Developmental Mechanisms of Fruit Diversification in Angiosperms and the Evolutionary Implications

The evolutionary origin of fruits played a pivotal role in promoting the dominance of angiosperms on the Earth as the fruits protect and nourish seeds and facilitate their dispersal through diverse mechanisms. Understanding the molecular networks underlying fruit development is a prerequisite for elucidating evolutionary mechanisms shaping fruit diversification, and particularly improving crop yield and quality of fruit in response to the rapid climate change in modern agricultural systems. In this article, we offer a comprehensive analysis of fruit classification, emphasising the intrinsic characteristics and their adaptive dispersal strategies in specific environments. Based on the studies in the model systems such as Arabidopsis thaliana and Solanum lycopersicum, we highlight recent advances in identifying novel components of the molecular networks involved in fruit development. We further discuss the evolutionary mechanisms that contribute to fruit diversification in the context of well-established phylogenetic frameworks, with examples from the Brassicaceae and Solanaceae families. A comparison between Brassicaceae and Solanaceae indicates the key module of fruit development is largely conserved in evolution. We propose the future research that integrates multidisciplinary evidence could help to better understand the mechanisms of fruit development and diversification, which ultimately contribute to improving crop yield and quality in practice.

Spatial Regulation of Rice Leaf Morphology by miRNA-Target Complexes During Viral Infection

Leaf morphogenesis is essential for plant growth and development, yet the mechanisms by which plant viruses induce changes in leaf shape are not well understood. Rice ragged stunt virus (RRSV) infection induces distinct morphological abnormalities in rice leaves, including leaf tip curling and serrated margins, through unknown pathogenic mechanisms. This study reveals that key regulatory microRNAs (miR164, miR319 and miR156) and their target genes (CUC, TCP and SPL) exhibit entirely opposite expression patterns in healthy and RRSV-infected leaves, indicating a profound impact on the leaf morphogenesis network. Significantly, the core protein OsCUC1, which typically functions by forming dimers, shows abnormal expression in the peripheral zone of the shoot apical meristem under viral infection, leading to disruptions in leaf development. OsTCP1 was found to dynamically regulate OsCUC1 dimer formation by modifying its subcellular localization and interacting with OsSPL14 and OsSPL17, thereby influencing their regulatory functions. Genetic disruptions of OsCUC1, OsTCP1 and OsSPL14/OsSPL17 enhance the severity of RRSV infection, demonstrating their critical involvement in the viral pathogenic strategy. The research uncovers a novel mechanism by which RRSV manipulates the expression and interactions of key regulatory factors, disrupting the delicate balance of the leaf morphogenesis network. These findings expand our understanding of viral manipulation of host development and provide a foundation for innovative strategies to enhance crop resilience.

Spexin expression in the human bile duct and perihilar cholangiocarcinoma

The bile duct transports bile fluid from the liver to the gallbladder and small intestine. It contains bioactive peptides, including galanin (GAL) and its receptors (GAL1-3-R). Spexin (SPX), a member of the GAL peptide family, activates GAL2-R and GAL3-R. Its expression in perihilar bile ducts or in perihilar cholangiocarcinoma (pCCA), the most common biliary cancer, is largely unknown. This study investigated SPX expression in healthy, cholestatic, and malignant bile duct tissues. Immunohistochemistry was used to evaluate SPX in healthy (n = 4), peritumoral (PIT) (n = 23) and pCCA (n = 34) tissues. Score values of SPX expression were calculated and statistically analyzed. In healthy and PIT tissues with or without cholestasis, SPX expression was predominantly observed in cholangiocytes and nerve fibers. In pCCA, tumor cells also expressed SPX. SPX levels were similar across healthy, peritumoral, and cholangiocytes/tumor cells. In a small pCCA patient cohort (n = 19), SPX expression did not correlate with tumor grade or patient survival (p = 0.0838). The substantial expression of SPX in cholangiocytes and nerve fibers in the bile duct indicates that SPX contributes via galaninergic signaling to gall bladder function. The presence of SPX in submucosal nerve fibers suggests a neuromodulatory role, possibly involving bile duct motility. SPX expression did not correlate with survival in pCCA, whereas previous findings on GAL suggest a prognostic value. This highlights the need for joint studies of SPX and GAL in larger cohorts.

Investigating the enhancement of neural differentiation of adipose-derived mesenchymal stem cell with Foeniculum vulgare nanoemulsions: An in vitro research

BACKGROUND

Neurons, distributed throughout the body, regulate various bodily functions. The recovery of the nervous system is often slow and can be irreversible. Currently, the approach of using mesenchymal stem cells (MSCs) in conjunction with conventional treatments for nervous system injuries is being explored. Nanoemulsions are systems designed for the nanoscale delivery of drug cargoes. Foeniculum vulgare (F. vulgare), a medicinal plant long utilized in complementary medicine, is the focus of this study. The aim is to utilize nanoemulsions of fennel to induce the differentiation of MSCs into neural-like cells in vitro.

MATERIALS AND METHODS

Human adipose-derived mesenchymal stem cells (hADSCs) were commercially purchased. These cells were cultured in DMEM medium containing 10 % fetal bovine serum and 1 % penicillin-streptomycin antibiotic. Based on a sequential extraction method, n-hexane (Hex), ethyl acetate (EtAc), and ethanolic extracts were obtained from the seeds of F. vulgare. To prepare the F. vulgare extract nanoemulsion, the aqueous phase (distilled water), the oily part (F. vulgare extract), Span 80 and Tween 20 were used. The optimal dose of F. vulgare nanoemulsion was determined using the MTT assay and acridine orange/ethidium bromide (AO/EB) staining. Neural differentiation was induced using a specialized differentiation medium on the MSCs, with the prepared nanoemulsions acting as inducers. The neural differentiation of the human differentiated hADSCs was studied and evaluated through Real-time PCR and immunocytochemistry (ICC) techniques on days 7 and 14.

RESULTS

The results obtained from the MTT and AO/EB tests indicated that the optimal dose of F. vulgare nanoemulsions is 1 μg/ml. Analysis of neural differentiation index gene expression revealed a significant (P ≤ 0.05) upregulation of MAP-2, β-tubulin III, and NSE genes on days 7 and 14 following treatment with the nanoemulsions. It is noteworthy that the nanoemulsion prepared from the hexane extract of the plant showed a significant increase in the expression of marker genes in the process of neural differentiation. Protein expression analysis demonstrated an increase in MAP-2, β-tubulin III, and NSE (gamma enolase) proteins in response to the nanoemulsion inducers compared to the control group (TCPS).

DISCUSSION

Overall, our findings indicate that F. vulgare nanoemulsions have a positive effect on the expression of genes and proteins related to neural differentiation in hADSCs. The proposed protocol may serve as a potential therapeutic strategy in complementary medicine for patients seeking to improve injuries to the nervous system. However, further studies and performance measurements are necessary in future research to confirm these results.

Novel high throughput 3D ECM remodeling assay identifies MEK as key driver of fibrotic fibroblast activity

In fibrotic tissues, activated fibroblasts remodel the collagen-rich extracellular matrix (ECM). Intervening with this process represents a candidate therapeutic strategy to attenuate disease progression. Models that generate quantitative data on 3D fibroblast-mediated ECM remodeling with the reproducibility and throughput needed for drug testing are lacking. Here, we develop a model that fits this purpose and produces combined quantitative information on drug efficacy and cytotoxicity. We use microinjection robotics to design patterns of fibrillar collagen-embedded fibroblast clusters and apply automated microscopy and image analysis to quantify ECM remodeling between-, and cell viability within clusters of TGFβ-activated primary human skin or lung fibroblasts. We apply this assay to compound screening and reveal actionable targets to suppress fibrotic ECM remodeling. Strikingly, we find that after an initial phase of fibroblast activation by TGFβ, canonical TGFβ signaling is dispensable and, instead, non-canonical activation of MEK-ERK signaling drives ECM remodeling. Moreover, we reveal that higher concentrations of two TGFβ receptor inhibitors while blocking canonical TGFβ signaling, in fact stimulate this MEK-mediated profibrotic ECM remodeling activity.

