International Journal of Molecular Sciences

25 pages, 2084 KB

Open AccessArticle

The Immune System in Antarctic and Subantarctic Fish of the Genus Harpagifer Is Affected by the Effects of Combined Microplastics and Thermal Increase

by Daniela P. Nualart, Pedro M. Guerreiro, Kurt Paschke, Stephen D. McCormick, Chi-Hing Christina Cheng and Luis Vargas-Chacoff

Int. J. Mol. Sci. 2025, 26(20), 9968; https://doi.org/10.3390/ijms26209968 (registering DOI) - 13 Oct 2025

Abstract

Rising ocean temperatures due to climate change, combined with the intensification of anthropogenic activity, may lead to changes in the physiology and distribution of native species. Compounding climate stress, microplastic particles (MPs) enter the oceans through wastewater and the breakdown of macroplastics. Depending [...] Read more.

Rising ocean temperatures due to climate change, combined with the intensification of anthropogenic activity, may lead to changes in the physiology and distribution of native species. Compounding climate stress, microplastic particles (MPs) enter the oceans through wastewater and the breakdown of macroplastics. Depending on their composition, they can be harmful and act as a vehicle for toxic substances, although their effects on native Antarctic and subantarctic species are unknown. Notothenioid fish are members of this group and are found inside and outside Antarctica, such as the Harpagifer, which has adapted to the cold and is particularly sensitive to thermal increases. Here, we aimed to evaluate the innate immune response in the head kidney, spleen, and foregut of two notothenoid fish, Harpagifer antarcticus and Harpagifer bispinis, exposed to elevated temperatures and PVC (polyvinyl chloride) microplastics. Adults from both species were collected on King George Island (Antarctica) and Punta Arenas (Chile), respectively. Specimens were assigned to a control group or exposed to a temperature increase (TI) or PVC microplastics (MPs), separately or in combination (MPs + TI). MP exposures were oral (gavage) for 24 h or aqueous (in a bath) for 24 and 48 h. Using real-time qPCR, we evaluated the relative gene expression of markers involved in the innate immune response, including tlr2 (toll-like receptor 2), tlr4 (toll-like receptor 4), myd88 (myeloid differentiation factor 88), nfkb (nuclear factor kb), il6 (interleukin 6), and il8 (irterleukin 8). We found differences between treatments when H. antarcticus and H. bispinis were exposed independently to MPs or thermal increase (TI) in the experiment with a cannula, showing an up-regulation in transcripts. In contrast, a down-regulation was observed when exposed in combination to MP + TI, which looked to be tissue-dependent. However, transcripts related to innate immunity in the bath experiment increased when exposure to both stressors was combined, mostly at 48 h. These results highlight the importance of evaluating the effects of multiple stressors, both independently and in combination, and whether these species will have the capacity to adapt or survive under these conditions, especially in waters where temperature is increasing and pollution is also rising, primarily from MP-PVC, a plastic widely used in various industries and among the population. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Immunology in Chile, 2nd Edition)

► Show Figures

Figure 1

27 pages, 18325 KB

Open AccessArticle

Prediction of Hyperinflammatory Phenotypes in Critically Ill Patients via Routine Clinical Data and IL-6: Towards Personalized Anti-Inflammatory Therapy

by Charlotte Linz, Alexander Shimabukuro-Vornhagen, Nina Hesse, Lucie Probst, Jorge Garcia Borrega, Dennis A. Eichenauer, Matthias Kochanek, Michael von Bergwelt-Baildon and Boris Böll

Int. J. Mol. Sci. 2025, 26(20), 9967; https://doi.org/10.3390/ijms26209967 (registering DOI) - 13 Oct 2025

Abstract

Interleukin-6 (IL-6) is a central mediator of systemic inflammation and is markedly elevated in critical illnesses, including sepsis, acute respiratory distress syndrome, and hyperinflammatory syndromes. Patient responses to immunomodulatory therapies vary, highlighting the need to better understand IL-6 regulation and its clinical implications. [...] Read more.

Interleukin-6 (IL-6) is a central mediator of systemic inflammation and is markedly elevated in critical illnesses, including sepsis, acute respiratory distress syndrome, and hyperinflammatory syndromes. Patient responses to immunomodulatory therapies vary, highlighting the need to better understand IL-6 regulation and its clinical implications. We retrospectively analyzed consecutive patients admitted to a medical intensive care unit in a quaternary academic center with a comprehensive cancer program, extracting clinical and laboratory data, including inflammatory markers and plasma IL-6 levels. Plasma IL-6 concentrations were measured using an electrochemiluminescence immunoassay. Survival analyses, multivariable adaptive Lasso regression, Bayesian logistic regression, and latent class analysis were performed to define determinants of IL-6 regulation, mortality, and inflammatory phenotypes. IL-6 levels were substantially elevated in sepsis (median 1150 pg/mL) and neutropenia (median 7866 pg/mL), with extreme concentrations exceeding 20,000 pg/mL when both were present. Although IL-6 across its full range was not independently predictive of intensive care unit mortality, dichotomized thresholds (≥200 pg/mL) correlated with lower survival. Advanced modeling defined a hyperinflammatory phenotype characterized by IL-6 ≥ 100 pg/mL and predicted mortality >40%, showing mortality of 58%, alongside distinct latent subgroups with heterogeneous inflammatory activity and outcomes. These results emphasize the prominent role of sepsis and neutropenia in driving IL-6 elevations and reveal inflammatory phenotypes with potential for risk stratification and targeted anti-cytokine therapy in critical illness. Full article

