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19 pages, 30475 KB  
Article
Tissue-Specific Detection of Autophagy and the Related Metabolites in Bombyx mori
by Qien Zhong, Jianghao Hu, Sheraz Ahmad, Xiaole Xie, Kang Li, Huiyu Yi and Ling Tian
Insects 2026, 17(9), 949; https://doi.org/10.3390/insects17090949 - 11 Sep 2026
Abstract
Tissue-specific autophagic remodeling drives larval tissue dismantling during lepidopteran metamorphosis, yet the metabolic regulators underlying tissue-autonomous autophagic heterogeneity remain incompletely defined. This study sought to dissect the linkage between lipid metabolic reprogramming and tissue-divergent autophagic potency in Bombyx mori. Spatiotemporal autophagic levels [...] Read more.
Tissue-specific autophagic remodeling drives larval tissue dismantling during lepidopteran metamorphosis, yet the metabolic regulators underlying tissue-autonomous autophagic heterogeneity remain incompletely defined. This study sought to dissect the linkage between lipid metabolic reprogramming and tissue-divergent autophagic potency in Bombyx mori. Spatiotemporal autophagic levels across larval tissues was profiled via BmAtg8–PE immunoblotting, BmAtg8 immunofluorescence, and LysoTracker Red lysosomal staining. Untargeted metabolomics was conducted on the fat body, midgut, posterior silk gland, and trachea at key metamorphic stages; differentially accumulated metabolites (DAMs) were processed through hierarchical clustering and KEGG functional enrichment. Autophagic activity was universally upregulated upon prepupal transition, with the posterior silk gland and trachea showing markedly higher autophagic levels, whereas the fat body and midgut maintained relatively lower autophagic activity in tissue-wide comparison. Lipids represented the most dynamically remodeled metabolite families; fatty acyls and their synthetic cascades were enriched in high-autophagy tissues, while glycerolipid and glycerophospholipid pathways prevailed in low-autophagy tissues. Integrative multi-omics and cytological evidence identify a correlative relationship between tissue-resolved lipid turnover and spatially segregated autophagic activation. This tissue-scale atlas establishes a fundamental resource for mechanistic exploration of lipid-autophagy crosstalk governing insect metamorphic development. Full article
(This article belongs to the Section Insect Physiology, Reproduction and Development)
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27 pages, 4259 KB  
Article
Combined Arctigenin and Curcumin Treatment Induces Redox and Metabolic Stress, AMPK Phosphorylation, and Apoptotic Signaling in Prostate Cancer Cells
by Moon-Kyun Cho, Sang-Han Lee, Hae-Seon Nam, Dongsic Choi and Yoon-Jin Lee
Nutrients 2026, 18(18), 2968; https://doi.org/10.3390/nu18182968 - 10 Sep 2026
Viewed by 178
Abstract
Background/Objectives: Prostate cancer remains a major cause of cancer-related mortality in men. Arctigenin (ATG) and curcumin (CUR) exhibit anticancer activity; however, their combined effects on redox and metabolic stress remain incompletely understood. This study investigated the anticancer effects of combined ATG and CUR [...] Read more.
Background/Objectives: Prostate cancer remains a major cause of cancer-related mortality in men. Arctigenin (ATG) and curcumin (CUR) exhibit anticancer activity; however, their combined effects on redox and metabolic stress remain incompletely understood. This study investigated the anticancer effects of combined ATG and CUR treatment in prostate cancer cells. Methods: PC-3 prostate cancer cells and normal human prostate epithelial (HPrEC) cells were treated with ATG and CUR alone or in combination. Cell viability, combination index, reactive oxygen species (ROS), GSH/GSSG ratio, ATP levels, AMPK phosphorylation, and apoptosis-related responses were evaluated. The contribution of oxidative stress was examined using N-acetyl-L-cysteine (NAC), and treatment effects were further assessed in three-dimensional (3D) spheroids. Results: Combined ATG and CUR treatment produced greater growth-inhibitory and apoptotic responses in PC-3 cells than in HPrEC cells and was synergistic under the tested condition in PC-3 cells. The combination increased ROS, reduced the GSH/GSSG ratio and ATP levels, increased AMPK phosphorylation, and enhanced apoptosis-related responses. NAC attenuated ROS accumulation, partially restored cell viability and ATP levels, and reduced caspase-3/7 activity in PC-3 cells. In 3D PC-3 spheroids, NAC also partially restored viability and ATP levels and attenuated increases in cleaved caspase-3 and cleaved PARP. Conclusions: Combined ATG and CUR treatment induces redox and metabolic stress and enhanced apoptotic responses in PC-3 cells, with weaker effects in HPrEC cells. NAC rescue supports a functional contribution of oxidative stress. These findings support an association between ROS-related metabolic stress, AMPK phosphorylation, and apoptotic signaling, while precise causal relationships require further investigation. Full article
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18 pages, 3537 KB  
Article
Serum Autophagy-Related Protein 5 and Clinically Defined Cognitive Status in Older Adults: A Plate-Stratified Cross-Sectional Study Across: Normal Cognition, Mild Cognitive Impairment, and Alzheimer’s Disease
by Kübra Erdoğan, Cemile Biçer, Rıdvan Erten, Kübra Kaya, Serap Boz, Hatice Turgut Şahin, Cemile Peker, Arzu Nevin Dağdemir, Büşragül Yılmaz, Aslıhan Yıldırım, Rana Tuna Doğrul, Hande Selvi Öztorun, Güneş Eken and Kamile Sılay
Medicina 2026, 62(9), 1722; https://doi.org/10.3390/medicina62091722 - 7 Sep 2026
Viewed by 191
Abstract
Background and Objectives: Impaired autophagy has been implicated in neurodegeneration, but circulating autophagy-related proteins have shown inconsistent associations with cognitive impairment. We compared serum autophagy-related protein 5 (ATG5) among older adults with normal cognition, mild cognitive impairment (MCI), and clinically diagnosed Alzheimer’s disease [...] Read more.
