Prognostic value of protein expression, tumor morphology and location within the pancreas in pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDA) of the head (hPDA) is more frequently diagnosed than PDA of the body/tail (btPDA) due to prevalent biliary obstruction symptoms, such as jaundice. hPDA is diagnosed and treated at an earlier stage than btPDA, leading to an improved prognosis. Data from 60 patients with PDA (30 patients with hPDA and 30 patients with btPDA) were analyzed, investigating tumor location (hPDA/btPDA) and clinical information [tumor size, lymph node metastasis, tumor stage and overall survival (OS)] depending on histological patterns [large duct pattern (PDA-L) and small duct pattern (PDA-S)], fibrotic focus (FF) and protein expression [GATA binding protein 6 (GATA6), cytokeratin 5/6, hepatocyte nuclear factor-1β (HNF1β), S100 calcium binding protein A4 (S-100A4), keratin 81 and transforming growth factor-β]. hPDA was significantly associated with tumor size, lymph node metastasis and more advanced stage. The worse OS was not related to tumor location, tumor size, lymph node metastasis or more advanced stage; however, GATA6 positivity was related to poor OS. Except for FF, PDA-L/PDA-S and immunostaining results were not associated with tumor location. PDA-L was related to S-100A4low, GATA6+ and HNF1β+. In the present study, tumor location did not influence tumor prognosis and histological pattern; otherwise, protein expression could influence PDA-L/PDA-S and OS. Therefore, histological classification may be useful in hPDA treatment.

Resveratrol ameliorates high‑fat diet‑induced insulin resistance via the DDIT4/mTOR pathway in skeletal muscle

Resveratrol (RSV) is a natural ingredient used in the treatment of diabetes mellitus. However, the antidiabetic mechanism of RSV is not clear. In the present study the antidiabetic mechanism of RSV was investigated using mice with high-fat diet (HFD)-induced insulin resistance (IR). C57BL/6J mice were divided into the following three groups: Control (CON), HFD, and HFD + RSV (RSV, 100 mg/kg body weight/day). Mice were administered RSV for 6 weeks; then biochemical and histological parameters, as well as gene and protein expression were detected. Compared with the CON group, the circulating levels of blood glucose, insulin, triglycerides, total cholesterol and high-density lipoprotein cholesterol, and area under the glucose curve were increased (P<0.05), the quantitative insulin sensitivity check index was decreased (P<0.05), and lipid accumulation in skeletal muscle was increased in the HFD group. RSV treatment was able to reverse this process and promote the IRS-1/PI3K/AKT/GLUT4 signaling pathway. Moreover, DNA damage-inducible transcript 4 (DDIT4) expression was upregulated, while the expression levels of mammalian target of rapamycin (mTOR) and p70 ribosomal protein S6 kinase were downregulated in the HFD + RSV group compared with the HFD group (P<0.05). Cell experiments inhibiting DDIT4 or activating mTOR also confirmed the role of these pathways. In summary, RSV ameliorated IR and glucose as well as lipid metabolism, and promoted the IRS-1/PI3K/AKT/GLUT4 signaling pathway through the DDIT4/mTOR signaling pathway in mice with HFD-induced IR.

POLR1D, a shared subunit of RNA polymerase I and III, modulates mTORC1 activity

The mechanistic target of rapamycin complex 1 (mTORC1) is a crucial nutrient sensor and a major regulator of cell growth and proliferation. While mTORC1 activity is frequently upregulated in cancer, the mechanisms regulating mTORC1 are not fully understood. POLR1D, a shared subunit of RNA polymerases I and III, is often upregulated in colorectal cancer (CRC) and mutated in Treacher-Collins syndrome. POLR1D, together with its binding partner POLR1C, forms a dimer that is believed to initiate the assembly of the multisubunit RNA polymerases I and III. Our data reveal an unexpected link between POLR1D and mTORC1 signalling. We found that the overproduction of POLR1D in human cells stimulates mTORC1 activity. In contrast, the downregulation of POLR1D leads to the repression of the mTORC1 pathway. Additionally, we demonstrate that a pool of POLR1D localises to the cytoplasm and interacts with the mTORC1 regulator RAGA and RAPTOR. Furthermore, POLR1D enhances the interaction between RAPTOR and RAGA and sustains mTORC1 activity under starvation conditions. We have identified a novel role for the RNA polymerase I/III subunit POLR1D in regulating mTORC1 signalling. Our findings suggest the existence of a new node in the already complex mTORC1 signalling network, where POLR1D functions to convey the cell's internal status, namely polymerase assembly, to this kinase.

Aberrant overexpression of m6A writer and reader genes in pediatric B-Cell Acute Lymphoblastic Leukemia (B-ALL)

BACKGROUND

m6A modification, regulated by writers (METTL3, METTL14), erasers (ALKBH5, FTO), and readers (IGF2BPs), is implicated in various cancers, including leukemias.

METHODS

In our study, we examined a cohort of 227 pediatric B-ALL patients (152 primary and 75 relapsed) and assessed the expression profiles of m6A machinery genes, including both writers and erasers, as well as the IGF2BP RNA-binding proteins, which are known as m6A readers. We also quantified the absolute percentage of m6A (m6A%). The correlation between m6A machinery gene expression and patient prognosis was studied using univariate and multivariate analyses.

RESULTS

Our analysis revealed a significant upregulation of m6A writers (METTL3 and METTL14), erasers (FTO), and m6A readers (IGF2BPs 1 and 3) in B-ALL patients, both in the primary and relapsed groups. m6A% levels were markedly higher in B-ALL samples than in controls. Multivariate analysis revealed that the expression of IGF2BP3, METTL3, and FTO genes, independently predicted lower overall survival and event-free survival in primary B-ALL patients.

CONCLUSIONS

Despite the collective dysregulation of the m6A machinery, the writers and readers appear to have a more dominant phenotype, as evidenced by the significantly elevated m6A% levels. This is the first study to analyze and establish the role of m6A machinery gene expression and its correlation with survival outcomes in a large group of B-ALL patients. These findings could aid in the development of new therapeutics targeting the m6A machinery and help predict relapse in pediatric B-ALL patients.

Effect of tristetraprolin on esophageal squamous cell carcinoma cell proliferation

BACKGROUND

Tristetraprolin (TTP) can inhibit the abnormal proliferation of malignant tumors but there are no studies involving TTP and esophageal squamous cell carcinoma (ESCC). We aimed to determine the effect of TTP on ESCC cell proliferation and to elucidate the underlying mechanism.

METHODS

The human ESCC cell line, KYSE-510, and the human ESCC cell line, KYSE-150, stably infected with tetracycline-inducible expression (Tet-on-TTP and Tet-on-EV, respectively) were screened with puromycin. After Tet-on-TTP KYSE-150 cells were treated with different concentrations of doxycycline [Dox] (0, 0.5, and 1 ug/mL), the levels of TTP mRNA and protein expression were detected by real-time fluorescent quantitative PCR and western blotting, respectively. The effects of TTP on proliferation and migration were estimated by CCK-8 and Transwell assays, respectively. Cell apoptosis and cell cycle were measured by flow cytometry. Cellular apoptosis-related gene protein expression was determined by western blotting.

RESULTS

TTP overexpression significantly inhibited KYSE-510 and KYSE-150 proliferation. TTP overexpression also significantly inhibited KYSE-150 migration. In addition, TTP expression upregulation promoted the KYSE-150 apoptosis and induced cell cycle arrest in the G2 phase, downregulated Bcl-2 expression, and upregulated Bax expression.

CONCLUSION

TTP inhibited ESCC cell proliferation, promoted ESCC cell apoptosis, and arrested cell cycle progression in the G2 phase.

Multi-organ proteome reveals different nursing ability between two honeybee srocks

High royal jelly production is an adaptive reproductive investment syndrome in honey bees that enhances their nursing ability to queen bee larvae. However, the biological basis of this reproduction investment at the multi-organ level remains elusive. In this study, proteome across 11 organs of two bee stocks: high royal jelly production bees (RJBs) and Italian bees (ITBs) was compared. Our analysis revealed significant differences in protein expression profiles in brain, fat body, mandibular gland, and Malpighian tubule, highlighting their crucial roles in regulating royal jelly secretion in RJBs. The increased energy turnover, protein synthesis, and lipid synthesis observed in RJBs compared to ITBs highlight their enhanced metabolic activity, which is essential for the robust secretion of royal jelly in RJBs. The elevated abundance of major royal jelly proteins (MRJPs), hexamerins, and vitellogenin suggests their critical contributions to the nutritional and material requirement necessary for royal jelly secretion. Furthermore, the high level of vitellogenin and juvenile hormone esterase may suppress juvenile hormones, which contribute to a strong royal jelly secretion and sensitivity of RJBs to larval pheromones relative to ITBs. This comprehensive dataset contributes to a better understanding of nursing behavior and reproductive investment in honey bees. Significiance. The royal jelly secretion syndrome is a colony level social trait dominated by the intricate interplay of multiple organs. However, previous studies have primarily focused on individual organs. In this study, the proteome of 11 organs was compared between high royal jelly production bees (RJBs) and Italian bees (ITBs) to provide knowledge on how multiple organs cooperate to boost the elevated royal jelly production by RJBs. Nutrition supply was sufficient at multiple organs of RJBs when compared to ITBs, indicating that nutrition plays an essential role in boosting energy metabolism, protein and lipid synthesis, and directly contributes to the amount of royal jelly secretion. The high level of secretion of storage proteins, such as MRJPs, hex, and vitellogenin, provides sufficient nutrition and material for royal jelly secretion. Moreover, the higher levels of vitellogenin and juvenile hormone esterase may suppress juvenile hormone synthesis, and contributing to stronger sense of RJBs to larval pheromone relative to ITBs. This suggests that nutrition can influence the hormone levels and sensory abilities of RJBs nurse bees to promote their royal jelly secretion ability. The reported data provide insights into the systematic regulation strategy of honeybee nursing behavior and reproductive investment.

