The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

A novel CD44-targeting aptamer recognizes chemoresistant mesenchymal stem-like TNBC cells and inhibits tumor growth

Triple-negative breast cancer (TNBC) represents a significant therapeutic challenge owing to the scarcity of targeted medicines and elevated recurrence rates. We previously reported the development of the nuclease-resistant RNA sTN58 aptamer, which selectively targets TNBC cells. Here, sTN58 aptamer was employed to capture and purify its binding target from the membrane protein fraction of cisplatin-resistant mesenchymal stem-like TNBC cells. Mass spectrometry in conjunction with aptamer binding assays across various cancer cell lines identified CD44 as the cellular target of sTN58. By binding to CD44, sTN58 inhibits the invasive growth and hyaluronic acid-dependent tube formation in chemoresistant TNBC cells, where CD44 serves as a key driver of tumor cell aggressiveness and stem-like plasticity. Moreover, in vivo studies demonstrated the aptamer's high tumor targeting efficacy and its capacity to significantly inhibit tumor growth and lung metastases following intravenous administration in mice with orthotopic TNBC. Overall, our findings reveal the striking potential of sTN58 as a targeting reagent for the recognition and therapy of cancers overexpressing CD44.

Effect of stationary phase surface chemistry and particle architecture in proteomics

The kinetic properties of four columns packed with fully porous particles and three with superficially porous particles were characterized for possible application in proteomic bottom-up analyses. All columns provided an attachment of hydrophobic C18 chains at the surface of the stationary phase. However, they differed in the additional attachment of polar groups and/or endcapping procedure. We have used the retention modeling protocol to explore the separation efficiency and maximal achievable peak capacity on tested columns. Almost all columns provided comparable maximal peak capacity in the range of 500 - 700 for the eight-hour gradient run. This confirms that the family of the stationary phases used in the bottom-up proteomics can be extended. In the case of fully porous particles, we found that the higher the column peak capacity, the higher the number of identified peptides in the simple proteomic sample, with approximately one identified peptide per peak capacity unit. On the contrary, in the case of the superficially porous particles, the number of identified peptides in the sample decreased with the higher column peak capacity. This trend can be overturned only when the lower amount of the sample is injected. Hence, when bottom-up proteomics is considered, the lower loadability of the superficially porous particles still needs to be addressed. Most stationary phases tested can be successfully used in the bottom-up analyses. However, the stationary phases with incorporated polar functional groups reduced the undesirable contribution of free silanol groups to peptide peak tailing and increased the information provided by LC-MS analysis.

Ion exchange- and enrichment-based technology applied to large-scale plasma proteomic analysis of breast cancer neoadjuvant chemotherapy

Mass spectrometry (MS) based proteomics provides unbiased quantification of all proteins in plasma, which can dynamically reflect individual health states in real time. However, large-scale proteomics studies are constrained by the excessive dynamic range of plasma proteome and low throughput. Herein, two kinds of magnetic metal-organic frameworks (MOFs) modified with ion exchange functional groups (denoted as MHP-UiO-66-SAX and MHP-HKUST-1-SCX) were designed and fabricated to exhibit large protein adsorption capability, which were combined with an automated Liquid-handling System, thus realizing in-depth, high-throughput and automated proteomics studies. The constructed workflow could automatically complete the sample preparation before MS within only six hours and nearly a thousand protein groups per sample could be quantified. In the cohort study of nearly one hundred breast cancer neoadjuvant chemotherapy (NC) plasma samples, two differentially expressed proteins previously reported as biomarkers were related with the pathological complete response (PCR) of the breast cancer, demonstrating the feasibility of the developed technology for preparing large-scale clinical samples and exhibiting the potential application in monitoring the effect of chemotherapy.

Deciphering immune dynamics in atherosclerosis: Inflammatory mediators as biomarkers and therapeutic target

BACKGROUND

Atherosclerosis, one of the main causes of cardiovascular disease, is driven by complex interactions between lipid metabolism and immune mechanisms in the vascular system. Regulatory molecules, particularly protein fragments derived from cytokines, chemokines and other immune-related proteins, play a central role in modulating inflammation and immune responses in atherosclerotic plaques.

RESULTS

Recent advances in peptidomics have revealed the dual role of immune system-derived peptides as indicators and effectors of atherosclerotic cardiovascular disease (ASCVD). Certain subsets of immune cells, such as pro-inflammatory monocytes and regulatory T cells, contribute to this peptide-mediated regulation. New findings suggest that these peptides may serve as diagnostic biomarkers and therapeutic targets in atherosclerosis.

CONCLUSION

This review highlights the translational relevance of immune-mediated peptides in ASCVD and emphasizes their diagnostic and therapeutic potential. By integrating peptidomics with immunology research, a new framework for understanding and targeting inflammation in atherosclerosis is proposed, opening new avenues for precision medicine in cardiovascular care.

Morpholino nicotinamide analogs of ponatinib, dual MNK, p70S6K inhibitors, display efficacy against lung and breast cancers

Therapeutic options for aggressive cancer types such as breast and lung remain limited; disease relapse and death occur in 30-60% of non-small cell lung cancer (NSCLC) patients, whereas in triple-negative breast cancer or TNBC, recurrence-free survival occurs in less than 30% patients. The kinases, MNK and p70S6K have been proposed as targets for the potential treatment of breast cancer (BC) and lung cancer but currently, no drug that was purposely designed to inhibit these kinases have been approved by the FDA for the treatment of BC or NSCLC. In this study, we have identified HSND80 (a morpholino nicotinamide analog of ponatinib) as a potent MNK/p70S6K inhibitor that has excellent activity against TNBC and NSCLC cell lines. HSND80 has a longer target residence time (τ) of 45 mins and 58 mins against MNK1 and MNK2 respectively, compared to τ of eFT508 (tomivosertib) against MNK1 and MNK2 (τ = 1 min and 5 min, respectively). Molecular dynamics simulation was used to provide some insights into the binding of HSND80 to MNK and p70S6K kinases. Western blotting analysis and phosphoproteomics analysis of the TNBC cell line, MDA-MB-231, revealed that phosphorylations of elF4E (MNK target) and elF4B and S6 (p70S6K targets) were reduced upon compound treatment, which is in line with the proposed mechanism of action; dual MNK/p70S6K targeting. HSND80 could be dosed orally at 15 and 30 mg/kg and at such doses, could reduce tumor volume in a syngeneic NSCLC mouse model.

Integrated synchrotron radiation-based fourier transform infrared (SR-FTIR) microscopy and tandem-mass spectrometry (LC-MS/MS) used to elucidate the apoptotic effect of chamuangone in A549 cells

Chamuangone, a natural compound extracted from Garcinia cowa leaves, has demonstrated potential in cancer therapeutics, but its effects on lung cancer cells remain unclear. This study investigates the apoptotic effects of Chamuangone on human lung adenocarcinoma cells (A549). The A549 cells were treated with Chamuangone, and the cytotoxic effects were evaluated using an MTT assay, revealing a dose-dependent inhibition of cell proliferation with an IC50 value of 19.43 μM. Annexin V assays further confirmed that Chamuangone induces apoptosis in A549 cells, showing increased levels of late apoptosis with higher concentrations. Synchrotron radiation-based Fourier transform infrared (SR-FTIR) microscopy provided insights into macromolecular changes, highlighting significant alterations in proteins, lipids, and nucleic acids. These structural changes in key cellular macromolecules were supported by proteomic analysis, which identified the upregulation of apoptosis-related proteins, including Peroxiredoxin-2 and Na+/H+ exchange regulatory cofactor NHE-RF1. Canonical pathway analysis indicated that Chamuangone affects oxidative phosphorylation and mitochondrial dysfunction, both crucial pathways for apoptosis. Additionally, upstream regulator analysis demonstrated significant inhibition of the epidermal growth factor receptor (EGFR), a key player in lung cancer progression. These findings suggest that Chamuangone triggers apoptosis through mitochondrial pathways and EGFR inhibition, positioning it as a promising therapeutic candidate for lung cancer treatment.

