Transcriptome Research Articles

AMP-activated protein kinase mediates (-)-epigallocatechin-3-gallate (EGCG) to promote lipid synthesis in mastitis cows

Mastitis, a serious threat to the health and milk production function of dairy cows decreases milk quality. Blood from three healthy cows and three mastitis cows were collected in this study and their transcriptome was sequenced using the Illumina HiSeq platform. Differentially expressed genes (DEGs) were screened according to the |log2FoldChange| > 1 and P-value < 0.05 criteria. Pathway enrichment and functional annotation were performed through KEGG and GO analyses. Finally, the mechanism of the AMP-activated protein kinase (AMPK) mediation of (-)-epigallocatechin-3-gallate (EGCG) to promote lipid metabolism in mastitis cows was analyzed in bovine mammary epithelial cells (BMECs). Transcriptome analysis revealed a total of 825 DEGs, with 474 genes showing increased expression and 351 genes showing decreased expression. The KEGG analysis of DEGs revealed that they were mainly linked to tumour necrosis factor, nuclear factor-κB signalling pathway, and lipid metabolism-related signalling pathway, whereas GO functional annotation found that DEGs were enriched in threonine and methionine kinase activity, cellular metabolic processes, and cytoplasm. AMPK expression, which is involved in several lipid metabolism pathways, was downregulated in mastitis cows. The results of in vitro experiments showed that the inhibition of AMPK promoted the expression of lipid synthesis genes in lipopolysaccharide-induced BMECs and that EGCG could promote lipid synthesis by decreasing the expression of AMPK and downregulating the expression of inflammatory factors in inflammatory BMECs. In conclusion, our study demonstrated that AMPK mediated EGCG to inhabit of inflammatory responses and promote of lipid synthesis in inflammatory BMECs.

Joint Genomic and Transcriptomic Analysis Reveals Candidate Genes Associated with Plumage Color Traits in Matahu Ducks

Plumage color is a key trait for identifying waterfowl breeds with significant economic importance. A white-feathered group has recently emerged within the native Matahu duck population, presenting an opportunity for breeding new lines. However, the genetic basis for this plumage variation is still unknown, necessitating further research. This study aims to identify the genetic mechanisms underlying the emergence of white-feathered individuals in the Matahu duck population through combined genome and transcriptome analysis, providing insights for selective breeding and the development of new white-feathered lines. In this study, a total of 1344 selected genes and 1406 significantly differentially expressed genes were identified through selection signal analysis and transcriptomic analysis, respectively. The functional enrichment of these genes revealed several key signaling pathways, including those related to cGMP-PKG, cAMP, PI3K-Akt, and MAPK. Furthermore, important candidate genes involved in melanin biosynthesis, such as MITF, MC1R, TYR, TYRP1, and ABCB6, were identified. Notably, 107 genes were detected by both methods, and, among these, DGKI, GPRC5B, HMX1, STS, ADGRA1, PRKAR2B, and HOXB9 are suggested to play a role in melanin formation and potentially influence plumage traits. Through the integrative approach combining genomic selection signals and transcriptomic analyses, we identified several candidate genes directly associated with plumage color, including MITF, TYR, TYRP1, and MC1R, along with multiple signaling pathways linked to melanin formation. We hypothesize that the expression of DGKI, GPRC5B, HMX1, STS, ADGRA1, PRKAR2B, and HOXB9, detected by both methods, may be closely related to the regulation of plumage color traits. These findings provide a foundational basis for further research aimed at elucidating the genetic mechanisms governing plumage color variation in ducks.

TRPV1 alleviates APOE4-dependent microglial antigen presentation and T cell infiltration in Alzheimer's disease

