochondrial oxygen consumption rate. Consistently, metabolomic and mitoproteomic analyses revealed a decrease in the abundance of several metabolites of the Krebs cycle and changes in the stoichiometry of the electron transport chain. Most importantly, ERMC destabilization by protein knockdown increased virus replication while dampening ZIKV-induced apoptosis. Overall, our results support the notion that flaviviruses hijack ERMCs to generate a cytoplasmic environment beneficial for sustained and efficient replication.

An accessible workflow for high-sensitivity proteomics using parallel accumulation-serial fragmentation (PASEF)

Deep and accurate proteome analysis is crucial for understanding cellular processes and disease mechanisms; however, it is challenging to implement in routine settings. In this protocol, we combine a robust chromatographic platform with a high-performance mass spectrometric setup to enable routine yet in-depth proteome coverage for a broad community. This entails tip-based sample preparation and pre-formed gradients (Evosep One) combined with a trapped ion mobility time-of-flight mass spectrometer (timsTOF, Bruker). The timsTOF enables parallel accumulation-serial fragmentation (PASEF), in which ions are accumulated and separated by their ion mobility, maximizing ion usage and simplifying spectra. Combined with data-independent acquisition (DIA), it offers high peak sampling rates and near-complete ion coverage. Here, we explain how to balance quantitative accuracy, specificity, proteome coverage and sensitivity by choosing the best PASEF and DIA method parameters. The protocol describes how to set up the liquid chromatography-mass spectrometry system and enables PASEF method generation and evaluation for varied samples by using the py_diAID tool to optimally position isolation windows in the mass-to-charge and ion mobility space. Biological projects (e.g., triplicate proteome analysis in two conditions) can be performed in 3 d with ~3 h of hands-on time and minimal marginal cost. This results in reproducible quantification of 7,000 proteins in a human cancer cell line in quadruplicate 21-min injections and 29,000 phosphosites for phospho-enriched quadruplicates. Synchro-PASEF, a highly efficient, specific and novel scan mode, can be analyzed by Spectronaut or AlphaDIA, resulting in superior quantitative reproducibility because of its high sampling efficiency.

Proteomics of the Dark-Ventral-Patch Sexual Signal in Male Red Deer

Sexual signals in animals encompass a variety of forms including visual, acoustic, and chemical signals that are fundamental for intra- and interspecific communication, including sexual selection processes. Among these, odor signals play a critical role. Chemical compounds involved in sexual signaling vary in nature, with lipids and proteins being particularly important. In the male Iberian red deer (Cervus elaphus hispanicus), the dark ventral patch has been identified as a key sexual signal during mating competition, associated with specific chemical compounds deposited during urination. Hair plays a significant role in this signaling due to its ability to retain compounds on the scales of the hair cuticle. In this study, we used a shotgun proteomic approach to investigate whether the ventral patch hair retains proteins on its surface that could reveal metabolic and cell-signaling adaptations potentially related to reproductive activity. Characterization of the origin and functionality of the proteins found in the hair of the dark ventral patch of male red deer, and their relationship to distinct metabolic pathways, provides an initial understanding of the potential role of these compounds in chemical communication in red deer intrasexual competition for mates.

A homo-FRET assay for patatin-specific proteolytic activity

The potato protein patatin embeds bioactive peptides that require targeted hydrolysis to be released as promising food additives. This study presents a patatin-specific protease assay for assessing a wide range of protease activities in high-throughput format. Conjugating patatin to the amine reactive fluorogenic BODIPY FL dye provided a stable protease substrate with efficient homo-FRET quenching at a low degree (7-8) of labeling. Compared to commercial BODIPY-casein, BODIPY-patatin provided higher fluorescence enhancement (by de-quenching) at high protease concentrations, while the sensitivity was generally comparable for both highly specific (e.g. Trypsin) and industrial relevant proteases (e.g. Alcalase and Neutrase) at low doses. For Chymotrypsin, BODIPY-patatin provided a 39 % response improvement at 5 ng dose. A peptide-centric analysis of mass spectrometry-based bottom-up proteomics data identified several BODIPY-labeling sites with varying occupancies in patatin, indicating heterogenous labeling under the applied conjugation conditions. BODIPY-labeled patatin complements commercial BODIPY-labeled casein as a globular, plant-based alternative for screening of proteolytic activity.

Modification of peroxidase activity and proteome in maize exposed to cadmium in the presence of galactoglucomannan oligosaccharides

We tested the effects of galactoglucomannan oligosaccharides (GGMOs) and/or cadmium (Cd) on peroxidase activity and the proteome in maize (Zea mays L.) roots and leaves. Our previous work confirmed that GGMOs ameliorate the symptoms of Cd stress in seedlings. Here, the plants were hydroponically cultivated for 7 days, and the protein content and peroxidase activity were estimated in intracellular, neutral cell wall, and acidic cell wall protein fractions. The peroxidase activity varied between the plant organs as well as among the fractions and treatments. The GGMOs in the presence of Cd did not significantly influence content of peroxidases but modulated their activity, which implies posttranslational regulation. The changes in the content of various proteins (e.g., related to the defence reactions, cell wall structure/metabolism, and activation of plant hormones) caused by GGMOs and Cd indicate possible protective mechanisms that improve the vitality of maize seedlings exposed to metal stress. GGMOs partially reverted Cd-induced protein disbalance, which was a reoccurring phenomenon of mitigation in leaves.

Efficient protein extraction for assessing food allergy risk in complex alternative protein matrices

Allergy to novel food proteins, due to diverse ingredients and innovative food processing technologies employed to achieve desired functional properties, is a major safety concern. Current allergy testing methods (ELISA and mass spectrometry) depend on high-quality protein extracts, meaning existing methods are often tailored to specific matrices. Therefore, a more efficient and general protein extraction method is desirable for comprehensive allergy risk assessment. Here, we developed a highly efficient and reproducible protein extraction method which achieved at least 80 % efficiency across several food matrices. Proteomics analysis of a plant-based meat using our optimized extraction method showed that higher extraction efficiency improved reproducibility of identified proteins. Moreover, higher protein extraction efficiency resulted in increased abundances of individual allergenic proteins. This underscores the relevance of our method for more accurate measurements of allergenic protein concentrations in allergy risk assessments.

