High-throughput Transcriptome Sequencing Research Articles

De novo assembly, gene annotation and marker development using illumina paired-end transcriptome sequences in nutmeg (Myristica fragrans Houtt.).

Nutmeg (Myristica fragrans) is a high-value spice crop widely utilized in culinary, medicinal, and industrial sectors. Despite its economic and cultural significance, genetic research on nutmeg is severely limited, hindering efforts to improve its cultivation and breeding programs. The lack of molecular markers and genetic tools has further constrained the development of superior trait varieties. Molecular markers are essential for genetic mapping, diversity studies, and marker-assisted selection, yet their application in nutmeg remains unexplored. This study utilized Illumina high-throughput paired-end transcriptome sequencing to explore the genetic framework of nutmeg, focusing on de novo assembly, gene annotation, and molecular marker development. RNA Sequencing (RNA-seq) was performed on leaf tissues from male and female trees to analyze differentially expressed genes. A total of 141,192 unigenes were assembled with an average length of 1117bp, achieving functional annotation in public databases like NR, Swiss-Prot, KEGG, and InterPro. De novo transcriptome assembly and functional annotation revealed ten candidate genes involved in sex determination. These candidate genes are associated with hormonal pathways, transcription factors, and reproductive development. Several primers/markers have been designed and validated using PCR. This research lays a foundation for genetic studies, marker-assisted breeding, and improved cultivation practices for nutmeg.

13-Methylpalmatine alleviates bleomycin-induced pulmonary fibrosis by suppressing the ITGA5/TGF-β/Smad signaling pathway.

13-Methylpalmatine alleviates bleomycin-induced pulmonary fibrosis by suppressing the ITGA5/TGF-β/Smad signaling pathway.

The IL-6 autocrine loop promoting IFN-γ-induced fibroblast senescence is involved in psychological stress-mediated exacerbation of vitiligo.

Psychological stress is the most common psychological comorbidity and a significant triggering factor of vitiligo. Moderate to severe psychological stress can markedly affect the efficacy of vitiligo treatment. However, the specific mechanisms underlying its involvement remain insufficiently studied. Chronic unpredictable mild stress (CUMS)-induced major depressive disorder (MDD)-like behavior was modeled in C57BL/6 mice alongside wild-type mice to investigate differences in vitiligo pathogenesis. White spot tissues from mouse tails were subjected to high-throughput transcriptomic sequencing (RNA-seq). In vitro experiments utilized β-galactosidase, P16, and P21 to assess IFN-γ-induced senescence. The effects of exogenous IL-6 on fibroblast senescence were assessed, and the role of blocking the IL-6 autocrine loop with an IL-6R inhibitor in reversing IFN-γ-induced fibroblast senescence was evaluated. CUMS-induced MDD -like mice exhibited significantly lower body mass index and sugar-water preference index compared to wild-type mice, and their vitiligo severity was markedly increased. Transcriptomic sequencing revealed significant upregulation of cellular senescence and JAK-STAT signaling pathways in white spot tissues of depressive-like vitiligo mice. In vitro findings indicated that IFN-γ induced fibroblast senescence via activation of the JAK2-STAT3 signaling pathway, which subsequently promoted melanocyte apoptosis and increased IL-6 secretion and IL-6R expression. Exogenous IL-6 further activated the JAK2-STAT3 signaling pathway, induced fibroblast senescence, and synergistically intensified IFN-γ-induced fibroblast senescence. Excessive activation of the IL-6 autocrine loop, synergizing with IFN-γ to aggravate fibroblast senescence and promote melanocyte apoptosis. Blocking the IL-6 autocrine loop may serve as an effective approach to mitigate the impact of CUMS on vitiligo pathogenesis and treatment efficacy.