BackgroundPersistent innate and adaptive immune responses in the brain contribute to the progression of Alzheimer’s disease (AD). APOE4, the most important genetic risk factor for sporadic AD, encodes apolipoprotein E4, which by itself is a potent modulator of immune response. However, little is known about the immune hub that governs the crosstalk between the nervous and the adaptive immune systems. Transient receptor potential vanilloid type 1 (TRPV1) channel is a ligand-gated, nonselective cation channel with Ca2+ permeability, which has been proposed as a neuroprotective target in AD.MethodsUsing Ca2+-sensitive dyes, dynamic changes of Ca2+ in microglia were measured, including exogenous Ca2+ uptake and endoplasmic reticulum Ca2+ release. The mRFP-GFP-tagged LC3 plasmid was expressed in microglia to characterize the role of TRPV1 in the autophagic flux. Transcriptomic analyses and flow cytometry were performed to investigate the effects of APOE4 on brain microglia and T cells from APOE-targeted replacement mice with microglia-specific TRPV1 gene deficiency.ResultsBoth APOE4 microglia derived from induced pluripotent stem cells of AD patients and APOE4-related tauopathy mouse model showed significantly increased cholesterol biosynthesis and accumulation compared to their APOE3 counterparts. Further, cholesterol dysregulation was associated with persistent activation of microglia and elevation of major histocompatibility complex II-dependent antigen presentation in microglia, subsequently accompanied by T cell infiltration. In addition, TRPV1-mediated transient Ca2+ influx mitigated cholesterol biosynthesis in microglia by suppressing the transcriptional activation of sterol regulatory element-binding protein 2, promoted autophagic activity and reduced lysosomal cholesterol accumulation, which were sufficient to resolve excessive immune response and neurodegeneration in APOE4-related tauopathy mouse model. Moreover, microglia-specific deficiency of TRPV1 gene accelerated glial inflammation, T cell response and associated neurodegeneration in an APOE4-related tauopathy mouse model.ConclusionsThe findings provide new perspectives for the treatment of APOE4-dependent neurodegeneration including AD.

The mitochondrial enzyme pyruvate carboxylase restricts pancreatic β-cell senescence by blocking p53 activation.

Defective glucose-stimulated insulin secretion (GSIS) and β-cell senescence are hallmarks in diabetes. The mitochondrial enzyme pyruvate carboxylase (PC) has been shown to promote GSIS and β-cell proliferation in the clonal β-cell lines, yet its physiological relevance remains unknown. Here, we provide animal and human data showing a role of PC in protecting β-cells against senescence and maintaining GSIS under different physiological and pathological conditions. β-cell-specific deletion of PC impaired GSIS and induced β-cell senescence in the mouse models under either a standard chow diet or prolonged high-fat diet feeding. Transcriptomic analysis indicated that p53-related senescence and cell cycle arrest are activated in PC-deficient islets. Overexpression of PC inhibited hyperglycemia- and aging-induced p53-related senescence in human and mouse islets as well as INS-1E β-cells, whereas knockdown of PC provoked senescence. Mechanistically, PC interacted with MDM2 to prevent its degradation via the MDM2 binding motif, which in turn restricts the p53-dependent senescent program in β-cells. On the contrary, the regulatory effects of PC on GSIS and the tricarboxylic acid (TCA) anaplerotic flux are p53-independent. We illuminate a function of PC in controlling β-cell senescence through the MDM2-p53 axis.

Comparative analysis of human and mouse transcriptomes during skin wound healing

Skin wound healing is a complex process which involves multiple molecular events and the underlying mechanism is not fully understood. We presented a comparative transcriptomic analysis of skin wound healing in humans and mice to identify shared molecular mechanisms across species. We analyzed transcriptomes from three distinct stages of the healing process and constructed protein-protein interaction networks to elucidate commonalities in the healing process. A substantial number of differentially expressed genes (DEGs) were identified in human transcriptomes, particularly upregulated genes before and after wound injury, and enriched in processes related to extracellular matrix organization and leukocyte migration. Similarly, the mouse transcriptome revealed thousands of DEGs, with shared biological processes and enriched KEGG pathways, highlighting a conserved molecular signature in skin wound healing. A total of 21 common DEGs were found across human comparisons, and 591 in mouse comparisons, with four genes (KRT2, MARCKSL1, MMP1, and TNC) consistently differentially expressed in both species, suggesting critical roles in mammalian skin wound healing. The expression trends of these genes were consistent, indicating their potential as therapeutic targets. The molecular network analysis identified five subnetworks associated with collagen synthesis, immunity, cell-cell adhesion, and extracellular matrix, with hub genes such as COL4A1, TLR7, TJP3, MMP13, and HIF1A exhibited significant expression changes before and after wound injury in humans and mice. In conclusion, our study provided a detailed molecular network for understanding the healing process in humans and mice, revealing conserved mechanisms that could help the development of targeted therapies across species.

Full-length transcriptome characterization and analysis of Carrizo Citrange and molecular insights into pathogen defense.