Analysis of gonadal transcriptome reveals core long non-coding RNA-mRNA regulatory network in sea cucumber Apostichopus japonicus

Apostichopus japonicus is a representative temperate sea cucumber species, that mainly inhabits in coastal zone of the continental shelf. With high nutritional value and important medical value, A. japonicus become an important commercial aquaculture species and produce significant economic value in recent years. A. japonicus has no sexual dimorphism that can be used to distinguish female and male individuals by external appearance and morphology. The phenotype sex can be only detected by dissecting and observing gonad tissue, thus the breeding efficiency could be greatly reduced. This limitation has hindered the advancement of selective breeding programs and sea cucumber industry. To investigate the genetic basis of reproductive biology in A. japonicus, advanced sequencing techniques, such as next- and third-generation sequencing, have been employed to explore the roles of non-coding RNAs and other genetic factors, offering new insights into sex determination mechanisms. To further gain a deeper understanding of the knowledge underlying lncRNAs in gonadal differentiation, we conducted a comparative transcriptome sequencing analysis of gonadal tissues from both sexes. In our research, a total of 3990 novel lncRNAs and 1441 differentially expressed lncRNAs were identified between female and male gonads. Additionally, a molecular regulatory network indicating lncRNA-mRNA interactions was constructed based on transcriptional profiles, which provide insights into the potential cis- and trans- target genes of lncRNAs. The gonadal transcriptome analysis identified a number of novel long non-coding RNAs involved in female and male reproduction process. Both cis- and trans-acting regulatory networks indicating lncRNA-mRNA interaction were constructed based on transcriptional profiles. These findings provide new insights into the lncRNA-mediated regulation of reproductive biology in marine invertebrates, indicating the crucial roles of long non-coding sequences in regulating expression profiles. Further, the GO and KEGG enrichment analyses of cis- and trans- targeted mRNA for differentially expressed lncRNA indicated that sexual reproduction (GO:0019953), germ cell development (GO:0007281), and negative regulation of hormone secretion (GO:0046888) are potentially involved in gonadal differentiation through the regulation of long non-coding sequences. Notably, besides the classical reproduction related signaling pathway like Gonadotropin-releasing hormone (GnRH) secretion (ko04929), several regulatory pathways, such as Epidermal growth factor receptor (ErbB) signaling pathway (ko04012), TGF-beta signaling pathway (ko04350), and neurotrophin signaling pathway (ko04722) were also enriched and potentially involved in sex differentiation and gonadal development.

DAF-18/PTEN protects LIN-35/Rb from CLP-1/CAPN-mediated cleavage to promote starvation resistance

Starvation resistance is a fundamental trait with profound influence on fitness and disease risk. DAF-18, the Caenorhabditis elegans ortholog of the tumor suppressor PTEN, promotes starvation resistance. PTEN is a dual phosphatase, and DAF-18 promotes starvation resistance as a lipid phosphatase by antagonizing insulin/IGF and PI3K signaling, activating the tumor suppressor DAF-16/FoxO. However, if or how DAF-18/PTEN protein-phosphatase activity promotes starvation resistance is unknown. Using genetic, genomic, bioinformatic, and biochemical approaches, we identified the C. elegans retinoblastoma/RB protein homolog, LIN-35/Rb, as a critical mediator of the effect of DAF-18/PTEN on starvation resistance. We show that DAF-18/PTEN protects LIN-35/Rb from cleavage by the μ-Calpain homolog CLP-1/CAPN, and that LIN-35/Rb together with the repressive DREAM complex promotes starvation resistance. We conclude that the tumor suppressors DAF-18/PTEN and LIN-35/Rb function in a linear pathway, with LIN-35/Rb and the rest of the DREAM complex functioning as a transcriptional effector of DAF-18/PTEN protein-phosphatase activity resulting in repression of germline gene expression. This work is significant for revealing a network of tumor suppressors that promote survival during cellular and developmental quiescence.

Fibroblasts fluctuating between mesenchyme and epithelium are involved in hair follicle mesenchyme development

The transition between the mesenchyme and epithelium contributes to the development of various tissues. During skin development, epithelial-mesenchymal transition in the ectodermal epithelia is involved in the development of the dermal mesenchyme in early embryos. However, the precise roles and functions of epithelial-mesenchymal/mesenchymal-epithelial transition in cutaneous development have not been fully elucidated. In this study, we aimed to elucidate these roles and functions in the neonatal mouse skin. We conducted single-cell RNA sequencing and immunohistochemical analyses to search for Pdgfra-expressing (Pα +) fibroblasts with transition activities to/from Krt5-expressing keratinocytes. We determined that the Pα +/Krt5-lineage (K5 lin+) fibroblasts significantly contributed to developing hair follicle dermal stem cells to generate lower dermal papilla cells and lower dermal sheath cells. In the developing mouse skin, K5 lin + fibroblasts appeared concurrently with hair follicle development and formed outer edge cells in the early dermal papilla on embryonic day 16.5. K5 lin + hair follicle mesenchymal cells were also maintained in aged mouse skin. These results provide insights into the role and function of the transition between the mesenchyme and epithelium in hair follicle development and maintenance.

Oxidative stress and central metabolism pathways impact epigenetic modulation in inflammation and immune response

Oxidative stress, metabolism, and epigenetics are deeply interconnected processes that collectively influence cellular function, health status, and contribute to disease progression. This review highlights the critical role of metabolic intermediates in epigenetic regulation, focusing on lactate, glutathione (GSH), and S-adenosylmethionine (SAM). Beyond its traditional role in energy metabolism, lactate modulates epigenetic mechanisms, influencing gene expression and cellular adaptation. Meanwhile, GSH and SAM serve as key regulators of DNA methylation and histone post-translational modifications, maintaining epigenetic homeostasis. These processes are tightly controlled by redox balance and oxidative stress, underscoring the intricate interplay between metabolism and epigenetic regulation. GSH depletion disrupts methylation homeostasis, while oxidative post-translational modifications (oxPTMs) on histones-including S-glutathionylation, carbonylation, and nitrosylation-alter chromatin architecture and transcriptional regulation. Additionally, we focus on histone lactylation, particularly its role in regulating innate and adaptive immune responses. We also explore how GSH and oxidative stress influence lactate levels, potentially inducing histone lactylation or S-glutathionylation through S,D-lactoylglutathione (LGSH), thereby impacting epigenetic regulation. By integrating insights into metabolic-epigenetic crosstalk, this review underscores the role of oxidative stress and central metabolic pathways in regulating epigenetic mechanisms, a concept known as "redox epigenetics." Understanding these intricate interactions offers new perspectives for therapeutic strategies aimed at restoring redox homeostasis and metabolic integrity to counteract disturbances in the epigenetic landscape.

Effects of CDC45 mutations on DNA replication and genome stability

Cdc45 is a non-catalytic subunit of the CMG helicase complex that is recruited to the autonomously replicating sequence at the onset of DNA replication. The Cdc45 protein is required for the initiation of DNA replication as well as for nascent DNA strand synthesis. It interacts with Mcm2 and Psf1 elements of CMG helicase, as well as with Sld3, an initiation factor, and Pol2, the catalytic subunit of DNA polymerase epsilon (Pol ε). In this study, we analyzed the effects of amino acid substitutions in the Cdc45 region involved in the interaction of this protein with Mcm2-7 (Cdc45-1), Psf1 (Cdc45-26), and Sld3 (Cdc45-25, Cdc45-35). We found that mutations in CDC45 resulted in defective DNA replication. Under permissive conditions, delayed DNA synthesis was observed. At restrictive temperatures, the mutant cells were unable to efficiently replicate DNA. However, after the initiation of DNA replication under permissive conditions, the four analyzed CDC45 mutants exhibited DNA synthesis under the restrictive conditions. Moreover, we observed increased mutation rates, mainly dependent on DNA polymerase zeta (Pol ζ), as well as increased incidence of replication errors. These findings confirm the essential function of Cdc45 in DNA replication initiation and demonstrate that impaired Cdc45 subunit has an impact on the fidelity of the nascent DNA strand synthesis. The changes in cell function observed in this study, related to defects in Cdc45 function, may help understand some diseases associated with CDC45.

From embryos to condensates: A developmental biologist's journey

I am the Huntington Sheldon Professor of Medical Discovery in the Department of Molecular Biology and Genetics in the School of Medicine at the Johns Hopkins University, where I have been running a lab for 30 years. Our research focusses on the molecular control of embryonic polarity and germline development, with an emphasis on asymmetric cell division and biomolecular condensates. We have uncovered mechanisms that localize proteins and RNAs in the cytoplasm by controlling protein diffusion and RNA condensation. My lab has also characterized a repressive program that launches the germline by inhibiting somatic gene expression in germline progenitors.

Effect of deubiquitinases in head and neck squamous cell carcinoma (Review)

HNSCC includes nasopharyngeal, laryngeal and oral cancers, and its pathogenesis is influenced by various factors. As an essential part of the ubiquitin (Ub)-proteasome system (UPS), deubiquitinating enzymes (DUBs) maintain the homeostasis of Ub molecules and influence the physiological functions of cells and disease processes by removing ubiquitinated proteins. Accumulating evidence has confirmed that the aberrant expression of DUBs is involved in cell proliferation, metastasis, and apoptosis during the development of HNSCC, with some acting as oncogenes and others as tumor-suppressor genes. In this review, the DUBs implicated in HNSCC were summarized and the mechanisms underlying abnormal DUBs expression in signaling pathways were discussed. In addition, given the important role of DUBs in tumorigenesis, recent studies were reviewed and agonists and inhibitors of DUBs were summarized to identify more effective therapeutic strategies.

