Cellular Mechanisms Research Articles

Single-nucleus transcriptomes reveal the underlying mechanisms of dynamic whitening in thermogenic adipose tissue in goats

BackgroundThermogenic adipose tissue, both beige and brown, experiences whitening as animals are exposed to warmth and age, but the potential mechanisms are not fully understood. In this study, we employed single-nucleus RNA-seq to construct a cell atlas during whitening progression and identified the characteristics of thermogenic adipocytes. ResultsOur histological studies and bulk transcriptome gene expression analysis confirmed that both perirenal and omental adipose tissues (pAT and oAT) exhibited progressive whitening in goats. Compared to the classic brown adipocytes in mice, goat thermogenic adipocytes were more closely related in gene expression patterns to human beige adipocytes, which was also confirmed by adipocyte type- and lineage-specific marker expression analysis. Furthermore, trajectory analysis revealed beige- and white-like adipocytes deriving from a common origin, coexisting and undergoing the transdifferentiation. In addition, differences in gene expression profiles and cell communication patterns (e.g., FGF and CALCR signaling) between oAT and pAT suggested a lower thermogenic capacity of oAT than that of pAT.ConclusionsWe constructed a cell atlas of goat pAT and oAT and descripted the characteristics of thermogenic adipocytes during whitening progression. Altogether, our results make a significant contribution to the molecular and cellular mechanisms behind the whitening of thermogenic adipocytes, and providing new insights into obesity prevention in humans and cold adaptation in animals.

Transcriptomic Profiling Unveils EDN3+ Meningeal Fibroblasts as Key Players in Sturge-Weber Syndrome Pathogenesis.

Sturge-Weber syndrome (SWS) is characterized by leptomeningeal vascular malformation, resulting in significant risks of life-threatening seizures and strokes. The current absence of specific treatments underscores the need to define the molecular and cellular mechanisms that drive the progression of SWS. Here, the transcriptome of 119 446 cells isolated from both malformed tissues and peri-lesion tissues from the brains of patients with SWS is examined. This comprehensive analysis finds a complex landscape of cell heterogeneity and distinct cell substate associated with the evolution of this disease are revealed. Notably, a unique fibroblast cluster and molecular mechanism are identified that contribute to the development of SWS. These findings not only expand the understanding of SWS but also open up promising avenues for therapeutic interventions.

Harnessing the fundamental roles of vitamins: the potent anti-oxidants in longevity.

Aging is a complex and heterogeneous biological process characterized by telomere attrition, genomic instability, mitochondrial dysfunction, and disruption in nutrient sensing. Besides contributing to the progression of cancer, metabolic disorders, and neurodegenerative diseases, these manifestations of aging also adversely affect organ function. It is crucial to understand these mechanisms and identify interventions to modulate them to promote healthy aging and prevent age-related diseases. Vitamins have emerged as potential modulators of aging beyond their traditional roles in health maintenance. There is an increasing body of evidence that hormetic effects of vitamins are responsible for activating cellular stress responses, repair mechanisms, and homeostatic processes when mild stress is induced by certain vitamins. It is evident from this dual role that vitamins play a significant role in preventing frailty, promoting resilience, and mitigating age-related cellular damage. Moreover, addressing vitamin deficiencies in the elderly could have a significant impact on slowing aging and extending life expectancy. A review of recent advances in the role of vitamins in delaying aging processes and promoting multiorgan health is presented in this article. The purpose of this paper is to provide a comprehensive framework for using vitamins as strategic tools for fostering longevity and vitality. It offers a fresh perspective on vitamins' role in aging research by bridging biological mechanisms and clinical opportunities.

Applications of Liquid-Liquid Phase Separation in Biosensing.

