Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis

Type I interferon protects against bone loss in periodontitis by mitigating an interleukin (IL)-17-neutrophil axis

Type I interferons (IFNs-I), a group of pleiotropic cytokines, critically modulate host response in various inflammatory diseases. However, the role of the IFN-I pathway in periodontitis remains largely unknown. In this report, we describe that the IFN-β levels in the gingival crevicular fluid of human subjects were negatively associated with periodontitis and clinical gingival inflammation. Disruption of IFN-I signaling worsened alveolar bone resorption in a ligature-induced periodontitis murine model. Deficiency of the IFN-I pathway resulted in an exaggerated inflammatory response in myeloid cells and drastically increased the interleukin-17 (IL-17)-mediated neutrophil recruitment in the gingiva. We further identified that the myeloid lineage-specific IFN-I response was essential in safeguarding against periodontal inflammation by suppressing the IL-17-producing γδ T cells in gingiva. IFN-I signaling also directly repressed osteoclastogenesis in monocytes, which are precursor cells for osteoclasts. Therefore, our findings demonstrate that an integral myeloid-specific IFN-I pathway protects against bone loss by keeping the IL-17-neutrophil axis in check and directly inhibiting osteoclast formation in periodontitis.

SLIT3-mediated intratumoral crosstalk induces neuroblastoma differentiation via a spontaneous regression-like program

BACKGROUND

Neuroblastoma, the most common pediatric extracranial solid tumor, has heterogeneous clinical outcomes ranging from malignant progression to spontaneous regression. With the highest frequency of the elusive spontaneous regression, low-risk INSS Stage 4S neuroblastoma represents an ideal model for mechanistic investigation. Spontaneous regression is often accompanied by tumor differentiation, but the mechanisms underlying this process remain largely unclear.

METHODS

Single-nucleus transcriptomics (snRNA-seq) data of neuroblastoma samples were obtained from the Synapse repository to investigate the composition of heterogeneous tumor cell clusters. The feature of the Stage 4S-specific tumor cell subpopulation was revealed through differential expression analysis, pathway enrichment analysis and pseudotime analysis, followed by clinical significance validation on public cohort datasets. The biological function of secreted SLIT3 was validated using multiple in vitro models, including recombinant protein treatment, conditioned medium treatment, and cell lines coculture, to confirm the intratumoral crosstalk effect. Orthotopic and subcutaneous xenograft models were established to verify SLIT3's in vivo function. Cellular bulk RNA-seq analysis was performed with or without SLIT3 recombinant protein treatment to discover the downstream pathways activated by SLIT3, followed by validation with specific pathway inhibitors.

RESULTS

Analysis of snRNA-seq revealed a distinct subpopulation of tumor cells within INSS Stage 4S neuroblastoma, characterized by a spontaneous regression-like program progressing toward differentiation. Activated SLIT-ROBO signaling was found in the Stage 4S-specific tumor cell subpopulation, which strongly correlated with favorable prognosis. Further investigation into the secreted ligands in SLIT-ROBO related pathways revealed that SLIT3 displayed the most potent enrichment in Stage 4S tumors and the strongest differentiation-inducing effect. In vitro experiments using recombinant SLIT3 protein, conditioned medium, and cell lines coculture consistently demonstrated the capacity of SLIT3 to induce neuroblastoma cell differentiation via intratumoral crosstalk, as evidenced by increased neurite outgrowth and elevated expression of neuronal differentiation markers. Both orthotopic xenograft and subcutaneous xenograft models demonstrated that SLIT3 expression suppressed tumor growth, leading to in vivo tumor differentiation. Mechanistically, PLCβ/PKC signaling mediates the SLIT3-induced neuroblastoma cell differentiation.

CONCLUSIONS

Stage 4S-specific tumor cell subpopulation exhibits a spontaneous regression-like program, from which SLIT3 mediates intratumoral crosstalk and promotes neuroblastoma differentiation via PLCβ/PKC signaling. These findings provide new insights into the mechanism of spontaneous regression in neuroblastoma and offer novel therapeutic targets for differentiation-based treatment strategies.

Sll1725, an ABC transporter in Synechocystis sp. PCC 6803 for the detoxification of cadmium ion stress

Cadmium threatens eco-environmental security and human health, but the interaction between cadmium and microalgae cells remains unknown. This research examined the molecular detoxification mechanism of Synechocystis sp. to cadmium. The results indicated that cadmium stress significantly inhibited chlorophyll a content and maximum photochemical quantum yield (Fv/Fm), with EC50 of 0.50 mg L-1. The differentially expressed genes/proteins (DEGs/DEPs) were significantly enriched in pathways of two-component system, translation, nucleotide metabolism, ribosome, photosynthesis and chlorophyll synthesis. 1073 DEGs and 338 DEPs were identified, and 84 DEGs/DEPs with consistent expression trends were obtained. Foldchange of Sll1725 ranked fourth in DEGs/DEPs but its function was unexplored. Phylogenetic analysis and 3D structure identified Sll1725 as an ABC transporter and molecular simulation determined its cadmium-efflux function. Under 0.50 mg L-1 cadmium stress, Δsll1725 had lower growth and Fv/Fm values than the wild-type. Meanwhile, the intracellular cadmium in Δsll1725 was higher, indicating that Sll1725 mitigated cadmium toxicity by efflux. The duckweed with overexpressed sll1725 exhibited cadmium tolerance. It could be deduced that Sll1725, belonged to ABC transporters, which played an important detoxification mechanism. These mutants might possess the potential for bioremediation. This study provides a basis for applying algal genetic resources in cadmium pollution treatment.

Pseudomonas sp. Strain ADAl3-4 Enhances Aluminum Tolerance in Alfalfa (Medicago sativa)

Aluminum toxicity severely inhibits root elongation and nutrient uptake, causing global agricultural yield losses. Dissolved Al3+ are accumulating in plants and subsequently entering food chains via crops and forage plants. Chronic dietary exposure to Al3+ poses a risk to human health. In this study, Pseudomonas sp. strain ADAl3-4, isolated from plant rhizosphere soil, significantly enhanced plant development and biomass. Phenotypic validation using Arabidopsis mutants showed that strain ADAl3-4 regulates plant growth and development under aluminum stress by reprogramming the cell cycle, regulating auxin and ion homeostasis, and enhancing the root absorption of Al3+ from the soil. Transcriptomic and biochemical analyses showed that strain ADAl3-4 promotes plant growth via regulating signal transduction, phytohormone biosynthesis, flavonoid biosynthesis, and antioxidant capacity, etc., under aluminum stress. Our findings indicate that Pseudomonas sp. strain ADAl3-4 enhances plant development and stress resilience under Al3+ toxicity through a coordinated multi-dimensional regulatory network. Furthermore, strain ADAl3-4 promoted the root absorption of aluminum rather than the transportation of Al to the aerial part, endowing it with application prospects.

Hyperacute intervention with DGMI for optimized stroke recovery: Modulating immune and inflammatory pathways in motor and sensory cortices

ETHNOPHARMACOLOGICAL RELEVANCE

Long-term neurological dysfunction following stroke significantly impairs patients' quality of life. Ginkgo biloba L (GBL), a traditional Chinese herbal medicine, has shown promise in treating ischemic stroke and related disorders. Diterpene Ginkgolides Meglumine Injection (DGMI), derived from GBL, has demonstrated improved recovery outcomes in stroke patients when administered during the hyperacute phase (HAP) in clinical studies, yet the underlying mechanisms remain elusive.

MATERIALS AND METHODS

Utilizing a Transient Middle Cerebral Artery Occlusion (tMCAO) model, we evaluated the effects of DGMI at varying doses and administration times on neurological function, brain injury, and identified key genes/pathways via RNA-seq and bioinformatics analyses, validated by RT-PCR. An in vitro LPS-induced astrocyte activation model was used to evaluate DGMI's anti-inflammatory effects.

RESULTS

DGMI administered during the hyperacute phase (HAP, 0.5 h post-tMCAO) exhibited superior neuroprotection compared to the acute phase (AP, 24 h post-tMCAO) in mice. HAP-DGMI significantly enhanced survival rates, reduced neurological deficit scores, infarct sizes, and neuronal apoptosis, with more pronounced improvements observed on days 3 and 7 post-tMCAO. Transcriptome sequencing revealed that HAP-DGMI more effectively normalized abnormal gene expression profiles, particularly in genes involved in immune and inflammatory pathways, in both motor (M1) and sensory (S1) cortices. Additionally, HAP-DGMI reversed a higher proportion of disease-characteristic pathways compared to AP.

CONCLUSIONS

These findings underscore the potential of early HAP intervention with DGMI in enhancing neuroprotection and functional recovery in AIS bymodulating key immune and inflammatory genes and pathways, providing experimental and theoretical support for the clinical application of DGMI.

A Guide to Basic RNA Sequencing Data Processing and Transcriptomic Analysis

RNA sequencing (RNA-Seq) has transformed transcriptomic research, enabling researchers to perform large-scale inspection of mRNA levels in living cells. With the growing applicability of this technique to many scientific investigations, the analysis of next-generation sequencing (NGS) data becomes an important yet challenging task, especially for researchers without a bioinformatics background. This protocol offers a beginner-friendly step-by-step guide to analyze NGS data (starting from raw .fastq files), providing the required codes with an explanation of the different steps and software used. We outline a computational workflow that includes quality control, trimming of reads, read alignment to the genome, and gene quantification, ultimately enabling researchers to identify differentially expressed genes and gain insights on mRNA levels. Multiple approaches to visualize this data using statistical and graphical tools in R are also described, allowing the generation of heatmaps and volcano plots to represent genes and gene sets of interest. Key features • Provides a beginner-friendly protocol for RNA-Seq analysis to obtain insights into gene expression. • Pipeline starts with raw .fastq files and involves analysis in command line/terminal and R (via RStudio). • Yields a variety of output files that represent mRNA levels amongst different samples. Output files include count files, heatmaps, ordered lists of DEGs, and volcano plots.

