Molecular Basis Research Articles

The genetic and molecular basis of a connexin-linked skin disease.

Erythrokeratodermia variabilis et progressiva (EKVP) is a rare hereditary skin disorder characterized by hyperkeratotic plaques and erythematous patches that progressively worsen with age. This disorder has been associated with variants in three connexin encoding genes (GJA1, GJB3, GJB4) and four unrelated genes (KRT83, KDSR, TRPM4, PERP). Most cases of connexin-linked EKVP exhibit an autosomal dominant mode of inheritance, with rare autosomal recessive cases. Collectively, evidence suggests that connexin variants associated with EKVP elicit a plethora of molecular defects including impaired gap junction (GJ) formation, dysregulated hemichannel and/or GJ channel function, cytotoxicity, dominant disruption of co-expressed connexins, and/or altered turnover kinetics. Here, we review the progress made in understanding the genetic and molecular basis of EKVP associated with connexin gene variants. We also discuss the landscape of treatment options used for this disorder and the future directions for research into this rare condition.

Membraneless organelles in health and disease: exploring the molecular basis, physiological roles and pathological implications

AbstractOnce considered unconventional cellular structures, membraneless organelles (MLOs), cellular substructures involved in biological processes or pathways under physiological conditions, have emerged as central players in cellular dynamics and function. MLOs can be formed through liquid-liquid phase separation (LLPS), resulting in the creation of condensates. From neurodegenerative disorders, cardiovascular diseases, aging, and metabolism to cancer, the influence of MLOs on human health and disease extends widely. This review discusses the underlying mechanisms of LLPS, the biophysical properties that drive MLO formation, and their implications for cellular function. We highlight recent advances in understanding how the physicochemical environment, molecular interactions, and post-translational modifications regulate LLPS and MLO dynamics. This review offers an overview of the discovery and current understanding of MLOs and biomolecular condensate in physiological conditions and diseases. This article aims to deliver the latest insights on MLOs and LLPS by analyzing current research, highlighting their critical role in cellular organization. The discussion also covers the role of membrane-associated condensates in cell signaling, including those involving T-cell receptors, stress granules linked to lysosomes, and biomolecular condensates within the Golgi apparatus. Additionally, the potential of targeting LLPS in clinical settings is explored, highlighting promising avenues for future research and therapeutic interventions.

Plumage polymorphism in the black sparrowhawk (Accipiter melanoleucus) is strongly associated with expression level of agouti signalling protein

Abstract Melanin-based plumage polymorphisms in birds are often associated with mutations in the melanogenesis genes, notably the melanocortin-1 receptor (MC1R), but may also arise through changes in the expression of these genes. Here we investigate the molecular basis of plumage polymorphism in both adult and juvenile black sparrowhawks (Accipiter melanoleucus), an African raptor that occurs in two adult colour morphs, light and dark, and also exhibits variation in juvenile plumage colouration. Our results confirmed that plumage differences in adult morphs were a result of differential deposition of eumelanin in their ventral contour feathers. No polymorphisms in the coding regions of the MC1R or the agouti signalling protein (ASIP) genes associated with adult colour morph were identified. However, lack of pigmentation in the developing breast feathers of light morph birds was strongly associated with elevated ASIP expression, and concomitant down-regulation of the downstream melanogenesis genes microphthalmia-associated transcription factor (MITF), tyrosinase (TYR) and tyrosinase-related protein 1 (TYRP1). Variation in the rufous coloured plumage of juveniles was found to be due to covariation in eumelanin and pheomelanin levels in dorsal and ventral contour feathers. As in adult birds, an inverse relationship between melanin pigmentation and ASIP expression was observed. This covariation between eumelanin and pheomelanin levels is not consistent with the pigment type-switching model of melanogenesis, where increased ASIP expression results in a switch from eumelanin to pheomelanin production. This highlights the need for caution when extrapolating results from model systems to other animals and the value of conducting research in wild species.