Robust collection and processing for label-free single voxel proteomics

With advanced mass spectrometry (MS)-based proteomics, genome-scale proteome coverage can be achieved from bulk tissues. However, such bulk measurement lacks spatial resolution and obscures tissue heterogeneity, precluding proteome mapping of tissue microenvironment. Here we report an integrated wet collection of single microscale tissue voxels and Surfactant-assisted One-Pot voxel processing method termed wcSOP for robust label-free single voxel proteomics. wcSOP capitalizes on buffer droplet-assisted wet collection of single voxels dissected by LCM to the tube cap and SOP voxel processing in the same collection cap. This method enables reproducible, label-free quantification of approximately 900 and 4600 proteins for single voxels at 20 µm × 20 µm × 10 µm (~1 cell region) and 200 µm × 200 µm × 10 µm (~100 cell region) from fresh frozen human spleen tissue, respectively. It can reveal spatially resolved protein signatures and region-specific signaling pathways. Furthermore, wcSOP-MS is demonstrated to be broadly applicable for OCT-embedded and FFPE human archived tissues as well as for small-scale 2D proteome mapping of tissues at high spatial resolutions. wcSOP-MS may pave the way for routine robust single voxel proteomics and spatial proteomics.

Integrated Multi-Omics Analyses of Synaptosomes Revealed Synapse-Centered Novel Targets in Alzheimer's Disease

Synapse dysfunction is an early event in Alzheimer's disease (AD) caused by various factors such as Amyloid beta, p-tau, inflammation, and aging. However, the exact molecular mechanism of synapse dysfunction in AD is largely unknown. To understand this, we comprehensively analyzed the synaptosome fraction in postmortem brain samples from AD patients and cognitively normal individuals. We conducted high-throughput transcriptomic analyses to identify changes in microRNA (miRNA) and mRNA levels in synaptosomes extracted from the brains of both unaffected individuals and those with Alzheimer's disease (AD). Additionally, we performed mass spectrometry analysis of synaptosomal proteins in the same sample group. These analyses revealed significant differences in the levels of miRNAs, mRNAs, and proteins between the groups. To further understand the pathways or molecules involved, we used an integrated omics approach and studied the molecular interactions of deregulated synapse miRNAs, mRNAs, and proteins in the samples from individuals with AD and the control group, which demonstrated the impact of deregulated miRNAs on their target mRNAs and proteins. Furthermore, the DIABLO analysis highlighted complex relationships between mRNAs, miRNAs, and proteins that could be key in understanding the pathophysiology of AD. Our study identified synapse-centered novel candidates that could be critical in restoring synapse dysfunction in AD.

Evaluation of Exosomal Proteins as Potential Biomarkers from RBC Stages of Plasmodium falciparum 3D7

Falciparum malaria relies extensively on cell-to-cell communication, and earlier research on the function of exosomal proteins derived from infected red blood cells (iRBCs) has been classified into numerous important roles. In this study, the exosomes were derived from Pf3D7-iRBCs cultured in vitro during synchronized trophozoite stages. The isolated exosomes were assessed using NTA, FE-SEM, and flow cytometry. Our study reported heterogeneous populations of exosomes during the infection. Additionally, label-free quantification based on LC/MS-MS for protein profiling revealed the presence of both parasitic and host (RBC) proteins; out of a total of 124 proteins detected, 20 Pf3D7 proteins and 80 RBC proteins were identified. Exosomal RBC protein expression is different in cRBCs-Exo and iRBCs-Exo, which shows how the parasite and RBCs interact with each other. Functional classification reported that the majority of these Pf3D7 proteins are uncharacterized with unknown functions, few of which are involved in biological processes such as regulation of complement activation, response to external stimuli, immune system-mediated signaling pathway, protein processing, etc. Hence, studying these exosomal proteins and comparing them to previous research has helped us understand how exosomes help cells to communicate in malaria. It may also reveal new potential biomarkers for diagnostic methods or therapies for malaria.

The RING Finger E3 Ligase RNF25 Protects DNA Replication Forks Independently of its Canonical Roles in Ubiquitin Signaling

The DNA damage response (DDR) mechanisms that allow cells to tolerate DNA replication stress are critically important for genome stability and cell viability. Using an unbiased genetic screen we identify a role for the RING finger E3 ubiquitin ligase RNF25 in promoting DNA replication stress tolerance. In response to DNA replication stress, RNF25-deficient cells generate aberrantly high levels of single-stranded DNA (ssDNA), accumulate in S-phase and show reduced mitotic entry. Using single-molecule DNA fiber analysis, we show that RNF25 protects reversed DNA replication forks generated by the fork remodeler HLTF from nucleolytic degradation by MRE11 and CtIP. Mechanistically, RNF25 interacts with the replication fork protection factor REV7 and recruits REV7 to nascent DNA after replication stress. The role of RNF25 in protecting replication forks is fully separable from its canonical functions in ubiquitin conjugation. This work reveals the RNF25-REV7 signaling axis as an important protective mechanism in cells experiencing replication stress.

The protein cargo of extracellular vesicles correlates with the epigenetic aging clock of exercise sensitive DNAmFitAge

Extracellular vesicles (EVs) are implicated in inter-organ communication, which becomes particularly relevant during aging and exercise. DNA methylation-based aging clocks reflect lifestyle and environmental factors, while regular exercise is known to induce adaptive responses, including epigenetic adaptations. Twenty individuals with High-fitness (aged 57.7 ± 9.8 years) and twenty Medium-Low-fitness (aged 57.5 ± 9.7 years) subjects provided blood samples. EVs were isolated from the samples using a size exclusion chromatography (SEC)-based method, and their protein content was analyzed by mass spectrometry (MS). Acceleration of the biological age estimator DNAmFitAge (AgeAccelFit) was associated with the protein cargo of EVs, whereas PhenoAge and GrimAge acceleration did not show a significant relationship. This finding suggests that the epigenetic aging-modulating role of exercise may involve inter-organ communication via EVs. Set Enrichment Analysis was performed to identify enriched Gene Ontology (GO) terms for sets of proteins that were either correlated with AgeAccelFit or detected exclusively in individuals with high levels of aerobic fitness. The protein cargo of EVs further suggests that inter-organ communication influences inflammation, the immune system, cellular repair, adhesion, metabolism and coagulation. Our findings help to understand the preventive role of exercise, which could be mediated in part by EVs.

Patient-Derived Xenografts of Triple-Negative Breast Cancer Enable Deconvolution and Prediction of Chemotherapy Responses

Combination chemotherapy remains essential for clinical management of triple-negative breast cancer (TNBC). Consequently, responses to multiple single agents cannot be delineated at the single patient level, even though some patients might not require all drugs in the combination. Herein, we conduct multi-omic analyses of orthotopic TNBC patient-derived xenografts (PDXs) treated with single agent carboplatin, docetaxel, or the combination. Combination responses were usually no better than the best single agent, with enhanced response in only ~13% of PDX, and apparent antagonism in a comparable percentage. Single-omic comparisons showed largely non-overlapping results between genes associated with single agent and combination treatments that could be validated in independent patient cohorts. Multi-omic analyses of PDXs identified agent-specific biomarkers/biomarker combinations, nominating high Cytokeratin-5 (KRT5) as a general marker of responsiveness. Notably, integrating proteomic with transcriptomic data improved predictive modeling of pathologic complete response to combination chemotherapy. PDXs refractory to all treatments were enriched for signatures of dysregulated mitochondrial function. Targeting this process indirectly in a PDX with HDAC inhibition plus chemotherapy in vivo overcomes chemoresistance. These results suggest possible resistance mechanisms and therapeutic strategies in TNBC to overcome chemoresistance, and potentially allow optimization of chemotherapeutic regimens.