Pediatric gliomas immunity challenges and immunotherapy advances

Pediatric gliomas, the most frequent brain tumors in children, are characterized by heterogeneity and a unique tumor immune microenvironment. They are categorized into different subtypes, including low-grade gliomas like pilocytic astrocytomas and high-grade gliomas such as diffuse midline gliomas and diffuse intrinsic pontine gliomas, each exhibiting distinct immunological profiles. The tumor immune microenvironment in pediatric gliomas is shaped by cellular and non-cellular components, including immune cells, cytokines, and the extracellular matrix, involved in tumor progression, immune evasion, and response to therapy. While pediatric low-grade gliomas often display an immunosuppressed microenvironment, high-grade gliomas are characterized by complex immune infiltrates and intricate immunosuppressive mechanisms. The blood-brain barrier further obscures immune cell recruitment and therapeutic delivery. Despite advances in understanding adult gliomas, the immunobiology of pediatric tumors is poorly investigated, with limited data on the interactions between glioma cells and immune populations such as T and natural killer cells, as well as tumor-associated macrophages. Herein, we provide an update of the current knowledge on tumor immune microenvironment interactions in pediatric gliomas, highlighting the immunosuppressive mechanisms and emerging immunotherapeutic strategies aiming at overcoming these barriers to improve clinical outcomes for affected children.

Alpha-Synuclein drives NURR1 and NLRP3 Inflammasome dysregulation in Parkinson's disease: From pathogenesis to potential therapeutic strategies

Parkinson's disease (PD), a progressive neurodegenerative disorder, is characterized by the loss of dopaminergic neurons and pathological aggregation of α-synuclein (α-Syn). Emerging evidence highlights the interplay between genetic susceptibility, neuroinflammation, and transcriptional dysregulation in driving PD pathogenesis. This review brings together the latest information on three important players: α-Syn, the transcription factor Orphan nuclear receptor (NURR1), and the NOD-like receptor 3 (NLRP3) inflammasome. Pathogenic α-syn aggregates cause damage to neurons by disrupting mitochondria and lysosomes and spreading in a way similar to prion proteins. They also turn on the NLRP3 inflammasome, which is a key player in neuroinflammation. NLRP3-driven release of pro-inflammatory cytokines exacerbates neurodegeneration and creates a self-sustaining inflammatory milieu. Meanwhile, reduced NURR1 activity, a pivotal modulator of dopaminergic neuron survival and development, exposes neurons to oxidative stress, neuroinflammation, and α-Syn toxicity, hence exacerbating disease progression. So, targeting this trio exhibits transformative potential against PD pathogenesis.

Therapeutic targeting the cGAS-STING pathway associated with protein and gene: An emerging and promising novel strategy for aging-related neurodegenerative disease

Neurodegenerative diseases (NDDs) represent a rapidly escalating global health challenge, contributing significantly to the worldwide disease burden and posing substantial threats to public health systems across nations. Among the many risk factors for neurodegeneration, aging is the major risk factor. In the context of aging, multiple factors lead to the release of endogenous DNA (especially mitochondrial DNA, mtDNA), which is an important trigger for the activation of the cGAS-STING innate immune pathway. Recent studies have identified an increasing role for activation of the cGAS-STING signaling pathway as a driver of senescence-associated secretory phenotypes (SASPs) in aging and NDDs. The cGAS-STING pathway mediates the immune sensing of DNA and is a key driver of chronic inflammation and functional decline during the aging process. Blocking cGAS-STING signaling may reduce the inflammatory response by preventing mtDNA release and enhancing mitophagy. Targeted inhibition of the cGAS-STING pathway by biological macromolecules such as natural products shows promise in therapeutic strategies for age-related NDDs. This review aims to systematically and comprehensively introduces the role of the cGAS-STING pathway in age-related NDDs in the context of aging while revealing the molecular mechanisms of the cGAS-STING pathway and its downstream signaling pathways and to develop more targeted and effective therapeutic strategies for NDDs.

Ascl1-mediated enhancement of GABAergic neuronal function in differentiated F11 cells under high glucose conditions

Gamma-aminobutyric acid (GABA)ergic neurons play a key role in pain modulation within the dorsal root ganglion (DRG), making them critical targets for therapeutic studies. This study utilized F11 cells as an in vitro model to examine GABAergic function under high-glucose conditions mimicking diabetic neuropathy. Differentiated F11 cells exhibited increased sensory neuronal marker expression and functional action potentials. Overexpression of the transcription factor Achaete-scute homolog 1 (Ascl1) via lentiviral vectors enhanced GABAergic characteristics, including upregulation of GAD65, GAD67, VGAT, and GABA release. Under high-glucose conditions, Ascl1 modulated pro-inflammatory cytokines (TNF-α, NF-κB, IL-1β), anti-inflammatory cytokines (IL-4, IL-10), and pain-related channels (TRPV1, TRPA1, Nav1.8), reversing pathological changes. Temporal control of Ascl1 during differentiation reduced hypersensitivity and improved cell viability, mediated by parvalbumin in a specific GABAergic subtype. These findings highlight the therapeutic potential of Ascl1 in neuropathic pain and the scalability of F11 cells for high-throughput screening of GABAergic therapeutics.

Drugging the Undruggable and beyond: Emerging precision oncology approaches to target acquired resistance to KRAS G12C and KRAS G12D inhibitors

Development of mutant specific KRAS inhibitors validated KRAS as a 'druggable' target. However, excellent initial efficacy was eventually overshadowed by failure to exhibit sustained clinical response, primarily due to acquired resistance. Some targeted therapies like SOS1, SHP2, and MEK inhibitors, in combination with mutant KRAS G12C inhibitors (G12Ci), are currently under clinical investigation with evidences of improving efficacy. However, a deep understanding of the underlying molecular pathways behind the acquired resistance is still at a nascent stage. Recent preclinical studies have uncovered a role of novel proteins and pathways responsible for resistance and their inhibition demonstrated a robust anticancer efficacy in combination. Plethora of combination therapy approaches are now being proposed with emergence of AXL, ULK1, Tissue factor, farnesyltransferase, etc. as targets to counter G12Ci resistance. This review summarizes in a comprehensive manner, some of the novel combination modalities to overcome G12Ci resistance, based on current understanding and with great potential to hit clinical success. Along with G12C, KRAS G12D (G12D) was also considered a formidable foe, until the discovery of selective inhibitors. However, eventual clinical resistance can eclipse the early success and requires an in-depth understanding of resistance mechanisms. Evidences of G12Ci resistance can be exploited as probable combination strategies to tackle ensuing resistance to G12D inhibitors (G12Di), and can translate in superior clinical efficacy. Early preclinical studies of G12Di in combination with ERBB, SOS1, AKT and immune-checkpoints inhibitors indicate encouraging response. This review further describes some of the early affirmations on combination strategies with G12Di. We postulate to go beyond 'Drugging the Undruggable' with advanced combination approaches mitigating G12C and G12D inhibitor resistance.

Molecular mechanisms of the anticancer action of fustin isolated from Cotinus coggygria Scop. in MDA-MB-231 triple-negative breast cancer cell line

The aim of the present work was to investigate some of the molecular mechanisms and targets of the anticancer action of the bioflavonoid fustin isolated from the heartwood of Cotinus coggygria Scop. in the triple-negative breast cancer cell line MDA-MB-231. For this purpose, we applied fluorescence microscopy analysis to evaluate apoptosis, necrosis, and mitochondrial integrity, wound healing assay to study fustin antimigratory potential and quantitative reverse transcription-polymerase chain reaction to analyze the expression of genes associated with cell cycle control, programmed cell death, metastasis, and epigenetic alterations. A complex network-based bioinformatic analysis was also employed for protein-protein network construction, hub genes identification, and functional enrichment. The results revealed a significant induction of early and late apoptotic and necrotic events, a slight alteration of the mitochondria-related fluorescence, and marked antimotility effect after fustin treatment. Of 34 analyzed genes, seven fustin targets were identified, of which CDKN1A, ATM, and MYC were significantly enriched in pathways such as cell cycle, intrinsic apoptotic signaling pathway in response to DNA damage and generic transcription pathway. Our findings outline some molecular mechanisms of the anticancer action of fustin pointing it out as a potential oncotherapeutic agent and provide directions for future in vivo research.