Citrus huanglongbing (HLB) is a major challenge that impacts the flourishing of the citrus industry. Therefore, analyzing the genomic information of HLB-resistant or tolerant citrus resources is crucial for breeding HLB-resistant citrus varieties. The Carrizo citrange, a hybrid of Citrus sinensis and Poncirus trifoliata, plays a pivotal role in citrus cultivation. However, its genetic explorations are difficult due to the absence of a reference genome or full-length transcriptome. In order to enhance our understanding of the genetic information of citrange, we conducted a full-length transcriptomic sequencing of multiple tissues from the Carrizo citrange using the PacBio Sequel II platform. Moreover, we performed gene ontology (GO) annotation, gene functional annotation, simple sequence repeats (SSR) types analysis, as well as identification of lncRNAs, alternative splicing events, and analysis of pathogen defense-related genes. Results showed that a total of 43,452 isoforms were generated, with 43,307 of them being annotated. GO annotation indicated the involvement of these isoforms in various biological processes, cellular components, and molecular functions. The coding sequence length of the isoforms ranged from 1,000 to 4,000 base pairs (bp). Moreover, we have discovered 54 varieties of transcription factors and regulators, along with 16 classifications of genes associated with resistance. Among all types of SSRs, trimer type SSRs were the most abundant. 130 lncRNAs were predicted to be highly reliable in the isoforms of the Carrizo citrange, with alternative splicing events identified, and the most frequent being retained intron. The analysis of gene family expansion and contraction revealed a significant increase in pathogen defense-related genes within the Carrizo citrange. The results of this study will be of great value for future investigations into gene function in citrange and for expanding the genetic pool for breeding citrus varieties resistant or tolerant to HLB.

Evolutionary divergent clusters of transcribed extinct truncated retroposons drive low mRNA expression and developmental regulation in the protozoan Leishmania

BackgroundThe Leishmania genome harbors formerly active short interspersed degenerated retroposons (SIDERs) representing the largest family of repetitive elements among trypanosomatids. Their substantial expansion in Leishmania is a strong predictor of important biological functions. In this study, we combined multilevel bioinformatic predictions with high-throughput genomic and transcriptomic analyses to gain novel insights into the diversified roles retroposons of the SIDER2 subfamily play in Leishmania genome evolution and expression.ResultsWe show that SIDER2 retroposons form various evolutionary divergent clusters, each harboring homologous SIDER2 sequences usually located nearby in the linear sequence of chromosomes. This intriguing genomic organization underscores the importance of SIDER2 proximity in shaping chromosome dynamics and co-regulation. Accordingly, we show that transcripts belonging to the same SIDER2 cluster can display similar levels of expression. SIDER2 retroposons are mostly transcribed as part of 3'UTRs and account for 13% of the Leishmania transcriptome. Genome-wide expression profiling studies underscore SIDER2 association generally with low mRNA expression. The remarkable link of SIDER2 retroposons with downregulation of gene expression supports their co-option as major regulators of mRNA abundance. SIDER2 sequences also add to the diversification of the Leishmania gene expression repertoire since ~ 35% of SIDER2-containing transcripts can be differentially regulated throughout the parasite development, with a few encoding key virulence factors. In addition, we provide evidence for a functional bias of SIDER2-containing transcripts with protein kinase and transmembrane transporter activities being most represented.ConclusionsAltogether, these findings provide important conceptual advances into evolutionary innovations of transcribed extinct retroposons acting as major RNA cis-regulators.

Spatial pattern and differential expression analysis with spatial transcriptomic data.

The emergence of spatial transcriptomic technologies has opened new avenues for investigating gene activities while preserving the spatial context of tissues. Utilizing data generated by such technologies, the identification of spatially variable (SV) genes is an essential step in exploring tissue landscapes and biological processes. Particularly in typical experimental designs, such as case-control or longitudinal studies, identifying SV genes between groups is crucial for discovering significant biomarkers or developing targeted therapies for diseases. However, current methods available for analyzing spatial transcriptomic data are still in their infancy, and none of the existing methods are capable of identifying SV genes between groups. To overcome this challenge, we developed SPADE for spatial pattern and differential expression analysis to identify SV genes in spatial transcriptomic data. SPADE is based on a machine learning model of Gaussian process regression with a gene-specific Gaussian kernel, enabling the detection of SV genes both within and between groups. Through benchmarking against existing methods in extensive simulations and real data analyses, we demonstrated the preferred performance of SPADE in detecting SV genes within and between groups. The SPADE source code and documentation are publicly available at https://github.com/thecailab/SPADE.