Abstract 5662: Deep-mining the antibody repertoires of transgenic mouse models with high-throughput single cell BCR and whole transcriptome sequencing

Abstract Transgenic mouse models are excellent tools to model human antibody response against antigens or disease of choice, given their ability to undergo diversification, in vivo affinity maturation, clonal selection and clonal expansion in their natural immune environment. Current antibody discovery methods lack the scale required to fully screen the antibody repertoire of transgenic mouse models to uncover maximum desirable antibody hits per discovery campaign. Here, we demonstrate our novel combinatorial barcoding approach to enable high-throughput single cell BCR and whole transcriptome profiling of transgenic mouse samples with unprecedented sensitivity, scalability, and flexibility. As a proof of concept, we profiled over 1 million cells from multiple transgenic mice that were either naive or immunized with antigens of interest to obtain hundreds of thousands of paired BCR clonotypes. Using the whole transcriptome data, we detected all B cell subpopulations including plasma cells at single cell resolution. We then used the paired heavy and light chain BCR data to detect productive chains in the majority of B cells revealing both unique and expanded clonotypes. In the expanded clonotype pool we found specific patterns of VDJ utilization and amino acid motifs compared to the naive pool. This method paves the way for high throughput screening of antibody repertoires from transgenic mice to allow for deep mining of repertoires for antibody discovery and therapeutic outcomes. Citation Format: Ajay Sapre, Alec Salvino, Guillermo Gallareta-Olivares, Efi Papalexi, Jose Jacob, Ashwath Kumar, Charles Roco, Alexander Rosenberg. Deep-mining the antibody repertoires of transgenic mouse models with high-throughput single cell BCR and whole transcriptome sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5662.

MiR-223-3p Mitigates Mitochondrial Dysfunction and Cementoblast Apoptosis in Orthodontic Root Resorption via FoxO3.

The aim of this study was to elucidate the roles of miR-223-3p in orthodontically induced inflammatory root resorption (OIIRR). We used high-throughput miRNA sequencing and transcriptome sequencing to analyze the differentially expressed miRNAs and mRNAs in OCCM-30 cells under hypoxia. Real-time quantitative PCR (RT-qPCR) and Western blotting were used to assess the expression of genes and proteins related to apoptosis, oxidative stress, and mitochondrial dysfunction. Fluorescence staining was employed to detect changes in cellular ROS (reactive oxygen species), MMP (mitochondrial membrane potential), and mtROS (mitochondrial ROS) expression. We found that miR-223-3p targeted FoxO3 to regulate apoptosis in cementoblasts under hypoxic conditions. Moreover, hypoxia-induced FoxO3 increased oxidative stress and induced mitochondrial dysfunction in cementoblasts, resulting in cell apoptosis. Administration of the ROS inhibitor NAC (N-acetyl cysteine) effectively reversed FoxO3-induced oxidative stress and mitochondrial dysfunction, thereby rescuing cell apoptosis. miR-223-3p targets FoxO3 and regulates the apoptosis of cementoblasts by improving oxidative stress and mitochondrial dysfunction. These findings may offer new insights into the mechanism of OIIRR.

Identification of a NEK7-related pyroptosis gene signature against pancreatic cancer and evaluation of its potential in tumor microenvironment remodeling via regulating inflammasome complex.

The treatment options for pancreatic ductal adenocarcinoma (PDAC) remain limited. It is therefore important to explore new therapeutic targets and strategies for better treatment and prognosis for patients with PDAC. NIMA-related kinase 7 (NEK7) is a serine/threonine kinase involved in PDAC development. Moreover, NEK7 was reported to regulate NLRP3 inflammasome and cell pyroptosis. To evaluate the role of NEK7 in PDAC, we performed RNA sequencing analysis in PDAC cells, and a series of bioinformatics analyses were employed to determine the biological function of NEK7 in PDAC. We identified a NEK7-Specific Pyroptosis Gene Set (NEK7-SPGS) by high-throughput transcriptome sequencing combining Gene Set Enrichment Analysis (GSEA). We reveal that NEK7-SPGS is highly associated with T helper cell infiltration and inflammatory response of PDAC. We therefore proposed that NEK7-SPGS might have potential for tumor microenvironment remodeling via T cells induced inflammatory response. Using dataset from TCGA database, we established a NEK7-SPGS-related prognostic signature for patients with PDAC. Subsequently, sensitivity estimation of chemotherapeutic drugs revealed a series of chemotherapy agents according to the NEK7-SPGS-related prognostic signature, including gemcitabine and paclitaxel, drugs that have been used as conventional agents for PDAC therapy. Meanwhile, we showed that the expression of SCAMP1, which is a member of NEK7-SPGS, was involved in the progression of PDAC in vivo and in vitro. We proposed a NEK7-specific pyroptosis gene signature and evaluated its potential in PDAC tumor microenvironment. The NEK7-SPGS-related prognostic signature could act as a prognostic biomarker and serve as therapeutic guidance in clinical application.

