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Keywords = serine phosphorylated pathway

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35 pages, 40681 KB  
Article
The Role of ULK3 in Cancer Progression: A Pan-Cancer Bioinformatics Analysis Integrated with Experimental Validation in Prostate Cancer
by Yangyang Han, Mengqi Zhang, Mannizire Rehemujiang, Xintong Li, Yimin Liu, Niuniu Zhang, Meng Sun, Yunbo Zhang, Ayshamgul Hasim and Mengjia Li
Int. J. Mol. Sci. 2026, 27(13), 6040; https://doi.org/10.3390/ijms27136040 - 5 Jul 2026
Viewed by 208
Abstract
Unc-51-like kinase 3 (ULK3) is a key member of the ULK serine/threonine kinase family. Aberrant ULK3 expression has been increasingly linked to tumorigenesis and malignant progression in multiple cancer types. However, the precise role of ULK3 in tumor initiation and progression remains incompletely [...] Read more.
Unc-51-like kinase 3 (ULK3) is a key member of the ULK serine/threonine kinase family. Aberrant ULK3 expression has been increasingly linked to tumorigenesis and malignant progression in multiple cancer types. However, the precise role of ULK3 in tumor initiation and progression remains incompletely understood. Leveraging integrated multi-omics data from The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression (GTEx) project, and the Clinical Proteomic Tumor Analysis Consortium (CPTAC), we systematically characterized the expression of ULK3 at both the transcript and protein levels across 33 cancer types. We also evaluated genomic alterations, prognostic significance, alternative splicing, pathway enrichment, tumor stemness, immune infiltration, and immunotherapy-related biomarkers. In parallel, we investigated the function of ULK3 in prostate cancer PC-3 cells using cellular localization analysis, wound-healing assays, and MTT assays. We further applied Connectivity Map (CMap) screening and molecular docking to identify candidate ULK3 activators. ULK3 was significantly upregulated in 13 cancer types, including Bladder Urothelial Carcinoma, Breast Invasive Carcinoma, and Lung Adenocarcinoma. In contrast, ULK3 was downregulated in Cholangiocarcinoma and Head and Neck Squamous Cell Carcinoma. High ULK3 expression was associated with poor overall survival in Adrenocortical Carcinoma, Kidney Renal Clear Cell Carcinoma, and Skin Cutaneous Melanoma. Copy number amplification contributed to ULK3 overexpression. A recurrent A206V missense mutation was detected in the protein kinase (Pkinase) domain. Genes co-expressed with ULK3 were enriched in RNA splicing, methylation, oxidative phosphorylation, and energy metabolism. ULK3 expression showed positive correlations with tumor stemness indices and m1A/m5C/m6A RNA modification regulators. From an immunological perspective, high ULK3 expression was associated with lower Immune Score, increased M2 macrophage infiltration, and co-expression of PD-L1, CTLA4, and LAG3 in most cancers. ULK3 expression was also correlated with Tumor Mutational Burden in Kidney Renal Clear Cell Carcinoma and Rectum Adenocarcinoma. In addition, ULK3 expression was associated with Microsatellite Instability in Brain Lower Grade Glioma, Lung Adenocarcinoma, and Uterine Corpus Endometrial Carcinoma. ULK3 overexpression promoted proliferation and migration in PC-3 cells. Cephaeline was screened as a putative ULK3 activator. Overall, ULK3 expression and amplification were associated with poor clinical outcomes, tumor stemness, immunosuppression, and RNA dysregulation. These findings highlight the potential value of ULK3 as a pan-cancer diagnostic and prognostic biomarker and as a predictor of immunotherapy response, particularly in prostate cancer. Full article
(This article belongs to the Special Issue Genetic and Molecular Markers in Prostate Cancer)
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14 pages, 2604 KB  
Article
Expression of Phosphomimetic OSTM1-T328E/S329D Variant Partially Restores Bone Resorption Defect in LRRK1-Deficient Mice
by Anakha Udayakumar, Yian Chen, Haibo Zhao, Subburaman Mohan and Weirong Xing
Biology 2026, 15(12), 964; https://doi.org/10.3390/biology15120964 - 19 Jun 2026
Viewed by 254
Abstract
LRRK1 is essential for osteoclast-mediated bone resorption, and loss of LRRK1 function causes osteopetrosis in mice and humans. However, the mechanisms by which LRRK1 regulates osteoclast activity remain incompletely defined. We previously identified that phosphorylation of OSTM1 at threonine 328 and serine 329 [...] Read more.