Short-term aircraft noise stress induces a fundamental metabolic shift in heart proteome and metabolome that bears the hallmarks of cardiovascular disease

Environmental stressors in the modern world can fundamentally affect human physiology and health. Exposure to stressors like air pollution, heat, and traffic noise has been linked to a pronounced increase in non-communicable diseases. Specifically, aircraft noise has been identified as a risk factor for cardiovascular and metabolic diseases, such as arteriosclerosis, heart failure, stroke, and diabetes. Noise stress leads to neuronal activation with subsequent stress hormone release that ultimately activates the renin-angiotensin-aldosterone system, increases inflammation and oxidative stress thus substantially affecting the cardiovascular system. However, despite the epidemiological evidence of a link between noise stress and metabolic dysfunction, the consequences of exposure at the molecular, metabolic level of the cardiovascular system are largely unknown. Here, we use a murine model system of short-term aircraft noise exposure to show that noise stress profoundly alters heart metabolism. Within 4 days of noise exposure, the heart proteome and metabolome bear the hallmarks of reduced potential for generating ATP from fatty-acid beta-oxidation, the tricarboxylic acid cycle, and the electron transport chain. This is accompanied by the increased expression of glycolytic metabolites, including the end-product, lactate, suggesting a compensatory shift of energy production towards anaerobic glycolysis. Intriguingly, the metabolic shift is reminiscent of what is observed in failing and ischaemic hearts. Mechanistically, we further show that the metabolic rewiring is likely driven by reactive oxygen species (ROS), as we can rescue the phenotype by knocking out NOX-2/gp91phox, a ROS inducer, in mice. Our results suggest that within a short exposure time, the cardiovascular system undergoes a fundamental metabolic shift that bears the hallmarks of cardiovascular disease. These findings underscore the urgent need to comprehend the molecular consequences of environmental stressors, paving the way for targeted interventions to mitigate health risks associated with chronic noise exposure in modern, environments heavily disturbed by noise pollution.

Multi-organ proteome reveals different nursing ability between two honeybee srocks

High royal jelly production is an adaptive reproductive investment syndrome in honey bees that enhances their nursing ability to queen bee larvae. However, the biological basis of this reproduction investment at the multi-organ level remains elusive. In this study, proteome across 11 organs of two bee stocks: high royal jelly production bees (RJBs) and Italian bees (ITBs) was compared. Our analysis revealed significant differences in protein expression profiles in brain, fat body, mandibular gland, and Malpighian tubule, highlighting their crucial roles in regulating royal jelly secretion in RJBs. The increased energy turnover, protein synthesis, and lipid synthesis observed in RJBs compared to ITBs highlight their enhanced metabolic activity, which is essential for the robust secretion of royal jelly in RJBs. The elevated abundance of major royal jelly proteins (MRJPs), hexamerins, and vitellogenin suggests their critical contributions to the nutritional and material requirement necessary for royal jelly secretion. Furthermore, the high level of vitellogenin and juvenile hormone esterase may suppress juvenile hormones, which contribute to a strong royal jelly secretion and sensitivity of RJBs to larval pheromones relative to ITBs. This comprehensive dataset contributes to a better understanding of nursing behavior and reproductive investment in honey bees. Significiance. The royal jelly secretion syndrome is a colony level social trait dominated by the intricate interplay of multiple organs. However, previous studies have primarily focused on individual organs. In this study, the proteome of 11 organs was compared between high royal jelly production bees (RJBs) and Italian bees (ITBs) to provide knowledge on how multiple organs cooperate to boost the elevated royal jelly production by RJBs. Nutrition supply was sufficient at multiple organs of RJBs when compared to ITBs, indicating that nutrition plays an essential role in boosting energy metabolism, protein and lipid synthesis, and directly contributes to the amount of royal jelly secretion. The high level of secretion of storage proteins, such as MRJPs, hex, and vitellogenin, provides sufficient nutrition and material for royal jelly secretion. Moreover, the higher levels of vitellogenin and juvenile hormone esterase may suppress juvenile hormone synthesis, and contributing to stronger sense of RJBs to larval pheromone relative to ITBs. This suggests that nutrition can influence the hormone levels and sensory abilities of RJBs nurse bees to promote their royal jelly secretion ability. The reported data provide insights into the systematic regulation strategy of honeybee nursing behavior and reproductive investment.

Revisiting toxins with transcriptomics-informed proteomics of venom glands and crude venom from Centruroides bicolor from Panama

The sting of the scorpion Centruroides bicolor causes a large morbidity in Panama. To characterize its venom, transcriptomic and proteomic analyses of the venom glands and the crude venom were performed. These two approaches utilized high-throughput sequencing to enhance the likelihood of detecting a wide range of venom proteins correlated with the venom proteome. After RNA venom gland extraction, a cDNA library was constructed and sequenced by RNA-seq. Also, the crude venom was digested using trypsin and chymotrypsin, and the resulting peptides were analyzed using a nano-LC-MS/MS. Notably, transcriptomic and proteomic venom approaches identified a hyaluronidase, alpha- and beta-neurotoxins that affect Na+ channels, CRISP proteins, metalloproteinases, transferrin, monooxygenase alpha-peptidyl-glycine, serine proteases, alpha pancreatic amylase, lysozyme, neurotoxins targeting K+ channels, neprilysin, scorpine, angiotensin-converting enzyme, insulin-like growth factor-binding domain proteins, nucleobindin-like proteins, and uncharacterized proteins. Interestingly, some of the venom proteins such as nucleobindin and angiotensin-converting enzymes have been not reported in the proteome, their predicted presence has only been previously derived from the genomic sequence of Centruroides sculpturatus and C. vittatus. These newly identified components enhance the understanding of the venomous nature of C. bicolor. SIGNIFICANCE: The proteins and peptides found in Centruroides bicolor venom by transcriptomic and proteomic analyses were assessed according to the protein and toxin databases available on public domains. Notably, some of the venom proteins such as nucleobindin and angiotensin-converting enzymes have been not reported in the proteome, their predicted presence has only been previously derived from the genomic sequence of Centruroides sculpturatus and C. vittatus. Moreover, enzymatic assays, including hyaluronidase, phospholipase A2, and proteolytic activity were conducted to confirm the presence or absence of those enzymes. Interestingly, neurotoxins from C. limbatus, a related species in the region, were found in the proteome but no mRNAs were identified in the transcriptome. These newly identified components enhance the understanding of the venomous nature of Centruroides bicolor.

MALDI Imaging and Spatial SILAC Proteomics of Three-Dimensional Multicellular Spheroids Dynamically Dosed with Doxorubicin-Encapsulating Liposomes

Microphysiological systems, such as multicellular spheroids, hold great promise for drug screening experiments. Spheroids may be dosed statically, where the drug is introduced to the growing chamber at one time point, or dynamically, where the drug is introduced via a fluidic component. Dynamic dosing can generate pharmacokinetic curves that more closely represent those seen in vivo than static dosing. In this work, we demonstrate the dynamic dosing of colorectal cancer spheroids in a 3D printed fluidic device with liposomal doxorubicin. Spheroids are valuable models to evaluate dynamic dosing, as they recapitulate the nutrient, oxygen, and pH gradients of solid tumors. Spheroids feature distinct cellular populations with a necrotic core, quiescent middle layer, and proliferative outer layer. Drug and liposome penetration are tracked with matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) and fluorescence imaging, showing that liposomal doxorubicin is stable to fluidic dosing and penetrates spheroids after 48 h. To provide a comprehensive pharmacodynamic profile of the distinct cellular regions within spheroids, we employ spatially stable isotopic labeling by amino acids in cell culture (spatial SILAC) proteomics to isotopically label the core and outer layers. Proteomic analysis reveals 714 upregulated proteins in the core upon treatment and 30 in the outer layers, as well as 103 downregulated proteins in the core and 1276 in the outer layers. Spatial SILAC uncovers the differential regulation of proteins associated with glycolysis, the TCA cycle, and lipid synthesis upon drug treatment between the spheroid core and outer layers. Using MALDI MSI and spatial SILAC proteomics, we interrogate the effects of dynamic dosing with liposomal doxorubicin on spheroid regions that would be overlooked by bulk analysis.

Data-Independent Acquisition-Based Quantitative Proteomics for Pairwise Comparison of Serum and Plasma

Human blood contains proteins secreted by various organs, but there is no consensus on whether serum or plasma is preferable for proteome studies. Mass spectrometry employing data-independent acquisition has emerged as a transformative methodology in proteomics, enabling reproducible large-scale quantification of proteomes during one LC-MS/MS analytical run and facilitating identification of potential markers and elucidation of biological processes. Here, we profiled the proteome data of ten paired plasma and serum samples in the initial sample set. Functional analysis revealed similarities and differences in biological functions and the preference for different organs between serum and plasma. Furthermore, comparative proteomic analysis highlighted the different proteomic characteristics. Plasma-overrepresented pathways were related to the phagosome and immune, while serum-overrepresented pathways were associated with amino acid metabolism, which were further validated by the follow-up sample set composed of eight paired plasma and serum samples. We have detected potential markers in plasma and serum for various cancers and explored their association with prognosis using data from the TCGA pan-cancer cohort and HPA database. Further assessment is required to validate the reproducibility of the quantification for these markers. Overall, this study highlights the commonality and specificity of plasma and serum at the molecular level, underscoring their respective utility in biological exploration and clinical applications.

The proteomic differences and expression of fatty acid-binding protein 6 (FABP6) associated with gastrointestinal injury in horses with oral administration of a clinical dose of phenylbutazone

BACKGROUND

Phenylbutazone (PBZ) can potentially induce gastrointestinal ulceration, and early detection of PBZ-induced gastroenteropathy will be useful for the diagnosis, treatment, and prevention of PBZ toxicity.