Background and Objectives: Impaired autophagy has been implicated in neurodegeneration, but circulating autophagy-related proteins have shown inconsistent associations with cognitive impairment. We compared serum autophagy-related protein 5 (ATG5) among older adults with normal cognition, mild cognitive impairment (MCI), and clinically diagnosed Alzheimer’s disease (AD), and examined its relationship with global cognitive performance. Materials and Methods: This single-centre cross-sectional study enrolled 164 older adults (55 with normal cognition, 55 with MCI, and 54 with clinically diagnosed AD). Cognitive status was determined through integrated clinical assessment rather than a single test cut-off. An enzyme-linked immunosorbent assay was employed to quantify serum ATG5, yielding quantifiable values for 156 participants, right-censored observations above the highest calibrator for six, and unmeasurable results for two. Since the two 96-well plates, drawn from one ELISA kit lot and processed on the same day, exhibited a substantial discrepancy in measurement scale across runs, they were analysed as distinct strata, with the principal group contrast estimated via a right-censored Tobit regression of log-transformed ATG5 within each plate, controlling for cognitive group, age and sex; a pooled plate-adjusted model also provided support. Supportive analyses used within-plate z-standardised ATG5. Associations with clinical variables were assessed using age- and sex-adjusted partial Spearman correlations with false discovery rate correction. Results: Across both analytical strata (plate 1 omnibus p = 0.293; plate 2 p = 0.264) and within the supportive pooled model (p = 0.143; AD vs. normal geometric mean ratio 0.89, 95% CI 0.73–1.09), serum ATG5 concentrations did not differ significantly between cognitive groups. Concentrations on plate 2 were 47% lower (GMR 0.53, 95% CI 0.45–0.62), a gap exceeding the inter-assay imprecision declared by the manufacturer and unexplained by the calibrator values from plate 2; since relative dispersion matched across both plates (likelihood ratio p = 0.730), the pattern suggests a multiplicative scale shift of unknown origin. Serum ATG5 levels were weakly associated with global cognitive performance assessed via the S-MMSE (partial ρ = 0.283, p < 0.001, FDR p = 0.010), an association that persisted after adjusting for education, albumin and folate and retained a similar magnitude within a linear model (β = 0.044, p = 0.014). Incorporating ATG5 into a model that included age, sex and education failed to enhance discrimination (ΔAUC +0.012 and +0.000). Conclusions: Serum ATG5 did not discriminate normal cognition, MCI, and clinically diagnosed AD. A weak rank-based association with S-MMSE was observed, but the effect was small. These findings do not support serum ATG5 as a diagnostic discriminator for clinically defined cognitive status. Full article
(This article belongs to the Section Epidemiology & Public Health)
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29 pages, 3090 KB  
Article
Protective Effect of Exogenous Quercetin Against Salt Stress in Triticum aestivum and Triticum durum
by Neonila V. Kononenko, Elena M. Lazareva and Larisa I. Fedoreyeva
Agronomy 2026, 16(17), 1727; https://doi.org/10.3390/agronomy16171727 - 4 Sep 2026
Viewed by 161
Abstract
Various stress factors lead to increased reactive oxygen species (ROS) formation and increased damage to various plant tissues. Data obtained using fluorescence microscopy show that under abiotic stress, the most intense ROS staining is observed in the epidermal and cortical cells of the [...] Read more.