SF3B4 regulates proliferation and apoptosis in hepatocellular carcinoma via alternative splicing and interaction with TRIM28 and SETD5

BackgroundSF3B4 encodes a core subunit of the U2-type spliceosome and is implicated in abnormal cell growth and tumorigenesis. However, its role in regulating gene expression and alternative splicing in hepatocellular carcinoma (HCC) remains inadequately understood.MethodsSF3B4 expression was downregulated in HCC cells, followed by high-throughput transcriptome sequencing to capture the transcriptomic changes induced by SF3B4. This approach facilitated the identification of potential targets regulated by SF3B4 at both the transcriptional and alternative splicing levels in HCC cells. Additionally, SF3B4-binding RNAs in Huh7 cells were identified through iRIP-seq. The RNA-seq data were subsequently analyzed to elucidate the molecular mechanisms by which SF3B4 affects gene expression and alternative splicing in HCC.ResultsDownregulation of SF3B4 promoted apoptosis and inhibited cell proliferation. In the RNA-seq data, the number of regulated alternative splicing events (RASE) significantly outnumbered the differentially expressed genes (DEGs), consistent with SF3B4’s role as a splicing factor that regulates a wide array of pre-mRNA splicing events. Furthermore, a total of 252 common RNA targets bound by SF3B4 were identified. Correlation analysis with RNA-seq data suggested that SF3B4 may bind to TRIM28, potentially modulating its mRNA expression levels. Additionally, SF3B4 may influence pre-mRNA alternative splicing by interacting with SETD5.ConclusionSF3B4 contributes to HCC progression by directly binding mRNAs and interacting with proteins, thereby regulating gene expression and alternative splicing.

Boosting the angiogenesis potential of self-assembled mesenchymal stem cell spheroids by size mediated physiological hypoxia for vascularized pulp regeneration.

Boosting the angiogenesis potential of self-assembled mesenchymal stem cell spheroids by size mediated physiological hypoxia for vascularized pulp regeneration.

Molecular Insights into Propofol's Neurotoxic Effects: Targeting the HTR1A/cAMP Signaling Pathway.

Propofol, a commonly used anesthetic in clinical practice, is favored for its rapid onset and short duration of action. Despite its widespread use, the potential neurotoxic effects of propofol remain insufficiently understood. This study utilized high-throughput transcriptome sequencing and network pharmacology to investigate the mechanisms by which propofol induces neurotoxicity in rat hippocampal neural progenitor cells (NPCs), focusing on the HTR1A/cAMP signaling pathway. Our findings reveal that propofol significantly inhibits the HTR1A/cAMP pathway, leading to altered expression of key genes that affect neuronal activity, inflammatory responses, and apoptosis. In vivo experiments further demonstrate that propofol impairs spatial learning and memory in rats, an effect that is partially reversed by overexpression of HTR1A. These results not only elucidate the molecular mechanisms underlying propofol-induced neuronal damage but also provide critical insights into the safe application of propofol in clinical settings.

Comparative transcriptome analysis of Isatis indigotica under different precipitation conditions.

Plant adaptation to environmental stress is crucial for improving crop resilience and productivity. The growth and yield of Isatis indigotica are significantly affected by water conditions. In this study, high-throughput transcriptome sequencing was performed on leaf samples from Isatis indigotica after different treatments: normal precipitation (CK), 40% rainfall reduction (R1), 80% rainfall reduction (R2), 40% rainfall enhancement (I1) and 80% rainfall enhancement (I2). Under 80% rainfall augmentation (I2), the malondialdehyde (MDA) content of Isatis indigotica leaves was the lowest, and the proline (pro) and catalase (CAT) activities were the highest. These findings indicate that normal precipitation conditions do not meet the optimal water requirements for the growth of Isatis indigotica and that appropriate irrigation can be used to improve the accumulation and quality of medicinal substances from this species. Transcriptome analysis of Isatis indigotica leaves compared with those in the control group (CK) revealed 896, 2551, 1294, and 3082 differentially expressed genes in the reduced rainfall reduction groups (R1, R2) and increased rainfall groups (I1, 12), respectively. The number of differentially expressed genes (DEGs) gradually increased with increasing rainfall and decreased after rainfall reduction. The GO enrichment results revealed that the DEGs were significantly enriched in functions such as cellular processes, metabolic processes, stimulus response, cell structure, and catalytic and binding activities. KEGG analysis revealed that metabolic pathways such as glutathione metabolism, phenylpropanoid biosynthesis, and plant hormone signaling were significantly enriched, with the greatest number of enriched genes. This study revealed 32 antioxidant system-related genes, 49 phenylpropanoid biosynthesis-related genes, and 49 plant hormone signaling pathway-related genes among the significantly enriched pathways. This study provides new insights into the regulation of Isatis indigotica leaves in response to different water contents at the molecular level. The findings also provide a reference for optimizing the field management of Isatis indigotica and improving the quality and yield of medicinal materials.