OBJECTIVES

To identify putative proteins associated with equine gastric ulcer syndrome after clinical dose (4.4 mg/kg) administration of PBZ by proteomic study.

STUDY DESIGN

In vivo experiments.

METHODS

Proteomic analysis using LC-MS/MS compared protein expression in serum and faeces of seven PBZ-treated horses with seven placebo-treated controls, and a novel putative biomarker was validated via enzyme-linked immunosorbent assay.

RESULTS

Differentially expressed proteins (DEPs) analysis on 5298 serum annotated proteins and 3538 faecal annotated proteins using the DESeq2 were performed between the control and treatment of EGUS groups. The results showed a list of 226 and 181 significant proteins in serum and faecal samples, respectively with a p adjust value <0.05. The proteomic serum and faeces samples were integrated into STITCH to illustrate PBZ interaction with bile acid homeostasis. FABP6 was significantly increased in PBZ-treated horses. The serum FABP6 concentration in the treatment group on Day 8 (1.80 ± 0.37 ng/mL) was higher than on Day 0 (1.15 ± 0.33 ng/mL, p = 0.01, 95% CI [-1.07, -0.25]). On Day 8, the serum FABP6 concentration in the treatment group was also higher than the control group (1.20 ± 0.48 ng/mL; p = 0.02, 95% CI [-1.10, -0.11]).

MAIN LIMITATIONS

Validation of all expressed proteins is a main limitation.

CONCLUSIONS

Administration of PBZ at a clinical dose of 4.4 mg/kg twice daily for 7 days may cause gastric mucosal damage. PBZ treatment increased the expression of SLC10A1 and FABP6, suggesting that early gastric mucosal injury may be linked to the bile acid pathway. Bile acids could potentially exacerbate PBZ-induced EGUS.

The TetR-like regulator Sco4385 and Crp-like regulator Sco3571 modulate heterologous production of antibiotics in Streptomyces coelicolor M512

Heterologous expression in well-studied model strains is a routinely applied method to investigate biosynthetic pathways. Here, we pursue a comparative approach of large-scale DNA-affinity-capturing assays (DACAs) coupled with semi-quantitative mass spectrometry (MS) to identify putative regulatory proteins from Streptomyces coelicolor M512, which bind to the heterologously expressed biosynthetic gene clusters (BGCs) of the liponucleoside antibiotics caprazamycin and liposidomycin. Both gene clusters share an almost identical genetic arrangement, including the location of promoter regions, as detected by RNA sequencing. A total of 2,214 proteins were trapped at the predicted promoter regions, with only three binding to corresponding promoters in both gene clusters. Among these, the overexpression of a yet uncharacterized TetR-family regulator (TFR), Sco4385, increased caprazamycin but not liposidomycin production. Protein-DNA interaction experiments using biolayer interferometry confirmed the binding of Sco4385 to Pcpz10 and PlpmH at different locations within both promoter regions, which might explain its functional variance. Sequence alignment allowed the determination of a consensus sequence present in both promoter regions, to which Sco4385 was experimentally shown to bind. Furthermore, we found that the overexpression of the Crp regulator, Sco3571, leads to a threefold increase in caprazamycin and liposidomycin production yields, possibly due to an increased expression of a precursor pathway.IMPORTANCEStreptomycetes are well-studied model organisms for the biosynthesis of pharmaceutically, industrially, and biotechnologically valuable metabolites. Their naturally broad repertoire of natural products can be further exploited by heterologous expression of biosynthetic gene clusters (BGCs) in non-native host strains. This approach forces the host to adapt to a new regulatory and metabolic environment. In our study, we demonstrate that a host regulator not only interacts with newly incorporated gene clusters but also regulates precursor supply for the produced compounds. We present a comprehensive study of regulatory proteins that interact with two genetically similar gene clusters for the biosynthesis of liponucleoside antibiotics. Thereby, we identified regulators of the heterologous host that influence the production of the corresponding antibiotic. Surprisingly, the regulatory interaction is highly specific for each biosynthetic gene cluster, even though they encode largely structurally similar metabolites.

Multi-omics analysis of SFTS virus infection in Rhipicephalus microplus cells reveals antiviral tick factors

The increasing prevalence of tick-borne arboviral infections worldwide necessitates advanced control strategies, particularly those targeting vectors, to mitigate the disease burden. However, the cellular interactions between arboviruses and ticks, especially for negative-strand RNA viruses, remain largely unexplored. Here, we employ a proteomics informed by transcriptomics approach to elucidate the cellular response of the Rhipicephalus microplus-derived BME/CTVM6 cell line to severe fever with thrombocytopenia syndrome virus (SFTSV) infection. We generate the de novo transcriptomes and proteomes of SFTSV- and mock-infected tick cells, identifying key host responses and regulatory pathways. Additionally, interactome analysis of the viral nucleoprotein (N) integrated host responses with viral replication and dsRNA-mediated gene silencing screen reveals two anti-SFTSV effectors: the N interacting RNA helicases DHX9 and UPF1. Collectively, our results provide insights into the antiviral responses of R. microplus vector cells and highlight critical SFTSV restriction factors, while enriching transcriptomic and proteomic resources for future research.

MCQR: Enhancing the Processing and Analysis of Quantitative Proteomics Data by Incorporating Chromatography and Mass Spectrometry Information

In the field of proteomics, generating biologically relevant results from mass spectrometry (MS) signals remains a challenging task. This is partly due to the fact that the computational strategies for converting MS signals into biologically interpretable data depend heavily on the MS acquisition method. Additionally, the processing and the analysis of these data vary depending on whether the proteomic experiment was performed with or without labeling, and with or without fractionation. Several R packages have been developed for processing and analyzing MS data, but they only incorporate identification and quantification data; none of them takes into account other invaluable information collected during MS runs. To address this limitation, we introduce MCQR, an alternative R package for the in-depth exploration, processing, and analysis of quantitative proteomics data generated from either data-dependent or data-independent acquisition methods. MCQR leverages experimental retention time measurements for quality control, data filtering, and processing. Its modular architecture offers flexibility to accommodate various types of proteomics experiments, including label-free, label-based, fractionated, or those enriched for specific post-translational modifications. Its functions, designed as simple building blocks, are user-friendly, making it easy to test parameters and methods, and to construct customized analysis scenarios. These unique features position MCQR as a comprehensive toolbox, perfectly suited to the specific needs of MS-based proteomics experiments.

B4 Raf-like MAPKKK RAF24 regulates Arabidopsis thaliana flowering time through HISTONE MONO-UBIQUITINATION 2

The timing of flowering is a critical agronomic trait governed by an extensive and sophisticated regulatory network. To date, limited understanding of how posttranslational modifications regulate flowering time exists. Here, using Arabidopsis, we resolve a role for the B4 Raf-like MAPKKK protein kinase RAF24 in regulating flowering time. Loss of RAPIDLY ACCELERATED FIBROSARCOMA24 (RAF24) led to premature flowering time through altered expression of FLC and FT. Comparative phosphoproteomic analysis of raf24 and wild-type plants revealed a list of known flowering-related phosphoproteins from distinct flowering pathways displaying downregulated phosphorylation. Of these, the RING-type ubiquitin ligase HISTONE MONO-UBIQUITINATION 2 (HUB2) lacked phosphorylation in the absence of RAF24. Absence of RAF24 induced H2Bub1 overaccumulation, with protein-protein interactome analysis of HUB2 in the presence and absence of RAF24 influencing HUB2 protein interaction partners, such as H2B. HUB2 was also found to physically interact with SUCROSE NONFERMENTING KINASE 2.4 (SnRK2.4) and SnRK2.6, known substrates of RAF24. Using phospho-mimetic and phospho-ablative plant lines, we then validated the importance of HUB2 phosphorylation at serine 314 (S314) in maintaining appropriate flowering time. Our findings uncovered a novel biological role of RAF24, as a higher-order flowering regulator, while further implicating HUB2 as a centerpiece of flowering time regulation.

Self-Iron-Enriched Bacterial Membrane Nanovesicles for Cascade and Multi-Modal Antitumor Therapy

The integration of microbiology and nanotechnology offers a novel strategy for cancer treatment. In this study, we innovatively propose the use of Pseudomonas aeruginosa bacterial membranes as nanocarriers. These membranes possess a simple and unique self-enriching property for iron, which, in addition to the inherent immune effects of the membrane itself, can facilitate tumor chemodynamic therapy through Fenton reactions. The system encapsulates the anticancer drug β-Lapachone, which can generate a large amount of hydrogen peroxide within cells, further serving as a substrate for the Fenton reaction, leading to a cascade reaction that achieves a synergistic effect of three therapeutic modalities in tumor treatment. Moreover, the aptamer AS1411 is used to enhance tumor targeting and optimize drug delivery within the tumor microenvironment. This investigation presents a multimodal antitumor strategy that demonstrates enhanced antitumor effects both in vitro and in vivo, providing a new paradigm for the antitumor application of bacterial membrane nanocarriers.

