Changes In Gene Expression Research Articles

Toxicity mechanism of metal-organic framework HKUST-1 and its carbonized product to Tetradesmus obliquus: Physiological and transcriptomic analysis.

Metal-organic frameworks (MOFs) are emerging materials with unique structures and properties, which have been widely used in many fields due to their various advantages. However, compared with its popular application research, the ecological safety of MOFs has rarely been reported. In this paper, a biological model, the common freshwater green algae Tetradesmus obliquus (T. obliquus) was used to study the effects of the copper-based MOF HKUST-1 and its carbonation product DHKUST-1 on the physiology and transcription level of the algae. A suite of advanced material characterization techniques has been utilized to multidimensionally reveal the physicochemical properties of HKUST-1 and its carbonation product. Notably, DHKUST-1 exhibit higher stability than HKUST-1 in aqueous environments, with lower ion release. During a 96-h exposure experiment, relevant indicators such as algae density, chlorophyll-a content and antioxidant enzyme activities were measured. Additionally, an intriguing IBR model was employed to comprehensively assess the toxicity of HKUST-1 and DHKUST-1 on the antioxidant system of T. obliquus. Furthermore, an in-depth analysis was conducted on the differential gene expression changes in T. obliquus under 10 mg/L HKUST-1 stress, exploring the impact on various pathways within algal cells. Briefly, the toxicity mechanism of HKUST-1 on T. obliquus is multi-involved. The findings of this study are expected to provide important basic data and references for the evaluation of the ecological safety of MOFs.

Constructing mechanosensitive signalling pathways de novo in synthetic cells.

Biological mechanotransduction enables cells to sense and respond to mechanical forces in their local environment through changes in cell structure and gene expression, resulting in downstream changes in cell function. However, the complexity of living systems obfuscates the mechanisms of mechanotransduction, and hence the study of these processes in vitro has been critical in characterising the function of existing mechanosensitive membrane proteins. Synthetic cells are biomolecular compartments that aim to mimic the organisation, functionality and behaviours of biological systems, and represent the next step in the development of in vitro cell models. In recent years, mechanosensitive channels have been incorporated into synthetic cells to create de novo mechanosensitive signalling pathways. Here, I will discuss these developments, from the molecular parts used to construct existing pathways, the functionality of such systems, and potential future directions in engineering synthetic mechanotransduction. The recapitulation of mechanotransduction in synthetic biology will facilitate an improved understanding of biological signalling through the study of molecular interactions across length scales, whilst simultaneously generating new biotechnologies that can be applied as diagnostics, microreactors and therapeutics.

Transcriptome analysis of liver injury of fatty liver disease induced by ALDH2 deficiency

Aldehyde dehydrogenase 2 (Aldh2) Glu504Lys mutation, common in East Asians, is linked to various alcohol-related pathologies, notably fatty liver disease. Recent findings suggest that high ethanol-producing Klebsiella pneumoniae(HiAlc Kpn) exacerbates liver injury in non-alcoholic fatty liver disease (NAFLD). Our study investigated the combined effects of Aldh2 deficiency and HiAlc Kpn on NAFLD liver injury, transcriptome analyses to unearth potential mechanisms and therapeutic targets. In our controlled experiment with Aldh2-deficient mice, we induced fatty liver via alcohol and HiAlc Kpn gavage, followed by comprehensive analyses to detect gene expression and epigenetic changes. The results showed that Aldh2-deficient mice were particularly vulnerable to ethanol and HiAlc Kpn, with notable gene expression changes in key metabolic and liver injury pathways. Our analysis identified crucial differentially expressed genes (DEGs) and pathways, highlighting the significant roles of genes like Cyp8b1, Cyp7a1, and Ugt2b1 in liver metabolism and suggesting them as therapeutic targets. The study underscores the impact of Aldh2 deficiency and HiAlc Kpn on NAFLD progression, revealing potential therapeutic strategies. Despite these insights, further research is needed to clarify the systemic effects on aldehyde metabolism and the full implications of Aldh2 deficiency and HiAlc Kpn in liver injury.

Proteins and DNA Sequences Interacting with Tanshinones and Tanshinone Derivatives.

