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Pathophysiology

Pathophysiology is an international, peer-reviewed, open access journal on the etiology, development, and elimination of pathological processes, published quarterly online by MDPI (since Volume 21, Issue 1 - 2020).
The International Society for Pathophysiology (ISP) is affiliated with Pathophysiology, serving as its official journal. Society members receive discounts on the article processing charges.
Indexed in PubMed | Quartile Ranking JCR - Q2 (Pathology)

All Articles (279)

Background: Rheumatoid arthritis (RA) is a systemic, pro-inflammatory, autoimmune disease that mainly affects the joints in a symmetrical manner. Differential proteomic profiling through Sequential Window Acquisition of all Theoretical Fragment Ion Mass Spectra (SWATH-MS/MS) helps in a better understanding of the RA pathogenesis. In this study, we compared the differentially upregulated proteins with those associated with fibrosis to gain a deeper understanding of the fibrotic aspect of RA. Methods: We analyzed plasma proteomics data, previously obtained by SWATH-MS/MS. Our focus was on proteins associated with Leucine Rich Alpha2glycoprotein1 (LRG1) and we employed an in silico method. Results: We identified common proteins between RA and fibrosis. Among them, LRG1 and Serine Protease Inhibitor Clade A, Member 1 (SERPINA1) showed a high co-expression score in the gene clusters. LRG1 is both pro-inflammatory and pro-fibrotic, while SERPINA1 is an anti-inflammatory protein that inhibits pro-inflammatory and pro-fibrotic molecules (Elastase). Further, docking studies and a simulation study of the docked complexes with the analysis of Hydrogen bonds, Solvent Accessible Surface Area (SASA), Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF) and Radius of gyration (Rg), suggested a strong interaction between the two partners, LRG1 and SERPINA1. Conclusions: Our study suggests that LRG1 may inhibit SERPINA1 and promote inflammation and fibrotic processes by disrupting SERPINA1’s primary function.

6 February 2026

Protein–Protein network analysis overlapping with RA and fibrosis. Venn diagram showing 14 common proteins between SWATH, RA, and fibrosis (A) and common interacting proteins (B). PCA analysis showing the correlations among FC, GDA score, and relevance score for the 14 common gene sets. GDA shows a negative correlation with FC and Relevance score, while FC and Relevance score are positively correlated (C). GDA score contributes more to the overall variation among the variables shown in the unit circle (D). Bar plot showing the variations among the variables with 49.5%, 28.6%, and 21.9% in PC1, PC2, and PC3, respectively (E). Gene distribution chart showing the cluster of LRG1, SERPINA1, SERPINA3, and Clu around the center, suggesting a close association among the variables (F).

Vitamin D Reprograms Non-Coding RNA Networks to Block Zika Virus in Human Macrophages

  • Julieta M Ramírez-Mejía,
  • Geysson Javier Fernandez and
  • Silvio Urcuqui-Inchima

Background: Zika virus (ZIKV), a mosquito-borne flavivirus, is associated with congenital malformations and neuroinflammatory disorders, highlighting the need to identify host factors that shape infection outcomes. Macrophages, key targets and reservoirs of ZIKV, orchestrate both antiviral and inflammatory responses. Methods: Vitamin D (VitD) has emerged as a potent immunomodulator that enhances macrophage antimicrobial activity and regulates inflammation. To investigate how VitD shapes macrophage responses to ZIKV, we reanalyzed publicly available RNA-seq and miRNA-seq datasets from monocyte-derived macrophages (MDMs) of four donors, differentiated with or without VitD and subsequently infected with ZIKV. Results: Differential expression analysis identified long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and mRNAs integrated into competing endogenous RNA (ceRNA) networks. In VitD-conditioned and ZIKV-infected MDMs, 65 lncRNAs and 23 miRNAs were significantly modulated. Notably, lncRNAs such as HSD11B1-AS1, Lnc-FOSL2, SPIRE-AS1, and PCAT7 were predicted to regulate immune and metabolic genes, including G0S2, FOSL2, PRELID3A, and FBP1. Among the miRNAs, let-7a and miR-494 were downregulated, while miR-146a, miR-708, and miR-378 were upregulated, all of which have been previously implicated in antiviral immunity. Functional enrichment analysis revealed pathways linked to metabolism, stress responses, and cell migration. ceRNA network analysis suggested that SOX2-OT and SLC9A3-AS1 may act as molecular sponges, modulating regulatory axes relevant to immune control and viral response. Conclusions: Despite limitations in sample size and experimental validation, this study provides an exploratory map of ncRNA–mRNA networks shaped by VitD during ZIKV infection, highlighting candidate molecules and pathways for further studies on host–virus interactions and VitD-mediated immune regulation.