Chemoproteomic Approach for Identifying Nuclear Arsenite-Binding Proteins

Trivalent arsenic, i.e., As(III), is the main form of arsenic species in the environment. Prolonged exposure to arsenicals through ingesting contaminated food and water has been implicated in the development of cancer and diabetes as well as cardiovascular and neurodegenerative diseases. A number of studies have been conducted to examine the mechanisms underlying the toxic effects of arsenite exposure, where As(III) was shown to displace Zn(II) and impair the functions of zinc-binding proteins. Considering that many zinc-binding proteins can bind to nucleic acids, we reason that systematic identification of arsenite-binding proteins in the nucleus may provide additional insights into the molecular targets of arsenite, thereby improving our understanding of the mechanisms of arsenic toxicity. Here, we conducted a quantitative proteomics experiment relying on affinity pull-down from nuclear protein lysate with a biotin-As(III) probe to identify nuclear arsenite-binding proteins. We uncovered a number of candidate As(III)-binding proteins that are involved in mRNA splicing, DNA repair, and replication. We also found that As(III) could bind to splicing factor 1 (SF1) and that this binding perturbs mRNA splicing in human cells. Together, our work provided insights into the mechanisms of As(III) toxicity by revealing new nuclear protein targets of As(III).

Proteomic profiling reveals common and region-specific protein signatures underlying tumor heterogeneity in cholangiocarcinoma

Cholangiocarcinoma (CCA), a neoplasm arising from biliary epithelial cells, is particularly widespread in Southeast Asia, with northeastern Thailand exhibiting the greatest prevalence attributed to Opisthorchis viverrini infection. This malignancy exhibits considerable molecular heterogeneity, leading to therapeutic resistance and recurrence. Comprehending its molecular mechanisms is essential for enhancing diagnostic and treatment approaches. Our research utilized multi-region LC-MS/MS proteomic analysis to investigate intratumor heterogeneity (ITH) in CCA. We examined 52 tumor areas and 13 neighboring tissues from 13 patients, concentrating on protein profiling, pathway analysis, differential protein expression, and the identification of shared and unique protein signatures. The findings indicated considerable inter-patient proteome variability, characterized by markedly distinct protein expressions among individuals, aligning with prior cancer research. Intra-tumor heterogeneity was apparent, with merely 18 proteins common to all tumor areas and patients, underscoring the intricacy of CCA. Significantly, the common proteins were associated with metabolic reprogramming and oxidative stress pathways, indicating possible indicators and therapeutic targets. This work highlights the significant proteome variability in CCA at both intra-tumor and inter-patient levels, underscoring the necessity for customized therapeutic approaches to tackle the disease's complexity and improve treatment outcomes.

Exhaled breath protein composition in patients hospitalised during the first wave of COVID-19

Coronavirus 2019 (COVID-19) leads to substantial morbidity and excess mortality all over the world which may be aggravated by the propensity of Severe Acute Respiratory Syndrome Coronavirus 2 to mutate. Mechanisms for development of severe COVID-19 are poorly understood. The air we exhale contains endogenous proteins and represents a highly accessible yet unexploited biological sample that can be collected without use of invasive procedures. We collected exhaled breath condensate samples from 28 patients hospitalised due to COVID-19 at admission and discharge using RTubes™. Bottom-up proteomic analysis of tandem mass-tag-labelled single exhaled breath samples was performed in 25 exhaled breath samples collected at admission and 13 samples collected at discharge using discovery-based nano-liquid chromatography-tandem mass spectrometry. In total, 232 proteins were identified in the exhaled breath samples after stringent data filtering. Most of the exhaled proteins were related to the immune systems function and regulation. The levels of four proteins, KRT77, DCD, CASP14 and SERPINB12 decreased from admission to discharge as patients generally recovered from the infection. These proteins are expressed in lung epithelium or macrophages and are associated with the regulation of inflammation drivers in COVID-19. In particular, the alarmins S100A8 and S100A9 accounted for 8% of the exhaled breath proteins. In conclusion, our study demonstrates that analysis of the exhaled breath protein composition can give insights into mechanisms related to inflammation and response to infections, and hereby also of severe COVID-19.Clinical Trial No: NCT04598620.

Differential Modulation of Endothelial Cell Functionality by LRP1 Expression in Fibroblasts and Cancer-Associated Fibroblasts via Paracrine signals and Matrix Remodeling

LRP1 is a multifunctional endocytosis receptor involved in the regulation of cancer cell aggressiveness, fibroblast phenotype and angiogenesis. In breast cancer microenvironment, cancer-associated fibroblasts (CAFs) play a crucial role in matrix remodeling and tumor niche composition. LRP1 expression was described in fibroblasts and CAFs but remains poorly understood regarding its impact on endothelial cell behavior and angiocrine signaling. We analyzed the angio-modulatory effect of LRP1 expression in murine embryonic fibroblasts (MEFs) and breast cancer-educated CAF2 cells. We employed conditioned media and fibroblast-derived matrices to model fibroblastic cells angiogenic effects on human umbilical vein endothelial cells (HUVEC). Neither the extracellular matrix assembled by MEFs knock-out for LRP1 (PEA-13) nor their secretome modify the migration of HUVEC as compared to wild-type. Conversely, LRP1-deficient CAF2 secretome and matrices stimulate endothelial cell migration. Using spheroids, we demonstrate that PEA-13 secretome does not affect HUVEC angio-invasion. By contrast, CAF2 secretome invalidated for LRP1 stimulates endothelial sprouting as compared to controls. In addition, it specifically stabilized peripheral VE-cadherin-mediated endothelial cell junctions. A global proteomic analysis revealed that LRP1 expression in CAFs orchestrates a specific mobilization of secreted matricial components, surface receptors and membrane-associated proteins at the endothelial cell surface, thereby illustrating the deep influence exerted by LRP1 in angiogenic signals emitted by activated fibroblasts.

Chronic ionizing radiation might suppress resistance to pathogens in aquatic plants without substantial oxidative stress

Chronic ionizing radiation causes elevated levels of DNA damage and reactive oxygen species in plants. Aquatic ecosystems in Chornobyl zone, a major radiological disaster site, are contaminated by harmful radionuclides. We focused on explaining the biochemical mechanisms responsible for the susceptibility of a wild aquatic plant (common reed, Phragmites australis) grown in Chornobyl zone to biotic stress. The fungal infection assay indicated that life in a radionuclide-contaminated environment might compromise plant immunity. Proteome profiling identified 1,867 proteins and we selected several dozen proteins with consistently higher and lower abundance in the samples from the littoral of contaminated lakes by hierarchical clustering. Discordant expression of coding genes pointed to posttranscriptional regulation. Proteins that accumulated in reed upon chronic irradiation suggested a biochemically stable phenotype with effective protection against reactive carbonyls. Simultaneously, proteins that depleted in plants collected from the littoral of radiologically contaminated lakes indicated worse stress resilience and enhanced susceptibility to biotic agents. Furthermore, the quantification of antioxidant enzyme activities and carbonylated proteins rebutted the idea about substantial oxidative stress in chronically irradiated plants. We advocate the necessity to consider increased pathogen sensitivity while developing policies for the management of radionuclide-contaminated areas.

Operational Taxon-Function Framework in MetaX: Unveiling Taxonomic and Functional Associations in Metaproteomics

Metaproteomics analyzes the functional dynamics of microbial communities by identifying peptides and mapping them to the most likely proteins and taxa. One challenge in this field lies in seamlessly integrating taxonomic and functional annotations to accurately represent the contributions of individual microbial taxa to functional diversity. We introduce MetaX, a comprehensive tool for analyzing taxon-function relationships in metaproteomics by mapping peptides to their lowest common ancestors and assigning functions based on proportional thresholds, ensuring accurate peptide-level mappings. Importantly, MetaX introduces the Operational Taxon-Function (OTF), a new conceptual unit for exploring microbial roles and interactions within ecosystems. Additionally, MetaX includes extensive statistical and visualization tools, establishing it as a robust platform for metaproteomics analysis. We validated MetaX by reanalyzing ex vivo gut microbiome metaproteomic data exposed to various sweeteners, yielding more detailed results than traditional protein analysis. Furthermore, using the peptide-centric approach and OTF, we observed that Parabacteroides distasonis significantly responds to certain sweeteners, highlighting its role in modifying specific metabolic functions. With its intuitive, user-friendly interface, MetaX facilitates a detailed study of the complex interactions between microbial taxa and their functions in metaproteomics. It enhances our understanding of microbial roles in ecosystems and health.

The plant-beneficial fungus Trichoderma harzianum T22 modulates plant metabolism and negatively affects Nezara viridula

BACKGROUND

Plant-beneficial fungi play an important role in enhancing plant health and resistance against biotic and abiotic stresses. Although extensive research has focused on their role in eliciting plant defences against pathogens, their contribution to induced resistance against herbivorous insects and the underlying mechanisms remain poorly understood. In this study, we used insect bioassays and untargeted metabolomics to investigate the impact of root inoculation of sweet pepper with the plant-beneficial fungus Trichoderma harzianum T22 on direct defence responses against the insect herbivore Nezara viridula.

