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.

Structural insights into the ubiquitin-independent midnolin-proteasome pathway

The protein midnolin (MIDN) augments proteasome activity in lymphocytes and dramatically facilitates the survival and proliferation of B-lymphoid malignancies. MIDN binds both to proteasomes and to substrates, but the mode of interaction with the proteasome is unknown, and the mechanism by which MIDN facilitates substrate degradation in a ubiquitin-independent manner is incompletely understood. Here, we present cryoelectron microscopy (cryo-EM) structures of the substrate-engaged, MIDN-bound human proteasome in two conformational states. MIDN induces proteasome conformations similarly to ubiquitinated substrates by using its ubiquitin-like domain to bind to the deubiquitinase RPN11 (PSMD14). By simultaneously binding to RPN1 (PSMD2) with its C-terminal α-helix, MIDN positions its substrate-carrying Catch domain above the proteasome ATPase channel through which substrates are translocated before degradation. Our findings suggest that both ubiquitin-like domain and C-terminal α-helix must bind to the proteasome for MIDN to stimulate proteasome activity.

NF-κB-mediated developmental delay extends lifespan in Drosophila

Developmental time (or time to maturity) strongly correlates with an animal's maximum lifespan, with late-maturing individuals often living longer. However, the genetic mechanisms underlying this phenomenon remain largely unknown. This may be because most previously identified longevity genes regulate growth rate rather than developmental time. To address this gap, we genetically manipulated prothoracicotropic hormone (PTTH), the primary regulator of developmental timing in Drosophila, to explore the genetic link between developmental time and longevity. Loss of PTTH delays developmental timing without altering the growth rate. Intriguingly, PTTH mutants exhibit extended lifespan despite their larger body size. This lifespan extension depends on ecdysone signaling, as feeding 20-hydroxyecdysone to PTTH mutants reverses the effect. Mechanistically, loss of PTTH blunts age-dependent chronic inflammation, specifically in fly hepatocytes (oenocytes). Developmental transcriptomics reveal that NF-κB signaling activates during larva-to-adult transition, with PTTH inducing this signaling via ecdysone. Notably, time-restricted and oenocyte-specific silencing of Relish (an NF-κB homolog) at early 3rd instar larval stages significantly prolongs adult lifespan while delaying pupariation. Our study establishes an aging model that uncouples developmental time from growth rate, highlighting NF-κB signaling as a key developmental program in linking developmental time to adult lifespan.

Improved synapsis dynamics accompany meiotic stability in Arabidopsis arenosa autotetraploids

During meiosis, the correct pairing, synapsis, and recombination of homologous chromosome pairs is critical for fertility of sexual eukaryotes. These processes are challenged in polyploids, which possess additional copies of each chromosome. Polyploidy thus provides a unique context to study how evolution can modify meiotic programs in response to challenges. We previously observed that in newly formed (neo-)polyploids of Arabidopsis arenosa, synapsis defects precede chromosomes associating in aberrant multivalent and univalent configurations. Here, we study synapsis dynamics in genotypes with varying levels of meiotic stability to ask whether efficient synaptic progression is a key component of evolving stable tetraploid meiosis. We develop a method to quantify synapsis dynamics using the progression of foci of the pro-crossover factor HEI10 as a reference. HEI10 initially appears at many small foci before accumulating only at crossover sites. In diploids, this transition begins while significant asynapsis is still present, though it quickly declines as HEI10 accumulates at fewer foci. In neo-tetraploids, suboptimal elongation of synaptic initiation sites and stalled synapsis, perhaps due to defective pairing, occurs before the onset of HEI10 accumulation. In established tetraploids, HEI10 accumulation begins only when synapsis is near complete, suggesting enhanced HEI10/synapsis codynamics (even compared to diploids). Hybrids generated by crossing neo- and established tetraploids exhibit intermediate phenotypes. We find the extent of asynapsis correlates positively with crossover numbers, and the frequency of multivalents and univalents, which can disturb chromosome segregation. Our work supports the hypothesis that improving the efficiency of synapsis is important for evolving polyploid meiotic stability.

Intercellular contractile force attenuates chemosensitivity through Notch-MVP-mediated nuclear drug export

Resistance to chemotherapeutics is one major challenge to clinical effectiveness of cancer treatment and is primarily interpreted by various biochemical mechanisms. This study establishes an inverse correlation between tumor cell contractility and chemosensitivity. In both clinical biopsies and cancer cell lines, high/low actomyosin-mediated contractile force attenuates/enhances the vulnerability to chemotherapy, which depends on intercellular force propagation. Cell-cell interaction force activates the mechanosensitive Notch signaling that upregulates the downstream effector major vault protein, which facilitates the export of chemotherapy drugs from nuclei, leading to the reduction of chemosensitivity. Cellular contractility promotes the tolerance of tumor xenografts to chemotherapy and sustains tumor growth in vivo, which can be reversed by the inhibition of contractile force, Notch signaling, or major vault protein. Further, the actomyosin-Notch signaling is associated with drug resistance and cancer recurrence of patients. These findings unveil a regulatory role of intercellular force in chemosensitivity, which could be harnessed as a promising target for cancer mechanotherapeutics.

Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES

Current genome sequencing initiatives across a wide range of life forms offer significant potential to enhance our understanding of evolutionary relationships and support transformative biological and medical applications. Species trees play a central role in many of these applications; however, despite the widespread availability of genome assemblies, accurate inference of species trees remains challenging due to the limited automation, substantial domain expertise, and computational resources required by conventional methods. To address this limitation, we present ROADIES, a fully automated pipeline to infer species trees starting from raw genome assemblies. In contrast to the prominent approach, ROADIES incorporates a unique strategy of randomly sampling segments of the input genomes to generate gene trees. This eliminates the need for predefining a set of loci, limiting the analyses to a fixed number of genes, and performing the cumbersome gene annotation and/or whole genome alignment steps. ROADIES also eliminates the need to infer orthology by leveraging existing discordance-aware methods that allow multicopy genes. Using the genomic datasets from large-scale sequencing efforts across four diverse life forms (placental mammals, pomace flies, birds, and budding yeasts), we show that ROADIES infers species trees that are comparable in quality to the state-of-the-art studies but in a fraction of the time and effort, including on challenging datasets with rampant gene tree discordance and complex polyploidy. With its speed, accuracy, and automation, ROADIES has the potential to vastly simplify species tree inference, making it accessible to a broader range of scientists and applications.

Muscle peripheral circadian clock drives nocturnal protein degradation via raised Ror/Rev-erb balance and prevents premature sarcopenia

How central and peripheral circadian clocks regulate protein metabolism and affect tissue mass homeostasis has been unclear. Circadian shifts in the balance between anabolism and catabolism control muscle growth rate in young zebrafish independent of behavioral cycles. Here, we show that the ubiquitin-proteasome system (UPS) and autophagy, which mediate muscle protein degradation, are each upregulated at night under the control of the muscle peripheral clock. Perturbation of the muscle transcriptional molecular clock disrupts nocturnal proteolysis, increases muscle growth measured over 12 h, and compromises muscle function. Mechanistically, the shifting circadian balance of Ror and Rev-erb regulates nocturnal UPS, autophagy, and muscle growth through altered TORC1 activity. Although environmental zeitgebers initially mitigate defects, lifelong muscle clock inhibition reduces muscle size and growth rate, accelerating aging-related loss of muscle mass and function. Circadian misalignment such as shift work, sleep deprivation, or dementia may thus unsettle muscle proteostasis, contributing to muscle wasting and sarcopenia.