LRRK1 is essential for osteoclast-mediated bone resorption, and loss of LRRK1 function causes osteopetrosis in mice and humans. However, the mechanisms by which LRRK1 regulates osteoclast activity remain incompletely defined. We previously identified that phosphorylation of OSTM1 at threonine 328 and serine 329 was compromised in LRRK1-deficient osteoclasts. To test the role for OSTM1 phosphorylation in LRRK1 regulation of osteoclast functions, we expressed a phosphomimetic OSTM1 variant in LRRK1-null osteoclasts. Overexpression of phosphomimetic, but not a dephosphomimetic variant, partially restored resorptive activity in LRRK1-deficient osteoclasts in vitro. To test OSTM1’s role in rescuing defective bone resorption in Lrrk1-null mice, we generated Ostm1-T328E/S329D knock-in (KI) mice and crossed them onto the Lrrk1-deficient background. Ostm1-T328E/S329D KI mice displayed normal skeletal development and bone remodeling. When crossed to the Lrrk1-deficient background, OSTM1-T328E/S329D expression increased osteoclast resorptive activity and bone formation and partially improved trabecular architecture, although bone volume remained unchanged. These findings demonstrate that OSTM1 phosphorylation contributes to LRRK1-dependent regulation of osteoclast function and identify the LRRK1–OSTM1 pathway as a mechanistic node controlling bone resorption. Our work provides new insight into the molecular basis of LRRK1-mediated osteoclast function and highlights OSTM1 phosphorylation as a potential therapeutic target for metabolic bone diseases. Full article
(This article belongs to the Section Cell Biology)
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22 pages, 25748 KB  
Article
q Is a Heterotrimeric G-Protein Subunit That Directs the Selectivity of PPARγ-Induced Gene Pathways Toward Energy-Related Processes Rather than Adiposity
by Evelyn A. Bates, Zachary A. Kipp, Wang-Hsin Lee, Genesee J. Martinez, Sally N. Pauss, Philipp E. Scherer and Terry D. Hinds
Metabolites 2026, 16(6), 418; https://doi.org/10.3390/metabo16060418 - 15 Jun 2026
Viewed by 354
Abstract
Background/Objectives: Signaling mediators of PPARγ influence pathways involved in adipogenesis, lipid storage, inflammation, energy-related processes, and glucose utilization. Recent research indicates that PPARγ coregulators, recruited or released during ligand binding, govern specific gene pathways. It was recently discovered that Gαq, a [...] Read more.
Background/Objectives: Signaling mediators of PPARγ influence pathways involved in adipogenesis, lipid storage, inflammation, energy-related processes, and glucose utilization. Recent research indicates that PPARγ coregulators, recruited or released during ligand binding, govern specific gene pathways. It was recently discovered that Gαq, a heterotrimeric G protein subunit, also signals to PPARγ and may significantly affect adipogenesis and glucose sensitivity. Methods: To explore Gαq’s role in adipocytes, we generated CRISPR-mediated Gαq (Gnaq) knockout (Gnaq KO) and scramble control cells from 3T3-L1 preadipocytes. Results: The absence of Gαq resulted in increased lipid accumulation and elevated serine 273 (but not serine 112) phosphorylation of PPARγ. Gαq deficiency also decreased mitochondrial abundance and respiration in response to PPARγ ligands such as rosiglitazone, pioglitazone, and troglitazone. RNA sequencing comparing differentiated Gnaq KO and control adipocytes identified over 800 differentially expressed genes, including those associated with enhanced lipid metabolism and reduced inflammation. Corresponding PamGene kinome profiling showed increased serine/threonine kinase activity and decreased phosphotyrosine kinase signaling in Gnaq KO adipocytes. Conclusions: These findings support Gαq as a regulator of adipocyte function, linking kinase signaling pathways to PPARγ-mediated transcription. This research provides mechanistic insights into targeting Gαq as a potential treatment for individuals with obesity and metabolic disorders. Full article
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19 pages, 3863 KB  
Article
The Involvement of the PI3K/AKT Pathway in Zn Alleviation of Heat Stress-Induced Damage to Broiler Jejunal Organoids
by Weizhen Song, Weiyun Zhang, Xi Lin, Hsiao-Ching Liu, Jack Odle, Miles Todd See, Shengchen Wang, Xiaoyan Cui, Chuanlong Wang, Liyang Zhang and Xugang Luo
Animals 2026, 16(10), 1492; https://doi.org/10.3390/ani16101492 - 13 May 2026
Viewed by 606
Abstract
The direct involvement of the phosphatidylinositol 3-kinase (PI3K)/serine threonine kinase (AKT) signaling pathway in the alleviation of the heat stress (HS)-induced damage to the integrity and barrier function of broiler jejunal organoids (JOs) by supplemental zinc (Zn) has not been confirmed. To verify [...] Read more.