Activating transcription factor-3 orchestrates the modulation of vascular anti-contractile activity and relaxation by governing the secretion of HDL-bound sphingosine-1-phosphate in perivascular adipose tissue

BACKGROUND AND PURPOSE

Perivascular adipose tissues (PVATs) play a critical role in modulating vascular homeostasis and protecting against cardiovascular dysfunction-mediated blood pressure dysregulation. We demonstrated that the activating transcription factor-3 (Atf3) gene in the PVAT is crucial for improving vascular wall tension abnormalities; however, its protective mechanism remains unclear. Herein, we aim to determine whether ATF3 regulates PVAT-derived relaxing factor (PVDRF) biosynthesis and if its secretion contributes to vasorelaxation.

EXPERIMENTAL APPROACH

This study employed an in vivo animal model using global Atf3-deficient mice, in vitro blood vessel myography, and biochemical analyses to evaluate ATF3-mediated PVDRF release and reactivity in the vasculature.

KEY RESULTS

Wild-type (WT) mouse thoracic aortic PVAT extracts significantly induced resting tone dilation and attenuated vasoconstrictor-induced contractile responses compared to Atf3-/- mice. Heat-stable PVAT extracts from WT mice caused sustained and reproducible vasodilation without tachyphylaxis in control aortic rings. Biochemical evaluation of PVDRF release revealed that Atf3-/- mice had lower sphingosine-1-phosphate (S1P) and HDL cholesterol (HDL-C) levels than WT mice. Furthermore, PVAT extracts from WT mice induced long-lasting vasorelaxation, which was significantly inhibited by the S1P3 receptor antagonist TY52156 and scavenger receptor class B type 1 receptor antagonist glyburide.

CONCLUSION AND IMPLICATIONS

ATF3 within the PVAT can modulate vascular function by strengthening sphingosine kinase 1 (sphk1)-S1P-S1P3 receptor lipid signalling and stimulating S1P binding to HDL to form the vasodilator HDL-S1P. ATF3 is an essential modulator for maintaining the physiological function of PVAT, providing a novel target for treatment of obesity-related cardiovascular diseases.

Fine Particulate Matter (PM2.5) and the Blood-Testis Barrier: An in Vivo and in Vitro Mechanistic Study

BACKGROUND

Fine particulate matter [particulate matter (PM) with aerodynamic diameter of ≤ 2.5 μ m (PM 2.5 )] is considered a major component of ambient PM. Exposure to PM 2.5 was shown to be associated with male reproductive system injury. Ferroptosis is regarded as an iron-dependent programmed cell death that is associated with the pathological process. It has been reported that SIRT1 has protective effects on the male reproductive system. However, the underlying mechanisms of exposure to PM 2.5 -induced testicular injury are still unexplored.

OBJECTIVES

In this study, we investigated the relationship between ferroptosis and male reproductive injury after exposure to PM 2.5 and the role of SIRT1/HIF-1 α signaling pathway in this process.

METHODS

We established a PM 2.5 exposure model in vivo and in vitro using Sertoli cell Sirt1 conditional knockout C57BL/6 (cKO) mice testes and primary Sertoli cells. Hematoxylin and eosin (H&E) staining were conducted to examine the histology of the mice testes. Sperm parameters and biotin tracer assay were conducted to evaluate the effects of exposure to PM 2.5 on the mice testes. Related markers and genes related to the blood-testis barrier (BTB) and ferroptosis were measured by quantitative real-time polymerase chain reaction (qPCR), western blot, and immunofluorescence assay. siRNA transfection was used to evaluate the potential mechanism.

RESULTS

Significant pathological damage and lower sperm quality were detected in mice testes exposed to PM 2.5 . We found that exposure to PM 2.5 damaged the BTB and inhibited the expression level of the BTB-related proteins (including Connexin 43, Occludin, Claudin 11, N-Cadherin and ZO-1). According to the enrichment analysis results, ferroptosis and HIF-1 α signaling pathway were significantly enriched in mice testes and primary Sertoli cells exposed to PM 2.5 . Subsequent experiments were conducted to verify the results of the enrichment analysis and revealed differences in the expression levels of HIF-1 α , ferroptosis-related genes (including GPX4, SLC7A11, ACSL4, and HO-1) and ferroptosis-related markers [including malondialdehyde (MDA), glutathione (GSH), and Fe 2 + ], associated with lower expression of SIRT1 after exposure to PM 2.5 . These results suggest that PM 2.5 exposure may be associated with ferroptosis and HIF-1 α signaling pathway in male reproductive dysfunction.

CONCLUSIONS

Taken together, in vivo and in vitro experiments verified that PM 2.5 exposure in mice may lead to testicular dysfunction through new pathways. https://doi.org/10.1289/EHP14447.

Taurine and proline promote lung tumour growth by co-regulating Azgp1/mTOR signalling pathway

Accurate metabolic biomarkers for lung cancer prognosis remain scarce but crucial. Taurine and proline, two metabolites, are consistently elevated across various cancer stages in previous studies, hinting at their potential role in disease progression. This study is the first to reveal how these metabolites contribute to poor prognosis. Transcriptomic analysis uncovered that taurine and proline downregulated Zinc-α2-glycoprotein (Azgp1), a gene linked to key metabolic pathways. Additionally, Azgp1 could also significantly affect downstream lipid metabolic pathways in lung cancer. Both taurine and proline influenced lipid metabolism via mammalian target of rapamycin (mTOR). When Azgp1 was overexpressed, lung cancer progression slowed significantly, alongside reduced mTOR activity. These findings underscore the pro-cancer role of taurine and proline, highlighting the Azgp1/mTOR axis as a vital, yet overlooked, pathway in lung cancer. This study not only advances our understanding but also identifies new therapeutic avenues.

Structural and Functional Insights into Targeting GCCG Sites in the EGFR Promoter by Two DNA Intercalators to Inhibit Breast Cancer Metastasis

Chemotherapeutic drugs are commonly used to treat cancers lacking targeted therapy options. However, their low specificity limits their treatment effectiveness. We report here that the cooperative binding of doxorubicin (Dox) with actinomycin D (ActD) enhances the specificity for consecutive GCCG sites in DNA. Using X-ray crystallography, we determined the crystal structure of ActD and Dox bound to d(AGCCGT)2 DNA. ActD intercalation at the GpC site induces a novel Dox binding mode at the adjacent CpG step. This ensures a snug fit, avoids steric clashes, and enhances the specificity. Transcriptome analysis revealed that combining Dox with ActD synergistically down-regulates EGFR in TNBC cells. Additionally, it reduces EGFR promoter activity. In vivo, the combination significantly suppresses tumor growth and outperforms the standard Dox and cyclophosphamide regimen in inhibiting metastasis. This study highlights targeting the activated EGFR pathway with sequence-specific DNA-targeting drug combinations as a potential TNBC treatment.

Comprehensive Transcriptomic Analysis of the Isolated Candida tropicalis with Enhanced Tolerance of Furfural Inhibitor

The Candida tropicalis (C. tropicalis) named YB-3 was isolated by the Atmospheric and room temperature plasma mutagenesis from 6.5 g/L furfural tolerance. The comprehensive transcriptomic analysis of YB-3 was performed. During the stress of furfural treatment, C. tropicalis YB-3 protected cells from oxidative stress damage by increasing the accumulation of the glutathione reductase gene and the expression of antioxidant enzymes, with the enhancement of the inositol phosphate synthase to maintain the structural integrity and transport function of the inner membrane system, thereby affecting the cells' tolerance. Through the gene knockout and exogenous verification, it was further confirmed that the pathways involved in the three genes of sulfate adenosine transferase gene, glutathione reductase gene, and inositol phosphate synthase gene had significant effects on improving the tolerance of the strain to furfural. The deep excavation of furfural-tolerant gene components and directional modification of C. tropicalis to enhance tolerance are key steps for improving the utilization rate of biomass.

Construction of RNA reference materials for improving the quantification of transcriptomic data

RNA reference materials and their corresponding reference datasets act as the 'ground truth' for the normalization of experimental values and are indispensable tools for reliably measuring intrinsically small differences in RNA-sequencing data, such as those between molecular subtypes of diseases in clinical samples. However, the variability in 'absolute' expression profiles measured across different batches, methods or platforms limits the use of conventional RNA reference datasets. We recently proposed a ratio-based method for constructing reference datasets. The ratio for a gene is defined as the normalized expression levels between two sample groups and produces more reliable values than the 'absolute' values obtained across diverse transcriptomic technologies and batches. Our gene ratios have been used for the successful generation of omics-wide reference datasets. Here, we describe a step-by-step process for establishing RNA reference materials and reference datasets, covering three stages: (1) reference materials, including material preparation, homogeneity testing and stability testing; (2) ratio-based reference datasets, including characterization, uncertainty estimation and orthogonal validation; and (3) applications, including definition of performance metrics, performing proficiency tests and diagnosing and correcting batch effects. This approach established the Quartet RNA reference materials and reference datasets (chinese-quartet.org) that have been approved as the first suite of nationally certified RNA reference materials by China's State Administration for Market Regulation. The protocol can be utilized to establish and apply reference materials to improve RNA-sequencing data quality in diverse clinical settings. The procedure can be completed in 2 d and requires expertise in molecular biology and bioinformatics.