RESULTS

We observed reduced relative growth rate of N. viridula on leaves of fungus-inoculated plants, with no change in mortality. Untargeted metabolomic analyses revealed that inoculation with T. harzianum did not affect the leaf metabolome in the absence of herbivory five weeks after inoculation. However, compared to non-inoculated plants, inoculated plants exhibited significant metabolic alterations in herbivore-damaged leaves following N. viridula feeding, while changes in the metabolic profile of distant leaves were less pronounced. Notably, metabolites involved in the shikimate-phenylpropanoid pathway, known to be involved in plant defence responses, displayed higher accumulation in damaged leaves of inoculated plants compared to non-inoculated plants.

CONCLUSION

Our results indicate that root inoculation with T. harzianum T22 affects plant defences against N. viridula, leading to reduced insect performance. Metabolite-level effects were primarily observed in damaged leaves, suggesting that the priming effect mainly results in localized metabolite accumulation at the site of attack. Future research should focus on identifying the detected compounds and determining their role in impairing N. viridula performance.

Retroviral adapters hijack the RNA helicase UPF1 in a CRM1/XPO1-dependent manner and reveal proviral roles of UPF1

The hijacking of CRM1 export is an important step of the retroviral replication cycle. Here, we investigated the consequences of this hijacking for the host. During HTLV-1 infection, we identified that this hijacking by the viral protein Rex favours the association between CRM1 and the RNA helicase UPF1, leading to a decreased affinity of UPF1 for cellular RNA and its nuclear retention. As a consequence, we found that the nonsense-mediated mRNA decay (NMD), known to have an antiviral function, was inhibited. Corroborating these results, we described a similar process with Rev, the functional homolog of Rex from HIV-1. Unexpectedly, we also found that, for HTLV-1, this process is coupled with the specific loading of UPF1 onto vRNA, independently of NMD. In this latter context, UPF1 positively regulates several steps of the viral replication cycle, from the nuclear export of vRNA to the production of mature viral particles.

SUMO2/3 modification of transcription-associated proteins controls cell viability in response to oxygen and glucose deprivation-mediated stress

Because limited oxygen and glucose supply to tissues is a serious challenge that cells must properly measure to decide between surviving or triggering cell death, organisms have developed accurate mechanisms for sensing and signaling these conditions. In recent years, signaling through posttranslational modification of proteins by covalent attachment of the Small Ubiquitin-like Modifier (SUMO) is gaining notoriety. Enhanced sumoylation in response to oxygen and glucose deprivation (OGD) constitutes a safeguard mechanism for cells and a new avenue for therapeutic intervention. However, indiscriminate global sumoylation can limit the therapeutic potential that a more precise action on selected targets would have. To clear up this, we have conducted a proteomic approach in P19 cells to identify specific SUMO targets responding to OGD and to investigate the potential that these targets and their sumoylation have in preserving cells from death. Proteins undergoing sumoylation in response to OGD are mostly related to transcription and RNA processing, and the majority of them are rapidly desumoylated when restoring oxygen and glucose (ROG), confirming the high dynamics of this modification. Since OGD is linked to brain ischemia, we have also studied cells differentiated into neurons. However, no major differences have been observed between the SUMO-proteomes of proliferating and differentiated cells. We show that the overexpression of the transcription factor SOX2 or the SUMO ligase PIAS4 has a manifest cell protective effect largely depending on their sumoylation, and that maintaining the sumoylation capacity of the coregulator NAB2 is also important to face OGD. Conversely, sumoylation of the pluripotency factor OCT4, which is sumoylated under OGD, and is a target of the SUMO protease SENP7 for desumoylation after ROG, seems to block its cell survival-promoting capacity. Thus, better outcomes in cell protection would rely on the appropriate combination of sumoylated and non-sumoylated forms of selected factors.

Conserved role of the SERK-BIR module in development and immunity across land plants

SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASES (SERKs), which are subfamily II of leucine-rich repeat receptor-like kinases (LRR-RLKs), play diverse roles in development and immunity in the angiosperm Arabidopsis thaliana. AtSERKs act as co-receptors for many LRR-RLKs, including BRASSINOSTEROID INSENSITIVE 1 (BRI1) and FLAGELLIN SENSITIVE 2 (FLS2).1,2,3,4 The conserved tyrosine (Y) residue in AtSERK3 is crucial for signaling specificity in differentiating BRI1- and FLS2-mediated pathways.5 BRI1-ASSOCIATED RECEPTOR KINASE 1 (BAK1)-INTERACTING RECEPTOR-LIKE KINASES (BIRs) interact with SERKs under resting conditions, negatively regulating SERK-mediated pathways.6,7 SERK and BIR are highly conserved in land plants, whereas BRI1 and FLS2 homologs are absent or poorly conserved in bryophyte lineages.8,9 The biological functions of SERK homologs in non-flowering plants are largely unknown. The genome of the liverwort Marchantia polymorpha encodes single homologs for SERK and BIR, namely MpSERK and MpBIR.9 We here show that Mpserk disruptants display growth and developmental defects with no observable sexual or vegetative reproduction. Complementation analysis revealed a contribution of the conserved Y residue of MpSERK to growth. Proximity-labeling-based interactomics identified MpBIR as a MpSERK interactor. Mpbir disruptants displayed defects in reproductive organ development. Patterns of development- and immunity-related gene expression in Mpserk and Mpbir were antagonistic, suggesting that MpBIR functions as an MpSERK repressor. The pathogenic bacterium Pseudomonas syringae pv. tomato DC3000 grew poorly on Mpbir, indicating a significant role of the MpSERK-MpBIR module in immunity. Taken together, we propose that the SERK-BIR functional module was already regulating both development and immunity in the last common ancestor of land plants.

All-at-once spatial proteome profiling of complex tissue context with single-cell-type resolution by proximity proteomics

Spatial proteomics enables in-depth mapping of tissue architectures, mostly achieved by laser microdissection-mass spectrometry (LMD-MS) and antibody-based imaging. However, trade-offs among sampling precision, throughput, and proteome coverage still limit the applicability of these strategies. Here, we propose proximity labeling for spatial proteomics (PSPro) by combining precise antibody-targeted biotinylation and efficient affinity purification for all-at-once cell-type proteome capture with sub-micrometer resolution from single tissue slice. With fine-tuned labeling parameters, PSPro shows reliable performance in benchmarking against flow cytometry- and LMD-based proteomic workflows. We apply PSPro to tumor and spleen slices, enriching thousands of proteins containing known markers from ten cell types. We further incorporate LMD into PSPro to facilitate comparison of cell subpopulations from the same tissue slice, revealing spatial proteome heterogeneity of cancer cells and immune cells in pancreatic tumor. Collectively, PSPro converts the traditional "antibody-epitope" paradigm to an "antibody-cell-type proteome" for spatial biology in a user-friendly manner. A record of this paper's transparent peer review process is included in the supplemental information.

Discovery of Proteoforms Associated with Alzheimer's Disease Through Quantitative Top-Down Proteomics

The complex nature of Alzheimer's disease (AD) and its heterogenous clinical presentation has prompted numerous large-scale -omic analyses aimed at providing a global understanding of the pathophysiological processes involved. AD involves isoforms, proteolytic products, and post-translationally modified proteins such as amyloid beta (Aβ) and microtuble-associated protein tau. Top-down proteomics (TDP) directly measures these species, and thus, offers a comprehensive view of pathologically relevant proteoforms that are difficult to analyze using traditional proteomic techniques. Here, we broadly explored associations between proteoforms and clinicopathological traits of AD by deploying a quantitative TDP approach across frontal cortex of 103 subjects selected from the ROS and MAP cohorts. The approach identified 1,213 proteins and 11,782 proteoforms, of which 154 proteoforms had at least one significant association with a clinicopathological phenotype. One important finding included identifying Aβ C-terminal truncation state as the key property for differential association between amyloid plaques and cerebral amyloid angiopathy (CAA). Furthermore, various N-terminally truncated forms of Aβ had noticeably stronger association with amyloid plaques and global cognitive function. Additionally, we discovered six VGF neuropeptides that were positively associated with cognitive function independent of pathological burden. The database of brain cortex proteoforms provides a valuable context for functional characterization of the proteins involved in Alzheimer's disease and other late-onset brain pathologies.