The direct involvement of the phosphatidylinositol 3-kinase (PI3K)/serine threonine kinase (AKT) signaling pathway in the alleviation of the heat stress (HS)-induced damage to the integrity and barrier function of broiler jejunal organoids (JOs) by supplemental zinc (Zn) has not been confirmed. To verify it, two experiments were conducted in the present study. In experiment 1, the optimal concentrations of PI3K/AKT inhibitor (PI3K-IN-1) or agonist (YS-49) were screened. In experiment 2, the role of PI3K/AKT in Zn alleviation of HS-induced damage to JOs was evaluated with three JO types as control groups under baseline incubation temperature (40 °C) plus a 3 (JOs types) × 3 (Zn sources) factorial design under high temperature (44 °C). The results showed that the optimal concentrations of the PI3K-IN-1 and YS-49 for effectively inhibiting and promoting (p < 0.001) phosphorylation of PI3K and AKT were 16 μmol/L and 9 μmol/L, respectively. Adding Zn, especially Zn proteinate with moderate chelation strength (Zn-Prot M), alleviated (p < 0.001) the HS-induced increases in diamine oxidase content and lactate dehydrogenase activity in the media and the HS-induced decreases in JOs budding percentage, proportions of 5-ethynyl-2′-deoxyuridine and proliferating cell nuclear antigen positive cells, and the phosphorylation of PI3K and AKT. PI3K/AKT inhibition or activation reduced or enhanced (p < 0.05) the above alleviating effect of Zn, especially Zn-Prot M. These results indicate that the PI3K/AKT signaling pathway mediated the alleviation of HS-induced damage to integrity and barrier function of broiler JOs by supplemental Zn, particularly Zn-Prot M via promotion of cell proliferation. Full article
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20 pages, 2135 KB  
Article
Identification of Cyclin L1 as a Host Factor Regulating Hepatitis B Virus Replication
by Collins Oduor Owino, Balakrishnan Chakrapani Narmada, Gian Yi Lin, Pauline Poh Kim Aw, Nivrithi Ganesh, Jovi Tan Siying, Marie-Laure Plissonnier, Thangavelu Thangavelu Matan, Niranjan Shirgaonkar, Pablo Bifani, Massimo Levrero, Giridharan Periyasamy, Seng Gee Lim and Ramanuj DasGupta
Viruses 2026, 18(5), 545; https://doi.org/10.3390/v18050545 - 8 May 2026
Viewed by 1359
Abstract
Background and Aims: Understanding regulatory interactions between hepatitis B virus (HBV) and host factors is essential for the development of next generation host-directed antiviral therapies and the achievement of a functional HBV cure. Here, we investigated HBV-induced alterations in host gene expression in [...] Read more.
Background and Aims: Understanding regulatory interactions between hepatitis B virus (HBV) and host factors is essential for the development of next generation host-directed antiviral therapies and the achievement of a functional HBV cure. Here, we investigated HBV-induced alterations in host gene expression in primary human hepatocytes (PHH) to identify host factors exploited by the virus for replication and persistence. Whole-transcriptome sequencing (WTS) of HBV-infected PHH identified host pathways with potential roles in the HBV life cycle. RNA interference-based functional screening of dysregulated candidate genes identified cyclin L1 (CCNL1) as a key host factor. RNAi-mediated knockdown of CCNL1 reduced HBV gene expression, including hepatitis B surface antigen (HBsAg). Mechanistically, CCNL1 regulates phosphorylation of the C-terminal domain (CTD) of RNA polymerase II (RNAPII) at serine 2 (S2), consistent with a role in transcriptional regulation. CCNL1 knockdown further reduced the binding of total and phospho- (Ser2/Ser5) RNAPII, pan-acetylated histone H3 (H3ac), and H3K27ac to HBV covalently closed circular DNA (cccDNA), indicating impaired cccDNA-dependent transcription. In addition, CCNL1 expression was elevated in chronic hepatitis B patients compared with those with resolved infection. Collectively, these data demonstrate that CCNL1 promotes HBV transcription and replication through modulation of RNAPII phosphorylation and chromatin-associated transcriptional activity, identifying CCNL1 as a potential host susceptibility factor for HBV. Importance: Hepatitis B virus infection remains a major threat to human health in areas with high prevalence. There is need to fully understand the complex interactions between the virus and human host factors/processes to support ongoing efforts to develop anti-HBV therapies that can be used with existing therapies to achieve a better cure. HBV relies on host cellular factors and biological processes to establish and maintain efficient infection, making host–virus interactions attractive targets for therapeutic intervention. Thus, identifying host factors that support and/or restrict HBV infection is essential for understanding the molecular basis of chronic HBV infection and for developing host-targeting anti-HBV drugs. This study identifies cyclin L1 (CCNL1) as a host susceptibility factor that promotes HBV transcription and replication through regulation of RNA polymerase II activity and or post-transcriptional mechanisms. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
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13 pages, 3129 KB  
Article
Simvastatin Attenuates Doxorubicin-Induced Inflammation in Human Cardiomyocytes
by Roberta Vitale, Rosaria Margherita Rispoli, Maria Carmela Di Marcantonio, Barbara Pala, Stefania Marzocco, Gabriella Mincione and Ada Popolo
Biomedicines 2026, 14(5), 1071; https://doi.org/10.3390/biomedicines14051071 - 8 May 2026
Viewed by 921
Abstract
Background/Objectives: Clinical application of Doxorubicin (Doxo) is limited by cardiotoxicity, a process strongly associated with an interplay between oxidative stress and inflammatory signaling, particularly Nuclear Factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation and Nucleotide oligomerization domain-like receptor family, pyrin domain containing [...] Read more.