Phase separation, particularly liquid-liquid phase separation (LLPS), has emerged as a powerful tool in biological research, offering unique advantages for visualizing and analyzing biomolecular interactions. This review highlights recent advances in leveraging LLPS to develop experimental techniques for studying protein-protein interactions (PPIs), protein-RNA interactions, and enzyme activity. The integration of LLPS with advanced techniques has expanded its applications, offering new possibilities for unraveling the complexities of cellular function and disease mechanisms. Looking forward, the development of more versatile, sensitive, and targeted LLPS-based methods is poised to transform molecular biology, providing deeper insights into cellular dynamics and facilitating therapeutic advancements.

Single-cell analysis reveals cellular heterogeneity, gene expression profiles, and pathway dynamics in acne vulgaris.

Acne vulgaris is a common dermatological condition, particularly in adolescents, and is associated with significant physical and psychological impacts. Its pathogenesis involves genetic factors, sebaceous gland dysfunction, inflammatory responses, and alterations in skin microbiota. Despite advancements in treatment, a comprehensive understanding of its cellular and molecular mechanisms remains limited, making therapeutic strategies challenging. Single-cell RNA sequencing (scRNA-seq) data from six acne vulgaris patients were obtained from the GEO database (GSE175817), filtered, and integrated. Differentially expressed genes (DEGs) were identified and subjected to functional enrichment analysis to explore the underlying pathogenesis. Gene set variation analysis (GSVA) was used to investigate metabolic pathway alterations, and ligand-receptor interactions were analyzed to examine cell-to-cell communication between lesional and non-lesional skin tissues. The integration of scRNA-seq data yielded the identification of eight distinct cell clusters, including endothelial cells, myeloid cells, lymphocytes, melanocytes, sebaceous gland cells, smooth muscle cells, keratinocytes and fibroblasts. The proportions of lymphoid and myeloid cells were found to be significantly different between the lesional and non-lesional sites. The differential expression of genes (DEGs) was found to be significantly specific to the different cell clusters. Abnormal intercellular communication was found to result in a substantial increase in the number and intensity of communications in the area of acne vulgaris lesions. Moreover, specific ligand-receptor pairs for SPP1 and IL6 associated with acne vulgaris were identified. Furthermore, the presence of specific alterations in metabolic pathways, including riboflavin metabolism, niacin metabolism, and lipoic acid metabolism, was observed. Our findings demonstrate the cellular heterogeneity and dysfunction of intercellular communication and metabolic signaling in the lesional skin tissues of patients with acne vulgaris. These findings have important implications for understanding the complex biological processes of acne vulgaris.

Overwriting an instinct: Visual cortex instructs learning to suppress fear responses.

Fast instinctive responses to environmental stimuli can be crucial for survival but are not always optimal. Animals can adapt their behavior and suppress instinctive reactions, but the neural pathways mediating such ethologically relevant forms of learning remain unclear. We found that posterolateral higher visual areas (plHVAs) are crucial for learning to suppress escapes from innate visual threats through a top-down pathway to the ventrolateral geniculate nucleus (vLGN). plHVAs are no longer necessary after learning; instead, the learned behavior relies on plasticity within vLGN populations that exert inhibitory control over escape responses. vLGN neurons receiving input from plHVAs enhance their responses to visual threat stimuli during learning through endocannabinoid-mediated long-term suppression of their inhibitory inputs. We thus reveal the detailed circuit, cellular, and synaptic mechanisms underlying experience-dependent suppression of fear responses.

Macrophages Unmasked: Their Pivotal Role in Driving Atherosclerosis in Systemic Lupus Erythematosus.

Systemic lupus erythematosus (SLE) is an autoimmune disease that significantly increases the risk of cardiovascular diseases, particularly atherosclerosis (AS). Understanding the shared pathogenic mechanisms underlying SLE and AS is crucial for developing effective therapeutic strategies. Macrophages, as pivotal immune cells, play a critical role in the initiation and progression of atherosclerotic plaques within the context of SLE. This review delves into the molecular and cellular mechanisms governing macrophage activation and differentiation in response to SLE-related inflammatory mediators, highlighting their roles in lipid metabolism, plaque stability, and immune regulation. Additionally, we discussed the current treatment modalities for SLE and their impact on macrophage functionality, exploring these effects for atherosclerotic progression. By elucidating the intricate relationship between macrophages, SLE pathophysiology, and AS progression, this review underscores the need for a multidisciplinary approach in managing SLE and its cardiovascular complications, aiming to improve patient survival and quality of life through tailored therapeutic interventions addressing both autoimmune and cardiovascular pathologies.