MGAT3 and MGAT5 overexpression alters the protein cargo of extracellular vesicles released by metastatic melanoma cells

Extracellular vesicles (EVs) are potential non-invasive diagnostic, prognostic and therapeutic tools. Additionally, they are important contributors to tumorigenesis. Glycosylation has been found to modulate the composition of the EV proteome. Increased amounts of β1,6-branched N-glycans, synthesized by N-acetylglucosaminyltransferase V (GnT-V), are most commonly observed in melanoma and are associated with decreased cell adhesion and increased metastasis. The opposite effect is caused by the addition of bisecting GlcNAc by N-acetylglucosaminyltransferase III (GnT-III). To date, the impact of these enzymes on EV cargo in melanoma remains unexplored. Flow cytometry was used to study the surface glycosylation of genetic variants of WM266-4 melanoma cells with induced overexpression of GnT-III or GnT-V encoding genes (MGAT3 or MGAT5) and EVs released by these cells. LC-MS/MS proteomics was applied to analyze the effect of altered glycosylation on the proteome of released EVs, followed by detailed bioinformatic analysis. Flow cytometry analysis revealed dynamic changes in the surface glycosylation of EVs derived from melanoma cells overexpressing MGAT3 or MGAT5. Induced overexpression of MGAT3 or MGAT5 also caused significant changes in the proteome of EVs. The proteomic analysis identified a total of 1770 microvesicular and 704 exosomal proteins that play different roles in melanoma progression, including those with established diagnostic/prognostic potential and those closely associated with melanoma onset. Proteomic profiling of EVs derived from cells overexpressing MGAT3 and MGAT5 revealed functional changes in EV protein content driven by glycosylation modifications. The study presented a potential multifaced application of melanoma-derived EVs for diagnostic and prognostic purposes.

Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data

Mass spectrometry is essential for analyzing and quantifying biological samples. The timsTOF platform is a prominent commercial tool for this purpose, particularly in bottom-up acquisition scenarios. The additional ion mobility dimension requires more complex data processing, yet most current software solutions for timsTOF raw data are proprietary or closed-source, limiting integration into custom workflows. We introduce rustims, a framework implementing a flexible toolbox designed for processing timsTOF raw data, currently focusing on data-dependent acquisition (DDA-PASEF). The framework employs a dual-language approach, combining efficient, multithreaded Rust code with an easy-to-use Python interface. This allows for implementations that are fast, intuitive, and easy to integrate. With imspy as its main Python scripting interface and sagepy for Sage search engine bindings, rustims enables fast, integrable, and intuitive processing. We demonstrate its capabilities with a pipeline for DDA-PASEF data including rescoring and integration of third-party tools like the Prosit intensity predictor and an extended ion mobility model. This pipeline supports tryptic proteomics and nontryptic immunopeptidomics data, with benchmark comparisons to FragPipe and PEAKS. Rustims is available on GitHub under the MIT license, with installation packages for multiple platforms on PyPi and all analysis scripts accessible via Zenodo.

Glycoproteomics Analysis of Triple Wild-Type Lung Adenocarcinoma Tissue Samples

Lung cancer has both high incidence and mortality, making it the leading cause of cancer-related mortality worldwide. It is a highly heterogeneous disease, with several histological subtypes and genetic alterations that influence prognosis and available treatment options. Here, we focus on the triple wild-type (TWT) subtype of lung adenocarcinoma (LUAD) that lacks the three most common actionable genetic alterations, subsequently making targeted therapies inaccessible. In this study, our aim was the mass spectrometry-based proteomic and N-glycoproteomic characterization of tumor and adjacent normal lung tissue regions from individuals (n = 12) with TWT LUAD. We found several proteins previously identified as potential prognostic or diagnostic biomarkers in LUAD and described dysregulated biological processes, giving an overview of the general differences between healthy and tumor tissue. Also, we highlight specific signatures detected using N-glycoproteomics and discuss their potential and importance based on data from databases and literature. To the best of our knowledge, this is the first N-glycoproteomics-focused study on TWT LUAD, and it could provide a valuable resource for further studies into this less well characterized subtype of lung cancer. For instance, we report altered N-glycosylation for several glycoproteins implicated in LUAD and other cancers that could have functional importance connected to the disease.

Unifying the analysis of bottom-up proteomics data with CHIMERYS

Proteomic workflows generate vastly complex peptide mixtures that are analyzed by liquid chromatography-tandem mass spectrometry, creating thousands of spectra, most of which are chimeric and contain fragment ions from more than one peptide. Because of differences in data acquisition strategies such as data-dependent, data-independent or parallel reaction monitoring, separate software packages employing different analysis concepts are used for peptide identification and quantification, even though the underlying information is principally the same. Here, we introduce CHIMERYS, a spectrum-centric search algorithm designed for the deconvolution of chimeric spectra that unifies proteomic data analysis. Using accurate predictions of peptide retention time, fragment ion intensities and applying regularized linear regression, it explains as much fragment ion intensity as possible with as few peptides as possible. Together with rigorous false discovery rate control, CHIMERYS accurately identifies and quantifies multiple peptides per tandem mass spectrum in data-dependent, data-independent or parallel reaction monitoring experiments.

Cdc48 plays a crucial role in redox homeostasis through dynamic reshaping of its interactome during early stationary phase

Most microbial cells on earth predominantly exist in non-proliferating, dormant conditions, such as the stationary state. The stationary phase is a crucial stage during the cellular lifespan, which requires homeostatic rewiring for long-term viability and rapid responses to environmental changes. Here, we show that entry to the stationary phase in yeast is accompanied by increased cytosolic and mitochondrial oxidation, imposing stress on the proteostasis network. We establish a functional link between redox and protein homeostasis, mediated by a key protein quality control member, Cdc48/p97/VCP. Comparative proteomic analysis of post-mitotic yeast cells reveals that while the global proteome remains largely stable during the first stages of stationary phase, the Cdc48 interactome undergoes significant remodeling, including altered interactions with antioxidants and its cofactors Shp1/Ubx1 and Ubx2. To challenge yeast Cdc48's capacity as a redox-switch protein during the early stages of the stationary phase, we utilized redox proteomics to map changes in reversible oxidation modification on Cdc48's cysteines upon entry to the stationary phase. We revealed the temporal and reversible oxidation of Cdc48-Cys115 as a key regulatory event essential for stationary-phase survival and interactome modulation. Cys115-to-serine mutation significantly reduced longevity and increased oxidative stress sensitivity, correlating with disrupted interactions between Cdc48 and antioxidants, and cofactor Shp1, specifically with the phosphorylated form of Shp1. Taken together, these findings identify a new thiol switch protein in the protein degradation pathway, while further defining novel roles for Cdc48 in reshaping the proteome during the yeast stationary phase.

A Site-Specific Photo-Crosslinking Proteomics Approach Provides Insights into Noncanonical Pyroptotic Caspase-4 Substrates

Inflammatory caspases (1/4/5) are key effectors in the process of pyroptosis by cleaving and activating the pore-forming protein gasdermin D (GSDMD). Unlike other caspases whose substrates have been well characterized, the substrates for caspase-4, which mediate noncanonical pyroptosis, remain poorly understood. Here, we combined noncanonical amino acids, photo-crosslinking, and proteomics to profile caspase-4 substrates, enabling the capture of transient protein interactions with activated caspase-4. A set of new substrates were identified by photo-crosslinking mass spectrometry, revealing the signaling pathway and biological process affected by pyroptosis. Notably, we found that AKT1 is cleaved at D108, which removes its autoinhibition and membrane localization domain, resulting in the release of activated AKT1. Our results also showed the precursor of caspase-5/12 could be cleaved by caspase-4 to form the p20/p10 active conformation, uncovering a previously unrecognized pyroptotic caspase cascade. Overall, this study presents an approach for identifying caspase-4 substrates and offers further understanding of noncanonical pyroptosis.

Structural determinants of mucins in influenza virus inhibition: The role of sialylated glycans and molecular size

Mucins are heavily glycosylated proteins that play a crucial role in protecting mucosal surfaces against pathogens, including influenza viruses. This study investigates the antiviral properties of bovine submaxillary mucins (BSM) as a model for oral mucins against the influenza virus (A/H3N2 subtype), focusing on glycan composition and mucin size. BSM was purified, and characterized by proteomic and glycomic analysis and its antiviral efficacy was assessed after selective removal of sialic acids, N-glycans, or all glycans via enzymatic and chemical treatments. We employed virus binding and inhibition assays, including microscale thermophoresis (MST) and hemagglutination inhibition (HAI), to characterize processed mucins for structure activity correlations. Removal of sialic acids reduced BSM's antiviral activity by over 10-fold, while complete glycan removal abolished it entirely, highlighting sialylated O-glycans as critical for viral inhibition. N-glycan removal had minimal impact on antiviral efficacy. A size-dependent antiviral effect was observed: smaller mucin fragments (∼50 and 330 kDa), which retained comparable O-glycosylation patterns, showed significantly reduced inhibition and viral binding affinity several orders of magnitude below intact BSM. These findings underscore the importance of mucin size and sialylated O-glycans in antiviral defense mechanisms against influenza.