Background/Objectives: Clinical application of Doxorubicin (Doxo) is limited by cardiotoxicity, a process strongly associated with an interplay between oxidative stress and inflammatory signaling, particularly Nuclear Factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation and Nucleotide oligomerization domain-like receptor family, pyrin domain containing 3 (NLRP3) inflammasome engagement. Identifying strategies capable of mitigating these interconnected pathways is of critical importance in cardio-oncology. Simvastatin (SIM) is a promising option since it modulates oxidative stress, inflammation, and cell death through its pleiotropic effects, so this study aimed to evaluate whether SIM attenuates Doxo-induced inflammatory responses. Methods: Human Cardiomyocyte (HCM) cells were pre-treated with SIM (10 µM) for 4 h and then co-exposed to SIM and Doxo (1 µM) for 20 h. Cytofluorimetric analysis was used to evaluate inducible nitric oxide synthase (iNOS), Connexin 43 (Cx43), and Cx43 phosphorylated at Serine 368 (pS368Cx43) levels. Real-time qPCR was performed to evaluate iNOS gene expression, while Nitric oxide (NO) release was evaluated by spectrophotometric analysis. Interleukin (IL)-1β, IL-18, IL-6, tumor necrosis factor alpha (TNF-α) production, and NLRP3 levels were evaluated by means of ELISA assay. Expression levels of inhibitor of nuclear factor kappa B alpha (IκB-α), Caspase-1, and Gasdermin D (GSDMD) were evaluated by Western Blot analysis. Nuclear translocation of NF-κB was evaluated by immunofluorescence assay. Results: In our experimental model, SIM significantly (p < 0.01) reduced Doxo-induced nitrite release, as well as iNOS gene expression (p < 0.05) and protein levels (p < 0.01). SIM also markedly attenuated Doxo-induced NF-κB signaling, pro-inflammatory cytokines production (TNF-α and IL-6, p < 0.01), and inflammosome-related responses (cleaved caspase-1, IL-1β, N-terminal domain of GSDMD), and NLRP3 expression p < 0.05). Additionally, SIM significantly attenuated the overexpression of Cx43 and its phosphorylated form (pS368Cx43), which are responsible for impairing intercellular communication and electrical coupling in cardiomyocytes and contribute to arrhythmias and conduction abnormalities characteristic of acute Doxo-induced cardiotoxicity. Conclusions: Overall, these findings demonstrate that SIM exerts a multifaceted cardioprotective effect against Doxo-induced injury, thereby targeting interconnected inflammatory and pro-arrhythmic pathways implicated in Doxo cardiotoxicity. Full article
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17 pages, 4375 KB  
Article
Characterization of Fiber-Type Composition and Phosphoproteins of Fast- and Slow-Growing Broilers
by Yi Li, Weiran Huo, Kaiqi Weng, Jinlu Liu, Yingjie Gu, Yuchun Cai, Yang Zhang, Yu Zhang, Xuming Hu, Guohong Chen and Qi Xu
Animals 2026, 16(9), 1311; https://doi.org/10.3390/ani16091311 - 24 Apr 2026
Viewed by 414
Abstract
Muscle fibers exhibit high plasticity: both the fast-twitch fiber type and slow-twitch fiber type can mutually transform under the regulation of phosphorylation. In this study, we characterized the muscle fiber profiles and phosphoproteomes of the m. extensor digitorum longus (EDL) and m. soleus [...] Read more.
Muscle fibers exhibit high plasticity: both the fast-twitch fiber type and slow-twitch fiber type can mutually transform under the regulation of phosphorylation. In this study, we characterized the muscle fiber profiles and phosphoproteomes of the m. extensor digitorum longus (EDL) and m. soleus (SOL) in slow-growing Xueshan chickens and fast-growing Ross 308 broilers. Fiber-type distribution was quantified by immunohistochemistry and RT-qPCR of MYH7B, MYH1A and MYH1B. TMT-based phosphoproteomics, combined with bioinformatic analysis, was used to identify differentially expressed phosphopeptides (DEPs) in two comparisons: Ross 308 SOL vs. Ross 308 EDL, and Xueshan EDL vs. Ross 308 EDL. The proportion of type I (slow-twitch) fibers in EDL was significantly higher in Xueshan chickens than in Ross 308 broilers (15.53% vs. 6.14%, p < 0.05), with no significant differences in fiber distribution or diameter between the SOL and EDL in Xueshan chickens (p > 0.05). A total of 3226 phosphopeptides corresponding to 1762 phosphoproteins were identified, with serine as the most abundant phosphorylated amino acid (73.92%). PDHA1, PHKB and PGAM1 were identified as the key DEPs common to both comparison groups. Bioinformatic analyses revealed that reversible site-specific phosphorylation regulates avian muscle fiber-type transformation mainly via the glycolysis/gluconeogenesis pathway. Full article
(This article belongs to the Section Poultry)
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21 pages, 1472 KB  
Article
A Recombinant Antibody Against Human DRP1 Serine 616 Phosphorylation Enables Detection of BRAFV600E-Associated Mitochondrial Division in Cancer
by Shanon T. Nizard, Yiyang Chen, Madhavika N. Serasinghe, Ruben Fernandez-Rodriguez, Kamrin D. Shultz, Jesminara Khatun, Anthony Mendoza, Jesse D. Gelles, Juan F. Henao-Martinez, Ioana Abraham-Enachescu, Md Abdullah Al Noman, Stella G. Bayiokos, J. Andrew Duty, Shane Meehan, Mihaela Skobe and Jerry Edward Chipuk
Antibodies 2026, 15(2), 38; https://doi.org/10.3390/antib15020038 - 20 Apr 2026
Viewed by 1350
Abstract
Background/Objectives: Mitochondria are dynamic organelles that continuously undergo balanced cycles of fusion and division to maintain optimal function. Mitochondrial division is mediated by Dynamin-Related Protein 1 (DRP1), a cytosolic large GTPase whose phosphorylation at serine 616 (DRP1-S616Ⓟ) promotes its translocation to the outer [...] Read more.