(This article belongs to the Special Issue Latest Advances in Cytokine Storm)

► Show Figures

Figure 1

11 pages, 581 KB

Open AccessArticle

Are Advanced Glycation End-Products and Skin Autofluorescence Associated with E-Selectin and Pulse Wave Velocity as Markers of Atherosclerosis Risk in Children with Obesity?

by Anna Medyńska, Anna Noczyńska and Danuta Zwolińska

Int. J. Mol. Sci. 2025, 26(20), 9966; https://doi.org/10.3390/ijms26209966 (registering DOI) - 13 Oct 2025

Abstract

Obesity is a risk factor for numerous complications, including atherosclerosis, the pathogenesis of which is complex. The aim of our study is to evaluate serum levels of E-selectin and hs-CRP and pulse wave velocity (PWV) as atherosclerosis risk factors and to explore their [...] Read more.

Obesity is a risk factor for numerous complications, including atherosclerosis, the pathogenesis of which is complex. The aim of our study is to evaluate serum levels of E-selectin and hs-CRP and pulse wave velocity (PWV) as atherosclerosis risk factors and to explore their relationship with advanced glycation end products (AGEs), methylgioxal (MG) and skin autofluorescence (sAF). We evaluated 125 children aged 8–18 years with simple obesity, stratified into two subgroups based on SDS BMI (Group I: 2–4; Group II:> 4), and compared them with 33 age-matched peers of normal weight. Children with obesity exhibited significantly elevated serum concentrations of AGEs, MG, E-selectin, and hs-CRP relative to the control group. Additionally, both height-normalized pulse wave velocity (SDS PWV) and sAF values were significantly higher in the children with obesity compared to their normal-weight counterparts. Except for sAF, which was elevated in children with obesity with a higher SDS BMI, no significant differences were observed among the subgroups of children. Positive correlations were observed between E-selectin and AGEs, MG and SDS PWV, as well as sAF and SDS BMI. Our findings indicate that children with obesity exhibit early signs of atherosclerotic changes, regardless of the degree of obesity. Moreover, circulating AGEs may represent a more reliable biomarker of atherosclerosis risk than sAF, as suggested by the strong positive correlation between AGEs and E-selectin. Further studies are warranted to validate these findings. Full article

(This article belongs to the Collection Feature Papers in Molecular Pathology, Diagnostics, and Therapeutics)

16 pages, 899 KB

Open AccessArticle

Terminalia chebula Fruit Extract Ameliorates Peripheral Edema by Inhibiting NF-κB and MAPK Signaling Pathways

by Sang-Hyup Lee, Sang-Yoon Kim, Yun-Gu Gwon, Su-Ha Lee, Ji-Soo Jeong, Je-Won Ko, Tae-Won Kim and Bong-Keun Choi

Int. J. Mol. Sci. 2025, 26(20), 9965; https://doi.org/10.3390/ijms26209965 (registering DOI) - 13 Oct 2025

Abstract

Peripheral edema is a pathological condition caused by abnormal fluid accumulation in the interstitial space due to elevated vascular permeability and inflammation. This study evaluated the therapeutic efficacy of Terminalia chebula fruit extract (TCE) in inflammation-induced peripheral edema and clarified its molecular mechanisms. [...] Read more.

Peripheral edema is a pathological condition caused by abnormal fluid accumulation in the interstitial space due to elevated vascular permeability and inflammation. This study evaluated the therapeutic efficacy of Terminalia chebula fruit extract (TCE) in inflammation-induced peripheral edema and clarified its molecular mechanisms. Using hydrogen peroxide (H₂O₂)-stimulated human umbilical vein endothelial cells (HUVECs), TCE was tested for effects on cell viability, inflammatory gene expression, intracellular reactive oxygen species, endothelial barrier integrity, and vascular endothelial growth factor (VEGF)-induced migration. Its influence on nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) and mitogen-activated protein kinase (MAPK) signaling was examined. In vivo, TCE was assessed in acetic acid-induced peritoneal vascular permeability and carrageenan-induced paw edema models, followed by histological analysis and serum tumor necrosis factor-α (TNF-α) measurement. TCE restored cell viability (76.2% to 94.8%), reduced TNF, IL6, and PTGS2 mRNA expression, and decreased reactive oxygen species by 27.2%. It enhanced barrier integrity, increased transendothelial electrical resistance, and inhibited VEGF-induced migration. TCE suppressed NF-κB and MAPK activation. In vivo, TCE reduced Evans blue extravasation by 41.6% and paw edema by 67.5%. Histology showed reduced dermal thickening and inflammatory infiltration, and serum TNF-α levels were lowered. TCE attenuates peripheral edema by preserving endothelial barrier function and suppressing inflammatory signaling, supporting its potential as a therapeutic agent for inflammation-associated vascular dysfunction and edema. Full article

(This article belongs to the Section Bioactives and Nutraceuticals)

19 pages, 1145 KB

Open AccessArticle

Checkpoint Blockade Efficacy in Uveal Melanoma Is Linked to Tumor Immunity, CD28, and CCL8

by Elias A. T. Koch, Renato Liguori, Afonso C. Alejandro, Stefan Schliep, Anne Petzold, Anja Wessely, Waltraud Fröhlich, Fulvia Ferrazzi, Julio Vera, Markus Eckstein, Carola Berking and Markus V. Heppt

Int. J. Mol. Sci. 2025, 26(20), 9964; https://doi.org/10.3390/ijms26209964 (registering DOI) - 13 Oct 2025

Abstract

For patients with metastatic uveal melanoma (UM), tebentafusp is currently the only systemic therapy approved by the EMA and FDA, but its use is limited to HLA-A*02:01-positive individuals. Immune checkpoint blockade (ICB) represents another option, though only a small subgroup of patients benefits, [...] Read more.