The developmental factor TBX3 engages with the Wnt/β-catenin transcriptional complex in colorectal cancer to regulate metastasis genes

Wnt signaling orchestrates gene expression in a plethora of processes during development and adult cell homeostasis via the action of nuclear β-catenin. Yet, little is known about how β-catenin generates context-specific transcriptional outcomes. Understanding this will reveal how aberrant Wnt/β-catenin signaling causes neoplasia specifically of the colorectal epithelium. We have previously identified the transcription factor TBX3 as a tissue-specific component of the Wnt/β-catenin nuclear complex during mouse forelimb development. In this study, we show that TBX3 is functionally active in human colorectal cancer (CRC). Here, genome-wide binding and transcriptomics analyses reveal that TBX3 regulates cancer metastasis genes in cooperation with Wnt/β-catenin. Proteomics proximity labeling performed across Wnt pathway activation shows that TBX3 engages with several transcription factors and chromatin remodeling complexes found at Wnt responsive elements (WRE). Protein sequence and structure analysis of TBX3 revealed short motifs, including an exposed Asn-Pro-Phe (NPF), that mediate these interactions. Deletion of these motifs abrogates TBX3's proximity to its protein partners and its ability to enhance the Wnt-dependent transcription. TBX3 emerges as a key modulator of the oncogenic activity of Wnt/β-catenin in CRC, and its mechanism of action exposes protein-interaction surfaces as putative druggable targets.

Niuhuang jiedu prescription alleviates realgar-induced dopaminergic and GABAergic neurotoxicity in Caenorhabditis elegans

ETHNOPHARMACOLOGICAL RELEVANCE

Niuhuang Jiedu (NHJD) is a Chinese medicine prescription containing realgar (As2S2), which is neurotoxic, and seven other traditional Chinese medicines (TCMs). However, whether the multiple TCMs contained in NHJD can mitigate the neurotoxicity of realgar is yet to be elucidated.

AIM OF THE STUDY

This study aimed to investigate the effect of NHJD on realgar-induced neurotoxicity and elucidate its underlying mechanisms.

MATERIAL AND METHODS

Caenorhabditis elegans was treated with realgar suspension (1-8 mg/mL) for 48 h. Transgenic nematode strains labeled with green fluorescent protein were used to evaluate neuronal structural damage. Locomotion and perception behaviors were assessed by measuring head thrashes, body bends, and chemotaxis. Oxidative stress was determined by detecting reactive oxygen species (ROS), lipofuscin, and glutathione-S-transferase-4 (GST-4) levels. Subsequently, a quantitative reverse transcription-polymerase chain reaction was employed to analyze gene expression associated with oxidative stress, whereas the role of the p38 MAPK pathway was investigated using KU25 nematodes. Finally, arsenic species in the nematodes were estimated using high-performance liquid chromatography-atomic fluorescence spectrometry. Data analysis was performed using analysis of variance or rank tests with SPSS 26.0.

RESULTS

Treatment of nematodes with 8 mg/mL realgar resulted in significant damage to dopaminergic and GABAergic neurons, impaired locomotor and perceptual behavior (at 4-8 mg/mL), and induced oxidative damage (at 2-8 mg/mL). A neuron-defective model was established using 8 mg/mL realgar to gauge the effects of NHJD on realgar-induced damage. The findings indicated that NHJD, containing the same dose of realgar, significantly alleviated neuronal damage and neurobehavioral impairment and increased ROS, lipofuscin, and GST-4 levels. In addition, NHJD reduced the expressions of oxidative stress-related genes (gst-4, skn-1, gcs-1, gss-1, ctl-2, ctl-3, and sod-1) compared with realgar alone. Nonetheless, significant differences in skn-1 expression, neurobehavior, ROS, or lipofuscin levels were not observed between the realgar and NHJD groups in KU25 nematodes. Moreover, arsenic methylation metabolites were not identified in the nematodes.

CONCLUSIONS

The multiple TCMs contained in NHJD effectively mitigated realgar-induced dopaminergic and GABAergic neurotoxicity in nematodes, and pmk-1 may play a crucial role in NHJD's alleviating realgar-induced neurotoxicity via the p38 MAPK signaling pathway.

Putrescine modulates alternative splicing of gonadotropin hormone-releasing hormone (GnRH) through differential regulation of splicing factors

Gonadotropin-releasing hormone (GnRH) plays a critical role in reproductive function, with its activity influenced by differential splicing that generates functionally distinct isoforms. However, the molecular mechanisms regulating GnRH pre-mRNA processing remain poorly understood. In this study, we investigated the effects of putrescine, a biogenic polyamine, on GnRH splicing and the expression of splicing regulatory factors. Transcriptome analysis revealed that putrescine treatment induces significant changes in the expression of splicing-related genes. Notably, putrescine enhanced the expression of both the full-length GnRH isoform (GnRH V1) and an exon-skipped variant (GnRH V2), with the latter exhibiting higher expression levels. Further analysis showed putrescine significantly upregulated key alternative splicing regulators, including SR proteins (SRSF11, SRSF12), RNA helicases (DDX26B, DDX6, DDX25), and Pre-mRNA processing factor (PRPF8), Splicing factor 3b (SF3B2). Conversely, HnRNPA3 and SF3B1 were downregulated. These findings suggest putrescine influences GnRH isoform expression through a dual mechanism: enhancing factors that promote alternative splicing while simultaneously attenuating components of the canonical splicing machinery. Our results provide novel insights into the molecular regulation of GnRH splicing and highlight putrescine as a potential modulator of reproductive function through alternative splicing mechanisms.

The essential role of E3 ubiquitin ligases in the pathogenesis of neurodevelopmental and psychiatric disorders: Cul3, Cul4, Ube3a, and ZNRF1

The ubiquitin-proteasome system (UPS) is a crucial proteolytic pathway responsible for maintaining cellular homeostasis by degrading specific substrates and misfolded proteins. Protein ubiquitination, a key post-translational modification, is mediated by three enzymes: E1 (activating enzyme), E2 (conjugating enzyme), and E3 (ligase enzyme). Among these, E3 ligase genes have been linked to various neurological disorders, emphasizing the need to understand their molecular mechanisms. This paper reviews recent studies on the substrates of various E3 ubiquitin ligases including Cul3, Cul4, Ube3a, and ZNRF1, and explains how their dysfunction contributes to neuronal impairments and disease phenotypes. By deepening our understanding of these mechanisms, this review aims to facilitate the development of targeted therapies and guide future research into neurodegenerative and neurodevelopmental disorders.

Integrative metabolic profiling of hypothalamus and skeletal muscle in a mouse model of cancer cachexia

Cancer cachexia is a multifactorial metabolic syndrome characterized by progressive weight loss, muscle wasting, and systemic inflammation. Despite its clinical significance, the underlying mechanisms linking central and peripheral metabolic changes remain incompletely understood. In this study, we employed a murine model of cancer cachexia induced by intraperitoneal injection of Lewis lung carcinoma (LLC1) cells to investigate tissue-specific metabolic adaptations. Cachectic mice exhibited reduced food intake, body weight loss, impaired thermoregulation, and decreased energy expenditure. Metabolomic profiling of serum, skeletal muscle, and hypothalamus revealed distinct metabolic shifts, with increased fatty acid and ketone body utilization and altered amino acid metabolism. Notably, hypothalamic metabolite changes diverged from peripheral tissues, showing decreased neurotransmitter-related metabolites and enhanced lipid-based energy signatures. Gene expression analysis further confirmed upregulation of glycolysis- and lipid oxidation-related genes in both hypothalamus and muscle. These findings highlight coordinated yet compartmentalized metabolic remodeling in cancer cachexia and suggest that hypothalamic adaptations may play a central role in the systemic energy imbalance associated with cachexia progression.