Background/Objectives: Mitochondria are dynamic organelles that continuously undergo balanced cycles of fusion and division to maintain optimal function. Mitochondrial division is mediated by Dynamin-Related Protein 1 (DRP1), a cytosolic large GTPase whose phosphorylation at serine 616 (DRP1-S616Ⓟ) promotes its translocation to the outer mitochondrial membrane and organelle division. Dysregulated mitochondrial division disrupts cellular homeostasis and contributes to disease pathogenesis, including cancer. Our prior work demonstrated that the oncogene-induced mitogen-activated protein kinase (MAPK) pathway constitutively phosphorylates DRP1 at serine 616, which is essential to cellular transformation and correlates with oncogene status in patient tissues. Similarly, DRP1-S616Ⓟ is subject to pharmacologic control by targeted therapies against oncogenic MAPK signaling. Methods: Building upon this foundation, we developed and characterized a recombinant murine monoclonal antibody (referred to as 3G11) with high specificity for human DRP1-S616Ⓟ, raised against a peptide derived from the human DRP1 sequence. Results: Using diverse experimental platforms, we demonstrate the robust utility of 3G11 to detect DRP1-S616Ⓟ in melanoma cell extracts and isolated organelles. Immunofluorescence revealed that pharmacologic inhibition of oncogenic MAPK signaling reduces DRP1-S616Ⓟ levels, which correlates with mitochondrial hyperfusion, while immunohistochemistry showed that elevated DRP1-S616Ⓟ expression in human tissues correlates with BRAFV600E disease. Conclusions: 3G11 is a new recombinant antibody for detecting DRP1-S616Ⓟ and supports studies of mitochondrial division in cancer. Together, these findings establish 3G11 as a specific, versatile, renewable, and cost-effective tool for studying mitochondrial division, with strong potential for clinical applications. Full article
(This article belongs to the Section Antibody Discovery and Engineering)
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16 pages, 1550 KB  
Review
Leucine-Rich Repeat Kinase 2 (LRRK2) in Glucose Metabolism and Metabolic–Neuroinflammatory Crosstalk
by Fumitaka Kawakami, Motoki Imai, Masanori Ogata, Toshiya Habata, Shun Tamaki, Rei Kawashima, Yoshifumi Kurosaki, Sayaka Miyai, Moragot Chatatikun, May Pyone Kyaw and Kenichi Ohba
Biomolecules 2026, 16(4), 588; https://doi.org/10.3390/biom16040588 - 15 Apr 2026
Viewed by 719
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a multidomain serine/threonine kinase and a major genetic contributor to Parkinson’s disease (PD). Although LRRK2 has been extensively studied in neurodegeneration, emerging evidence indicates that it also plays a critical role in systemic metabolism. LRRK2 regulates glucose [...] Read more.