For patients with metastatic uveal melanoma (UM), tebentafusp is currently the only systemic therapy approved by the EMA and FDA, but its use is limited to HLA-A*02:01-positive individuals. Immune checkpoint blockade (ICB) represents another option, though only a small subgroup of patients benefits, and no reliable predictive biomarkers are available to date. The aim of this study was therefore to identify parameters associated with favorable ICB response. Tumor samples and clinical data from 30 patients were analyzed. Group A (n = 16) showed clinical benefit, while Group B (n = 14) experienced disease progression. NanoString^® analyses revealed 258 upregulated genes in Group A, including IDO1, CD28, and CCL8. The enriched pathways were predominantly linked to immune activation, leukocyte adhesion, and responses to external stimuli. Immunohistochemistry confirmed significantly higher CD28 expression on infiltrating immune cells in Group A, while a machine learning approach identified CCL8 as a predictive marker with ~78% accuracy. Overall survival differed significantly between the groups. These findings indicate that patients responding to ICB display tumors with enhanced immune activation. CD28 and CCL8 emerged as promising candidates and should be validated in prospective studies to determine their clinical utility. Full article

(This article belongs to the Special Issue Skin Cancer: From Molecular Pathophysiology to Novel Treatment)

► Show Figures

Figure 1

12 pages, 1237 KB

Open AccessArticle

HSP90 Inhibition Disrupts 27-Hydroxycholesterol-Induced Inflammatory Signaling in Monocytic Cells

by Jaesung Kim, Munju Kwon, Dongha Park, Nakyung Kang, Yonghae Son, Ninib Baryawno, Byoung Soo Kim, Sik Yoon, Sae-Ock Oh, Dongjun Lee and Koanhoi Kim

Int. J. Mol. Sci. 2025, 26(20), 9963; https://doi.org/10.3390/ijms26209963 (registering DOI) - 13 Oct 2025

Abstract

27-Hydroxycholesterol (27OHChol), a cholesterol metabolite, induces inflammatory responses in monocytic cells and promotes their differentiation into mature dendritic cells. Here, we examined whether inhibition of heat shock protein 90 (HSP90) modulates these responses. Treatment with ganetespib, a selective HSP90 inhibitor, significantly reduced chemokine [...] Read more.

27-Hydroxycholesterol (27OHChol), a cholesterol metabolite, induces inflammatory responses in monocytic cells and promotes their differentiation into mature dendritic cells. Here, we examined whether inhibition of heat shock protein 90 (HSP90) modulates these responses. Treatment with ganetespib, a selective HSP90 inhibitor, significantly reduced chemokine CCL2 expression, lowering monocytic cell migration. It also suppressed matrix metalloproteinase-9 (MMP-9) expression and attenuated the lipopolysaccharide (LPS) response otherwise amplified by 27OHChol. Furthermore, ganetespib decreased mature dendritic cell markers (CD80, CD83, CD88) and restored endocytic activity, indicating a less activated state. These changes suggest that HSP90 regulates 27OHChol-induced pro-inflammatory activation via its client proteins. To explore this mechanism, we examined the phosphorylation status of signaling proteins. 27OHChol enhanced phosphorylation of Akt and its downstream targets, S6 and 4E-BP1 within the Akt/mTORC1 pathway. Ganetespib reduced total and phosphorylated Akt and 4E-BP1, and selectively inhibited S6 phosphorylation without altering total protein level. Collectively, these findings demonstrate that HSP90 inhibition by ganetespib mitigates 27OHChol-driven monocytic cell activation through suppression of the HSP90-Akt/mTORC1 axis. Targeting this pathway may provide a promising therapeutic strategy for metabolic inflammation associated with oxysterols. Full article

(This article belongs to the Special Issue Dialogue Between Inflammation and Immunity: From Mechanism to Therapy)

16 pages, 750 KB

Open AccessArticle

Peptide Mapping for Sequence Confirmation of Therapeutic Proteins and Recombinant Vaccine Antigens by High-Resolution Mass Spectrometry: Software Limitations, Pitfalls, and Lessons Learned

by Mateusz Dobrowolski, Małgorzata Urbaniak and Tadeusz Pietrucha

Int. J. Mol. Sci. 2025, 26(20), 9962; https://doi.org/10.3390/ijms26209962 (registering DOI) - 13 Oct 2025

Abstract

Peptide mapping is a well-established method for confirming the identity of therapeutic proteins as part of batch release testing and product characterization for regulatory filings. Traditionally based on enzymatic digestion followed by reversed-phase liquid chromatography and UV detection, the method has evolved with [...] Read more.