Hydrogen sulfide repairs testicular damage induced by heat stress in rats.

Heat stress can cause testicular damage and affect male fertility. The gasotransmitter hydrogen sulfide (H2S) is involved in various physiological and pathophysiological processes, with antioxidant and anti-inflammation effects. The aim of this study was to investigate whether H2S could reduce the testicular damage caused by heat stress. In this study, we constructed a rat heat-stress model and treated it with H2S. Histopathology, high-throughput sequencing, bioinformatics analysis and molecular biology methods were used to investigate whether H2S donor NaHS could alleviate heat stress-induced testicular injury and to explore the underlying mode of action of H2S. Heat stress reduced testis index, sperm quality, sex hormone levels and disturbed testicular structures. High-throughput transcriptome sequencing and Gene Ontology (GO) enrichment analyses showed that genes involved in inflammation were upregulated in the heat stress group compared to the control group. H2S treatment increased testis index, sperm quality and attenuated pathological alternation and hormone disorder in rats exposed to heat stress. Furthermore, H2S administration reversed increased inflammatory factors tumor necrosis factor-α, interleukin-1β and interleukin-6, and resulted in a significant decrease in malondialdehyde levels and in increased activity of catalase and ratio of reduced/oxidized glutathione compared to the heat stress group. This study suggests that H2S donor NaHS can effectively restore testicular damage caused by heat stress in rats by inhibiting inflammation and oxidative stress.

RBM39 promotes hepatocarcinogenesis by regulating RFX1's alternative splicing and subsequent activation of integrin signaling pathway.

Alternative splicing (AS) is crucial for tumor cells as it regulates protein expression and produces various protein isoforms, which can have diverse or even opposing roles in tumor growth and metastasis. Despite its significance, the role of AS and related splicing factors, particularly splicing-related messenger ribonucleoproteins (mRNPs), in hepatocarcinogenesis, is poorly understood. High-throughput transcriptome sequencing of HCC patients revealed that the spliceosome pathway might play a significant role in HCC development. Through the combined analysis of the three gene clusters, the splicing factor RBM39 was identified, which was highly expressed in HCC tumor tissues with prognostic value. Functional studies showed that silencing RBM39 inhibited cell proliferation, migration, and invasion via the integrin pathway. By performing RNA immunoprecipitation sequencing (RIP-seq), we found that RBM39 combined to RFX1 pre-mRNA and regulated alternative splicing of exon 2. Mechanistically, the exon 2 skipping in RFX1, influenced by high RBM39 expression in HCC cells, led to the production of an N-terminal truncated RFX1, which lost the transcriptional repression ability on oncogenic collagen genes. High RBM39 expression enhances the malignant capabilities of HCC cells by regulating the alternative splicing of RFX1 and subsequently activating the FAK/PI3K/AKT signaling pathway.

Fresh Rehmanniae Radix regulates cholesterol metabolism disorder in mice fed with high-fat and high-cholesterol diet via FXR-mediated bile acid reabsorption

