Rescue of a unique ovine parainfluenza virus type 3 strain via Red/ET assembly

Parainfluenza virus type 3 (PIV3) is an important pathogen that causes respiratory disease in humans and many animals, but ovine infection has been rarely reported. In this study, a strain of ovine parainfluenza virus type 3 (OPIV3) was isolated from a sheep farm in Tianjin, China, and named TJ2022. Phylogenetic analysis indicated a high homology between the TJ2022 strain and the OPIV3 TX01 strain. Compared with the TX01 strain, TJ2022 showed 17 and 13 unique amino acid mutations in the P and L proteins, respectively, and possessed a distinct gene end sequence, suggesting unique genetic evolution of TJ2022. Three-dimensional structural prediction analysis of the L protein indicated that characteristic mutations in the L protein may affect the virus's replication capacity. Host immune response analysis showed that the expression levels of IFN-α, IFN-β, and interferon stimulated genes (Mx1, IFI6, ISG15, and OAS1) were significantly elevated after TJ2022 infection. Furthermore, using the Red/ET homologous recombination system, we constructed an infectious clone of OPIV3 dependent on the T7 promoter (rTJ2022). The rTJ2022 exhibited genetic stability, growth kinetics, and host cell immune response similar to TJ2022. This study establishes the foundation for exploring OPIV3 infection and defense mechanisms, epidemiology, and the potential development of live vector vaccines.

Long-term nucleus basalis cholinergic lesions alter the structure of cortical vasculature, astrocytic density and microglial activity in Wistar rats

Basal forebrain cholinergic neurons (BFCNs) are the sole source of cholinergic innervation to the cerebral cortex and hippocampus in humans and the primary source in rodents. This system undergoes early degeneration in Alzheimer's disease. BFCNs terminal synapses are involved in the regulation of the cerebral blood flow by making classical synaptic contacts with other neurons. Additionally, they are located in proximity to cortical cerebral blood vessels, forming connections with various cell types of the neurovascular unit (NVU), including vascular smooth muscle cells, endothelial cells, and astrocytic end-feet. However, the effects of the BFCNs input on NVU components remain unresolved. To address this issue, we immunolesioned the nucleus basalis by administering bilateral stereotaxic injections of the cholinergic immunotoxin 192-IgG-Saporin in 2.5-month-old Wistar rats. Seven months post-lesion, we observed a significant reduction in cortical vesicular acetylcholine transporter-immunoreactive synapses. This was accompanied by changes in the diameter of cortical capillaries and precapillary arterioles, as well as lower levels of vascular endothelial growth factor A (VEGF-A). Additionally, the cholinergic immunolesion increased the density of cortical astrocytes and microglia in the cortex. At these post-BFCN-lesion stages, astrocytic end-feet exhibited an increased co-localization with arterioles. The number of microglia in the parietal cortex correlated with cholinergic loss and exhibited morphological changes indicative of an intermediate activation state. This was supported by decreased levels of proinflammatory mediators IFN-γ, IL-1β, and KC/GRO (CXCL1), and by increased expression of M2 markers SOCS3, IL4Rα, YM1, ARG1, and Fizz1. Our findings offer a novel insight: that the loss of nucleus basalis cholinergic input negatively impacts cortical blood vessels, NVU components, and microglia phenotype.

Wnt3a is an early regulator of the Wolffian duct directionality via the regulation of apicobasal cell polarity

The Wolffian duct is a pair of epithelial ductal structures along the body axis that induces nephron development by interaction with the metanephric mesenchyme. The interaction between the mesenchyme and the ureteric bud derived from the Wolffian duct is mediated by Wnt ligands, the loss of which results in kidney agenesis. Nonetheless, the early contribution of Wnt signaling to Wolffian duct formation remains unclear. We therefore examined these dynamics in knockout and transgenic mouse embryos. The Wnt signal reporter was active in the extending Wolffian duct, and Wnt3a-knockout embryos exhibited a fragmented and misdirectional Wolffian duct. Apicobasal polarity was disrupted under Wnt3a-deficiency. These findings suggest that Wnt3a plays an important role in Wolffian duct development by regulating apicobasal polarity.

Non-coding RNA RMRP governs RAB31-dependent MMP secretion, enhancing ovarian cancer invasion

Non-coding RNAs (ncRNAs) are frequently dysregulated in various cancers and have been implicated in the etiology and progression of cancer. Ovarian cancer, the most fatal gynecological cancer, has a poor prognosis and a high patient fatality rate due to metastases. In this study, we classified patients with ovarian cancer into three groups based on their ncRNA expression levels. Notably, an ncRNA transcribed by RNA polymerase III, RNA component of mitochondrial RNA processing endoribonuclease (RMRP), is highly expressed in a group with a poor prognosis. Functional assays using SKOV3 and HeyA8 human ovarian cancer cell lines revealed that while RMRP modulation had no significant effect on cell viability, it markedly enhanced cell invasion. Knockdown and ectopic expression experiments demonstrated that RMRP promotes the secretion of matrix metalloproteinase (MMP)-2 and -9, thereby facilitating ovarian cancer cell invasiveness. Transcriptomic analysis further revealed a positive correlation between RMRP expression and genes involved in cellular localization, including RAB31, a member of the Ras-related protein family. Notably, RAB31 knockdown abrogated the pro-invasive effects of RMRP, identifying it as a key downstream effector in SKOV3 and HeyA8 cells. In addition, MechRNA analysis identified RAB31 as a putative RMRP-interacting transcript. These findings establish RMRP as a critical regulator of RAB31-dependent MMP secretion and ovarian cancer cell invasion. Moreover, our results suggest that RMRP could serve as a promising prognostic biomarker for ovarian cancer.

Testes-specific protease 50 heightens stem-like properties and improves mitochondrial function in colorectal cancer

AIMS

The progression of colorectal cancer (CRC) is driven by a small subset of cancer stem-like cells (CSCs), and mitochondrial function is essential for maintaining their stemness. TSP50, a novel identified oncogene, has been found to promote cell proliferation in multiple cancer types. In this study, we detected the regulatory role of TSP50 in regulating CSC-like properties and mitochondrial mass in CRC.

MATERIALS AND METHODS

First, TSP50 expression and clinical relevance were analyzed via clinical databases and immunohistochemical (IHC). Subsequently, bioinformatic analyses, CRC cell lines, tumorsphere cultures, and mouse xenograft models were utilized to evaluate the relationship between TSP50 and CSC-like properties as well as mitochondrial mass. Finally, immunofluorescence, immunoprecipitation, and Western blotting were performed to dissect the regulatory mechanisms of TSP50, followed by rescue experiments conducted both in vitro and in vivo.

KEY FINDINGS

TSP50 was overexpressed in CRC tissues, correlating with poor drug response and shorter overall survival (OS). Meanwhile, TSP50 was shown to enhance CSC-like properties in both CRC cells and mouse xenograft models, while concurrently increasing mitochondrial mass and reducing ROS levels, these effects were partially reversed by inhibition of the PI3K/AKT pathway. Mechanistic investigations revealed that TSP50-induced activation of PI3K/AKT signaling is primarily mediated by the enhanced catalytic activity of PI3K p110α subunit.

SIGNIFICANCE

Collectively, TSP50 drives CRC malignancy by promoting CSC-like properties and enhancing mitochondrial function through PI3K/AKT signaling. These findings identify TSP50 as a potential therapeutic target for eliminating CSC-like cells and improving clinical outcomes in CRC treatment.

IGF1R activates FOXP3-β-catenin signaling to promote breast cancer development

PURPOSE

Forkhead box P3 (FOXP3), a key marker of regulatory T cells (Tregs), is crucial for Treg differentiation and development. Emerging evidence suggests that FOXP3 is also expressed in various tumor cells; however, its role in tumor progression remains controversial. This study aimed to elucidate the impact of FOXP3 on breast cancer development.

METHODS

Breast cancer cell lines, including HCC1937, HCC1806, Hs 578T, MDA-MB-231, and MCF-7, along with xenograft mouse models, to assess the effects of FOXP3 on cell proliferation and tumor growth. FOXP3 expression in human breast cancer samples was analyzed using quantitative PCR and immunohistochemistry analyses. Cell proliferation and invasion were evaluated through MTS and transwell assays, respectively. Chromatin immunoprecipitation (ChIP) assays were performed to determine FOXP3 binding to the β-catenin gene promoter.