Peptide mapping is a well-established method for confirming the identity of therapeutic proteins as part of batch release testing and product characterization for regulatory filings. Traditionally based on enzymatic digestion followed by reversed-phase liquid chromatography and UV detection, the method has evolved with technological advancements to incorporate mass spectrometry (MS), enabling more detailed structural insights. Residue-level confirmation of amino acid sequences requires MS/MS fragmentation, which produces large amounts of data that must be processed using specialized software. In regulated environments, the use of academic algorithms is often limited by validation requirements, making it necessary to rely on commercially approved tools, although their built-in scoring systems have limitations that can affect sequence assignment accuracy. Here, we present representative examples of incorrect peptide assignments generated by commercial software. In antibody sequence analysis, misidentifications resulted from isobaric and near-isobaric dipeptides (e.g., SA vs. GT). Additional examples from the analysis of SARS-CoV-2 spike protein variants revealed software-induced artifacts, including artificial succinylation of aspartic acid residues to compensate for sequence mismatches, and incorrect deamidation site assignments due to misinterpretation of isotopic peaks. These findings underscore the necessity for expert manual review of MS/MS data, even when using validated commercial platforms, and highlight the molecular challenges in distinguishing true sequence variants from software-driven artifacts. Full article

(This article belongs to the Section Biochemistry)

16 pages, 940 KB

Open AccessArticle

Comparative Effects of Trichoderma guizhouense NJAU4742 and Bacillus velezensis SQR9 on Growth and Pb Accumulation in Salix suchowensis

by Ruifang Huang, Baosong Wang, Ming Xu, Dezong Sui and Xudong He

Int. J. Mol. Sci. 2025, 26(20), 9961; https://doi.org/10.3390/ijms26209961 (registering DOI) - 13 Oct 2025

Abstract

Soil lead (Pb) contamination poses a severe threat to agricultural sustainability and food security. Phytoremediation offers a green alternative for remediation, yet its efficiency is limited by poor plant tolerance and restricted metal uptake. In this study we investigated the functional roles of [...] Read more.

Soil lead (Pb) contamination poses a severe threat to agricultural sustainability and food security. Phytoremediation offers a green alternative for remediation, yet its efficiency is limited by poor plant tolerance and restricted metal uptake. In this study we investigated the functional roles of the microbial inoculants Trichoderma guizhouense NJAU4742 and Bacillus velezensis SQR9 in enhancing the performance of Salix suchowensis P1024 grown in Pb-contaminated soil. NJAU4742 significantly increased plant biomass by 34% (p < 0.05), accompanied by increased soil microbial biomass and higher activities of urease, acid phosphatase, and sucrase. In contrast, SQR9 strongly enhanced Pb accumulation by 19% (p < 0.05), which was accompanied by upregulated antioxidant enzymes, reduced lipid peroxidation, and elevated cysteine levels. Random forest and correlation analyses demonstrated that soil nutrient cycling indices (urease, MBC, sucrase) were key predictors of biomass, whereas antioxidant defenses (POD, CAT) primarily explained Pb accumulation. These findings provide new insights into the distinct contributions of NJAU4742 and SQR9 to willow growth and Pb remediation, and provide a basis for developing more effective microbe-assisted phytoremediation strategies. Full article

(This article belongs to the Section Molecular Plant Sciences)

29 pages, 2053 KB

Open AccessReview

Targeting Granulin Haploinsufficiency in Frontotemporal Dementia: From Genetic Mechanisms to Therapeutics

by Eva Bagyinszky and Seong Soo A. An

Int. J. Mol. Sci. 2025, 26(20), 9960; https://doi.org/10.3390/ijms26209960 (registering DOI) - 13 Oct 2025

Abstract

Frontotemporal dementia (FTD) is the second most common early-onset dementia after Alzheimer’s disease, characterized by progressive neurodegeneration primarily in the frontal and temporal lobes. Granulin (GRN) gene for encoding the progranulin (PGRN) protein was a key genetic contributor to FTD. PGRN [...] Read more.

Frontotemporal dementia (FTD) is the second most common early-onset dementia after Alzheimer’s disease, characterized by progressive neurodegeneration primarily in the frontal and temporal lobes. Granulin (GRN) gene for encoding the progranulin (PGRN) protein was a key genetic contributor to FTD. PGRN was a multifunctional protein involved in lysosomal function, neuroinflammation, and neuronal survival. This review discusses the contributions of GRN haploinsufficiency to FTD pathogenesis with an emphasis on genetic mutations, downstream cellular consequences, relevant animal and cellular models, and emerging therapeutic strategies. Loss-of-function mutations in GRN were responsible up to ~50% reduction in PGRN levels, resulting in lysosomal dysfunction, TDP-43 aggregation, impaired microglial homeostasis, and enhanced neuroinflammation. Multiple in vitro and in vivo models recapitulated these pathological features. Novel therapeutic approaches, such as AAV-mediated gene therapy, stop codon readthrough compounds, SORT1 inhibitors, and antisense oligonucleotides, were investigated to restore PGRN levels and to mitigate disease progressions. However, challenges included the oncogenic risks of overexpression and the limited translational success in clinical trials to date. Targeting GRN haploinsufficiency became a promising avenue for FTD therapy. Improved models and refined delivery systems would be essential to develop safe and effective treatments. Future work should also focus on biomarker-guided interventions in presymptomatic mutation carriers. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Genetics and Genomics)

► Show Figures

Figure 1

29 pages, 1598 KB

Open AccessReview

Roles of Tumor-Infiltrating Lymphocytes and Antitumor Immune Responses as Predictive and Prognostic Markers in Patients with Breast Cancer Receiving Neoadjuvant Chemotherapy

by Ryungsa Kim, Takanori Kin and Koji Arihiro

Int. J. Mol. Sci. 2025, 26(20), 9959; https://doi.org/10.3390/ijms26209959 (registering DOI) - 13 Oct 2025

Abstract

Tumor-infiltrating lymphocytes (TILs) are thought to play important roles in tumor shrinkage and survival prolongation in patients with breast cancer receiving neoadjuvant chemotherapy (NAC). TILs are mononuclear immune cells such as lymphocytes and plasma cells, including CD4+ and CD8+ T cells, natural killer [...] Read more.