Comparative analyses of morphology and temporal floral organ transcriptome provide insights into the development of staminodes in Globba racemosa (Zingiberaceae)

Staminode, the most conspicuous floral organ in Zingiberaceae, which greatly contributes to the ornamental value of flowers in this family. Meanwhile, staminode is a key innovation in Zingiberaceae, which is hypothesized to have originated from the fertile stamen. Previous morphological and gene expression analyses have provided evidence for this hypothesis. However, in Zingiberaceae, little is known about the gene expression dynamics of the staminode compared to other floral organs at transcriptomic level, and the molecular mechanisms underlying identity specification of the staminodes remain unresolved. In this study, by using G. racemosa, an ornamental plant in Zingiberaceae, we first traced the flower development of G. racemosa, with special attention to the development of the two types of staminodes (the labellum and the outer androecial member), to explore the morphological differences between staminodes and the fertile stamen. Then, by combining a full-length transcriptome and comparative transcriptome data from seven types of floral organs at four developmental stages, we identified candidate genes that are specifically, preferentially, or differentially expressed in the labellum and the outer androecial member compared to other floral organs. Using weighted gene co-expression network analysis (WGCNA), we further identified several modules that are significantly correlated with the labellum and the outer androecial member. Lastly, by examining the expression patterns of four well-known gene regulatory networks, which, according to previous studies, are presumed to be involved in the identity specification and morphogenesis of staminodes in Zingiberaceae, we found other potential regulators for the development of staminodes of G. racemosa. Notably, we found that on the one hand, the labellum and the outer androecial member shared some genes with the fertile stamen, providing evidence for the stamen origin of staminodes in Zingiberaceae; on the other hand, the labellum, outer androecial member, and petal also share many genes, explaining the morphological similarity among labellum, outer androecial member, and petal. Thus, in terms of regulatory mechanisms, the staminodes in G. racemosa may represent a complex of stamen and petal characteristics. In summary, our results offer valuable resources for further research on gene functions and lay the foundation for future analyses of the molecular mechanisms underlying staminode development in Zingiberaceae.

Optimization of genome editing by CRISPR ribonucleoprotein for high efficiency of germline transmission of Sox9 in zebrafish

Primordial germ cells (PGCs) are the first germline stem cells to emerge during early embryonic development and are essential for the propagation and survival of species. Genome editing creates mutagenesis possibilities in vivo, but the generation of precise mutations in PGCs is still challenging. Here, we report an optimized approach for highly efficient genome editing via introducing biallelic variations in early embryos in zebrafish. We adopted an extended, GC-rich, and chemically modified sgRNA along with microinjection of the CRISPR ribonucleoprotein (RNP) complex into the yolk sac at the 1-cell stage. We found that genome editing of Sox9a generated a high proportion of heterozygotes with edited alleles in the F1 generation, indicating biallelic editing. Deep sequencing and mapping the edited cells from early embryos to future tissues revealed that the edited founder has a dominantly edited allele, sox9a M1, accounting for over 99 % of alleles in the testis. Specifically, all offspring of the founder inherited the edited allele, suggesting nearly complete editing of the alleles in early germline cells. Overall, the optimization delineates biallelic editing of sox9a in early embryos and transmission of edited alleles to offspring, thus presenting a method to create a desired genetic mutation line of Sox9a avoiding lengthy traditional crossbreeding.

Structural analysis of EPOP BC-box binding to the elongin BC complex

The elongin BC complex (ELOBC) interacts with BC-box-containing proteins and plays a role in various cellular processes, including transcriptional regulation and ubiquitination. Elongin BC and polycomb repressive complex 2-associated protein (EPOP) contains a BC-box motif in its N-terminal region and influences cancer cell proliferation and differentiation. A previous study showed that a BC-box containing an EPOP-derived peptide suppresses cancer cell growth and induces apoptosis by disrupting the interaction between the ELOBC and its partner proteins. Here, we report the crystal structure of the EPOP BC-box peptide bound to the ELOBC and compare it with the structures of other BC-box-containing proteins in complex with the ELOBC. The overall structure of interactions between the BC-box and the ELOC was similar across different complexes, indicating a conserved binding mode. Our structural analysis revealed that the strictly conserved leucine residue (Leu40) within the BC-box of EPOP, which was previously suggested to be critical for interactions between the BC-box and the ELOC, was deeply embedded in the hydrophobic pocket of the ELOC protein. This study provided structural insights into BC-box-mediated protein-protein interactions and may serve as a fundamental resource for developing small molecules that modulate the interactions between ELOBC and BC-box-containing proteins.

Long-term aerobic exercise enhances liver health: miRNA regulation and oxidative stress alleviation

This study aims to investigate the effects of long-term aerobic exercise on liver health in aging rats. As age increases, the continuous accumulation of endogenous reactive oxygen species (ROS) damages hepatocytes, leading to liver function decline and the development of diseases such as cirrhosis and liver cancer. Using an 18-month-old rat model, we implemented an eight-month aerobic exercise regimen to systematically evaluate its hepatoprotective effects. The results showed that aerobic exercise effectively reduced oxidative stress and inflammation levels in liver tissue, decreased the expression of cell cycle regulator P53 and inflammatory regulator NF-κB protein, upregulated NRF2 protein expression, improved mitochondrial function, and inhibited the progression of ferroptosis. These beneficial effects were achieved through the upregulation of miR-21 and miR-224 expression induced by exercise. These microRNAs inhibit the translation of MAP2K3 and MAPK14, thereby suppressing the activation of the P38 MAPK pathway. We further found that inhibiting P38 MAPK can enhance cellular antioxidant and anti-inflammatory capabilities, reversing hepatocyte damage caused by hydrogen peroxide. These results demonstrate that long-term aerobic exercise can reprogram aging-related oxidative stress and metabolic pathology by regulating miRNAs and the P38 MAPK pathway, thereby helping to prevent age-related liver diseases.

Buthionine sulfoximine acts synergistically with doxorubicin as a sensitizer molecule on different tumor cell lines

The chemotherapeutic drug doxorubicin (DOX) has been widely used for treating solid tumors attributed to its antiproliferative effectiveness; however, its clinical use is limited due to side effects, including cardiotoxicity, myelosuppression, and drug resistance. Combining DOX with buthionine sulfoximine (BSO), a glutathione (GSH) synthesis inhibitor, showed promising results in overcoming these adverse effects, potentially reducing the required DOX dose while maintaining efficacy. The aim of the present study was to examine the effects of different concentrations of BSO and DOX, both individually and in combination, utilizing B16/F10 (murine melanoma), SNB-19 (human glioblastoma), S180 (murine sarcoma), and SVEC4-10 (murine endothelial) cell lines. Cell viability, migration, and clonogenicity were assessed using the following assays MTT, scratch, and colony formation. Antioxidant levels of GSH, as well as activities catalase (CAT), and superoxide dismutase (SOD) were measured. BSO alone exhibited minimal cytotoxic effects, while DOX alone reduced cell viability significantly. The combination of BSO+DOX decreased IC50 values for most cell lines, demonstrating a synergistic effect, especially in B16/F10, S180, and SVEC4-10 cells. BSO+DOX combination significantly inhibited cell migration and clonogenicity compared to DOX alone. While GSH levels were decreased with BSO+DOX treatment activities of CAT and SOD increased following DOX administration but remained unchanged by BSO. These results suggest that BSO may be considered a valuable tool to improve DOX therapeutic efficacy, particularly in cases of chemotherapy-resistant tumors, as BSO enhances DOX activity while potentially reducing systemic chemotherapeutic drug toxicity.

APE1 promotes lung adenocarcinoma through G4-mediated transcriptional reprogramming of urea cycle metabolism

Lung adenocarcinoma (LUAD) remains the leading cause of cancer deaths worldwide. Apurinic/apyrimidinic endonuclease 1 (APE1), an enzyme integral to DNA repair and redox signaling, is notably upregulated in LUAD. Here we reveal that APE1 amplification, primarily via allele duplication, strongly correlates with poor prognosis in LUAD patients. Using human LUAD cell lines and a KRAS-driven mouse model, we showed that APE1 deletion hampered cell proliferation and tumor growth, highlighting its role in tumorigenesis. Mechanistically, APE1 promoted the transcription of urea cycle genes CPS1 and ARG2 by modulating the presence of G-quadruplex (G4) structures in their promoter regions. APE1 loss disrupted the urea cycle and pyrimidine metabolism, inducing metabolic reprogramming and growth arrest, which could be rescued by CPS1 or pyrimidine restoration. These findings uncover APE1's role in transcriptional regulation of urea cycle metabolic reprogramming via G4 structure, providing a potential therapeutic target LUAD patients with elevated APE1 expression.