Challenges and Insights in Absolute Quantification of Recombinant Therapeutic Antibodies by Mass Spectrometry: An Introductory Review

This review describes mass spectrometry (MS)-based approaches for the absolute quantification of therapeutic monoclonal antibodies (mAbs), focusing on technical challenges in sample treatment and calibration. Therapeutic mAbs are crucial for treating cancer and inflammatory, infectious, and autoimmune diseases. We trace their development from hybridoma technology and the first murine mAbs in 1975 to today's chimeric and fully human mAbs. With increasing commercial relevance, the absolute quantification of mAbs, traceable to an international standard system of units (SI units), has attracted attention from science, industry, and national metrology institutes (NMIs). Quantification of proteotypic peptides after enzymatic digestion using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) has emerged as the most viable strategy, though methods targeting intact mAbs are still being explored. We review peptide-based quantification, focusing on critical experimental steps like denaturation, reduction, alkylation, choice of digestion enzyme, and selection of signature peptides. Challenges in amino acid analysis (AAA) for quantifying pure mAbs and peptide calibrators, along with software tools for targeted MS data analysis, are also discussed. Short explanations within each chapter provide newcomers with an overview of the field's challenges. We conclude that, despite recent progress, further efforts are needed to overcome the many technical hurdles along the quantification workflow and discuss the prospects of developing standardized protocols and certified reference materials (CRMs) for this goal. We also suggest future applications of newer technologies for absolute mAb quantification.

Tandem mass tag-based proteomic analysis of granulosa and theca interna cells of the porcine ovarian follicle following in vitro treatment with vitamin D3 and insulin alone or in combination

This study was performed to investigate the proteomic basis underlying the interaction between vitamin D3 (VD) and insulin (I) within ovarian follicle using the pig as a model. Porcine antral follicles were incubated in vitro for 12 h with VD alone and I alone or in combination (VD + I) or with no treatment as the control (C). In total, 7690 and 7467 proteins were identified in the granulosa and theca interna compartments, respectively. Comparative proteomic analysis revealed 97 differentially abundant proteins (DAPs) within the granulosa layer and 11 DAPs within the theca interna layer. In the granulosa compartment, VD affected proteome leading to the promotion of cell proliferation, whereas I influenced mainly proteins related to cellular adhesion. The VD + I treatment induced granulosa cell proliferation probably via the DAPs involved in DNA synthesis and the cell cycle regulation. In the theca interna layer, VD alone or in co-treatment with I affected DAPs associated with cholesterol transport and lipid and steroid metabolic processes that was further confirmed by diminished lipid droplet accumulation. SIGNIFICANCE: The application of quantitative proteomics demonstrated for the first time the complexity of VD and I interactions in porcine ovarian follicle, providing a framework for understanding the molecular mechanisms underlying their cross-talk. Although identified DAPs were related to crucial ovarian processes, including the granulosa cell proliferation and cholesterol transport in the theca interna layer, novel molecular pathways underlying these processes have been proposed. The identified unique proteins may serve as indicators of VD and I interactions in both follicle layers, and could be useful biomarkers of ovarian pathologies characterized by impaired VD and I levels, such as polycystic ovary syndrome.

Intraspecific venom variation in the Iberian asp viper (Vipera aspis zinnikeri) across natural and intensive agricultural habitats

Snake venom composition varies at different levels. To date, comparative venom studies have seldom taken into account the role of habitat type in the occurrence of snake venom variation. Here we investigated the presence of venom variation across different populations of the Iberian asp viper (Vipera aspis zinnikeri) inhabiting two contrasting habitats: natural vs. intensive agricultural. We used shotgun proteomics to describe the protein composition of the venoms of six adults from two distinct localities. Furthermore, to test whether local conditions and habitat can alter venom composition in this taxon, we compared the SDS-PAGE profiles of 40 adult venoms from six populations, three in natural habitats and three in intensive agricultural environments. The venoms were composed of 21 toxin families, of which five (CTL, PLA2, VEGF, svSP, and svMP) comprised 69-82 % of each proteome. The relative abundances of toxin families varied considerably at inter- and intra-population levels. Linear regression performed on non-metric multidimensional scaling values showed a significant effect of locality of origin and habitat type on the differences detected between individual SDS-PAGE venom profiles. Our results suggest the presence of regional variation in V. a. zinnikeri venom, potentially reinforcing the role of local pressures in shaping snake venom composition. SIGNIFICANCE: This work provides the first proteomic characterization of the venom of the Iberian asp viper, Vipera aspis zinnikeri, obtained by means of shotgun proteomics. The statistical analysis of 40 individual SDS-PAGE venom profiles highlights that venom variation in this taxon can be associated with geographical origin and habitat type of the area where each viper was collected. Our results suggest the presence of regional variation in V. a. zinnikeri venom, reinforcing the role that local pressures may play as drivers of snake venom variation.

Multi-omics reveals the mechanism of Trimethylamine N-oxide derived from gut microbiota inducing liver fatty of dairy cows

BACKGROUND

Trimethylamine N-oxide (TMAO) is a metabolite produced by gut microbiota, and its potential impact on lipid metabolism in mammals has garnered widespread attention in the scientific community. Bovine fatty liver disease, a metabolic disorder that severely affects the health and productivity of dairy cows, poses a significant economic burden on the global dairy industry. However, the specific role and pathogenesis of TMAO in bovine fatty liver disease remain unclear, limiting our understanding and treatment of the condition. This study aims to construct a bovine fatty liver cell model using an integrated approach that combines transcriptomic, proteomic, and metabolomic data. The objective is to investigate the impact of TMAO on lipid metabolism at the molecular level and explore its potential regulatory mechanisms.

RESULTS

We established an in vitro bovine fatty liver cell model and conducted a comprehensive analysis of cells treated with TMAO using high-throughput omics sequencing technologies. Bioinformatics methods were employed to delve into the regulatory effects on lipid metabolism, and several key genes were validated through RT-qPCR. Treatment with TMAO significantly affected 4790 genes, 397 proteins, and 137 metabolites. KEGG enrichment analysis revealed that the significantly altered molecules were primarily involved in pathways related to the pathology of fatty liver disease, such as metabolic pathways, insulin resistance, hepatitis B, and the AMPK signaling pathway. Moreover, through joint analysis, we further uncovered that the interaction between TMAO-mediated AMPK signaling and oxidative phosphorylation pathways might be a key mechanism promoting lipid accumulation in the liver.