Tumor-infiltrating lymphocytes (TILs) are thought to play important roles in tumor shrinkage and survival prolongation in patients with breast cancer receiving neoadjuvant chemotherapy (NAC). TILs are mononuclear immune cells such as lymphocytes and plasma cells, including CD4+ and CD8+ T cells, natural killer cells, B cells, macrophages, regulatory T cells (Tregs), and myeloid/dendritic cells. The pre-NAC presence of more T cells and fewer Tregs in biopsy samples of primary breast tumors is known to contribute to tumor shrinkage and prolonged survival. This review was conducted to elucidate these roles in patients with breast cancer treated with NAC. Publications selected for inclusion in this review were identified by a PubMed search for articles published in English, performed using the terms “breast cancer”, “neoadjuvant chemotherapy”, “tumor-infiltrating lymphocyte”, “pathological complete response”, and “immune response”. The search was completed in July 2024. The functional roles of TILs in the achievement of these outcomes may vary by tumor subtype; increases and decreases in TIL levels before and after NAC have been shown to have conflicting effects. Biomarkers have been reported to predict local responses in the tumor microenvironment (e.g., immune-related gene signatures) and systemic immune responses (e.g., neutrophil-to-lymphocyte and platelet-to-lymphocyte ratios). Immune gene signatures and immune cell infiltration do not appear to be universally associated with tumor response or outcome in patients with breast cancer treated with NAC. The functional roles of TILs in breast tumor response and breast cancer survival may vary by tumor subtype, and conflicting results for the same subtypes may be due to differences in NAC regimens, immune responses, tumor heterogeneity, sample size, and the technical methods used to evaluate TILs in tumor samples. Full article

(This article belongs to the Section Molecular Immunology)

► Show Figures

Figure 1

18 pages, 1310 KB

Open AccessArticle

Plasma with Added Protease Inhibitors Improves Alpha- and Beta-CGRP Measurement Compared to Serum: Towards a Reliable Biomarker for Chronic Migraine

by Lucía de la Guerra-Sasián, Gabriel Gárate, Jorge Madera, Sara Pérez-Pereda, Marta Pascual-Mato, Vicente González-Quintanilla, Julio Pascual and María Muñoz-San Martín

Int. J. Mol. Sci. 2025, 26(20), 9958; https://doi.org/10.3390/ijms26209958 (registering DOI) - 13 Oct 2025

Abstract

The neuropeptide calcitonin gene-related peptide (CGRP), especially a-CGRP, is central in migraine pathophysiology. Although CGRP is a therapeutic target and potential biomarker, inconsistencies in measurement procedures need to be further studied for reliable results. This study aims to analyze factors influencing plasma CGRP [...] Read more.

The neuropeptide calcitonin gene-related peptide (CGRP), especially a-CGRP, is central in migraine pathophysiology. Although CGRP is a therapeutic target and potential biomarker, inconsistencies in measurement procedures need to be further studied for reliable results. This study aims to analyze factors influencing plasma CGRP measurement. Chronic migraine (CM) patients were recruited in our Headache Unit. Blood samples were collected before and during treatment with CGRP monoclonal antibodies, processed and stored. Levels of CGRP were measured with isoform-specific enzyme-linked immunosorbent assay (ELISA) tests. Statistical tests were used to assess concentration changes and group differences. The addition of protease inhibitors (PIs) to plasma samples significantly increased a-CGRP level detection, with a smaller effect on β-CGRP. No correlation was found between the a- and β-CGRP levels in plasma. The plasma-PI samples showed higher CGRP concentrations than in serum. The a-CGRP levels decreased during treatment while the β-CGRP levels remained stable. a-CGRP and age correlated negatively, but no sex-related differences were observed either for a- or β-CGRP. PI improved CGRP detection in plasma. The a-CGRP levels, which were influenced by age, decreased with specific treatment, suggesting its potential role as a biomarker. In contrast, β-CGRP remained stable, suggesting independent regulation of both isoforms. Full article

(This article belongs to the Section Biochemistry)

21 pages, 3935 KB

Open AccessArticle

Polyporusterone B Alleviates Inflammatory Injury via Suppression of Pro-Inflammatory Cytokine Production

by Dan Song, Yanru Zhang, Jialu Yuan, Xiaohua Hao, Shizhuo Chen, Xinjie Zhao and Yaomeng Yang

Int. J. Mol. Sci. 2025, 26(20), 9957; https://doi.org/10.3390/ijms26209957 (registering DOI) - 13 Oct 2025

Abstract

Polyporusterone B, a triterpene carboxylic acid isolated from Polyporus umbellatus Fries, exhibits anti-cancer and anti-hemolytic activities; however, its anti-inflammatory properties and underlying mechanisms remain unelucidated. We studied the anti-inflammatory effects of Polyporusterone B using lipopolysaccharide (LPS)-stimulated Raw264.7 murine macrophages (in vitro) and LPS-induced [...] Read more.