Detecting ribosome collisions with differential rRNA fragment analysis in ribosome profiling data

It has become clear in recent years that ribosomes regularly stall during translation. Such translation impairment has many causes, including exposure to ribotoxic stress agents, the presence of specific RNA structures or sequences, or a shortage of amino acids or translation factors. If they are not resolved, stalled ribosomes can lead to ribosome collisions that are continuously surveilled by various sensor proteins. This in turn initiates a cascade of signalling events that can change the physiology and behaviour of cells. However, measuring changes in collision abundance has proved challenging, and as a result, the importance of collision-mediated biological responses is still unclear. Here, we show that computational analyses of standard ribosome profiling (Ribo-seq) data enable the prediction of changes in ribosome collisions between conditions. This is achieved by using the known 3D structure of collided ribosomes to define the ribosomal RNA (rRNA) positions that are differentially digested by RNases during the Ribo-seq protocol. Comparison of the relative rRNA reads at these positions allows the relative quantification of collisions between samples, an approach we call differential ribosome collisions by Analysis of rRNA Fragments (dricARF). When applied to public datasets across multiple organisms, our approach detects changes in collision events with unprecedented accuracy and sensitivity. In addition to providing supplementary evidence for ribosome collisions, our tool has the potential to uncover novel biological processes that are mediated by them. dricARF is available as part of the ARF R package and can be accessed through https://github.com/fallerlab/ARF.

Interactions between radiotherapy resistance mechanisms and the tumor microenvironment

BACKGROUND

Resistance to radiotherapy (RT) presents a significant clinical challenge in management of cancer. Recent evidence points to specific mechanisms of resistance within the tumor microenvironment (TME), which we aim to discuss, with the aim of overcoming the clinical challenge.

METHODS

We performed the narrative review using PubMed and Web of Science databases to identify studies that reported the regulative network and treatments of RT resistance from TME perspectives.

RESULTS

RT significantly changes the immune TME of cancers, which is closely appearing to play a key role in RT resistance (RTR) by modulating immune cell infiltration and function. Various phenotypes are involved in the development of RTR, such as autophagy, senescence, oxidative stress, cell polarization, ceramide metabolism, and angiogenesis in the TME. Key genes and pathways are also implicated in RTR, including immune and inflammatory cytokines, TGF-β, P53, the NF-κB pathway, the cGAS/STING pathway, the ERK and AKT pathway, and the STAT pathway. Based on the mechanism of RTR in the TME, many proposed routes to overcome RTR, several specifically target the TME including targeting fibroblast activation protein, exosomes management, nanomedicine, and immunotherapy. Many challenges in RT resistance still need to be further explored with emerging investigative methods, such as artificial intelligence, genetic technologies, and bioengineering.

CONCLUSIONS

The complex interactions between RT and TME significantly affect the efficiency of RT. Novel approaches to overcome this clinical difficulty are promising, which needs future work to further explore and identify better treatment strategies.

A biochemical screening platform to target chromatin states using condensates as a tool

Chromatin states define cell fates and consequently dysfunctional chromatin states drive disease. Conventional approaches to target dysfunctional chromatin states typically rely on targeting a defined, structured binding pocket of a specific chromatin protein. However, drugs developed from targeting single chromatin proteins have often failed in the clinic due to toxicity from broad non-specific effects on the genome. Substantial previous work has indicated that the function of a given chromatin state is encoded in the context-dependent protein-protein interactions (PPIs) between the Intrinsically disordered regions (IDRs) and folded domains of the multiple constituents. Currently, there are no drug discovery approaches that target the complex multivalent protein interactions within a given dysfunctional chromatin state. Therefore, new methods are required to target chromatin within specific conformational contexts for better translation into humans. Prior discoveries from our group and others have shown that chromatin intrinsically forms condensates through weak, yet specific, multivalent interactions between itself and other components. Using this intrinsic property of chromatin, we have developed a new screening method to address this technology gap and identify modulators of dysfunctional chromatin states for drug discovery. Here, we show that we can recreate different chromatin contexts as phase-separated condensates that have distinct biochemical and biophysical properties. Furthermore, we have scaled the technology into a screening platform and identify small molecules that modulate chromatin states specifically based on their chromatin context. We anticipate that such specific targeting of a disease driving chromatin assembly would reduce off-target effects, translate better into humans and open a new landscape of therapeutic possibilities for targeting complex, multivalent interactions.

Immunosenescence in skeletal muscle: The role-play in cancer cachexia chessboard

With the increase in life expectancy, age-related conditions and diseases have become a widespread and relevant social burden. Among these, immunosenescence and cancer cachexia play a significant often intertwined role. Immunosenescence is the progressive aging decline of both the innate and adaptive immune systems leading to increased infection susceptibility, poor vaccination efficacy, autoimmune disease, and malignancies. Cancer cachexia affects elderly patients with cancer causing severe weight loss, muscle wasting, inflammation, and reduced response to therapies. Whereas the connections between immunosenescence and cancer cachexia have been raising attention, the molecular mechanisms still need to be completely elucidated. This review aims at providing the current knowledge about the interplay between immunosenescence, skeletal muscle, and cancer cachexia, analyzing the molecular pathways known so far to be involved. Finally, we highlight potential therapeutic strategies suited for elderly population aimed to block immunosenescence and to preserve muscle mass in cachexia, also presenting the analysis of the current state-of-the-art of related clinical trials.

Bud, branch, breathe! Building a mammalian lung over space and time

Many mammalian organs, such as the mammary and lachrymal glands, kidney and lungs develop by the process known as branching morphogenesis. An essential feature of this process is the reciprocal interaction between the inner branched tubular epithelium and the surrounding mesenchyme to optimize the final amount of epithelial tissue that is generated for specific functions. To achieve this expansion the initial epithelial population undergoes repeated rounds of bud formation, branch outgrowth and tip bifurcations, with each repertoire requiring dynamic changes in cell behavior. The process of branching morphogenesis was first studied experimentally by Grobstein and others who showed that the embryonic epithelium did not develop without so-called inductive signals from the mesenchyme. However, it was not known whether this activity was uniformly distributed throughout the mesoderm or localized to specific regions. The mouse lung was seen as a powerful system in which to investigate such questions since its early branching is highly stereotypic, both in vivo and in culture. This advantage was exploited by two young scientists, Alescio and Cassini, who used grafting techniques with explanted embryonic mouse lungs. They showed that mesenchyme from around distal buds could induce ectopic buds in the trachea and other non-branching regions of the epithelium. At the same time, distal regions denuded of their mesoderm failed to develop further. They speculated that inductive factors that promote bud formation and continued outgrowth in competent endoderm are specifically localized within the distal mesenchyme, establishing a conceptual framework for future experimentation. Since then, advances in many areas of biology and bioengineering have enabled the identification of gene regulatory networks, signaling pathways and biomechanical properties that mediate lung branching morphogenesis. However, a quantitative model of how these parameters are coordinated over space and time to control the pattern and scale of branching and the overall size of the lung, still remains elusive.

Engineering colloidal systems for cell manipulation, delivery, and tracking

Men-made colloidal systems are widely presented across various aspects of biomedical science. There is a strong demand for engineering colloids to tailor their functions and properties to meet the requirements of biological and medical tasks. These requirements are not only related to size, shape, capacity to carry bioactive compounds as drug delivery systems, and the ability to navigate via chemical and physical targeting. Today, the more challenging aspects of colloid design are how the colloidal particles interact with biological cells, undergo internalization by cells, how they reside in the cell interior, and whether we can explore cells with colloids, intervene with biochemical processes, and alter cell functionality. Cell tracking, exploitation of cells as natural transporters of internalized colloidal carriers loaded with drugs, and exploring physical methods as external triggers of cell functions are ongoing topics in the research agenda. In this review, we summarize recent advances in these areas, focusing on how colloidal particles interact and are taken up by mesenchymal stem cells, dendritic cells, neurons, macrophages, neutrophils and lymphocytes, red blood cells, and platelets. The engineering of colloidal vesicles with cell membrane fragments and exosomes facilitates their application. The perspectives of different approaches in colloid design, their limitations, and obstacles on the biological side are discussed.