Various stress factors lead to increased reactive oxygen species (ROS) formation and increased damage to various plant tissues. Data obtained using fluorescence microscopy show that under abiotic stress, the most intense ROS staining is observed in the epidermal and cortical cells of the root cap and division zones. Increased ROS formation under abiotic stress activates the antioxidant system in wheat. The expression level of the MnSOD and Cu/ZnSOD genes in the Orenburgskaya 22 wheat variety (Triticum aestivum) is more than twice that in the Zolotaya variety (Triticum durum). An amount of 150 mM NaCl activates MnSOD and Cu/ZnSOD gene expression in the Orenburgskaya 22 wheat variety, increases glutathione (GSH) content, and activates GSH-associated enzymes. Therefore, different wheat genotypes have different mechanisms for neutralizing ROS. The antioxidant quercetin reduces ROS formation and also promotes antioxidant system activation in the Orenburgskaya 22 variety and has virtually no effect on the Zolotaya variety. However, it does reduce ROS before and after NaCl treatment in both wheat genotypes. Salt stress causes an increase in the number of small and large autophagosomes in root cells of Triticum durum wheat, while, in Triticum aestivum, large vacuoles not marked by ATG8 and small autophagosomes near the nucleus form in root cortex cells. Treatment of control plants with quercetin does not increase the number of autophagosomes. Treatment with quercetin after salt stress does not increase the number of ATG8-marked autophagosomes in cells of either genotype. Treatment with quercetin before salt exposure leads to an increase in the number of autophagosomes in durum wheat cells. PCR analysis of autophagy genes revealed features of the initiation of autophagosome formation. Thus, quercetin exerts a protective effect against salt stress. However, its use is limited to plants with high flavonoid content. Quercetin may have promising applications in agriculture. Full article
(This article belongs to the Section Plant-Crop Biology and Biochemistry)
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27 pages, 2542 KB  
Article
Genome-Wide Differentiation, Inbreeding, and Candidate Selection Loci in Local Vietnamese Pig Breeds
by Van Thanh Nguyen, Nguyen Van Ba and Duy Ngoc Do
Int. J. Mol. Sci. 2026, 27(17), 7897; https://doi.org/10.3390/ijms27177897 - 4 Sep 2026
Viewed by 238
Abstract
Vietnam harbors exceptional genetic diversity among at least 26 indigenous pig breeds. We analyzed genome-wide single-nucleotide polymorphism (SNP) data from 90 animals representing 15 local Vietnamese breeds and six Landrace pigs using principal component analysis, the windowed fixation index (FST), cross-population extended haplotype [...] Read more.
Vietnam harbors exceptional genetic diversity among at least 26 indigenous pig breeds. We analyzed genome-wide single-nucleotide polymorphism (SNP) data from 90 animals representing 15 local Vietnamese breeds and six Landrace pigs using principal component analysis, the windowed fixation index (FST), cross-population extended haplotype homozygosity (XP-EHH), within-population integrated haplotype score (iHS), and runs of homozygosity (ROHs). The population structure was consistent with a north–south differentiation axis, and Ba Xuyen showed elevated heterozygosity, providing suggestive evidence of a European genetic contribution; the f3 statistic was positive (f3 = +0.015), and formal evidence of admixture requires a significantly negative f3, so this criterion was not met. Integration of FST and XP-EHH identified GPC5, E2F6, NOS1, and TLR4 as top Northern candidate loci and CRYM/ZP2 as the leading Central candidate locus, and these windows were recovered at both the 90th and 95th percentile thresholds, indicating analytical robustness rather than independent biological validation. iHS was elevated at E2F6 in Northern breeds (|iHS| = 3.04) and at NOS1 across all regional groups (|iHS| = 2.66–3.36). Breed-level phenotypic XP-EHH, based on published breed descriptions and coat color rather than individual body-composition measurements, identified GALNT2 as a candidate shared across breed groups; HCAR1 and ATG10 as candidates specific to the extreme-fat/prolific breed group; and EFNA5 and HIPK2 as candidates specific to the medium-bodied breed group. ROHs identified Soc, Co, and Hung as breeds warranting particular attention in conservation planning due to elevated autozygosity. Because each breed was represented by only six individuals, and because no individual-level phenotypic measurements were available, all findings are reported as exploratory population-genomic signals requiring replication in larger cohorts. Overall, we describe genomic differentiation and candidate selection signatures among local Vietnamese pig breeds and provide a foundation for further genomic studies of these breeds. Full article
(This article belongs to the Special Issue Advances in Molecular Research of Animal Genetics and Genomics)
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13 pages, 2643 KB  
Article
Berberine Chloride Suppresses Melanogenesis in B16-F1 Melanoma Cells in Association with ERK and Autophagy-Related Signaling
by HwaJeong Ryu, Ho Jae Lim and Jung Eun Park
Cosmetics 2026, 13(5), 225; https://doi.org/10.3390/cosmetics13050225 - 31 Aug 2026
Viewed by 184
Abstract
Skin pigmentation is regulated by intrinsic and extrinsic factors and is closely associated with melanogenesis and cellular homeostasis. Autophagy is a cellular self-digestion process that contributes to homeostatic regulation, but its role in melanogenesis remains to be further clarified. This study investigated whether [...] Read more.