Interleukin-22 inhibits right ventricular remodelling by a unique mechanism in a pulmonary artery constriction model

Abstract Background Fibrosis and remodeling of right ventricle (RV) are associated with prognosis in patients with RV failure. Interleukin-22 (IL-22) is a member of the IL-10 cytokine family, play roles in tissue protection and wound repair. We have previously shown that IL-22 plays an important role in cardiac remodeling after acute myocardial infarction; however, the role of IL-22 in RV fibrosis and remodeling remains elusive. Purpose We investigated the role of IL-22 in the pathogenesis of RV remodeling during pressure overload. Methods Pulmonary artery banding (PAB) is performed by placing a 6-0 suture around the pulmonary artery over a 24 G needle in wild type mice (C57BL/6J) and IL-22 knockout mice (IL-22 KO). Only mice with moderate pulmonary artery stenosis (peak pressure gradient across the pulmonary band: 25–40 mmHg at 1 week after surgery by echo Doppler) were included in the study protocol. Four weeks after PAB, RV function was measured by echocardiography and real-time PCR analysis was performed to measure Col1a1, Col3a1, BNP, and transcriptome analysis was performed. Survival confirmation of mice with moderate pulmonary artery stenosis was also performed up to 56 days. Results IL-22 KO mice had significantly higher 56-day mortality rate compared with WT mice after PAC (p&amp;lt;0.01). Four weeks after PAB, IL-22 KO mice showed markedly increased RV weight (IL-22 KO mice vs. wild-type mice; RV/LV+IVS: 0.48±0.05 vs 0.40±0.02, P=0.002). IL-22 KO mice exhibited significant RV enlargement and RV dysfunction 4 weeks after PAB. (IL-22 KO mice vs wild type mice; RVEDV: 10±2.3mm2 vs 12.9±3.1mm2, P=0.005, TAPSE: 10.8±1.8mm vs 9.5±1.7mm, P=0.04, FAC: 35.2±7.8% vs 23±6.0%, P&amp;lt;0.001). The expressions of Col1a1 and Col3a1 were no difference between in IL22-KO mice and Wild mice. However, BNP, a cardioprotective marker, tended to be lower in IL-22KO mice. The transcriptome analysis also showed that the group of fibrosis-related genes that are elevated in PAC in WT mice were less elevated in IL-22 KO mice. Conclusion These results suggest that IL-22 is involved in RV remodelling during RV pressure loading without a general mechanism.

Transcriptomic analysis of cellular senescence induced by ectopic expression of ATF6α in human breast cancer cells.

The transcriptomic profile of cellular senescence is strongly associated with distinct cell types, the specific stressors triggering senescence, and temporal progression through senescence stages. This implies the potential necessity of conducting separate investigations for each cell type and a stressor inducing senescence. To elucidate the molecular mechanism that drives endoplasmic reticulum (ER) stress-induced cellular senescence in MCF-7 breast cancer cells, with a particular emphasis on the ATF6α branch of the unfolded protein response. We conducted transcriptomic analysis on MCF-7 cells by ectopic expression of ATF6α. Transcriptomic sequencing was conducted on MCF-7 cells at 6 and 9 hours post senescence induction through ATF6α ectopic expression. Comprehensive analyses encompassing enriched functional annotation, canonical pathway analysis, gene network analysis, upstream regulator analysis and gene set enrichment analysis were performed on Differentially Expressed Genes (DEGs) at 6 and 9 hours as well as time-related DEGs. Regulators and their targets identified from the upstream regulator analysis were validated through RNA interference, and their impact on cellular senescence was assessed by senescence-associated β-galactosidase staining. ATF6α ectopic expression resulted in the identification of 12 and 79 DEGs at 6 and 9 hours, respectively, employing criteria of a false discovery rate < 0.05 and a lower fold change (FC) cutoff |log2FC| > 1. Various analyses highlighted the involvement of the UPR and/or ER Stress Pathway. Upstream regulator analysis of 9 hour-DEGs identified six regulators and eleven target genes associated with processes related to cytostasis and 'cell viability and cell death of connective tissue cells.' Validation confirmed the significance of MAP2K1/2, GPAT4, and PDGF-BB among the regulators and DDIT3, PPP1R15A, and IL6 among the targets. Transcriptomic analyses and validation reveal the importance of the MAP2K1/2/GPAT4-DDIT3 pathway in driving cellular senescence following ATF6α ectopic expression in MCF-7 cells. This study contributes to our understanding of the initial molecular events underlying ER stress-induced cellular senescence in breast cancer cells, providing a foundation for exploring cell type- and stressor-specific responses in cellular senescence induction.