α‑ketoglutarate protects against septic cardiomyopathy by improving mitochondrial mitophagy and fission

Septic cardiomyopathy is a considerable complication in sepsis, which has high mortality rates and an incompletely understood pathophysiology, which hinders the development of effective treatments. α‑ketoglutarate (AKG), a component of the tricarboxylic acid cycle, serves a role in cellular metabolic regulation. The present study delved into the therapeutic potential and underlying mechanisms of AKG in ameliorating septic cardiomyopathy. A mouse model of sepsis was generated and treated with AKG via the drinking water. Cardiac function was assessed using echocardiography, while the mitochondrial ultrastructure was examined using transmission electron microscopy. Additionally, in vitro, rat neonatal ventricular myocytes were treated with lipopolysaccharide (LPS) as a model of sepsis and then treated with AKG. Mitochondrial function was evaluated via ATP production and Seahorse assays. Additionally, the levels of reactive oxygen species were determined using dihydroethidium and chloromethyl derivative CM‑H2DCFDA staining, apoptosis was assessed using a TUNEL assay, and the expression levels of mitochondria‑associated proteins were analyzed by western blotting. Mice subjected to LPS treatment exhibited compromised cardiac function, reflected by elevated levels of atrial natriuretic peptide, B‑type natriuretic peptide and β‑myosin heavy chain. These mice also exhibited pronounced mitochondrial morphological disruptions and dysfunction in myocardial tissues; treatment with AKG ameliorated these changes. AKG restored cardiac function, reduced mitochondrial damage and corrected mitochondrial dysfunction. This was achieved primarily through increasing mitophagy and mitochondrial fission. In vitro, AKG reversed LPS‑induced cardiomyocyte apoptosis and dysregulation of mitochondrial energy metabolism by increasing mitophagy and fission. These results revealed that AKG administration mitigated cardiac dysfunction in septic cardiomyopathy by promoting the clearance of damaged mitochondria by increasing mitophagy and fission, underscoring its therapeutic potential in this context.

Cross-taxa extrapolation: Is there a role for thyroid hormone conjugating liver enzymes during amphibian metamorphosis?

Chemical safety assessment includes evaluating the potential to disrupt the endocrine system in humans and wildlife. The thyroid hormone system shows high complexity which is conserved across vertebrates, allowing biological read-across between regulatory important taxa, namely mammals and amphibians. Potential thyroid disruption in aquatic vertebrates is typically investigated by activity assays (Amphibian Metamorphosis Assay (AMA), Xenopus Eleutheroembryo Thyroid Assay). Since neither assay is designed to provide detailed mechanistic information, mode of action analyses often rely on mammalian data, assuming overall cross-vertebrate conservation. This manuscript elaborates on the imperative that, despite overall conservation, the T-modality in metamorphosing amphibians needs to be understood in detail to justify biological read-across between mammals and amphibians. To this end, we revisit the AMA regarding amphibian developmental physiology, and the T-modality regarding mechanistic cross-vertebrate conservation. The importance of a mechanistic understanding for read-across is showcased based on the AMA's apparent insensitivity to at least one category of prototypical liver enzyme inducers. From a regulatory perspective, deeper mechanistic understanding is needed, not only to strengthen the scientific basis for designing testing strategies and interpreting study results, but also to allow the identification of data gaps and thus development of New Approach Methodologies (NAMs) to minimize vertebrate testing.

Loss of non-muscle myosin II Zipper leads to apoptosis-induced compensatory proliferation in Drosophila

Drosophila Non-muscle myosin II Zipper (Zip) belongs to a functionally divergent class of molecular motors that play a vital role in various cellular processes including cell adhesion, cell migration, cell protrusion, and maintenance of polarity via its cross-linking property with actin. To further determine its role in cell proliferation and apoptosis, we carried out Zip loss of function studies that led to compromised epithelial integrity in Drosophila wing imaginal discs as evident from the perturbed expression pattern of cell-cell junction proteins Cadherin, Actin, and Armadillo. Disruption of these adhesion proteins resulted in the cells undergoing apoptosis as evident from the increased level of effector caspase, cDcp-1. The induction of cell death due to the loss of function of Zip was accompanied by proliferation as apparent from increased PH3 staining. The control of apoptosis-induced compensatory proliferation lies under the caspase cascade. We carried out experiments that suggested that the apical caspase Dronc is responsible for the apoptosis-induced compensatory proliferation due to the loss of Zip function and not the effector caspase Drice/Dcp-1. Further, it was observed that Dronc leads to the subsequent activation of Jun N-terminal kinase pathway (JNK) pathway and Wingless (Wg) mitogen that diffuse to the neighboring cells and prompt them to undergo cell division. Taken together, our results suggest that loss of function of Zip leads to apoptosis-induced compensatory proliferation.

POLR1F promotes proliferation and stemness of anaplastic thyroid cancer by activating F2R/p38 MAPK signaling

Anaplastic thyroid cancer (ATC) is one of the most aggressive cancers characterized by a rapid growth rate. Dysregulation of RNA polymerase (Pol) is critical for cancer development. However, little is known about its role and mechanism in ATC. In the present study, the expression of Pol family members is screened in a large-cohort proteome containing 113 ATCs and 20 normal thyroid samples. Combined with the mRNA levels and gene dependency scores, we find that RNA Polymerase I Subunit F (POLR1F) is significantly upregulated in ATC tissues with the strongest gene effect among the Pol family members. The results are confirmed in ATC tissues and cell lines, revealing that POLR1F mainly locates in the nucleus and expresses stronger than that in normal thyrocytes. Silencing POLR1F in ATC cell lines significantly inhibit cell proliferation, colony formation, and sphere sizes. POLR1F knockdown dramatically reduces ATC tumor growth in both zebrafish and nude mouse xenograft models. RNA sequencing reveals that the coagulation factor thrombin receptor (F2R) is a downstream target of POLR1F, which participates in the p38 MAPK pathway. POLR1F promotes the H3K4 methylation at the F2R promoter by reducing the binding of demethylase KDM5C to H3K4me3, thereby enhancing F2R transcription. These results demonstrate that POLR1F maintains ATC stemness and growth by activating F2R/p38 MAPK signaling, shedding light on the essential role of POLR1F in ATC progression.

The clinical-grade CBP/ p300 inhibitor CCS1477 represses the global NRF2-dependent cytoprotective transcription program and re-sensitizes cancer cells to chemotherapeutic drugs

Constitutive activation of NRF2 provides a selective advantage to malignant tumour clones through the hijacking of the NRF2-dependent cytoprotective transcriptional program, which allows the cancer cells to survive and thrive in the chemically stressful tumour niche, whilst also providing resistance to anti-cancer drugs due to the upregulation of xenobiotic metabolizing enzymes and drug efflux pumps. Through a small-molecule epigenetic screen carried out in KEAP1 mutant lung cancer cells, in this study, we identified CCS1477 (Inobrodib) to be an inhibitor of the global NRF2-dependent transcription program. Mechanistically, CCS1477 is able to repress NRF2's cytoprotective response through the inhibition of its obligate transcriptional activator partner CBP/p300. Importantly, in addition to repressing NRF2-dependent anti-oxidative stress and xenobiotic metabolizing enzyme gene expression, CCS1477 treatment is also able to reverse the chemoresistance phenotype and re-sensitize NRF2-activated tumour cells to anti-cancer drugs. Furthermore, in co-culture experiments of KEAP1 mutant cancer cells with primary human T cells, CCS1477 treatment suppressed the acquisition of the T cell exhaustion transcriptional state, which should function to augment the anti-cancer immune response. Thus, CCS1477-mediated inhibition of CBP/p300 represents a novel therapeutic strategy with which to target the currently untreatable tumours with aberrant NRF2 activation.

Non-canonical Wnt co-receptors ROR1/ROR2 are differentially regulated by hypoxia in colon cancer cells

ROR1 and ROR2 co-receptors are transducers of non-canonical Wnt responses that promote an aggressive phenotype in several cancer types, including colon cancer. It has been demonstrated that hypoxia promotes tumor progression through the action of Hypoxia Inducible Factors (HIFs). An in silico analysis revealed that ROR2 is overexpressed in the advanced clinical stages of colon cancer. In line with this, ROR1 and ROR2 were found to be only expressed in malignant colon cells compared to non-malignant ones. The blockade of either ROR1 or ROR2 impaired colon cancer cells' colony formation abilities and the migration capacity of them. Additionally, the silencing of the ROR2 co-receptor blocked the metastatic ability of colon cancer cells in a xenografted mice model. We found that while silencing HIF-1α did not significantly reduce ROR1 or ROR2 expression, inhibiting HIF-2α and HIF-3α expression greatly decreased the protein levels of both co-receptors in colon cancer cells. The HIF-1α subunit expression is induced in acute hypoxia, whereas HIF-2α and HIF-3α show higher activity in chronic hypoxia, which may be functionally relevant since hypoxia induced a decrease in the constitutive active β-catenin transcriptional activity in SW480 cells. While both ROR1 and ROR2 stimulate proliferation and migration under normoxic conditions, the exposure of cells to hypoxia increased the expression of ROR1 or ROR2, depending on the Wnt cellular context, Thus, our results indicate that hypoxia partially represses β-catenin transcriptional activity and activates non-canonical Wnt signaling by regulating ROR1/ROR2 expression to induce an aggressive migrating and metastatic phenotype in colon cancer cells.