Near-infrared photobiomodulation therapy on HD10.6 human sensory neurons cell culture.

We investigated the molecular effects of near-infrared photobiomodulation therapy (PBMT) on HD10.6 human sensory neuron cell cultures. This study explores the utility of PBMT in modulating the functionality of sensory neurons in vitro with a potential translational effect on analgesia, a significant concern in clinical settings, particularly in pediatrics where non-invasive treatments are crucial. HD10.6 human sensory neuron cell model was employed in the study. The 800 and 970 PBMT was tested on the cells and mitochondria related parameters and TRP channel functionality were evaluated after irradiation. We found that PBMT affects mitochondrial dynamics and reduces oxidative stress, influenced calcium ion flow, pivotal in nociception signaling, and modified the expression of TRPV1 and TRPA1 receptors post-irradiation. This study observed a potential impact of PBMT on sensory neurons through various cellular mechanisms. These findings may contribute to the understanding of PBMT's mechanistic effects on human sensory neurons, not yet explored in in-vitro model, pointing to its potential utility as a supportive treatment for non-invasive pain management in pediatric care.

Biomechanical Insights into the Proteomic Profiling of Cells in Response to Red Light Absorption.

Photobiomodulation (PBM) is a promising non-invasive therapy for tissue repair, but its underlying cellular mechanisms are not fully understood. In this study, the biomechanical and proteomic responses of three cell types - keratinocytes (HACAT), fibroblasts (L929), and osteoblasts (OFCOLII) - exposed to red light (633 nm) are investigated using atomic force microscopy (AFM) and mass spectrometry-based proteomic analysis. Red light absorption resulted in cell-type-specific changes in viscoelastic properties, with fibroblasts exhibiting increased fluidity, reduced stiffness, and enhanced motility. Conversely, keratinocytes exhibited intensity-dependent responses, while osteoblasts appeared to be relatively insensitive to irradiation conditions. Proteomic profiling identified key signaling pathways involved in immune response, ATP production, and stress regulation. The immune and ATP pathways are strongly linked to the modulation of viscoelastic properties, particularly in fibroblasts, while weaker correlations wereobserved in keratinocytes. Cytoskeletal remodeling, primarily within the F-actin network, is identified as the main driver of mechanical alterations, with additional contributions from microtubules and intermediate filaments. These findings provide new insights into how red light absorption modulates cellular viscoelasticity through cytoskeletal remodeling, with potential applications in optimizing light-based therapies for tissue regeneration and diseasetreatment.

Postbiotics as a Therapeutic Tool in Alzheimer's Disease: Insights into Molecular Pathways and Neuroprotective Effects.

Alzheimer's disease (AD) is a progressive neurodegenerative disease, characterized by oxidative stress, neuroinflammation, mitochondrial dysfunction, neurotransmitter imbalance, tau hyperphosphorylation, and amyloid beta (Aβ) accumulation in brain regions. The gut microbiota (GM) has a major impact on brain function due to its bidirectional interaction with the gut through the gut-brain axis. The gut dysbiosis has been associated with neurological disorders, emphasizing the importance of gut homeostasis in maintaining appropriate brain function. The changes in the composition of microbiomes influence neuroinflammation and Aβ accumulation by releasing pro-inflammatory cytokines, decreasing gut and blood-brain barrier (BBB) integrity, and microglial activation in the brain. Postbiotics, are bioactive compounds produced after fermentation, have been shown to provide several health benefits, particularly in terms of neuroinflammation and cognitive alterations associated with AD. Several research studies on animal models and human have successfully proven the effects of postbiotics on enhancing cognition and memory in experimental animals. This article explores the protective effects of postbiotics on cellular mechanisms responsible for AD pathogenesis and studies highlighting the influence of postbiotics as a total combination and specific compounds, including short-chain fatty acids (SCFAs). In addition, postbiotics act as a promising option for future research to deal with AD's progressive nature and improve an individual's life quality using microbiota modulation.