Genomic insights into climate change-induced forest dieback in Abies alba hotspots of decline

AbstractUnderstanding adaptive genetic responses to climate change is an issue of utmost importance to improve conservation policies and adaptive management. This study deeps on it, focusing on rear-edge silver fir (Abies alba) forests, where decline has been reported and linked to climatic stressors, such as warming and recurrent drought events. Hotspots and coldspots of forest decline and mortality were defined. Different sets of single nucleotide polymorphisms (SNPs), namely genome-wide and adaptive, were used to study their genetic characteristics, aiming to identify differences in genetic diversity between vigor classes (declining and non-declining trees) and age cohorts (adult trees and saplings). Global DNA methylation levels were assessed to investigate a possible role of epigenetic processes in adaptation to stressful environments. Parentage and relatedness analysis were conducted to track the genetic lineage of trees from each site. Our findings indicate that, even though adaptive SNPs seem to provide more insightful information than the genome-wide set, the optimal approach for evolutionary studies is a combination of both. Changes in adaptive genomic diversity and DNA methylation were observed between vigor classes, revealing the existence of a molecular basis behind the ongoing decline events in silver forests. Besides, trees’ relatives display a higher mixture of origins in coldspots, which could provide a temporary refuge for the species’ genetic diversity and adaptive potential. All in all, both genetic and epigenetic characteristics should be considered in order to comprehend how forest trees respond to climate stress to achieve adaptation to climate change.

A Critical Review of Recent Advances in Maize Stress Molecular Biology

With the intensification of global climate change and environmental stress, research on abiotic and biotic stress resistance in maize is particularly important. High temperatures and drought, low temperatures, heavy metals, salinization, and diseases are widespread stress factors that can reduce maize yields and are a focus of maize-breeding research. Molecular biology provides new opportunities for the study of maize and other plants. This article reviews the physiological and biochemical responses of maize to high temperatures and drought, low temperatures, heavy metals, salinization, and diseases, as well as the molecular mechanisms associated with them. Special attention is given to key transcription factors in signal transduction pathways and their roles in regulating maize stress adaptability. In addition, the application of transcriptomics, genome-wide association studies (GWAS), and QTL technology provides new strategies for the identification of molecular markers and genes for maize-stress-resistance traits. Crop genetic improvements through gene editing technologies such as the CRISPR/Cas system provide a new avenue for the development of new stress-resistant varieties. These studies not only help to understand the molecular basis of maize stress responses but also provide important scientific evidence for improving crop tolerance through molecular biological methods.

Abstract A006: Investigating the effects of fibroblasts derived from the primary versus the metastatic organ on 3D biomimetic models of pancreatic cancer

