Interstitial lung disease (ILD) is an umbrella term representing a heterogeneous group of restrictive lung disorders with destructive abnormalities in the lung interstitium. The overlapping clinical onset of various ILD subtypes poses significant challenges in diagnosis and management of the disease. Various omics technologies have explored disease-specific molecular markers, crucial for understanding the complex pathophysiology underlying disease progression. Proteomics, a rapidly advancing high-throughput omics tool, captures dynamic protein changes within a biological system, depicting its actual functional state. This enables comprehensive proteome profiling, facilitating the identification of specific biomarkers and pathways, thereby enhancing diagnostic precision and paving the way for targeted therapeutic interventions. This review highlights recent proteomic discoveries in idiopathic pulmonary fibrosis, autoimmune ILDs, exposure-related ILDs, and sarcoidosis, including emerging therapeutic avenues. It summarizes dysregulated pathways and potential biomarkers crucial for differential diagnosis, prognosis, disease progression, and treatment responses. The pathogenesis of ILD involves complex interactions of complement activation, humoral immune responses, and extracellular matrix organization pathways, and the expression levels of these pathway mediators vary across ILD stages and subtypes. Further validation of these pathways and their mediators through multicentric, large-cohort studies across diverse geographical locations is needed to enhance disease understanding and develop ”true” clinical biomarkers.

Modified electroconvulsive therapy (MECT) is an effective treatment for mood and psychiatric disorders and provides rapid and significant improvements in severe symptoms of several mental health conditions. The basis and molecular mechanisms underlying the therapeutic effects of MECT are poorly understood. We attempted to compare the urinary proteome of each depressive patient before and after electroconvulsive therapy. 54 urinary proteomes from 9 patients were analyzed, including before and after MECT. Due to the heterogeneity of depression disorder, comparing the urine proteome of each person before and after treatment was used. Common differential protein and biological process were thought to contribute most to the changes caused by MECT. The common biological processes enriched by differential proteins through GO analysis with most patients mainly included cell adhesion (9/9 patients), immune response (7/9), axon guidance (7/9), and oxidation stress (7/9). Moreover, the common biological pathways identified by Ingenuity Pathway Analysis software showed that acute phase response signaling (7/9 patients), NRF2-mediated oxidative stress response (7/9), synaptogenesis signaling pathway (5/9), and ephrin B signaling (5/9) were all upregulated among each patient and were involved in promoting synaptic plasticity and neuroplasticity. Common biological processes and pathways top distributed in urine were reported about resulting in increased excitatory synaptic activity, which were related to the mechanism of MECT in the treatment of mental illnesses. In addition, the common differential proteins CSPG4, CBG, APP, NCAM1, and ARSA were suspected to be related to memory loss, memory damage, and memory formation, which might be the effects of MECT.

Aims: In this study, we propose a non-invasive approach utilizing quantitative proteomics analysis of urine samples to identify potential biomarkers for gastric cancer. Methods: Urine samples were collected from 30 gastric cancer patients, 30 early-stage gastric cancer patients, and 30 healthy controls at Beijing Shijitan and Beijing Friendship Hospitals. For further confirmation, we correlated our findings with The Cancer Genome Atlas database, which uses tandem mass tag tagged quantitative proteomics. Results: In individuals with advanced gastric cancer compared to control group, 376 urine proteins were differentially expressed, while 191 urine proteins were differentially expressed in individuals with early gastric cancer compared to control group. An analysis of gene ontology revealed that these differentially expressed proteins are primarily involved in cell adhesion, biological adhesion, and negative regulation. Through a comprehensive analysis that considered high FC value, low p-value, and alignment with existing literature, we identified five potential urine proteins (PYGB, ITGB3, COL1A1, and TNFRSF12A) as showing differential expression between the AGC and CG groups，three potential urine proteins (HSPA8, CTSL, and FTL) as showing differential expression between the EGC and CG groups. Conclusion: Understanding the roles and pathways of differentially expressed proteins has clarified the molecular mechanisms of gastric cancer.