RESULTS

FOXP3 expression was elevated in advanced breast cancer and correlates with poor clinical outcomes. FOXP3 directly binds to β-catenin gene promoter - 986 to - 1168 region to facilitate β-catenin transcription, consequently resulting in increased breast cancer cell proliferation, migration, and invasion in vitro and tumor growth in vivo. Furthermore, IGF1R activated FOXP3-β-catenin signaling to promote breast tumor growth. Moreover, elesclomol, a potent copper ionophore, significantly inhibited FOXP3 expression to suppress breast tumor growth.

CONCLUSION

This study indicates that FOXP3 plays an oncogenic role in breast cancer development and suggests that targeting IGF1R-FOXP3-β-catenin signaling may be a putative therapeutic strategy for human breast cancer treatment.

Macrophage Changes and High-Throughput Sequencing in Aging Mouse Intervertebral Disks

Background

Intervertebral disk (IVD) degeneration is associated with lower back pain and aging; however, the mechanisms underlying age-related changes and the changes in macrophage polarization in aging intervertebral disks require further elucidation. The aim of this study was to evaluate changes in macrophages, the differential expression of senescence genes, and their relationship with hub genes in IVDs during aging in mice.

Methods

Twenty-eight male wild C57 mice aged 4 weeks were divided into two groups. Four mice per group were selected for high-throughput sequencing and 10 for tail IVD immunohistochemical analysis. Adult and aged mouse IVD specimens were stained with hematoxylin-eosin, Fast Green, and Alcian Blue to determine collagen (Col) 1, Col2, proteoglycan, P16, P21, P53, CD11b, CD86, CD206, IL-1, TGF-β, and IL-4 expression. High-throughput sequencing was performed on adult and aged mouse IVD tissues.

Results

Aged mouse IVDs showed reduced height and marked degeneration, with decreased Col2 and proteoglycan expression and increased Col1 expression. The expression of senescence markers, senescence-associated IL-1, TGF-β, and IL-4, and macrophage-related markers, CD11b, CD86, and CD206, increased markedly with age. High-throughput sequencing revealed 1975 differentially expressed genes in adult and aged mice, with 797 genes showing upregulated expression (top five: Kcna7, Mmp9, Panx3, Myl10, and Bglap) and 1178 showing downregulated expression (top five: Srd5a2, Slc38a5, Gm47283, Npy, and Pcdh8). Gene Ontology and pathway enrichment analyses highlighted aging-related cellular components, biological processes, and metabolic pathways. The identified hub genes included Cox5a, Ndufs6, and Ndufb9.

Conclusions

Disk senescence and reduced height in aged mice are linked to upregulated expression of senescence-associated phenotypes and macrophage polarization markers. These findings suggest that macrophages and differential gene expression play key roles in age-related IVD degeneration, indicating that they can be used as potential targets for therapeutic intervention.

Vegfr3 activation of Pkd2l1+ CSF-cNs triggers the neural stem cell response in spinal cord injury

Activating adult neural stem cells (NSCs) located within the spinal cord niche is considered a promising therapeutic approach for treating spinal cord injury (SCI). Cerebrospinal fluid (CSF)-contacting neurons expressing Pkd2l1 exhibit phenotypic and molecular traits similar to those of adult NSCs. However, the mechanism responsible for regulating the activation of Pkd2l1+ CSF-cNs still needs to be discovered. This research demonstrated that Pkd2l1+ CSF-cNs have a high concentration of vascular endothelial growth factor receptor 3 (Vegfr3) and that SCI results in elevated Vegfr3 levels. The overexpression of Vegfr3 in Pkd2l1+CSF-cNs induced potential NSC activation. Blocking Vegfr3 led to a significant reduction in the percentage of active Pkd2l1+ CSF-cNs, suggesting that Vegfr3 is involved in controlling the shift from dormancy to activation in these cells. In vivo, the downregulation of Vegfr3 by SAR131475 inhibited Pkd2l1+CSF-cN proliferation and maintained self-renewal. Injection of vascular endothelial growth factor C (Vegf-C) into the lateral ventricle of adult mice confirmed the involvement of Vegfr3 in activating Pkd2l1+ CSF-cNs. Vegf-C administration significantly increased the number of activated Pkd2l1+ CSF-cNs. Mechanistically, Vegfr3 primed quiescent Pkd2l1+ CSF-cNs for cell cycle reentry by enabling the activation of PI3K/Akt signaling. The activation of Vegfr3 may enhance SCI outcomes by promoting neuronal survival and facilitating the recovery of motor function in mice. Together, our findings highlight that Vegfr3 is a crucial functional regulator of Pkd2l1+ CSF-cNs, governing the transition from NSC quiescence to activation.

VRK2 kinase pathogenic pathways in cancer and neurological diseases

The VRK2 ser-thr kinase, belonging to the dark kinome, is implicated in the pathogenesis of cancer progression, neurological and psychiatric diseases. The VRK2 gene codes for two isoforms. The main isoform (VRK2A) is mainly located in the cytoplasm, and anchored to different types of membranes, such as the endoplasmic reticulum, mitochondria and nuclear envelope. The VRK2A isoform interacts with signaling modules assembled on scaffold proteins such as JIP1 or KSR1, forming stable complexes and blocking the activation of regulatory signaling pathways by altering their intracellular localization and the balance among them. VRK2 regulates apoptosis, nuclear membrane organization, immune responses, and Cajal bodies. Wild-type VRK2 is overexpressed in tumors and contributes to cancer development. In cells and tumors with low levels of nuclear VRK1, VRK2 generates by alternative splicing a shorter isoform (VRK2B) that lacks the C-terminal hydrophobic tail and permits its relocation to nuclei. Furthermore, rare VRK2 gene variants are associated with different neurological or psychiatric diseases such as schizophrenia, epilepsy, bipolar disorder, depression, autism, circadian clock alterations and insomnia, but their pathogenic mechanism is unknown. These diseases are a likely consequence of an altered balance among different signaling pathways that are regulated by VRK2.

The Impact of VEGF-C-Induced Dural Lymphatic Vessel Growth on Ischemic Stroke Pathology

Timely relief of edema and clearance of waste products, as well as promotion of anti-inflammatory immune responses, reduce ischemic stroke pathology, and attenuate harmful long-term effects post-stroke. The discovery of an extensive and functional lymphatic vessel system in the outermost meningeal layer, dura mater, has opened up new possibilities to facilitate post-stroke recovery by inducing dural lymphatic vessel (dLV) growth via a single injection of a vector encoding vascular endothelial growth factor C (VEGF-C). In the present study, we aimed to improve post-stroke outcomes by inducing dLV growth in mice. We injected mice with a single intracerebroventricular dose of adeno-associated viral particles encoding VEGF-C before subjecting them to transient middle cerebral artery occlusion (tMCAo). Behavioral testing, Gadolinium (Gd) contrast agent-enhanced magnetic resonance imaging (MRI), and immunohistochemical analysis were performed to define the impact of VEGF-C on the post-stroke outcome. VEGF-C improved stroke-induced behavioral deficits, such as gait disturbances and neurological deficits, ameliorated post-stroke inflammation, and enhanced an alternative glial immune response. Importantly, VEGF-C treatment increased the drainage of brain interstitial fluid (ISF) and cerebrospinal fluid (CSF), as shown by Gd-enhanced MRI. These outcomes were closely associated with an increase in the growth of dLVs around the region where we observed increased vefgc mRNA expression within the brain, including the olfactory bulb, cortex, and cerebellum. Strikingly, VEGF-C-treated ischemic mice exhibited a faster and stronger Gd-signal accumulation in ischemic core area and an enhanced fluid outflow via the cribriform plate. In conclusion, the VEGF-C-induced dLV growth improved the overall outcome post-stroke, indicating that VEGF-C has potential to be included in the treatment strategies of post-ischemic stroke. However, to maximize the therapeutic potential of VEGF-C treatment, further studies on the impact of an enhanced dural lymphatic system at clinically relevant time points are essential.