Coevolution of Drosophila-type timeless with partner clock proteins

Drosophila-type timeless (dTIM) is a key clock protein in fruit flies, regulating rhythmicity and light-mediated entrainment. However, functional experiments indicate that its contribution to the clock differs in various insects. Therefore, we conducted a comprehensive phylogenetic analysis of dTIM across animals and dated its origin, gene duplications, and losses. We identified variable and conserved protein domains and pinpointed animal lineages that underwent the biggest changes in dTIM. While dTIM modifications are only mildly affected by changes in the PER protein, even the complete loss of PER in echinoderms had no impact on dTIM. However, changes in dTIM always co-occur with the loss of CRYPTOCHROMES or JETLAG. This is exemplified by the remarkably accelerated evolution of dTIM in phylloxera and aphids. Finally, alternative d-tim splicing, characteristic of Drosophila melanogaster temperature-dependent function, is conserved to some extent in Diptera, albeit with unique alterations. Altogether, this study pinpoints major changes that shaped dTIM evolution.

Plexin B2 in physiology and pathophysiology of the central nervous system

The Plexin protein family was initially found in 1995, comprising subfamilies from Plexin A to Plexin D. Plexin B2, a member of the Plexin subfamily, has widespread expression in many human organs and tissues, particularly in the nervous system where expression levels are significantly heightened. The biological roles of Plexin B2 are mostly determined by its protein structure and functional domains. These domains regulate the binding selectivity and affinity for ligands. Ligand binding activates signal transduction pathways, resulting in regulatory effects on several biological processes. This includes managing brain growth and change, keeping angiogenesis and vascular homeostasis in check, and preventing the start, growth, and metastasis of cancer. Plexin B2 has also been associated with the onset of many nervous system illnesses. Plexin B2 aids in the invasion and spread of malignant cells, facilitates nerve healing following spinal cord damage, and plays a role in the etiology of schizophrenia. This article thoroughly examines the existing research on Plexin B2 and its importance in central nervous system biology. Simultaneously, it investigates the regulatory function of Plexin B2 across many cell types in the central nervous system, specifically neural stem cells, neurons, microglia, and astrocytes. This study examines the current knowledge of Plexin B2's role in central nervous system diseases, including schizophrenia, spinal cord injury, neuroblastoma, and fear memory. Overall, the prospects for the clinical translation of Plexin B2 are promising. However, challenges related to specificity and drug delivery must be addressed. Future research could explore the integration of nanodrug delivery systems to enhance the clinical application of Plexin B2-targeted therapies.

A high-throughput differential chemical genetic screen uncovers genotype-specific compounds altering plant growth

The identification of chemical compounds regulating plant growth in a genetic context can greatly enhance our understanding of biological mechanisms. Here, we have developed a high-throughput phenotype-directed chemical screening method in plants to compare two genotypes and identify small molecules inducing genotype-specific phenotypes. We used Arabidopsis thaliana wild type and mus81, a DNA repair mutant, and screened off-patent drugs from the Prestwick library to selectively identify molecules affecting mus81 growth. We developed two complementary convolutional neural networks (CNN)-based image segmentation and classification programs to quantify Arabidopsis seedling growth. Using these approaches, we detected that about 10% of Prestwick molecules cause altered growth in both genotypes, suggesting their toxic effects on plant growth. We identified three Prestwick molecules specifically affecting mus81. Overall, we developed a straightforward, accurate, and adaptable methodology for performing high-throughput screening of chemical libraries in a time-efficient manner, accelerating the discovery of genotype-specific chemical regulators of plant growth.

Regulation of pericentromeric DNA loop size via Scc2-cohesin interaction

Cohesin exhibits DNA loop extrusion when bound to the ATPase activator Scc2 (NIPBL in humans), which has been proposed to organize higher-order chromosome folding. In budding yeast, most chromosome-bound cohesins lack Scc2. How the Scc2-cohesin interaction is regulated on the chromosome and its physiological consequences remain unclear. Here, we show that the deletion of both ECO1 and WPL1, two known cohesin regulators, but not either alone, caused Scc2-cohesin co-localization in metaphase, particularly around centromeres, using calibrated chromatin immunoprecipitation sequencing (ChIP-seq). Eco1's mitotic activity was required to prevent this co-localization in Δwpl1. We also demonstrate that Scc2-cohesin co-localization enlarged pericentromeric DNA loops, linking centromeres to genome sites hundreds of kilobases away, and delayed mitotic chromosome segregation. These findings suggest that Wpl1 and Eco1 cooperatively regulate Scc2-cohesin interaction, restrict pericentromeric DNA loop size, and facilitate chromosome segregation.

Anti-fibrotic, muscle-promoting antibody-drug conjugates for the improvement and treatment of DMD

Fibrosis, characterized by the deposition of excess and disorganized extracellular matrix (ECM), is a key pathological hallmark of multiple diseases, including Duchenne muscular dystrophy (DMD). Aiming to inhibit fibrosis progression, we generated an antibody-drug conjugate (ADC) that delivers an innovative small molecule conjugate to inhibit the ECM-modifying enzyme Lysyl oxidase (LOX) specifically in fibrotic lesions by targeting M2 macrophages. Administration of the ADC to mdx mice, the murine model of DMD, results in ADC accumulation in fibrotic muscles without affecting healthy tissues. Long-term ADC treatments of adult mdx mice lead to inhibition of the fibrotic process and to significant improvement of cardiac and skeletal muscle function. Our study demonstrates that targeted inhibition of LOX-dependent fibrotic diseases, such as DMD, facilitates improved outcomes for muscular dystrophies.

Differentiation of human pluripotent stem cells into urothelial organoids via transient activation of WNT signaling

The cloaca is a transient structure that forms in the terminal hindgut giving rise to the rectum dorsally and the urogenital sinus ventrally. Similarly, human hindgut cultures derived from human pluripotent stem cells generate human colonic organoids (HCOs) which also contain co-developing urothelial tissue. In this study, our goal was to identify pathways involved in cloacal patterning and apply this to human hindgut cultures. RNA sequencing (RNA-seq) data comparing dorsal versus ventral cloaca in e10.5 mice revealed that WNT signaling was elevated in the ventral versus dorsal cloaca. Inhibition of WNT signaling in hindgut cultures maintained their differentiation toward colonic organoids. WNT activation promoted differentiation toward human urothelial organoids (HUOs). HUOs contained developmental stage specific cell types present in mammalian urothelial tissue including co-developing mesenchyme. Therefore, HUOs offer a powerful in vitro model for dissecting the regulatory pathways that control the dynamic emergence of stage specific cell types within the human urothelium.

FGFR4 inhibition augments paclitaxel-induced cell death in ovarian cancer

OBJECTIVES

Epithelial ovarian cancer (EOC) is the most lethal gynecological malignancy, which has a high mortality rate due to frequent tumor recurrence. The development of drug resistance against the first-line chemotherapeutic agent, such as paclitaxel/Taxol®, represents a critical reason. The mechanisms of paclitaxel resistance remain largely unknown, and druggable drivers which can be targeted to prevent or revert paclitaxel resistance also need to be identified.

METHODS

Phos-tag-based screens in cells treated with paclitaxel were used to identify key regulators involved in paclitaxel resistance, such as fibroblast growth factor receptor 4 (FGFR4). The functional role of FGFR4 in regulating paclitaxel resistance was further identified using apoptosis assays, which included the identification of apoptotic marker levels and activities. The involvement of FGFR4 downstream signaling pathways involved in paclitaxel resistance were identified through western blotting and quantitative PCR. Their roles in regulating paclitaxel resistance were also validated using apoptosis assays. Immunofluorescent staining was performed to identify the synergy of paclitaxel and FGFR4 inhibition.

RESULTS

Functional in vitro and in vivo studies demonstrate that FGFR4 depletion suppresses ovarian cancer cell proliferation, migration, and tumor growth. Importantly, FGFR4 silencing or specific inhibition can sensitize ovarian cancer cells to paclitaxel, whereas FGFR4 overexpression confers paclitaxel resistance. Mechanistically, FGFR4 regulates paclitaxel sensitivity in EOC cells through modulating the expression of the anti-apoptotic protein B-cell lymphoma-extra large (Bcl-xL) via MEK-ERK-RSK signaling pathway. The inhibition of Bcl-xL or MEK-ERK-RSK signaling can also enhance paclitaxel-stimulated cytotoxicity.

CONCLUSION

These findings indicate that targeting FGFR4 can be a promising novel strategy to overcome paclitaxel resistance and improve the outcomes of EOC patients.

Ligand preference of EphB2 receptor is selectively regulated by N-glycosylation

The Eph receptors and their ephrin ligands play important roles in cell communication and neuron development. Eph interacts with ephrin in a complex manner. Here, we found ephrin-B2 instead of well-recorded ephrin-A5 specifically recognize and activate EphB2 receptor in primary cortical neurons. Domain-swapping and N/Q mutagenesis results show that the ectodomain of EphB2 and its N-glycosylation sites are critical for the ephrin binding selectivity. The N265, N336, N428, and N482Q mutant EphB2 cannot distinguish ephrin-B2 from ephrin-A5. Furthermore, the N-glycosylation sites in EphB2 are evolutionarily conserved and the N-glycan-directed binding strategy is commonly used in other Eph family members. A gain-of-function EphB6 mutant restores its ephrin-B2 binding ability. Finally, EphB2 is robustly glycosylated in the mouse brain and N-glycosylation is required for EphB2 signaling-induced cell rounding and dendritic spine formation. Collectively, our findings provide a molecular basis to understand the exquisite Eph/ephrin interaction preferences.