Diabetic cystopathy (DCP) is a prevalent urinary complication in diabetes. Late-stage DCP can cause chronic urinary retention, significantly impacting the patient’s quality of life and even posing a risk to their lives. Therefore, it is crucial to investigate the pathogenesis and pathological characteristics of DCP. This study aims to utilize proteomics-related methods to uncover the pathogenesis of DCP by analyzing the differential protein expression profiles in the bladder tissue of diabetic rats and normal rats. Morphological analysis revealed notable changes in the bladder tissue of diabetic rats, including significant inflammatory cell infiltration and collagen fiber deposition. Immunohistological examination demonstrated increased apoptosis and decreased proliferation in the bladder tissue of diabetic rats. Quantitative proteomic analysis identified a total of 280 differentially expressed proteins between the two groups, with 193 proteins being down-regulated and 87 proteins being up-regulated. Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways indicated significant changes in protein expression profiles and signaling pathways in the bladder of diabetic rats. Additionally, transcription factor analysis revealed that the insulin-like growth factor-related protein family was the most affected. This study provides valuable evidence for identifying potential genes for the treatment of diabetic bladder.

Non-invasive methods are necessary for the diagnostic and follow-up of metabolic dysfunction-associated steatohepatitis (MASH). This study aims to perform a proteomic analysis on serum and liver samples from morbid obese (MO) women to identify key mediators of MASH. HPLC-MS/MS proteomics was conducted on serum and liver samples from a cohort of 174 MO women classified by liver histology: 44 normal liver (NL), 66 simple steatosis (SS) and 64 MASH. Serum proteomics identified 257 proteins. The MASH individuals had 13 altered proteins, 11 upregulated and 2 downregulated. Altered proteins are primarily involved in molecular pathways of the initial triggering and complement cascade (50%). Liver proteomics identified 2081 proteins, with 72 upregulated and 84 downregulated in MASH. These proteins are mostly involved in molecular pathways of amino acid metabolism (31,25%), antimicrobial peptides (20%), fatty acid metabolism (17,5%). We identified 13 altered proteins in serum of MASH: increased levels of fructose-bisphosphate aldolase, clusterin, collectin-10 and -11, scavenger receptor cysteine-rich-M130, attractin, pigment epithelium-derived factor, vitronectin, complement factor-H, thrombospondin-4 and apolipoprotein-AIV and decreased levels of sex hormone-binding globulin and adiponectin. These proteins can be part of a panel of biomolecules for the diagnosis or follow-up of MASH.

Purpose: Pulmonary hypertension (PH) is a chronic complications of sickle cell disease (SCD) with limited known biomarkers, beyond increases in plasma brain natriuretic peptide levels. Experimental Design: We conducted a proof-of-concept study to identify serum protein biomarkers that were differentially expressed in SCD patients with elevated tricuspid regurgitation velocity (TRV – a noninvasive marker of PH). Results: We found 41 out of 92 target proteins that were significantly different between the non-elevated (TRV≤2.6 m/sec; N = 35) and highly elevated TRV group (TRV≥2.9 m/sec; N = 35, p<0.05). Six of them passed a Bonferroni correction (p value < 0.0005) including T-cell surface glycoprotein, lymphotactin, SLAM family member 7, galectin-9, TNF-related apoptosis-inducing ligand receptor 2, and tumor necrosis factor receptor superfamily member 11A . We observed up to a 1.2-fold increase in the high TRV group for these six proteins. These six proteins had strong positive correlation with serum NT-proBNP levels (a positive control marker elevated in PH (r >= 0.44). Additionally, these markers correlated with other clinical parameters of PH in SCD. Conclusion: Circulatory protein markers of the immune response are increased in SCD patients with elevated TRV as compared to those without elevated TRV.