Extrinsic induction of apoptosis and tumor suppression via the p53–Reprimo–Hippo–YAP/TAZ–p73 pathway

Tumor progression is suppressed by inherent cellular mechanisms such as apoptosis. The p53 tumor suppressor gene is the most commonly mutated gene in human cancer and plays a pivotal role in tumor suppression. RPRM is a target gene of p53 known to be involved in tumor suppression, but its molecular function has remained elusive. Here, we report that Reprimo (the protein product of RPRM) is secreted and extrinsically induces apoptosis in recipient cells. We identified FAT1, FAT4, CELSR1, CELSR2, and CELSR3, members of the protocadherin family, as receptors for Reprimo. Subsequent analyses revealed that Reprimo acts upstream of the Hippo-YAP/TAZ-p73 axis and induces apoptosis by transactivating various proapoptotic genes. In vivo analyses further support the tumor-suppressive effects of secreted Reprimo. These findings identify the p53-Reprimo-Hippo-YAP/TAZ-p73 axis as an extrinsic apoptosis pathway that plays a crucial role in tumor suppression. Our finding of the innate tumor eliminator Reprimo and the downstream pathway offers a promising avenue for the pharmacological treatment of cancer.

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

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

DNA Methylation in Long-term Memory.

Understanding neural mechanisms of memory has been one of the key questions in biology. Long-term memory specifically, allows one to travel mentally without constraints of time and space (1). A long-term memory must have gone through a series of temporal processes: encoding, consolidation, storage, and retrieval. Decades of studies have revealed cellular and molecular mechanisms underlying each process. In this paper, we will first review the emerging concept of memory engrams and technologies of engram labeling, as these methods provide a new avenue to study the molecular mechanisms for memory. Then, we will focus on DNA methylation and its role in long-term memory. Lastly, we will discuss some key remaining questions in this field and their implications in memory-related disease.

UV-induced reorganization of 3D genome mediates DNA damage response

While it is well-established that UV radiation threatens genomic integrity, the precise mechanisms by which cells orchestrate DNA damage response and repair within the context of 3D genome architecture remain unclear. Here, we address this gap by investigating the UV-induced reorganization of the 3D genome and its critical role in mediating damage response. Employing temporal maps of contact matrices and transcriptional profiles, we illustrate the immediate and holistic changes in genome architecture post-irradiation, emphasizing the significance of this reconfiguration for effective DNA repair processes. We demonstrate that UV radiation triggers a comprehensive restructuring of the 3D genome organization at all levels, including loops, topologically associating domains and compartments. Through the analysis of DNA damage and excision repair maps, we uncover a correlation between genome folding, gene regulation, damage formation probability, and repair efficacy. We show that adaptive reorganization of the 3D genome is a key mediator of the damage response, providing new insights into the complex interplay of genomic structure and cellular defense mechanisms against UV-induced damage, thereby advancing our understanding of cellular resilience.

Local endoreduplication of the host is a conserved process during Phytomyxea–host interaction