Abstract Pancreatic ductal adenocarcinoma (PDAC) is the 3rd leading cause of cancer death in the United States with a 5-year survival rate of only 13%. Early diagnosis is very difficult and thus 53% of patients are diagnosed after metastasis has already occurred, with the liver being the most frequently affected site. Both primary tumors and metastases have dense desmoplastic stroma due to a high percentage of fibroblasts within the tumor microenvironment (TME). Previously, we developed a tunable 3D biomimetic model of the liver metastatic niche (LMN) to investigate how local fibroblasts affect tumor growth and chemoresistance in PDAC liver metastasis. This study aims to investigate the contributions of fibroblasts at the primary versus metastatic sites. We used matched primary PDAC and liver metastatic (LM) organoids derived from the Kras+/LSL-G12D; Trp53+/LSL-R172H; Pdx1-Cre (“KPC”) genetically engineered mouse model. This allows us to compare the effects of primary PDAC cancer associated fibroblasts (CAFs) and liver metastasis associated fibroblasts (MAFs) on tumor cell growth and chemoresistance. Rheometry analyses were conducted to study the impact of local fibroblasts on the extracellular matrix (ECM) stiffness. Our results showed that both storage and loss moduli were enhanced only when PDAC CAFs were present in the co-cultured gels compared to gels with MAFs. Additionally, the 3D biomimetic model showed fibroblasts increased tumor growth and chemoresistance to gemcitabine, only when they were derived from the same site as the tumor cells. This highlighted the importance of studying the organ-specific microenvironment to develop better treatment options for patients with metastatic PDAC. To delve deeper into the molecular basis of these observations, we conducted RNA-sequencing to identify and compare the gene expression profiles in primary and metastatic tumor organoids exposed to conditioned media from CAFs and MAFs using a transwell membrane co-culture model. Our results showed significant differences in gene expression based on the type of fibroblasts co-cultured with the organoids. Moreover, we investigated the role of MAF-derived exosomes on LM growth and chemoresistance using exosome depletion and direct exosome addition to LM organoids. Lastly, we performed exosomes size and distribution characterizations using dynamic light scattering (DLS) analysis. Taken together, these findings highlight the critical role of the organ-specific microenvironment in tumor progression and the necessity of targeted therapies to improve patient outcomes in metastatic PDAC. Our results underscore the importance of developing a tunable 3D biomimetic model of the LMN, as it enables the testing of novel therapeutic strategies designed to disrupt interactions between MAFs and tumor cells, and potentially advancing treatments for metastatic PDAC. Citation Format: Mahsa Pahlavanneshan, Weikun Xiao, Eileen Fung, Vaidhyanathan Mahaganapathy, Chae Young Eun, Chang-Il Hwang, Shannon Mumenthaler, Reginald Hill. Investigating the effects of fibroblasts derived from the primary versus the metastatic organ on 3D biomimetic models of pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr A006.

Abstract C006: Tumor-associated macrophages drive prostate cancer progression via IL-1β signaling

Abstract Inflammation is linked to prostate cancer progression. Inflammatory cell infiltrates are commonly observed in prostate biopsies, and inflammation-induced lesions (proliferative inflammatory atrophy, PIA) are precursors of prostate cancer. However, the mechanism by which inflammation impacts prostate cancer progression is poorly understood. Here, we investigated the significance of inflammation on prostate cancer progression using a cMyc-driven prostate adenocarcinoma mouse model (Hi-Myc). We observed a robust tumor-associated macrophage (TAM) infiltrate early during progression of Hi-Myc tumors. Depleting TAMs led to a decrease in both tumor weight and invasive area, demonstrating the functional importance of TAMs in tumor maintenance. To elucidate the molecular basis of how TAMs influence tumor progression, we collected Hi-Myc tumors throughout cancer development from the precursor stage of prostatic intraepithelial neoplasia to prostate adenocarcinoma and performed single-cell RNA sequencing (scRNA-seq). Our study revealed that a gene signature of strong IL-1β signaling activation was observed in TAMs from Hi-Myc tumors, but not in macrophages from wild-type prostates. Importantly, IL-1β neutralization led to delayed tumor progression with reduced tumor weight and invasive area. Furthermore, blocking IL-1β signaling decreased TAM infiltration, suggesting a positive feedback loop created by TAMs. To understand the effect of IL-1β on cancer cell invasion, we used a protease-dependent fluorescent probe to investigate the activity of major extracellular matrix degraders and found that IL-1β neutralization impairs MMP activity, likely through loss of expression by tumor cells and macrophages. To further investigate the targets of IL-1β signaling, we analyzed Il1r1 expression levels across all cell types and found the highest levels in cancer-associated fibroblasts (CAFs). Moreover, CAFs expressed elevated levels of the myeloid chemokines Ccl2, Csf1, Cxcl1, Cxcl2 as well as Il6 compared to fibroblasts from wild-type prostates. In vitro studies of wild-type prostate fibroblasts treated with recombinant IL-1β confirmed that IL-1β directly upregulates expression of these inflammatory cytokines and chemokines. In addition, IL-1β directly promotes proliferation of tumor-derived prostate cancer organoids in vitro. Overall, our study suggests that TAMs and CAFs cooperatively drive pro-tumorigenic IL-1β signaling in prostate cancer, demonstrating a direct mechanistic link between inflammation and prostate cancer progression. Citation Format: Young Sun Lee, Jimmy L. Zhao, Max Land, Joseph Chan, Perianne Smith, Roshan Sharma, Sanjay Kottapalli, Linda Fong, Zhenghao Chen, Cathy Wang, Jesse Kirkpatrick, Ava Soleimany, Samir Zaidi, Kayla Lawrence, Amanda Kulick, Teng Han, Zhen Sun, Philip Watson, Anuradha Gopalan, Ojasvi Chaudhary, Tianhao Xu, Ignas Masilionis, Ronan Chaligne, Dana Rathkopf, Michael Morris, Sangeeta Bhatia, Michael Haffner, Dana Pe'er, Charles Sawyers. Tumor-associated macrophages drive prostate cancer progression via IL-1β signaling [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr C006.