Leucine-rich repeat kinase 2 (LRRK2) is a multidomain serine/threonine kinase and a major genetic contributor to Parkinson’s disease (PD). Although LRRK2 has been extensively studied in neurodegeneration, emerging evidence indicates that it also plays a critical role in systemic metabolism. LRRK2 regulates glucose homeostasis through modulation of insulin signaling, vesicle trafficking, mitochondrial function, and inflammatory responses. Studies using LRRK2 knockout and knock-in models, including the pathogenic G2019S mutation, have revealed abnormalities in insulin sensitivity, adipose tissue inflammation, hepatic glucose production, and skeletal muscle metabolism. Mechanistically, LRRK2 phosphorylates Rab GTPases, thereby controlling insulin receptor trafficking and GLUT4 translocation. In addition, LRRK2 influences mitochondrial dynamics and reactive oxygen species production, linking metabolic stress to inflammatory signaling. Importantly, LRRK2 also regulates innate immune pathways, including TLR4–NFκB signaling and inflammasome activation, thereby connecting peripheral metabolic dysfunction to neuroinflammation. Here, we propose an integrated metabolic–neuroinflammatory crosstalk model in which LRRK2 functions as a molecular coordinator linking peripheral metabolic dysfunction to central neurodegeneration. In this framework, systemic metabolic stress—characterized by insulin resistance, chronic inflammation, advanced glycation end product (AGE) accumulation, and blood–brain barrier disruption—drives microglial activation and neurodegenerative processes. Understanding this systemic axis may provide new therapeutic opportunities targeting both metabolic dysfunction and neurodegeneration in PD. Full article
(This article belongs to the Section Cellular Biochemistry)
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21 pages, 633 KB  
Review
The Gut–Kidney–Metabolic Axis: Impact of Gut-Derived Uremic Toxins on Insulin Resistance in Diabetic Kidney Disease
by Charlotte Delrue, Margaux Vinckier, Reinhart Speeckaert, Stefania Marzocco and Marijn M. Speeckaert
Int. J. Mol. Sci. 2026, 27(8), 3472; https://doi.org/10.3390/ijms27083472 - 13 Apr 2026
Viewed by 760
Abstract
Chronic kidney disease (CKD), especially diabetic kidney disease (DKD), is characterized not only by progressive loss of renal function but also by profound metabolic disturbances, including insulin resistance (IR). Emerging evidence implicates gut-derived uremic toxins as mediators linking intestinal dysbiosis to metabolic and [...] Read more.
Chronic kidney disease (CKD), especially diabetic kidney disease (DKD), is characterized not only by progressive loss of renal function but also by profound metabolic disturbances, including insulin resistance (IR). Emerging evidence implicates gut-derived uremic toxins as mediators linking intestinal dysbiosis to metabolic and renal injury. Several microbial metabolites, for example, indoxyl sulfate, p-cresyl sulfate, and trimethylamine-N-oxide, are known to accumulate in CKD due to decreased renal excretion and altered tubular secretion. In vitro and in vivo experiments indicate that these gut-derived nephrotoxins impair insulin signaling pathways in cells. This results in increased production of reactive oxygen species, activation of stress kinases, higher levels of inflammatory cytokines, and inhibitory serine phosphorylation of insulin receptor substrates. Consequently, phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt) signaling is impaired, reducing cellular glucose uptake. At the same time, these toxins induce endothelial dysfunction and mitochondrial damage, not only causing systemic IR but also contributing to the progression of kidney disease. Observational data link higher plasma toxin levels with components of IR, rapid loss of renal function as measured by estimated glomerular filtration rate, and a high risk of cardiovascular events in CKD patients. Although causality in humans remains unproven, interventions targeting the microbiota, toxin binding, and oxidative stress pathways show promise. We propose an integrated gut–kidney–metabolic framework in which dysbiosis-driven toxin production may amplify IR and DKD progression. Full article
(This article belongs to the Special Issue Molecular Insights into Diabetic Nephropathy)
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14 pages, 1607 KB  
Article
Rapamycin Prevents Sulfate-Reducing Bacteria-Induced Effects on Snail and GSK-3 and Impaired Intestinal Barrier
by Sudha B. Singh, Cody A. Braun, Amanda Carroll-Portillo and Henry C. Lin
Microorganisms 2026, 14(4), 781; https://doi.org/10.3390/microorganisms14040781 - 30 Mar 2026
Viewed by 735
Abstract
Desulfovibrio spp. are sulfate-reducing bacteria (SRB) associated with conditions such as inflammatory bowel disease (IBD) that are linked to intestinal barrier dysfunction (leaky gut). Previously, we reported that Desulfovibrio vulgaris (DSV) caused increased intestinal permeability by upregulating nuclear transcription factor Snail. However, the [...] Read more.