Polyporusterone B, a triterpene carboxylic acid isolated from Polyporus umbellatus Fries, exhibits anti-cancer and anti-hemolytic activities; however, its anti-inflammatory properties and underlying mechanisms remain unelucidated. We studied the anti-inflammatory effects of Polyporusterone B using lipopolysaccharide (LPS)-stimulated Raw264.7 murine macrophages (in vitro) and LPS-induced endotoxin shock in C57BL/6 mice (in vivo). Results showed that Polyporusterone B (1, 5, and 10 μM) had no cytotoxicity toward Raw264.7 cells, but significantly inhibited LPS-induced production of nitric oxide (NO) and pro-inflammatory cytokines (tumor necrosis factor (TNF-α), interleukin 1β (IL-1β), and interleukin 6 (IL-6)) in a concentration- and time-dependent manner, as demonstrated by Griess assay, qPCR, and ELISA. Western blot analysis revealed that Polyporusterone B suppressed LPS-induced phosphorylation of mitogen-activated protein kinases (ERK, P38, and NK) and reduced phosphorylation-mediated degradation of inhibitor of κBα (IκBα). Immunofluorescence and immunohistochemical staining further confirmed that Polyporusterone B blocked nuclear translocation of nuclear factor kappa-B (NF-κB)/Rel A in both Raw264.7 cells and mouse tissues. In the in vivo model, Polyporusterone B pretreatment significantly mitigated LPS-induced multi-organ pathological damage (e.g., lung edema, hepatic inflammation, renal hemorrhage) and downregulated tissue levels of TNF-α, IL-1β, and IL-6. These findings suggest that Polyporusterone B exerts anti-inflammatory effects by inhibiting the mitogen-activated protein kinase (MAPK) and NF-κB signaling pathways, suggesting its potential as a therapeutic candidate for inflammatory diseases. Full article

(This article belongs to the Special Issue Cytokines in Inflammation and Health)

27 pages, 15602 KB

Open AccessArticle

Dissecting Melanoma Ecosystem Heterogeneity from Molecular Characteristics to Genetic Variation at Single-Cell Resolution

by Congxue Hu, Liyuan Li, Tengyue Li, Baobin Qi, Wanqi Mi, He Yu, Kaiyue Yang, Qi Ou, Xia Li and Yunpeng Zhang

Int. J. Mol. Sci. 2025, 26(20), 9956; https://doi.org/10.3390/ijms26209956 (registering DOI) - 13 Oct 2025

Abstract

Melanoma shows heterogeneity across body sites like skin, acral skin, and the uvea, driven by molecular characteristics and genetic variations. However, comparative studies exploring the heterogeneity of melanoma across different anatomical sites remain limited, hindering a comprehensive understanding of its underlying biology. We [...] Read more.

Melanoma shows heterogeneity across body sites like skin, acral skin, and the uvea, driven by molecular characteristics and genetic variations. However, comparative studies exploring the heterogeneity of melanoma across different anatomical sites remain limited, hindering a comprehensive understanding of its underlying biology. We proposed a research framework through bioinformatics to analyze the tumor ecosystems of cutaneous, acral, and uveal melanoma, from molecular characteristics to genetic variations at single-cell resolution. We found that oxidative phosphorylation (OXPHOS) is a critical driver of tumor cell evolution, with abnormal ribosomal gene and tumor suppressor expression observed in uveal melanoma (UM). Additionally, we screened for potential drug targets and drugs against tumor cells. In the immune microenvironment, acral melanoma (AM) and UM exhibit stronger immunosuppressive characteristics compared to cutaneous melanoma (CM). OXPHOS contributes to T cell cytotoxicity dysregulation in CM and AM, while interferon-γ is crucial in UM. Tumor cells may also induce T cell dysfunction through biological signals such as MIF-CD74 and HLA-E-NKG2A. This study offers valuable insights into melanoma heterogeneity, providing a comprehensive research framework for understanding the distinct molecular and immune characteristics of CM, AM, and UM, and potentially guiding the development of therapeutic strategies tailored to each melanoma subtype. Full article

(This article belongs to the Section Molecular Informatics)

► Show Figures

Graphical abstract

8 pages, 241 KB

Open AccessEditorial

Transcription Factors in Plant Gene Expression Regulation

by Piotr Szymczyk

Int. J. Mol. Sci. 2025, 26(20), 9955; https://doi.org/10.3390/ijms26209955 (registering DOI) - 13 Oct 2025

Abstract

Gene expression is a fundamental element in the process of genetic information flow [...] Full article

(This article belongs to the Special Issue Transcription Factors in Plant Gene Expression Regulation)

21 pages, 2320 KB

Open AccessArticle

Precision Profiling of Disease Progression in Murine Models of Sepsis and Septic Shock

by Stewart D. Ramsay, Declan E. Kilgariff, Benjamin J. Young, Mark P. Plummer, Marni A. Nenke, Emily J. Meyer, David J. Torpy and Richard L. Young

Int. J. Mol. Sci. 2025, 26(20), 9954; https://doi.org/10.3390/ijms26209954 (registering DOI) - 13 Oct 2025

Abstract

Septic shock has an unacceptably high mortality rate and unmet need for new therapeutics. Murine models are crucial for research, yet methodologies often differ. This study characterised standard- and high-grade caecal ligation and puncture (CLP) murine models of septic shock by integrating ultraminiature [...] Read more.