Transcriptional regulation of daily sleep amount by TCF4-HDAC4-CREB complex in mice

Histone deacetylase HDAC4/5 cooperates with cAMP response element-binding protein (CREB) in the transcriptional regulation of daily sleep amount downstream of LKB1-SIK3 kinase cascade in mice. Here, we report a significant enrichment of the E-box motifs for the basic loop-helix-loop (bHLH) proteins near the CREB- and HDAC4-binding sites in the mouse genome. Adeno-associated virus-mediated expression of class I bHLH transcription factors, such as TCF4, TCF3, or TCF12, across the mouse brain neurons reduces the duration of rapid eye movement sleep (REMS) and non-REMS (NREMS). TCF4 requires its bHLH domain to regulate REMS or NREMS amount, of which the latter is mostly independent of the E-box-binding activity. Consistent with that TCF4 interacts with CREB and HDAC4 via the bHLH domain, TCF4 relies on CREB and partly on HDAC4 to regulate NREMS/REMS amount. Conversely, the ability of CREB to regulate sleep duration also requires its binding to TCF4 and HDAC4. Together, these results indicate that TCF4, HDAC4, and CREB could function cooperatively in the transcriptional regulation of daily sleep amount in mice.

Detecting the distribution patterns of histone lactylation in the mouse testis at different developmental stages

Lactate is a key glycolytic metabolite that serves as an energy substance and signaling molecule. Lactylation, a recently characterized posttranslational modification (PTM), has been identified in histone and nonhistone proteins. Compelling evidence suggests that this lactate-related epigenetic modification potently regulates gene expression under physiological and pathological conditions. However, the distribution of this histone modification in the testis remains largely unknown. In this study, we investigated the expression dynamics of histone acetyltransferases (HATs), histone deacetylases (HDACs), and the lactate-regulating enzyme hexokinase 2 (HK2), and examined the cellular distribution of several types of histone lactylation, which have been identified as important for transcription and chromatin accessibility, in mouse testes during critical postnatal developmental stages. The results revealed that the expression levels of the lactylation-associated transcripts were developmentally regulated and that the histone lactylation, including H3K9la, H3K12la and H4K18la were present in spermatogenic and Sertoli cells at postnatal days (PD) 0, 6, 21, and 60. However, signals for H3K5la and H3K14la were not detected in gonocytes at PD0 and signal for H3K14la was not detected in mature Sertoli cells or spermatogonia of adult testes. Furthermore, a lack of lactate dehydrogenase a (Ldha) in Sertoli cells impacted the localization of several histone lactylation modifications in spermatogenic cells. Notably, H4K12la was specifically detected in zygotene and diplotene spermatocytes in the control testis, whereas it was present mainly in spermatogonia of Lhda Sertoli cell conditional knockout testis (Ldha-cKO). The results of this study lay a foundation for further understanding the role of lactylation modification in spermatogenesis and provide important data for further dissectting the role of Sertoli cell-derived lactate in germ cell development.

Innovative injectable, self-healing, exosome cross-linked biomimetic hydrogel for cartilage regeneration

The limited self-healing capacity of cartilage hinders its repair and regeneration at the defect sites. Recent research into small-molecular compounds has shown promise in achieving a better regeneration of cartilage. In this study, we encapsulate kartogenin (KGN) and transforming growth factor β1 (TGF-β1) within mesenchymal stem cells derived exosomes (EKT), and then coated them with succinylated chitosan (sCH) to create positively charged exosomes, termed CEKT. These CEKT exhibit exceptional chondrogenic promoting capabilities shown during in vitro studies with bone marrow derived mesenchymal stem cells (BMSCs). They also can penetrate deep into cartilage tissue derived from porcine knee joints guided by their positive charge. Subsequently, a dynamic exosomes-crosslinked hydrogel (Gel-CEKT) is fabricated by crosslinking CEKT with oxidized chondroitin sulfate (oCS) and Wharton's jelly (WJ) through imine bond formation. Physicochemical studies revealed the injectability, excellent adhesive, and self-healing abilities of this hydrogel, which enables minimally invasive and precise treatment of cartilage defects, assisted by the enriched and sustained administration of CEKT. In vitro cell experiments show that Gel-CEKT can efficiently recruit BMSCs and significantly promote the gene expression of Sox9 and protein expression of collagen II and aggrecan. Furthermore, we show in a rat model of cartilage defect that the Gel-CEKT demonstrates superior performance compared to Gel@EKT, which has freely encapsulated exosomes in the hydrogel. The freely encapsulated exosomes are rapidly released, whereas the exosome-crosslinked gel structure ensures sustained retention and functionality at the site of defect. This leads to impressive outcomings, including extensive new cartilage tissue formation, a smoother cartilage surface, significant chondrocyte production, and seamless integration with orderly and continuous structure formation between cartilage and subchondral bone. This study underscores the potential of exosomes-crosslinked hydrogels as a novel and promising therapeutic approach for clinical cartilage regeneration.

Lipid nanoparticle (LNP) mediated mRNA delivery in neurodegenerative diseases

Neurodegenerative diseases (NDD) are characterized by the progressive loss of neurons and the impairment of cellular functions. Messenger RNA (mRNA) has emerged as a promising therapy for treating NDD, as it can encode missing or dysfunctional proteins and anti-inflammatory cytokines or neuroprotective proteins to halt the progression of these diseases. However, effective mRNA delivery to the central nervous system (CNS) remains a significant challenge due to the limited penetration of the blood-brain barrier (BBB). Lipid nanoparticles (LNPs) offer an efficient solution by encapsulating and protecting mRNA, facilitating transfection and intracellular delivery. This review discusses the pathophysiological mechanisms of neurological disorders, including Parkinson's disease (PD), Alzheimer's disease (AD), multiple sclerosis (MS), Huntington's disease (HD), ischemic stroke, spinal cord injury, and Friedreich's ataxia. Additionally, it explores the potential of LNP-mediated mRNA delivery as a therapeutic strategy for these diseases. Various approaches to overcoming BBB-related challenges and enhancing the delivery and efficacy of mRNA-LNPs are discussed, including non-invasive methods with strong potential for clinical translation. With advancements in artificial intelligence (AI)-guided mRNA and LNP design, targeted delivery, gene editing, and CAR-T cell therapy, mRNA-LNPs could significantly transform the treatment landscape for NDD, paving the way for future clinical applications.

Molecular mechanisms affected by boron deficiency in root and shoot meristems of plants

Boron deficiency is an abiotic stress that negatively impacts plant growth and yield worldwide. Boron deficiency primarily affects the development of plant meristems- stem cells critical for all post-embryonic tissue growth. The essential role of boron in meristem development was first established in 1923. It remains unclear whether boron directly integrates into meristem molecular signalling pathways. In addition to its stabilizing function in the primary cell wall, growing evidence suggests roles for boron in various molecular processes including phytohormone cascades. These indications enhance a mechanistic understanding of why boron is crucial for proper meristem development. In this review we compile and discuss molecular pathways influenced by boron availability in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), rice (Oryza sativa), and oilseed rape (Brassica napus) with a focus on the auxin-, ethylene-, and cytokinin-mediated hormone cascades. We particularly compare and contrast phenotypic and molecular adaptations of shoot and root meristems to boron deficiency and pinpoint tissue-specific differences.

Gibberellins: extending the Green Revolution

The Green Revolution more than doubled crop yields and food production in crop species such as wheat and rice. This was primarily accomplished by altering the gibberellin (GA) signaling pathway to reduce plant height and prevent plants from falling over when growth was promoted with fertilizer application. Similar approaches have not been successfully accomplished in other grass crop species, such as maize, due to pleiotropic deleterious traits that arise from altering the GA pathway. This review highlights new findings in GA research across grass crop species. We have primarily focused on the developmental role of GAs in plant architecture and growth. We discuss how alteration of GA effects could be used to alter plant morphology and development of ideal plant ideotypes for grass crop species. To further extend the Green Revolution and improve food production from cereal crop species, targeted and tissue-specific regulation of the GA pathway will have to be undertaken.