Tanshinones, biologically active diterpene compounds derived from Salvia miltiorrhiza, interact with specific proteins and DNA sequences, influencing signaling pathways in animals and humans. This study highlights tanshinone-protein interactions observed at concentrations achievable in vivo, ensuring greater physiological relevance compared to in vitro studies that often employ supraphysiological ligand levels. Experimental data suggest that while tanshinones interact with multiple proteomic targets, only a few enzymes are significantly affected at biologically relevant concentrations. This apparent paradox may be resolved by tanshinones' ability to bind DNA and influence enzymes involved in gene expression or mRNA stability, such as RNA polymerase II and human antigen R protein. These interactions trigger secondary, widespread changes in gene expression, leading to complex proteomic alterations. Although the current understanding of tanshinone-protein interactions remains incomplete, this study provides a foundation for deciphering the molecular mechanisms underlying the therapeutic effects of S. miltiorrhiza diterpenes. Additionally, numerous tanshinone derivatives have been developed to enhance pharmacokinetic properties and biological activity. However, their safety profiles remain poorly characterized, limiting comprehensive insights into their medicinal potential. Further investigation is essential to fully elucidate the therapeutic and toxicological properties of both native and modified tanshinones.

Novel photocrosslinking chemical probes utilized for high-resolution spatial transcriptomics.

The architecture of cells and the tissue they form within multicellular organisms are highly complex and dynamic. Cells optimize their function within tissue microenvironments by expressing specific subsets of RNAs. Advances in cell tagging methods enable spatial understanding of RNA expression when merged with transcriptomics. However, these techniques are currently limited by the spatial resolution of the tagging, the number of RNAs that can be sequenced, and multiplexing to isolate spatially-distinct cells within the same tissue landscape. To address these limitations, we developed CrossSeq, which employs photocrosslinking fluorescent probes and confocal microscopy activation to demarcate user-defined regions of interest on fixed cells for multiplexed spatial transcriptomic analysis. We investigate phenyl azide and diazirine crosslinking scaffolds and define their photoactivity profiles. We then deploy the aryl azide scaffold with three fluorophores for multiplexing on glyoxal fixed cells and analyze the defined populations using flow cytometry. Finally, we apply CrossSeq to investigate an in vitro MDA-MB-231-LM2 metastatic cancer migration model to evaluate changes in gene expression at the migratory cell front versus the exterior population. We anticipate this new technology will be a valuable tool addition as it will enable easier access to spatial transcriptomic analysis for the scientific community using conventional microscopy and analysis techniques.

Development of BACE2-IN-1/tranylcypromine-based compounds to induce steroidogenesis-dependent neuroprotection.

Traumatic brain injury (TBI) constitutes a significant burden on global healthcare systems, especially affecting younger populations, where it is a leading cause of disability and mortality. Current treatments for TBI mainly focus on preventing further brain damage and controlling symptoms. However, despite these approaches, several clinical needs remain unmet. Revelations from single-cell RNA sequencing (scRNA-seq) performed to determine cell-type heterogeneity and gene expression changes in brain tissue indicated that brain trauma increases the expression of lysine-specific demethylase 1 (LSD1) and secretase 2 (BACE2). To capitalize on this finding, a medicinal chemistry campaign was conducted to pragmatically insert tranylcypromine, an LSD1 inhibitor, into a carefully designed BACE2 inhibitory template (BACE2-IN-1). Additionally, tranylcypromine was structurally modified to enhance the effects of LSD1 inhibition in TBI. As a result, a tractable neuroprotective agent, BACE2-IN-1/tranylcypromine-based compound 4, was identified, showing potential to maintain Neuro-2a cell survival by alleviating mitochondrial damage after oxidative stress. Compound 4 also restored TBI-mediated inhibition of the cholesterol biosynthetic pathway (mevalonate pathway) and damage of redox metabolism, increasing neuroprotective effects. Furthermore, behavioral assays, including nest-building and cognitive performance tests, demonstrated significant improvement in mice post-TBI following treatment with compound 4. Taken together, the outcomes of this study validate the favorable effects of inhibiting LSD1 and beta-secretase in mitigating mitochondrial stress and promoting neurometabolic recovery in TBI. These findings pave the way for the development of rationally designed inhibitors as promising neuroprotective agents, potentially addressing unmet clinical needs in TBI treatment.