Combining KPNA2 and FOXM1 Expression as Prognostic Markers and Therapeutic Targets in Hormone Receptor-Positive, HER2-Negative Breast Cancer

Background/Objectives: Breast cancer remains the leading malignancy affecting women worldwide, with significant mortality rates. This study aimed to evaluate the prognostic significance of FOXM1 expression specifically in hormone receptor-positive, HER2-negative (HR+HER2-) breast cancer patients with high KPNA2 expression, and to identify potential FOXM1-targeted therapeutic strategies for this patient subgroup. Methods: We analyzed RNA sequencing and microarray data from three independent cohorts: Mackay Memorial Hospital patient samples, The Cancer Genome Atlas, and Gene Expression Omnibus databases. The expression levels of KPNA2, FOXM1, CCNB1, and CCNB2 were evaluated, with particular emphasis on stratifying patients based on KPNA2 expression levels. Their associations with clinical outcomes were assessed using Gene Set Enrichment Analysis and survival analyses. Results: While KPNA2 expression showed strong positive correlations with FOXM1, CCNB1, and CCNB2 across all datasets, our analysis revealed a distinct prognostic pattern in HR+HER2- breast cancer patients with high KPNA2 expressions. In this specific subgroup, low FOXM1 expression emerged as a favorable prognostic indicator, despite the generally poor prognosis associated with high KPNA2 levels. Gene Set Enrichment Analysis demonstrated significant enrichment of the G2/M checkpoint pathway in high KPNA2-expressing patients, suggesting potential therapeutic vulnerability to FOXM1 inhibition in this subgroup. Conclusions: This study establishes FOXM1 expression as a critical prognostic marker, specifically in KPNA2-high HR+HER2- breast cancer patients, where low FOXM1 levels correlate with improved survival outcomes. These findings suggest that FOXM1 inhibition could be particularly effective in patients with high KPNA2 expression, offering a novel therapeutic strategy for this specific molecular subtype. Several FOXM1 inhibitors, including thiostrepton and FDI-6, warrant investigation as potential targeted treatments for KPNA2-high HR+HER2- breast cancer patients.

E3 ligase TRIM8 suppresses lung cancer metastasis by targeting MYOF degradation through K48-linked polyubiquitination

Ubiquitination is a posttranslational modification that regulates tumour progression-associated proteins through the ubiquitin‒proteasome system, making E3 ligases potential antitumour targets. Here, we report that TRIM8, a member of the TRIM family and an E3 ligase, can act as a tumour suppressor in non-small cell lung cancer (NSCLC). Both gain- and loss-of-function experiments revealed that TRIM8 inhibits the proliferation, colony formation, migration and invasion of NSCLC cells. Experiments with a xenograft model showed that TRIM8 expression suppresses tumour metastasis in vivo. Moreover, low expression of TRIM8 was associated with poor overall survival in both the Taiwanese and GEO lung cancer cohorts. TRIM8 overexpression in lung cancer cells reduced MYOF expression, and restoring MYOF rescued cell migration in TRIM8-overexpressing cells. TRIM8 targeted MYOF for K48-linked ubiquitination, facilitating proteasome-mediated degradation and subsequently suppressing the extracellular secretion of MMPs. Our results provide new insights into the contribution of TRIM8 to lung cancer progression, suggesting that TRIM8 is a new biomarker and a novel therapeutic target for lung cancer.

Differential gene expression in Clostridium perfringens during pre-and post-infection phases and in jejunal tissues of broilers with necrotic enteritis induced by Clostridium perfringens alone and its coinfection with Eimeria

The pathogenesis of necrotic enteritis (NE) involves complex gene regulation at both the bacterial cell and host tissue levels, yet many aspects remain incompletely understood. This study aims to compare the differential transcriptome of the netB-positive Clostridium perfringens strain, CP54, before and after infection. Differentially expressed genes and pathways were also examined in jejunal tissues from CP54-induced and CP54-Eimeria coinfected NE models to identify potential targets for mitigating NE. Forty-one-day-old Cobb straight-run broilers were assigned to four groups: CP and Eimeria coinfection group (EimCP), Eimeria infection group (Eim), CP54 infection group (CP), and untreated control (CTL). Subclinical and severe NE models were established by oral infection with CP54 alone and CP54-Eimeria coinfection, respectively. Three post-infection CP54 strains (CPd1, CPd2, and CPd3) were isolated from necrotic jejunal mucosa in the EimCP group and analyzed alongside pre-infection CP54 using 4-plex bacterial RNA sequencing (RNA-seq). Jejunal tissues were collected and analyzed for differentially expressed genes between groups via tissue RNA-seq. The results showed that post-infection CP54 strains exhibited unique gene regulation patterns associated with environmental adaptation, including upregulation of oxidation-reduction processes, oxidoreductase activity, and downregulation of pyrimidine metabolism. However, no differential expressed virulence genes, including cpa, colA, lepB, luxS, nanI, netB, and cpb2, were identified between the pre- and post-infection CP54 cells. In host tissues, the analysis revealed significant activation of cytokine-cytokine receptor interactions and Toll-like receptor pathways that contribute to inflammatory responses. Upregulating IL8, IL12B, and INHBA played a key role in activating these pathways. Additionally, NE-infected jejunal tissues displayed suppressed PPAR pathway activity and increased p53 signaling. These changes suggest a significant role for apoptosis, immune regulation, and lipid metabolism in the progression of the disease. In summary, this study identifies key genes and transcripts associated with NE at both the bacterial and host levels, offering perspectives on the pathways driving disease progression and host-pathogen interactions. These findings provide crucial insights for developing effective prevention and control strategies, ultimately reducing NE risks and associated losses in the broiler industry.

Neurotensin-neurotensin receptor 2 signaling in adipocytes suppresses food intake through regulating ceramide metabolism

Neurotensin (NTS) is a secretory peptide produced by lymphatic endothelial cells. Our previous study revealed that NTS suppressed the activity of brown adipose tissue via interactions with NTSR2. In the current study, we found that the depletion of Ntsr2 in white adipocytes upregulated food intake, while the local treatment of NTS suppressed food intake. Our mechanistic study revealed that suppression of NTS-NTSR2 signaling enhanced the phosphorylation of ceramide synthetase 2, increased the abundance of its products ceramides C20-C24, and downregulated the production of GDF15 in white adipose tissues, which was responsible for the elevation of food intake. We discovered a potential causal and positive correlation between serum C20-C24 ceramide levels and human food intake in four populations with different ages and ethnic backgrounds. Together, our study shows that NTS-NTSR2 signaling in white adipocytes can regulate food intake via its direct control of lipid metabolism and production of GDF15. The ceramides C20-C24 are key factors regulating food intake in mammals.

The STING antagonist SN-011 ameliorates cisplatin induced acute kidney injury via suppression of STING/NF-κB-mediated inflammation

Acute kidney injury (AKI) is a critical clinical syndrome associated with both innate and adaptive immune responses and thus increases mortality. Nevertheless, specific therapeutics for AKI are scarce so far. Recent studies have revealed that knockout of STING alleviate AKI, suggesting that STING could be an attractive target for AKI therapy. SN-011, a promising STING inhibitor, has not been reported in studies of its anti-AKI activity. In this study, we sought to examine the effects of SN-011 on AKI and explore its underlying mechanism. Our findings indicate that SN-011 could modulate the NF-κB and MAPK pathways, suppress the expression of inflammatory factors, and decrease ROS release in the cisplatin-induced cell model. In addition, SN-011 blocked the nuclear translocation of NF-κB p65, further mitigating the inflammatory response. In vivo, SN-011 enhanced survival rates and alleviated renal dysfunction. According to gene set enrichment analysis of sequencing data from mouse kidneys, we further confirm that SN-011 modulates the NF-κB and MAPK pathways. Our study suggests that SN-011 could be an attractive anti-inflammatory agent for further anti-AKI research.

Chronic heat stress upregulates pyruvate metabolic process and gluconeogenesis but downregulates immune responses in Sahiwal cattle

Climate change and growing population and their strain on animal production are the impending challenges that the developing countries, like India, need to tackle in the coming days. This study aimed to detect and analyze the uncharacterized variation in the gene expression patterns with the change of condition, from thermoneutral to chronic hot-humid, in the Sahiwal cattle, one of the best breeds of milk-producing cattle in India, known for being heat-tolerant. Using RNA-Seq analysis on peripheral blood mononuclear cells (PBMCs), 4021 differentially expressed mRNAs (2772 upregulated, 1249 downregulated) and 1303 differentially expressed long non-coding RNAs (769 upregulated, 534 downregulated) were identified, with the thresholds of false discovery rate < 0.05 and|log2(fold change)| > 2. Significantly (p-adjusted < 0.05) overrepresented Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Reactome pathways were analyzed, revealing upregulation of processes like pyruvate metabolic process, gluconeogenesis, ion transmembrane transport, neuropeptide signaling pathway, and animal organ development, with genes like SHH, GRK1, CHRM3, CAMK2A, and HSPB7 were upregulated, while translation and immune responses, with genes like RPS3, EEF1A1, TNF, BoLA-DRB3, and UBB were downregulated. Analysis of cis-mRNAs of DE-lncRNAs showed presence of both up- and down-regulated cis-mRNAs for both up- and down-regulated lncRNAs indicating existence of positive and negative regulation of mRNA expression by lncRNAs. Managemental nudges that decrease metabolic heat generation, like betaine and chromium supplementation, and increase heat dissipation, like microenvironment cooling, should be utilized. This study highlights the role of pyruvate metabolism and gluconeogenesis in coping up with heat stress and offers an improved understanding of the heat stress response of Sahiwal cattle along with the genes and pathways responsible for it.