The effects of green light-emitting diode irradiation and inducer factors on the differentiation of human adipose tissue-derived mesenchymal cells into myocardial-like cells

Physical factors like LED light can influence cell behavior, impacting stem cell proliferation and differentiation. Stem cell-based therapies offer a promising alternative to heart transplantation for cardiac conditions like myocardial infarction. This study evaluated the effects of green LED light (530 nm) and a biochemical inducer cocktail (oxytocin and ascorbic acid) on human adipose tissue-derived mesenchymal stem cells (hAD-MSCs) differentiation into cardiomyocyte-like cells. hAD-MSCs were treated with LED, the cocktail, and their combination. Cardiomyogenic markers NKX2.5, GATA4, cTnI, and CX43 were assessed via real-time PCR and western blotting. LED and the cocktail enhanced cardiac gene expression and protein synthesis, but their combination showed significantly higher effects, especially on day 7. This study demonstrates for the first time that green LED light combined with oxytocin and ascorbic acid can enhance hAD-MSC cardiac differentiation, supporting its potential in regenerative therapies following human studies.

Diverse roles of ethylene in maize growth and development, and its importance in shaping plant architecture

The gaseous plant hormone ethylene is a key developmental and growth regulator, and a pivotal endogenous response signal to abiotic and biotic interactions, including stress. Much of what is known about ethylene biosynthesis, perception, and signaling comes from decades of research primarily in Arabidopsis thaliana and other eudicot model systems. In contrast, detailed knowledge on the ethylene pathway and response to the hormone is markedly limited in maize (Zea mays L.), a global cereal crop that is a major source of calories for humans and livestock, as well as a key industrial biofeedstock. Recent reports of forward screens and targeted reverse genetics have provided important insight into conserved and unique differences of the ethylene pathway and downstream responses. Natural and edited allelic variation in the promoter regions and coding sequences of ethylene biosynthesis and signaling genes alters maize shoot and root architectures, and plays a crucial role in biomass and grain yields. This review discusses recent advances in ethylene research in maize, with an emphasis on the role of ethylene in regulating growth and development of the shoot and root systems, and ultimately how this crucial hormone impacts plant architecture and grain yield.

Sex-Biased Gene Expression of RNAi Pathway Components in the Sea Lice Caligus rogercresseyi

RNA interference (RNAi) is a conserved mechanism for post-transcriptional gene regulation and a critical process of arthropod immunity. This study investigates RNAi-associated genes in Caligus rogercresseyi, an ectoparasitic sea louse that poses significant challenges to salmon aquaculture. In that regard, 16 RNAi-associated genes were identified by in silico analysis, including Cr-AGO1, Cr-CNOT1, Cr-DCR, Cr-SND1, and Cr-XRN1. Phylogenetic analysis demonstrated clustering with homologous sequences from other arthropods, particularly the ectoparasitic copepod Lepeophtheirus salmonis. RNA-Seq analyses revealed developmentally regulated expression patterns, with RNAi-associated genes clustered into four distinct expression profiles. Quantitative PCR (qPCR) validation confirmed significant male-biased expression for several key genes, including Cr-AGO1 (109-fold increase), Cr-DCR (22-fold), Cr-XRN1 (22-fold), Cr-SND1 (fourfold), and Cr-CNOT1 (threefold), suggesting potential roles in male reproductive processes such as spermatogenesis. Cr-DDX6, Cr-Drosha, and Cr-XPO5, potentially involved in oocyte development and RNA transport, exhibited female-biased expression. These results provide new insights into RNAi-associated gene expression in C. rogercresseyi, uncovering significant developmental and sex-biased expression patterns. Characterizing these critical genes establishes a foundation for exploring control strategies based on the RNAi process, targeting sex-biased and developmentally essential genes. Such treatments could reduce reproductive success in sea lice while minimizing environmental impact, offering a sustainable alternative for managing caligidosis in aquaculture.

Decoding microRNA arm switching: a key to evolutionary innovation and gene regulation

miRNA arm switching is a pivotal regulatory mechanism that allows organisms to fine-tune gene expression by selectively utilizing either the 5p or 3p strand of a miRNA duplex. This process, conserved across species, facilitates adaptive responses to developmental cues, environmental changes, and disease states. By dynamically altering strand selection, arm switching reshapes gene regulatory networks, contributing to phenotypic diversity and evolutionary innovation. Despite its growing recognition, the mechanisms driving arm switching-such as thermodynamic properties and enzyme-mediated processing-remain incompletely understood. This review synthesizes current findings, highlighting arm switching as a highly conserved mechanism with profound implications for the evolution of regulatory networks. We explore how this phenomenon expands miRNA functionality, drives phenotypic plasticity, and co-evolves with miRNA gene duplications to fuel the diversification of biological functions across taxa.

Tracing mitochondrial marks of neuronal aging in iPSCs-derived neurons and directly converted neurons

This study aims to determine if neurons derived from induced pluripotent stem cells (iPSCsNs) and directly converted neurons (iNs) from the same source cells exhibit changes in mitochondrial properties related to aging. This research addresses the uncertainty around whether aged iPSCsNs retain aging-associated mitochondrial impairments upon transitioning through pluripotency while direct conversion maintains these impairments. We observe that both aged models exhibit characteristics of aging, such as decreased ATP, mitochondrial membrane potential, respiration, NAD+/NADH ratio, and increased radicals and mitochondrial mass. In addition, both neuronal models show a fragmented mitochondrial network. However, aged iPSCsNs do not exhibit a metabolic shift towards glycolysis, unlike aged iNs. Furthermore, mRNA expression differed significantly between aged iPSCsNs and aged iNs. The study concludes that aged iPSCsNs may differ in transcriptomics and the aging-associated glycolytic shift but can be a valuable tool for studying specific feature of mitochondrial neuronal aging in vitro alongside aged iNs.

Emergence of CpG-cluster blanket methylation in aged tissues: a novel signature of epigenomic aging

Aging is accompanied by widespread DNA methylation changes across the genome. While age-related methylation studies typically focus on individual CpGs, cluster analysis provides more robust data and improved interpretation. We characterized age-associated CpG-cluster methylation changes in mouse spleens, peripheral blood mononuclear cells, and livers. We identified a novel signature termed blanket methylations (BMs), fully methylated CpG clusters absent in young tissues but appearing in aged tissues. BM formation was locus- and cell-dependent, with minimal overlap among tissues. Statistical analysis, heterogeneity assessment, and random modeling demonstrated that BMs arise through nonrandom mechanisms and correlate with accelerated aging. Notably, BMs appeared in chronologically young mice with progeroid or disease-driven aging, including in 4-month-old Zmpste24-/- (lifespan ∼5 months) and 3-month-old Huntington's disease model mice (lifespan ∼4 months). The detection of BMs in purified CD4+ T cells demonstrated that their occurrence is intrinsic to aging cells rather than a result of infiltration from other tissues. Further investigation revealed age-related downregulation of zinc-finger-CxxC-domain genes, including Tet1 and Tet3, which protect CpG islands from methylation. Importantly, TET1 or TET3 depletion induced BM formation, linking their loss to age-associated methylation drift. These findings establish BMs as a robust marker of epigenomic aging, providing insight into age-related methylation changes.

Massively parallel jumping assay decodes Alu retrotransposition activity

The human genome contains millions of copies of retrotransposons that are silenced but many of these copies have potential to become active if mutated, having phenotypic consequences, including disease. However, it is not thoroughly understood how nucleotide changes in retrotransposons affect their jumping activity. Here, we develop a massively parallel jumping assay (MPJA) that tests the jumping potential of thousands of transposons en masse. We generate a nucleotide variant library of four Alu retrotransposons containing 165,087 different haplotypes and test them for their jumping ability using MPJA. We found 66,821 unique jumping haplotypes, allowing us to pinpoint domains and variants vital for transposition. Mapping these variants to the Alu-RNA secondary structure revealed stem-loop features that contribute to jumping potential. Combined, our work provides a high-throughput assay that assesses the ability of retrotransposons to jump and identifies nucleotide changes that have the potential to reactivate them in the human genome.