Ergosterol-induced immune response in barley involves phosphorylation of phosphatidylinositol phosphate metabolic enzymes and activation of diterpene biosynthesis

Lipids play crucial roles in plant-microbe interactions, functioning as structural components, signaling molecules, and microbe-associated molecular patterns (MAMPs). However, the mechanisms underlying lipid perception and signaling in plants remain largely unknown. Here, we investigate the immune responses activated in barley (Hordeum vulgare) by lipid extracts from the beneficial root endophytic fungus Serendipita indica and compare them to responses elicited by chitohexaose and the fungal sterol ergosterol. We demonstrate that S. indica lipid extract induces hallmarks of pattern-triggered immunity (PTI) in barley. Ergosterol emerged as the primary immunogenic component and was detected in the apoplastic fluid of S. indica-colonized barley roots. Notably, S. indica colonization suppresses the ergosterol-induced burst of reactive oxygen species (ROS) in barley. By employing a multi-omics approach, which integrates transcriptomics, phosphoproteomics, and metabolomics, we provide evidence for the phosphorylation of phosphatidylinositol phosphate (PIP) metabolic enzymes and activation of diterpene biosynthesis upon exposure to fungal lipids. Furthermore, we show that phosphatidic acid (PA) enhances lipid-mediated apoplastic ROS production in barley. These findings indicate that plant lipids facilitate immune responses to fungal lipids in barley, providing new insights into lipid-based signaling mechanisms in plant-microbe interactions.

Circadian Proteomics Reassesses the Temporal Regulation of Metabolic Rhythms by Chlamydomonas Clock

Circadian clocks execute temporal regulation of metabolism by modulating the timely expression of genes. Clock regulation of mRNA synthesis was envisioned as the primary driver of these daily rhythms. mRNA oscillations often do not concur with the downstream protein oscillations, revealing the importance to study protein oscillations. Chlamydomonas reinhardtii is a well-studied miniature plant model. We quantitatively probed the Chlamydomonas proteome for two subsequent circadian cycles using high throughput SWATH-DIA mass spectrometry. We quantified > 1000 proteins, half of which demonstrate circadian rhythms. Among these rhythmic proteins, > 90% peak around subjective midday or midnight. We uncovered key enzymes involved in Box C/D pathway, amino acid biosynthesis, fatty acid (FA) biosynthesis and peroxisomal β-oxidation of FAs are driven by the clock, which were undocumented from earlier transcriptomic studies. Proteins associated with key biological processes such as photosynthesis, redox, carbon fixation, glycolysis and TCA cycle show extreme temporal regulation. We conclude that circadian proteomics is required to complement transcriptomic studies to understand the complex clock regulation of organismal biology. We believe our study will not only refine and enrich the evaluation of temporal metabolic processes in C. reinhardtii but also provide a novel understanding of clock regulation across species.

Pharmacological targeting of BMAL1 modulates circadian and immune pathways

The basic helix-loop-helix PER-ARNT-SIM (bHLH-PAS) proteins BMAL1 and CLOCK heterodimerize to form the master transcription factor governing rhythmic gene expression. Owing to connections between circadian regulation and numerous physiological pathways, targeting the BMAL1-CLOCK complex pharmacologically is an attractive entry point for intervening in circadian-related processes. In this study, we developed a small molecule, Core Circadian Modulator (CCM), that targets the cavity in the PASB domain of BMAL1, causing it to expand, leading to conformational changes in the PASB domain and altering the functions of BMAL1 as a transcription factor. Biochemical, structural and cellular investigations validate the high level of selectivity of CCM in engaging BMAL1, enabling direct access to BMAL1-CLOCK cellular activities. CCM induces dose-dependent alterations in PER2-Luc oscillations and orchestrates the downregulation of inflammatory and phagocytic pathways in macrophages. These findings collectively reveal that the BMAL1 protein architecture is inherently configured to enable the binding of chemical ligands for functional modulation.

Engineered orthogonal and obligate bacterial commensalism mediated by a non-standard amino acid

Microorganisms can be genetically engineered for intrinsic biological containment based on synthetic chemical provision. However, reliance on an exogenous chemical limits the contexts where a contained microorganism could survive. Here we design an orthogonal obligate commensalism in Escherichia coli that autonomously creates environments permissive for survival of a partner microbe. We engineer one E. coli strain (the producer) to biosynthesize a non-standard amino acid (nsAA) from simple carbon sources through heterologous expression. We engineer a second E. coli strain (the utilizer) to rely on the same nsAA for growth as a synthetic auxotroph, with a 14-day escape rate of 2.8 × 10-9 escapees per colony-forming unit. Co-culture experiments show utilizer dependence on the producer, with no escape detected during co-inoculation of ~107 colony-forming units of utilizer and a non-producer E. coli strain. Dependence is maintained within a simplified synthetic maize root-associated community. This work provides ecological insights and presents a potential biocontainment strategy independent of an exogenous chemical.

The role of indole-3-acetic acid and characterization of PIN transporters in complex streptophyte alga Chara braunii

Auxin, indole-3-acetic acid (IAA), is a key phytohormone with diverse morphogenic roles in land plants, but its function and transport mechanisms in algae remain poorly understood. We therefore aimed to explore the role of IAA in a complex, streptophyte algae Chara braunii. Here, we described novel responses of C. braunii to IAA and characterized two homologs of PIN auxin efflux carriers: CbPINa and CbPINc. We determined their localization in C. braunii using epitope-specific antibodies and tested their function in heterologous land plant models. Further, using phosphoproteomic analysis, we identified IAA-induced phosphorylation events. The thallus regeneration assay showed that IAA promotes thallus elongation and side branch development. Immunolocalization of CbPINa and CbPINc confirmed their presence on the plasma membrane of vegetative and generative cells of C. braunii. However, functional assays in tobacco BY-2 cells demonstrated that CbPINa affects auxin transport, whereas CbPINc does not. The IAA is effective in the acceleration of cytoplasmic streaming and the phosphorylation of evolutionary conserved targets such as homolog of RAF-like kinase. These findings suggest that, although canonical PIN-mediated auxin transport mechanisms might not be fully conserved in Chara, IAA is involved in morphogenesis and fast signaling processes.

Plasma protein corona of liposomes loaded with a phospholipid-allocolchicinoid conjugate enhances their anti-inflammatory potential

Today colchicine is considered as a possible new treatment for cardiovascular diseases. Its physiological effects have been shown to be primarily due to the intra-leukocyte concentrations. Nanoparticulate formulations could help accumulation of colchicine in phagocytic cells. Previously we formulated liposomes loaded with a colchicine analog in the form of an enzyme-responsive conjugate with phosphatidylcholine (aC-PC) and showed acceptable stability of the formulation in human plasma. Here, we investigated how protein coronas formed on a series of aC-PC-bearing liposomes in human plasma affected their interactions with leukocytes and endothelial cells. Liposome-protein complexes were analyzed by shotgun proteomics. Liposomes 25C with the highest load of aC-PC (25 %) were distinguished by a three times more massive protein corona and specific profile of proteins, including enrichment with ApoD and galectin-3-binding protein, which may affect the inflammation-associated signaling. Differences in the protein coronas did not noticeably affect liposome uptake by cultured monocytes and endotheliocytes, although the level of uptake decreased in the presence of plasma proteins. Nor did the composition of liposomes affect the course of phagocytosis by leukocytes in the blood ex vivo. The effects of protein coronas were manifested in the suppression of the production of inflammatory chemokine MCP-1 (and to a much lesser extent IL-8) by stimulated peripheral blood monocytes about 1.5 times compared with naked liposomes. In the case of liposomes 25C the inhibition was complete. These liposomes are considered the most promising for further preclinical studies.

Whole-exome tumor-agnostic ctDNA analysis enhances minimal residual disease detection and reveals relapse mechanisms in localized colon cancer

In stage 2-3 colon cancer (CC), postsurgery circulating tumor DNA (ctDNA) assessment is crucial for guiding adjuvant chemotherapy (ACT) decisions. While existing assays detect ctDNA and help identify high-risk persons with CC for recurrence, their limited sensitivity after surgery poses challenges in deciding on ACT. Additionally, a substantial portion of persons with CC fail to clear ctDNA after ACT, leading to recurrence. In this study, we performed whole-exome sequencing (WES) of ctDNA at different time points in participants with relapsed CC in two independent cohorts, alongside transcriptomic and proteomic analyses of metastases, to enhance comprehension of progression mechanisms. A plasma WES-based tumor-agnostic assay demonstrated higher sensitivity in detecting minimal residual disease (MRD) compared to current assays. Immune evasion appears to be the primary driver of progression in the localized CC setting, indicating the potential efficacy of immunotherapy for microsatellite stability in persons with CC. Organoid modeling further supports the promising potential of targeted therapy in eradicating MRD, surpassing conventional treatments.