This study aims to investigate the potential effect of the water extract of fresh Rehmanniae Radix on hypercholesterolemia in mice that was induced by a high-fat and high-cholesterol diet and explore its possible mechanism from bile acid reabsorption. Male C57BL/6 mice were randomly assigned into the following groups: control, model, low-and high-dose(4 and 8 g·kg~(-1), respectively) fresh Rehmanniae Radix, and positive drug(simvastatin, 0.05 g·kg~(-1)). Other groups except the control group were fed with a high-fat and high-cholesterol diet for 6 consecutive weeks to induce hypercholesterolemia. From the 6th week, mice were administrated with corresponding drugs daily via gavage for additional 6 weeks, while continuing to be fed with a high-fat and high-cholesterol diet. Serum levels of total cholesterol(TC), triglycerides(TG), low density lipoprotein-cholesterol(LDL-c), high density lipoprotein-cholesterol(HDL-c), and total bile acid(TBA), as well as liver TC and TG levels and fecal TBA level, were determined by commercial assay kits. Hematoxylin-eosin(HE) staining, oil red O staining, and transmission electron microscopy were performed to observe the pathological changes in the liver. Three livers samples were randomly selected from each of the control, model, and high-dose fresh Rehmanniae Radix groups for high-throughput transcriptome sequencing. Differentially expressed genes were mined and KEGG pathway enrichment analysis was performed to predict the key pathways and target genes of the water extract of fresh Rehmanniae Radix in the treatment of hypercholesterolemia. RT-qPCR was employed to measure the mRNA levels of cholesterol 7α-hydroxylase(CYP7A1) and cholesterol 27α-hydroxylase(CYP27A1) in the liver. Western blot was employed to determine the protein levels of CYP7A1 and CYP27A1 in the liver as well as farnesoid X receptor(FXR), apical sodium-dependent bile acid transporter(ASBT), and ileum bile acid-binding protein(I-BABP) in the ileum. The results showed that the water extract of fresh Rehmanniae Radix significantly lowered the levels of TC and TG in the serum and liver, as well as the level of LDL-c in the serum. Conversely, it elevated the level of HDL-c in the serum and TBA in feces. No significant difference was observed in the level of TBA in the serum among groups. HE staining, oil red O staining, and transmission electron microscopy showed that the water extract reduced the accumulation of lipid droplets in the liver. Further mechanism studies revealed that the water extract of fresh Rehmanniae Radix significantly down-regulated the protein levels of FXR and bile acid reabsorption-related proteins ASBT and I-BABP. Additionally, it enhanced CYP7A1 and CYP27A1, the key enzymes involved in bile acid synthesis. Therefore, it is hypothesized that the water extract of fresh Rehmanniae Radix may exert an anti-hypercholesterolemic effect by regulating FXR/ASBT/I-BABP signaling, inhibiting bile acid reabsorption, and increasing bile acid excretion, thus facilitating the conversion of cholesterol to bile acids.

Transcriptomic Analysis Reveals the Biosynthesis Mechanism of Coixol Under Salicylic Acid Treatment

Background: Coix (Coix lacryma-jobi L.) is cultivated as medicine and food homologous resources containing various active components. As one of its main ingredients, coixol possesses the biological activities of fever reduction, pain relief, tumor suppression, blood glucose, and pressure decrease. However, the biosynthesis mechanism of coixol in coix is still unclear. Methods: In this study, different dosages of salicylic acid (SA) were applied to coix plants, and the contents of coixol from different parts were detected by an ultra-performance liquid chromatography–tandem mass spectrometry (UPLC–MS/MS). The biosynthesis pathway of coixol was determined by high-throughput transcriptome sequencing analysis and the genes were then verified by qRT-PCR. Results: SA treatment significantly increased plant height, root length, and fresh weight and increased the coixol contents in the root, stem, leaf, and seed. In total, eight enzyme-encoding genes were screened out as the key genes in the biosynthesis of coixol. The bioaccumulation of coixol was mainly through benzoxazinoid biosynthetic metabolic pathway (ko00402). Conclusions: These findings not only pointed the way for increasing the content of coixol in cultivation but also provided a reference for further elucidation of the gene functions involved in the bioaccumulation of coixol.

Dynamic Immune Response Landscapes of Avian Peripheral Blood Post-Vaccination Against Infectious Bronchitis Virus Infection.

Background/Objectives: Despite decades of extensive vaccinations against avian infectious bronchitis virus (IBV) infection, outbreaks caused by constantly emerging variants due to genome recombination between different viral strains, including vaccine strains, occur annually worldwide. The development of novel vaccines with favorable safety and effectiveness is required but is hindered by a limited understanding of vaccination against IBV. Methods: Here, we performed a comprehensive analysis of the in vivo dynamics of peripheral blood mononuclear cells (PBMCs) in specific pathogen-free chickens inoculated with the widely used live attenuated IBV vaccine strain H120 at single-cell level, using high-throughput single-cell transcriptome sequencing (scRNA-seq). Results: High-quality sequencing dataset for four scRNA-seq data containing the transcriptomes of 29,846 individual chicken PBMCs were obtained, defining 22 populations and 7 cell types based on distinct molecular signatures and known markers. Further integrative analysis constructed the time series dynamic cell transition and immune response landscapes within the two weeks post-prime vaccination against IBV. Enhanced crosstalk between antigen-presenting cells and T lymphocytes was revealed as early as four days post-vaccination. The specific immune cell populations and their comprehensive cellular and molecular networks involved in the initiation phase of antiviral adaptive immune responses were elucidated in details. Conclusions: Our study provides a comprehensive view of the dynamic initiation of immune responses in chickens against IBV infection at the cellular and molecular levels, which provides theoretical support and potential solutions for the future rational design of safe and effective vaccines, the augmentation of the efficacy of current vaccines, and the optimization of immune programs.