Two independent regulatory mechanisms synergistically contribute to P450-mediated insecticide resistance in a lepidopteran pest, Spodoptera exigua

BACKGROUND

Cytochrome P450 enzymes play a pivotal role in the detoxification of plant allelochemicals and insecticides. Overexpression of P450 genes has been proven to be involved in insecticide resistance in insects. However, the molecular mechanisms underlying the regulation of P450 genes in insects are poorly understood.

RESULTS

Here, we determine that upregulation of CYP321B1 confers resistance to organophosphate (chlorpyrifos) and pyrethroid (cypermethrin and deltamethrin) insecticides in the resistant Spodoptera exigua strain. Enhanced expression of transcription factors CncC/Maf contributes to the increase in the expression of CYP321B1 in the resistant strain. Reporter gene assays and site-directed mutagenesis analyses confirm that a specific binding site is crucial for binding CncC/Maf to activate the expression of CYP321B1. In addition, creation of a new binding site resulting from the cis-mutations in the promoter region of CYP321B1 in the resistant strain facilitates the binding of the POU/homeodomain transcription factor Nubbin, and further enhances the expression of this P450 gene. Furthermore, we authenticate that changes in both trans- and cis-regulatory elements in the promoter region of CYP321B1 act in combination to modulate the promoter activity in a synergistic manner.

CONCLUSIONS

Collectively, these results demonstrate that two distinct but synergistic mechanisms coordinately result in the overexpression of CYP321B1 involved in insecticide resistance in an agriculturally important insect pest, S. exigua. The information on mechanisms of metabolic resistance could help to understand the development of resistance to insecticides by other pests and contribute to designing effective integrated pest management strategies for the pest control.

Multiplexing light-inducible recombinases to control cell fate, Boolean logic, and cell patterning in mammalian cells

Light-inducible regulatory proteins are powerful tools to interrogate fundamental mechanisms driving cellular behavior. In particular, genetically encoded photosensory domains fused to split proteins can tightly modulate protein activity and gene expression. While light-inducible split protein systems have performed well individually, few multichromatic and orthogonal gene regulation systems exist in mammalian cells. The design space for multichromatic circuits is limited by the small number of orthogonally addressable optogenetic switches and the types of effectors that can be actuated by them. We developed a library of red light-inducible recombinases and directed patterned myogenesis in a mesenchymal fibroblast-like cell line. To address the limited number of light-inducible domains (LIDs) responding to unique excitation spectra, we multiplexed light-inducible recombinases with our "Boolean logic and arithmetic through DNA excision" (BLADE) platform. Multiplexed optogenetic tools will be transformative for understanding the role of multiple interacting genes and their spatial context in endogenous signaling networks.

A BRASSINOSTEROID INSENSISTIVE 1 receptor kinase ortholog is required for sex determination in Ceratopteris richardii

Most ferns, unlike all seed plants, are homosporous and produce sexually undifferentiated spores. Sex ratio in many homosporous species is environmentally established by the secretion of antheridiogen from female/hermaphrodite gametophytes. Nearby undetermined gametophytes perceive antheridiogen, which induces male development. In the fern Ceratopteris richardii (Ceratopteris), hermaphroditic (her) mutants develop as hermaphrodites even in the presence of antheridiogen. Modern sequencing and genomic tools make the molecular identification of mutants in the 11-Gbp genome of this fern possible. We mapped 2 linked mutants, her7-14 and her7-19, to the same 16-Mbp interval on chromosome 29 of the Ceratopteris genome. An ortholog of the receptor kinase gene BRASSINOSTEROID INSENSITIVE 1 (BRI1) within this interval encoded a deletion mutation in her7-14 and a missense mutation in her7-19. Three other linked her mutants encoded missense mutations in the same gene, which we name HER7. Consistent with a function as a receptor kinase, HER7-GFP fusion protein localized to the plasma membrane and cytoplasm. Analysis of gene expression showed that brassinosteroid biosynthesis was upregulated in hermaphrodites compared with male gametophytes. Our work demonstrates that HER7 is required for sex determination in Ceratopteris and opens avenues for studying the evolution of antheridiogen systems.

Decoding the dual role of autophagy in cancer through transcriptional and epigenetic regulation

Autophagy is a conserved catabolic process that is essential for maintaining cellular homeostasis by degrading and recycling damaged organelles and misfolded proteins. In cancer, autophagy exhibits a context-dependent dual role: In early stages, autophagy acts as a tumor suppressor by preserving genomic integrity and limiting oxidative stress. In advanced stages, autophagy supports tumor progression by facilitating metabolic adaptation, therapy resistance, immune evasion, and metastasis. This review highlights the molecular mechanisms underlying this dual function and focuses on the transcriptional and epigenetic regulation of autophagy in cancer cells. Key transcription factors, including the MiT/TFE family, FOXO family, and p53, as well as additional regulators, are discussed in the context of stress-responsive pathways mediated by mTORC1 and AMPK. A deeper understanding of the transcriptional and epigenetic regulation of autophagy in cancer is crucial for developing context-specific therapeutic strategies to either promote or inhibit autophagy depending on the cancer stage, thereby improving clinical outcomes in cancer treatment.

Prmt1-mediated methylation regulates Ncoa4 stability to transactivate Adamts genes and promote bone extracellular matrix degradation in chronic hematogenous osteomyelitis

BACKGROUND

Protein arginine methyltransferases (Prmts) are essential regulators of various biological processes and have been implicated in the pathogenesis of numerous diseases. However, their role in osteomyelitis remains poorly understood.

METHODS

A mouse model of chronic hematogenous osteomyelitis (CHOM) was established by intravenous inoculation with Staphylococcus aureus (S. aureus). Gene and protein expression levels were quantified using RT-qPCR and immunoblot analysis, respectively. Protein interactions were determined via immunoprecipitation and co-immunoprecipitation assays. In vitro and in vivo assays were employed to evaluate protein methylation and ubiquitination. Bone destruction was assessed through histological staining.

RESULTS

Among 9 Prmt members, Prmt1 was the only one significantly upregulated in osteomyelitis-affected mice. Our findings revealed that the inflammatory microenvironment specifically upregulated Prmt1 expression in osteoblasts and osteocytes, which facilitated its interaction with the transcriptional activator Ncoa4 (nuclear receptor coactivator 4) and mediated Ncoa4 arginine methylation, thereby enhancing Ncoa4 protein stability. Methylated Ncoa4 formed a transcriptional complex with the histone acetyltransferase Cbp (CREB-binding protein) and transcription factor Ap1 (Activator protein 1), driving the expression of four Adamts genes (Adamts3/8/12/14) that promoted extracellular matrix (ECM) degradation in osteoblasts and osteocytes. In contrast, depletion or pharmacological inhibition of Prmt1 prevented Ncoa4 methylation upon stimulation with pro-inflammatory cytokines, leading to Ncoa4 ubiquitination by Rnf8 (Ring finger protein 8) E3 ligase and subsequent proteasomal degradation, eventually leading to downregulation of Adamts expression. Importantly, treatment with Prmt1 inhibitors TCE-5003 and MS023 significantly mitigated bone ECM degradation and prevented osteomyelitis progression in S. aureus-infected mice.

CONCLUSION

These findings identify Prmt1 as a pivotal regulator of bone ECM degradation in osteomyelitis through stabilization of Ncoa4 and highlight Prmt1 as a promising therapeutic target for osteomyelitis treatment.