Skin pigmentation is regulated by intrinsic and extrinsic factors and is closely associated with melanogenesis and cellular homeostasis. Autophagy is a cellular self-digestion process that contributes to homeostatic regulation, but its role in melanogenesis remains to be further clarified. This study investigated whether berberine chloride (BBC), an isoquinoline alkaloid, modulates melanin production through autophagy-related signaling in B16-F1 melanoma cells. Tyrosinase activity was examined by tyrosinase zymography, extracellular melanin levels in the culture supernatant were measured after BBC treatment, and the expression of melanogenesis-, mitogen-activated protein kinase (MAPK)-, and autophagy-related proteins was analyzed by Western blotting. BBC inhibited tyrosinase activity and reduced extracellular melanin levels in a dose-dependent manner. BBC also increased phosphorylated extracellular signal-regulated kinase (p-ERK) levels while decreasing melanogenesis-related protein expression. In addition, BBC modulated MAPK signaling and the expression of autophagy-associated proteins. Small interfering RNA-mediated knockdown of Atg5, Beclin1, or ERK partially restored extracellular melanin levels in BBC-treated cells. These findings suggest that BBC suppresses melanogenesis in B16-F1 melanoma cells in association with ERK and autophagy-related signaling. Full article
(This article belongs to the Section Cosmetic Dermatology)
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24 pages, 3971 KB  
Article
AgeViva Modulates Inflammatory Responses, Autophagy, and Mitochondrial Homeostasis in BV-2 Cells and C. elegans
by Federica Armeli, Emily Schifano, Beatrice Mengoni, Arianna Montanari, Martina Menin, Laura Pompa, Maria Luisa Crudeli, Thomas Lenz, Trevor Archer, Daniela Uccelletti and Rita Businaro
Metabolites 2026, 16(9), 625; https://doi.org/10.3390/metabo16090625 - 28 Aug 2026
Viewed by 182
Abstract
Background: Oxidative stress, neuroinflammation, impaired autophagy, and mitochondrial dysfunction are major contributors to ageing and neurodegenerative diseases. This study investigated whether AgeViva could counteract these processes by modulating redox balance, inflammation, autophagy, and mitochondrial function. Methods: The effects of AgeViva were [...] Read more.
Background: Oxidative stress, neuroinflammation, impaired autophagy, and mitochondrial dysfunction are major contributors to ageing and neurodegenerative diseases. This study investigated whether AgeViva could counteract these processes by modulating redox balance, inflammation, autophagy, and mitochondrial function. Methods: The effects of AgeViva were evaluated using two complementary experimental models: lipopolysaccharide (LPS)-stimulated BV2 microglial cells and Caenorhabditis elegans (C. elegans) nematodes. In BV2 cells, the expression of inflammatory, autophagy-related, and antioxidant response genes, including NRF2, SOD, and GPX, was evaluated by RT-qPCR, while cell viability was assessed by Trypan Blue exclusion assay. In C. elegans, lifespan, healthspan parameters, ROS accumulation, mitochondrial integrity, membrane potential, and the expression of stress-response, longevity, and autophagy-related genes were analyzed following AgeViva supplementation. Results: In LPS-stimulated BV2 cells, AgeViva significantly reduced the expression of mRNA the pro-inflammatory cytokines Interleukin-1 beta (IL-1β) and Tumor Necrosis Factor alpha (TNF-α) while increasing Interleukin-10 (IL-10) levels, AgeViva also induced changes in autophagy-related transcripts, such as modulation of microtubule-associated protein 1a/1b-Light Chain (LC3) and Sequestosome 1 (p62) expression, activated antioxidant-related gene expression, increasing the expression of Superoxide Dismutase 1(SOD1) and Glutathione Peroxidase (GPX). In C. elegans, AgeViva supplementation extended lifespan and improved healthspan parameters, including locomotor activity and pharyngeal pumping. Treated nematodes showed reduced cytosolic and mitochondrial ROS accumulation, preservation of mitochondrial network integrity, and maintenance of mitochondrial-associated fluorescence, reflecting mitochondrial content and/or membrane potential during ageing. Molecular analyses revealed modulation of key pathways involved in stress resistance and longevity, including Insulin-like Growth Factor 1 (Insulin/IGF-1) signaling Dauer Formation-2 and 16 (DAF-2/DAF-16), Skinhead-1 (SKN-1/Nrf2) signaling, and autophagy-related genes, like Ligating (lgg-1), Autophagy-Related-7 (atg-7), Autophagy Related-18 (atg-18), uncoordinated-51 (unc-51), and ectopic p-granules autophagy protein 5 (epg-5). Conclusions: AgeViva promotes healthy ageing by modulating oxidative stress, inflammation, autophagy, and mitochondrial homeostasis. Full article
(This article belongs to the Special Issue Autophagy and Antioxidant Pathways in Neurodegenerative Diseases)
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16 pages, 7952 KB  
Article
Sex-Associated Effects of Thioredoxin Reductase Inhibition in Hyperoxia-Induced Lung Injury in Adult Mice
by Katelyn Dunigan-Russell, Matthew Ryan Smith, Hua Zhong, ViLinh Tran, Dean P. Jones, Lynette K. Rogers and Trent Tipple
Metabolites 2026, 16(9), 623; https://doi.org/10.3390/metabo16090623 - 28 Aug 2026
Viewed by 303
Abstract
Background: Supraphysiological levels of oxygen are often used as therapy for acute respiratory distress and severe pulmonary morbidities but can cause excessive generation of reactive oxygen species resulting in oxidative and inflammatory injury. Aurothioglucose (ATG), an FDA-approved, gold-containing pharmaceutical, potently and irreversibly inhibits [...] Read more.