CONCLUSIONS

Our study provides new insights into the role of TMAO in the pathogenesis of bovine fatty liver disease and offers a scientific basis for developing more effective treatment strategies.

Aminoglycoside tolerance in Vibrio cholerae engages translational reprogramming associated with queuosine tRNA modification

Tgt is the enzyme modifying the guanine (G) in tRNAs with GUN anticodon to queuosine (Q). tgt is required for optimal growth of Vibrio cholerae in the presence of sub-lethal aminoglycoside concentrations. We further explored here the role of the Q34 in the efficiency of codon decoding upon tobramycin exposure. We characterized its impact on the overall bacterial proteome, and elucidated the molecular mechanisms underlying the effects of Q34 modification in antibiotic translational stress response. Using molecular reporters, we showed that Q34 impacts the efficiency of decoding at tyrosine TAT and TAC codons. Proteomics analyses revealed that the anti-SoxR factor RsxA is better translated in the absence of tgt. RsxA displays a codon bias toward tyrosine TAT and overabundance of RsxA leads to decreased expression of genes belonging to SoxR oxidative stress regulon. We also identified conditions that regulate tgt expression. We propose that regulation of Q34 modification in response to environmental cues leads to translational reprogramming of transcripts bearing a biased tyrosine codon usage. In silico analysis further identified candidate genes which could be subject to such translational regulation, among which DNA repair factors. Such transcripts, fitting the definition of modification tunable transcripts, are central in the bacterial response to antibiotics.

LncPepAtlas: a comprehensive resource for exploring the translational landscape of long non-coding RNAs

Long non-coding RNAs were commonly viewed as non-coding elements. However, they are increasingly recognized for their ability to be translated into proteins, thereby playing a significant role in various cellular processes and diseases. With developments in biotechnology and computational algorithms, a range of novel approaches are being applied to investigate the translation of long non-coding RNA (lncRNAs). Herein, we developed the LncPepAtlas database (http://www.cnitbiotool.net/LncPepAtlas/), which aims to compile multiple evidences for the translation of lncRNAs and annotations for the upstream regulation of lncRNAs across various species. LncPepAtlas integrated compelling evidence from nine distinct sources for the translation of lncRNAs. These include a dataset comprising 2631 publicly available Ribo-seq samples from nine species, which has been collected and analysed. LncPepAtlas offers extensive annotation for lncRNA upstream regulation and expression profiles across various cancers, tissues or cell lines at transcriptional and translational levels. Importantly, it enables novel antigen predictions for lncRNA-encoded peptides. By identifying numerous peptide candidates that could potentially bind to major histocompatibility complex class I and II molecules, this work may provide new insights into cancer immunotherapy. The function of peptides were inferred by aligning them with experimentally detected proteins. LncPepAtlas aims to become a convenient resource for exploring translatable lncRNAs.

Investigating proteogenomic divergence in patient-derived xenograft models of ovarian cancer

Within ovarian cancer research, patient-derived xenograft (PDX) models recapitulate histologic features and genomic aberrations found in original tumors. However, conflicting data from published studies have demonstrated significant transcriptional differences between PDXs and original tumors, challenging the fidelity of these models. We employed a quantitative mass spectrometry-based proteomic approach coupled with generation of patient-specific databases using RNA-seq data to investigate the proteogenomic landscape of serially-passaged PDX models established from two patients with distinct subtypes of ovarian cancer. We demonstrate that the utilization of patient-specific databases guided by transcriptional profiles increases the depth of human protein identification in PDX models. Our data show that human proteomes of serially passaged PDXs differ significantly from their patient-derived tumor of origin. Analysis of differentially abundant proteins revealed enrichment of distinct biological pathways with major downregulated processes including extracellular matrix organization and the immune system. Finally, we investigated the relative abundances of ovarian cancer-related proteins identified from the Cancer Gene Census across serially passaged PDXs, and found their protein levels to be unstable across PDX models. Our findings highlight features of distinct and dynamic proteomes of serially-passaged PDX models of ovarian cancer.

Distinct Proteomic Brain States Underlying Long-Term Memory Formation in Aversive Operant Conditioning

Long-term memory (LTM) formation relies on de novo protein synthesis; however, the full complement of proteins crucial to LTM formation remains unknown in any system. Using an aversive operant conditioning model of aerial respiratory behavior in the pond snail mollusk, Lymnaea stagnalis (L. stagnalis), we conducted a transcriptome-guided proteomic analysis on the central nervous system (CNS) of LTM, no LTM, and control animals. We identified 366 differentially expressed proteins linked to LTM formation, with 88 upregulated and 36 downregulated in LTM compared to both no LTM and controls. Functional annotation highlighted the importance of balancing protein synthesis and degradation for LTM, as indicated by the upregulation of proteins involved in proteasome activity and translation initiation, including EIF2D, mRNA levels of which were confirmed to be upregulated by conditioning and implicated nuclear factor Y as a potential regulator of LTM-related transcription in this model. This study represents the first transcriptome-guided proteomic analysis of LTM formation ability in this model and lays the groundwork for discovering orthologous proteins critical to LTM in mammals.

Ribosomes translocation into the spore of Bacillus subtilis is highly organised and requires peptidoglycan rearrangements

In the spore-forming bacterium Bacillus subtilis transcription and translation are uncoupled and the translational machinery is located at the cell poles. During sporulation, the cell undergoes morphological changes including asymmetric division and chromosome translocation into the forespore. However, the fate of translational machinery during sporulation has not been described. Here, using microscopy and mass spectrometry, we show the localisation of ribosomes during sporulation in wild type and mutant Bacillus subtilis. We demonstrate that ribosomes are associated with the asymmetric septum, a functionally important organelle in the cell's developmental control, and that SpoIIDMP-driven peptidoglycan rearrangement is crucial for ribosomes packing into the forespore. We also show that the SpoIIIA-SpoIIQ 'feeding-tube' channel is not required for ribosome translocation. Our results demonstrate that translation and translational machinery are temporally and spatially organised in B. subtilis during sporulation and that the forespore 'inherits' ribosomes from the mother cell. We propose that the movement of ribosomes in the cell may be mediated by the bacterial homologs of cytoskeletal proteins and that the cues for asymmetric division localisation may be translation-dependent. We anticipate our findings to elicit more sophisticated structural and mechanistic studies of ribosome organisation during bacterial cell development.