Phytochrome-interacting factors PIF4 and PIF5 directly regulate autophagy during leaf senescence in Arabidopsis.

During leaf senescence, autophagy plays a critical role by removing damaged cellular components and participating in nutrient remobilization to sink organs. However, how AUTOPHGAY (ATG) genes are regulated during natural leaf senescence remains largely unknown. In this study, we attempted to identify upstream transcriptional regulator(s) of ATGs and their molecular basis during leaf senescence in Arabidopsis through the combined analyses of promoter binding, autophagy flux, and genetic interactions. We found that PIF4 and PIF5 (PIF4/PIF5) directly bind to the promoters of the ATG5, ATG12a, ATG12b, ATG8a, ATG8e, ATG8f, and ATG8g, inducing their transcription. These target ATGs are downregulated in pif4, pif5, and pif4pif5 mutants, resulting in decreased autophagic activity and slower degradation of chloroplast proteins and chlorophyll. Conversely, overexpression of ATG8s accelerated protein degradation with early leaf senescence. Moreover, our data suggests partial suppression of the pif4pif5 phenotype by ATG8a overexpression. PIF4/PIF5 also influences senescence induced by nutrient starvation, another hallmark of the autophagy pathway. Furthermore, we observed that the PIF4/PIF5-ATG regulatory module may contribute to seed maturation. Our study not only unveils transcriptional regulators of autophagy in natural leaf senescence but also underscores the potential role of PIF4/PIF5 as functional regulators in leaf senescence and nutrient remobilization.

EL HÁBITO DE FUMAR Y SU INFLUENCIA EN LA CONSOLIDACIÓN ÓSEA: UNA REVISIÓN INTEGRADORA

Smoking is considered one of the risk factors for various diseases, not only related to the respiratory system but also influencing the physiological processes of various organs and body systems. This article aims to deepen the understanding of the effects of smoking on bone healing by analyzing its molecular, cellular, and clinical bases. This process is subject to possible direct or indirect interferences from chemical substances such as nicotine. It is important to note that, besides conventional cigarettes, there is also indiscriminate use of electronic cigarettes, which, according to an analysis conducted by Pérez and Duarte (2022), have considerably higher nicotine levels than traditional cigarettes. Another study conducted by González et al. (2021) highlights the increasing popularity of these devices among young people, underscoring the importance of preventive measures. According to the National Institute of Traumatology and Orthopedics (INTO), inhaling tobacco smoke increases bone tissue healing time by 60%, thus delaying the body's ability to heal injuries and compromising bone absorption. The clinical repercussions of smoking on the quality and speed of bone recovery after fractures and orthopedic procedures are identified to improve understanding and develop specific clinical strategies and interventions for smoking patients. The specific objectives of this research were to: investigate the molecular and cellular mechanisms of the bone healing process, analyze the effects of smoking on the quality of the formed tissue, evaluate the influence of smoking on the bone healing time in patients after fracture or orthopedic surgery, and finally propose therapeutic strategies and preventive measures to improve bone healing. To this end, a bibliographic search was conducted on articles relevant to the topic using various means. The selection of articles was based on three stages, choosing those that met the inclusion criteria. During the development of this article, it is observed that smoking is an extended and ancestral practice, being a constant and emerging health problem. Additionally, it is considered a modifiable risk factor for decreasing bone density. In conclusion, the need for specific strategies to address complications in bone healing in smoking patients is highlighted.