A rare stop-gain SNP mutation in BrGL2 causes aborted trichome development in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

KEY MESSAGE

A rare stop-gain SNP mutation in BrGL2 confers short hair phenotype of Chinese cabbage via bulked-segregant analysis sequencing, fine-mapping and gene silencing analysis. Trichomes negatively affect the quality of Chinese cabbage, a leafy vegetable crop in the family Brassicaceae. The short hair trait is caused by abnormal trichome development. In this study, the BraA07g025490.3C gene was identified as a candidate gene for the short hair trait in Chinese cabbage by BSA-seq and fine-mapping analyses. It was subsequently named BrGL2 because of its strong homology to AtGL2 (At1g79840). Sequence analysis indicated that a C to G single-nucleotide polymorphism (SNP) mutation in the sixth exon of BrGL2 produced a premature stop codon in the HCW (short hair) line, resulting in a loss-of-function mutation of BrGL2. This stop-gain SNP mutation was found exclusively in the HCW line, and not in 524 diverse B. rapa accessions. Further analysis by virus-induced gene silencing showed that the knock-down of BrGL2 in HN19-G lines (wild-type hair) reduced the size of leaf trichomes. BrGL2 affected trichome development probably by impacting the expression of downstream transcription factor genes and cell wall-related genes, as determined by comparative transcriptome analyses of wild type and short hair lines. On the basis of the identification and verification of the key stop-gain SNP mutation in BrGL2 resulting in aborted trichome development in Chinese cabbage, we propose a model for trichome development.

Profiling and functional characterization of long noncoding RNAs during human tooth development

The regulatory processes in developmental biology research are significantly influenced by long non-coding RNAs (lncRNAs). However, the dynamics of lncRNA expression during human tooth development remain poorly understood. In this research, we examined the lncRNAs present in the dental epithelium (DE) and dental mesenchyme (DM) at the late bud, cap, and early bell stages of human fetal tooth development through bulk RNA sequencing. Developmental regulators co-expressed with neighboring lncRNAs were significantly enriched in odontogenesis. Specific lncRNAs expressed in the DE and DM, such as PANCR, MIR205HG, DLX6-AS1, and DNM3OS, were identified through a combination of bulk RNA sequencing and single-cell analysis. Further subcluster analysis revealed lncRNAs specifically expressed in important regions of the tooth germ, such as the inner enamel epithelium and coronal dental papilla (CDP). Functionally, we demonstrated that CDP-specific DLX6-AS1 enhanced odontoblastic differentiation in human tooth germ mesenchymal cells and dental pulp stem cells. These findings suggest that lncRNAs could serve as valuable cell markers for tooth development and potential therapeutic targets for tooth regeneration.

LC-MS/MS based metabolomics reveals the mechanism of skeletal muscle regeneration

BACKGROUND

Skeletal muscle possesses a robust regenerative capacity and can effectively repair itself following injury. However, research on the metabolic changes during skeletal muscle regeneration in large animals remains relatively limited. Therefore, in this study, we used pigs as a model and applied non-targeted LC-MS/MS metabolomic technology to reveal the metabolic changes during skeletal muscle regeneration, and conducted an in-depth exploration of important signaling pathways, which can provide a reference for further research on the mechanisms promoting skeletal muscle regeneration.

METHODS

In this study, we used 18 piglets aged 35 days and weighing 7.10 ± 0.90 kg to construct a skeletal muscle regeneration model. These piglets were randomly divided into three treatment groups (n = 6) and injected with cardiotoxins (CTX) in the right longissimus dorsi muscle. They were euthanized on the 1st, 4th, and 16th days post-injection to collect right longissimus dorsi muscle samples as the treatment group. Additionally, the left longissimus dorsi muscle of piglets on the 4th day post-injection was selected as the control group. Phenotypic changes in skeletal muscle regeneration were determined through H&E staining, immunofluorescence, and Western Blot analysis, and LC-MS/MS untargeted metabolomics technology was utilized to explore the differential expressed metabolites (DEMs) involved in skeletal muscle regeneration.

RESULTS

Phenotyping results showed that the regeneration model showed 3 stages of inflammation, regeneration and remodeling, which indicated successful model construction. Non-targeted LC-MS/MS metabolomics analysis showed significant differences in the structure of metabolites in these 3 stages. (1) In the inflammatory stage, a total of 198 DEMs were identified, which were mainly enriched in the pathways regulating the inflammatory response. (2) in the repair stage, 264 DEMs were identified, which were mainly enriched in pathways that inhibit inflammatory response and promote protein synthesis. (3) During the remodeling stage, 102 DEMs were identified, which were mainly enriched in the pathways that inhibit protein depletion and promote protein deposition. Temporal expression analysis revealed metabolites consistent with changes in the skeletal muscle regeneration process and found that these metabolite functions were mainly enriched in inhibiting inflammatory responses, alleviating myofibrillar lysis, and promoting muscle growth. Among them, (R)-Lipoic acid, 8-Hydroxyguanosine, and Uridine 5'-monophosphate maybe key metabolites associated with skeletal muscle regeneration.

CONCLUSION

The skeletal muscle regeneration mechanism was systematically explored, and the metabolite time series analysis during skeletal muscle regeneration revealed some key metabolites that reflect the degree of skeletal muscle damage.

Neuroimmune signaling mediates astrocytic nucleocytoplasmic disruptions and stress granule formation associated with TDP-43 pathology

Alterations in transactivating response region DNA-binding protein 43 (TDP-43) are prevalent in amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and other neurological disorders. TDP-43 influences neuronal functions and might also affect glial cells. However, specific intracellular effects of TDP-43 alterations on glial cells and underlying mechanisms are not clear. We report that TDP-43 dysregulation in mouse and human cortical astrocytes causes nucleoporin mislocalization, nuclear envelope remodeling, and changes in nucleocytoplasmic protein transport. These effects are dependent on interleukin-1 (IL-1) receptor activity and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling and are associated with the formation of cytoplasmic stress granules. Stimulation of IL-1 receptors and NF-κB signaling are necessary and sufficient to induce astrocytic stress granules and rapid nucleocytoplasmic changes, which are broadly alleviated by inhibition of the integrated stress response. These findings establish that TDP-43 alterations and neuroimmune factors can induce nucleocytoplasmic changes through NF-κB signaling, revealing mechanistic convergence of proteinopathy and neuroimmune pathways onto glial nucleocytoplasmic disruptions that may occur in diverse neurological conditions.

One organ to infect them all: the Cuscuta haustorium

BACKGROUND

Research on the parasitic plant genus Cuscuta has flourished since the genomes of several of its species were published. Most of the research revolves around the iconic infection organ that secures the parasite's sustenance: the haustorium. Interest in understanding the structure-function-regulation relationship of the haustorium is based as much on the wish to find ways to keep the parasite under control as on the opportunities it offers to shed light on various open questions in plant biology.

SCOPE

This review will briefly introduce parasitism among plants, using the genus Cuscuta as the main example, before presenting its haustorium alongside the terminology that is used to describe its architecture. Possible evolutionary origins of this parasitic organ are presented. The haustorium is then followed from its initiation to maturity with regard to the molecular landscape that accompanies the morphological changes and in light of the challenges it must overcome before gaining access to the vascular cells of its hosts. The fact that Cuscuta has an unusually broad host range stresses how efficient its infection strategy is. Therefore, particular consideration will be given in the final section to a comparison with the process of grafting, being the only other type of tissue connection that involves interspecific vascular continuity.

CONCLUSIONS

Studies on Cuscuta haustoriogenesis have revealed many molecular details that explain its success. They have also unearthed some mysteries that wait to be solved. With a better understanding of the complexity of the infection with its combination of universal as well as host-specific elements that allow Cuscuta to parasitize on a wide range of host plant species, we may be many steps closer to not only containing the parasite better but also exploiting its tricks where they can serve us in the quest of producing more and better food and fodder.