IL20RA Is the Key Factor Contributing to the Stronger Antioxidant Capacity of Rongchang Pig Sertoli Cells

Variations in disease resistance among pig breeds have been extensively documented, with Sertoli cells (SCs) playing a pivotal role in spermatogenesis. Infections can induce oxidative stress, which can lead to damage to these cells. This study aimed to compare the levels of oxidative stress in SCs from Rongchang and Landrace pig breeds following LPS challenge. SCs were isolated, cultured, and stimulated with LPS to assess cell viability and markers of oxidative stress. Cell viability was evaluated along with oxidative stress markers such as reactive oxygen species (ROS), mitochondrial superoxide, malondialdehyde, and antioxidant enzymes. Mitochondrial function was assessed using JC-1 and Calcein AM probes. Transcriptomic analysis identified differentially expressed genes (DEGs), while ingenuity pathway analysis (IPA) explored enriched pathways. IL20RA, identified through transcriptomics, was validated using the siRNA knockdown technique. The results showed that Rongchang SCs exhibited lower levels of oxidative stress compared to Landrace SCs along with higher activity of antioxidant enzymes. IL20RA emerged as a key regulator since its knockdown affected mitochondrial superoxide production and catalase secretion. The findings suggest that Rongchang SCs possess superior antioxidant capacity, possibly due to the IL20RA-mediated protection of mitochondria, thereby providing insights into breed-specific resistance against oxidative stress and highlighting the role of IL20RA in maintaining stem cell function.

The combination of decitabine with multi-omics confirms the regulatory pattern of the correlation between DNA methylation of the CACNA1C gene and atrial fibrillation

Background

Studies have shown that DNA methylation of the CACNA1C gene is involved in the pathogenesis of various diseases and the mechanism of drug action. However, its relationship with atrial fibrillation (AF) remains largely unexplored.

Objective

To investigate the association between DNA methylation of the CACNA1C gene and AF by combining decitabine (5-Aza-2'-deoxycytidine, AZA) treatment with multi-omics analysis.

Methods

HepG2 cells were treated with AZA to observe the expression of the CACNA1C gene, which was further validated using gene expression microarrays. Pyrosequencing was employed to validate differentially methylated sites of the CACNA1C gene observed in DNA methylation microarrays. A custom DNA methylation dataset based on the MSigDB database was combined with ChIP-sequencing and RNA-sequencing data to explore the regulatory patterns of DNA methylation of the CACNA1C gene.

Results

Treatment of HepG2 cells with three different concentrations of AZA (2.5 µM, 5.0 µM, and 10.0 µM) resulted in 1.6, 2.5, and 2.9-fold increases in the mRNA expression of the CACNA1C gene, respectively, compared to the DMSO group, with statistical significance at the highest concentration group (p < 0.05). Similarly, AZA treatment of T47D cells showed upregulated mRNA expression of the CACNA1C gene in the gene expression microarray results (adj P < 0.05). DNA methylation microarray analysis revealed that methylation of a CpG site in intron 30 of the CACNA1C gene may be associated with AF (adj P < 0.05). Pyrosequencing of this site and its adjacent two CpG sites demonstrated significant differences in DNA methylation levels between AF and sinus rhythm groups (p < 0.05). Subsequent multivariate logistic regression models confirmed that the DNA methylation degree of these three sites and their average was associated with AF (p < 0.05). Additionally, the UCSC browser combined with ChIP-sequencing revealed that the aforementioned region was enriched in enhancer markers H3K27ac and H3K4me1. Differential expression and pathway analysis of RNA-sequencing data ultimately identified ATF7IP and KAT2B genes as potential regulators of the CACNA1C gene.

Conclusion

The DNA methylation levels at three CpG sites in intron 30 of the CACNA1C gene are associated with AF status, and potentially regulated by ATF7IP and KAT2B.

Trait responses, nonconsumptive effects, and the physiological basis of Helicoverpa armigera to bat predation risk

Predation reduces the population density of prey, affecting its fitness and population dynamics. Few studies have connected trait changes with fitness consequences in prey and the molecular basis and metabolic mechanisms of such changes in bat-insect systems. This study focuses on the responses of Helicoverpa armigera to different predation risks, focusing on echolocating bats and their calls. Substantial modifications were observed in the nocturnal and diurnal activities of H. armigera under predation risk, with enhanced evasion behaviors. Accelerated development and decreased fitness were observed under predation risks. Transcriptomic and metabolomic analyses indicated that exposure to bats induced the upregulation of amino acid metabolism- and antioxidant pathway-related genes, reflecting shifts in resource utilization in response to oxidative stress. Exposure to bat predation risks enhanced the activity of DNA damage repair pathways and suppressed energy metabolism, contributing to the observed trait changes and fitness decreases. The current results underscore the complex adaptive strategies that prey species evolve in response to predation risk, enhancing our understanding of the predator-prey dynamic and offering valuable insights for innovative and ecologically informed pest management strategies.

Impact of photoaging on the chemical and cytotoxic properties of nanoscale zeolitic imidazolate framework-8

This study investigated the influence of photoaging on a nanoscale metal-organic framework (MOF), truncated rhombic dodecahedron nano-zeolitic imidazolate framework-8 (nZIF-8), focusing on its oxidative stress, inflammation, and implications for pulmonary diseases. We observed significant photodegradation-induced transformations in nZIF-8, characterized by a reduction in particle size from 200.5 to 101.4 nm and notable structural disintegration after prolonged exposure to simulated solar radiation. This alteration resulted in a marked decrease in oxidative cytotoxicity in BEAS-2B cells, which was attributed to changes in surface properties and reduced reactive oxygen species (ROS) production. Gene expression analysis further revealed a decrease in cytotoxic and inflammatory responses, which potentially lowers the risk of chronic obstructive pulmonary disease (COPD). Aged nZIF-8 also showed diminished capacity to induce pro-inflammatory cytokines and influence COPD-related gene expression, reducing its potential to exacerbate COPD pathogenesis. Our findings highlight the critical need for comprehensive safety evaluations of these materials, while considering their long-term environmental and biological impacts. The diminished cytotoxicity and inflammatory potential of aged nZIF-8 highlighted its enhanced suitability for broader applications, indicating that photoaging may lead to safer and more sustainable material utilization.

Nuclear factors NF-YC3 and NF-YBs positively regulate arbuscular mycorrhizal symbiosis in tomato

The involvement of nuclear factor Y (NF-Y) in transcriptional reprogramming during arbuscular mycorrhizal symbiosis has been demonstrated in several plant species. However, a comprehensive picture is lacking. We showed that the spatial expression of NF-YC3 was observed in cortical cells containing arbuscules via the cis-regulatory element GCC boxes. Moreover, the NF-YC3 promoter was transactivated by the combination of CYCLOPS and autoactive calcium and calmodulin-dependent kinase (CCaMK) via GCC boxes. Knockdown of NF-YC3 significantly reduced the abundance of all intraradical fungal structures and affected arbuscule size. BCP1, SbtM1, and WRI5a, whose expression associated with NF-YC3 levels, might be downstream of NF-YC3. NF-YC3 interacted with NF-YB3a, NF-YB5c, or NF-YB3b, in yeast (Saccharomyces cerevisiae) and in planta, and interacted with NF-YA3a in yeast. Spatial expression of 3 NF-YBs was observed in all cell layers of roots under both mock and mycorrhizal conditions. Simultaneous knockdown of 3 NF-YBs, but not individually, reduced the fungal colonization level, suggesting that there might be functional redundancy of NF-YBs to regulate AM symbiosis. Collectively, our data suggest that NF-YC3 and NF-YBs positively regulate AM symbiosis in tomato, and arbuscule-related NF-YC3 may be an important downstream gene of the common symbiosis signaling pathway.

Integrative analysis of genetics, epigenetics and RNA expression data reveal three susceptibility loci for smoking behavior in Chinese Han population

Despite numerous studies demonstrate that genetics and epigenetics factors play important roles on smoking behavior, our understanding of their functional relevance and coordinated regulation remains largely unknown. Here we present a multiomics study on smoking behavior for Chinese smoker population with the goal of not only identifying smoking-associated functional variants but also deciphering the pathogenesis and mechanism underlying smoking behavior in this under-studied ethnic population. After whole-genome sequencing analysis of 1329 Chinese Han male samples in discovery phase and OpenArray analysis of 3744 samples in replication phase, we discovered that three novel variants located near FOXP1 (rs7635815), and between DGCR6 and PRODH (rs796774020), and in ARVCF (rs148582811) were significantly associated with smoking behavior. Subsequently cis-mQTL and cis-eQTL analysis indicated that these variants correlated significantly with the differential methylation regions (DMRs) or differential expressed genes (DEGs) located in the regions where these variants present. Finally, our in silico multiomics analysis revealed several hub genes, like DRD2, PTPRD, FOXP1, COMT, CTNNAP2, to be synergistic regulated each other in the etiology of smoking.