Omic AI reveals new autophagy regulators from the Atg1 interactome in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, Atg1 is a core autophagy-related (Atg) protein kinase (PK) in regulating macroautophagy/autophagy, by physically interacting with numerous other proteins, or by phosphorylating various substrates. It is unclear how many Atg1-interacting partners and substrates are also involved in regulating autophagy. Here, we conducted transcriptomic, proteomic and phosphoproteomic profiling of Atg1-dependent molecular landscapes during nitrogen starvation-triggered autophagy, and detected 244, 245 and 217 genes to be affected by ATG1 in the autophagic process at mRNA, protein, and phosphorylation levels, respectively. Based on the Atg1 interactome, we developed a novel artificial intelligence (AI) framework, inference of autophagy regulators from multi-omic data (iAMD), and predicted 12 Atg1-interacting partners and 17 substrates to be potentially functional in autophagy. Further experiments validated that Rgd1 and Whi5 are required for bulk autophagy, as well as physical interactions and co-localizations with Atg1 during autophagy. In particular, we demonstrated that 2 phosphorylation sites (p-sites), pS78 and pS149 of Whi5, are phosphorylated by Atg1 to regulate the formation of Atg1 puncta during autophagy initiation. A working model was illustrated to emphasize the importance of the Atg1-centered network in yeast autophagy. In addition, iAMD was extended to accurately predict Atg proteins and autophagy regulators from other PK interactomes, indicating a high transferability of the method. Taken together, we not only revealed new autophagy regulators from the Atg1 interactome, but also provided a useful resource for further analysis of yeast autophagy.

Antibody-guided identification of Achromobacter xylosoxidans protein antigens in cystic fibrosis

Persistent bacterial airway infection is a hallmark feature of cystic fibrosis (CF). Achromobacter spp. are gram-negative rods that can cause persistent airway infection in people with CF (pwCF), but the knowledge of host immune responses to these bacteria is limited. The aim of this study was to investigate if patients develop antibodies against Achromobacter xylosoxidans, the most common Achromobacter species, and to identify the bacterial antigens that induce specific IgG responses. Seven serum samples from pwCF with Achromobacter infection were screened for antibodies against bacteria in an ELISA coated with A. xylosoxidans, A. insuavis, or Pseudomonas aeruginosa. Sera from pwCF with or without P. aeruginosa infection (n = 22 and 20, respectively) and healthy donors (n = 4) were included for comparison. Serum with high titers to A. xylosoxidans was selected for affinity purification of bacterial antigens using serum IgGs bound to protein G beads. The resulting IgG-antigen complexes were then analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Selected antigens of interest were produced in recombinant form and used in an ELISA to confirm the results. Four of the seven patients with Achromobacter infection had serum antibodies against Achromobacter. Using patient serum-IgG for affinity purification of A. xylosoxidans proteins, we identified eight antigens. Three of these, which were not targeted by anti-P. aeruginosa antibodies, were expressed recombinantly for further validation: dihydrolipoyl dehydrogenase (DLD), type I secretion C-terminal target domain-containing protein, and domain of uncharacterized function 336 (DUF336). While specific IgG against all three recombinant antigens was confirmed in the patient serum with high titers against Achromobacter, DLD and DUF336 showed the least binding to serum IgG from pwCF without Achromobacter spp. infection. Using serum IgG affinity purification in combination with LC-MS/MS and confirming the results using ELISA against recombinant proteins, we have identified bacterial antigens from A. xylosoxidans.IMPORTANCEAchromobacter species are opportunistic pathogens that can cause airway infections in people with cystic fibrosis. In this patient population, persistent Achromobacter infection is associated with low lung function, but the knowledge about bacterial interactions with the host is currently limited. In this study, we identify protein antigens that induce specific antibody responses in the host. The identified antigens may potentially be useful in serological assays, serving as a complement to culturing methods for the diagnosis and surveillance of Achromobacter infection.

TAF2 condensation in nuclear speckles links basal transcription factor TFIID to RNA splicing factors

TFIID is an essential basal transcription factor, crucial for RNA polymerase II (pol II) promoter recognition and transcription initiation. The TFIID complex consists of the TATA binding protein (TBP) and 13 TBP-associated factors (TAFs) that contain intrinsically disordered regions (IDRs) with currently unknown functions. Here, we show that a conserved IDR drives TAF2 to nuclear speckle condensates independently of other TFIID subunits. Quantitative mass spectrometry analyses reveal TAF2 proximity to RNA splicing factors including specific interactions of the TAF2 IDR with SRRM2 in nuclear speckles. Deleting the IDR from TAF2 does not majorly impact global gene expression but results in changes of alternative splicing events. Further, genome-wide binding analyses suggest that the TAF2 IDR impedes TAF2 promoter association by guiding TAF2 to nuclear speckles. This study demonstrates that an IDR within the large multiprotein complex TFIID controls nuclear compartmentalization and thus links distinct molecular processes, namely transcription initiation and RNA splicing.

Expanding the Allelic and Clinical Heterogeneity of Movement Disorders Linked to Defects of Mitochondrial Adenosine Triphosphate Synthase

BACKGROUND

Defects of mitochondrial ATP synthase (ATPase) represent an emerging, yet incompletely understood group of neurodevelopmental diseases with abnormal movements.

OBJECTIVE

The aim of this study was to redefine the phenotypic and mutational spectrum of movement disorders linked to the ATPase subunit-encoding genes ATP5F1A and ATP5F1B.

METHODS

We recruited regionally distant patients who had been genome or exome sequenced. Fibroblast cultures from two patients were established to perform RNA sequencing, immunoblotting, mass spectrometry-based high-throughput quantitative proteomics, and ATPase activity assays. In silico three-dimensional missense variant modeling was performed.

RESULTS

We identified a patient with developmental delay, myoclonic dystonia, and spasticity who carried a heterozygous frameshift c.1404del (p.Glu469Serfs*3) variant in ATP5F1A. The patient's cells exhibited significant reductions in ATP5F1A mRNA, underexpression of the α-subunit of ATPase in association with other aberrantly expressed ATPase components, and compromised ATPase activity. In addition, a novel deleterious heterozygous ATP5F1A missense c.1252G>A (p.Gly418Arg) variant was discovered, shared by three patients from two families with hereditary spastic paraplegia (HSP). This variant mapped to a functionally important intersubunit communication site. A third heterozygous variant, c.1074+1G>T, affected a canonical donor splice site of ATP5F1B and resulted in exon skipping with significantly diminished ATP5F1B mRNA levels, as well as impaired ATPase activity. The associated phenotype consisted of cerebral palsy (CP) with prominent generalized dystonia.

CONCLUSIONS

Our data confirm and expand the role of dominant ATP5F1A and ATP5F1B variants in neurodevelopmental movement disorders. ATP5F1A/ATP5F1B-related ATPase diseases should be considered as a cause of dystonia, HSP, and CP. © 2025 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

An atlas of ferroptosis-induced secretomes

Cells undergoing regulated necrosis systemically communicate with the immune system via the release of protein and non-protein secretomes. Ferroptosis is a recently described iron-dependent type of regulated necrosis driven by massive lipid peroxidation. While membrane rupture occurs during ferroptosis, a comprehensive appraisal of ferroptotic secretomes and their potential biological activity has been lacking. Here, we apply a multi-omics approach to provide an atlas of ferroptosis-induced secretomes and reveal a novel function in macrophage priming. Proteins with assigned DAMP and innate immune system function, such as MIF, heat shock proteins (HSPs), and chaperones, were released from ferroptotic cells. Non-protein secretomes with assigned inflammatory function contained oxylipins as well as TCA- and methionine-cycle metabolites. Interestingly, incubation of bone marrow-derived macrophages (BMDMs) with ferroptotic supernatants induced transcriptional reprogramming consistent with priming. Indeed, exposure to ferroptotic supernatants enhanced LPS-induced cytokine production. These results define a catalog of ferroptosis-induced secretomes and identify a biological activity in macrophage priming with important implications for the fine-tuning of inflammatory processes.

High-confidence glycosomal membrane protein inventory unveils trypanosomal peroxin PEX15

Trypanosomatid parasite infections cause Chagas disease, human African trypanosomiasis, and leishmaniasis, affecting over 12 million people worldwide. Glycosomes, the peroxisome-related organelles of trypanosomes, are essential for survival, making their metabolic functions and biogenesis mediated by peroxins (PEXs) suitable drug targets. We report a comprehensive protein inventory of glycosomal membranes, defined through advanced subcellular membrane protein profiling combined with quantitative mass spectrometry and including 28 high-confidence glycosomal membrane proteins. We validate four previously unknown glycosomal membrane proteins, including a tail-anchored protein, which we show to be the long-sought Trypanosoma PEX15. Despite low sequence similarity, Trypanosoma PEX15 exhibits structural and topological similarities with its yeast and human counterparts, and it is essential for glycosome biogenesis and parasite survival. Considering the low degree of conservation with its human counterpart, PEX15 is a promising target for drug development. This inventory is an important resource for characterizing glycosome biology and therapeutic development.