The Exoproteome and Surfaceome of Toxigenic Corynebacterium diphtheriae 1737 and Its Response to Iron Restriction and Growth on Human Hemoglobin

Toxin-producing Corynebacterium diphtheriae strains are the etiological agents of the severe upper respiratory disease, diphtheria. A global phylogenetic analysis revealed that biotype gravis is particularly lethal as it produces diphtheria toxin and a range of other virulence factors, particularly when it encounters low levels of iron at sites of infection. To gain insight into how it colonizes its host, we have identified iron-dependent changes in the exoproteome and surfaceome of C. diphtheriae strain 1737 using a combination of whole-cell fractionation, intact cell surface proteolysis, and quantitative proteomics. In total, we identified 1414 of the predicted 2265 proteins (62%) encoded by its reference genome. For each protein, we quantified its degree of secretion and surface exposure, revealing that exoproteases and hydrolases predominate in the exoproteome, while the surfaceome is enriched with adhesins, particularly DIP2093. Our analysis provides insight into how components in the heme-acquisition system are positioned, showing pronounced surface exposure of the strain-specific ChtA/ChtC paralogues and high secretion of the species-conserved heme-binding HtaA protein, suggesting it functions as a hemophore. Profiling the response of the exoproteome and surfaceome after microbial exposure to human hemoglobin and iron limitation reveals potential virulence factors that may be expressed at sites of infection. Data are available via ProteomeXchange with identifier PXD051674.

Structures of Saccharolobus solfataricus initiation complexes with leaderless mRNAs highlight archaeal features and eukaryotic proximity

The archaeal ribosome is of the eukaryotic type. TACK and Asgard superphyla, the closest relatives of eukaryotes, have ribosomes containing eukaryotic ribosomal proteins not found in other archaea, eS25, eS26 and eS30. Here, we investigate the case of Saccharolobus solfataricus, a TACK crenarchaeon, using mainly leaderless mRNAs. We characterize the small ribosomal subunit of S. solfataricus bound to SD-leadered or leaderless mRNAs. Cryo-EM structures show eS25, eS26 and eS30 bound to the small subunit. We identify two ribosomal proteins, aS33 and aS34, and an additional domain of eS6. Leaderless mRNAs are bound to the small subunit with contribution of their 5'-triphosphate group. Archaeal eS26 binds to the mRNA exit channel wrapped around the 3' end of rRNA, as in eukaryotes. Its position is not compatible with an SD:antiSD duplex. Our results suggest a positive role of eS26 in leaderless mRNAs translation and possible evolutionary routes from archaeal to eukaryotic translation.

Salivary peptidomic profiling of chronic gingivostomatitis in cats by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry and nanoscale liquid chromatography-tandem mass spectrometry

BACKGROUND

Chronic gingivostomatitis in cats (FCGS) is a moderately to severely painful condition, potentially caused by inadequate immune response to oral antigenic stimulation. Salivary peptidome analysis can identify inflammatory protein mediators and pathways involved in oral mucosal immune activation and may indicate potential therapeutic options for FCGS.

OBJECTIVE

Evaluate the diversity and abundance of salivary peptides in cats with FCGS using matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and nanoscale liquid chromatography-tandem mass spectrometry (nano LC-MS/MS).

ANIMALS

Thirty-two cats with FCGS and 18 healthy controls.

METHODS

Case-control cross-sectional study. We compared the salivary peptide profiles of diseased and healthy cats. The diagnosis of FCGS was confirmed by histopathology. Saliva samples were analyzed for viral infections using polymerase chain reaction (PCR), peptide mass fingerprint (PMF) using MALDI-TOF MS, and peptide identification using nano LC-MS/MS.

RESULTS

Distinct clusters of peptide profiles were observed between groups. In FCGS, 26 salivary peptides were altered, including apolipoprotein A1, nuclear receptor subfamily 1 group I member 3, fibrinogen alpha chain, interleukin 2 receptor gamma, interleukin 23 receptor, hemoglobin subunit alpha, and serpin peptidase inhibitor clade A (alpha-1 antiproteinase, antitrypsin) member 12, protein-tyrosine-phosphatase, and cholinergic receptor nicotinic alpha 10 subunit. Protein-anti-inflammatory drug interaction networks were observed.

CONCLUSIONS AND CLINICAL IMPORTANCE

Peptide mass fingerprint and peptide profiles identified distinct clusters between FCGS and healthy cats. The 9 novel salivary peptide markers were associated with the JAK/STAT and PI3K/Akt pathways and immune responses. These potentially noninvasive biomarkers may facilitate understanding of FCGS pathophysiology and guide future therapeutic research.

Global analysis of endogenous protein disorder in cells

Disorder and flexibility in protein structures are essential for biological function but can also contribute to diseases, such as neurodegenerative disorders. However, characterizing protein folding on a proteome-wide scale within biological matrices remains challenging. Here we present a method using a bifunctional chemical probe, named TME, to capture in situ, enrich and quantify endogenous protein disorder in cells. TME exhibits a fluorescence turn-on effect upon selective conjugation with proteins with free cysteines in surface-exposed and flexible environments-a distinctive signature of protein disorder. Using an affinity-based proteomic approach, we identify both basal disordered proteins and those whose folding status changes under stress, with coverage to proteins even of low abundance. In lymphoblastoid cells from individuals with Parkinson's disease and healthy controls, our TME-based strategy distinguishes the two groups more effectively than lysate profiling methods. High-throughput TME fluorescence and proteomics further reveal a universal cellular quality-control mechanism in which cells adapt to proteostatic stress by adopting aggregation-prone distributions and sequestering disordered proteins, as illustrated in Huntington's disease cell models.

Impact of increasingly complex cell culture conditions on the proteome of human periodontal ligament stem cells

AIMS

Human periodontal ligament stem cells (hPDLSCs) exhibit an enormous potential to regenerate periodontal tissue. However, their translatability to the clinical setting is constrained by technical difficulties in standardizing culture conditions. The aim was to assess complex culture conditions using a proteomic-based protocol to standardize multi-layer hPDLSC cultivation methodology.

MATERIALS AND METHODS

hPDLSC-derived constructs were created with varying biological complexity. The simplest constructs were monolayer sheets of hPDLSCs cultured with fetal bovine serum (FBS) or Plasma Rich in Growth Factors supernatant (PRGFsn). The most complex constructs were triple-layered cell structures cultured with PRGFsn, with or without PRGF fibrin membrane (mPRGF). Ultrastructure and proteomic analyses were performed on these constructs.

RESULTS

PRGF supernatant improved protein expression related to extracellular matrix, adhesion, proliferation, and migration in hPDLSCs. PRGF fibrin scaffold upregulates proteins for cell activation, respiration, and electron transport. hPDLSCs on fibrin membrane show robust osteogenic potential through differential protein expression (ossification, tissue remodeling, morphogenesis, or cell migration) and overall homeostasis relative to less complex structures.

CONCLUSION

Our data reveal the far-reaching potential of 3-dimensional constructs in combination with PRGF technology in periodontal regenerative applications.