Desulfovibrio spp. are sulfate-reducing bacteria (SRB) associated with conditions such as inflammatory bowel disease (IBD) that are linked to intestinal barrier dysfunction (leaky gut). Previously, we reported that Desulfovibrio vulgaris (DSV) caused increased intestinal permeability by upregulating nuclear transcription factor Snail. However, the signaling mechanisms underlying this effect remain unclear. Glycogen synthase kinase-3 (GSK-3) is a serine/threonine kinase that maintains intestinal barrier integrity and negatively regulates Snail and promotes its degradation by proteasomes. Rapamycin has been shown to protect the intestinal barrier and is also known to activate GSK-3. In this study, we investigated whether DSV disrupts intestinal barrier function through modulation of GSK-3 signaling and whether rapamycin could counteract these effects. Using a previously established DSV-induced paracellular permeability model using polarized Caco-2 monolayers, here, we showed that DSV induced inhibitory phosphorylation of GSK-3. Pretreatment of cells with rapamycin prevented DSV- induced phospho- inactivation of GSK-3, suppressed Snail expression and nuclear localization, and significantly reduced DSV-induced barrier permeability. Inhibition of proteasomal degradation with MG132 abolished the protective effects of rapamycin on barrier permeability, supporting a role for GSK-3–mediated proteasomal regulation of Snail. Together, these findings identify GSK-3 signaling as a novel mechanism underlying DSV-induced intestinal barrier dysfunction and highlight rapamycin as a potential therapeutic approach strategy to protect intestinal barrier integrity in response to DSV. Specifically, targeting the GSK-3/Snail pathway may represent a promising strategy to mitigate SRB-associated intestinal barrier disruption. Full article
(This article belongs to the Special Issue The Microbial Pathogenesis)
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36 pages, 1662 KB  
Review
CMGC Kinases in Viral Infection and Human Disease
by Oluwamuyiwa T. Amusan and Hongyan Guo
Pathogens 2026, 15(4), 366; https://doi.org/10.3390/pathogens15040366 - 30 Mar 2026
Viewed by 1044
Abstract
Cellular processes rely heavily on protein phosphorylation, a mechanism essential for organismal physiology and pathology. The CMGC family comprises a large group of serine/threonine kinases defined by a conserved catalytic core and closely related kinase domains. While several CMGC members have been extensively [...] Read more.
Cellular processes rely heavily on protein phosphorylation, a mechanism essential for organismal physiology and pathology. The CMGC family comprises a large group of serine/threonine kinases defined by a conserved catalytic core and closely related kinase domains. While several CMGC members have been extensively studied, others, including the RCK and CDKL subfamilies, remain less studied. Here, we synthesize current knowledge of CMGC kinases, emphasizing their structural organization, mechanisms of activation, and roles in infection and disease. CMGC kinases such as CDKs and DYRKs are activated downstream of growth factor signaling to drive proliferative programs. In contrast, other CMGC members respond to cellular stress signals, including stress cytokines, and function during quiescence or adverse conditions to regulate antiproliferative and pro-survival pathways. Through these context-dependent activities, CMGCs govern fundamental cellular processes, including growth, metabolism, transcription, and genome integrity. Although individual CMGC kinases operate within distinct signaling cascades, substantial crosstalk exists among their pathways. Both DNA and RNA viruses exploit host CMGC networks to reprogram the intracellular environment and enhance replication. While CMGC–virus interactions are often proviral, specific CMGC-mediated antiviral responses have been described, notably in SARS-CoV-2 infection. Collectively, CMGC kinases occupy a central position in cellular homeostasis and disease. Full article
(This article belongs to the Special Issue Pathogen–Host Interactions: Death, Defense, and Disease)
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18 pages, 9974 KB  
Article
Serine 89 Phosphorylation Controls Nuclear Localization and Transcriptional Activity of ARID3B
by Micneya Landeros-Rodriguez, Krishna Ailiani, Richard Dahl and Karen D. Cowden Dahl
Cells 2026, 15(7), 612; https://doi.org/10.3390/cells15070612 - 30 Mar 2026
Viewed by 911
Abstract
Transcription factors that control stem cell programs are central drivers of cancer progression, metastasis, and therapy resistance. ARID3B, a DNA-binding protein overexpressed across multiple tumor types, expands the cancer stem cell population by regulating these pathways. Yet, how ARID3B is regulated remains largely [...] Read more.
Transcription factors that control stem cell programs are central drivers of cancer progression, metastasis, and therapy resistance. ARID3B, a DNA-binding protein overexpressed across multiple tumor types, expands the cancer stem cell population by regulating these pathways. Yet, how ARID3B is regulated remains largely unknown. Here, we uncover phosphorylation at Serine 89 as a critical switch controlling ARID3B localization and function. We used site-directed mutagenesis to generate phospho-dead (S89A) and phospho-mimetic (S89D) ARID3B constructs, and we generated a phospho-specific antibody for S89. With these tools, we showed that phosphorylation confines ARID3B to the nucleus in ovarian cancer and glioblastoma cells, as well as in human tissues, while unphosphorylated ARID3B can localize to the nucleus, cytoplasm, and membrane. Functionally, S89D mirrors wild-type ARID3B in regulating key transcriptional programs, whereas S89A diverges, consistent with altered subcellular localization. Chromatin immunoprecipitation confirms that direct gene regulation is enhanced in WT ARID3B and S89D compared to cells expressing S89A. Collectively, these findings reveal phosphorylation as a previously unrecognized molecular switch that dictates ARID3B’s localization and transcriptional activity, providing novel insights into cancer stem cell regulation and identifying a potential targetable vulnerability in aggressive tumors. Full article
(This article belongs to the Section Cell Signaling)
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20 pages, 9448 KB  
Article
Dissecting the Phospho-Regulatory Landscape of Protein Kinase N1 (PKN1) and Its Downstream Signaling: Functional Insights into the Activity-Dependent and Disease-Relevant Phosphosites
by Sreeshma Ravindran Kammarambath, Leona Dcunha, Athira Perunelly Gopalakrishnan, Yashi Shailendra Gautam, Furqaan Ahmed Basha, Prathik Basthikoppa Shivamurthy, Inamul Hasan Madar and Rajesh Raju
Int. J. Mol. Sci. 2026, 27(5), 2137; https://doi.org/10.3390/ijms27052137 - 25 Feb 2026
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Abstract
Protein Kinase N1 (PKN1) is a PKC-related serine/threonine kinase of the AGC group within the eukaryotic protein kinase superfamily (ePK) that orchestrates oncogenic, metabolic, and cytoskeletal signaling. Despite these critical roles, the phosphorylation-dependent regulatory network of PKN1 remains largely undefined. We performed a [...] Read more.