BackgroundEndoreduplication, a modified cell cycle, involves cells duplicating DNA without undergoing mitosis. This phenomenon is frequently observed in plants, algae, and animals. Biotrophic pathogens have been demonstrated to induce endoreduplication in plants to secure more space or nutrients.MethodsIn this study, we investigated the endoreduplication process triggered by two phylogenetically distant Rhizaria organisms—Maullinia spp. (in brown algae) and Plasmodiophora brassicae (in plants)—by combining fluorescent in situ hybridization (FISH) with nuclear area measurements.ResultsWe could confirm that Plasmodiophora brassicae (Plasmodiophorida) triggers endoreduplication in infected plants. For the first time, we also demonstrated pathogen-induced endoreduplication in brown algae infected with Maullinia ectocarpii and Maullinia braseltonii (Phagomyxida). We identified molecular signatures of endoreduplication in RNA-seq datasets of P. brassicae-infected Brassica oleracea and M. ectocarpii-infected Ectocarpus siliculosus.DiscussionCell cycle switch proteins such as CCS52A1 and B in plants, CCS52 in algae, and the protein kinase WEE1 in plants were upregulated in RNA-seq datasets hinting at a potential role in the phytomyxean-induced transition from mitotic cell cycle to endocycle. By demonstrating the consistent induction of endoreduplication in hosts during phytomyxid infections, our study expands our understanding of Phytomyxea–host interaction. The induction of this cellular mechanism by phytomyxid parasites in phylogenetically distant hosts further emphasizes the importance of endoreduplication in these biotrophic interactions.

Translocating gut pathobiont Enterococcus gallinarum induces T H 17 and IgG3 anti-RNA–directed autoimmunity in mouse and human

Chronic autoimmune diseases often lead to long-term sequelae and require lifelong immunosuppression because of an incomplete understanding of the triggers and drivers in genetically predisposed patients. Gut bacteria that escape the gut barrier, known as translocating gut pathobionts, have been implicated as instigators and perpetuators of extraintestinal autoimmune diseases in mice. The gut microbial contributions to autoimmunity in humans remain largely unclear, including whether specific pathological human adaptive immune responses are triggered by such pathobionts. Here, we show that the translocating pathobiont Enterococcus gallinarum can induce both human and mouse interferon-γ + T helper 17 (T H 17) differentiation and immunoglobulin G3 (IgG3) subclass switch of anti– E. gallinarum RNA antibodies, which correlated with anti-human RNA autoantibody responses in patients with systemic lupus erythematosus (SLE) and autoimmune hepatitis, two extraintestinal autoimmune diseases. E. gallinarum RNA, but not human RNA, triggered Toll-like receptor 8 (TLR8), and TLR8-mediated human monocyte activation promoted human T H 17 induction by E. gallinarum . Translocation of the pathobiont triggered increased anti-RNA autoantibody titers that correlated with renal autoimmune pathophysiology in murine gnotobiotic lupus models and with disease activity in patients with SLE. These studies elucidate cellular mechanisms of how a translocating gut pathobiont induces systemic human T cell– and B cell–dependent autoimmune responses and provide a framework for developing host- and microbiota-derived biomarkers and targeted therapies in autoimmune diseases.

Cellular mechanisms underlying overreaching in skeletal muscle following excessive high-intensity interval training.

Overreaching (OR) can be defined as a decline in physical performance resulting from excessive exercise training, necessitating days to weeks recovery. Impairments in the contractile function of skeletal muscle are believed to be a primary factor contributing to OR. However, the cellular mechanism triggering OR remains unclear. The purpose of this study was to elu idate the mechanisms underlying OR. Rats' plantar flexor muscles were subjected to repeated electrical stimulations mimicking excessive high-intensity interval training (HIIT) daily for 13 consecutive days, and isometric torques were monitored. The torque was measured one day after HIIT, and subsequently, the physiological function of type II fibers was analyzed by using mechanically-skinned-fiber technique. Eleven out of 17 rats exhibited torque decline, while others did not. Thus, the rats were divided into OR and non-overreaching (NOR) groups. Skinned fibers from the gastrocnemius (GAS) muscles of both groups showed decreased depolarization-induced force and increased myofibrillar Ca2+ sensitivity.However, the fibers from the OR group, but not the NOR group, exhibited a decrease in myofibrillar maximal force. Biochemical analyses of a superficial region of GAS muscle revealed that α-actinin 2 content was increased in the NOR group, but not the OR group, whereas calpain-3 autolysis was increased in the OR group, but not the NOR group. These findings shed light on the cellular mechanism underlying OR: OR following excessive HIIT was induced by a decreased myofibrillar maximal force, while Ca2+ sensitivity was increased.