Galectin-9 activates host immune response and improve immunoprotection of Onychostoma macrolepis against Aeromonas hydrophila infection

Galectin-9 (Gal-9) belongs to a family of the glycan-binding proteins (GBPs) and is known to restrict bacterial activity via interacting with pathogen associated molecular pattern (PAMPs). However, the underlying immune mechanism of endogenous Gal-9 on fish against bacterial infection is still unclear. In this study, effects of Gal-9 from Onychostoma macrolepis (OmGal-9) on expression of immune-related genes were measured by HEK293T. The immune response of O. macrolepis with OmGal-9 overexpression to Aeromonas hydrophila (A. hydrophila) infection (1.65 × 108 CFU/mL) was evaluated by tissue bacterial load, fish survival rate and transcriptome analysis. The results showed that OmGal-9 displayed a punctate distribution in the nucleus and cytoplasm of HEK293T cells. Compared to cells transfected with the empty vector (EV group), recombinant plasmid pEGFP-Gal9 treatment (Gal9 group) significantly down-regulated the expression of immune-related genes TNFα, STAT3, MyD88, LCK, and p52 of HEK293T cells stimulated with LPS at 24 h, while up-regulated IκBα and caspase-1 (P < 0.05). The activities of catalase (CAT), superoxide dismutase (SOD), the total antioxidant capacity (T-AOC), alkaline phosphatase (AKP), acid phosphatase (ACP), and lysozyme (LZM) of O. macrolepis were significantly increased on 7 days in Gal9 group compared to EV group (P < 0.05). The bacterial load of liver, spleen, and kidney of O. macrolepis infected with A. hydrophila in Gal9 group at 24 h was significantly lower than that in EV group (P < 0.05), and the survival rate had increased from 15 % to 35 %. A comparative transcriptome analysis between the Gal9 and EV group identified 305 differentially expressed genes (DEGs). The analysis showed that OmGal-9 might play an important regulatory role in glycolysis/gluconeogenesis, fatty acid degradation, and ascorbate and aldarate metabolism. Moreover, the immune-related DEGs were predominantly enriched in eleven pathways, with the most important three of them being linked to innate immunity: NOD-like, C-type lectin and Toll-like receptor signaling pathway. Taking together, OmGal-9 can enhance the resistance of fish to bacterial diseases by improving immune system function and activating immune-related pathways.

Fatty acid synthase inhibitor cerulenin hinders liver cancer stem cell properties through FASN/APP axis as novel therapeutic strategies

Hepatocellular carcinoma (HCC) poses significant treatment challenges due to high postoperative recurrence rates and the limited effectiveness of targeted medications. Researchers have identified the unique metabolic profiles of cancer stem cells (CSCs) as the primary drivers of cancer recurrence, metastasis, and drug resistance. Therefore, to address the therapeutic conundrum, this study focused on rewinding metabolic reprogramming of CSCs as a novel therapeutic strategy. HCC CSCs exhibited elevated fatty acid (FA) metabolism compared with parental cells. To specifically target FA metabolism in CSCs, we utilized cerulenin, a fatty acid synthase (FASN) inhibitor. Surprisingly, cerulenin can diminish CSC-like characteristics, including stemness gene expression, spherogenicity, tumorigenicity, and metastatic potential. In addition, sorafenib, a multikinase inhibitor used as targeted therapy for advanced HCC, was employed in combination with cerulenin, demonstrating a great synergistic effect, particularly in CSCs. Importantly, our RNA sequencing analysis disclosed that the amyloid protein precursor (APP) is a crucial downstream effector of FASN in regulating CSC properties. We found that APP plays a crucial role in CSCs' characteristics that can be inhibited by cerulenin. By focusing on FA metabolism, this study identified the FASN/APP axis as a viable target to develop a more potent therapy strategy for advanced HCC.

Comprehensive Transcriptomic Analysis Reveals Defense-Related Genes and Pathways of Rice Plants in Response to Fall Armyworm (Spodoptera frugiperda) Infestation

Rice (Oryza sativa L.) serves as a substitute for bread and is a staple food for half of the world's population, but it is heavily affected by insect pests. The fall armyworm (Spodoptera frugiperda) is a highly destructive pest, threatening rice and other crops in tropical regions. Despite its significance, little is known about the molecular mechanisms underlying rice's response to fall armyworm infestation. In this study, we used transcriptome analysis to explore the global changes in gene expression in rice leaves during a 1 h and 12 h fall armyworm feeding. The results reveal 2695 and 6264 differentially expressed genes (DEGs) at 1 and 12 h post-infestation, respectively. Gene Ontology (GO) and KEGG enrichment analyses provide insights into biological processes and pathways affected by fall armyworm feeding. Key genes associated with hormone regulation, defense metabolic pathways, and antioxidant and detoxification processes were upregulated, suggesting the involvement of jasmonic acid (JA) signaling, salicylic acid biosynthesis pathways, auxin response, and heat shock proteins in defense during 1 h and 12 h after fall armyworm infestation. Similarly, key genes involved in transcriptional regulation and defense mechanisms reveal the activation of calmodulins, transcription factors (TFs), and genes related to secondary metabolite biosynthesis. Additionally, MYB, WRKY, and ethylene-responsive factors (ERFs) are identified as crucial TF families in rice's defense response. This study provides a comprehensive understanding of the molecular dynamics in rice responding to fall armyworm infestation, offering valuable insights for developing pest-resistant rice varieties and enhancing global food security. The identified genes and pathways provide an extensive array of genomic resources that can be used for further genetic investigation into rice herbivore resistance. This also suggests that rice plants may have evolved strategies against herbivorous insects. It also lays the groundwork for novel pest-resistance techniques for rice.

Assessing and mitigating batch effects in large-scale omics studies

Batch effects in omics data are notoriously common technical variations unrelated to study objectives, and may result in misleading outcomes if uncorrected, or hinder biomedical discovery if over-corrected. Assessing and mitigating batch effects is crucial for ensuring the reliability and reproducibility of omics data and minimizing the impact of technical variations on biological interpretation. In this review, we highlight the profound negative impact of batch effects and the urgent need to address this challenging problem in large-scale omics studies. We summarize potential sources of batch effects, current progress in evaluating and correcting them, and consortium efforts aiming to tackle them.

Selective Effect of DNA N6-Methyladenosine Modification on Transcriptional Genetic Variations in East Asian Samples

Genetic variations and DNA modification are two common dominant factors ubiquitous across the entire human genome and induce human disease, especially through static genetic variations in DNA or RNA that cause human genetic diseases. DNA N6-methyladenosine (6mA) methylation, as a new epigenetic modification mark, has been widely studied for regulatory biological processes in humans. However, the effect of DNA modification on dynamic transcriptional genetic variations from DNA to RNA has rarely been reported. Here, we identified DNA, RNA and transcriptional genetic variations from Illumina short-read sequencing data in East Asian samples (HX1 and AK1) and detected global DNA 6mA modification using single-molecule, real-time sequencing (SMRT) data. We decoded the effects of DNA 6mA modification on transcriptional genetic variations in East Asian samples and the results were extensively verified in the HeLa cell line. DNA 6mA modification had a stabilized distribution in the East Asian samples and the methylated genes were less likely to mutate than the non-methylated genes. For methylated genes, the 6mA density was positively correlated with the number of variations. DNA 6mA modification had a selective effect on transcriptional genetic variations from DNA to RNA, in which the dynamic transcriptional variations of heterozygous (0/1 to 0/1) and homozygous (1/1 to 1/1) were significantly affected by 6mA modification. The effect of DNA methylation on transcriptional genetic variations provides new insights into the influencing factors of DNA to RNA transcriptional regulation in the central doctrine of molecular biology.

Molecular analyses of the tubby-like protein gene family and their response to salt and high temperature in the foxtail millet (Setaria italica)

Tubby-like proteins (TLPs) are a group of proteins found in both eukaryotes and prokaryotes. They are significant in various physiological and biochemical processes, especially in plants' response to abiotic stress. However, the role of TLP in foxtail millet (Setaria italica) remains unclear. The millet genome has 16 members of the TLP family with typical Tub domains, which can be sorted into five subgroups based on gene structure, motif, and protein domain distribution. SiTLPs were discovered to be predominantly located in the nucleus and also had extracellular distribution. The interspecific evolutionary analysis indicated that SiTLPs had a closer evolutionary relationship with monocots and were consistent with the morphological classification of foxtail millet. When subjected to salt stress, the abundance of SiTLP was affected, and qRT-PCR results showed that the expression levels of certain SiTLP members were induced by salt stress while others remained unresponsive. Except for SiTLP14, all other SiTLP genes were up-regulated in response to high-temperature stress, implying a potentially crucial role for SiTLP in mitigating high-temperature-induced damage. This study provides valuable insights into understanding the functional significance of the TLP gene family in foxtail millet.

Transcriptome Analysis of Differentially Expressed Genes and Molecular Pathways Involved in C2C12 Cells Myogenic Differentiation

Muscles are essential tissues responsible for movement, stability, and metabolism, playing a crucial role in human health and well-being. A comprehensive understanding of muscle differentiation processes is imperative for combating muscle degenerative diseases such as muscular dystrophy. In this study, C2C12 cells were induced to differentiate into myotubes in vitro. Phenotypic changes were observed utilizing Gimsa and immunofluorescent staining techniques. RNA sequencing was conducted at distinct time points (0, 2, 4, and 7 days) during the differentiation process. To elucidate the underlying molecular mechanisms, differential expression analysis, gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and Gene Set Enrichment Analysis (GSEA) were performed. Soft clustering of time series gene expression was employed to establish the expression patterns of differentially expressed genes (DEGs) at various time points during myogenesis. Additionally, quantitative reverse transcription PCR was utilized to validate gene expression from RNA-seq data at the mRNA level. Throughout the myogenic differentiation of C2C12 cells, notable morphological changes were observed, with myoblasts forming multinucleated myotubes by day 4 and plump elongated structures by day 7. Gene expression analysis revealed a substantial increase in DEGs as differentiation progressed, with a significant rise in DEGs from day 0 to day 7. Enrichment analysis highlighted key biological processes and pathways involved, including signal transduction and immune system processes, as well as pathways like chemokine and calcium signaling. Noise-robust soft clustering identified distinct temporal gene expression patterns, categorizing genes into upregulated, downregulated, and biphasic response clusters. The MYH family exhibited diverse expression changes, with Myh3, Myh13, Myh6, Myh7, Myh2, Myh8, Myh14, Myh7b, Myh1, and Myh4 upregulated, Myh10, Myh9, and Myh12 downregulated. Key transcription factors displayed dynamic expression patterns, which was crucial for the regulation of myoblast differentiation. A comprehensive and dynamic transcriptomic analysis of the C2C12 myoblast differentiation process has significantly enhanced our understanding of the key genes and biological pathways involved in myogenesis.