Revenge unraveling the fortress: Exploring anticancer drug resistance mechanisms in BC for enhanced therapeutic strategies

Breast cancer (BC) is the most prevalent form of cancer in women worldwide and the main cause of cancer-related fatalities in females. BC can be classified into various types based on where cancer has begun to grow or spread, specific characteristics that influence how cancer behaves, and treatment choices. BC is multifaceted, and due to its diverse nature, the mechanisms involved are complex and have not yet been understood. Overexpression and expression of various factors involved in the functioning of mechanisms lead to abnormal changes, providing an environment supporting cancer cell growth. Understanding BC risk factors and early diagnosis through screening techniques like mammography and diagnostic techniques such as imaging and biopsies has advanced significantly. A wide range of treatment options, including surgery, radiation, chemotherapy, targeted treatments, and hormonal therapies, are now available. Daily advancements are being made in the clinical treatment of BC. Still, BC drug resistance cases remain highly prevalent and are currently one of the biggest problems faced by medical science. To increase response rates and possibly lengthen survival, there is a critical requirement for novel medicines with minimal sensitivity to overcome drug resistance. This review classifies different mechanisms that are involved in the development of BC and workable pharmacological targets and explains how they relate to the development of BC drug resistance. By concentrating on the mechanisms covered in this review, we can have a deep understanding of different mechanisms and learn innovative ways to develop novel therapeutics for the disease to combat medication resistance.

Membrane-associated ring-CH-type finger 2 protects against metabolic dysfunction-associated fatty liver disease by targeting fatty acid synthase

OBJECTIVE

Metabolic dysfunction-associated fatty liver disease (MAFLD) has emerged as an important public health concern that poses a significant threat to human health and imposes a substantial economic burden. Research has demonstrated that ubiquitin ligase-mediated substrate protein ubiquitination is a pivotal factor influencing liver lipid homeostasis and metabolic abnormalities in MAFLD. Nevertheless, the specific enzyme molecules implicated in this regulatory process remain to be elucidated. We have published a transcriptome-overexpressing ubiquitin ligase, membrane-associated ring-CH-type finger 2 (MARCH2), in HepG2 cells, and subsequent reanalysis of these transcriptome data revealed a close association between MARCH2 and lipid metabolism.

METHODS

By employing a range of methodologies, including recombinant adeno-associated virus (rAAV) transduction, lentiviral transduction, immunoblotting, quantitative PCR, tissue section staining, ubiquitination assays, serum biochemical analysis, immunoprecipitation, and mass spectrometry, this study investigated the functions and mechanisms of MARCH2 in the progression of MAFLD at the molecular, cellular, and organismal levels.

RESULTS

Overexpression of MARCH2, but not its catalytically inactive ligase variant, inhibited lipid accumulation in HepG2 cells. Additionally, MARCH2 undergoes K48-linked self-polyubiquitination and subsequent proteasomal degradation in response to oleic acid/palmitic acid stimulation. Furthermore, knockout of MARCH2 exacerbates the progression of MAFLD-related phenotypes, including increased body weight, impaired glucose tolerance, reduced insulin sensitivity, hypercholesterolemia, hepatic lipid accumulation, and steatosis, in high-fat diet-fed mice, irrespective of sex. Mechanistically, MARCH2 facilitates the polyubiquitination and degradation of fatty acid synthase (FASN) in the de novo lipogenesis pathway. And liver-specific overexpression of MARCH2 by rAAV effectively reduces FASN levels and further ameliorates MAFLD in ob/ob mice.

CONCLUSIONS

MARCH2 undergoes self-ubiquitination and plays an important role in maintaining the liver lipid homeostasis of MAFLD, and drug intervention in the MARCH2-FASN axis is a promising approach for treating systemic metabolic abnormalities in MAFLD.

IL-4 alters TLR7-induced B cell developmental program in lupus

TLR7 stimulation of T-bet+CD11c+IgD-CD27- double-negative 2 (DN2) B cells is crucial for autoantibody formation in systemic lupus erythematosus (SLE). Here, we show that administration of IL-4 for five weeks significantly reduced autoantibodies and T-bet+CD11c+ IgD- B cells in autoimmune BXD2 mice treated with R848, a TLR7 agonist. Single-cell transcriptomics analysis indicates that following two doses of in vivo administration, IL-4 redirected development toward follicular, CD23+ germinal center (GC), and DN4-like memory B cells compared to treatment with R848 alone. While IL-4 enhanced genes related to antigen processing and presentation, it also suppressed R848-induced Ki67+ GC B cells in vivo. In vitro stimulation of SLE patient B cells with a DN2 polarizing cocktail revealed that IL-4 reduced the expression of interferon response and DN2 signature genes, promoting a population of CD23+T-bet- DN4 B population. These findings suggest that developmental reprogramming by IL-4 counteracts TLR7-promoted DN2 and GC B cells in SLE.

Paving the way for bacteria-based drug delivery: biohybrid microrobots emerging from microrobotics and synthetic biology

Advances in microrobotics and synthetic biology are paving the way for innovative solutions to long-standing challenges in drug delivery. Both fields have independently worked on engineering bacteria as a therapeutic system, focusing on enhancing propulsion, cargo delivery, detection, and biocompatibility. Bacteria, with their inherent adaptability and functional versatility, serve as an ideal foundation for these efforts, enabling them to navigate complex biological environments such as the human body. This review explores the convergence of microrobotics and synthetic biology, which has catalysed the development of biohybrid bacterial microrobots that integrate the strengths of both disciplines. By incorporating external control modalities - such as light, ultrasound, and magnetic fields - these hybrid systems address the limitations of purely microrobotic or biological approaches, offering new opportunities to enhance precision and efficacy in targeted therapies. However, realising the full potential of biohybrid bacterial microrobots requires overcoming critical challenges, such as ensuring compatibility between biological and synthetic components, scaling manufacturing processes, and defining regulatory pathways tailored to living therapeutics. Addressing these hurdles through joint, interdisciplinary research efforts, can unlock the transformative possibilities of these systems in modern medicine.

Surfactin accelerates Bacillus subtilis pellicle biofilm development

Surfactin is a biosurfactant produced by many B. subtilis strains with a wide variety of functions from lowering surface tension to allowing motility of bacterial swarms, acting as a signaling molecule, and even exhibiting antimicrobial activities. However, the impact of surfactin during biofilm formation has been debated with variable findings between studies depending on the experimental conditions. B. subtilis is known to form biofilms at the solid-air, the solid-medium, and the liquid-air interfaces, the latter of which is known as a pellicle biofilm. Pellicle formation is a complex process requiring coordinated movement to the liquid-air interface and subsequent cooperative production of biofilm matrix components to allow robust pellicle biofilm formation. This makes pellicle formation a promising model system for assaying factors in biofilm formation and regulation. Here, we assayed the influence of surfactin and additional metabolites on the timing of pellicle biofilm formation. Using time-lapse imaging, we assayed pellicle formation timing in 12 B. subtilis isolates and found that one, MB9_B4, was significantly delayed in pellicle formation by approximately 10 h. MB9_B4 was previously noted to lack robust surfactin production. Indeed, deletion of surfactin synthesis in the other isolates delayed pellicle formation. Further, pellicle delay was rescued by addition of exogeneous surfactin. Testing reporters of biofilm-related gene expression revealed that induction of pellicle formation was caused by a combination of increased gene expression of one of the biofilm components and promotion of growth.

Molecular insights into human soleus muscle atrophy development: long-term dry immersion effects on the transcriptomic profile and posttranslational signaling

Muscle disuse results in complex signaling alterations followed by structural and functional changes, such as atrophy, force decrease, and slow-to-fast fiber-type shift. Little is known about human skeletal muscle signaling alterations under long-term muscle disuse. In this study, we describe the effects of 21-day dry immersion on human postural soleus muscle. We performed both transcriptomic analysis and Western blots to describe the states of the key signaling pathways regulating soleus muscle fiber size, fiber type, and metabolism. Twenty-one-day dry immersion resulted in both slow-type and fast-type myofibers atrophy, downregulation of rRNA content, and mTOR signaling. Twenty-one-day dry immersion also leads to slow-to-fast fiber-type and gene expression shift, upregulation of p-eEF2, p-CaMKII, p-ACC content and downregulation of NFATc1 nuclear content. It also caused massive gene expression alterations associated with calcium signaling, cytoskeletal parameters, and downregulated mitochondrial signaling (including fusion, fission, and marker of mitochondrial density).NEW & NOTEWORTHY The main findings of our study are as follows: 1) The soleus slow fibers atrophy after 21-day dry immersion (DI) does not exceed that after 7-day DI; 2) The soleus ubiquitin ligases expression after 21-day DI returns to its initial level; 3) The soleus slow fibers atrophy after 21-day DI is accompanied by a mitochondrial apparatus structural markers decrease; 4) The soleus fibers signaling pathways restructuring process during 21-day DI is carried out in a complex manner.