Browning of inguinal white adipose tissue by the novel lignan (-)-secoisolariciresinol 4-O-methyl ether attenuates diet-induced obesity through mitochondrial and peroxisomal activation

Studies indicate that the induction and activation of brown and beige adipocytes, which can enhance energy expenditure, may be beneficial for managing obesity and its associated diseases. This study investigated whether a novel lignan (-)-secoisolariciresinol 4-O-methyl ether (S4M) obtained from arctigenin inhibited diet-induced obesity by the browning of white adipose tissue (WAT). S4M treatment inhibited adipogenesis and lipid accumulation in white-induced 3T3-L1 adipocytes and in zebrafish embryonic development. Moreover, S4M treatment promoted browning in white adipocytes by increasing TOM20, UCP1, and PGC1α protein levels and consequently upregulating the mitochondrial content. S4M treatment significantly promoted mitochondrial fission by increasing the expression of DRP1. Furthermore, it enhanced peroxisomal biogenesis and function by inducing PEX13, ACOX1, and catalase. Mdivi-1, a mitochondrial dynamics inhibitor, diminished the browning effect of white adipocytes by the S4M treatment. This study found that S4M treatment inhibited weight gain in high-fat diet-induced obese mice, decreased the weight of WAT, and increased the abundance and function of mitochondria and peroxisomes in inguinal WAT, suggesting that S4M treatment could increase energy expenditure. The results suggest that S4M has potential as a therapeutic agent for combating obesity and its associated metabolic disorders.

Genome-wide identification and expression analysis of the SIRT gene family in Nile tilapia (Oreochromis niloticus)

The sirtuin (SIRT) family is a nicotine adenine dinucleotide (NAD+)-dependent class III histone deacetylase, which is widely involved in numerous physiological processes of organisms, such as metabolism, reproduction, and immunity. Here, based on the genomics database, comprehensive analysis of the SIRT gene in Nile tilapia (Oreochromis niloticus) was analyzed using bioinformatics methods and quantitative real-time PCR. The nine SIRT genes of O. niloticus (OnSIRT) were distributed on eight chromosomes. The OnSIRTs contain distinct sequences from 3 exons in OnSIRT4 to 16 exons in OnSIRT2, however, they share conserved domains and protein motifs. Phylogenetic analysis shows that the OnSIRTs belong to four subfamilies and are highly conserved in teleosts, and evolution is characterized primarily by purification selection. The OnSIRT genes showed diversified expression patterns in fourteen tissues of O. niloticus. OnSIRT2, OnSIRT3, OnSIRT3.2, OnSIRT6, and OnSIRT7 are mainly expressed in the gonads, especially in the ovary. OnSIRT1 and OnSIRT4 are mainly expressed in the kidney. OnSIRT5a is mainly expressed in the stomach, however, OnSIRT5b is mainly expressed in the liver and spleen. The results of this study provide a basis information for further exploration of the function and molecular mechanism of the SIRT gene family in teleosts.

Rooted in Communication: Exploring Auxin-Salicylic Acid Nexus in Root Growth and Development

Plant hormones are pivotal in orchestrating diverse aspects of growth and developmental processes. Among various phytohormones, auxin and salicylic acid (SA) stand out as important regulators, often exerting opposing effects on overall plant growth. Essentially, research has indicated that auxin and SA-mediated pathways exhibit mutual antagonism during pathogen challenge. Additionally, in recent years, significant advancements have been made in uncovering the molecular intricacies that govern the action and interplay between these two phytohormones during various essential growth-related processes. In this discussion, we briefly delve into the genetic and molecular mechanisms involved in auxin and SA antagonism. We then analyse in detail how this dialogue impacts critical aspects of root development, with an emphasis on the transcriptional and protein regulatory networks. Finally, we propose the potential of exploring their interaction in various other aspects of below ground root growth processes. Understanding this relationship could provide valuable insights for optimizing and enhancing crop growth and yields.

Role of Atg3, Atg5 and Atg12 in the crosstalk between apoptosis and autophagy in the posterior silk gland of Bombyx mori

Autophagy is a cellular mechanism that enhances cell survival in response to various stressors, including nutrient deprivation; however, it also plays a pivotal role in the regulation of programmed cell death. This study examined the effects of autophagy-related genes Atg3, Atg5 and Atg12 on apoptosis and autophagy during the degeneration of the posterior silk gland in Bombyx mori, employing RNA interference techniques. Apoptosis-specific markers and autophagic processes were evaluated in both control and treatment groups. The knockdown of all three genes resulted in a significant reduction in autophagy, modifications in the apoptosis process, aberrant expression of p53 and impaired lysosomal function. It was determined that Atg3 is involved in the regulation of intracellular mitochondrial homeostasis. Following the silencing of Atg5, evidence was obtained indicating the gene's role in regulating lysosomal pH. Notably, the loss of Atg3 and Atg5 was associated with an increase in apoptotic markers, whereas the silencing of Atg12 inhibited apoptosis. Elevated levels of the p53 transcription factor following gene silencing suggested a potential interaction between these genes and p53. Our findings further underscore the importance of autophagy-mediated cell death, involving Atg3, Atg5 and Atg12, in the proper progression of degeneration in the posterior silk gland. A comprehensive understanding of the molecular mechanisms that mediate the interaction between apoptosis and autophagy is essential for elucidating their roles in both physiological and pathological contexts.

Deubiquitinating enzyme USP2 regulates brown adipose tissue thermogenesis via controlling EBF2 stabilization

OBJECTIVE

The activation of brown adipose tissue (BAT) promotes energy expenditure is recognized as a promising therapeutic strategy for combating obesity. The deubiquitinating enzyme family members are widely involved in the process of energy metabolism. However, the specific deubiquitinating enzyme member that affects the BAT thermogenesis remains largely unexplored.

METHODS

Adeno-associated virus, lentivirus and small molecule inhibitor were applied to generate USP2 gain- or loss-of-function both in vivo and in vitro. OxyMax comprehensive laboratory animal monitoring system, seahorse and transmission electron microscopy were used to determine the energy metabolism. Quantitative proteomics, immunofluorescence staining and co-immunoprecipitation were performed to reveal the potential substrates of USP2.

RESULTS

USP2 is upregulated upon thermogenic activation in adipose, and has a close correlation with UCP1 mRNA levels in human adipose tissue. BAT-specific Usp2 knockdown or systemic USP2 inhibition resulted in impaired thermogenic programs both in vivo and in vitro. Conversely, overexpression of Usp2 in BAT conferred protection against high-fat diet-induced obesity and associated metabolic disorders. Proteome-wide analysis identified EBF2 as the substrate of USP2 that mediates the thermogenic function of USP2 in BAT.

CONCLUSIONS

Our data demonstrated the vital role of USP2 in regulating BAT activation and systemic energy homeostasis. Activation of USP2-EBF2 interaction could be a potential therapeutic strategy against obesity.

FOXM1 cooperates with ERα to regulate functional β-cell mass

The transcription factor forkhead box (FOX)M1 regulates β-cell proliferation and insulin secretion. Our previous work demonstrates that expressing a constitutively active form of FOXM1 (FOXM1*) in β-cells increases β-cell function, proliferation, and mass in male mice. However, in contrast to what is observed in males, we demonstrate here that in female mice expression of FOXM1* in β-cells does not affect β-cell proliferation or glucose tolerance. Similarly, FOXM1* transduction of male but not female human islets enhances insulin secretion in response to elevated glucose. We therefore examined the mechanism behind this sexual dimorphism. Estrogen contributes to diabetes susceptibility differences between males and females, and estrogen receptor (ER)α is the primary mediator of β-cell estrogen signaling. Moreover, in breast cancer cells, ERα and FOXM1 work together to drive gene expression. We therefore examined whether FOXM1 and ERα functionally interact in β-cells. FOXM1* rescued elevated fasting glucose, glucose intolerance, and homeostatic model assessment of β-cell function (HOMA-B) in female mice with a β-cell-specific ERα deletion. Furthermore, in the presence of estrogen, the FOXM1 and ERα cistromes exhibit significant overlap in βTC6 β-cells. In addition, FOXM1 and ERα binding sites frequently occur in complex enhancers co-occupied by other islet transcription factors. These data indicate that FOXM1 and nuclear ERα cooperate to regulate β-cell function and suggest a general mechanism contributing to the lower incidence of diabetes observed in women.NEW & NOTEWORTHY Here we investigate why the effects of increasing FOXM1 activity in β-cells observed in male mice are not seen in female mice. ERα likely collaborates with FOXM1 and other transcription factors to enhance gene expression related to β-cell function. Higher estrogen levels in females may contribute to their increased insulin secretion and the more severe consequences of losing transcription factors like FOXM1 in males. Overall, these findings shed light on sex differences in diabetes susceptibility.