Serum taurine affects lung cancer progression by regulating tumor immune escape mediated by the immune microenvironment

INTRODUCTION

Taurine is a naturally occurring sulfonic acid involved in various physiological and pathological processes, such as the regulation of calcium signaling, immune function, inflammatory response, and cellular aging. It has the potential to predict tumor malignant transformation and formation. Our previous work discovered the elevated taurine in lung cancer patients. However, the precise impact and mechanism of elevated serum taurine levels on lung cancer progression and the suitability of taurine or taurine-containing drinks for lung cancer patients remain unclear.

OBJECTIVES

Our study aimed to systematically investigate the role of taurine in lung cancer, with the ultimate goal of contributing novel strategies for lung cancer treatment.

METHODS

Lung cancer C57 and nude mice models, RNA sequencing, and stable transfection were applied to explored the effects and mechanisms of taurine on lung cancer. Tissues of 129 non-small cell lung cancer (NSCLC) patients derived from 2014 to 2017 for immunohistochemistry were collected in Taihe Hospital.

RESULTS

Low doses of taurine, as well as taurine-infused beverages at equivalent doses, significantly enhanced lung tumor growth. Equally intriguing is that the promoting effect of taurine on lung cancer progression wanes as the dosage increases. The Nuclear factor erythroid 2-like 1 (Nfe2l1 or Nrf1)-reactive oxygen species (ROS)-PD-1 axis may be a potential mechanism for dual role of taurine in lung cancer progression. However, taurine's impacts on lung cancer progression and the anti-tumor function of Nfe2l1 were mainly determined by the immune competence. Taurine inhitited lung tumor growth probably by inhibiting NF-κB-mediated inflammatory responses in nude mice rather than by affecting Nfe2l1 function. As patients age increased, Nfe2l1 gene and protein gradually returned to the levels observed in healthy individuals, but lost its anti-lung cancer effects.

CONCLUSIONS

Taurine emerges as a potential biomarker for lung cancer progression, predicting poor prognosis and unsuitability for specific patients. Lung cancer patients, especially young patients, should be conscious of potential effects of taurine-containing drinks. Conversely, taurine or its drinks may be more suitable for older or immune-deficient patients.

Defining the activity of pro-reparative extracellular vesicles in wound healing based on miRNA payloads and cell type-specific lineage mapping

Small extracellular vesicles (EVs) are released by cells and deliver biologically active payloads to coordinate the response of multiple cell types in cutaneous wound healing. Here we used a cutaneous injury model as a donor of pro-reparative EVs to treat recipient diabetic obese mice, a model of impaired wound healing. We established a functional screen for microRNAs (miRNAs) that increased the pro-reparative activity of EVs and identified a down-regulation of miR-425-5p in EVs in vivo and in vitro associated with the regulation of adiponectin. We tested a cell type-specific reporter of a tetraspanin CD9 fusion with GFP to lineage map the release of EVs from macrophages in the wound bed, based on the expression of miR-425-5p in macrophage-derived EVs and the abundance of macrophages in EV donor sites. Analysis of different promoters demonstrated that EV release under the control of a macrophage-specific promoter was most abundant and that these EVs were internalized by dermal fibroblasts. These findings suggested that pro-reparative EVs deliver miRNAs, such as miR-425-5p, that stimulate the expression of adiponectin that has insulin-sensitizing properties. We propose that EVs promote intercellular signaling between cell layers in the skin to resolve inflammation, induce proliferation of basal keratinocytes, and accelerate wound closure.

Elucidating the Role of SlBBX31 in Plant Growth and Heat-Stress Resistance in Tomato

Heat stress inhibits plant growth and productivity. Among the main regulators, B-box zinc-finger (BBX) proteins are well-known for their contribution to plant photomorphogenesis and responses to abiotic stress. Our research pinpoints that SlBBX31, a BBX protein harboring a conserved B-box domain, serves as a suppressor of plant growth and heat tolerance in tomato (Solanum lycopersicum L.). Overexpressing (OE) SlBBX31 in tomato exhibited yellowing leaves due to notable reduction in chlorophyll content and net photosynthetic rate (Pn). Furthermore, the pollen viability of OE lines obviously decreased and fruit bearing was delayed. This not only affected the fruit setting rate and the number of plump seeds but also influenced the size of the fruit. These results indicate that SlBBX31 may be involved in the growth process of tomato, specifically in terms of photosynthesis, flowering, and the fruiting process. Conversely, under heat-stress treatment, SlBBX31 knockout (KO) plants displayed superior heat tolerance, evidenced by their improved membrane stability, heightened antioxidant enzyme activities, and reduced accumulation of reactive oxygen species (ROS). Further transcriptome analysis between OE lines and KO lines under heat stress revealed the impact of SlBBX31 on the expression of genes linked to photosynthesis, heat-stress signaling, ROS scavenging, and hormone regulation. These findings underscore the essential role of SlBBX31 in regulating tomato growth and heat-stress resistance and will provide valuable insights for improving heat-tolerant tomato varieties.

Fine particulate matter (PM2.5) induces testosterone disruption by triggering ferroptosis through SIRT1/HIF-1α signaling pathway in male mice

Fine particulate matter (PM2.5), a significant component of air pollution particulate matter, is inevitable and closely associated with increasing male reproductive disorder. However, the testicular targets of PM2.5 and its toxicity related molecular mechanisms are still not fully understood. In this study, the conditional knockout (cKO) mice and primary Leydig cells were used to explore the testicular targets of PM2.5 and the related underlying mechanisms. First, apparent the structure impairment of seminiferous tubules, Leydig cells vacuolization, decline of serum testosterone and sperm quality reduction were found in male wild-type (WT) and Sirt1 knockout mice after exposure to PM2.5. Enrichment analyses revealed that differentially expressed genes (DEGs) were enriched in steroid hormone biosynthesis, ferroptosis, and HIF-1 signaling pathway in the mice testes after exposure to PM2.5, which were subsequently verified by the molecular biological analyses. Notably, similar enrichment analyses results were also observed in primary Leydig cells after treatment with PM2.5. In addition, Knockdown of Sirt1 significantly increased PM2.5-induced expression and activation of HIF-1α, which was in parallel to the changes of cellular iron levels, oxidative stress indicators and the ferroptosis markers. In conclusion, this highlights that PM2.5 triggers ferroptosis via SIRT1/HIF-1α signaling pathway to inhibit testosterone synthesis in males. These findings provide a novel research support for the study that PM2.5 causes male reproductive injury.

Assessing the impact of transcriptomics data analysis pipelines on downstream functional enrichment results

Transcriptomics is widely used to assess the state of biological systems. There are many tools for the different steps, such as normalization, differential expression, and enrichment. While numerous studies have examined the impact of method choices on differential expression results, little attention has been paid to their effects on further downstream functional analysis, which typically provides the basis for interpretation and follow-up experiments. To address this, we introduce FLOP, a comprehensive nextflow-based workflow combining methods to perform end-to-end analyses of transcriptomics data. We illustrate FLOP on datasets ranging from end-stage heart failure patients to cancer cell lines. We discovered effects not noticeable at the gene-level, and observed that not filtering the data had the highest impact on the correlation between pipelines in the gene set space. Moreover, we performed three benchmarks to evaluate the 12 pipelines included in FLOP, and confirmed that filtering is essential in scenarios of expected moderate-to-low biological signal. Overall, our results underscore the impact of carefully evaluating the consequences of the choice of preprocessing methods on downstream enrichment analyses. We envision FLOP as a valuable tool to measure the robustness of functional analyses, ultimately leading to more reliable and conclusive biological findings.

Insights into the Early Steps of the Symbiotic Interaction between Soybean (Glycine max) and Sinorhizobium fredii Symbiosis Using Transcriptome, Small RNA, and Degradome Sequencing

Symbiotic nitrogen fixation carried out by the soybean-rhizobia symbiosis increases soybean yield and reduces the amount of nitrogen fertilizer that has been applied. MicroRNAs (miRNAs) are crucial in plant growth and development, prompting an investigation into their role in the symbiotic interaction of soybean with partner rhizobia. Through integrated small RNA, transcriptome, and degradome sequencing analysis, 1215 known miRNAs, 314 of them conserved, and 187 novel miRNAs were identified, with 44 differentially expressed miRNAs in soybean roots inoculated with Sinorhizobium fredii HH103 and a ttsI mutant. The study unveiled that the known miRNA gma-MIR398a-p5 was downregulated in the presence of the ttsI mutation, while the target gene of gma-MIR398a-p5, Glyma.06G007500, associated with nitrogen metabolism, was upregulated. The results of this study offer insights for breeding high-efficiency nitrogen-fixing soybean varieties, enhancing crop yield and quality.

Nuclear factor interleukin 3 and metabolic dysfunction-associated fatty liver disease development

This study investigates sex-specific effects in a gain-of-function model to evaluate Nfil3 function in relation to high-fat diet (HFD)-induced metabolic dysfunction-associated steatotic liver disease (MASLD) and gut microbiota (GM)-induced alterations in the bile acid (BA) profile. MASLD is induced in both wild type and Nfil3-deficient (NKO) C57BL/6 J mice through an HFD. The hepatic immune response is evaluated using flow cytometry, revealing that NKO mice exhibit lower body weight, serum triglyceride (TG) levels, tissue injury, inflammation, and fat accumulation. The Nfil3 deletion reduces macrophage counts in fibrotic liver tissues, decreases proinflammatory gene and protein expression, and diminishes gut barrier function. Alpha and beta diversity analysis reveal increased GM alpha diversity across different sexes. The Nfil3 gene deletion modifies the BA profile, suggesting that negative feedback through the Nfil3-FXR-FGF15 axis facilitates BA recycling from the liver via enterohepatic circulation. Therefore, inhibiting Nfil3 in the liver offers a viable treatment approach for MASLD.