Protein Kinase N1 (PKN1) is a PKC-related serine/threonine kinase of the AGC group within the eukaryotic protein kinase superfamily (ePK) that orchestrates oncogenic, metabolic, and cytoskeletal signaling. Despite these critical roles, the phosphorylation-dependent regulatory network of PKN1 remains largely undefined. We performed a large-scale phosphoproteomic data integration of publicly available human datasets (892 profiling datasets and 191 differential datasets) to identify recurrent PKN1 phosphorylation sites. This analysis identified two predominant PKN1 phosphosites, S562 and S916, that were frequently observed and differentially regulated across studies. The S916 maps to a turn motif (TM) in the AGC group of kinases, which is evolutionarily conserved among PKN paralogs, while S562 is non-conserved and appears to be PKN1-specific. Co-regulation and enrichment analyses suggest that S916 is associated with insulin/AMPK signaling and metabolic pathways, whereas S562 co-occurs with phosphosites involved in cell division, cytoskeletal regulation, and microtubule cytoskeleton organization. Integrating predicted and experimentally validated kinases, substrates, and interactors, we reconstructed a phospho-regulatory network that positions PKN1 at the crossroads of cytoskeleton organization and metabolic signaling. To assess the disease relevance of these phosphorylation events, we integrated transcriptomic and phosphoproteomic data from the hepatocellular carcinoma database (HCCDB). PKN1 was markedly up-regulated in HCC, and its phosphorylation at S916 was positively co-regulated with multiple oncogenic and proliferation-associated protein phosphosites. These results predict S562 and S916 as potential sites for targeted biochemical validation and functional experiments. The identification of S562 and S916 as key regulatory sites provides new mechanistic insight into PKN1 activation and highlights potential avenues for therapeutic targeting. Full article
(This article belongs to the Special Issue The Role of Protein Kinase in Health and Diseases)
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19 pages, 6731 KB  
Article
Phosphoproteomic Profiling of Multiple Myeloma Based on Ex Vivo Drug Sensitivity Resistance Testing Identifies Phosphorylation Signatures Associated with Drug Response
by Katie Dunphy, Ellen Purcell, Caroline A. Heckman, Paul Dowling, Despina Bazou and Peter O’Gorman
Biomolecules 2026, 16(2), 323; https://doi.org/10.3390/biom16020323 - 19 Feb 2026
Viewed by 903
Abstract
Multiple myeloma (MM) is characterised by the clonal expansion of plasma cells in the bone marrow followed by end-organ damage. Despite a significant increase in the five-year survival rate in recent years, MM is still considered an incurable disease as patients will repeatedly [...] Read more.
Multiple myeloma (MM) is characterised by the clonal expansion of plasma cells in the bone marrow followed by end-organ damage. Despite a significant increase in the five-year survival rate in recent years, MM is still considered an incurable disease as patients will repeatedly relapse and develop resistance to standard-of-care therapies. A central theme for the personalization of MM therapy is understanding the biological mechanisms of drug resistance and identifying clinically relevant biomarkers of therapeutic response. Highly effective protocols for the enrichment of phosphorylated peptides followed by high-resolution mass spectrometry makes possible the quantitation of thousands of site-specific phosphorylation events, principally on serine, threonine or tyrosine residues. In this study, phosphoproteomic analysis of 20 MM patient cell lysates was performed, stratified based on their ex vivo drug response profiles to Bortezomib and Lenalidomide, two of the most foundational therapeutic agents in the management of MM. In this study, patients who are highly sensitive to these drugs show increased phosphorylation of proteins concerned with translation and RNA processing including the spliceosome, RNA transport and RNA binding pathways, while highly resistant patients demonstrated an increased phosphorylation of proteins involved with tight junctions, the Rap1 signalling pathway and the phosphatidylinositol signalling system. This study has established a phosphoproteomic dataset displaying unique phosphorylation signatures associated with drug sensitivity in MM patient plasma cells. The identification of phosphorylation signatures associated with drug resistance provides the foundation for further exploration of these mechanisms and associated signalling pathways to further characterise drug resistance mechanisms in MM and identify promising biomarkers of therapeutic response and targets for drug re-sensitization in MM. Full article
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