Mechanical force-driven cell competition ensures robust morphogen gradient formation

Morphogen gradients provide positional data and maintain tissue patterns by instructing cells to adopt distinct fates. In contrast, morphogen gradient-forming tissues undergo dynamic morphogenetic movements that generate mechanical forces and can disturb morphogen signal transduction. However, the interactions between morphogen gradients and these forces remain largely unknown. In this study, we described how mechanical force-mediated cell competition corrects noisy morphogen gradients to ensure robust tissue patterns. The Wnt/β-catenin morphogen gradient-that patterns the embryonic anterior-posterior axis-generates cadherin-actomyosin interaction-mediated intercellular tension gradients-termed mechano-gradients. Naturally generated unfit cells that produce noisy Wnt/β-catenin gradients induce local deformation of the mechano-gradients. Neighboring fit cells sense this deformation, resulting in the activation of Piezo family mechanosensitive calcium channels and secretion of annexinA1, which specifically kills unfit cells to recover morphogen gradients. Therefore, mechanical force-mediated cell competition between the morphogen-receiver cells supports robust gradient formation. Additionally, we discuss the potential roles of mechanical force-driven cell competition in other contexts, including organogenesis and cancer.

Synthetic microbial community maintains the functional stability of aerobic denitrification under environmental disturbances: Insight into the mechanism of interspecific division of labor

Understanding how synthetic microbial community (SMC) respond to environmental disturbances is the key to realizing SMC engineering applications. Here, dibutyl phthalate (DBP) and levofloxacin (LOFX) were used as environmental disturbances to study their effects on the aerobic denitrification functional stability of SMC composed of Pseudomonas aeruginosa N2 (PA), Acinetobacter baumannii N1(AC) and Aeromonas hydrophila (AH). The results showed that aerobic denitrification efficiency could be maintained at about 93 % under DBP or LOFX disturbance, and interspecific communication was mainly carried out through N-butyryl-L-homoserine lactone (C4-HSL) and N-(3-oxododecanoyl)-L-homoserine lactone (3OC12-HSL), correspondingly. DBP and LOFX induced the acceleration of tricarboxylic acid (TCA) cycle, which facilitated the energy flux and extracellular polymeric substances (EPS) production, thereby allowing SMC to adapt to disturbances. Under DBP disturbance, DBP stimulated phenazine-1-carboxylic acid production to accelerate electron transfer from the quinone pool to complex III, resulting in an increase in electron transfer activity. Up-regulation of complex I, complex III and heme synthesis genes under LOFX disturbance led to enhanced denitrification enzymes expression and electron transfer efficiency. SMC re-regulated different metabolic pathways to build metabolic networks to maintain normal metabolic activity under different disturbances. Overall, SMC maintained functional stability through the labor division in modulation of interspecific communication, formation of defensive barriers, promotion of energy flux, directional transfer of electron flux, and reconstruction of metabolic networks. DBP stimulated AH and PA to occupy functional dominance, while LOFX induced AC and PA to play a major role. The understanding of the stability mechanism under different environmental disturbances provides valuable guidance for stability maintenance and engineering applications of SMC.

Antibodies targeting ADAM17 reverse neurite outgrowth inhibition by myelin-associated inhibitors

Upon spinal cord injury, axons attempting to regenerate need to overcome the repulsive actions of myelin-associated inhibitors, including the myelin-associated glycoprotein, Nogo-A, and the oligodendrocyte myelin glycoprotein. These inhibitors bind and signal through a neuronal receptor/co-receptor/transducer complex composed of NgR1, Lingo-1, and p75. Consequently, p75 is cleaved by alpha secretase followed by gamma-secretase, triggering downstream signaling that inhibits axonal regrowth. ADAM10 and ADAM17 are both known to function as alpha secretases in neurons. Here we show that ADAM17, and not ADAM10, is the alpha secretase that recognizes and cleaves p75, when it is a part of a 5-component neuron-myelin signaling complex comprising NgR1, Lingo-1, p75, GT1b, and a myelin inhibitor. Importantly, we demonstrate the ability of inhibitory anti-ADAM17 mAbs to abrogate the cleavage of p75 in a neuroblastoma-glioma cell line and reverse the neurite outgrowth inhibition by myelin-associated inhibitors.

Discovery and biological evaluation of carborane-containing derivatives as TEAD auto palmitoylation inhibitors

Transcriptional enhanced associate domain (TEAD) proteins are key downstream effectors of the Hippo signaling pathway that play a crucial role in various cell processes including tissue development, regeneration, cell proliferation and cancer. TEADs contain a hydrophobic auto-palmitoylation pocket that can bind palmitic acid and stabilize TEADs from being degraded. Inhibitors targeting this palmitoylation pocket typically consist of hydrophobic pharmacophores. Carboranes is a cage-shaped molecule exhibiting superior hydrophobicity compared to adamantane or phenyl groups. Herein, we incorporated carborane into known TEAD inhibitors for better interaction with the hydrophobic palmitate pocket. Compounds 1f and 1l are identified as TEAD transcription inhibitors with strong anti-proliferation and anti-migration activities toward prostate cancer cell lines. They also significantly reduced TEAD-regulated downstream gene expressions.

Prognostic and Potential Therapeutic Roles of PRKDC Expression in Lung Cancer

PRKDC is a key factor involved in the ligation step of the non-homologous end joining pathway. Its dysfunction has proven to be a biomarker for radiosensitivity of cancer cells. However, the prognostic value of PRKDC and its underlying mechanisms have not been clarified yet. In this study, we found that PRKDC overexpressed in lung adenocarcinoma (LUAD) and is significantly related to unfavorable survival, while downregulation of PRKDC is link to inflamed tumor immune signature. Our further in vitro results also showed a potent antitumor efficacy of PRKDC inhibitors alone or combined with cisplatin in human lung cancer cells. This study demonstrated that PRKDC is a potential prognostic biomarker, immunotherapy target, and promising combination candidate for chemotherapy for lung cancer, and highlighted the potential of PRKDC-targeted inhibitors for the treatment of lung cancer.

Antipsychotic-induced hyperprolactinemia: Toxicologic mechanism and the increased breast cancer risk

Antipsychotic drugs are effective at improving both the positive and negative symptoms of schizophrenia as well as the manic phase of bipolar disorder. Whether an antipsychotic is termed typical or atypical is related to the xenobiotic's propensity to cause extrapyramidal side effects. However, with a few exceptions, drugs of both classes of antipsychotics are known to cause hyperprolactinemia. As many breast cancers are responsive to prolactin concentrations, the persistent increase in prolactin of the antipsychotics has implications for public health and carcinogenesis. The objective of this study was to review the extant literature on hyperprolactinemia due to antipsychotics, and to determine the risk imposed by those drugs on human breast cancer. A summary risk of breast cancer with use of any antipsychotic was found to be 1.19 (95 % confidence interval 1.10-1.30). When limiting usage of antipsychotics to 5 or more years, the summary risk increased to 1.26 (95 % confidence interval 1.12-1.43). And when limited to those studies who evaluated only those medications with the greatest increase in prolactin, the risk increased to 1.59 (95 % confidence interval 1.37-1.85). Given this increased risk of breast cancer, stronger warnings about this increased risk are warranted, and regular monitoring of prolactin levels and breast cancer screening should be part of the management plan for these patients.

A refined Golgi-Cox method for the staining of embryonic neurons in the mouse brain

The Golgi-Cox stain remains a valuable technique used to investigate the morphology of individual neurons. Despite this, Golgi-Cox staining protocols are predominantly designed to impregnate adult neurons. Protocols optimised for the staining of immature embryonic mouse neurons have been previously developed but have limitations, including being time-consuming and being reliant on the use of expensive commercial kits. Here, we present a simple and inexpensive method for Golgi-Cox staining of embryonic neurons in the mouse brain. We identified that a 60 minute, 4 % paraformaldehyde (PFA) brain fixation step, followed by a wash with distilled water prior to immersion in Golgi-Cox solution was critical to the success of the stain. By altering the duration of the wash step, the visualisation of different populations across the neuraxis of neurons could be emphasised. Shorter washes enabled cortical neurons to be readily distinguished, whereas extending the wash steps was needed to enable subcortical neurons to be delineated.