A real-world multi-center RNA-seq benchmarking study using the Quartet and MAQC reference materials

Translating RNA-seq into clinical diagnostics requires ensuring the reliability and cross-laboratory consistency of detecting clinically relevant subtle differential expressions, such as those between different disease subtypes or stages. As part of the Quartet project, we present an RNA-seq benchmarking study across 45 laboratories using the Quartet and MAQC reference samples spiked with ERCC controls. Based on multiple types of 'ground truth', we systematically assess the real-world RNA-seq performance and investigate the influencing factors involved in 26 experimental processes and 140 bioinformatics pipelines. Here we show greater inter-laboratory variations in detecting subtle differential expressions among the Quartet samples. Experimental factors including mRNA enrichment and strandedness, and each bioinformatics step, emerge as primary sources of variations in gene expression. We underscore the profound influence of experimental execution, and provide best practice recommendations for experimental designs, strategies for filtering low-expression genes, and the optimal gene annotation and analysis pipelines. In summary, this study lays the foundation for developing and quality control of RNA-seq for clinical diagnostic purposes.

Microplastic exposure disturbs sleep structure, reduces lifespan, and decreases ovary size in Drosophila melanogaster

The organ-specific toxicity resulting from microplastic (MP) exposure has been extensively explored, particularly concerning the gut, liver, testis, and lung. However, under natural conditions, these effects are not restricted to specific organs or tissues. Investigating whether MP exposure presents a systemic threat to an entire organism, impacting factors such as lifespan, sleep, and fecundity, is essential. In this study, we investigated the effects of dietary exposure to two different doses of MPs (1-5 μm) using the terrestrial model organism Drosophila melanogaster. Results indicated that the particles caused gut damage and remained within the digestive system. Continuous MP exposure significantly shortened the lifespan of adult flies. Even short-term exposure disrupted sleep patterns, increasing the length of daytime sleep episodes. Additionally, one week of MP exposure reduced ovary size, with a trend towards decreased egg-laying in mated females. Although MPs did not penetrate the brain or ovaries, transcriptome analysis revealed altered gene expression in these tissues. In the ovary, Gene Ontology (GO) analysis indicated genotoxic effects impacting inflammation, circadian regulation, and metabolic processes, with significant impacts on extracellular structure-related pathways. In the brain, GO analysis identified changes in pathways associated with proteolysis and carbohydrate metabolism. Overall, this study provides compelling evidence of the systemic negative effects of MP exposure, highlighting the urgent need to address and mitigate environmental MP pollution.

Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling

Certified RNA reference materials are indispensable for assessing the reliability of RNA sequencing to detect intrinsically small biological differences in clinical settings, such as molecular subtyping of diseases. As part of the Quartet Project for quality control and data integration of multi-omics profiling, we established four RNA reference materials derived from immortalized B-lymphoblastoid cell lines from four members of a monozygotic twin family. Additionally, we constructed ratio-based transcriptome-wide reference datasets between two samples, providing cross-platform and cross-laboratory 'ground truth'. Investigation of the intrinsically subtle biological differences among the Quartet samples enables sensitive assessment of cross-batch integration of transcriptomic measurements at the ratio level. The Quartet RNA reference materials, combined with the ratio-based reference datasets, can serve as unique resources for assessing and improving the quality of transcriptomic data in clinical and biological settings.

A comprehensive workflow for optimizing RNA-seq data analysis

BACKGROUND

Current RNA-seq analysis software for RNA-seq data tends to use similar parameters across different species without considering species-specific differences. However, the suitability and accuracy of these tools may vary when analyzing data from different species, such as humans, animals, plants, fungi, and bacteria. For most laboratory researchers lacking a background in information science, determining how to construct an analysis workflow that meets their specific needs from the array of complex analytical tools available poses a significant challenge.

RESULTS

By utilizing RNA-seq data from plants, animals, and fungi, it was observed that different analytical tools demonstrate some variations in performance when applied to different species. A comprehensive experiment was conducted specifically for analyzing plant pathogenic fungal data, focusing on differential gene analysis as the ultimate goal. In this study, 288 pipelines using different tools were applied to analyze five fungal RNA-seq datasets, and the performance of their results was evaluated based on simulation. This led to the establishment of a relatively universal and superior fungal RNA-seq analysis pipeline that can serve as a reference, and certain standards for selecting analysis tools were derived for reference. Additionally, we compared various tools for alternative splicing analysis. The results based on simulated data indicated that rMATS remained the optimal choice, although consideration could be given to supplementing with tools such as SpliceWiz.

CONCLUSION

The experimental results demonstrate that, in comparison to the default software parameter configurations, the analysis combination results after tuning can provide more accurate biological insights. It is beneficial to carefully select suitable analysis software based on the data, rather than indiscriminately choosing tools, in order to achieve high-quality analysis results more efficiently.

Identification of anti-fibrotic and pro-apoptotic bioactive compounds from Ganoderma formosanum and their possible mechanisms in modulating TGF-β1-induced lung fibrosis

ETHNOPHARMACOLOGICAL RELEVANCE

The Compendium of Materia Medica and the Classic of Materia Medica, the two most prominent records of traditional Chinese medicine, documented the therapeutic benefits of Ganoderma sinense particularly in addressing pulmonary-related ailments. Ganoderma formosanum, an indigenous subspecies of G. sinense from Taiwan, has demonstrated the same therapeutic properties.

AIM OF THE STUDY

The aim of this study is to identify bioactive compounds and evaluate the potential of G. formosanum extracts as a novel treatment to alleviate pulmonary fibrosis (PF). Using an in-house drug screening platform, two-stage screening was performed to determine their anti-fibrotic efficacy.

METHODS AND MATERIALS

G. formosanum was fractionated into four partitions by solvents of different polarities. To determine their antifibrotic and pro-apoptotic properties, the fractions were analyzed using two TGF-β1-induced pulmonary fibrosis cell models (NIH-3T3) and human pulmonary fibroblast cell lines, immunoblot, qRT-PCR, and annexin V assays. Subsequently, transcriptomic analysis was conducted to validate the findings and explore possible molecular pathways. The identification of potential bioactive compounds was achieved through UHPLC-MS/MS analysis, while molecular interaction study was investigated by multiple ligands docking and molecular dynamic simulations.

RESULTS

The ethyl acetate fraction (EAF) extracted from G. formosanum demonstrated substantial anti-fibrotic and pro-apoptotic effects on TGF-β1-induced fibrotic models. Moreover, the EAF exhibited no discernible cytotoxicity. Untargeted UHPLC-MS/MS analysis identified potential bioactive compounds in EAF, including stearic acid, palmitic acid, and pentadecanoic acid. Multiple ligands docking and molecular dynamic simulations further confirmed that those bioactive compounds possess the ability to inhibit TGF-β receptor 1.

CONCLUSION

Potential bioactive compounds in G. formosanum were successfully extracted and identified in the EAF, whose anti-fibrotic and pro-apoptotic properties could potentially modulate pulmonary fibrosis. This finding not only highlights the EAF's potential as a promising therapeutic candidate to treat pulmonary fibrosis, but it also elucidates how Ganoderma confers pulmonary health benefits as described in the ancient texts.

Observation of Agonistic Behavior in Pacific White Shrimp (Litopenaeus vannamei) and Transcriptome Analysis

Agonistic behavior has been identified as a limiting factor in the development of intensive L. vannamei aquaculture. However, the characteristics and molecular mechanisms underlying agonistic behavior in L. vannamei remain unclear. In this study, we quantified agonistic behavior through a behavioral observation system and generated a comprehensive database of eyestalk and brain ganglion tissues obtained from both aggressive and nonaggressive L. vannamei employing transcriptome analysis. The results showed that there were nine behavior patterns in L. vannamei which were correlated, and the fighting followed a specific process. Transcriptome analysis revealed 5083 differentially expressed genes (DEGs) in eyestalk and 1239 DEGs in brain ganglion between aggressive and nonaggressive L. vannamei. Moreover, these DEGs were primarily enriched in the pathways related to the energy metabolism process and signal transduction. Specifically, the phototransduction (dme04745) signaling pathway emerges as a potential key pathway for the adjustment of the L. vannamei agonistic behavior. The G protein-coupled receptor kinase 1-like (LOC113809193) was screened out as a significant candidate gene within the phototransduction pathway. Therefore, these findings contribute to an enhanced comprehension of crustacean agonistic behavior and provide a theoretical basis for the selection and breeding of L. vannamei varieties suitable for high-density aquaculture environments.

IFI16 promotes the progression of clear cell renal cell carcinoma through the IL6/PI3K/AKT axis

BACKGROUND

Clear cell renal cell carcinoma (ccRCC) is a common disease in the urinary system, with a high incidence and poor prognosis in advanced stages. Although γ-interferon-inducible protein 16 (IFI16) has been reported to play a role in various tumors, its involvement in ccRCC remains poorly documented, and the molecular mechanisms are not yet clear.

METHODS

We conducted bioinformatics analysis to study the expression of IFI16 in ccRCC using public databases. Additionally, we analyzed and validated clinical specimens that we collected. Subsequently, we explored the impact of IFI16 on ccRCC cell proliferation, migration, and invasion through in vitro and in vivo experiments. Furthermore, we predicted downstream molecules and pathways using transcriptome analysis and confirmed them through follow-up experimental validation.