3 February 2026

Alteration of lncRNA profiles by Vitamin D in Zika virus–infected MDMs. (a) Distribution of differentially expressed non-coding RNAs identified in ZIKV-D3-MDMs, categorized as lincRNAs, pseudogenes, antisense lncRNAs, divergent lncRNAs, miRNAs, and tRNAs. The total number of differentially expressed ncRNAs is indicated. (b) Principal component analysis (PCA) of differentially expressed lncRNAs across the four experimental conditions (MDM, D3-MDM, ZIKV-MDM, and ZIKV-D3-MDM). Each point represents a biological replicate, and the percentage of variance explained by each principal component is shown. (c) Pie chart illustrating the proportion of up-regulated, down-regulated, and unaffected lncRNAs in response to Vitamin D treatment in ZIKV-infected MDMs. (d) K-means clustering of up-regulated lncRNAs based on their normalized expression profiles across the four experimental groups. Each panel represents one cluster, and bars indicate mean relative expression values ± SEM. Representative lncRNAs for each cluster are indicated. (e) K-means clustering of down-regulated lncRNAs using the same analytical approach as in (d). (f) Summary table listing the up-regulated and down-regulated lncRNAs associated with each expression cluster identified by k-means clustering. The number of lncRNAs per cluster (n) is indicated.

Amyloid Beta Oligomers as Early Triggers of Neuronal Cytoskeleton Dysfunction in Alzheimer’s Disease

  • Yadira Gasca-Martínez,
  • Miguel Angel Ontiveros-Torres and
  • José Jaime Jarero-Basulto
  • + 1 author

Alzheimer’s disease (AD) is characterized by progressive cognitive decline, with amyloid beta oligomers (AβOs) emerging as the most neurotoxic species and acting as early triggers of cellular alterations. Before the appearance of other protein aggregates, AβOs disrupt the dynamics and stability of the neuronal cytoskeleton, a structure essential for maintaining neuronal morphology, axonal transport, and synaptic plasticity. Experimental evidence demonstrates that AβOs promote microtubule disassembly, Tau hyperphosphorylation, reduced kinesin levels, impaired axonal transport, and alterations in actin dynamics through the LIMK–cofilin signaling pathway. In addition, increased levels of neurofilament light chain have been identified as an early biomarker of axonal damage. Notably, these cytoskeletal disturbances arise in the absence of extensive neuronal death, underscoring the cytoskeleton as a critical early target in AD pathogenesis. In this review, we analyze cytoskeletal alterations induced by AβOs in neurons and discuss how these changes may contribute to disrupted neuronal communication, a defining early hallmark of AD pathology.

3 February 2026

Schematic representation of APP processing pathways. The non-amyloidogenic pathway involves cleavage of APP by α-secretase followed by γ-secretase, preventing Aβ formation. In contrast, in the amyloidogenic pathway, β-secretase cleaves APP to generate sAPPβ, followed by a second cleavage by γ-secretase, resulting in the release of Aβ peptide into extracellular space (pathological pathway). Elements were adapted from Server Medical Art (https://smart.servier.com), licensed under Creative Commons Attribution 4.0 (https://creativecommons.org/licenses/by/4.0).
  • Feature Paper
  • Article
  • Open Access

Background: AMP-activated protein kinase (AMPK) acts as a key energy sensor that negatively regulates skeletal muscle mass. Zinc is an essential trace element that is required for myogenic differentiation and protein synthesis, while zinc deficiency has been associated with muscle atrophy in vivo. However, how zinc status modulates AMPK activation itself or alters downstream responses to AMPK signaling in muscle cells remains unclear. Methods: C2C12 myotubes were cultured under zinc-depleted (ZnD), zinc-sufficient (20 μM; Zn20), or zinc-supplemented (40 μM; Zn40) conditions. AMPK was activated by AICAR, and zinc status–dependent responses were evaluated using molecular and morphological analyses. Results: AICAR increased intracellular zinc levels in Zn20 and Zn40 but not in ZnD. Zinc transporter expression exhibited gene-specific regulation: Zip3 was upregulated across all zinc conditions, Zip14 was significantly induced in ZnD and Zn40, and Zip10 was selectively upregulated in Zn40. AICAR induced myotube atrophy in all groups; however, the reduction in myotube diameter was significantly greater under zinc-depleted conditions. Zinc depletion was associated with transcriptional upregulation of FoxO1, FoxO3, Atrogin-1, and MuRF1 in response to AICAR, while AMPK activation and suppression of S6K1 phosphorylation occurred to a similar extent regardless of zinc status. Conclusions: These findings indicate that zinc availability does not alter AMPK activation itself but modulates downstream atrophic responses to AMPK signaling. Under conditions of AMPK activation, adequate zinc availability is accompanied by increased intracellular zinc levels and stress-responsive ZIP regulation, which may limit excessive atrophic gene induction, whereas zinc depletion increases susceptibility to AMPK-induced atrophic responses in skeletal muscle cells.

2 February 2026

Zinc depletion is associated with increased susceptibility to AMPK-induced myotube atrophy. (A) Representative Western blot showing phosphorylated and total AMP-activated protein kinase (pAMPK and AMPK) after AICAR stimulation (1 mM, 24 h) in C2C12 myotubes cultured under zinc-depleted (ZnD), zinc-sufficient (Zn20; 20 μM ZnSO4), or zinc-supplemented (Zn40; 40 μM ZnSO4) conditions. GAPDH was used as a loading control. (B) Representative phase-contrast images of myotubes (scale bar = 100 μm) and quantitative analysis of mean myotube diameter. Data are presented as mean ± SEM (n = 3 in each group). ** p < 0.01. Statistical comparisons include Control vs. AICAR within each zinc condition, as well as comparisons among zinc conditions where indicated. Zn20 (20 μM ZnSO4) was used as a zinc-sufficient reference condition for comparative analyses in this in vitro system.

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Pathophysiology - ISSN 1873-149X