Proteomes

Background: Obesity is a major risk factor for type 2 diabetes (T2D); however, the molecular links between these conditions are not fully understood. Methods: We performed an integrative serum proteomics study on samples from 134 individuals (healthy controls, patients with obesity and/or T2D) using both data-independent (DIA) and data-dependent (DDA) liquid chromatography-mass spectrometry approaches, complemented by phosphopeptide enrichment, kinase activity prediction, network and pathway analyses to get more information on the different proteoforms involved in the pathophysiology of the diseases. Results: We identified 235 serum proteins, including 13 differentially abundant proteins (DAPs) between groups. Both obesity and T2D were characterized by activation of complement and coagulation cascades, as well as alterations in lipid metabolism. Ingenuity Pathway Analysis^® (IPA) revealed shared canonical pathways, while phosphorylation-based regulation differentiated the two conditions. Elevated hemopexin (HPX), vitronectin (VTN), kininogen-1 (KNG1) and pigment epithelium-derived factor (SERPINF1), along with decreased adiponectin (ADIPOQ) and apolipoprotein D (APOD), indicated a pro-inflammatory, pro-coagulant serum profile. Network analyses of antimicrobial and immunomodulatory peptides (AMPs) revealed strong overlaps between immune regulation and lipid metabolism. Phosphoproteomics and kinase prediction highlighted altered CK2 and AGC kinase activities in obesity, suggesting signaling-level modulation. Conclusions: Our comprehensive proteomic and phosphoproteomic profiling reveals overlapping yet distinct molecular signatures in obesity and T2D, emphasizing inflammation, complement activation and phosphorylation-driven signaling as central mechanisms that potentially contribute to disease progression and therapeutic targeting.

Background: Rabies is among the oldest known zoonotic viral diseases and is caused by members of the Lyssavirus genus. The prototype species, Lyssavirus rabies, effectively evades the host immune response, allowing the infection to progress unnoticed until the onset of clinical signs. At this stage, the disease is irreversible and invariably fatal, with definitive diagnosis possible only post-mortem. Given the advances in modern proteomics, this study aimed to identify potential protein biomarkers for antemortem diagnosis of rabies in dogs, which are the principal reservoir hosts of the rabies virus. Methods: Two hundred and thirty-one samples (brain tissues (BT), cerebrospinal fluids (CSF), and serum (SR) samples) were collected from apparently healthy dogs brought for slaughter for human consumption in South-East and North-Central Nigeria. All the BT were subjected to a direct fluorescent antibody test to confirm the presence of lyssavirus antigen, and 8.7% (n = 20) were positive. Protein extraction, quantification, reduction, and alkylation were followed by on-bead (HILIC) cleanup and tryptic digestion. The resulting peptides from each sample were injected into the Evosep One LC system, coupled to the timsTOF HT MS, using the standard dia-PASEF short gradient data acquisition method. Data was processed using Spectronaut^TM (v19). An unpaired t-test was performed to compare identified protein groups (proteins and their isoforms) between the rabies-infected and uninfected BT, CSF, and SR samples. Results: The study yielded 54 significantly differentially abundant proteins for the BT group, 299 for the CSF group, and 280 for the SR group. Forty-five overlapping differentially abundant proteins were identified between CSF and SR, one between BT and CSF, and two between BT and SR; none were found that overlapped all three groups. Within the BT group, 33 proteins showed increased abundance, while 21 showed decreased abundance in the rabies-positive samples. In the CSF group, 159 proteins had increased abundance and 140 had decreased abundance in the rabies-positive samples. For the SR group, 215 proteins showed increased abundance, and 65 showed decreased abundance in the rabies-positive samples. Functional enrichment analysis revealed that pathways associated with CSF, spinocerebellar ataxia, and neurodegeneration were among the significant findings. Conclusion: This study identified canonical proteins in CSF and SR that serve as candidate biomarkers for rabies infection, offering insights into neuronal dysfunction and potential tools for early diagnosis.

Background: Non-muscle invasive bladder cancer (NMIBC) comprises high-grade (HG) and low-grade (LG) variants, classified by aggressiveness, recurrence risk, and stage—either non-invasive (pTa) or invading the lamina propria (pT1). Cystoscopy remains the diagnostic gold standard, with no less-invasive alternatives, while molecular mechanisms driving tumorigenesis and treatment response are poorly understood. Methods: To address this gap, we conducted a preliminary top-down proteomic study on fresh biopsies from pTa-LG and pT1-HG NMIBC at initial diagnosis to identify molecular differences and potential prognostic biomarkers. Results: Distinct protein profiles were observed between stages. Highly abundant proteins in pT1-HG were associated with nitric oxide biosynthesis, signal transduction, inhibition of apoptosis, protein folding, and immune response. Proteins of low abundance were related to cellular localization, cytoskeleton organization, cell adhesion, phagocytosis, and tissue development. Notably, multiple proteoforms of PDC6I/ALIX, a protein implicated in the regulation of apoptosis, proliferation, and PD-L1 surface presentation, were significantly downregulated in pT1-HG tumors. Furthermore, the abundance of proteins such as GANAB, GALE, THIC, SEPT8, and MYDGF/C19orf10 correlated with tumor size, suggesting their potential as prognostic biomarkers. Conclusions: These proteins, taken together, indicate that they may serve as valuable prognostic markers, offering a path toward more personalized management of NMIBC beyond the traditional one-size-fits-all approach.