Septic shock has an unacceptably high mortality rate and unmet need for new therapeutics. Murine models are crucial for research, yet methodologies often differ. This study characterised standard- and high-grade caecal ligation and puncture (CLP) murine models of septic shock by integrating ultraminiature arterial telemetry with comprehensive plasma biomarker analysis. Standard-grade and high-grade CLP was performed in 8–10 week old, male C57BL/6 mice (n = 98), with a subset implanted with arterial telemetry to monitor real-time circulatory function. Plasma markers of inflammation and organ damage were measured at multiple intervals up to 168 h post-CLP. Standard-grade and high-grade CLP showed distinct progressions; episodes of hypotension began 5–6 h after CLP in 30% of standard-grade and all high-grade CLP mice, with respective 168 h mortality of 40% and 71%. Recurrent episodes of hypotension 5–39 h after CLP were universally lethal. The coincidence of hypotension and elevated plasma lactate defined the onset of septic shock after high-grade CLP, which was always lethal. Inflammatory cytokines and markers of liver, renal, and cardiac damage were markedly elevated to 168 h after high-grade CLP, in contrast to standard-grade CLP, which returned to baseline by 48 h. Elevated plasma IL-6, TNFα, and corticosterone, along with reduced albumin, were significantly correlated with mortality. In conclusion, this research refines murine CLP models by providing a precise, dynamic map of the progression to septic shock. The high-grade CLP model consistently models early and late-stage physiological deterioration and serves as a robust model for evaluating the efficacy of novel therapies aimed at human septic shock. Full article

(This article belongs to the Section Molecular Endocrinology and Metabolism)

► Show Figures

Figure 1

20 pages, 4019 KB

Open AccessArticle

Assessing the Anti-Cryptococcus Antifungal Potential of Artemisinin

by Maphori Maliehe, Jacobus Albertyn and Olihile M. Sebolai

Int. J. Mol. Sci. 2025, 26(20), 9953; https://doi.org/10.3390/ijms26209953 (registering DOI) - 13 Oct 2025

Abstract

Cryptococcus neoformans (C. neoformans) has emerged as a global pathogen of concern. While much is known about its pathobiology, its management is complicated by strains displaying non-fluconazole susceptibility. This contribution assessed the repurposing of artemisinin (ART) as an anti-Cryptococcus antifungal. [...] Read more.

Cryptococcus neoformans (C. neoformans) has emerged as a global pathogen of concern. While much is known about its pathobiology, its management is complicated by strains displaying non-fluconazole susceptibility. This contribution assessed the repurposing of artemisinin (ART) as an anti-Cryptococcus antifungal. An in vitro susceptibility assay was performed to assess the drug response of cells. To establish the ART mode of action, assays examining mitochondrial health were set up. The phagocytosis efficiency of a murine macrophage cell line towards ART-treated and non-treated cells was determined. To complement this, the immunomodulatory effects of ART were further characterised in Galleria mellonella (G. mellonella) by assessing haemocytes’ phagocytosis and expression of immune genes, i.e., insect metalloproteinase inhibitor (IMPI) and hemolin, essential for the insect antimicrobial response. In the end, the survival rate of infected larvae was calculated. We established that ART was antifungal, with cell death triggered by the uncoupling of the cytochrome c (cyt c) from the mitochondria, leading to activation of caspase-3-dependent-like apoptosis. Moreover, treatment induced ultrastructural changes with treated cells appearing more deformed than non-treated cells (p < 0.05). Treatment also increased the susceptibility of cells towards both macrophage and haemocyte phagocytosis compared to non-treated cells (p < 0.05). Importantly, treatment seemed to weaken the cells, decreasing their virulence potential based on analysis of the expression of the immune gene markers, which translated into treatment rescuing 75% of the larvae infected with 0.1 ART-treated cells. These preliminary findings support the repurposing of ART as an anti-Cryptococcus antifungal. Full article

(This article belongs to the Special Issue Antifungal Drug Discovery: Progresses, Challenges, Opportunities, 2nd Edition)

► Show Figures

Figure 1

17 pages, 5676 KB

Open AccessArticle

Jumping Translocation Breakpoint Expression in Midgestation Mouse Embryos

by Carley McGrath, Taniya M Jayaweera, Thomas Lufkin, Costel C. Darie, Anca-Narcisa Neagu and Petra Kraus

Int. J. Mol. Sci. 2025, 26(20), 9952; https://doi.org/10.3390/ijms26209952 (registering DOI) - 13 Oct 2025

Abstract

Jumping translocations (JTs) can lead to partial trisomies. A breakpoint within the gene known as Jumping Translocation Breakpoint (JTB) has previously been associated with JTs involving the long arm of human chromosome 1 (1q). These 1q+ amplifications are frequently observed in [...] Read more.