Wall shear stress modulates metabolic pathways in endothelial cells

IntroductionHemodynamic forces play a crucial role in modulating endothelial cell (EC) behavior, significantly influencing blood vessel responses. While traditional in vitro studies often explore ECs under static conditions, ECs are exposed to various hemodynamic forces in vivo. This study investigates how wall shear stress (WSS) influences EC metabolism, focusing on the interplay between WSS and key metabolic pathways.ObjectivesThe aim of this study is to examine the effects of WSS on EC metabolism, specifically evaluating its impact on central carbon metabolism and glycolysis using transcriptomics and tracer metabolomics approaches.MethodsECs were exposed to WSS, and transcriptomic analysis was performed to assess gene expression changes related to metabolic pathways. Tracer metabolomics was used to track metabolic fluxes, focusing on glutamine and glycolytic metabolism. Additionally, chemical inhibition of glutamate dehydrogenase was conducted to evaluate its role in EC fitness under WSS.ResultsTranscriptomic data revealed upregulation of glutamine and glutamate pathways, alongside downregulation of glycolytic activity in ECs exposed to WSS. Tracer metabolomics confirmed that WSS promotes glutamine anaplerosis into the Krebs cycle, while decreasing glycolytic metabolism. Suppression of glutamate dehydrogenase impaired EC fitness under WSS conditions.ConclusionOur findings illuminate that ECs subjected to WSS exhibit a preference for glutamine as a key nutrient source for central carbon metabolism pathways, indicating diminished reliance on glycolysis. This study elucidates the nutritional predilections and regulatory mechanisms governing EC metabolism under WSS in vitro, underscoring the pivotal role of physical stimuli in shaping EC metabolic responses.

Drought Response in the Transcriptome and Ionome of Wild and Domesticated Lablab purpureus L. Sweet, an Underutilized Legume.

Hunger remains a prevalent issue worldwide, and with a changing climate, it is expected to become an even greater problem that our food systems are not adapted to. There is therefore a need to investigate strategies to fortify our foods and food systems. Underutilized crops are farmed regionally, are often adapted to stresses, including droughts, and have great nutritional profiles, potentially being key for food security. One of these crops, Lablab purpureus L Sweet, or lablab, is a legume grown for humans or as fodder and shows remarkable drought tolerance. Understanding of lablab's molecular responses to drought and drought's effects on its nutritional qualities is limited and affects breeding potential. Using transcriptomics at three time points, changes in gene expression in response to drought were investigated in wild and domesticated lablab. The effect of drought on the elemental profile of lablab leaves was investigated using ionomics to assess drought's impact on nutritional quality. Differences in drought response between wild and domesticated lablab accessions were revealed, which were mainly due to differences in the expression of genes related to phosphorus metabolic response, cell wall organization, and cellular signaling. The leaves of wild and domesticated lablab accessions differed significantly in their elemental concentrations, with wild accessions having higher protein, zinc, and iron concentrations. Drought affected the concentration of some elements, with potential implications for the use of lablab under different environments. Overall, this study is an important first step in understanding drought response in lablab with implications for breeding and improvement of drought-tolerant lablab.

Comparative Analysis of Iodine Levels, Biochemical Responses, and Thyroid Gene Expression in Rats Fed Diets with Kale Biofortified with 5,7-Diiodo-8-Quinolinol.

Iodine is a key micronutrient essential for the synthesis of thyroid hormone, which regulates metabolic processes and maintains overall health. Despite its importance, iodine deficiency is a global health issue, leading to disorders such as goiter, hypothyroidism, and developmental abnormalities. Biofortification of crops with iodine is a promising strategy to enhance the dietary iodine intake, providing an alternative to iodized salt. Curly kale (Brassica oleracea var. sabellica) is a nutrient-rich vegetable high in vitamins A, C, K; minerals; fiber; and bioactive compounds with antioxidant, anti-inflammatory, and detoxifying properties. This study evaluates the effects of diets containing iodine-biofortified curly kale ('Oldenbor F1' and 'Redbor F1') on iodine content, tissue iodine levels, and various biochemical parameters in laboratory rats. The biofortified curly kale was enriched with 5,7-diiodo-8-quinolinol. The iodine content in the AIN-93G (control) diet and the non-biofortified curly kale diets did not differ significantly. However, diets with 5,7-diiodo-8-quinolinol biofortified kale showed significantly higher iodine levels compared with the control diets. Tissue analysis revealed the highest iodine concentrations in the liver and kidneys of rats fed diets with biofortified curly kale, indicating better iodine bioavailability. Biochemical analysis showed that rats fed the biofortified kale diet had lower total cholesterol (TC) and triglyceride (TG) levels compared with rats fed the control diet. Additionally, the biofortified diet improved the liver function markers (ALAT, ASAT) and reduced oxidative stress markers (TBARS). The study also investigated the expression of thyroid-related genes (Slc5A5, Tpo, Dio1, Dio2) in response to diets containing biofortified kale. The results demonstrated significant changes in gene expression, indicating adaptive mechanisms to dietary iodine levels and the presence of bioactive compounds in the biofortified kale. The study also observed variations in uric acid levels, with lower concentrations in rats fed a diet with biofortified curly kale. Biofortified curly kale supports thyroid function and improves liver and kidney health by reducing oxidative stress and modulating key biochemical and genetic markers. These findings suggest that biofortified curly kale can effectively increase dietary iodine intake as a nutritional intervention to address iodine deficiency and promote overall health.