Parkinson’s disease (PD) is neuropathologically characterized by the progressive degeneration of dopaminergic (DA) neurons in the substantia nigra pars compacta (SNpc), affecting 10 million people worldwide. Rosmarinic acid (RA), a polyphenol found in plants like rosemary (Rosmarinus officinalis), is known for its intriguing biological properties and potential antioxidant and neuroprotective effects. In a previous study we showed that RA treatment prevented hyperlocomotion in mice with MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine)-induced parkinsonism and improved the monoaminergic system in healthy animals. However, the molecular mechanisms underlying RA’s action in PD remain unclear. In this study, we treated MPTP-induced PD animals (C57BL/6 male mice) with RA orally at a dose of 100 mg/kg for 15 days and examined the proteome of substantia nigra (SN) to identify possible regulatory targets of RA treatment to shed some lights into its neuroprotective effects. Quantitative proteomics revealed that RA treatment regulated proteins associated with oxidative phosphorylation (OXPHOS), glutamatergic synapse, and vesicular cycle signaling pathway. We identified 371 proteins significantly regulated in response to RA administration (255 upregulated and 116 downregulated). Notably, some cellular targets of RA treatment reported here, including mGluR2/mGluR3/EAAT - proteins from the glutamatergic system - and proteins from the Complex I of the electron transport chain are promising targets for therapeutic intervention. These findings highlight the molecular differences between MPTP-induced PD mice and those treated with RA, providing insights on the molecular basis behind the neuroprotective effects of RA and revealing potential PD signatures that warrant further investigation.

The effective prioritization of drug resistance mutations affecting protein folding and interactions is crucial for treatment success. To address this, a bioinformatics pipeline, AMIA, is introduced, integrating various structural analysis tools into a simplified workflow. By optimizing computational resources, data transformations are automated, enhancing scalability and reproducibility. AMIA automates mutation introduction into protein structures, calculates polar interaction changes, and analyses protein fold energy through pre-established software tools. Furthermore, it includes automated molecular dynamics analysis, reducing the need for constant user input and output management. This open-source pipeline facilitates the visualization of mutation effects on protein structure and dynamic states, aiding in prioritizing variants for experimental validation. AMIA (available at: https://github.com/kbrown3687524/amia) streamlines computational analysis, contributing to improved treatment regimen development against drug-resistant mutations.

Purpose: Traumatic brain injury (TBI), including pediatric abusive head trauma (AHT), is the leading cause of death and disability in children and young adults worldwide. The current understanding of trauma-induced molecular changes in the brain of human subjects with intracranial haemorrhage (ICH) remains inadequate and requires further investigation to improve the outcome and management of TBI in the clinic. Calcium-mediated damage at the site of brain injury has been shown to activate several catalytic enzymes. Experimental design: Serine hydrolases (SHs) are major catalytic enzymes involved in the biochemical pathways of blood coagulation, systemic inflammation and neuronal signaling. Here we investigated activity-based protein profiling (ABPP) by measuring the activity status of SH enzymes in the serum of infants with severe ICH as a consequence of AHT or atraumatic infants who died of sudden infant death syndrome (SIDS). Results: Our proof-of-principle study revealed significantly reduced physiological activity of dozens of metabolic SHs in the serum of infants with severe AHT compared to the SIDS group, with some of the enzymes being related to neurodevelopment and basic brain metabolism.

Anti-VEGF therapy is commonly used to treat proliferative diabetic retinopathy (PDR), but the exact mechanism of VEGF signaling is not fully understood. Using data-independent acquisition mass spectrometry (DIA-MS), we analyzed proteomic changes in aqueous humor (AH) samples collected before and one week after intravitreal ranibizumab (IVR) treatment from 10 PDR patients to discover potential biomarkers. Resultantly, 875 proteins were quantified and 26 proteins were significantly altered in response to IVR treatment in PDR. Further investigation through gene ontology (GO) and pathway analysis revealed that these differentially expressed proteins were primarily involved in extracellular matrix (ECM) and platelet degranulation signaling. Protein-protein interaction analysis highlighted five hub proteins (COL3A1, DPT, VEGFA, SPP1, SERPING1) that were found to be ECM components. Enzyme-linked immunosorbent assay (ELISA) confirmed the decreased levels of VEGFA and increased levels of DPT proteins after IVR treatment in another 8 samples of AH in 4 PDR patients. Our study provided novel insights into aqueous proteins of PDR following IVR treatment. Targeting the ECM pathway, particularly the elevation of DPT protein, may provide a deeper understanding of the anti-VEGF resistance and VEGF signaling in PDR.