Machine learning-based screening of asthma biomarkers and related immune infiltration.

Asthma has an annual increasing morbidity rate and imposes a heavy social burden on public healthcare systems. The aim of this study was to use machine learning to identify asthma-specific genes for the prediction and diagnosis of asthma. Differentially expressed genes (DEGs) related to asthma were identified by examining public sequencing data from the Gene Expression Omnibus, coupled with the support vector machine recursive feature elimination and least absolute shrinkage and selection operator regression model. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene set enrichment analysis and correlation analyses between gene and immune cell levels were performed. An ovalbumin-induced asthma mouse model was established, and eukaryotic reference transcriptome high-throughput sequencing was performed to identify genes expressed in mouse lung tissues. Thirteen specific asthma genes were obtained from our dataset analysis (LOC100132287, CEACAM5, PRR4, CPA3, POSTN, LYPD2, TCN1, SCGB3A1, NOS2, CLCA1, TPSAB1, CST1, and C7orf26). The GO analysis demonstrated that DEGs linked to asthma were primarily related to positive regulation of guanylate cyclase activity, gpi anchor binding, peptidase activity and arginine binding. The renin-angiotensin system, arginine biosynthesis and arginine and proline metabolism were the key KEGG pathways of DEGs. Additionally, the genes CEACAM5, PRR4, CPA3, POSTN, CLCA1, and CST1 expression levels were positively associated with plasma cells and resting mast cells. The mouse model revealed elevated nos2 and clca1 expression in the asthmatic mouse group compared with that in normal mice, which was consistent with the findings in asthmatic patients. This study identified new marker genes for the prediction and diagnosis of asthma, which can be further validated and applied clinically.

AdipoR1 enhances the radiation resistance via ESR1/CCNB1IP1/cyclin B1 pathway in hepatocellular carcinoma cells

Hepatocellular carcinoma is one of the most common malignant tumors, and radiotherapy plays a pivotal role in its therapeutic regimen. However, radiotherapy resistance is the main cause of therapeutic failure in patients. Our previous study revealed that Adiponectin Receptor 1 (AdipoR1) is involved in regulating radiation resistance in liver cancer patients treated with stereotactic body radiotherapy. To explore the mechanism, we performed high-throughput transcriptome sequencing of hepatocellular carcinoma cells with stable knockdown of AdipoR1. KEGG enrichment analysis indicated that the cell cycle and ubiquitination degradation pathways may be involved in the regulation of radiation resistance by AdipoR1.The knockdown of AdipoR1 can attenuate the radiation-induced G2/M phase arrest through cyclin B1.By the ubiquitination IP assay and a rescue experiment, we confirmed that CCNB1IP1 regulated the ubiquitination and degradation of cyclin B1. Combined with information from transcription factor database and AdipoR1 transcriptome sequencing, these results showed that estrogen receptor 1 (ESR1) may be a transcription factor of CCNB1IP1. We found that AdipoR1 promoted the translocation of ESR1 from the cytoplasm to the nucleus, and ESR1 inhibited the transcription of CCNB1IP1.Therefore, we propose that AdipoR1 regulates the ubiquitination level, cell cycle progression, and radiation resistance of HCC cells through the “AdipoR1 /ESR1/CCNB1IP1/cyclin B1” axis. This study will promote the development of novel targeted radiosensitizing drugs.