Phosphoproteomic Analysis of Signaling Pathways in Lymphomas

Cellular fate is regulated by intricate signal transduction mediated by posttranslational protein modifications like phosphorylation to transmit information. As other cancer types, lymphomas frequently show dysregulation of signaling pathways that contribute to malignant transformation and tumor progression. For example, in diffuse large B-cell lymphoma the B-cell antigen receptor was identified as an oncogenic driver mediating cellular growth and survival signals. Thus, the elucidation of these complex signaling networks is crucial to gain insight into the mechanisms underlying tumorigenesis and to identify target proteins for innovative therapeutic approaches.Here, we describe a mass spectrometry-based phosphoproteomic approach for the global analysis of intracellular signaling events and their dynamics. The workflow combines phosphopeptide enrichment and fractionation with liquid chromatography-coupled mass spectrometry for the amino acid site-specific identification and quantification of thousands of phosphorylation events. Such global signaling analyses have great potential for the elucidation of oncogenic pathomechanisms, diagnostic biomarkers, and drug targets.

Clinical functional proteomics of intercellular signalling in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) has an atypical, highly stromal tumour microenvironment (TME) that profoundly contributes to its poor prognosis1. Here, to better understand the intercellular signalling between cancer and stromal cells directly in PDAC tumours, we developed a multidimensional proteomic strategy called TMEPro. We applied TMEPro to profile the glycosylated secreted and plasma membrane proteome of 100 human pancreatic tissue samples to a great depth, define cell type origins and identify potential paracrine cross-talk, especially that mediated through tyrosine phosphorylation. Temporal dynamics during pancreatic tumour progression were investigated in a genetically engineered PDAC mouse model. Functionally, we revealed reciprocal signalling between stromal cells and cancer cells mediated by the stromal PDGFR-PTPN11-FOS signalling axis. Furthermore, we examined the generic shedding mechanism of plasma membrane proteins in PDAC tumours and revealed that matrix-metalloprotease-mediated shedding of the AXL receptor tyrosine kinase ectodomain provides an additional dimension of intercellular signalling regulation in the PDAC TME. Importantly, the level of shed AXL has a potential correlation with lymph node metastasis, and inhibition of AXL shedding and its kinase activity showed a substantial synergistic effect in inhibiting cancer cell growth. In summary, we provide TMEPro, a generically applicable clinical functional proteomic strategy, and a comprehensive resource for better understanding the PDAC TME and facilitating the discovery of new diagnostic and therapeutic targets.

Engineered nascent living human tissues with unit programmability

Leveraging human cells as materials precursors is a promising approach for fabricating living materials with tissue-like functionalities and cellular programmability. Here we describe a set of cellular units with metabolically engineered glycoproteins that allow cells to tether together to function as macrotissue building blocks and bioeffectors. The generated human living materials, termed as Cellgels, can be rapidly assembled in a wide variety of programmable three-dimensional configurations with physiologically relevant cell densities (up to 108 cells per cm3), tunable mechanical properties and handleability. Cellgels inherit the ability of living cells to sense and respond to their environment, showing autonomous tissue-integrative behaviour, mechanical maturation, biological self-healing, biospecific adhesion and capacity to promote wound healing. These living features also enable the modular bottom-up assembly of multiscale constructs, which are reminiscent of human tissue interfaces with heterogeneous composition. This technology can potentially be extended to any human cell type, unlocking the possibility for fabricating living materials that harness the intrinsic biofunctionalities of biological systems.

Single-Cell Multi-Omics Analysis of In Vitro Post-Ovulatory-Aged Oocytes Revealed Aging-Dependent Protein Degradation

Once ovulated, the oocyte has to be fertilized in a short time window or it will undergo post-ovulation aging (POA), whose underlying mechanisms are still not elucidated. Here, we optimized single-cell proteomics methods and performed single-cell transcriptomic, proteomic, and phosphoproteomic analysis of fresh, POA, and melatonin-treated POA oocytes. POA oocytes showed downregulation of most differentially expressed proteins, with little correlation with mRNA expression, and the protein changes can be rescued by melatonin treatment. MG132 treatment rescued the decreased fertilization and polyspermy rates and upregulated fragmentation and parthenogenesis rates of POA oocytes. MG132-treated oocytes displayed health status at proteome, phosphoproteome, and fertilization ability similar to fresh oocytes, suggesting that protein stabilization might be the underlying mechanism for melatonin to rescue POA. The important roles of proteasome-mediated protein degradation during oocyte POA revealed by single-cell multi-omics analyses offer new perspectives for increasing oocyte quality during POA and improving assisted reproduction technologies.

Cross-Linking Mass Spectrometry to Capture Protein Network Dynamics of Cell Membranome

Interactions among proteins are fundamental in driving functions and activities that regulate cell biology, mechanotransduction, and cell-to-cell communication/recognition. Recently, cross-linking mass spectrometry (XL-MS) has emerged as a powerful tool for interaction discovery and characterization, driving the enlightenment of novel binding partners otherwise undetected. Covalent linkages of two amino acid residues of proteins (or within complexes) in close proximity can be identified by MS, thus providing structural insights such as distance restraints or unraveling interaction dynamics.The XL-MS workflow described here is applied to map the plasma membrane protein (PMP) networks since they play important roles in the modulation of diverse molecular processes, including transport, signal transduction, endocytosis, and secretion. The strategy includes cross-linking of PMP-enriched fractions, label-free nanoLC-MS/MS, and bioinformatics data analysis. "Membranome" interconnections constitute around 30% of the mammalian proteome and 60% of all drug targets. Exploring such networks under different biological conditions is a promising and unbiased approach to depicting regulatory pathways that govern cell behavior.

Sex-dependent efficacy of sphingosine-1-phosphate receptor agonist FTY720 in mitigating Huntington's disease

Huntington's disease (HD) is a debilitating neurodegenerative disorder characterized by severe motor deficits, cognitive decline and psychiatric disturbances. An early and significant morphological hallmark of HD is the activation of astrocytes triggered by mutant huntingtin, leading to the release of inflammatory mediators. Fingolimod (FTY), an FDA-approved sphingosine-1-phosphate (S1P) receptor agonist is used to treat multiple sclerosis (MS), a neuroinflammatory disease, and has shown therapeutic promise in other neurological conditions. Our study aimed to investigate the therapeutic potential of FTY for treating HD by utilizing a well-characterized mouse model of HD (zQ175dn) and wild-type littermates. The study design included a crossover, long-term oral treatment with 1 mg/kg to 2 mg/kg FTY from the age of 15-46 weeks (n = 128). Different motor behavior and physiological parameters were assessed throughout the study. The findings revealed that FTY rescued disease-related body weight loss in a sex-dependent manner, indicating its potential to regulate metabolic disturbances and to counteract neurodegenerative processes in HD. FTY intervention also rescued testicular atrophy, restored testis tissue structure in male mice suggesting a broader impact on peripheral tissues affected by huntingtin pathology. Histological analyses of the brain revealed delayed accumulation of activated astrocytes contributing to the preservation of the neural microenvironment by reducing neuroinflammation. The extent of FTY-related disease improvement was sex-dependent. Motor functions and body weight improved mostly in female mice with sustained estrogen levels, whereas males had to compensate for the ongoing, disease-related testis atrophy and the loss of androgen production. Our study underscores the beneficial therapeutic effects of FTY on HD involving endogenous steroid hormones and their important anabolic effects. It positions FTY as a promising candidate for therapeutic interventions targeting various aspects of HD pathology. Further studies are needed to fully evaluate its therapeutic potential in patients.