RESULTS

IFI16 was significantly upregulated in ccRCC tissue and correlated with poor patient prognosis. In vitro, IFI16 promoted ccRCC cell proliferation, migration, and invasion, while in vivo, it facilitated subcutaneous tumor growth and the formation of lung metastatic foci. Knocking down IFI16 suppressed its oncogenic function. At the molecular level, IFI16 promoted the transcription and translation of IL6, subsequently activating the PI3K/AKT signaling pathway and inducing epithelial-mesenchymal transition (EMT).

CONCLUSION

IFI16 induced EMT through the IL6/PI3K/AKT axis, promoting the progression of ccRCC.

RAF1 gene fusions are recurrent driver events in infantile fibrosarcoma-like mesenchymal tumors

Infantile fibrosarcomas (IFS) and congenital mesoblastic nephroma (CMN) are rare myofibroblastic tumors of infancy and early childhood commonly harboring the ETV6::NTRK3 gene fusion. IFS/CMN are considered as tumors with an 'intermediate prognosis' as they are locally aggressive, but rarely metastasize, and generally have a favorable outcome. A fraction of IFS/CMN-related neoplasms are negative for the ETV6::NTRK3 gene rearrangement and are characterized by other chimeric proteins promoting MAPK signaling upregulation. In a large proportion of these tumors, which are classified as IFS-like mesenchymal neoplasms, the contributing molecular events remain to be identified. Here, we report three distinct rearrangements involving RAF1 among eight ETV6::NTRK3 gene fusion-negative tumors with an original histological diagnosis of IFS/CMN. The three fusion proteins retain the entire catalytic domain of the kinase. Two chimeric products, GOLGA4::RAF1 and LRRFIP2::RAF1, had previously been reported as driver events in different cancers, whereas the third, CLIP1::RAF1, represents a novel fusion protein. We demonstrate that CLIP1::RAF1 acts as a bona fide oncoprotein promoting cell proliferation and migration through constitutive upregulation of MAPK signaling. We show that the CLIP1::RAF1 hyperactive behavior does not require RAS activation and is mediated by constitutive 14-3-3 protein-independent dimerization of the chimeric protein. As previously reported for the ETV6::NTRK3 fusion protein, CLIP1::RAF1 similarly upregulates PI3K-AKT signaling. Our findings document that RAF1 gene rearrangements represent a recurrent event in ETV6::NTRK3-negative IFS/CMN and provide a rationale for the use of inhibitors directed to suppress MAPK and PI3K-AKT signaling in these cancers. © 2024 The Pathological Society of Great Britain and Ireland.

Reference-free inferring of transcriptomic events in cancer cells on single-cell data

BACKGROUND

Cancerous cells' identity is determined via a mixture of multiple factors such as genomic variations, epigenetics, and the regulatory variations that are involved in transcription. The differences in transcriptome expression as well as abnormal structures in peptides determine phenotypical differences. Thus, bulk RNA-seq and more recent single-cell RNA-seq data (scRNA-seq) are important to identify pathogenic differences. In this case, we rely on k-mer decomposition of sequences to identify pathogenic variations in detail which does not need a reference, so it outperforms more traditional Next-Generation Sequencing (NGS) analysis techniques depending on the alignment of the sequences to a reference.

RESULTS

Via our alignment-free analysis, over esophageal and glioblastoma cancer patients, high-frequency variations over multiple different locations (repeats, intergenic regions, exons, introns) as well as multiple different forms (fusion, polyadenylation, splicing, etc.) could be discovered. Additionally, we have analyzed the importance of less-focused events systematically in a classic transcriptome analysis pipeline where these events are considered as indicators for tumor prognosis, tumor prediction, tumor neoantigen inference, as well as their connection with respect to the immune microenvironment.

CONCLUSIONS

Our results suggest that esophageal cancer (ESCA) and glioblastoma processes can be explained via pathogenic microbial RNA, repeated sequences, novel splicing variants, and long intergenic non-coding RNAs (lincRNAs). We expect our application of reference-free process and analysis to be helpful in tumor and normal samples differential scRNA-seq analysis, which in turn offers a more comprehensive scheme for major cancer-associated events.

Systematic characterization of gene families and functional analysis of PvRAS3 and PvRAS4 involved in rosmarinic acid biosynthesis in Prunella vulgaris

Prunella vulgaris is an important material for Chinese medicines with rosmarinic acid (RA) as its index component. Based on the chromosome-level genome assembly we obtained recently, 51 RA biosynthesis-related genes were identified. Sequence feature, gene expression pattern and phylogenetic relationship analyses showed that 17 of them could be involved in RA biosynthesis. In vitro enzymatic assay showed that PvRAS3 catalyzed the condensation of p-coumaroyl-CoA and caffeoyl-CoA with pHPL and DHPL. Its affinity toward p-coumaroyl-CoA was higher than caffeoyl-CoA. PvRAS4 catalyzed the condensation of p-coumaroyl-CoA with pHPL and DHPL. Its affinity toward p-coumaroyl-CoA was lower than PvRAS3. UPLC and LC-MS/MS analyses showed the existence of RA, 4-coumaroyl-3',4'-dihydroxyphenyllactic acid, 4-coumaroyl-4'-hydroxyphenyllactic acid and caffeoyl-4'-hydroxyphenyllactic acid in P. vulgaris. Generation and analysis of pvras3 homozygous mutants showed significant decrease of RA, 4-coumaroyl-3',4'-dihydroxyphenyllactic acid, 4-coumaroyl-4'-hydroxyphenyllactic acid and caffeoyl-4'-hydroxyphenyllactic acid and significant increase of DHPL and pHPL. It suggests that PvRAS3 is the main enzyme catalyzing the condensation of acyl donors and acceptors during RA biosynthesis. The role of PvRAS4 appears minor. The results provide significant information for quality control of P. vulgaris medicinal materials.

Analysis of the mechanism of curcumin against osteoarthritis using metabolomics and transcriptomics

Curcumin, a polyphenolic compound derived from the turmeric plant (Curcuma longa), has been extensively studied for its anti-inflammatory and anti-proliferative properties. The safety and efficacy of curcumin have been thoroughly validated. Nevertheless, the underlying mechanism for treating osteoarthritis remains ambiguous. This study aims to reveal the potential mechanism of curcumin in treating osteoarthritis by using metabolomics and transcriptomics. Firstly, we validated the effect of curcumin on inflammatory factors in human articular chondrocytes. Secondly, we explored the cellular metabolism mechanism of curcumin against osteoarthritis using cell metabolomics. Thirdly, we assessed the differences in gene expression of human articular chondrocytes through transcriptomics. Lastly, to evaluate the essential targets and elucidate the potential mechanism underlying the therapeutic effects of curcumin in osteoarthritis, we conducted a screening of the proteins within the shared pathway of metabolomics and transcriptomics. Our results demonstrated that curcumin significantly decreased the levels of inflammatory markers, such as IL-β, IL-6, and TNF-α, in human articular chondrocytes. Cell metabolomics identified 106 differential metabolites, including beta-aminopropionitrile, 3-amino-2-piperidone, pyrrole-2-carboxaldehyde, and various other components. The transcriptomic analysis yielded 1050 differential mRNAs. Enrichment analysis showed that the differential metabolites and mRNAs were significantly enriched in seven pathways, including glycine, serine, and threonine metabolism; pentose and glucuronate interconversions; glycerolipid metabolism; histidine metabolism; mucin-type o-glycan biosynthesis; inositol phosphate metabolism; and cysteine and methionine metabolism. A total of 23 key targets were identified to be involved in these pathways. We speculate that curcumin may alleviate osteoarthritis by targeting key proteins involved in glycine, serine, and threonine metabolism; inhibiting pyruvate production; and modulating glycolysis.

Attenuating mitochondrial dysfunction and morphological disruption with PT320 delays dopamine degeneration in MitoPark mice

BACKGROUND

Mitochondria are essential organelles involved in cellular energy production. Changes in mitochondrial function can lead to dysfunction and cell death in aging and age-related disorders. Recent research suggests that mitochondrial dysfunction is closely linked to neurodegenerative diseases. Glucagon-like peptide-1 receptor (GLP-1R) agonist has gained interest as a potential treatment for Parkinson's disease (PD). However, the exact mechanisms responsible for the therapeutic effects of GLP-1R-related agonists are not yet fully understood.

METHODS

In this study, we explores the effects of early treatment with PT320, a sustained release formulation of the GLP-1R agonist Exenatide, on mitochondrial functions and morphology in a progressive PD mouse model, the MitoPark (MP) mouse.

RESULTS

Our findings demonstrate that administration of a clinically translatable dose of PT320 ameliorates the reduction in tyrosine hydroxylase expression, lowers reactive oxygen species (ROS) levels, and inhibits mitochondrial cytochrome c release during nigrostriatal dopaminergic denervation in MP mice. PT320 treatment significantly preserved mitochondrial function and morphology but did not influence the reduction in mitochondria numbers during PD progression in MP mice. Genetic analysis indicated that the cytoprotective effect of PT320 is attributed to a reduction in the expression of mitochondrial fission protein 1 (Fis1) and an increase in the expression of optic atrophy type 1 (Opa1), which is known to play a role in maintaining mitochondrial homeostasis and decreasing cytochrome c release through remodeling of the cristae.

CONCLUSION

Our findings suggest that the early administration of PT320 shows potential as a neuroprotective treatment for PD, as it can preserve mitochondrial function. Through enhancing mitochondrial health by regulating Opa1 and Fis1, PT320 presents a new neuroprotective therapy in PD.