Relation of Alzheimer's disease-related TDP-43 proteinopathy to metrics from diffusion tensor imaging (DTI) and neurite orientation dispersion and density imaging (NODDI)

Transactive response DNA-binding protein 43 kDa (TDP-43) deposition is linked to regional brain atrophy in Alzheimer's disease (AD), but diffusion changes associated with AD-related TDP-43 proteinopathy remain underexplored. This study evaluates the potential of diffusion tensor imaging (DTI) and neurite orientation dispersion and density imaging (NODDI) as in vivo markers for detecting TDP-43 proteinopathy in AD. We analyzed DTI and NODDI metrics in 49 cases with AD neuropathologic changes, categorized by postmortem TDP-43 status. Diffusion metrics from the temporal lobe gray and white matter regions and key white matter tracts were compared between TDP-43-positive and negative cases. Group differences were significant in the left hippocampus, amygdala, and uncinate fasciculus after adjusting for age, Braak neurofibrillary tangle (NFT) stage and APOE ε4 status. TDP-43-positive cases showed increased mean diffusivity (MD) and altered neurite density index (NDI) and orientation dispersion index (ODI). Area under the receiver operating characteristic curve (AUROC) analysis revealed high predictive accuracy for amygdala ODI (AUC = 0.809, sensitivity = 0.81, specificity = 0.76), hippocampal MD (AUC = 0.763, sensitivity = 0.81, specificity = 0.67), and uncinate fasciculus MD (AUC = 0.782, sensitivity = 0.88, specificity = 0.61). Combined, DTI/NODDI predictors demonstrated stronger discriminative ability (AUC = 0.856, sensitivity = 0.88, specificity = 0.76). These findings suggest that AD-related TDP-43 proteinopathy is associated with specific diffusion changes in the left temporal lobe. DTI and NODDI metrics, particularly MD, NDI, and ODI, may improve the antemortem detection of TDP-43 pathology in AD.

Genetic architecture of anthocyanin pigment traits and purple spot (Stemphylium vesicarium) resistance in an F1 pseudo-testcross population of asparagus

Stemphylium vesicarium (Wallr.) Simmons is a plant pathogenic fungus causing purple spot in both fern and spears of asparagus (Asparagus officinalis L.). Although the fern can be sprayed with fungicides to control the disease, pesticide applications during spear harvest are restricted. Infected spears can develop prominent pigmentation at lesion sites, reducing marketable yield. Breeding resistant asparagus cultivars with decreased lesion numbers and reduced purpling at the site of infection is considered the most economical and sustainable approach to combat this disease. The objectives of this study were to determine the genetic architectures of, and relationships among, anthocyanin pigment expression in spear scale leaves (ALS) and spear lesions (APS) and purple spot levels in spears (NPS) and fern (PSF). Traits were phenotyped over 2 years under natural conditions in an F1 pseudo-testcross population, and quantitative trait loci (QTL) were mapped. ALS, APS, NPS, and PSF were not correlated, suggesting independent regulation of the anthocyanin pathway in scale leaves and lesions and no relationship between pigment and disease. Segregation, 3 red:1 purple and 3 red:13 purple, was observed in scale leaves and lesions, respectively. Two stable QTL for each of ASL, APS, and NPS, one tentative QTL for ASL, four tentative QTL for APS, two tentative QTL for NPS, and three tentative QTL for PSF were identified. Candidate genes were found for four loci. This study advances the genetic understanding of anthocyanin pigmentation at a tissue-specific level, and purple spot disease severity in spears and fern, supporting future breeding efforts.

Targeting mitochondrial ribosomal protein expression by andrographolide and melatonin for colon cancer treatment

Colospheroids contain colon cancer stem cells (CSCs) that cause colorectal cancer metastasis (mCRC). Colorectal cancer (CRC) is the second leading cause of cancer-related deaths in the U.S. Little is known about the role of mitochondria in the survival and metastatic ability of CSCs. In this study, we investigate the effect of andrographolide (AGP) and melatonin (MLT) on mitochondrial dynamics (including fusion and fission) and the expression of mitochondrial ribosomal proteins (MRPs). Our results show that AGP and MLT synergistically reduce the total active mitochondrial mass, downregulate fusion and fission proteins, reduce OXPHOS proteins, and lead to CSC growth inhibition via Nrf2 and KEAP1 signaling. Microarray revealed 4389 differentially expressed mRNAs in the AGP and MLT combination compared to the control. Results exhibiting a three-fold induction/reduction were validated by qRT-PCR and immunoblot. MRPS6, a mitochondrial ribosomal (Mitoribosome) small subunit protein, was dramatically downregulated by AGP + MLT treatment compared to control. MRPS6 inhibition by siRNA reduced mCRC cell viability. Molecular docking-based protein-ligand interactions showed that AGP has direct physical interaction with MRPS6 and increases the binding affinity of MLT to MRPS6. This drug combination downregulated genes in the NRF2 (NFE2L2) pathway in CSCs. MRPS6 may be directly linked to CSC proliferation and could be a therapeutic target for this population. Functionally, MRPS6 knockdown significantly reduced colony formation, with enhanced suppression in AGP + MLT-treated cells. In xenograft models, the AGP-MLT combination synergistically decreased MRPS6 expression and increased apoptosis, as evidenced by TUNEL assays, demonstrating the therapeutic potential of targeting MRPS6 in CRC.

DPP-IV and FAS inhibitory peptides: therapeutic alternative against diabesity

Diabesity is a modern epidemic that indicates a strong association between obesity and diabetes. Key enzymes have been identified in the development and progression of both diseases, DPP-IV in glucose uptake and FAS in fatty acid synthesis. In both cases, the molecular mechanisms of how each one acts separately have been described, and which are the key inhibitory drugs and molecules for each one. However, although it is known that there is an association between both clinically and molecularly, the mechanism has not been elucidated; therefore, this review focuses on proposing a mechanism of convergence of DPP-IV and FAS in diabesity, and the possible mode of action in which bioactive peptides obtained from plant and animal sources can inhibit these two enzymes in a similar way as drugs do.

Peering into the Bacterial Cell: From Transcription to Functional Genomics

I started my faculty career in 1981 at the UW-Madison in the Department of Bacteriology and moved to the University of California, San Francisco in 1993, where I am a Professor in the Departments of Microbiology and Immunology and Cell and Tissue Biology. In this article, I first review my contributions to understanding the molecular biology of the bacterial transcriptional apparatus and the global role of alternative sigmas (σs), a major pillar of bacterial transcriptional control. I then discuss my role in spearheading the development of bacterial systems biology, specifically to the genome-wide phenotyping approaches necessary for rapid understanding of gene function and the molecular basis of pathway connections across the bacterial universe.

Exploring the mechanism of fibronectin extra domain B in the tumor microenvironment and implications for targeted immunotherapy and diagnostics (Review)

Fibronectin extra domain B (FN‑EDB) is a unique domain of FN), whose expression is significantly upregulated in the tumor microenvironment (TME). FN‑EDB plays a key role in tumor cell adhesion, angiogenesis and invasion, and is closely related to tumor malignancy and poor prognosis. Moreover, the high expression of FN‑EDB in multiple cancer types makes it a potential therapeutic target. However, comprehensive studies of the mechanism of FN‑EDB in different cancer types and its potential as therapeutic targets are lacking. The present study aimed to explore the general role of FN‑EDB in multiple types of cancer and to integrate the knowledge of cell biology, molecular biology and immunology, so as to give a comprehensive understanding of the role of FN‑EDB in TME. Furthermore, by focusing on the use of FN‑EDB in clinical diagnosis and treatment, the potential of targeting FN‑EDB as a diagnostic and therapeutic target was evaluated and the progress in clinical trials of these drugs was discussed. By searching web sites such as PubMed and web of science, various high‑quality studies including RNA sequencing, drug experiments, cell experiments, animal models, clinical randomized controlled experiments and large‑scale cohort studies were collected, with sufficient evidence to support a comprehensive evaluation of the function and potential application of FN‑EDB. The present study revealed the general role of FN‑EDB in multiple types of cancer and evaluated its potential as a diagnostic and therapeutic target. It also provided a basis for future development of more effective and precise cancer therapies.