Potential role of formononetin as a novel natural agent in Alzheimer's disease and osteoporosis comorbidity.

The growing aging population has led to an increase in the prevalence of Alzheimer's disease (AD) and osteoporosis (OP), both of which significantly impair quality of life. The comorbid nature of these conditions suggests a shared genetic etiology, the understanding of which is crucial for developing targeted therapies. This study aims to explore the shared genetic etiology underlying AD and OP, using a system biology approach to identify potential therapeutic targets and natural compounds for treatment. We employed Weighted Gene Co-Expression Network Analysis (WGCNA) with molecular docking strategies to uncover the genetic links between AD and OP. MT2A and CACNA1C were identified as key pleiotropic hub genes potentially linking AD and OP. Molecular docking was utilized to screen for compounds with therapeutic potential, leading to the identification of formononetin as a compound with significant binding affinity to these hub genes. Quantitative real-time PCR (qRT-PCR) validation was conducted to confirm the gene expression changes in disease models. Our study indicate that formononetin exhibits strong binding affinity to the identified hub genes, MT2A and CACNA1C. qRT-PCR validation confirmed the upregulation of these genes in disease models, which was mitigated upon treatment with formononetin, suggesting a reversal of disease markers. This study advances our understanding of the genetic intersections between AD and OP and positions formononetin as a promising natural agent for further translational research. Formononetin's multi-target potential makes it a valuable candidate for managing these comorbid conditions, meriting further investigation and development as a therapeutic strategy.

Evaluation of Cinnamon Essential Oil and Its Emulsion on Biofilm-Associated Components of Acinetobacter baumannii Clinical Strains.

Acinetobacter baumannii, one of the most dangerous pathogens, is able to form biofilm structures and aggravate its treatment. For that reason, new antibiofilm agents are in need, and new sources of antibiofilm compounds are being sought from plants and their products. Cinnamon essential oil is associated with a wide spectrum of biological activities, but with a further improvement of its physicochemical properties it could provide even better bioavailability. The aim of this work was the evaluation of the antibiofilm properties of cinnamon essential oil and its emulsion. In order to evaluate the antibiofilm activity, crystal violet assay was performed to determine biofilm biomass. The main components of the biofilm matrix were measured as well as the motile capacity of the tested strains. Gene expression was monitored with RT-qPCR, while treated biofilms were observed with Raman spectroscopy. A particularly strong potential against pre-formed biofilm with a decreased biomass of up to 66% was found. The effect was monitored not only with regard to the whole biofilm biomass, but also on the individual components of the biofilm matrix such as exopolysaccharides, proteins, and eDNA molecules. Protein share drops in treated biofilms demonstrated the most consistency among strains and rose to 75%. The changes in strain motility and gene expressions were investigated after the treatments were carried out. Raman spectroscopy revealed the influence of the studied compounds on chemical bond types and the components present in the biofilm matrix of the tested strains. The results obtained from this research are promising regarding cinnamon essential oil and its emulsion as potential antibiofilm agents, so further investigation of their activity is encouraged for their potential use in biomedical applications.