Background: Supraphysiological levels of oxygen are often used as therapy for acute respiratory distress and severe pulmonary morbidities but can cause excessive generation of reactive oxygen species resulting in oxidative and inflammatory injury. Aurothioglucose (ATG), an FDA-approved, gold-containing pharmaceutical, potently and irreversibly inhibits thioredoxin reductase 1, and ATG treatment preserves reduced glutathione levels and attenuates hyperoxic lung injury. Methods: Adult C3H mice were treated with saline or ATG and exposed to room air (RA) or >95% O2. All mice had succumbed or were euthanized at 200 h of >95% O2. In a separate cohort euthanized at 72 h, prior to the appearance of oxygen toxicity, lung tissues were collected for metabolomic analyses. Comparisons were performed between RA and >95% O2 exposure, saline and ATG treatment, and male and female. Results: In <95% O2, differences in survival between the sexes with and without ATG treatment were observed. ATG-treated females survived longer than all other hyperoxia-exposed groups. Features in the glutathione and selenoprotein pathways were significantly different. Metabolomic analysis revealed keratan sulfate (KS) biosynthesis and glycosphingolipid (GSL) biosynthesis as the primary pathways affected in the saline O2 vs. ATG O2 comparison. Carnitine shuttle was identified as the primary pathway between the sexes both with ATG and O2. Conclusions: The current data suggest that the improved survival of hyperoxia-exposed, ATG-treated, female C3H mice may be driven by alterations in glutathione synthesis, energy production, and metabolism resulting in decreased lung injury. These findings may provide direction for further research to improve outcomes after hyperoxia exposure. Full article
(This article belongs to the Topic Animal Models of Human Disease 3.0)
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11 pages, 851 KB  
Case Report
Carbimazole-Induced Severe Acquired Aplastic Anemia in a Patient with Graves’ Disease: A Case Report
by Rahaf A. Alghamdi, Hind A. Alshankiti, Adel F. Al-Marzouki and Yara M. Daous
Reports 2026, 9(3), 287; https://doi.org/10.3390/reports9030287 - 26 Aug 2026
Viewed by 233
Abstract
Background and Clinical Significance: Carbimazole is a widely used medication to treat Graves’ disease, although it can rarely cause acquired aplastic anemia, a complication that happens in less than 0.01% of people. Case Presentation: We report a 36-year-old woman treated with supratherapeutic dose [...] Read more.
Background and Clinical Significance: Carbimazole is a widely used medication to treat Graves’ disease, although it can rarely cause acquired aplastic anemia, a complication that happens in less than 0.01% of people. Case Presentation: We report a 36-year-old woman treated with supratherapeutic dose carbimazole who, after approximately six months of treatment, developed high grade fever, severe menorrhagia, spontaneous epistaxis, and pancytopenia. Her bone marrow biopsy showed severe bone marrow failure with only 5% cellularity and trilineage hypoplasia. Other potential causes were ruled out. Immediate discontinuation of carbimazole was done, and supportive care, including blood transfusions, broad-spectrum antibiotics, G-CSF, and eltrombopag, was started. The patient deteriorated during her hospital stay, developed neutropenic sepsis and acute respiratory failure from diffuse alveolar hemorrhage, which required intubation and pulse steroid therapy. She was stabilized and discharged, with a referral to a tertiary medical center for starting antithymocyte globulin (ATG) immunosuppressive therapy, which she subsequently completed; two months after discharge she was transfusion independent with near-normalization of her blood counts. Conclusions: This case serves as a stark reminder of how lethal thionamide-induced bone marrow failure can be, highlighting the vital need for immediate drug cessation, swift intensive care, and thorough patient education on early warning signs. Full article
(This article belongs to the Section Endocrinology/Metabolism)
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27 pages, 44874 KB  
Article
Genome-Wide Identification of the GmATG Gene Family and Its Response to Multiple Biotic and Abiotic Stresses in Soybean (Glycine max)
by Ling Yang, Jingyi Fan, Enguang Ren, Shuo Yang and Dandan Hu
Genes 2026, 17(9), 996; https://doi.org/10.3390/genes17090996 - 24 Aug 2026
Viewed by 323
Abstract
Background: Autophagy plays a central role in maintaining cellular homeostasis, regulating growth and development, and responding to multiple stresses. Autophagy-related genes (ATGs) play critical roles in autophagy, yet their functional diversity in soybean (Glycine max) remains underexplored. Methods: Genome-wide identification of [...] Read more.