Abstract Purpose The main objective of this study is to characterize and analyze modified peptides in DBS samples. This includes deciphering their specific PTMs and understanding their potential impact on the population or disease cohort under study. Experimental design Using mass spectrometry-based proteomic approaches, we performed a comprehensive analysis of DBS samples. Our focus was on the identification and quantification of modified peptides. We also took advantage of recent advances in DBS mass spectrometry to ensure accurate detection and quantification. Results A comprehensive analysis identified 976 modified peptides in DBS samples. Of these, a subset of 211 peptides was consistently present in all samples, highlighting their potential biological importance and relevance. This indicates a diverse spectrum of PTMs in the proteome of DBS samples. Conclusions and clinical relevance Integration of mass spectrometry and proteomics has revealed a broad spectrum of modified peptides in DBS samples and highlighted their importance in biological processes and disease progression. Accurate detection of these PTMs may be critical for risk stratification and disease management. This study improves the understanding of molecular mechanisms underlying biological processes and disease development, providing important insights for clinical applications.

Acute glaucoma’s main sign is acute ocular hypertension (AOH), leading to retinal ganglion cell (RGC) death and irreversible visual loss. However, there is currently no approved effective therapy for this condition. This research aimed to identify the major regulators and the overall protein changes involved in AOH-induced RGC death. Mass-spectrometry was used to analyze proteomic patterns in the retinal protein extracts from the AOH and sham-group, and then Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway studies were performed. In proteomics analysis, we identified 92 proteins in the AOH group compared to the control group, with 58 proteins being up-regulated and 34 proteins being down-regulated. Western blot and biochemical assay analyses identified changes in Fatty acid-binding protein 7 (FABP7), and caveolin-1(Cav-1) that were related to fatty acid metabolism and ocular inflammatory signaling. Moreover, variations in the expression of the proteins Galectin-1 (Gal-1), S100 calcium-binding protein A6 (S100a6), and Visinin-like protein-1 (VILIP) was shown, all of which were associated to the process of neuronal ischemia. Our investigation demonstrated that neuroinflammation and fatty acid metabolism were involved in retinal impairment following AOH, offering a potential therapeutic strategy for acute glaucoma.

Venous Thromboembolism (VTE) remains a significant cause of morbidity and mortality worldwide. Rivaroxaban, a direct oral factor Xa inhibitor, mediates anti-inflammatory and cardiovascular-protective effects besides its well-established anticoagulant properties; yet, these remain poorly characterized. Extracellular vesicles (EVs) are considered proinflammatory messengers regulating a myriad of (patho)physiological processes and may be highly relevant to the pathophysiology of VTE. The effects of Rivaroxaban on circulating EVs in VTE patients remain unknown. We have established that differential EV biosignatures are found in patients with non-valvular atrial fibrillation anticoagulated with Rivaroxaban versus warfarin. Here, we investigated whether differential proteomic profiles of circulating EVs could also be found in patients with VTE. We performed comparative label-free quantitative proteomic profiling of enriched plasma EVs from VTE patients anticoagulated with either Rivaroxaban or warfarin using a tandem mass spectrometry approach. Of the 181 quantified proteins, 6 were found to be either exclusive to, or enriched in, Rivaroxaban-treated patients. Intriguingly, these proteins form a cluster tightly involved in negative feedback regulation of inflammatory and coagulation pathways, suggesting that EV proteomic signatures may reflect both Rivaroxaban’s anti-coagulatory and anti-inflammatory potential. These findings may be of translational relevance towards characterizing the emerging anti-inflammatory and cardioprotective mechanisms associated with this therapy.