Loss of tissue-type plasminogen activator causes multiple developmental anomalies

Abstract Hydrocephalus and Dandy-Walker malformation are among the most common congenital brain anomalies. We identified three consanguineous families with both obstructive hydrocephalus and Dandy-Walker malformation. To understand the molecular basis of these anomalies, we conducted genome-wide sequencing in these families. We identified three homozygous truncating variants in the PLAT gene in the four affected family members. All of them showed tetraventricular hydrocephalus. In two individuals, a membrane at the inferior aspect of the fourth ventricle was likely the cause of their hydrocephalus. Three cases exhibited Dandy-Walker malformation whereas the two oldest individuals displayed intellectual disability. PLAT encodes the tissue-type plasminogen activator, a serine protease whose main function is to cleave the proenzyme plasminogen to produce active plasmin. Interestingly, plasminogen deficiency has also been shown to cause obstructive hydrocephalus and Dandy-Walker malformation, suggesting that loss of PLAT causes these defects by disrupting plasmin production. In summary, we describe a recessive disorder characterized by obstructive hydrocephalus, Dandy-Walker malformation and intellectual disability in individuals with loss-of-function variants in PLAT. This discovery further strengthens the involvement of the plasminogen pathway in the pathogenesis of these developmental disorders.

Small, but mitey: investigating the molecular genetic basis formite domatia development and intraspecific variation in Vitisriparia using transcriptomics.

Here, we investigated the molecular genetic basis of mite domatia, structures on the underside of leaves that house mutualistic mites, and intraspecific variation in domatia size in Vitis riparia (riverbank grape). Domatia and leaf traits were measured, and the transcriptomes of mite domatia from two genotypes of V. riparia with distinct domatia sizes were sequenced to investigate the molecular genetic pathways that regulate domatia development and intraspecific variation in domatia traits. Key trichome regulators as well as auxin and jasmonic acid are involved in domatia development. Genes involved in cell wall biosynthesis, biotic interactions, and molecule transport/metabolism are upregulated in domatia, consistent with their role in domatia development and function. This work is one of the first to date that provides insight into the molecular genetic bases of mite domatia. We identified key genetic pathways involved in domatia development and function, and uncovered unexpected pathways that provide an avenue for future investigation. We also found that intraspecific variation in domatia size in V. riparia seems to be driven by differences in overall leaf development between genotypes.

HC-HA/PTX3 from Human Amniotic Membrane Induced Differential Gene Expressions in DRG Neurons: Insights into the Modulation of Pain

Background: The biologics derived from human amniotic membranes (AMs) demonstrate potential pain-inhibitory effects in clinical settings. However, the molecular basis underlying this therapeutic effect remains elusive. HC-HA/PTX3 is a unique water-soluble regenerative matrix that is purified from human AMs. We examined whether HC-HA/PTX3 can modulate the gene networks and transcriptional signatures in the dorsal root ganglia (DRG) neurons transmitting peripheral sensory inputs to the spinal cord. Methods: We conducted bulk RNA-sequencing (RNA-seq) of mouse DRG neurons after treating them with HC-HA/PTX3 (15 µg/mL) for 10 min and 24 h in culture. Differential gene expression analysis was performed using the limma package, and Gene Ontology (GO) and protein–protein interaction (PPI) analyses were conducted to identify the networks of pain-related genes. Western blotting and in vitro calcium imaging were used to examine the protein levels and signaling of pro-opiomelanocortin (POMC) in DRG neurons. Results: Compared to the vehicle-treated group, 24 h treatment with HC-HA/PTX3 induced 2047 differentially expressed genes (DEGs), which were centered on the ATPase activity, receptor–ligand activity, and extracellular matrix pathways. Importantly, PPI analysis revealed that over 50 of these DEGs are closely related to pain and analgesia. Notably, HC-HA/PTX3 increased the expression and signaling pathway of POMC, which may affect opioid analgesia. Conclusions: HC-HA/PTX3 induced profound changes in the gene expression in DRG neurons, centered around various neurochemical mechanisms associated with pain modulation. Our findings suggest that HC-HA/PTX3 may be an important biological active component in human AMs that partly underlies its pain inhibitory effect, presenting a new strategy for pain treatment.