Intrinsically weak sex chromosome drive through sequential asymmetric meiosis

Meiotic drivers are selfish genetic elements that bias their own transmission, violating Mendel's Law of Equal Segregation. It has long been recognized that sex chromosome-linked drivers present a paradox: Their success in transmission can severely distort populations' sex ratio and lead to extinction. This paradox is typically solved by the presence of suppressors or fitness costs associated with the driver, limiting the propagation of the driver. Here, we show that Stellate (Ste) in Drosophila melanogaster represents a novel class of X chromosome-linked driver that operates with an inherent mechanism that weakens its drive strength. Ste protein asymmetrically segregates into Y-bearing cells during meiosis I, subsequently causing their death. Unexpectedly, Ste segregates asymmetrically again during meiosis II, sparing half of the Y-bearing spermatids from Ste-induced defects, thereby weakening the drive strength. Our findings reveal a mechanism by which sex chromosome drivers avoid suicidal success.

A cross-tissue transcriptomic approach decodes glucocorticoid receptor-dependent links to human metabolic phenotypes

Glucocorticoids, acting through the glucocorticoid receptor (GR), control metabolism, maintain homeostasis, and enable adaptive responses to environmental challenges. Their function has been comprehensively studied, leading to identification of numerous tissue-specific GR-dependent mechanisms. Abundant evidence shows that GR-triggered responses differ across tissues, however, the extent of this specificity was not comprehensively explored. It is also unknown how particular GR-induced molecular patterns are translated into profile of higher-level human traits. Here, we examine cross-tissue effects of GR activation on gene expression. We assessed changes induced by stimulation with GR agonist, dexamethasone in nine tissues (adrenal cortex, perigonadal adipose tissue, hypothalamus, liver, kidney, anterior thigh muscle, pituitary gland, spleen, and lungs) in adult male C57BL/6 mice, using whole-genome microarrays. Dexamethasone induced balanced transcriptional responses across all examined tissues with 585 identified dexamethasone-regulated transcripts, including 446 with significant treatment-tissue interaction effects. Clustering analysis revealed sixteen GR-dependent patterns, including those universal across tissues and tissue-specific. We leveraged existing gene annotations and created new annotation sets based on chromatin immunoprecipitation sequencing, recent large-scale genome-wide association studies, and human transcriptome collections. As expected, GR-dependent transcripts were associated with essential metabolic processes (glycolysis/gluconeogenesis, lipid-metabolism) and inflammation-related pathways. Beyond these, we found novel links between regulated gene patterns and human phenotypic traits, like reticulocyte count or blood triglyceride levels. Overall effects of GR stimulation are well coordinated and closely linked to biological roles of tissues and organs. Our findings provide novel insights into complex systemic and tissue-specific actions of glucocorticoids and their potential impacts on human physiology and pathology.

Self-propagating wave drives morphogenesis of skull bones in vivo

Cellular motion is a key feature of tissue morphogenesis and is often driven by migration. However, migration need not explain cell motion in contexts where there is little free space or no obvious substrate, such as those found during organogenesis of mesenchymal organs including the embryonic skull. Through ex vivo imaging, biophysical modeling, and perturbation experiments, we find that mechanical feedback between cell fate and stiffness drives bone expansion and controls bone size in vivo. This mechanical feedback system is sufficient to propagate a wave of differentiation that establishes a collagen gradient which we find sufficient to describe patterns of osteoblast motion. Our work provides a mechanism for coordinated motion that may not rely upon cell migration but on emergent properties of the mesenchymal collective. Identification of such alternative mechanisms of mechanochemical coupling between differentiation and morphogenesis will help in understanding how directed cellular motility arises in complex environments with inhomogeneous material properties.

Dopamine D2 receptor agonists abrogate neuroendocrine tumour angiogenesis to inhibit chemotherapy-refractory small cell lung cancer progression

Small cell lung cancer (SCLC) is difficult to treat due to its aggressiveness, early metastasis, and rapid development of resistance to chemotherapeutic agents. Here, we show that treatment with a dopamine D2 receptor (D2R) agonist reduces tumour angiogenesis in multiple in vivo xenograft models of human SCLC, thereby reducing SCLC progression. An FDA-approved D2R agonist, cabergoline, also sensitized chemotherapy-resistant SCLC tumours to cisplatin and etoposide in patient-derived xenograft models of acquired chemoresistance in mice. Ex vivo, D2R agonist treatment decreased tumour angiogenesis through increased apoptosis of tumour-associated endothelial cells, creating a less favourable tumour microenvironment that limited cancer cell proliferation. In paired SCLC patient-derived specimens, D2R was expressed by tumour-associated endothelial cells obtained before treatment, but D2R was downregulated in SCLC tumours that had acquired chemoresistance. D2R agonist treatment of chemotherapy-resistant specimens restored expression of D2R. Activation of dopamine signalling is thus a new strategy for inhibiting angiogenesis in SCLC and potentially for combatting chemotherapy-refractory SCLC progression.

Extracellular PKM2 modulates cancer immunity by regulating macrophage polarity

Tumor controls its immunity by educating its microenvironment, including regulating polarity of tumor associated macrophages. It is well documented that cancer cells release PKM2 to facilitate tumor progression. We report here that the extracellular PKM2 (EcPKM2) modulates tumor immunity by facilitating M2 macrophage polarization in tumors. EcPKM2 interacts with integrin αvβ3 on macrophage to activate integrin-FAK-PI3K signal axis. Activation of FAK-PI3K by EcPKM2 suppresses PTEN expression, which subsequently upregulates arginase1 (Arg1) expression and activity in macrophage to facilitate M2 polarity. Our studies uncover a novel and important mechanism for modulation of tumor immunity. More importantly, an antibody against PKM2 that disrupts the interaction between EcPKM2 and integrin αvβ3 is effective in converting M2 macrophages to M1 macrophages in tumors, suggesting a new therapeutic strategy and target for cancer therapies. Combination of the anti-PKM2 antibody with checkpoint blockades provides enhanced treatment effects.

Molecular Studies on Plant Telomeres: Expanding Horizons in Plant Biology

The integrity of plant genomes is intricately safeguarded by telomeres, the protective caps located at the ends of the chromosome. This review provides a comprehensive analysis of the molecular mechanisms governing the structure, maintenance, and dynamics of plant telomeres, highlighting their genetic and epigenetic regulation and their pivotal roles in plant development, longevity, stress adaptation, and disease resistance. Recent advancements, such as next-generation sequencing and single-molecule imaging, have revolutionized our understanding of telomere biology, unveiling new insights into telomerase activity and telomere-associated genetic variants. Additionally, the review also discusses the challenges and future directions of telomere research, including the potential applications of telomere biology in plant breeding and genetic engineering.

Endothelial cell metabolism in cardiovascular physiology and disease

Endothelial cells are multifunctional cells that form the inner layer of blood vessels and have a crucial role in vasoreactivity, angiogenesis, immunomodulation, nutrient uptake and coagulation. Endothelial cells have unique metabolism and are metabolically heterogeneous. The microenvironment and metabolism of endothelial cells contribute to endothelial cell heterogeneity and metabolic specialization. Endothelial cell dysfunction is an early event in the development of several cardiovascular diseases and has been shown, at least to some extent, to be driven by metabolic changes preceding the manifestation of clinical symptoms. Diabetes mellitus, hypertension, obesity and chronic kidney disease are all risk factors for cardiovascular disease. Changes in endothelial cell metabolism induced by these cardiometabolic stressors accelerate the accumulation of dysfunctional endothelial cells in tissues and the development of cardiovascular disease. In this Review, we discuss the diversity of metabolic programmes that control endothelial cell function in the cardiovascular system and how these metabolic programmes are perturbed in different cardiovascular diseases in a disease-specific manner. Finally, we discuss the potential and challenges of targeting endothelial cell metabolism for the treatment of cardiovascular diseases.