Transcriptome of Arabidopsis thaliana Plants Exposed to Human Parasites Cryptosporidium parvum and Giardia lamblia

Pathogen infection in animals and plants is recognized in a relatively similar manner by the interaction of pattern recognition receptors on the host cell surface with pathogen-associated molecular patterns on the pathogen surface. Previous work demonstrates that animal pathogenic bacteria can be recognized by plant receptors and alter transcriptome. In this work, we have hypothesized that exposure to human parasites, Cryptosporidium parvum and Giardia lamblia, would also trigger pathogen response in plants, leading to changes in transcriptome. Detached Arabidopsis leaves were exposed for one hour to heat-inactivated Cryptosporidia or Giardia. The transcriptome profile showed large changes in gene expression with significant overlap between two parasites, including upregulated GO terms “cellular response to chitin”, “response to wounding”, “response to oomycetes”, “defense response to fungus”, “incompatible interaction”, and “activation of innate immune response”, and downregulated GO terms “positive regulation of development”, “cell surface”, “regulation of organ growth”, “wax biosynthetic process”, “leaf and shoot morphogenesis”. Uniquely downregulated GO terms in response to Cryptosporidia were GO terms related to chromatin remodelling, something that was not reported before. To conclude, it appears that while Cryptosporidia or Giardia are not pathogens of Arabidopsis, this plant possesses various mechanisms of recognition of pathogenic components of parasites.

Gene Expression Correlates with Disability and Pain Intensity in Patients with Chronic Low Back Pain and Modic Changes in a Sex-Specific Manner.

Chronic low back pain (cLBP) lacks clear physiological explanations, and the treatment options are of limited effect. We aimed to elucidate the underlying biology of cLBP in a subgroup of patients with Modic changes type I (suggestive of inflammatory vertebral bone marrow lesions) by correlating gene expression in blood with patient-reported outcomes on disability and pain intensity and explore sex differences. Patients were included from the placebo group of a clinical study on patients with cLBP and Modic changes. Blood was collected at the time of inclusion, after three months, and after one year, and gene expression was measured at all time points by high-throughput RNA sequencing. The patients reported disability using the Roland-Morris Disability Questionnaire, and pain intensity was assessed as a mean of three scores on a 0-10 numeric rating scale: current LBP, worst LBP within the last two weeks, and mean LBP within the last two weeks. The gene expression profiles were then correlated to the reported outcomes. Changes in gene expression over time correlated significantly with changes in both disability and pain. The findings showed distinct patterns in men and women, with negligible overlap in correlated genes between the sexes. The genes involved were enriched in immunological pathways, particularly T cell receptor complex and immune responses related to neutrophils. Several of the genes harbour polymorphisms that previously have been found to be associated with chronic pain. Taken together, our results indicate gender differences in the underlying biology of disability and pain intensity in patients with low back pain.

The Sub-inhibitory Effect of Azithromycin and Ciprofloxacin on <i>virF</i> Gene Expression in Enteroinvasive <i>Escherichia coli</i> and <i>Shigella flexner</i>i

Background: Bacillary dysentery is an invasive bacterial gastroenteritis that damages the colon epithelium and leads to bloody diarrhea. Enteroinvasive Escherichia coli (EIEC) and Shigella flexneri are two major etiologic agents of the disease. The virF gene is a transcriptional regulator of the virulence genes involved in the invasion of these bacteria. Previous studies have shown that sub-minimum inhibitory concentrations (sub-MICs) of antibiotics have significant effects on bacterial virulence. Objectives: This study aimed to evaluate the effects of sub-MICs of ciprofloxacin and azithromycin on S. flexneri and EIEC. Methods: Prototype strains of both bacteria were treated with sub-MICs of 1/2, 1/4, and 1/8 of ciprofloxacin and azithromycin antibiotics. Changes in the expression of the virF gene in antibiotic-treated samples compared to control samples were analyzed using relative real-time polymerase chain reaction (PCR). Results: The mean expression of the virF gene in all sub-MICs of ciprofloxacin was increased in both S. flexneri and EIEC, while a down-regulation was observed in sub-MICs of azithromycin. These gene expression changes were dose-dependent. Conclusions: The results demonstrated that the virulence of S. flexneri and EIEC is affected by sub-MICs of azithromycin and ciprofloxacin. Given that azithromycin, unlike ciprofloxacin, reduces the severity of infection at sub-MICs, it is a more appropriate choice with a lower risk for treating acute infections caused by these bacteria.