Background: Autophagy plays a central role in maintaining cellular homeostasis, regulating growth and development, and responding to multiple stresses. Autophagy-related genes (ATGs) play critical roles in autophagy, yet their functional diversity in soybean (Glycine max) remains underexplored. Methods: Genome-wide identification of GmATG genes was performed using sequence similarity and domain-based searches against the Wm82.gnm4 reference genome, followed by characterization of physicochemical properties, chromosomal distribution, phylogenetic relationships, gene duplication, conserved motifs, gene structure, three-dimensional structural, and promoter cis-acting elements. Tissue-specific expression and multiple stresses response were examined using transcriptome data and profiled by RT-qPCR. Results: A total of 60 GmATG genes belonging to 20 subfamilies were identified in soybean. Gene family expansion was predominantly driven by fragment duplication (33 gene pairs), with the ATG8 family expanding to 12 members, and pan-genomic analysis uncovered prominent copy number variation (6–9 copies) in the ATG18 family. GmATG genes showed distinct expression patterns in response to multiple abiotic and biotic stresses. Specifically, GmATG18f was significantly induced by phosphorus deficiency in the low-phosphorus-tolerant soybean variety Nannong 94-156. GmATG8g, GmATG9d and GmATG13d showed a typical expression trend of initial increase followed by decrease, with expression levels peaking at 6–12 h after salt stress treatment. GmATG8g and GmATG9d were rapidly upregulated at the early drought stress stage, while GmATG13a maintained sustained upregulation. In response to Phomopsis stem rot, GmATG7a/8h/8i/11/13d/18e/18f displayed differential expression in resistant and susceptible soybean materials. Conclusions: This study systematically characterizes the composition, expansion and stress response patterns of the GmATG gene family, revealing functional differentiation among family members. The identified key candidate genes, including abiotic-stress-regulated GmATG8g/9d/13d/18f and biotic-stress-regulated GmATG7a/8h/8i/11/13d/18e/18f, provide valuable genetic resources for the molecular breeding of stress-tolerant soybean. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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15 pages, 13610 KB  
Article
Organellar Genome Analysis of the Red Alga Rhodymenia intricata (Rhodophyta, Florideophyceae) and Its Phylogenetic Analysis
by Maheshkumar Prakash Patil, Yong Jun Park, Jeong Woo Cho, Kwangsup Lee, Shin-Ichi Kitamura, Ganesh Bansi Patil, Rakesh Eshwarlal Mutha, Jong-Oh Kim and Kyunghoi Kim
Life 2026, 16(9), 1391; https://doi.org/10.3390/life16091391 - 24 Aug 2026
Viewed by 282
Abstract
Red algae (Rhodophyta) are an ancient lineage of photosynthetic eukaryotes that play important roles in marine ecosystems. However, genomic information for many species within the order Rhodymeniales remains limited, particularly for mitochondrial genomes. In this study, we sequenced, assembled, and analyzed the complete [...] Read more.
Red algae (Rhodophyta) are an ancient lineage of photosynthetic eukaryotes that play important roles in marine ecosystems. However, genomic information for many species within the order Rhodymeniales remains limited, particularly for mitochondrial genomes. In this study, we sequenced, assembled, and analyzed the complete mitochondrial genome (mitogenome) of Rhodymenia intricata to investigate its genome organization, gene content, and phylogenetic position within Rhodymeniales. The mitogenome of R. intricata is a circular DNA molecule of 26,213 bp containing 49 genes, including 25 protein-coding genes (PCGs), 21 tRNA genes, and 3 rRNA genes. The genome shows a strong A + T bias (70.9%) and positive AT and GC skews, typical of red algal mitogenomes. Comparative analysis with other Rhodymeniales mitogenomes revealed generally conserved gene content and organization, with several lineage-specific features such as the presence of the rpl20 gene, an additional open reading frame (orf148), and three rRNA genes (rnl, rns, and rns5). Codon usage analysis indicated a preference for leucine and isoleucine codons and dominant start and stop codons (ATG and TAA). Phylogenetic analysis based on a concatenated dataset of 23 mitochondrial PCGs strongly supported the monophyly of Rhodymeniales and confirmed the close relationship between R. intricata and R. pseudopalmata. Overall, this study presents the first complete mitogenome of R. intricata and expands mitogenomic resources for Rhodymeniales, providing new insights into mitogenome evolution and phylogenetic relationships in red algae. Full article
(This article belongs to the Section Genomics and Proteomics)
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19 pages, 4966 KB  
Article
YAP1 Is Associated with Cumulus Expansion-Related Factor Expression and Autophagy-Related Signaling in Yak Cumulus Cells
by Tiantian Zhang, Meng Wang, Xin Ma, Tingting Lu, Qiyong Zuo, Qian Zhang, Libin Wang and Yangyang Pan
Animals 2026, 16(17), 2636; https://doi.org/10.3390/ani16172636 - 22 Aug 2026
Viewed by 246
Abstract
Cumulus expansion is important for oocyte maturation, but its molecular regulation in yak remains unclear. This study examined the association of Yes-associated protein 1 (YAP1) with cumulus expansion-related and autophagy-related molecular markers in cumulus cells isolated from yak cumulus–oocyte complexes collected from ovarian [...] Read more.