Cathepsin S: A key drug target and signalling hub in immune system diseases

The lysosomal cysteine protease cathepsin S supports host defence by promoting the maturation of MHC class-II proteins. In contrast, increased cathepsin S activity mediates tissue destructive immune responses in autoimmune and inflammatory diseases. Therefore, cathepsin S is a key target in drug discovery programs. Here, we critically reviewed the specific mechanisms by which cathepsin S mediates autoimmune and hyperinflammatory responses to identify new targets for therapeutic immunomodulation. To this end, we performed literature review utilizing PubMed, drug database of US FDA, European Medicines Agency and the Drug-Gene Interaction Database. Cathepsin S destroys T cell epitopes and reduces endogenous antigen diversity, impairing negative selection of autoreactive T cells that could recognize these epitopes. Moreover, cathepsin S critically regulates inflammatory disease severity by generating proinflammatory molecules (PAR-1, PAR-2, IL-36γ, Fractalkine, Endostatin, Ephrin-B2), inactivating anti-inflammatory mediators (SLPI) and degrading molecules involved in antimicrobial and immunomodulatory responses (surfactant protein-A, LL-37, beta-defensins), inter-endothelial/-epithelial barrier function, gene repair and energy homeostasis. These pathways could be targeted by repositioning of existing drugs. These findings suggest that inhibiting cathepsin S or a specific downstream target of cathepsin S by repositioning of existing drugs could be a promising strategy for treating autoimmune and inflammatory diseases. Current cathepsin S inhibitors in clinical trials face challenges, highlighting the need for innovative inhibitors that function effectively in various cellular compartments with differing pH levels, without targeting the shared catalytic site of cysteine cathepsins.

A central role for Numb/Nbl in multiple Shh-mediated axon repulsion processes

Sonic hedgehog (Shh) is an axon guidance molecule that can act as either a chemorepellent or a chemoattractant, depending on the neuron type and their developmental stage. In the developing spinal cord, Shh initially attracts commissural axons to the floor plate and later repels them after they cross the midline. In the developing visual system, Shh repels ipsilateral retinal ganglion cell (iRGC) axons at the optic chiasm. Although Shh requires the endocytic adaptor Numb for attraction of spinal commissural axons, the molecular mechanisms underlying Shh dual function in attraction and repulsion are still unclear. In this study, we show that Numb is essential for two Shh-mediated repulsion processes: iRGC axon repulsion at the optic chiasm and antero-posterior commissural axon repulsion in the spinal cord. Therefore, Numb is required for Shh-mediated attraction and repulsion. These results position Numb as a central player in the non-canonical Shh signaling pathway mediating axon repulsion.

Potentials of peroxisome proliferator-activated receptor (PPAR) α, β/δ, and γ: An in-depth and comprehensive review of their molecular mechanisms, cellular Signalling, immune responses and therapeutic implications in multiple diseases

Peroxisome proliferator-activated receptors (PPARs), ligand-activated transcription factors, have emerged as a key regulator of various biological processes, underscoring their relevance in the pathophysiology and treatment of numerous diseases. PPARs are primarily recognized for their critical role in lipid and glucose metabolism, which underpins their therapeutic applications in managing type 2 diabetes mellitus. Beyond metabolic disorders, they have gained attention for their involvement in immune modulation, making them potential targets for autoimmune-related inflammatory diseases. Furthermore, PPAR's ability to regulate proliferation, differentiation, and apoptosis has positioned them as promising candidates in oncology. Their anti-inflammatory and anti-fibrotic properties further highlight their potential in dermatological and cardiovascular conditions, where dysregulated inflammatory responses contribute to disease progression. Recent advancements have elucidated the molecular mechanisms of different PPAR isoforms, including their regulation of key signalling pathways such as NF-κB and MAPK, which are crucial in inflammation and cellular stress responses. Additionally, their interactions with co-factors and post-translational modifications further diversify their functional roles. The therapeutic potential of various PPAR agonists has been extensively explored, although challenges related to side effects and target specificity remain. This growing body of evidence underscores the significance of PPARs in understanding the molecular basis of diseases and advancing therapeutic interventions, paving way for targeted treatment approach across a wide spectrum of medical conditions. Here, we provide a comprehensive and detailed perspective of PPARs and their potential across different health conditions to advance our understanding, elucidate underlying mechanisms, and facilitate the development of potential treatment strategies.

PRMT1 Upregulates SIRT6 by Enhancing Arginine Methylation of E2F7 to Inhibit Vascular Smooth Muscle Cell Senescence in Aortic Dissection

Aortic dissection (AD) is a highly alarming clinical condition of the aorta, with a significant mortality rate. Vascular smooth muscle cell (VSMC) senescence dominantly promotes AD progression. This study planned to clarify the exact functions and mechanisms of protein arginine methyltransferase 1 (PRMT1), E2F7, and Sirtuin 6 (SIRT6) in the VSMC senescence of the AD model. Angiotensin II (Ang II) and β-Aminopropionitrile (BAPN) were used to treat VSMCs or C57BL/6J mice to establish the AD in vitro or in vivo model. Protein expressions were examined by western blot, IHC, and IF staining. Histological change or cell senescence was monitored using H&E or senescence-associated-β-galactosidase (SA-β-gal) staining. Enzyme-Linked Immunosorbent Assay (ELISA) assays were utilized to evaluate senescence-associated secretory phenotype markers' levels. The binding interactions between E2F7 and SIRT6 or PRMT1 and E2F7 were verified by the luciferase reporter, ChIP Co-IP, and GST-pull-down analysis. The ubiquitination levels of E2F7 were assessed using ubiquitination assays. PRMT1, E2F7, and SIRT6 protein levels were decreased in the Ang II-treated VSMCs of the AD model. Moreover, E2F7 repressed cell senescence by transcriptionally regulating SIRT6 in the AD model. PRMT1 silencing promoted cell senescence of VSMCs under Ang II. Further, PRMT1-mediated arginine methylation could maintain the protein stability of E2F7. PRMT1 restrained cell senescence of VSMCs via the E2F7/SIRT6 axis in the AD model. PRMT1 enhanced arginine methylation of E2F7, leading to the upregulation of SIRT6, thereby inhibiting the senescence of VSMCs in the AD model.

Downregulation of EZH2 Promotes Renal Epithelial Cellular Senescence and Kidney Aging

Renal epithelial cell senescence and kidney aging have become the focus of scientific investigation. However, how epigenetic regulation in these processes remains elusive. Enhancer of zeste homolog 2 (EZH2), a histone methyltransferase, regulates trimethylation of histone H3 at lysine 27 (H3K27me3) and plays an important role in renal pathophysiology. In this study, we show that the expression of EZH2 is decreased in naturally aged and irradiation (IR)-induced mouse kidneys, as well as in IR-induced human renal cortical tubular epithelial (RCTE) cells through proteasome-mediated degradation. Inhibition of EZH2 with its specific inhibitor 3-DZNeP promotes tubular cell senescence and kidney aging characterized by an increase in the expression of senescence markers, including p16 and p21, in mouse kidneys and in IR-induced RCTE cells. We show that EZH2 represses the transcription of p16 through trimethylation of H3K27me3, which directly binds to the promoter of p16. EZH2 represses the transcription of p21 through directly binding to the promoter of p21, and this process is involved in its interaction with p53 and its phosphorylation by ataxia-telangiectasia mutated (ATM), a critical protein involved in the cellular response to DNA damage. Inhibition of ATM with its inhibitor decreased the phosphorylation of EZH2 and the binding of EZH2 to the promoter of p21 in IR-treated RCTE cells in a p53-dependent manner. This study suggests that EZH2 plays a critical role in preventing kidney aging and DNA-damage-induced renal tubular cellular senescence, in which senescence and kidney aging also result in the destabilization of EZH2, forming a negative feedback loop.

Advancements in the study of DLK1 in the pathogenesis of diabetes

DLK1, as a membrane-bound protein, has been extensively studied in the field of cancer research. As a ligand downstream of the Notch pathway, it broadly influences developmental and metabolic processes in the body. With deeper research, it has been found that DLK1 can induce the synthesis and secretion of insulin through the ERK and AKT pathways, playing a crucial role in the development of metabolic diseases. Diabetes mellitus (DM) is a chronic metabolic disorder characterized by insufficient insulin production by the pancreas or inadequate utilization of insulin by the body. This article aims to review the relationship between DLK1 and diabetes, recent research advancements, and to discuss future research directions and challenges.

PARP-1 gene promoter region may be associated with progression in multiple sclerosis

Multiple Sclerosis (MS) is a leading cause of disability among young adults. Most cases begin with relapsing-remitting MS (RRMS) and can transition to secondary progressive MS (SPMS) over time. It is known that the inflammatory status of the central nervous system changes during the progression of MS. Poly (ADP-ribose) polymerase-1 (PARP-1) is an enzyme involved in several cellular processes. Our study aimed to investigate the relationship between MS and the PARP-1 gene. We analyzed the PARP-1 gene's missense polymorphism rs1136410, promoter region polymorphism rs7527192, and 3'UTR polymorphism rs8679 in 123 MS patients and 168 healthy controls using the PCR-RFLP method. We examined genotype and allele frequency distributions among case-control groups and clinical subgroups. We observed that the CC genotype of rs7527192 polymorphism was increased in SPMS patients compared to controls. We also found that the CC genotype and C allele frequency were increased in the EDSS score > 3-6 group compared to healthy controls. The C allele frequency was increased in EDSS score > 3-6 compared to those with ≤ 3 and ≥ 6. When the results observed in our study are evaluated with the known effect of PARP-1 on the inflammasome pathway, we suggest that rs7527192 may be effective in the progression process through the activity of the PARP-1 inflammasome pathway.