Investigation into biased signaling, glycosylation, and drug vulnerability of acute myeloid leukemia

Understanding and harnessing biased signaling offers significant potential for developing novel therapeutic strategies or enhancing existing treatments. By managing biased signaling, it is possible to minimize adverse effects, including toxicity, and to optimize therapeutic outcomes by selectively targeting beneficial pathways. In the context of acute myeloid leukemia (AML), a highly aggressive blood cancer characterized by the rapid proliferation of abnormal myeloid cells in the bone marrow and blood, the dysregulation of these signaling pathways, particularly those involving G protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs), significantly contributes to disease progression and therapeutic resistance. Traditional therapies for AML often struggle with resistance and toxicity, leading to poor patient outcomes. However, by exploiting the concept of biased signaling, researchers may be able to design drugs that selectively activate pathways that inhibit cancer cell growth while avoiding those that contribute to resistance or toxicity. Glycosylation, a key post-translational modification (PTM), plays a crucial role in biased signaling by altering receptor conformation and ligand-binding affinity, thereby affecting the outcome of biased signaling. Chemokine receptors like CXCR4, which are often overexpressed and heavily glycosylated in AML, serve as targets for therapeutic intervention. By externally inducing or inhibiting specific PTMs, it may be possible to further refine therapeutic strategies, unlocking new possibilities for developing more effective and less toxic treatments. This review highlights the importance of understanding the dynamic relationship between glycosylation and biased signaling in AML, which is essential for the development of more effective treatments and overcoming drug resistance, ultimately leading to better patient outcomes.

Intratumor HIF-1α modulates production of a cachectic ligand to cause host wasting

Tumor-host interactions play critical roles in cancer-associated cachexia. Previous studies have identified several cachectic proteins secreted by tumors that impair metabolic homeostasis in multiple organs, leading to host wasting. The molecular mechanisms by which malignant tumors regulate the production or secretion of these cachectic proteins, however, still remain largely unknown. In this study, we used different Drosophila cachexia models to investigate how malignant tumors regulate biosynthesis of ImpL2, a conserved cachectic protein that inhibits systemic insulin/IGF signaling and suppresses anabolism of host organs. Through bioinformatic and biochemical analysis, we found that hypoxia-inducible factor HIF-1α/Sima directly binds to the promoter region of ImpL2 gene for the first time, promoting its transcription in both tumors and non-tumor cells. Interestingly, expressing HphA to moderately suppress HIF-1α/Sima activity in adult yki 3SA gut tumors or larval scrib 1 Ras V12 disc tumors sufficiently decreased ImpL2 expression and improved organ wasting, without affecting tumor growth. We further revealed conserved regulatory mechanisms conserved across species, as intratumor HIF-1α enhances the production of IGFBP-5, a mammalian homolog of fly ImpL2, contributing to organ wasting in both tumor-bearing mice and patients. Therefore, our study provides novel insights into the mechanisms by which tumors regulate production of cachectic ligands and the pathogenesis of cancer-induced cachexia.

Comparative transcriptome analysis identified genes involved in ovarian development in Takifugu rubripes

Ovarian development is a complex process involving multiple genes, but the molecular mechanisms underlying this process in Takifugu rubripes remain poorly understood. This study aimed to identify genes associated with ovarian development in T. rubripes and to investigate the regulatory mechanisms of oocyte maturation. Transcriptome data were compared across four different developmental stages (stage II to V) to identify differentially expressed genes (DEGs) and perform GO and KEGG enrichment analysis. The expression patterns of randomly selected genes were then validated by qPCR. The results yielded a total of 1,289,401,820 raw data from all libraries, with 16,929 DEGs identified across all comparison groups. The DEGs were predominantly enriched in ovarian steroidogenesis, estrogen-mediated signaling, and TGF-beta signaling pathways. The qPCR analysis showed that cyp17a1 was identified as being expressed at similar levels in stage II and III. Thereafter, cyp17a1 was observed to undergo a continuous increase in expression from stage III to V. cyp19a1, nanos1, foxl2 and ar were identified as being expressed at similar levels at stage II and III, then increase in expression from stage III to IV and subsequent downregulation from stage IV to V. hsd17b1 was identified as being expressed at similar levels at stage II and IV. This study represents a transcriptomic study of ovarian development in female T. rubripes. Several essential ovarian-related genes and sex-related biological pathways were identified. The results will improve our understanding of the molecular mechanisms underlying ovarian development in this species.

A BiP-centric View of Endoplasmic Reticulum Functions and of My Career

After completing my post-doctoral training at the University of Alabama, Birmingham and a brief period on the faculty there, I joined the Department of Tumor Cell Biology at St. Jude Children's Research Hospital in 1987 as an Assistant Member and started my independent research program. For the following 37 years, I led a relatively small basic research group comprised at various times of post-doctoral fellows, graduate students, undergraduate students, and research technicians; many of whom I am still in contact. Last year I closed the lab and transitioned to an emeritus position at St. Jude. I continue to maintain several research collaborations covering areas of research that have long been dear to my heart. My post-doctoral studies on BiP revealed that it controlled immunoglobulin assembly and transport, and as such, played a critical role in the fidelity of the immune response. My lab continued to define BiP's functions in protein folding and subunit assembly, as well as, in degradation of proteins that failed to mature properly using biochemical, cell-based, and biophysical analyses. Several ER localized co-factors that regulate the activity of BiP and allow it to contribute to its multiple ER functions were identified by our group. These include DnaJ family members and nucleotide change factors. Through a variety of collaborative studies, we pursued BiP's functions in maintaining the permeability barrier of the translocon, contributing to ER calcium stores, and regulating the up-stream transducers of the UPR, a stress response that is activated by the accumulation of unfolded proteins in the ER.

PagSND1-B1 Regulates Wood Formation by Influencing Phosphorus Absorption and Distribution in Poplar

In natural environments, the growth and development of trees are continuously affected by phosphorus (P) starvation stress. However, the mechanisms through which trees balance stem growth and P distribution remain unknown. This study found that in the woody model species poplar, the P loss in stems is more severe than that in roots and leaves under P starvation conditions, thereby inhibiting stem development and reducing the expression of numerous genes related to wood formation, including PagSND1-B1. Intriguingly, overexpression of PagSND1-B1 in poplar enhances resistance to P starvation and promotes xylem development. Further analysis demonstrated that PagSND1-B1 can directly and positively regulate the phosphorus transporter PagPHT1;5a. Analysis of P content changes in leaves, stems and roots of transgenic poplar before and after treatment indicated that overexpression of PagSND1-B1 disrupts the normal P redistribution procedure, leading to increased P accumulation in stems, which is beneficial for xylem development. Therefore, PagSND1-B1 participates in the phosphorus absorption and homoeostasis of poplar by modulating PagPHT1;5a. This study provides valuable insights into the regulatory function of PagSND1-B1 in wood formation and the process by which trees balance phosphorus distribution and xylem development.

Elucidating the Molecular Landscape of Cystic Kidney Disease: Old Friends, New Friends and Some Surprises

Cystic kidney diseases (CyKD) are a diverse group of disorders affecting more than 1 in 1000 individuals. Over 120 genes are implicated, primarily encoding components of the primary cilium, transcription factors, and morphogens. Prognosis varies greatly by molecular diagnosis. Causal variants are not identified in 10%-60% of individuals due to our limited understanding of CyKD. To elucidate the molecular landscape of CyKD, we queried the CAG Biobank using the ICD10 codes N28.1, Q61.1, Q61.11, Q61.19, Q61.2, Q61.3, and Q61.8 to identify individuals with CyKD. One hundred eight individuals met clinical criteria for CyKD and underwent proband-only exome sequencing. Causal variants were identified in 86/108 (80%) individuals. The most common molecular diagnoses were PKD1-related autosomal dominant polycystic kidney disease (32/108; 30%) and autosomal recessive polycystic kidney disease (21/108; 19%). Other common molecular diagnoses were ciliopathy syndromes (7/108; 6.5%) and Tuberous Sclerosis (6/108; 5.6%). Seven individuals had variants in genes not previously associated with CyKD (7/108; 6.5%). Candidate genes were identified in five individuals (5/108; 4.5%). Discordance between molecular and clinical diagnosis was present in two individuals. We demonstrate a high molecular diagnosis rate in individuals with CyKD that can result in diagnostic reclassification, supporting a role for genetic testing in CyKD.