Cumulus expansion is important for oocyte maturation, but its molecular regulation in yak remains unclear. This study examined the association of Yes-associated protein 1 (YAP1) with cumulus expansion-related and autophagy-related molecular markers in cumulus cells isolated from yak cumulus–oocyte complexes collected from ovarian follicles. YAP1 was overexpressed or knocked down, and YAP1-overexpressing cultures were additionally treated with 3-methyladenine (3-MA). Transcript abundance was assessed by RT-qPCR and interpreted descriptively, whereas protein abundance was evaluated by Western blotting; representative immunofluorescence and mCherry-GFP-LC3B images were also examined. YAP1 overexpression significantly increased HAS2 and PTGS2 protein abundance, while PTX3 and TNFAIP6 showed non-significant upward trends; YAP1 knockdown significantly reduced all four proteins. YAP1 manipulation was also associated with changes in Beclin-1, ATG5, p62, and the LC3B-II/LC3B-I ratio. Compared with YAP1 overexpression alone, 3-MA co-treatment significantly reduced HAS2, PTGS2, PTX3, TNFAIP6, Beclin-1, and ATG5, increased p62, and numerically reduced the LC3B-II/LC3B-I ratio without statistical significance. These findings support an association between YAP1 and cumulus expansion-related molecular programs and are consistent with partial involvement of 3-MA-sensitive, autophagy-associated signaling. Direct functional assays and pathway-specific validation are required to establish causality. Full article
(This article belongs to the Section Cattle)
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27 pages, 11965 KB  
Article
Estradiol Ameliorates Postmenopausal Bladder Dysfunction by Restoring Mitophagy via the miRNA-200/KLF4/mTOR Signaling Pathway
by Kuang-Shun Chueh, Jian-He Lu, Jing-Wen Mao, Bin-Nan Wu, Cheng-Yu Long, Zhi-Feng Miao, Tai-Jui Juan, Rong-Jyh Lin, Shu-Mien Chuang, Mei-Chen Shen, Ting-Wei Sun, Mei-Chin Lu and Yung-Shun Juan
Int. J. Mol. Sci. 2026, 27(17), 7529; https://doi.org/10.3390/ijms27177529 - 22 Aug 2026
Viewed by 287
Abstract
Postmenopausal ovarian hormone deficiency (OHD) contributes to overactive bladder (OAB) through oxidative stress, mitochondrial dysfunction, and dysregulated estrogen receptor (ER) signaling. This study investigated whether estradiol (E2) alleviates dysfunction by modulating the ER/Smad/miRNA-200/KLF4/mTOR signaling pathway to restore mitochondrial quality control. Thirty female Sprague-Dawley [...] Read more.
Postmenopausal ovarian hormone deficiency (OHD) contributes to overactive bladder (OAB) through oxidative stress, mitochondrial dysfunction, and dysregulated estrogen receptor (ER) signaling. This study investigated whether estradiol (E2) alleviates dysfunction by modulating the ER/Smad/miRNA-200/KLF4/mTOR signaling pathway to restore mitochondrial quality control. Thirty female Sprague-Dawley rats were initially allocated to Sham, Ovariectomy (OVX) and OVX + E2 group; after attrition during the 12-month protocol, six surviving animals per group were included in the principal analyses. The OVX + E2 group received daily intramuscular E2 (IM, 30 μg/kg/day) for one month. Bladder function was assessed via micturition volume and frequency by metabolic cages, cystometrograms, and contractility assays. Mechanisms were analyzed using immunofluorescence, Western blotting, transmission electron microscopy (TEM), and miRNA sequencing. OVX rats exhibited significant overactivity and compromised contractility, accompanied by upregulated ERα and downregulated ERβ/GPER. Molecularly, OHD was associated with the upregulation of the miRNA-200 family (miRNA-200a-3p, miRNA-200b-3p and miRNA-200b-5p), which was accompanied by reduced levels of KLF4 and autophagy proteins (ATG7, ATG12 and Beclin-1), as well as elevated p-mTOR expression. TEM revealed the accumulation of damaged mitochondria with ultrastructural features associated with impaired mitophagy. However, E2 treatment ameliorated these abnormalities. These improvements were associated with the restoration of TGF-β/Smad signaling, downregulation of selected miRNA-200 family members, recovery of KLF4 level, and increased expression of autophagy-related markers, accompanied by improved mitochondrial ultrastructural integrity. This cellular restoration might be correlated with improved urodynamic parameters. E2 might exert therapeutic effects by improving mitochondrial quality, potentially via the ER/Smad/miRNA-200/KLF4 signaling pathway. These findings provided mechanistic insights into estrogen-mediated protection and highlight this proposed signaling pathway as a therapeutic target for postmenopausal OAB. Full article
(This article belongs to the Special Issue Autophagy and Apoptosis in Mammal Cells)
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19 pages, 10493 KB  
Article
Whole-Exome Sequencing Identifies Candidate Genomic Features Associated with Response to Platinum-Based Chemotherapy and Ixabepilone-Based Treatment in Ovarian Cancer
by Tobias M. P. Hartwich, Stefania Bellone, Orazio De Tommasi, Sarah Ottum, Victoria Ettorre, Michelle Greenman, Namrata Sethi, Cem Demirkiran, Kevin Y. Yang, Ammal Abbasi, Ludmil B. Alexandrov and Alessandro D. Santin
Int. J. Mol. Sci. 2026, 27(17), 7524; https://doi.org/10.3390/ijms27177524 - 22 Aug 2026
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Abstract
Carboplatin/paclitaxel (CP) chemotherapy is the cornerstone of therapy for advanced stage ovarian cancer (OC). However, despite initial sensitivity, this regimen cannot avoid the emergence of resistance. Ixabepilone ± bevacizumab (IB) is a combination recently added to NCCN guidelines for the treatment of platinum-resistant [...] Read more.