Protein Sample Preparation for Bottom-Up, Label-Free Quantitative Proteomics of Adipose Tissue

Adipose tissue (AT) is a complex, multifunctional endocrine organ that plays a significant role in animal evolution and human disease. Profiling of the proteome, or the set of proteins produced by a cell or tissue at a given time, can be used to explore the myriad functions of adipose tissue and understand its role in health and disease. The main challenges of adipose tissue proteomics include the high lipid and low protein content of the tissue and association of many proteins with lipid droplets. Here, we present a protocol for gel-free, label-free, bottom-up, relative quantitative proteomics of adipose tissue based on findings from the literature and our laboratory that yields reproducible protein and peptide identification rates while minimizing cost and processing time. This approach involves tissue homogenization, protein precipitation from homogenates, solubilization and denaturation of proteins in a buffer containing 5% sodium deoxycholate (SDC, an acid-insoluble detergent) and 5 mM tris(2-carboxyethyl)phosphine (TCEP, a reducing agent), alkylation with chloroacetamide, and in-solution tandem digestion with trypsin and Lys-C enzymes in the presence of 1% SDC. Acidification of peptides efficiently removes SDC prior to desalting and mass spectrometry. This method has been used successfully in our laboratory by both experienced researchers and those with limited technical backgrounds, including high school, undergraduate, and graduate students. We have identified >1500 proteins in adipose tissue of non-model mammals (e.g., blubber of marine mammals) spanning a dynamic range of 105 using this approach, including proteins of interest for comparative physiology such as adipokines, metabolic and antioxidant enzymes, lipid droplet proteins, metabolite transporters, and mitochondrial proteins, among others.

The Lipid Droplet Protein DHRS3 Is a Regulator of Melanoma Cell State

Lipid droplets are fat storage organelles composed of a protein envelope and lipid-rich core. Regulation of this protein envelope underlies differential lipid droplet formation and function. In melanoma, lipid droplet formation has been linked to tumor progression and metastasis, but it is unknown whether lipid droplet proteins play a role. To address this, we performed proteomic analysis of the lipid droplet envelope in melanoma. We found that lipid droplet proteins were differentially enriched in distinct melanoma states; from melanocytic to undifferentiated. DHRS3, which converts all-trans-retinal to all-trans-retinol, is upregulated in the MITFLO/undifferentiated/neural crest-like melanoma cell state and reduced in the MITFHI/melanocytic state. Increased DHRS3 expression is sufficient to drive MITFHI/melanocytic cells to a more undifferentiated/invasive state. These changes are due to retinoic acid-mediated regulation of melanocytic genes. Our data demonstrate that melanoma cell state can be regulated by expression of lipid droplet proteins which affect downstream retinoid signaling.

Outstanding enrichment of ladderane lipids in anammox bacteria: Overlooked effect of pH

Ladderane lipids synthesised by anammox bacteria hold significant potential for applications in jet fuel, drug delivery, and optoelectronics. Despite the widespread use of anammox bacteria in nitrogen removal from wastewater, the optimal conditions for maximising ladderane production remain unclear, limiting their broader application. To address this, we operated a fed-batch bioreactor with anammox bacteria, gradually adjusting the pH from 6.5 to 7.5 while regularly sampling for microbial community composition (Illumina sequencing), proteins, and ladderane lipids (UHPLC-HRMS). Our findings reveal that ladderane production positively correlates with rising pH increasing nearly fivefold as pH rose from 6.5 to 7.5, with a notable shift towards lipids containing two ladderane alkyl chains at higher pH. However, the conditions at an alkaline pH range also induced mild stress in anammox bacteria, as evidenced by our proteomic and microbial community data. Therefore, we propose maintaining a pH above 7.5 to enrich ladderane-rich anammox biomass but emphasise the need for gradual adaptation. This approach could optimise anammox installations for producing high-value ladderane lipids from wastewater.

Structural characterization and proteomic profiling of oviposition secretions across three rice planthopper species

Insect oviposition secretions play crucial roles during the reproductive process, yet systematic studies on their structural characterization and protein compositions remain limited. This study investigated the oviposition secretions of three major rice pests: the brown planthopper (Nilaparvata lugens, BPH), small brown planthopper (Laodelphax striatella, SBPH), and white-backed planthopper (Sogatella furcifera, WBPH). Ultrastructural observation revealed differences in the oviposition secretions of them. The eggs of BPH and SBPH were adhered to rice tissue by abundant secretions, while WBPH eggs were embedded deeper within the leaf sheath with less secretions. Proteomic analysis identified 111, 98, and 66 oviposition secretion proteins (OSPs) in BPH, SBPH, and WBPH, respectively. 4 common protein subgroups were shared among them, along with varying numbers of shared subgroups between species pairs. Notably, the majority of OSPs were exclusively found in one species, indicating the existence of both similar and specialized functions unique to each planthopper species. The functions of 4 uncharacterized OSPs (Nl.chr07.0363, Nl.chr12.078, Nl.chr11.716, Nl.scaffold.0714) that were uniquely identified in the BPH were studied by maternal RNAi. Downregulation of each of these 4 protein-coding genes led to a significant decrease in egg production and hatchability. Moreover, knockdown of Nl.chr12.078 or Nl.chr07.0363 also disrupt the secretory function of the lateral oviduct. In conclusion, this study provides insights into the structural characteristics and protein components of the oviposition secretions of BPH, SBPH, and WBPH, which could serve as potential targets for RNAi-based pest control and lay a foundation for future studies on insect-plant interactions mediated by oviposition secretions.

Isolation and Identification of Nuclear Protein Complexes Using GFP-Tagged Arabidopsis Lines and IP-MS Approach

Immunoprecipitation coupled with mass spectrometry (IP-MS) is a powerful method that enables the identification of protein-protein interactions and isolation of protein complexes. When optimized to work with plant material, it proved to be suitable for the isolation of different types of nuclear complexes from Arabidopsis. Here, we describe a detailed protocol for the isolation of chromatin remodeling and polycomb repressive complexes using Arabidopsis lines that express GFP-tagged proteins as baits, directly from whole-cell extracts or after nuclei enrichment. We describe different experimental variations of the key steps in the protocol and discuss the analysis and interpretation of the IP-MS data.