Histological analysis of anterior eye development in the brown anole lizard (Anolis sagrei).

For all vertebrates, the anterior eye structures work together to protect and nourish the eye while ensuring that light entering the eye is correctly focused on the retina. However, the anterior eye structure can vary significantly among different vertebrates, reflecting how the structures of the anterior eye have evolved to meet the specific visual needs of different vertebrate species. Although conserved pathways regulate fundamental aspects of anterior eye development in vertebrates, there may also be species-specific differences underlying structural variation. Our knowledge of the cellular and molecular mechanisms underlying the development of structures of the anterior eye comes mainly from work in mammals, chicks, some amphibians, and small teleosts such as zebrafish. Our understanding of anterior eye development would benefit from comparative molecular studies in diverse vertebrates. A promising lizard model is the brown anole, Anolis sagrei, which is easily raised in the laboratory and for which genome editing techniques exist. Here, we provide a detailed histological analysis of the development of the anterior structures of the eye in A. sagrei, which include the cornea, iris, ciliary body, lens, trabecular meshwork, and scleral ossicles. The development of the anterior segment in anoles follows a pattern similar to other vertebrates. The lens forms first, followed by the cornea, iris, ciliary body, and tissues involved in the outflow of the aqueous humor. The development of the iris and ciliary body begins temporally and then proceeds nasally. Scleral ossicle development is generally comparable to that reported for chicks and turtles. Anoles have a remarkably thin cornea and a flat ciliary body compared to the eyes of mammals and birds. This study highlights several features in anoles and represents a deeper understanding of reptile eye development.

Recent Developments in 14-3-3 Stabilizers for Regulating Protein-Protein Interactions: An Update.

14-3-3 proteins play a crucial role in the regulation of protein-protein interactions, impacting various cellular processes and disease mechanisms. Recent advancements have led to the development of stabilizers that enhance the binding of 14-3-3 proteins to clients, presenting promising therapeutic potentials. This perspective provides an updated overview of the latest developments in the field of 14-3-3 stabilizers, with a focus on their design, synthesis, and biological evaluation. We discuss the structural basis for the interaction between 14-3-3 proteins and their ligands, highlighting key modifications that enhance binding affinity and selectivity. Additionally, we explore the therapeutic applications of 14-3-3 stabilizers across major therapeutic areas such as cancer, metabolic disorders, and neurodegenerative diseases. By summarizing recent research findings and technological advancements, this perspective aims to shed light on the current state of 14-3-3 stabilizer developments and outline future directions for optimizing these compounds as effective therapeutic agents.

Efficacy and Cellular Mechanism of Biomimetic Marine Adhesive Protein-Based Coating Against Skin Photoaging.

Skin photoaging is a problem worldwide, clinically often accompanied by collagen decline, increased wrinkles, loss of skin elasticity, structurally weakened skin, and other complications,which urgently demand effective treatment strategies. The biosafety and efficacy of single-function therapies for repairing skin photoaging are still challenging for clinical medicine today. At present, numerous studies report that the wet adhesive proteins driven from marine organisms play a critical role in the biomedical material field, particularly in aquatic environments. In this study, a natural recombinant protein-based coating from scallop byssal protein is prepared to investigate the efficacy and cellular mechanism in accelerating the repair of UVB-induced photoaging in a mouse model. In vitro experiments demonstrate the safety of the coating and its efficacy in enhancing cell adhesion, spreading, proliferation, and migration. Additionally, the coating effectively scavenges reactive oxygen species, promotes the expression of cell adhesion molecules and anti-apoptotic proteins, and inhibits inflammatory responses. In animal tests, the coating exhibited remarkable adsorption properties, showing significant potential for in situ regenerative therapy, as evidenced by its ability to protect against UVB-induced skin photoaging and oxidative stress. These findings suggest that Sbp9Δ coating provides a simple, safe, and innovative strategy for treating skin photoaging.