FOXG1 Improves Cognitive Function in Alzheimer's Disease by Promoting Endogenous Neurogenesis

Strategies aimed at enhancing the capacity of neural stem cells (NSCs) to generate multipotential, proliferative, and migratory cell populations capable of efficient neuronal differentiation are crucial for structural repair following neurodegenerative damage. The role of Forkhead-box gene 1 (FOXG1) in pattern formation, cell proliferation, and specification has been established. However, its involvement in Alzheimer's disease (AD) remains largely unknown. Here, we investigated the association between Foxg1 gene variants and AD-like behavioral deficits, amyloid-β (Aβ) aggregate formation, as well as p21 expression. Furthermore, we explored whether targeting the FOXG1-regulated cell cycle contributes to the promotion of adult neurogenesis in the context of AD. In this study, we successfully induced overexpression of FOXG1 in the hippocampus of AD brains through adeno-associated virus-Foxg1 infusion. Activation of FOXG1 rescued spatial learning disabilities, short-term memory deficits, and sensorimotor gating impairments observed in AD transgenic animals. By inhibiting p21 WAF1/cyclin-dependent kinase interacting protein 1 (p21cip1/waf1)-mediated cell cycle arrest, FOXG1 facilitates the activation and proliferation of NSCs. Additionally, the Foxg1 gene promotes an increase in precursor population size and enhances neuroblast differentiation. These combined effects on proliferation and differentiation lead to the generation of postmitotic neurons within the hippocampus in AD animals. Together, these findings demonstrate the importance of cooperation between FOXG1 and p21 for maintaining NSC self-renewal while facilitating neuronal lineage progression and contributing to endogenous neurogenesis during AD. Elevating levels of FOXG1 either pharmacologically or through alternative means could potentially serve as a therapeutic strategy for treating AD.

tRF-23-R9J89O9N9:A novel liquid biopsy marker for diagnosis of hepatocellular carcinoma

BACKGROUND

Non-coding small RNA, specifically tRNA-derived small RNAs (tsRNAs), are readily detectable in cancer patients, exhibit remarkable stability, and are present in high abundance. They play a significant role in tumor development. However, the clinical significance of serum tsRNAs in hepatocellular carcinoma (HCC) remains poorly understood. In this study, we explored the impact of a novel tsRNA, named tRF-23-R9J89O9N9, in the adjuvant diagnosis, disease monitoring, and prognosis assessment of HCC.

METHODS

The tRF-23-R9J89O9N9 was identified as the target molecule through screening the The Cancer Genome Atlas(TCGA) database. Its expression levels were measured using qRT-PCR. Various methods, including agarose gel electrophoresis, Sanger sequencing, gradient dilution experiments, room temperature stability tests, and repeated freeze-thaw assessments, were employed to evaluate the performance of tRF-23-R9J89O9N9. The correlation between tRF-23-R9J89O9N9 levels and clinicopathological parameters was analyzed using the χ2 test. The diagnostic value of tRF-23-R9J89O9N9 in HCC was assessed with ROC curve analysis, while the prognostic value was evaluated using Kaplan-Meier curves.

RESULTS

Serum tRF-23-R9J89O9N9 expression levels were significantly elevated in HCC patients, while levels in postoperative patients were restored to those of healthy subjects. Additionally, the expression of tRF-23-R9J89O9N9 related to TNM stage(P = 0.009), lymph node metastasis(P＜0.0001), and degree of differentiation(P＜0.0001). Furthermore, the combination of AFP, PIVKA-II, and CEA greatly improved the diagnostic value for HCC. Serum tRF-23-R9J89O9N9 was also identified as a potential biomarker for dynamic monitoring and prognosis of HCC.

CONCLUSIONS

tRF-23-R9J89O9N9 may regard as a potential novel biomarker for the adjuvant diagnosis of HCC.

KMT2D: A key emerging epigenetic regulator in head and neck diseases and tumors

Histone modifications are critical determinants of chromatin accessibility and gene expression, both of which are intrinsically linked to human development and disease. Lysine methyltransferase 2D (KMT2D), a prominent member of the H3K4 methyltransferase family, is ubiquitously expressed across human tissues. Recent studies have found that it can regulate gene expression and signal pathway opening and closing in more than one way, playing an important role in cell proliferation and cell cycle homeostasis. Although previous studies have identified KMT2D as a potentially pivotal factor in the development and pathology of head and neck tissues, the regulatory networks associated with KMT2D in various complex head and neck diseases remain incompletely elucidated. This review seeks to consolidate recent findings on KMT2D's involvement in head and neck diseases, thereby laying the groundwork for future research into its mechanistic role in disease progression. A deeper understanding of KMT2D's functions and regulatory mechanisms is essential for advancing our comprehension of histone modifications and for the development of diagnostic tools and targeted therapeutic strategies for head and neck diseases.

Zebrafish as a preclinical model for diabetes mellitus and its complications: From monogenic to gestational diabetes and beyond

With diabetes currently affecting 537 million people globally, innovative research approaches are urgently required. Zebrafish (Danio rerio) has emerged as a pivotal model organism in diabetes research, particularly valuable for developmental biology studies and preclinical therapeutic validation. Its rapid life cycle, optical transparency, and genetic tractability collectively enable efficient longitudinal observation of pathological progression and pharmacological responses. Utilizing zebrafish models, researchers have elucidated fundamental mechanisms governing islet development, β-cell dysfunction, and metabolic dysregulation. These experimental systems have significantly advanced our understanding of various diabetes subtypes, including type 1, type 2, gestational, and monogenic forms, while also facilitating mechanistic studies of diabetic complications such as retinopathy and nephropathy. Recent model refinements, particularly in simulating monogenic disorders and pregnancy-associated metabolic changes, promise to deepen our comprehension of disease pathophysiology and therapeutic interventions. Nevertheless, a persistent limitation lies in their incomplete recapitulation of human-specific physiological complexity and multi-organ metabolic interactions, factors that may influence translational applicability. Despite these constraints, zebrafish-based research continues to provide an indispensable platform for diabetes investigation, holding significant promise for alleviating the escalating global burden of this metabolic disorder.

DDX37 and DDX50 Maintain Genome Stability by Preventing Transcription-dependent R-loop Formation

R-loops consist of an RNA-DNA hybrid and a displaced single-stranded DNA strand that play a central role in several biological processes. However, as the presence of aberrant R-loops forms a significant threat to genome stability, R-loop formation and resolution is strictly controlled by RNAse H and helicases. In a screening for RNA helicases, previously described as RNA-DNA hybrid interactors, that control genome integrity, we identified for the first time DDX37 and DDX50. Depletion of DDX37 and DDX50 promotes DNA damage, as demonstrated by H2AX phosphorylation and increased comet tail length. In addition, knock down of these RNA helicases decreases the DNA replication track length and leads to RPA focus formation, results that are indicative of replication stress. Downregulation of DDX37 and DDX50 triggers an increase in RNA-DNA hybrids, that can be reverted by the overexpression of RNase H1. Interestingly, inhibition of transcription prevented the increased RNA-DNA hybrid formation and DNA damage upon DDX37 or DDX50 depletion. Together these results demonstrate that DDX37 and DDX50 are important for resolving RNA-DNA hybrids appearing during transcription and thereby preventing DNA damage by replication stress.

Aging and Lifestyle Modifications for Preventing Aging-Related Diseases

The pathogenesis of various chronic diseases is closely associated with aging. Aging of the cardiovascular system promotes the development of severe cardiovascular diseases with high mortality, including atherosclerosis, coronary heart disease, and myocardial infarction. Similarly, aging of the nervous system promotes the development of neurodegenerative diseases, such as Alzheimer's disease, which seriously impairs cognitive function. Aging of the musculoskeletal system is characterized by decreased function and mobility. The molecular basis of organ aging is cellular senescence, which involves multiple cellular and molecular mechanisms, such as impaired autophagy, metabolic imbalance, oxidative stress, and persistent inflammation. Given the ongoing demographic shift toward an aging society, strategies to delay or reduce the effects of aging have gained significance. Lifestyle modifications, such as exercise and calorie restriction, are now recognized for their anti-aging effects, their capacity to reduce modification, their potential to prolong lifespan, and their capacity to lower the risk of cardiovascular disease. This review elucidates the molecular mechanisms and application significance of various anti-aging approaches at the molecular level, based on research progress in aging. It aims to provide a reference for the prevention and treatment of age-related diseases in progressively aging societies.