Insights on Wet and Dry Workflows for Human Gut Metaproteomics

The human gut microbiota (GM) is a community of microorganisms that resides in the gastrointestinal (GI) tract. Recognized as a critical element of human health, the functions of the GM extend beyond GI well-being to influence overall systemic health and susceptibility to disease. Among the other omic sciences, metaproteomics highlights additional facets that make it a highly valuable discipline in the study of GM. Indeed, it allows the protein inventory of complex microbial communities. Proteins with associated taxonomic membership and function are identified and quantified from their constituent peptides by liquid chromatography coupled to mass spectrometry analyses and by querying specific databases (DBs). The aim of this review was to compile comprehensive information on metaproteomic studies of the human GM, with a focus on the bacterial component, to assist newcomers in understanding the methods and types of research conducted in this field. The review outlines key steps in a metaproteomic-based study, such as protein extraction, DB selection, and bioinformatic workflow. The importance of standardization is emphasized. In addition, a list of previously published studies is provided as hints for researchers interested in investigating the role of GM in health and disease states.

Phosphorylation of SNW1 protein associated with equine melanocytic neoplasm identified in serum and feces

Equine melanocytic neoplasm (EMN) represents a form of skin tumor observed predominantly in grey horses aged over 15 years. Despite its prevalence, current therapeutic and preventive strategies for EMN have been subject to limited investigation. This study endeavors to shed light on potential phosphoproteins present in equine serum and fecal samples, potentially linked to EMN, with a specific focus on functional interactions in EMN pathogenesis. We examined 50 samples (25 serum, 25 feces), divided into three groups based on EMN severity: normal (n = 16), mild (n = 18), and severe EMN (n = 16). Equine phosphoproteome analysis identified 2,359 annotated serum phosphoproteins and 2002 annotated fecal phosphoproteins through differentially expressed proteins (DEPs). KEGG analysis emphasized the role of environmental information processing. Notably, the integrin NF-kappaB binding P-TEFb to stimulate transcriptional elongation signaling pathway, involving SNW1 protein, was implicated in early stage of EMN development in both serum and fecal samples. This highlights SNW1's potential role in mediating transcriptional processes, offering a novel marker within environmental information processing. This study enhances understanding of EMN mechanisms in horses, suggesting early detection through non-invasive methods and identifying a functional pathway involving SNW1, which could inform future treatment and prevention strategies.

Proteomic profiling of kidney biopsies in nephrotic syndrome

Background

Minimal change disease (MCD) and focal segmental glomerulosclerosis (FSGS) are patterns of kidney injury observed in the filtering units of the kidney known as glomeruli. These histological patterns are seen in kidney biopsies from individuals with idiopathic nephrotic syndrome (iNS), which occurs in both children and adults. However, there is some indication that MCD and FSGS are within the same phenotypic spectrum.

Methods

From the NURTuRE cohort of individuals with NS, we performed laser microdissection and mass spectrometry analysis of kidney biopsy samples to identify proteomic patterns of disease. 56 individuals with iNS segregated by histological pattern (37 MCD and 19 FSGS) across three age groups: early childhood (0-6 years), late childhood (6-18 years) and adult (>18 years).

Results

We found no distinct clustering of proteomic profiles between MCD and FSGS, but identified global differences in glomerular cell and extracellular matrix composition related to both histological pattern and age. The proteomic data are available via ProteomeXchange with identifier PXD053362.

Conclusions

The lack of distinct clustering between MCD and FSGS in our study suggests shared biological processes between these injury patterns of iNS, supporting the hypothesis that they are part of the same disease spectrum. The global differences observed in glomerular cell and extracellular matrix composition suggest involvement of diverse biogeological processes as different patterns of iNS manifests in different age groups. This study also demonstrates the feasibility of pooling bioresources, central processing of heterogeneous tissue samples, and developing laser-microdissection and proteomic analysis methodology.

The α1- and β1-Subunits of Nitric Oxide-Sensitive Guanylyl Cyclase in Pericytes of Healthy Human Dental Pulp

Nitric oxide-sensitive guanylyl cyclase (NO-GC) is a heterodimeric enzyme with an α- and a β-subunit. In its active form as an α1β1-heterodimer, NO-GC produces cyclic guanosine-3',5'-monophophate (cGMP) to regulate vasodilation and proliferation of vascular smooth muscle cells (VSMCs). In contrast to VSMCs, only a few studies reported on the expression of the NO-GC α1β1-heterodimer in human pericytes. Since NO-GC is a marker for platelet-derived growth factor-β (PDGFRβ)-positive pericytes, we investigated whether NO-GC is expressed in its active α1β1-heterodimer in pericytes of healthy human dental pulp. In our previous studies, we developed and validated an antibody against the α1-subunit of human NO-GC. Here, we developed a new antibody against the β1-subunit of human NO-GC and validated it by immunoblot, mass spectrometry, and immunohistochemistry on tissue samples from humans and NO-GC knockout (GCKO) mice. Using both antibodies, we detected α1- and β1-subunits of NO-GC in pericytes of pre-capillary arterioles, capillaries, and post-capillary venules in dental pulp of decalcified and non-decalcified human molars. We concluded that NO-GC as an active α1β1-heterodimer may be involved in the regulation of vascular permeability, vascular stability, organ homeostasis, and organ regeneration in healthy human dental pulp.

Embracing native diversity to enhance the maximum quantum efficiency of photosystem II in maize

The sustainability of maize cultivation would benefit tremendously from early sowing, but is hampered by low temperatures during early development in temperate climates. We show that allelic variation within the gene encoding subunit M of the NADH-dehydrogenase-like (NDH) complex (ndhm1) in a European maize landrace affects several quantitative traits that are relevant during early development in cold climates through NDH-mediated cyclic electron transport around photosystem I, a process crucial for photosynthesis and photoprotection. Beginning with a genome-wide association study for maximum potential quantum yield of photosystem II in dark-adapted leaves (Fv/Fm), we capitalized on the large phenotypic effects of a hAT transposon insertion in ndhm1 on multiple quantitative traits (early plant height [EPH], Fv/Fm, chlorophyll content, and cold tolerance) caused by the reduced protein levels of NDHM and associated NDH components. Analysis of the ndhm1 native allelic series revealed a rare allele of ndhm1 that is associated with small albeit significant improvements of Fv/Fm, photosystem II efficiency in light-adapted leaves (ΦPSII), and EPH compared with common alleles. Our work showcases the extraction of favorable alleles from locally adapted landraces, offering an efficient strategy for broadening the genetic variation of elite germplasm by breeding or genome editing.