Gene-environment interactions in the influence of maternal education on adolescent neurodevelopment using ABCD study.

Maternal education was strongly correlated with adolescent brain morphology, cognitive performances, and mental health. However, the molecular basis for the effects of maternal education on the structural neurodevelopment remains unknown. Here, we conducted gene-environment-wide interaction study using the Adolescent Brain Cognitive Development cohort. Seven genomic loci with significant gene-environment interactions (G×E) on regional gray matter volumes were identified, with enriched biological functions related to metabolic process, inflammatory process, and synaptic plasticity. Additionally, genetic overlapping results with behavioral and disease-related phenotypes indicated shared biological mechanism between maternal education modified neurodevelopment and related behavioral traits. Finally, by decomposing the multidimensional components of maternal education, we found that socioeconomic status, rather than family environment, played a more important role in modifying the genetic effects on neurodevelopment. In summary, our study provided analytical evidence for G×E effects regarding adolescent neurodevelopment and explored potential biological mechanisms as well as social mechanisms through which maternal education could modify the genetic effects on regional brain development.

Architecture and activation of single-pass transmembrane receptor guanylyl cyclase.

The heart, in addition to its primary role in blood circulation, functions as an endocrine organ by producing cardiac hormone natriuretic peptides. These hormones regulate blood pressure through the single-pass transmembrane receptor guanylyl cyclase A (GC-A), also known as natriuretic peptide receptor 1. The binding of the peptide hormones to the extracellular domain of the receptor activates the intracellular guanylyl cyclase domain of the receptor to produce the second messenger cyclic guanosine monophosphate. Despite their importance, the detailed architecture and domain interactions within full-length GC-A remain elusive. Here we present cryo-electron microscopy structures, functional analyses and molecular dynamics simulations of full-length human GC-A, in both the absence and the presence of atrial natriuretic peptide. The data reveal the architecture of full-length GC-A, highlighting the spatial arrangement of its various functional domains. This insight is crucial for understanding how different parts of the receptor interact and coordinate during activation. The study elucidates the molecular basis of how extracellular signals are transduced across the membrane to activate the intracellular guanylyl cyclase domain.

Exploring the Molecular Basis of Anticancer Activity in Various Moss Species Against Colorectal Cancer Cells

Background: Mushrooms are shown to protect against the side effects of cancer. Therefore, mushrooms with proven anticancer properties and active ingredients are fascinating in the search for new cancer drugs. Objective: In this study, the effects of extracts from Hericium coralloides (M1), Lactarius deliciosus (M2), Lepista nuda (M3), Pleurotus ostreatus (M4), and Suillus collitinus (M5) together on HCT116 were investigated. Mesenchymal stem cells (MSCs) were used to study the effect on healthy cells. Methods: MTT was used to determine cell viability. Dose-response curves were generated, the IC50 values of the compounds were calculated, and the effect of the extracts was compared using it. The FTIR was used to analyze the quantitative changes of the cellular components. Results and Discussion: The evaluation of the IC50 values of all fungal species showed that they reduced the cell viability of HCT116 cells. In contrast, no significant reduction in cell viability was observed in MSCs. Changes in the ratio of cell membrane lipids, proteins, and cell nucleic acids between control and fungal-treated HCT116 cells were detected by FTIR. Many of the chemotherapeutic agents are of plant origin, and many resources should still be explored to inhibit the side effects of cancer therapy. Conclusion: The data obtained through this experiment will serve as a reference for studies to be a new source of anticancer drugs in modern pharmacology.

Machine learning-driven discovery of novel therapeutic targets in diabetic foot ulcers.