Potential role of Sigma-1 receptor inhibition and ER stress-related pathways in upregulating definitive endoderm markers in human embryonic stem cells

Endoplasmic reticulum (ER) stress and unfolded protein response (UPR) participate in stem cell proliferation, differentiation, and apoptosis. Sigma-1 receptor (S1R) is a unique ER chaperon protein that regulates ER stress and UPR. Here, we examine the effects of S1R inhibition on pluripotency and differentiation of human embryonic stem cells (hESCs). hESCs were treated with different doses of an S1R inhibitor (BD 1047), and we investigated the expressions of different pluripotency and lineage-specific genes. The BD-treated hESCs showed increased SRY-box transcription factor 17 (SOX17) expression [definitive endoderm-specific protein], and reductions in NANOG expression and in the number of alkaline phosphatase (ALP)-positive colonies. In silico gene expression analysis of three datasets that contained the hESCs-derived DE samples (GSE98324, GSE63592, GSE52658) was performed to investigate the ER stress-related gene expression patterns during DE differentiation. In silico analysis revealed that UPR-related genes upregulated during DE differentiation and CCL2 was the only gene present in all three DE datasets. qRT-PCR and immunostaining showed that CCL2, eIF2A, ATF4, XBP1, GRP78, DDIT3, DNAJB9, and PDIA5 which are UPR related marker genes were all upregulated in both the BD-treated hESCs and female and male hESC-derived DE cells. The results of this study suggest possible roles for S1R, ER stress-related genes, and the CCL2 pathway during differentiation of hESCs into DE. These potential new targets may improve the efficiency of protocols used to differentiate endodermal lineages.

Effects of polystyrene microparticles exposures on spermatogenic cell differentiation and reproductive endpoints in male mice

The widespread distribution of microplastics in the environment has raised concerns about their potential implications for human health. Microplastics accumulate in animals and humans, but the risks associated with these pollutants are not fully understood. This study aimed to investigate the effects of polystyrene microplastics on the male reproductive system. The 0.1 μm polystyrene (PS) could accumulate in the testicular tissue and spermatogonia GC-1, while 1 μm PS was not easy to enter and accumulate in the testicular tissue and cells. Mice continuously exposed for 3-months to 0.1 μm PS demonstrated lower fertility and inhibited spermatogonium differentiation compared to control mice. The 0.1 μm PS were dispersed throughout the seminiferous tubule of the testis. Metabolic reprogramming was found to be involved in these processes. Histone methylation and autophagy-related pathways showed significant differences following PS treatment in testis tissue and GC-1 cells. Our findings suggest that chronic exposure to 0.1 μm PS inhibited spermatogenic cell differentiation and impaired fertility in male mice. We propose that abnormal epigenetic modifications in 0.1 μm PS exposed mice contributed to the dysregulation of glycolytic enzymes, and that the impaired autophagic pathway exacerbated the accumulation of glycolytic enzymes further. Glycolysis plays a critical role in the regulation of spermatogenic cell differentiation, and its regulation partially alleviated the impairments associated with PS exposure. In conclusion, our findings suggest that chronic exposure to nanoplastics PS inhibited spermatogenic cell differentiation and impaired fertility in male mice via disrupted epigenetic modification and metabolic dysregulation.

P.1 and P.2 SARS-CoV-2 Brazilian variants activate the unfolded protein response with a time and pathway specificity

COVID-19 is a human respiratory syndrome caused by the infection of the SARS-CoV-2 virus that has a high rate of infection and mortality. Viruses modulate the host machinery by altering cellular mechanisms that favor their replication. One of the mechanisms that viruses exploit is the protein folding and processing of post-translational modifications that occur in the endoplasmic reticulum (ER). When ER function is impaired, there is an accumulation of misfolded proteins leading to endoplasmic reticulum stress (ER stress). To maintain homeostasis, cells trigger an adaptive signaling mechanism called the Unfolded Protein Response (UPR) which helps cells deal with stress, but under severe conditions, can activate the apoptotic cell death mechanism. This study elucidated an activation of a diversity of molecular mechanisms by Brazilian variants of SARS-CoV-2 by a time-resolved and large-scale characterization of SARS-CoV-2-infected cells proteomics and immunoblotting. Furthermore, it was shown that pharmacological UPR modulation could reduce viral release by counteracting the different viral activations of its cellular response. Analysis of human clinical specimens and disease outcomes focusing on ER stress reinforces the importance of UPR modulation as a host regulatory mechanism during viral infection and could point to novel therapeutic targets. SIGNIFICANCE: Since the emergence of SARS-CoV-2 and the consequent COVID-19 pandemic, the rapid emergence of variants of this new coronavirus has been a cause for concern since many of them have significantly higher rates of transmissibility and virulence, being called Variants of Concern (VOC). In this work, we studied the VOCs Gamma (P.1) and Zeta (P.2), also known as Brazilian variants. Constant evidence has reported that there are particularities related to each variant of SARS-CoV-2, with different rates of transmissibility, replication and modulation of host biological processes being observed, in addition to the mutations present in the variants. For this reason, this work focused on infections caused by the Brazilian variants of SARS-CoV-2 in different cell lines, in which we were able to observe that the infections caused by the variants induced endoplasmic reticulum stress in the infected cells and activated the UPR pathways, presenting specific modulations of each variant in this pathway. Furthermore, transcriptome analysis of patients revealed a correlation between ER-related genes and COVID-19 progression. Finally, we observed that the use of UPR modulators in host cells decreased viral release of all variants without affecting cell viability. The data presented in this work complement the observations of other studies that aim to understand the pathogenicity of SARS-CoV-2 VOCs and possible new therapeutic strategies, mainly targeting biological processes related to the endoplasmic reticulum.

Comparative Perspectives on Neuropeptide Function and Social Isolation

Chronic social isolation alters behavior across animal species. Genetic model organisms such as mice and flies provide crucial insight into the molecular and physiological effects of social isolation on brain cells and circuits. Here, we comparatively review recent findings regarding the function of conserved neuropeptides in social isolation in mice and flies. Analogous functions of 3 classes of neuropeptides-tachykinins, cholecystokinins, and neuropeptide Y/F-in the two model organisms suggest that these molecules may be involved in modulating behavioral changes induced by social isolation across a wider range of species, including humans. Comparative approaches armed with tools to dissect neuropeptidergic function can lead to an integrated understanding of the impacts of social isolation on brain circuits and behavior.

Obesity prevention by different exercise protocols (HIIT or MICT) involves beige adipocyte recruitment and improved mitochondrial dynamics in high-fat-fed mice

AIM

This study evaluated the effects of high-intensity interval training (HIIT) and moderate-intensity continuous training (MICT) on UCP1-dependent and UCP1-independent thermogenic and mitochondrial dynamics markers in the inguinal sWAT of high-fat-fed mice.

METHODS

Sixty male C57BL/6 mice (3 months old) were divided into six experimental groups: control diet (C), C + HIIT (C-HIIT), C + MICT (C-MICT), high-fat diet (HF), HF + HIIT (HF-HIIT) and HF + MICT (HF-MICT). The diet and exercise protocols started simultaneously and lasted ten weeks.

RESULTS

HIIT and MICT prevented body mass gain and fat pad expansion, improved insulin sensitivity, and induced browning in C-fed and HF-fed animals. Chronic intake of a HF diet caused adipocyte hypertrophy with a proinflammatory adipokine profile and impaired the expression of thermogenic and mitochondrial dynamics markers. However, both exercise intensities increased anti-inflammatory adipokine concentrations and improved gene markers of mitochondrial dynamics, resulting in sustained UCP1-dependent and UCP1-independent thermogenic markers and maintenance of the beige phenotype in inguinal sWAT. The principal component analysis placed all trained groups opposite the HF group and near the C group, ensuring the effectiveness of HIIT and MICT to prevent metabolic alterations.

CONCLUSIONS

This study provides reliable evidence that, regardless of intensity, exercise is a strategy to prevent obesity by reducing body fat accumulation and inducing browning. The anti-inflammatory adipokine profile and the increased expression of UCP1-dependent and UCP1-independent thermogenic markers sustained active beige adipocytes and mitochondrial enhancement to halt metabolic disturbances due to HF-feeding in exercised mice.