Integrative whole-genome methylation and transcriptome analysis reveals epigenetic modulation of glucose metabolism by dietary berberine in blunt snout bream (Megalobrama amblycephala)

The present research was designed to explore the epigenetic mechanism by which dietary berberine (BBR) affects glucose metabolism in fish. Blunt snout bream (Megalobrama amblycephala) is susceptible to disturbances in glucose metabolism when subjected to prolonged high-carbohydrate diets. This study aimed to elucidate whether BBR can enhance glucose regulation in M. amblycephala via modulating DNA methylation levels. Fish (average weight of 20.36 ± 1.44 g) were administered a normal-carbohydrate diet (NC, 30 % carbohydrate), a high-carbohydrate diet (HC, 43 % carbohydrate), or a high-carbohydrate diet supplemented with 50 mg/kg berberine (HB) for 10 weeks. Subsequently, global DNA methylation level, whole-genome bisulfite sequencing (WGBS), RNA-seq, bisulfite sequencing PCR, and real-time quantitative PCR were employed to analyze the DNA methylation patterns and transcription results of the liver genome. The findings indicated that high carbohydrate diets induced glucose metabolism disorders in M. amblycephala, whereas BBR mitigated these metabolic disturbances by reducing methylation levels. WGBS results revealed that CG-type cytosine methylation predominated, and that DNA methylation mainly occurred in promoter, intron, and exon regions. Furthermore, analyses demonstrated a negative correlation between DNA methylation around the transcriptional start site and gene expression levels for 47 genes. Functional enrichment analysis revealed that these genes were associated with 60 KEGG pathways, including 12 genes implicated in the amelioration of insulin resistance, reduction of gluconeogenesis, and maintenance of glucose homeostasis. Consequently, we generated a comprehensive catalog of liver DNA methylation in M. amblycephala, which provides a foundational framework for future investigations into the epigenetic regulation of glucose metabolism by BBR.

Identification of ZNF384 as a regulator of epigenome in leukemia

Leukemia is a complex hematologic cancer driven by genetic and epigenetic changes that impact gene expression. Understanding these molecular mechanisms is essential for improving leukemia diagnosis and prognosis. This study examines the role of the zinc finger protein ZNF384 in the epigenome and its influence on gene regulation in leukemia. We analyzed next-generation sequencing data from The Encyclopedia of DNA Elements (ENCODE), integrating datasets such as chromatin immunoprecipitation sequencing (ChIP-seq) of ZNF384 and regulatory histone marks, RNA sequencing (RNA-seq), and Hi-C data from K562 and GM12878 cells. Additionally, we used RNA-seq from K562 ZNF384 knock-down (KD) cells generated via CRISPR interference (CRISPRi) to validate our findings. This enabled us to explore the chromatin interaction patterns of ZNF384 and its regulatory impact. Our results demonstrate that ZNF384 associates with promoters and enhancers in K562 and GM12878 cells, facilitating increased transcription levels. We also found ZNF384 enriched at topologically associating domain (TAD) boundaries and chromatin loops, suggesting a role in three-dimensional (3D) chromatin organization. Furthermore, we identified a significant binding of ZNF384 at SINE-Alu elements in both K562 and GM12878 cells. In summary, this study highlights the regulatory role of ZNF384 in the leukemia epigenome and its impact on gene expression. Understanding the oncogenic implications of ZNF384 may improve leukemia diagnosis and prognosis.

Calpain inhibition in a transgenic model of calpastatin overexpression facilitates reversal of myocardial hypertrophy

AIMS

It was recently demonstrated that the intracellular signalling phosphatase calcineurin is subject to cleavage by the protease calpain, resulting in a truncated calcineurin fragment that is a strong inductor of myocardial hypertrophy. We now address the question of whether inhibition of calpain function in cardiomyocytes, and thereby prevention of calcineurin truncation, attenuates development of myocardial hypertrophy.

METHODS AND RESULTS

We generated a transgenic mouse model with conditional cardiac calpastatin overexpression (CAST OE) and compared their cardiac hypertrophic response to angiotensin-II (AngII) with that of non-induced control animals. Angiotensin-II osmotic mini-pumps were removed 3 weeks after implantation and cardiac hypertrophy was re-evaluated 3 weeks after pump removal. Induction of calpastatin overexpression resulted in 88% inhibition of calpain activity and suppressed calcineurin truncation. In CAST OE mice, basal phenotype and AngII-induced myocardial hypertrophy were comparable with non-induced controls (mean heart to body weight ratios ± SD in milligrams per gram: CAST OE, 4.8 ± 0.4; CAST OE + AngII, 7.1 ± 0.5; non-induced, 4.9 ± 0.4; non-induced + AngII, 7.2 ± 0.4). However, CAST OE mice demonstrated a complete reversal of hypertrophy when angiotensin-II was removed, whereas hypertrophy persisted in non-induced controls (CAST OE 5.0 ± 0.5; non-induced 7.0 ± 0.4; P < 0.0001). Persistent hypertrophy in controls was accompanied by nuclear accumulation of truncated calcineurin and elevated activity of the Nuclear Factor of Activated T-cells pathway. Moreover, we found that truncated calcineurin was insufficiently ubiquitinylated compared with its full-length form and thus escaped degradation over several weeks in our in vivo experiments.

CONCLUSIONS

Our data demonstrate that calpain-mediated cleavage results in nuclear accumulation of a truncated, constitutively active and degradation-resistant calcineurin isoform that sustains a long-term myocardial hypertrophic response to angiotensin-II beyond withdrawal of the stimulus. Cardiomyocyte specific calpain inhibition by transgenic calpastatin overexpression prevented the post-stimulus myocardial hypertrophic response.

PVAT adipocyte: energizing, modulating, and structuring vascular function during normotensive and hypertensive states

Hypertension represents the most common form of cardiovascular disease. It is characterized by significant remodeling of the various layers of the vascular system, including the outermost layer: the perivascular adipose tissue (PVAT). Given the tissue's pivotal role in regulating blood pressure, a comprehensive understanding of the changes that occur within PVAT during the progression of hypertension is essential. This article reviews the mechanisms through which PVAT modulates blood pressure, including the secretion of bioactive soluble factors, provision of mechanical support, and adipose-specific functions such as adipogenesis, lipogenesis, lipolysis, and extracellular matrix remodeling. Additionally, this review emphasizes the influence of hypertension on each of these regulatory mechanisms, thereby providing a deeper insight into the pathophysiological interplay between hypertension and PVAT biology.

Wolfram syndrome 2 gene (CISD2) deficiency disrupts Ca2+-mediated insulin secretion in β-cells

OBJECTIVE

Diabetes, characterized by childhood-onset, autoantibody-negativity and insulin-deficiency, is a major manifestation of Wolfram syndrome 2 (WFS2), which is caused by recessive mutations of CISD2. Nevertheless, the mechanism underlying β-cell dysfunction in WFS2 remains elusive. Here we delineate the essential role of CISD2 in β-cells.

METHODS

We use β-cell specific Cisd2 knockout (Cisd2KO) mice, a CRISPR-mediated Cisd2KO MIN6 β-cell line and transcriptomic analysis.

RESULTS

Four findings are pinpointed. Firstly, β-cell specific Cisd2KO in mice disrupts systemic glucose homeostasis via impairing β-granules synthesis and insulin secretion; hypertrophy of the β-islets and the presence of a loss of identity that affects certain β-cells. Secondly, Cisd2 deficiency leads to impairment of glucose-induced extracellular Ca2+ influx, which compromises Ca2+-mediated insulin secretory signaling, causing mitochondrial dysfunction and, thereby impairing insulin secretion in the MIN6-Cisd2KO β-cells. Thirdly, transcriptomic analysis of β-islets reveals that Cisd2 modulates proteostasis and ER stress, mitochondrial function, insulin secretion and vesicle transport. Finally, the activated state of two potential upstream regulators, Glis3 and Hnf1a, is significantly suppressed under Cisd2 deficiency; notably, their downstream target genes are deeply involved in β-cell function and identity.

CONCLUSIONS

These findings provide mechanistic insights and form a basis for developing therapeutics for the effective treatment of diabetes in WFS2 patients.

Milk-derived exosomes as functional nanocarriers in wound healing: Mechanisms, applications, and future directions

Wound healing presents a significant challenge in healthcare, imposing substantial physiological and economic burdens. While traditional treatments and stem cell therapies have shown benefits, milk-derived exosomes (MDEs) offer distinct advantages as a cell-free therapeutic approach. MDEs, isolated from mammalian milk, are characterized by their biocompatibility, ease of acquisition, and high yield, making them a promising tool for enhancing wound repair. This review provides a comprehensive analysis of the composition, sources, and extraction methods of MDEs, with a focus on their therapeutic role in both acute and diabetic chronic wounds. MDEs facilitate wound healing through the delivery of bioactive molecules, modulating key processes such as inflammation, angiogenesis, and collagen synthesis. Their ability to regulate complex wound-healing pathways underscores their potential for widespread clinical application. This review highlights the importance of MDEs in advancing wound management and proposes strategies to optimize their use in regenerative medicine.