Jumping translocations (JTs) can lead to partial trisomies. A breakpoint within the gene known as Jumping Translocation Breakpoint (JTB) has previously been associated with JTs involving the long arm of human chromosome 1 (1q). These 1q+ amplifications are frequently observed in cancer. JTB was initially mapped to the Epidermal Differentiation Complex (EDC) at 1q21, and earlier studies primarily focused on its role in malignant or adult tissues. Using updated genomic data, we refined the mapping of JTB. We employed RNA in situ hybridization (RISH) to visualize Jtb expression with organ, tissue, and cell-level resolution. We demonstrate that human JTB and murine Jtb are located outside the EDC. In midgestational wild-type mouse embryos, Jtb is expressed in multiple tissues, including the developing heart and vertebral column, and shows partial overlap with the expression of early markers of the neural crest cell lineage. Our findings suggest that the oncogenic potential associated with human JTB translocations is likely unrelated to its previously assumed location within the EDC. Full article

(This article belongs to the Section Macromolecules)

► Show Figures

Figure 1

22 pages, 2098 KB

Open AccessReview

Mammary Gland Microbiota in Benign Breast Diseases

by Nikita I. Ukraincev, Maria I. Kashutina, Larisa I. Kasatkina, Adkhamzhon B. Abduraimov and Yury V. Zhernov

Int. J. Mol. Sci. 2025, 26(20), 9951; https://doi.org/10.3390/ijms26209951 (registering DOI) - 13 Oct 2025

Abstract

The human microbiome is a critical factor in health and disease. While its association with breast cancer (BC) has been increasingly studied, this review provides a dedicated synthesis of the microbiota’s role in benign breast diseases (BBDs)—a common yet microbiologically overlooked spectrum of [...] Read more.

The human microbiome is a critical factor in health and disease. While its association with breast cancer (BC) has been increasingly studied, this review provides a dedicated synthesis of the microbiota’s role in benign breast diseases (BBDs)—a common yet microbiologically overlooked spectrum of conditions. The primary aim of this work is to consolidate the current understanding of the composition, origins, and functional mechanisms of the mammary gland (MG) microbiota specifically in the context of BBD and to evaluate its potential for novel diagnostic and therapeutic targets. We detail the distinct MG microbiota, formed via exogenous (e.g., cutaneous, translocation) and endogenous (e.g., enteromammary, lymphohematogenous) pathways, and its interaction with the host through estrogen metabolism, immunomodulation, and epigenetic modifications. This narrative review reveals unique dysbiotic patterns in BBD, characterized by distinct microbial signatures, such as the enrichment of Corynebacterium kroppenstedtii in granulomatous mastitis and the presence of Staphylococcus aureus in fibroadenomas and lactational mastitis. Furthermore, specific gut microbial profiles are identified in BBD patients, including an increased abundance of genera such as Clostridium and Faecalibacterium, alongside a decrease in Collinsella and Alistipes compared to healthy controls. These specific taxa represent compelling candidates for diagnostic biomarkers. We conclude that microbial dysbiosis is a significant component of BBD pathogenesis. A paradigm shift toward multi-omics approaches and mechanistic studies is now essential to translate these associations into clinical applications. Understanding the BBD-specific microbiome holds the promise of revolutionizing patient care through microbiota-based diagnostics for differentiating benign subtypes and novel, personalized therapeutic strategies aimed at restoring microbial homeostasis. Full article

(This article belongs to the Section Molecular Microbiology)

► Show Figures

Figure 1

23 pages, 863 KB

Open AccessReview

microRNAs as Biomarkers and Therapeutic Targets in Rheumatoid Arthritis

by Filip Machaj, Magdalena Chmielewska-Jeznach, Anna Koryszewska-Bagińska, Damian Malinowski, Andrzej Pawlik and Gabriela Olędzka

Int. J. Mol. Sci. 2025, 26(20), 9950; https://doi.org/10.3390/ijms26209950 (registering DOI) - 13 Oct 2025

Abstract

Rheumatoid arthritis (RA) is a prevalent autoimmune disease characterized by chronic joint inflammation. Its pathophysiology involves complex interactions among immune cells, leading to joint damage, primarily in the synovial membrane. MicroRNAs (miRs), single-stranded non-coding RNAs, play a critical role in regulating pathways affecting [...] Read more.

Rheumatoid arthritis (RA) is a prevalent autoimmune disease characterized by chronic joint inflammation. Its pathophysiology involves complex interactions among immune cells, leading to joint damage, primarily in the synovial membrane. MicroRNAs (miRs), single-stranded non-coding RNAs, play a critical role in regulating pathways affecting RA progression, particularly in fibroblast-like synoviocytes and peripheral blood mononuclear cells. Key pathways influenced by miRs include NF-κB, apoptosis, PI3K/AKT signaling, and cytokine production. Dysregulated miRs impact cell proliferation, survival, and inflammatory responses. This review explores not only the role of miRs in RA pathogenesis, but also highlights their potential as biomarkers for early detection and severity prediction. Moreover, therapeutic approaches targeting miRs, including mimics and inhibitors, show promise in animal models, with methods like intra-articular administration being favored due to better efficacy and reduced side effects. While early studies highlight potential pathways for RA treatment, challenges remain in translating these findings into safe and effective clinical therapies. Full article

(This article belongs to the Special Issue miRNA in Human Diseases)

► Show Figures

Figure 1

Journal Description

International Journal of Molecular Sciences

Latest Articles

Journal Menu

Journal Browser

Highly Accessed Articles

Latest Books

E-Mail Alert

News

Topics

Conferences

Special Issues

Topical Collections

Further Information

Guidelines

MDPI Initiatives

Follow MDPI