An NF-κB-regulated cytokine enhances the antiviral resistance of silkworm, Bombyx mori

Insect NF-κB-like factor, Relish, is activated by viral infection and induces the production of antiviral proteins. In this study, we performed a transcriptomic analysis of BmE cells expressing the active form of BmRelish (BmRelishact) and identified BmVago-like as the most strongly-induced secreted-protein. Expression of BmVago-like was specifically triggered by Bombyx mori Nucleo Polyhedro Virus (BmNPV) infection and regulated by BmSTING-BmRelish pathway. Incubating the fresh culture of cells with supernatant medium of BmVago-like expressing cells or recombinant BmVago-like protein (rBmVago-like) significantly increased antiviral resistance. On the contrary, reducing the expression of Bmvago-like by RNA interference (RNAi) in BmE cells as well as in silkworm larvae impaired antiviral response. Furthermore, we constructed transgenic silkworm line over-expressing BmVago-like (BmVago-likeOV) and found they had markedly lower viral load and higher survival rate after BmNPV infection compared with the wild-type control. Co-immunoprecipitation assay showed Bmintegrin β1 interacts with BmVago-like and it was involved in BmVago-like mediated antiviral response. Finally, we found the expression level of signalling molecules in the JAK-STAT pathway increased in rBmVago-like-treated cells and BmVago-likeOV silkworm larvae but decreased in RNAi-treated cells. In summary, our research uncovered an inducible antiviral response in silkworm mediated by cytokine BmVago-like, which is the downstream effector of BmSTING-BmRelish pathway and functions as an antiviral cytokine.

A systematic evaluation of the therapeutic potential of endogenous-ADAR editors in cancer prevention and treatment

Adenosine deaminases acting on RNA (ADAR) enzymes constitute a natural cellular mechanism that induces A-to-I(G) editing, introducing genetic changes at the RNA level. Recently, interest in the endogenous-ADAR editor has emerged for correcting genetic mutations, consisting of a programmed oligonucleotide that attracts the native ADAR, thereby offering opportunities for medical therapy. Here, we systematically chart the scope of cancer mutations that endogenous-ADAR can correct. First, analyzing germline single nucleotide variants in cancer predisposition genes, we find that endogenous-ADAR can revert a fifth of them, reducing the risk of cancer development later in life. Second, examining somatic mutations across various cancer types, we find that it has the potential to correct at least one driver mutation in over a third of the samples, suggesting a promising future treatment strategy. We also highlight key driver mutations that are amenable to endogenous-ADAR, and are thus of special clinical interest. As using endogenous-ADAR entails delivering relatively small payloads, the prospects of delivering endogenous-ADAR to various cancers seem promising. We expect that the large scope of correctable mutations that are systematically charted here for the first time will pave the way for a new era of cancer treatment options.

Machine learning unravels the mysteries of glioma typing and treatment

Gliomas, which are complex primary malignant brain tumors known for their heterogeneous and invasive nature, present substantial challenges for both treatment and prognosis. Recent advancements in whole-genome studies have opened new avenues for investigating glioma mechanisms and therapies. Through single-cell analysis, we identified a specific cluster of cancer cell-related genes within gliomas. By leveraging diverse datasets and employing non-negative matrix factorization (NMF), we developed a glioma subtyping method grounded in this identified gene set. Our exploration delved into the clinical implications and underlying regulatory frameworks of the newly defined subtype classification, revealing its intimate ties to glioma malignancy and prognostic outcomes. Comparative assessments between the identified subtypes revealed differences in clinical features, immune modulation, and the tumor microenvironment (TME). Using tools such as the limma R package, weighted gene co-expression network analysis (WGCNA), machine learning methodologies, survival analyses, and protein-protein interaction (PPI) networks, we identified key driver genes influencing subtype differentiation while quantifying associated outcomes. This study not only sheds light on the biological mechanisms within gliomas but also paves the way for precise molecular targeted therapies within this intricate disease landscape.

HUWE1-mediated ubiquitination and degradation of oxidative damage repair gene ATM maintains mitochondrial quality control system in lens epithelial cells

Mitochondrial dysfunction, resulting from a diminished oxidative damage repair capacity of mitochondrial DNA (mtDNA) in peripheral lens epithelial cells (LECs), is a key pathogenic mechanism in age-related cortical cataract (ARCC). This study aims to investigate the potential role of the E3 ligase HUWE1 and its ubiquitination substrate, the oxidative damage repair gene ATM, in the pathogenesis of ARCC. Our findings reveal that ATM protein expression is downregulated in human peripheral lens epithelial cells and the turbid cortex, correlating with increased expression of HUWE1. Overexpression of ATM is shown to repair damaged mtDNA, protect mitochondria in LECs from oxidative damage, inhibit mitochondrial fission, enhance mitochondrial biogenesis and mitophagy, and prevent LECs apoptosis. Conversely, overexpression of HUWE1 may negate the protective effects of ATM via the ubiquitination pathway, promote oxidative stress-induced mitochondrial damage, increase the expression of mitochondrial fission proteins Drp1/Fis1, lead to mitochondrial network fragmentation and LECs apoptosis. In a SD rat lens model ex vitro, the ATM inhibitor AZD0156 exacerbated lens opacity, whereas the mitochondrial fission inhibitor Mdivi-1 restored lens transparency. These results suggest that modulating key molecules involved in oxidative damage repair and mitochondrial fission pathways could enhance mitochondrial quality control, paving the way for the development of targeted molecular therapies for the prevention and treatment of ARCC.

N6-methyladenosine RNA modification in stomach carcinoma: Novel insights into mechanisms and implications for diagnosis and treatment

N6-methyladenosine (m6A) RNA methylation is crucially involved in the genesis and advancement of gastric cancer (GC) by controlling various pathobiological aspects including gene expression, signal transduction, metabolism, cell death, epithelial-mesenchymal transition, angiogenesis, and exosome function. Despite its importance, the exact mechanisms by which m6A modification influences GC biology remain inadequately explored. This review consolidates the latest advances in uncovering the mechanisms and diverse roles of m6A in GC and proposes new research and translational directions. Key regulators (writers, readers, and erasers) of m6A, such as METTL3/14/16 and WTAP, significantly affect cancer progression, anticancer immune response, and treatment outcomes. m6A modification also impacts immune cell infiltration and the tumor microenvironment, highlighting its potential as a diagnostic and prognostic marker. Interactions between m6A methylation and non-coding RNAs offer further novel insights into GC development and therapeutic targets. Targeting m6A regulators could enhance immunotherapy response, overcome treatment resistance, and improve oncological and clinical outcomes. Models based on m6A can precisely predict treatment response and prognosis in GC. Additional investigation is needed to fully understand the mechanisms of m6A methylation and its potential clinical applications and relevance (e.g., as precise markers for early detection, prediction of outcome, and response to therapy and as therapeutic targets) in GC. Future research should focus on in vivo studies, potential clinical trials, and the examination of m6A modification in other types of cancers.

Exploring the connection between dementia and cardiovascular risk with a focus on ADAM10

Alzheimer's disease (AD) represents a leading cause of dementia, characterized by progressive cognitive and functional decline. Although extensive research has unraveled critical aspects of AD pathology, its etiology remains incompletely understood, urging further exploration into potential risk factors. Growing evidence underscores a significant link between cardiovascular disease (CVD) risk factors and AD, with modifiable lifestyle elements - such as physical inactivity, high low-density lipoprotein (LDL) levels, obesity, hypertension, atherosclerosis, and diabetes - emerging as contributors to cerebrovascular damage and neurodegeneration. ADAM10, a disintegrin and metalloproteinase involved in the non-amyloidogenic processing of amyloid precursor protein (APP), has garnered interest for its dual role in cardiovascular and neurodegenerative processes. ADAM10's regulation of neuroinflammation, endothelial function, and proteolytic cleavage of APP potentially moderates amyloid-β (Aβ) peptide formation, thus influencing both cardiovascular and brain health. Given these interconnected roles, this narrative review investigates whether ADAM10-driven vascular dysfunction accelerates neurodegeneration, how lipid metabolism influences ADAM10 activity in CVD and AD, and whether targeting ADAM10 could offer a dual-benefit therapeutic strategy to mitigate disease burden. By exploring epidemiological data, clinical studies, and molecular pathways, we aim to clarify ADAM10's bridging function between AD and cardiovascular risk, offering a new perspective into therapeutic opportunities to alleviate the dual burden of these interrelated conditions.