Coupling genome-wide continuous perturbation with biosensor screening reveals the potential targets in yeast isopentanol synthesis network

The increasing consumption of fossil fuels is contributing to global resource depletion and environmental pollution. Branched-chain higher alcohols, such as isopentanol and isobutanol, have attracted significant attention as next-generation biofuels. Biofuel production through microbial fermentation offers a green, sustainable, and renewable alternative to chemical synthesis. While enhanced production of isopentanol has been achieved in a variety of chassis, the fermentation yield has not yet reached levels suitable for industrial-scale production. In this study, we employed a continuous perturbation tool to construct a genome-scale perturbation library, combined with an isopentanol biosensor to screen for high-yielding mutants. We identified five high-yielding mutants, each exhibiting an increased glucose conversion rate and isopentanol titer. The F2 strain, in particular, achieved an isopentanol titer of 1.57 ± 0.014 g/L and a yield of 14.04 ± 0.251 mg/g glucose (10% glucose), surpassing the highest values reported to date in engineered Saccharomyces cerevisiae. Systematic transcriptome analysis of the isopentanol synthesis, glycolysis, glycerol metabolism, and ethanol synthesis pathways revealed that MPC, OAC1, BAT2, GUT2, PDC6, and ALD4 are linked to efficient isopentanol production. Further analysis of differentially expressed genes (DEGs) identified 17 and 12 co-expressed DEGs (co-DEGs) in all mutants and the two second-round mutants, respectively. In addition, we validated the knockout or overexpression of key co-DEGs. Our results confirmed the critical roles of HOM3 and DIP5 in isopentanol production, along with genes associated with the aerobic respiratory chain (SDH3, CYT1, COX7, ROX1, and ATG41) and cofactor balance (BNA2 and NDE1). Additionally, functional analysis of the co-DEGs revealed that MAL33 is associated with the synthesis of branched-chain higher alcohols, expanding the intracellular metabolic network and offering new possibilities for green, cost-effective biofuel production.

Kidney deletions of Cyp27b1 fail to reduce serum 1,25(OH)2D3

Vitamin D metabolism is controlled through the kidney mitochondrial P450 enzymes 1α-hydroxylase (CYP27B1) and 24-hydroxylase (CYP24A1) that activate and degrade the endocrine vitamin D hormone (1,25(OH)2D3), respectively. We recently demonstrated that extrarenal cells can make 1,25(OH)2D3 with adequate vitamin D supplementation by targeted mass spectrometry imaging in our Cyp27b1 kidney enhancer deletion mouse model that lacks circulating 1,25(OH)2D3 (M1/M21-DIKO mouse). Based on these observations, we selectively deleted Cyp27b1 (Cyp27b1fl/fl) from the mouse kidney using the Six2- and Pax8-cre drivers that target tubule and nephron development to see if we could recapitulate the remarkable phenotype of the M1/M21-DIKO mice. While Six2-cre/Cyp27b1fl/fl mice had a mild phenotype, Pax8-cre/Cyp27b1fl/fl mice had a marked elevation of parathyroid hormone and a reduction in bone mineral density. The vitamin D metabolic profile in the Pax8-cre/Cyp27b1fl/fl clearly indicated a dysfunction in the CYP24A1 enzyme with reductions in 24,25(OH)2D3 and 25(OH)D3-26,23-lactone with an accompanying elevation of 25(OH)D3. However, despite these compensatory reductions in CYP24A1 derived metabolites and apparent deletion of Cyp27b1 in the kidney, the 1,25(OH)2D3 levels were not changed from wildtype in either mouse. Like 24,25(OH)2D3, the 1,24,25(OH)3D3 levels were also reduced. These data highlight the robust homeostatic mechanisms to salvage 1,25(OH)2D3, point towards potential compensatory mechanisms of 1,25(OH)2D3 production from non-kidney tissues, and reinforce the utility of the M1/M21-DIKO model as a non-global deletion of Cyp27b1 with reductions in serum 1,25(OH)2D3 to be used to understand the complexity of vitamin D metabolism in health and inflammatory disease.

Cell competition as an emerging mechanism and therapeutic target in cancer

Cell competition, as an internal quality control mechanism that constantly monitor cell fitness and eliminate unfit cells, maintains proper embryogenesis and tissue integrity during early development and adult homeostasis. Recent studies have revealed that cell competition functions as a tumor-suppressive mechanism to defend against cancer by removing neoplastic cell, which however, is hijacked by tumor cells and drive cell competition in favor of mutant cells, thereby promoting cancer initiation and progression. In this review, with a special focus on mammalian systems, we discuss the latest insights into the mechanisms regulating cell competition and its dual role in tumor development. We also provide current strategies to modulate the direction of cell competition for the prevention and treatment of cancers.

The R337C mutation in the p53 oligomerization domain affects the regulatory domain and its ability to bind response elements: Evidence based on structural and biophysical studies

The homotetrameric form of p53 is critical for performing essential functions like maintaining genomic stability and preventing uncontrolled cell proliferation. In part, these crucial functions are mediated by the p53 C-terminal region (CTR) containing the tetramerization/oligomerization domain (TD/OD) and regulatory domain (RD), responsible for maintaining the protein's oligomeric state and regulating its function. Mutations in the tetramerization domain reduce the transactivation potential and alter the transactivation specificity of p53. This study investigates the effect of high-frequency tetramerization missense mutation p53R337C on protein stability, oligomeric state, and its ability to bind the DNA response elements. For the first time using CD and FTIR spectroscopy, we have shown that the p53 regulatory domain (residues 363-393) and oligomerization domain (residues 327-355) possess a characteristic alpha helix secondary structure, which is enhanced upon binding to DNA, implicating stabilization of the domain. The mutation R337C in the OD impacts the secondary and tertiary structure of p53 CTR, leading to the loss of secondary structure and the formation of unstable tetramers, as shown by CD and DSC thermal studies. Surprisingly, the secondary structure of mutant p53 CTR partially stabilized upon binding to the DNA sequence. Our data suggests that the unstable p53R337C tetramer exhibits weaker binding to the DNA promoter sequence with decreased transcription activity, consistent with previous cell-based assays. Our study conclude that the loss of salt-bridge interactions between Arg337 and Asp352 in the intra-dimer of p53 leads to the formation of unstable tetramers, and the DNA-binding ability of the regulatory domain.

Disinfectants and one health review: The role of reactive oxygen species in the bactericidal activity of chlorine against Salmonella

Salmonella are among the most common foodborne pathogens in humans, and they are associated with mild to severe diseases commonly referred to as salmonellosis. The genus resides in various animals' intestinal tracts, including humans. It is one of the most diverse genera of bacteria, including over 2500 serovars. Consumption of poultry products contaminated with Salmonella is a significant source of disease transmission in humans. Because of this food safety concern, the poultry industry and governments spend billions of dollars on Salmonella containment methods. However, a completely effective strategy is yet to be established. Chlorine has been commonly used as a disinfectant in the poultry industry. In humans, antibiotic therapy is the primary means for managing Salmonella infection. However, widespread use of both compounds at sub-inhibitory concentrations has allowed resistant strains to emerge and rapidly spread globally. Both antimicrobial compounds involve generating reactive oxygen species (ROS) as a bactericidal mechanism of action. However, ROS generation and its association with bacterial survival and growth inhibition have not been widely explored. Thus, a better understanding of ROS generation during antimicrobial treatments may help devise better Salmonella containment strategies.

Drug design for cyclin-dependent kinase 9 (CDK9) inhibitors in silico

Despite the potential of cyclin-dependent kinase 9 (CDK9) as a novel target for various malignancies and HIV replication in infected cells, no effective inhibitors have been developed. In the preceding study, we deciphered a hidden cavity in CDK9 upon molecular dynamics (MD) simulation of the CDK9/CyclinT1/Tat trimolecular complex. This cavity is located near the CDK9 ATP pocket (continuous cavity I, CCI) and extends to the cyclin T1 (CycT1) contact surface (CCII and CCIII). In this study, we searched for compounds similar to previously identified CDK9 inhibitors using cheminformatics to identify compounds that are better suited to this hidden cavity. We identified compounds that effectively targeted CCII and CCIII of CDK9. We confirmed their inhibitory effects on the CDK9/CycT1 complex in vitro. As these inhibitory compounds target only a portion (CCII and CCIII cavities) of CDK9, we examined their combinatorial effects with the known CDK inhibitor BS-181. As expected, this combination exerted an additive inhibitory effect on CDK9 expression. These findings confirm the presence of a CDK9 hidden cavity that was revealed transiently by MD simulations, thus providing promising evidence for the development of CDK9 inhibitors.