To utilize machine learning for identifying treatment response genes in diabetic foot ulcers (DFU). Transcriptome data from patients with DFU were collected and subjected to comprehensive analysis. Initially, differential expression analysis was conducted to identify genes with significant changes in expression levels between DFU patients and healthy controls. Following this, enrichment analyses were performed to uncover biological pathways and processes associated with these differentially expressed genes. Machine learning algorithms, including feature selection and classification techniques, were then applied to the data to pinpoint key genes that play crucial roles in the pathogenesis of DFU. An independent transcriptome dataset was used to validate the key genes identified in our study. Further analysis of single-cell datasets was conducted to investigate changes in key genes at the single-cell level. Through this integrated approach, SCUBE1 and RNF103-CHMP3 were identified as key genes significantly associated with DFU. SCUBE1 was found to be involved in immune regulation, playing a role in the body's response to inflammation and infection, which are common in DFU. RNF103-CHMP3 was linked to extracellular interactions, suggesting its involvement in cellular communication and tissue repair mechanisms essential for wound healing. The reliability of our analysis results was confirmed in the independent transcriptome dataset. Additionally, the expression of SCUBE1 and RNF103-CHMP3 was examined in single-cell transcriptome data, showing that these genes were significantly downregulated in the cured DFU patient group, particularly in NK cells and macrophages. The identification of SCUBE1 and RNF103-CHMP3 as potential biomarkers for DFU marks a significant step forward in understanding the molecular basis of the disease. These genes offer new directions for both diagnosis and treatment, with the potential for developing targeted therapies that could enhance patient outcomes. This study underscores the value of integrating computational methods with biological data to uncover novel insights into complex diseases like DFU. Future research should focus on validating these findings in larger cohorts and exploring the therapeutic potential of targeting SCUBE1 and RNF103-CHMP3 in clinical settings.

Dab2 is required for the scavenging function of lymphatic endothelial cells in the zebrafish meninges.

To date it is only partially understood how the brain is cleared of waste products resulting from its high metabolic activity, although this process has important implications for the development and progression of neurodegenerative diseases. Lymphatic vessels play a central role in maintaining fluid and tissue homeostasis, and the recent description of meningeal lymphatic vessels within the dura mater of mice, human and zebrafish has raised considerable interest in unraveling the function of these vessels. In zebrafish, brain lymphatic endothelial cells (BLECs) constitute an additional meningeal lymphatic endothelial cell population. These highly endocytically active cells contribute to the clearance of the brain, but the molecular basis of this scavenging activity is only poorly understood. Here, we report on the characterization of zebrafish disabled 2 (dab2) mutants. Embryos lacking maternally provided dab2 show defective venous sprouting from the caudal vein plexus at 26hpf. Furthermore, we show that the cargo-specific adaptor protein is specifically expressed in BLECs, and that BLECs are significantly impeded in their capacity to internalize specific substrates injected into the cerebrospinal fluid upon loss of zygotic dab2. Our work therefore identifies Dab2 as an important member of the molecular machinery mediating the scavenging function of BLECs in the meninges.

Unraveling the Amino Acid Synthesis in Maturity Sesame Seeds Based on the Integrative Analysis of Transcriptome and Metabolome

ABSTRACTSesame plays a vital role in food industry due to its high oil yield, antioxidant potential, and substantial protein content. Notably, there are significant differences in amino acid composition in sesame seeds at various developmental stages. However, the molecular basis and regulatory mechanism underlying amino acid production largely remain unexplored. To unravel these mechanisms, we analyzed the metabolome and transcriptome profiles of a sesame variety across four distinct growth stages (S1–S4). Our analysis identified a total of 17 amino acids, with glutamic acid (Glu), arginine (Arg), proline (Pro), and tyrosine (Tyr) exhibiting significantly higher abundances in mature stages. This increased abundance correlated with the elevated expression of genes involved in amino acid synthesis and regulatory genes. Using weighted gene co‐expression network analysis, we discovered modules associated with glutathione metabolism, arginine biosynthesis, proline, and tyrosine synthesis, along with candidate genes that regulate amino acid production and metabolism. Notably, the differential expression of genes within the amino acid pathways resulted in significant variations in the contents of Glu, Arg, Pro, and Tyr at the mature stage (28 days after flowering, S4) compared to other growth stages. Correlation analysis revealed strong association among the enzymes glutamine synthetase (GS), glutamate/aspartate–prephenate aminotransferase (PAT), and polyamine oxidase (PAO) with the 17 amino acids, suggesting their potential role in the amino acid synthesis. Our findings provide novel insights into the synthesis and accumulation of amino acids during the growth stages of sesame seeds, highlighting key regulatory genes and metabolic pathways involved in this process. Our study lays the groundwork for future studies aiming to enhance the nutritional quality and yield of sesame varieties.