Downregulation of DDIT4 levels with borneol attenuates hepatotoxicity induced by gilteritinib

Gilteritinib, a multi-target kinase inhibitor, is currently used as standard therapy for acute myeloid leukemia. However, approximately half of the patients encounter liver-related adverse effects during the treatment with gilteritinib, which limiting its clinical applications. The underlying mechanisms of gilteritinib-induced hepatotoxicity and the development of strategies to prevent this toxicity are not well-reported. In our study, we utilized JC-1 dye, and MitoSOX to demonstrate that gilteritinib treatment leads to hepatocytes undergoing p53-mediated mitochondrial apoptosis. Furthermore, qRT-PCR analysis revealed that DNA damage-inducible transcript 4 (DDIT4), a downstream target of p53, was upregulated following gilteritinib administration and was identified as a key factor in gilteritinib-induced hepatotoxicity. After drug screening and western blot analysis, borneol, a bicyclic monoterpenoid, was found to decrease the protein level of DDIT4. This is the first compound found to downregulate DDIT4 levels and ameliorate hepatic injury caused by gilteritinib. Our findings suggest that high levels of DDIT4 are the primary driver behind gilteritinib-induced liver injury, and that borneol could potentially be a clinically safe and feasible therapeutic strategy by inhibiting DDIT4 levels.

Role of SMYD2 in gastrointestinal cancer progression (Review)

Gastrointestinal cancer is one of the most prevalent malignancies in humans and is often associated with a poor prognosis. Understanding the molecular mechanisms underlying cancer progression and severity is essential for the development of effective cancer therapies. Abnormal protein methylation is associated with the occurrence and advancement of cancer, highlighting the importance of protein methyltransferase research. SET and MYND domain-containing protein 2 (SMYD2), a lysine methyltransferase, has emerged as a promising small molecule target for cancer treatment. Notably, SMYD2 is implicated in the pathogenesis of several diseases, including gastrointestinal cancer. SMYD2 is closely associated with the tumorigenesis, proliferation, migration and other biological processes of gastrointestinal cancer, indicating its potential as a novel therapeutic target. The present review offers an in-depth analysis of SMYD2, covering its structural characteristics, regulatory pathways and functional significance. By assessing the biological roles and therapeutic potential of SMYD2, the current review presents fresh insights and perspectives for advancing research in different types of gastrointestinal cancer.

The GWAS candidate far upstream element binding protein 3 (FUBP3) is required for normal skeletal growth, and adult bone mass and strength in mice

Bone mineral density (BMD) and height are highly heritable traits for which hundreds of genetic loci have been linked through genome wide association studies (GWAS). FUBP3 is a DNA and RNA binding protein best characterised as a transcriptional regulator of c-Myc, but little is known about its role in vivo. Single nucleotide polymorphisms in FUBP3 at the 9q34.11 locus have been associated with BMD, fracture and height in multiple GWAS, but FUBP3 has no previously established role in the skeleton. We analysed Fubp3-deficient mice to determine the consequence of FUBP3 deficiency in vivo. Mice lacking Fubp3 had reduced survival to adulthood and impaired skeletal growth. Bone mass was decreased, most strikingly in the vertebrae, with altered trabecular micro-architecture. Fubp3 deficient bones were also weak. These data provide the first functional demonstration that Fubp3 is required for normal skeletal growth and development and maintenance of adult bone structure and strength, indicating that FUBP3 contributes to the GWAS association of 9q34.11 with variation in height, BMD and fracture.

Structure-based optimization of TEAD inhibitors: Exploring a novel subpocket near Glu347 for the treatment of NF2-mutant cancer

The Hippo signaling pathway is critical for regulating cell growth, tissue homeostasis, and organ size. Dysregulation of this pathway has been associated with a range of pathologies, especially cancer, through its modulation of downstream effectors-Yes-associated protein (YAP) and the transcriptional coactivator with PDZ-binding motif (TAZ). These proteins bind to transcriptional enhanced associate domain (TEAD) proteins and function as transcription factors in the nucleus, producing oncogenic target genes such as CTGF and CYR61. TEAD proteins require palmitoylation via a covalent bond with cysteine in the central pocket to bind YAP/TAZ. Therefore, competitive inhibition that prevents palmitoylation could serve as an effective anticancer strategy. In this study, we analyzed the crystal structures of the known inhibitor VT-105 bound to TEAD3 to identify new binding spots that were previously unexplored, with the aim of discovering more potent compounds using structure-based drug design. Consequently, we identified a novel hydrogen-bonding site and discovered C-2, which effectively binds to this site, as confirmed by X-ray crystallography. Furthermore, C-2 exhibited stable pharmacokinetic properties and demonstrated impressive efficacy in a mouse xenograft model.

Bacterial Regulatory Circuits are Linked and Extended by Small RNAs

I was lucky to start my research career as the molecular biology revolution was taking hold, providing a constantly increasing set of tools and questions to investigate. Starting from a fascination with bacteria and their ability to adapt to different conditions, I've investigated post-translational mechanisms and their role in the ability of E. coli to respond to stress. My research career has been primarily at the National Institutes of Health, where I run a group within the Laboratory of Molecular Biology, NCI and hold the title of NIH Distinguished Investigator. Our lab has been interested in both energy-dependent proteolysis, discussed very briefly here, and small regulatory RNAs (sRNAs). The major group of such sRNAs act by pairing with target mRNAs with the aid of the RNA chaperone Hfq, mediating both positive and negative regulation of translation and mRNA stability. Both in our own lab and in a continuing and highly productive collaboration with the laboratory of Gisela (Gigi) Storz, we have used global approaches to identify novel sRNAs, identified how many of them are regulated, both at the level of transcription and stability, and worked on understanding the role of these sRNAs in regulatory networks. Our continued work explores regulators of sRNA and Hfq function. Here, Gigi and I have split summaries of our findings, and hope that our two chapters will be read together.

Assessing bioavailability and the toxicity of resveratrol nanoparticles: Insights from an in vivo chicken embryonic model

This study evaluates the bioavailability, developmental toxicity, genotoxicity, and estrogenic effects (EA) of resveratrol nanoparticles (NPs) stabilized by Tween 80 and carboxymethyl chitosan (CMCS) using chicken embryonic models. Tween NPs exhibited smaller sizes (93.18 nm), and more homogeneous distribution compared to CMCS NPs (267.92 nm). Resveratrol-loaded CMCS NPs achieved a peak serum concentration (Cmax) of 0.462 μg/mL at 60 min, while Tween NPs showed lower bioavailability (Cmax = 0.16 μg/mL). CMCS NPs induced a higher mortality (45.0 %) at 760 μg/kg compared to Tween NPs (25.0 %) and resveratrol (0 %). Without loaded with resveratrol, Tween Empty NPs and CMCS Empty NPs showed higher mortality (51.5 % and 60.7 %, respectively). As capping agents, Tween 80 showed minimal mortality but induced malformation of 15.8 % at higher dose. CMCS increased mortality (30 %) and malformation (10 %) at 10 mg/kg. Empty NPs induced higher lipoperoxidation and DNA damage than resveratrol-loaded NPs. Tween Empty NPs significantly elevated DNA damage (p < 0.0001), while CMCS Empty NPs exhibited no genotoxic effects. Estrogen-responsive apolipoprotein II (ApoII) gene expression was significantly upregulated in the Tween Empty group (9.51 ± 3.27-fold), indicating potential EA of the nanocarrier. These findings highlight both the NPs and nanocarriers must be evaluated in safety of nano-formulations.