Trypanosoma cruzi cell cycle progression exhibits minimal variation in histone PTMs with unique histone H4 acetylation pattern

Histones are crucial proteins in eukaryotic cells that undergo extensive posttranslational modifications (PTMs) such as methylation, acetylation, and phosphorylation, which are associated to chromatin structure, gene expression, DNA damage/repair and cell cycle. In Trypanosoma cruzi, the primary sequence of histones differs from that of other eukaryotes. Despite this, they display a vast range of PTMs, though their modulation throughout the cell cycle remains largely unexplored. In this study, we investigated the dynamic modulation of histone PTMs across G1/S, S, and G2/M phases of T. cruzi cell cycle using hydroxyurea- synchronized parasites. We applied a workflow that included histone derivatization, trypsin digestion followed by a high-resolution mass spectrometry and data independent analysis. Quantitative analysis of 141 histone peptide isoforms revealed that there are only minor variations in histone PTM levels throughout the cell cycle. The H3K76 trimethylation remained predominant throughout all phases, with an increase in monomethylation during G2/M. Additionally, hyperacetylation of the N-terminal region of histone H4 was observed, particularly at lysine residues 2, 5, and 10, suggesting their importance in cell cycle progression. Striking, acetylation of histone H4 at K2 and K5 increases during the S-phase, mirroring the H4K5acK12ac pattern observed in mammals, which are related to histone nuclear import and chromatin deposition. Overall, the results suggest that the T. cruzi cell cycle maintains stable global levels of histone PTMs, relying on variations in only a few specific PTMs. Further investigations are warranted to elucidate the functional significance of these PTMs and their impact on cell cycle regulation and chromatin dynamics in T. cruzi. SIGNIFICANCE: Histone posttranslational modifications (PTMs) are key regulators of chromatin architecture and cellular processes such as gene expression and cell cycle control. In Trypanosoma cruzi, the etiological agent of Chagas disease, histones have a distinct primary structure compared to other eukaryotes, yet they display a wide variety of PTMs. This study provides a comprehensive analysis of histone PTM dynamics across the G1/S, S, and G2/M phases of the T. cruzi cell cycle, revealing that global histone PTM levels remain largely stable, with variations in a few specific marks. Notably, the study highlights the increased acetylation of histone H4 at lysines 2 and 5 during the S-phase, contrasting with the well-conserved acetylation at lysines 5 and 12 observed in mammals involved in nuclear import and chromatin assembly. These findings underscore the evolutionary divergence and functional specificity of histone modifications and provide a foundation for further investigations into their roles in parasite biology, with potential implications for understanding chromatin dynamics and identifying novel therapeutic targets.

Regulation of autophagy: Insights into O-GlcNAc modification mechanisms

Autophagy is a "self-eating" biological process that degrades cytoplasmic contents to ensure cellular homeostasis. Its response to stimuli occurs in two stages: Within a few to several hours of exposure to a stress condition, autophagic flow rapidly increases, which is mediated by post-translational modification (PTM). Subsequently, the transcriptional program is activated and mediates the persistent autophagic response. O-linked β-N-acetylglucosamine (O-GlcNAc) modification is an inducible and dynamically cycling PTM; mounting evidence suggests that O-GlcNAc modification participates in the total autophagic process, including autophagy initiation, autophagosome formation, autophagosome-lysosome fusion, and transcriptional process. In this review, we summarize the current knowledge on the emerging role of O-GlcNAc modification in regulating autophagy-associated proteins and explain the different regulatory effects on autophagy exerted by O-GlcNAc modification.

ZLN005, a PGC-1α agonist, delays photoreceptor degeneration by enhancing mitochondrial biogenesis in a murine model of retinitis pigmentosa

Retinitis pigmentosa (RP) is a hereditary neurodegenerative disease characterized by the degeneration of photoreceptors caused by mutations in various genes. Increasing evidence suggests that mitochondrial biogenesis plays a critical role in many neurodegenerative diseases. This study investigated the role of mitochondrial biogenesis in rd1 mice, a widely recognized model of RP. Male C57BL/6 mice and age-matched rd1 mice were used for in vivo experiments, while H2O2 was employed on 661w cells to establish an in vitro model. Our findings revealed that mitochondrial biogenesis and the regulatory PGC-1α/NRF-1/TFAM pathway were significantly downregulated in rd1 mice. Treatment with ZLN005, a PGC-1α agonist, markedly improved visual function in rd1 mice and alleviated thinning of the retinal outer nuclear layer. Additionally, ZLN005 enhanced mitochondrial biogenesis and restored mitochondrial function in photoreceptors. Further analysis in vitro confirmed that ZLN005 rescued photoreceptor degeneration by promoting mitochondrial biogenesis through the PGC-1α/NRF-1/TFAM pathway. In summary, our results highlight the critical role of mitochondrial biogenesis and the PGC-1α/NRF-1/TFAM pathway in the progression of RP. This offers a potential strategy to delay photoreceptor degeneration in RP by maintaining mitochondrial function and could be combined with existing therapies for improving treatment outcomes through synergistic pathways.

Proteomics and phosphoproteomics analysis of acute pancreatitis alleviated by forsythoside B

Acute pancreatitis (AP) is a common acute abdominal condition in clinical practice, associated with high morbidity and mortality rates. Forsythia constitutes a component of traditional Chinese medicinal decoctions used for clinical AP treatment; however, the efficacy of its active monomer in treating AP has yet to be completely substantiated. Here, we engineered an AP cell and mouse model by administering a combination of caerulein and LPS. In vitro experiments utilizing AR42J cells demonstrated that forsythoside B (FST·B) was the most effective monomer in mitigating cellular inflammation. Subsequently, a comprehensive evaluation of FST·B concentrations and efficacy was performed in animal models. Next Mass spectrometry analysis of pancreatic from AP mice treated with 50 mg/kg FST·B was conducted to elucidate its primary regulatory molecular signaling and key targets. FST·B effectively mitigated pathological damage in mice with acute pancreatitis, leading to a reduction in the expression of inflammatory cytokines in both pancreatic tissue and serum. Proteomics and phosphoproteomic profiles revealed that FST·B significantly enhanced the level of oxidative phosphorylation and spliceosome pathway in the AP mice. This research provides initial evidence of the regulatory molecular signals and targets of FST·B in AP, laying a potential foundation for its clinical use in treating AP. SIGNIFICANCE: Acute pancreatitis (AP) is a common acute abdominal condition in clinical practice, associated with high morbidity and mortality rates, and the global incidence of AP has increased by approximately 25 % over the past 15 years. Despite the complexity of AP's causes and the high susceptibility of proteins to degradation during lesions, systems biology studies, such as proteomics, have been limited in investigating the molecular mechanisms involved in its pharmacological treatment. Forsythoside B, a phenylethanol glycoside isolated from the air-dried fruit of forsythia, is a traditional oriental anti-inflammatory drug commonly used in clinical practice. We demonstrated in the AP mouse model that forsythoside B can alleviate pancreatic inflammatory damage in vivo. To elucidate the molecular mechanisms underlying the anti-inflammatory effect of forsythoside B, a comprehensive proteomic and phosphoproteomic analysis was conducted on AP mice models prior to and subsequent to forsythoside B intervention. Finally, 1640 significantly differentially expressed proteins, 1448 significantly differentially expressed phosphoproteins corresponding to 2496 significantly differentially expressed phosphosites were identified. Functional analysis revealed that forsythoside B significantly enhanced the level of oxidative phosphorylation in the AP mice in proteomic profiles, and the spliceosome pathway at the phosphorylation level was significantly affected by forsythoside B. This research provides initial evidence of the regulatory molecular signals and targets of forsythoside B in AP, laying a potential foundation for its clinical use in treating AP.

Why do histone monomethylation and dimethylation cause a significant difference in binding to LEDGF?

Lens epithelium-derived growth factor (LEDGF) is a chromatin-binding protein. It regulates gene transcription and is associated with acquired immunodeficiency syndrome and cancer. Its PWWP domain binds to histone H3 at K36 (H3K36). The binding affinity depends on H3K36 methylation. To investigate this dependency, we performed molecular dynamics simulations of the PWWP domain and histone fragments. We found that not only hydrophobic interaction but also electrostatic interaction is important. The binding is not maintained with nonmethylated and monomethylated H3K36 because the tips of these H3K36s form hydrogen bonds with water molecules, while dimethylated and trimethylated H3K36 form no such hydrogen bond, making this binding stable.

Phase behavior and dissociation kinetics of lamins in a polymer model of progeria

One of the key structural proteins in the eukaryotic cell nucleus is lamin. Lamins can assemble into a two-dimensional protein meshwork at the nuclear periphery, known as the nuclear lamina, which provides rigidity and shape to the nucleus. Mutations in lamin proteins that alter the structure of the nuclear lamina underlie laminopathic diseases, including Hutchinson-Gilford Progeria Syndrome (HGPS). Experiments have shown that, compared to healthy cells, lamin supramolecular structures (e.g., protofilaments) assemble into a thicker lamina in HGPS, where they form highly stable nematic microdomains at the nuclear periphery, reminiscent of liquid crystals. This significantly alters the morphological and mechanical properties of the nucleus. In this study, we investigate the aggregation of lamin fibrous structures and their dissociation kinetics from the nuclear periphery by modeling them as coarse-grained, rod-like polymer chains confined within a rigid spherical shell. Our model reproduces the formation of multidirectional nematic domains at the nuclear surface and the reduced lamin dissociation observed in HGPS nuclei by adjusting lamin concentration, lamin-lamin (head-tail), and lamin-shell association strengths. While nematic phase formation requires relatively strong lamin-shell affinity under any non-vanishing inter-lamin attraction, the thickness of the lamina layer is primarily controlled by the head-tail association strength in the model. Furthermore, the unbinding kinetics of lamin chains from the lamina exhibit a concentration-dependent facilitated dissociation, suppressed by strong intra-lamin interactions, reminiscent of diseased nuclei. Overall, our calculations reveal the physical mechanisms by which mutations affecting native lamin interactions and concentration could lead to an abnormal nuclear lamina in laminopathic diseases.