Deciphering SPP1-related macrophage signaling in the pathogenesis of intervertebral disc degeneration

This study delved into the molecular mechanisms underlying mechanical stress-induced intervertebral disc degeneration (msi-IDD) through single-cell and high-throughput transcriptome sequencing in mouse models and patient samples. Results exhibited an upsurge in macrophage presence in msi-IDD intervertebral disc (IVD) tissues, with secreted phosphoprotein 1 (SPP1) identified as a pivotal driver exacerbating degeneration via the protein kinase RNA-like endoplasmic reticulum kinase/ activating transcription factor 4/ interleukin-10 (PERK/ATF4/IL-10) signaling axis. Inhibition of SPP1 demonstrated promising outcomes in mitigating msi-IDD progression in both in vitro and in vivo models. These findings underscore the therapeutic promise associated with the modulation of the PERK signaling pathway in IDD, shedding light on the pathogenesis of msi-IDD and proposing a promising avenue for intervention strategies.Graphical abstract1) Macrophage Regulation in IDD: SPP1 activates the PERK/ATF4/IL-10 signaling axis in macrophages, increasing IL-10 production, essential for inhibiting msi-IDD progression.2) Effective Intervention: Inhibition of SPP1 in macrophages shows potential for therapeutic intervention, significantly mitigating msi-IDD progression in mouse models.3) Mechanical Stress Insights: Highlights the critical role of mechanical stress in intervertebral disc degeneration, establishing a link between macrophage activity and IDD pathogenesis through advanced molecular profiling.

A Comparative Transcriptome and Proteome Analysis of the Molecular Mechanism Underlying Anterior to Dorsal Eye Rotation in the Celestial-Eye Goldfish (Carassius auratus).

Goldfish (Carassius auratus), subjected to millennia of artificial selection and breeding, have diversified into numerous ornamental varieties, such as the celestial-eye (CE) goldfish, noted for its unique dorsal eye rotation. Previous studies have primarily focused on anatomical modifications in CE goldfish eyes, yet the molecular underpinnings of their distinctive eye orientation remain poorly understood. This study employed high-throughput transcriptome and proteome sequencing on 110-day-old full-sibling CE goldfish, which displayed either anterior or upward eye rotations. Verification of these findings was conducted using quantitative PCR (qPCR) for transcriptomic data and parallel reaction monitoring (PRM) for proteomic analysis. Our research identified 73,685 genes and 7717 proteins, pinpointing 8 common differentially expressed genes (DEGs) and proteins (DEPs) implicated in cytoskeleton remodeling, cell adhesion, apoptosis, and optic nerve regeneration. Enrichment analyses further delineated pathways associated with apoptosis, necroptosis, and cell adhesion molecules. The results indicated a significant role for genes involved in cytoskeletal dynamics, nervous system function, and apoptotic processes in the dorsal eye rotation of CE goldfish. Analyses of abnormalities in ocular membrane structures, along with disturbances in lipid and protein synthesis metabolism and energy metabolism during developmental stages, provided compelling evidence for the potential use of CE goldfish as a model organism in studying human eye-related disorders. This investigation provided the first comprehensive transcriptomic and proteomic overview of eye rotation in CE goldfish, offering insights crucial for the genetic breeding of new ornamental fish varieties.

Transcript Changes of Placental Tissue in Gestational Diabetes Mellitus Based on Transcriptome Sequencing.

This study aims to identify key genes that may be involved in the pathogenesis of gestational diabetes mellitus and to preliminarily elucidate the underlying mechanisms. High-throughput transcriptome sequencing was employed to identify Differentially expressed genes (DEGs) in placental tissue samples of GDM and normal pregnant women. Functional and pathway analyses of these DEGs were conducted using bioinformatics databases. Significant DEGs were validated through real-time quantitative PCR in conjunction with relevant literature. In comparison to the normal pregnancy group, 435 DEGs were identified in the GDM group, comprising 128 upregulated and 307 downregulated genes. GO enrichment analysis revealed that DEGs were primarily associated with biological processes, such as cellular processes, biological regulation, regulation of biological processes, and response to stimuli. Cell component enrichment analysis indicated their association with cellular anatomical entities and protein-containing complexes. Molecular function enrichment analysis highlighted their roles in binding and catalytic activities. KEGG pathway enrichment analysis indicated the involvement of DEGs in signalling pathways related to PI3K-Akt signaling pathway and ECM-receptor interaction. qRT-PCR validation of five randomly selected DEGs confirmed consistent expression trends with RNA-Seq quantification. YWHAB, LEP, CCL21, PAPPA2, and SFN may be potential biological markers for the diagnosis of GDM, involved in the occurrence and development of GDM, and have certain value for disease prediction and diagnosis.