Rationally Designed Self-Derived Peptides Kill Escherichia coli by Targeting BamA and BamD Essential for Outer Membrane Protein Biogenesis

There is an urgent need to develop antibiotics with new mechanisms of action for combating antibiotic-resistant bacteria, particularly against Gram-negative pathogens that severely threaten human health. Here, we introduce the rational design and comprehensive characterization of self-derived antibacterial peptides that specifically target Escherichia coli BamA and BamD, vital components of the β-barrel assembly machine (BAM) for the folding and membrane integration of outer membrane proteins (OMPs) in Gram-negative bacteria. Among the three BamA-targeted peptides, BamA543-551, which corresponds to an extracellular loop of BamA, exhibits remarkable bactericidal activity against OM-permeabilizedE. coli cells. Similarly, among four BamD-targeted peptides, BamD163-187 corresponding to a BamA-interacting α-helix exhibits potent bactericidal activity. Notably, both BamA543-551 and BamD163-187 are able to kill other OM-permeabilized Gram-negative pathogens but not Gram-positive ones, and fusion with a cell membrane-penetrating peptide enabled them to directly kill intactE. coli cells. Further, both of them significantly change the cell membrane integrity ofE. coli, induce the accumulation of misfolded OmpF, and reduce the level of folded OmpF. In particular, in vivo photo-cross-linking analysis indicates that BamA543-551 disrupts the direct interaction between BamA and periplasmic chaperone SurA in livingE. coli cells, thus offering insights into their mode of action. Collectively, our findings confirm the potential of BamA and BamD as promising antibiotic targets and suggest that BamA- and BamD-derived peptides can be candidates for antibiotic development.

Integration of photoperiod and time-restricted feeding on the circadian gene rhythms in juvenile salmon

The circadian clock has evolved to synchronize animal behaviour and physiology with the external environment. Present in almost all cells, the clock is made up of a transcription-translation feedback loop that is responsive to cues such as light/dark cycles (photoperiod) and the time of feeding. Chinook salmon (Oncorhynchus tshawytscha) is a fish species whose clock is thought to be adapted in natural populations according to their latitude, where photoperiod variation can be extreme in northern spring/summer conditions. Here, we probed for the expression of circadian clock genes in four tissues of juvenile Chinook salmon under different environmental conditions. We find that the circadian clock is optimal when photoperiod is coupled with regular feeding during daylight hours. We further tested the effects of constant light and time-restricted feeding, environmental factors that are known to affect daily gene expression rhythms, on the expression of clock genes, appetite-regulating hormones, and metabolic regulators in the intestine of juvenile Chinook. We find that overall constant light is chrono-disruptive irrespective of the timing of food. The resulting disruption in gene expression produces aberrant rhythms, and affects glucose homeostasis, despite an increase in growth. Our data suggests photoperiod and time-restricted feeding could be optimized in Chinook aquaculture and raise the question of whether and how photoperiod changes are compensated in northern-adapted populations.

KAT5 regulates neurodevelopmental states associated with G0-like populations in glioblastoma

Quiescence cancer stem-like cells may play key roles in promoting tumor cell heterogeneity and recurrence for many tumors, including glioblastoma (GBM). Here we show that the protein acetyltransferase KAT5 is a key regulator of transcriptional, epigenetic, and proliferative heterogeneity impacting transitions into G0-like states in GBM. KAT5 activity suppresses the emergence of quiescent subpopulations with neurodevelopmental progenitor characteristics, while promoting GBM stem-like cell (GSC) self-renewal through coordinately regulating E2F- and MYC- transcriptional networks with protein translation. KAT5 inactivation significantly decreases tumor progression and invasive behavior while increasing survival after standard of care. Further, increasing MYC expression in human neural stem cells stimulates KAT5 activity and protein translation, as well as confers sensitivity to homoharringtonine, to similar levels to those found in GSCs and high-grade gliomas. These results suggest that the dynamic behavior of KAT5 plays key roles in G0 ingress/egress, adoption of quasi-neurodevelopmental states, and aggressive tumor growth in gliomas.

Cocultured amniotic stem cells and cardiomyocytes in a 3-D acellular heart patch reduce the infarct size and left ventricle remodeling: promote angiogenesis in a porcine acute myocardial infarction model

BACKGROUND

Acute myocardial infarction (AMI) induces significant myocardial damage, ultimately leading to heart failure as the surrounding healthy myocardial tissue undergoes progressive deterioration due to excessive mechanical stress.

METHODS

This study aimed to investigate myocardial regeneration in a porcine model of AMI using an acellular amniotic membrane with fibrin-termed an amnion bilayer (AB) or heart patch-as a cellular delivery system using porcine amniotic stem cells (pASCs) and autologous porcine cardiomyocytes (pCardios). Fifteen pigs (aged 2-4 months, weighing 50-60 kg) were randomly assigned to three experimental groups (n = 5): control group (AMI induction only), pASC group (pASC transplantation only), and coculture group (pASC and pCardio transplantation). AMI was induced via posterior left ventricular artery ligation and confirmed through standard biomarkers. After eight weeks, histological and molecular analyses were conducted to assess myocardial regeneration.

RESULTS

Improvement in regional wall motion abnormality (RWMA) was observed in 60% of the coculture group, 25% of the pASC group, and none in the control group. Histological analysis of the control group revealed extensive fibrosis with pronounced lipomatosis, particularly at the infarct center. In contrast, pASC and coculture groups exhibited minimal fibrotic scarring at both the infarct center and border regions. Immunofluorescence analysis demonstrated positive α-actinin expression in both the pASC and coculture groups, with the coculture group displaying sarcomeric structures-an organization absent in control group. RNA expression levels of key cardiomyogenic markers, including cardiac troponin T (cTnT), myosin heavy chain (MHC), and Nkx2.5, were significantly elevated in the treatment groups compared to the controls, with the coculture group exhibiting the highest MHC expression. The expression of c-Kit was also increased in both treatment groups relative to the control. Conversely, apoptotic markers p21 and Caspase-9 were highest in the control group, while coculture group exhibited the lowest p53 expression.

CONCLUSION

Epicardial transplantation of an acellular amniotic heart patch cocultured with cardiomyocytes and pASCs demonstrated superior cardiomyogenesis after eight weeks compared to pASC transplantation alone or control conditions. The coculture system was found to enhance the cardiac regeneration process, as evidenced by improved RWMA, distinct sarcomeric organization, reduced fibrotic scarring, and lower apoptotic gene expression.

Most human DNA replication initiation is dispersed throughout the genome with only a minority within previously identified initiation zones

BACKGROUND

The identification of sites of DNA replication initiation in mammalian cells has been challenging. Here, we present unbiased detection of replication initiation events in human cells using BrdU incorporation and single-molecule nanopore sequencing.

RESULTS

Increases in BrdU incorporation allow us to measure DNA replication dynamics, including identification of replication initiation, fork direction, and termination on individual nanopore sequencing reads. Importantly, initiation and termination events are identified on single molecules with high resolution, throughout S-phase, genome-wide, and at high coverage at specific loci using targeted enrichment. We find a significant enrichment of initiation sites within the broad initiation zones identified by population-level studies. However, these focused initiation sites only account for ~ 20% of all identified replication initiation events. Most initiation events are dispersed throughout the genome and are missed by cell population approaches. This indicates that most initiation occurs at sites that, individually, are rarely used. These dispersed initiation sites contrast with the focused sites identified by population studies, in that they do not show a strong relationship to transcription or a particular epigenetic signature.

CONCLUSIONS

We show here that single-molecule sequencing enables unbiased detection and characterization of DNA replication initiation events, including the numerous dispersed initiation events that replicate most of the human genome.