Enhancement of adipose stem cell quality via Cu‐MON: Transcriptome and bioinformatics analysis of normal and diabetic stem cells

AbstractTransplanted adipose stem cells (ASC) have a low survival rate in the body, and there are not many ASC that can be effectively used, which weakens their tissue repair function. Based on this status quo, a new type of copper‐based metal–organic network (Cu‐MON) was used to pretreat cells to regulate cell activity in order to improve the efficacy of cell therapy or reduce the number of cells used, thus reducing the cost of clinical treatment. Gene expression changes before and after Cu‐MON treatment of normal donor adipose stem cells (ND‐ASC) and type 2 diabetes mellitus adipose stem cells (T2DM‐ASC) were evaluated through RNA sequencing, KEGG and GO enrichment analysis. The results showed that Cu‐MON improved ASC cell quality by regulating immune response and promoting paracrine secretion. IL‐17 signaling pathway and IL‐6, CXCL8, and MMP‐9 were key pathways and necessary genes that affected the ability of stem cells. In addition, Cu‐MON also improved stem cell antiviral ability through Type I interferon signaling pathway. Our research showed that Cu‐MON had improved the cell quality of ASC by regulating immune response, promoting paracrine secretion, and improving antiviral capabilities. This approach to biomaterial pretreatment is fast, convenient, and relatively safe, and provides new strategies for improving the efficiency of cell therapies.

Syringin inhibits the crosstalk between macrophages and fibroblast-like synoviocytes to treat rheumatoid arthritis via PDE4.

Syringin (SRG) is well-known for its anti-inflammatory effects. However, its pharmacological mechanisms against rheumatoid arthritis (RA) are not fully understood. We assessed the anti-RA effects of SRG using a collagen-induced arthritis (CIA) rat model. And, we employed single-cell RNA sequencing (scRNA-seq) to analyze the changes in cell types and gene expression in the synovial tissues. Building on these observations, we investigated the effects of SRG on M1 macrophage polarization and RA-fibroblast-like synoviocytes (FLS) proliferation. Our findings highlighted the anti-RA effects of SRG on CIA rat. scRNA-seq of rat synovial tissues revealed significant changes in M1 and RA-FLS. Specifically, SRG decreased the levels of inflammatory factors in the supernatants of LPS and IFN-γ induced THP-1 cells and downregulated M1-polarized markers in these cells. Further analysis indicated that SRG's regulation of phosphodiesterase 4 (PDE4) and its associated factors was crucial for its anti-M1 polarization effects. Besides, we found that SRG inhibited the activation of FLS in vivo but showed no direct effects on RA-FLS in vitro. However, in RA-FLS, co-cultured with supernatant from SRG-treated M1-polarized THP-1 cells exhibited lower ability of cell proliferation and activation as compared to co-cultured with supernatant from M1-polarized THP-1 cells. By integrating scRNA-seq analysis with in vivo and in vitro validations, our study revealed that SRG achieved its anti-RA effects by blocking the interaction between macrophages and RA-FLS, with PDE4 playing a central role. This study may provide a novel research paradigm in studying the multi-cell regulatory mechanisms of natural compounds.

Hyperosmotic stress-induced NLRP3 inflammasome activation via the mechanosensitive PIEZO1 channel in dry eye corneal epithelium.

PIEZO1 modulates the inflammatory response by translating mechanical signals from osmotic pressure into biological processes. This study investigates the functional role of PIEZO1 in activating the NLRP3 inflammasome in corneal epithelial cells under hyperosmotic stress and evaluates its contribution to the pathogenesis of dry eye disease (DED). In the in vitro experiments, immortalized human corneal epithelial cells (HCECs) were cultured under hyperosmotic conditions (450mOsm). For in vivo studies, a dry eye disease mouse model was established by subcutaneous injection of scopolamine (SCOP) in C57BL/6 mice. After successfully inducing the dry eye model, corneal epithelial cell damage was assessed through corneal fluorescein staining scores and TUNEL assays. Protein expression levels were examined via western blotting and immunofluorescence staining, while mRNA expression was analyzed using quantitative RT-PCR. Activation of the NLRP3 inflammasome was evaluated by measuring IL-1β protein cleavage and the formation of ASC speckles. In the DED model, activation of the NLRP3 inflammasome was detected in corneal epithelial cells, along with increased expression of PIEZO1. The PIEZO1-specific agonist Yoda1 induced upregulation of NLRP3 inflammasome-related gene expression and triggered NLRP3 inflammasome activation. Conversely, silencing PIEZO1 using siRNA or inhibiting its activity suppressed hyperosmotic stress-induced changes in NLRP3 inflammasome-related gene expression and activation. In vivo, PIEZO1 inhibition effectively prevented NLRP3 inflammasome activation in corneal epithelial cells and restored the damaged phenotype associated with dry eye disease. Hyperosmotic stress-induced activation of the NLRP3 inflammasome in corneal epithelial cells is mediated through PIEZO1 activation. The identification of PIEZO1's role in this DED-related pathophysiological response highlights its potential as a therapeutic target for mitigating inflammation in clinical settings.