XAF1 antagonizes TRIM28 activity through the assembly of a ZNF313-mediated destruction complex to suppress tumor malignancy.

X-linked inhibitor of apoptosis-associated factor 1 (XAF1) is a stress-inducible pro-apoptotic protein that is commonly inactivated in multiple human cancers. Nevertheless, the molecular basis for its tumor suppression function remains largely uncharacterized. Here we report that XAF1 antagonizes the oncogenic activity of tripartite motif containing 28 (TRIM28) ubiquitin E3 ligase through zinc finger protein 313 (ZNF313)-induced ubiquitination and proteasomal degradation. XAF1 exerts apoptosis-promoting effect more strongly in TRIM28+/+ versus XAF1-/- tumor cells and suppresses tumor cell growth, migration, invasion, and epithelial-to-mesenchymal transition and xenograft tumor growth in a highly TRIM28-dependent fashion. Mechanistically, XAF1 interacts directly with the RING domains of TRIM28 and ZNF313 through the ZF6 and ZF7 domain, respectively, thereby facilitating ZNF313 interaction with and ubiquitination of TRIM28. A mutant XAF1 lacking either ZF6 or ZF7 domain exhibits no activity to promote TRIM28 ubiquitination. By destabilizing TRIM28, XAF1 blocks TRIM28-driven ubiquitination of p53 and RLIM, p53-HDAC1 interaction, and TWIST1 stabilization. Intriguingly, TRIM28 destabilizes XAF1 through K48-linked polyubiquitination and proteasomal degradation to protect tumor cells from apoptotic stress, indicating its role as an intrinsic antagonist against XAF1 and the antagonistic interplay of XAF1 and TRIM28. XAF1 expression is inversely correlated with TRIM28 expression in cancer cell lines and tumor tissues and more tightly associated with the survival of TRIM28-high versus TRIM28-low patients. Together, this study uncovers a novel mechanism by which XAF1 suppresses tumor malignancy and an important role for XAF1-TRIM28 interplay in governing stress response, illuminating the mechanistic consequence of its alteration during tumorigenic process.

Elucidating the gastroprotective mechanisms of Imperata cylindrica Beauv.var. major (Nees) C.E.Hubb through UHPLC-MS/MS and systems network pharmacology.

Imperata cylindrica Beauv.var. major (Nees) C.E.Hubb., commonly known as BaiMaoGen (BMG), a medicinal and edible traditional Chinese medicinal (TCM) herb commonly used in health supplements, has been observed to offer protective effects against gastrointestinal disorders. However, the specific bioactive compounds and their molecular mechanisms have not been fully elucidated. This study employed ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) and systematic network pharmacology to analyze and identify the key active components and their interactions with biological targets. Thirty-six main active compounds, including 3,4-dihydroxybenzoic acid and p-hydroxybenzoic acid, were identified and analyzed for their interaction with key protein targets using molecular docking and dynamic simulations. This combined approach highlighted the therapeutic pathways involved, particularly the PI3K/AKT signaling pathways, providing new insights into the molecular basis of BMG's gastroprotective effects. Our findings suggested that BMG's complex multi-target action can potentially be harnessed to develop effective treatments for gastrointestinal toxicity.