Suppressing SPARC gene with siRNA exerts therapeutic effects and inhibits MMP-2/9 and ADAMTS1 overexpression in a murine model of ischemia/reperfusion-induced acute kidney injury

Secreted protein acidic and rich in cysteine (SPARC), a collagen-binding matricellular protein, is reported to facilitate inflammation and fibrosis in various tissues including the kidneys. Ischemia/reperfusion (I/R) is a major process of acute kidney injury. To investigate whether SPARC inhibition might attenuate renal I/R injury, we injected small interfering RNA (siRNA) targeting SPARC into male BALB/c mice one day before 45 min of renal ischemia followed by 72 h of reperfusion. Serum creatinine concentration, blood urea nitrogen, histological tubular damage, tubulointerstitial fibrosis, and expression of collagen I and transforming growth factor-β were increased after I/R. Expression of 4-hydroxy-2-nonenal, an oxidative stress marker, and the inflammatory cytokines monocyte chemoattractant protein-1 and tumor necrosis factor-α, were also upregulated in I/R kidneys. Overexpression of SPARC mRNA was observed after I/R, and immunohistochemistry revealed that SPARC was localized mainly in damaged tubuloepithelial cells. Additionally, a disintegrin and metalloproteinase with thrombospondin type 1 motif (ADAMTS1) expression colocalized with SPARC. Injection of siRNA targeting SPARC attenuated renal dysfunction, histological abnormalities, collagen deposition, oxidative stress, and renal inflammation. In addition, SPARC gene knockdown suppressed the I/R-induced increases in ADAMTS1 and matrix metalloproteinase-2/9 expression. In conclusion, I/R-induced SPARC could be a novel therapeutic target against acute kidney injury.

BCOR-rearranged sarcomas: In silico insights into altered domains and BCOR interactions

BCOR (BCL-6 corepressor) rearranged small round cell sarcoma (BRS) represents an uncommon soft tissue malignancy, frequently characterized by the BCOR::CCNB3 fusion. Other noteworthy fusions include BCOR::MAML3, BCOR::CLGN, BCOR::MAML1, ZC3H7B::BCOR, KMT2D::BCOR, CIITA::BCOR, RTL9::BCOR, and AHR::BCOR. The BCOR gene plays a pivotal role in the Polycomb Repressive Complex 1 (PRC1), essential for histone modification and gene silencing. It interfaces with the Polycomb group RING finger homolog (PCGF1). This study employed comprehensive in silico methodologies to investigate the structural and functional effects of BCOR fusion events in BRS. The analysis revealed significant alterations in the domain architecture of BCOR, which resulted in the loss of BCL6-regulated transcriptional repression. Furthermore, IUPred3 prediction indicated a significant increase in disorder in the C-terminal regions of the BCOR in the fusion proteins. A detailed analysis of the physicochemical properties by ProtParam revealed a decrease in isoelectric point, stability, and hydrophobicity. The analysis of protein structures predicted by AlphaFold3 using the PRODIGY algorithm revealed statistically significant deviations in binding affinities for BCOR-PCGF1 dimers and a non-canonical PRC1 variant tetramer compared to the wild-type BCOR. The findings provide a comprehensive summary and elucidation of the fusion proteome associated with BRS, suggesting a substantial impact on the stability and functionality of the fusion proteins, thereby contributing to the oncogenic mechanisms underlying BRS. In this study, we provide the first compilation and comparative analysis of the known BCOR fusions of BRS and introduce a new in silico approach to enhance a better understanding of the molecular basis of BRS.

Pre-existing DNA methylation signatures in the prefrontal cortex of alcohol-naïve nonhuman primates define neural vulnerability for future risky ethanol consumption

Alcohol use disorder (AUD) is a highly prevalent, complex, multifactorial and heterogeneous disorder, with 11 % and 30 % of adults meeting criteria for past-year and lifetime AUD, respectively. Identification of the molecular mechanisms underlying risk for AUD would facilitate effective deployment of personalized interventions. Studies using rhesus monkeys and rats, have demonstrated that individuals with low cognitive flexibility and a predisposition towards habitual behaviors show an increased risk for future heavy drinking. Further, low cognitive flexibility is associated with reduced dorsolateral prefrontal cortex (dlPFC) function in rhesus monkeys. To explore the underlying unique molecular signatures that increase risk for chronic heavy drinking, a genome-wide DNA methylation (DNAm) analysis of the alcohol-naïve dlPFC-A46 biopsy prior to chronic alcohol self-administration was conducted. The DNAm profile provides a molecular snapshot of the alcohol-naïve dlPFC, with mapped genes and associated signaling pathways that vary across individuals. The analysis identified 1,463 differentially methylated regions (DMRs) related to unique genes that were strongly associated with average ethanol intake consumed over 6 months of voluntary self-administration. These findings translate behavioral phenotypes into neural markers of risk for AUD, and hold promise for parallel discoveries in risk for other disorders involving impaired cognitive flexibility. SIGNIFICANCE: Alcohol use disorder (AUD) is a highly prevalent and heterogeneous disorder. Prevention strategies to accurately identify individuals with a high risk for AUD, would help reduce the prevalence, and severity of AUD. Our novel epigenomic analysis of the alcohol-naïve nonhuman primate cortex provides a molecular snapshot of the vulnerable brain, pointing to circuitry and molecular mechanisms associated with cortical development, synaptic functions, glutamatergic signaling and coordinated signaling pathways. With a complex disorder like AUD, having the ability to identify the molecular mechanisms underlying AUD risk is critical for better development of personalized effective treatments.

S-phase kinase-associated protein 1 inhibits orbital fibroblasts adipogenesis to improve thyroid-associated ophthalmopathy (TAO)

Thyroid-associated ophthalmopathy (TAO), a localized manifestation of Graves' disease, involves complex autoimmune interactions leading to orbital tissue inflammation and remodeling. The pathophysiology of TAO is marked by significant orbital connective tissue and fat pad expansion, mononuclear cell infiltration, and fibrosis, ultimately affecting eye motility and quality of life. This study explores the role of S-phase kinase-associated protein 1 (SKP1) in the adipogenic differentiation of orbital fibroblasts (OFs), a key process in TAO. Using bioinformatics analysis of gene expression profiles from TAO patients (GSE105149 and GSE58331), SKP1 was identified as a critical regulator of adipogenesis. Experimental validation confirmed that SKP1 expression is significantly downregulated in TAO-derived OFs under adipogenic differentiation for 10 days, correlating with elevated lipid accumulation and increased expression levels of adipogenic markers. Furthermore, downregulation of SKP1 promotes adipogenic differentiation, while upregulation inhibits this process in OFs in vitro and in TAO mice models in vivo. Mechanistically, SKP1 was shown to modulate the PI3K/AKT signaling, with downregulation activating and upregulation inhibiting the pathway, thereby influencing adipogenesis. In summary, SKP1 exerts a crucial regulatory effect on TAO pathogenesis and might act as an underlying therapeutic target for mitigating OFs adipogenesis in TAO.

Genome-wide identification, evolution and expression of pax gene family members in mandarin fish (Siniperca chuatsi)

The pax gene family is involved in the development process through its extensive effects on cell proliferation, differentiation, and apoptosis. Herein, the whole pax gene family members of mandarin fish (Siniperca chuatsi) were first identified and characterized. By comparing pax gene family members from another 13 representative animals, an expansion of pax gene family members was observed in teleosts. In mandarin fish, a total of 15 potential pax gene family members, distributed on 13 chromosomes, were found, which shared conserved synteny with other teleosts. The expression profiles revealed that members of pax gene family showed time-specific expression profiles during embryonic and gonad development in mandarin fish, which indicated they might play a specific role in organogenesis during embryonic development and the process of gonad development and differentiation. Our research will lay a good foundation for further functional investigation of pax gene family during fish embryonic and gonad development.

Electroactive membranes enhance in-situ alveolar ridge preservation via spatiotemporal electrical modulation of cell motility

Post-extraction alveolar bone resorption invariably compromises implant placement and aesthetic restoration outcomes. Current non-resorbable membranes exhibit limited efficacy in alveolar ridge preservation (ARP) due to insufficient cell recruitment and osteoinductive capabilities. Herein, we introduce a multifunctional electroactive membrane (PPy-BTO/P(VDF-TrFE), PB/PT) designed to spatiotemporally regulate cell migration and osteogenesis, harmonizing with the socket healing process. Initially, the membrane's endogenous-level surface potential recruits stem cells from the socket. Subsequently, adherent cell-migration-triggered forces generate on-demand piezopotential, stimulating intracellular calcium ion fluctuations and activating the Ca2+/calcineurin/NFAT1 signaling pathway via Cav3.2 channels. This enhances cell motility and osteogenic differentiation predominantly in the coronal socket region, counteracting the natural healing trajectory. The membrane's self-powered energy supply, proportional to cell migration velocity and manifested as nanoparticle deformation, mitigates ridge shrinkage, both independently and in conjunction with bone grafts. This energy-autonomous membrane, based on the spatiotemporal modulation of cell motility, presents a novel approach for in-situ ARP treatment and the development of 4D bionic scaffolds.

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.