Functionally-informed fine-mapping identifies genetic variants linking increased CHD1L expression and HIV restriction in monocytes

Human Immunodeficiency Virus Type 1 (HIV) set-point viral load is a strong predictor of disease progression and transmission risk. A recent genome-wide association study in individuals of African ancestries identified a region on chromosome 1 significantly associated with decreased HIV set-point viral load. Knockout of the closest gene, CHD1L, enhanced HIV replication in vitro in myeloid cells. However, it remains unclear if HIV spVL associated variants are associated with CHD1L gene expression changes. Here we apply a heuristic fine-mapping approach to prioritize combinations of variants that explain the majority of set-point viral load variance and identify variants likely driving the association. We assess the combined impact of these variants on CHD1L regulation using publicly available sequencing studies, and test the relationship between CHD1L expression and set-point viral load using imputed CHD1L expression from monocytes. Taken together, this work characterizes genetically regulated CHD1L expression and further expands our knowledge of CHD1L-mediated HIV restriction in monocytes.

Assays to Enhance Metabolic Phenotyping in the Kidney.

The kidney is highly metabolically active, and injury induces changes in metabolism that can impact repair and fibrosis progression. Changes in expression of metabolism-related genes and proteins provide valuable data, but functional metabolic assays are critical to confirm changes in metabolic activity. Stable isotope metabolomics are the gold standard, but these involve considerable cost and specialized expertise. Both the Seahorse bioflux assays and substrate oxidation assays in tissues ex vivo are two relatively cost-effective assays for interrogating metabolism. Many institutions have access to Seahorse bioflux analyzers, which can easily and quickly generate data, but guidelines to enhance reproducibility are lacking. We investigate how variables (e.g. primary versus immortalized cells, time in culture) impact the data generated by Seahorse bioflux analyzers. In addition, we show the utility of 3H-palmitate, a new approach for assessing fatty acid oxidation in the kidney, in uninjured and injured kidney cortices. The 3H-palmitate substrate oxidation assays also demonstrate significant sex-dependent and strain-dependent differences in rates of fatty acid oxidation. These data should facilitate metabolic interrogation in the kidney field with enhanced reproducibility.

Using the AP1 Transcription Factor FOSL1 to Assess the Exacerbation of Psoriasis.

The transcription factor AP1 plays a crucial role in the proliferation, apoptosis, and terminal differentiation of epidermal keratinocytes. This study aimed to clarify whether the subunit of AP1, FOSL1 protein, can be used to assess the exacerbation of psoriasis by evaluating its changes in protein and mRNA levels in cultured epidermal keratinocytes and skin specimens of the patients prescribed with bathwater PUVA (Psoralen and UVA) therapy. This study aimed to investigate FOSL1, a subunit of the transcription factor AP-1, as a potential biomarker for psoriasis by examining its protein and mRNA expression in skin specimens from patients undergoing bathwater PUVA (Psoralen and UVA) therapy and cultured epidermal keratinocytes. The distribution of FOSL1 in patients' skin was explored by immunohistochemistry. Changes in gene and protein expression were quantitatively assessed by qPCR and ELISA, respectively. Immunohistochemistry analysis revealed that FOSL1 accumulated in lesional skin. The expression of FOSL1 significantly increased during disease flare-ups but decreased following the treatment with bathwater PUVA therapy. Furthermore, silencing FOSL1 led to a marked reduction in the expression of ten FOSL1 target genes associated with the disease. Our study suggests that FOSL1 shows potential as a biomarker for psoriasis. This is supported by two key findings: first, the expression of FOSL1 correlates with disease activity, and second, its expression is linked to changes in the expression of genes previously implicated in the pathogenesis of psoriasis, namely MMP1, MMP9, IVL, CCNA2, CCL2, HMOX1, PLAU, PLAUR, and THBD.