Carboplatin/paclitaxel (CP) chemotherapy is the cornerstone of therapy for advanced stage ovarian cancer (OC). However, despite initial sensitivity, this regimen cannot avoid the emergence of resistance. Ixabepilone ± bevacizumab (IB) is a combination recently added to NCCN guidelines for the treatment of platinum-resistant OC. It would be desirable to identify biomarkers able to differentiate patients who are resistant to CP and IB, and biomarkers that identify which patients may benefit from IB treatment. We analyzed whole-exome-sequencing (WES) data from 49 OC patients exposed to CP, including 28 platinum-sensitive vs. 21 platinum-resistant, and 31 additional platinum-resistant patients, including 16 responders (i.e., CR/PR) vs. 15 non-responders (SD/PD) to ixabepilone ± bevacizumab. Comprehensive genetic analyses were performed to identify alterations correlated with resistance to CP and IB. WES analysis of CP responders vs. non-responders revealed differences in HRD-signatures (p < 0.05), OS (p < 0.005) and gain/loss-of-function in multiple genes associated with tumor growth/progression including but not limited to ACVR2A, INHBA, MAP3K7, ATG5, SGK1, FYN, RSPO3, NOD1 and LRRK2. WES analysis of platinum-resistant IB-treated patients revealed additional nominally significant genes and deranged pathways including gains in the DROSHA and SDHA genes in responders vs. non-responders (p < 0.05). Patients harboring HRD-signatures showed significantly higher sensitivity to CP and prolonged survival compared to HRD-negative patients. Alterations in genes associated with tumor growth/progression correlated with resistance to CP regimen and may represent novel “druggable” candidate biomarkers for the targeted treatment of CP/IB-resistant patients. Further validation in independent cohorts and preclinical experiments in CP/IB-resistant models are warranted to establish the clinical utility of these findings. Full article
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23 pages, 13646 KB  
Article
Repetitive Compressive Loading Downregulates the Expression of Autophagy-Related Factors, Autophagy Capacity and Cellular Activity in Human Osteoarthritic Chondrocytes
by Satomi Sato, Hideaki Iwata, Takeaki Yamamoto, Shu Somemura, Masahiro Takemoto, Yuki Takahashi-Suzuki, Yodo Sugishita, Hiroto Fujiya, Naoki Haraguchi and Kazuo Yudoh
Int. J. Mol. Sci. 2026, 27(16), 7485; https://doi.org/10.3390/ijms27167485 - 21 Aug 2026
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Abstract
Mechanical stress is thought to be involved in the pathogenesis and pathophysiology of osteoarthritis (OA). However, much remains to be elucidated regarding how chondrocytes sense and respond to mechanical stress (stress sensing and response factors). Additionally, it still remains unclear whether there are [...] Read more.
Mechanical stress is thought to be involved in the pathogenesis and pathophysiology of osteoarthritis (OA). However, much remains to be elucidated regarding how chondrocytes sense and respond to mechanical stress (stress sensing and response factors). Additionally, it still remains unclear whether there are defensive responses and mechanisms to protect against pathological agents and mechanical stress in articular cartilage tissue. This study was designed to determine whether repetitive mechanical force, at physiologic levels, affects the expression of factors regulating autophagy such as the autophagy-related proteins ATG5, Beclin-1, and Parkin, and the autophagy process as well as cellular activity in cultured chondrocytes. Three-dimensional cultured tissue was generated from human chondrocytes using a collagen sponge scaffold. After physiological mechanical loading of the 3D cell–collagen sponge construct, comparative analyses of expression levels of ATG5, Beclin-1, and Parkin were performed in human chondrocytes. Chondrocyte activity and Transmission Electron Microscopy (TEM) analysis for detecting autophagy process were also analyzed with or without repetitive compressive loading. In chondrocytes, 60 min or 180 min repetitive compressive loading significantly decreased the expression of ATG5, Beclin-1 and Parkin in comparison with the non-loading group. TEM analysis indicated that, in normal chondrocytes of the non-loading group, the autophagy process was shown to be progressing. In contrast, repetitive loading decreased the number of autophagosomes and autolysosomes in chondrocytes. In addition, numerous degenerated organelles that had not undergone autophagy were observed within the chondrocytes under repetitive loading. The ATG5 and Beclin-1 proteins are known to play crucial roles in regulating cellular autophagy. Furthermore, repetitive mechanical loading caused a decreased expression of Parkin, a mitophagy regulator in chondrocytes. Our results indicate for the first time that a decrease in mitophagy, as well as cellular autophagy, in response to mechanical stress, even at the physiologic level, leads to the accumulation of defective mitochondria and abnormal cellular proteins, resulting in reduced chondrocyte activity and affecting the maintenance of cartilage tissue homeostasis, ultimately contributing to the progression of OA. Full article
(This article belongs to the Section Molecular Biology)
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