Integrated plasma proteomics and myocardial tissue transcriptomics reveal elevated fibrosis markers in arrhythmogenic cardiomyopathy patients

Abstract Background Arrhythmogenic cardiomyopathy (ACM) is characterized by myocardial fibrofatty replacement and ventricular arrhythmias, with potential progression to heart failure. This study aims to identify ACM-specific biomarkers for improved prognosis and possible treatment strategies. Methods RNA sequencing and transcriptome analyses were performed in cardiomyocytes of 10 ACM patients, 10 dilated cardiomyopathy patients and 10 healthy controls. Analyses were performed using liquid chromatography and mass spectrometry. Additionally, plasma protein expression was assessed in 38 ACM patients and 24 healthy controls using the Proximity Extension Assay (Olink®). A standardized bicycle exercise test was performed in 11 ACM patients and controls and blood was obtained before and after exercise. Results Myocardial tissue transcriptomics identified several upregulated molecules associated with extracellular matrix formation and immune response in ACM. Plasma protein sequencing revealed upregulation of proteins involved in metabolic pathways, inflammation, and fibrosis. Integration of these analyses identified key soluble profibrotic markers such as Fibulin-3, Endostatin and C-X-C motif chemokine 10 (CXCL10) in plasma of ACM patients. After exercise, Fibulin-3 levels increased in ACM patients compared to controls. These findings were further validated using enzyme-linked immunosorbent assay (ELISA). Conclusion This comprehensive analysis revealed distinct proteomic and transcriptomic signatures in ACM patients' plasma and cardiomyocytes. The integrative analysis identified several upregulated profibrotic markers in ACM. Our Findings may advance diagnostic and prognostic strategies and offer potential therapeutic targets.

Genetics of Some Wool Traits in Sheep: A Review

Greasy fleece yield, staple length and fibre diameter are complex quantitative traits influenced by various genetic and environmental factors. Among non-genetic factors year of birth, gender of lamb, centre of rearing, parity and type of birth are known to influence wool traits in different sheep genetic resources. To develop effective breeding objectives and accurately evaluate genetic potential, more precise analysis of genetic parameters and correlations between growth traits is essential. However, inconsistent results were observed across breeds and studies, highlighting the need for breed-specific optimization strategies. Greasy fleece yield, fibre diameter and staple length are critical determinants of wool quality and quantity. Wool traits are moderately (20–50%) to highly heritable (≥50%), so improving quality and quantity of a wool clip can happen even after one generation. The significant variations observed among breeds underscore the need for breed-specific optimization strategies. By integrating genetic and environmental factors, sheep breeders and producers can develop effective breeding programs, improve wool production, and enhance profitability. Wool traits are moderately to highly heritable, however, very low and very high estimates have also been reported in different sheep genetic resources. The heritability estimates correspond to the genetic variation in a trait. Gene mapping has identified chromosomal regions influencing fibre quality and production, enabling more efficient selection of superior wool production. Recent studies have employed various techniques to investigate the impact of fibre-related genes, including the candidate gene approach, transcriptome analysis and genome-wide association studies. It is concluded that wool traits being quantitative in nature are governed by different genes and are influenced by genetic and different environmental factors.

Somatic DICER1-Mutant Benign Thyroid Nodules in Adults: A Group of Follicular Nodular Disease With Continuous Growth.

Germline DICER1 mutations cause familial multinodular goiter (MNG). However, the prevalence of somatic DICER1 mutations in non-MNG benign thyroid nodules and their characteristics remain unknown. Adult-onset thyroid nodules with a pathological diagnosis were genotyped via targeted sequencing. DICER1-mutant nodules were assessed clinically and pathologically. Organoids were established to investigate follicular formation and growth. Transcriptomic analysis was conducted to evaluate transcriptional features, which were validated by immunofluorescence. Among 931 adult-onset thyroid nodules, we identified 13 benign thyroid nodules with DICER1 hotspot mutations. The majority harbored a somatic DICER1 hotspot mutation with a somatic DICER1 truncating variant. Clinically, 38.5% of the DICER1-mutant nodules exhibited substantial growth. DICER1-mutant nodules with durations longer than 2 years were substantially enlarged (P=.0448). Pathologically, all DICER1-mutant nodules were defined as thyroid follicular nodular disease (TFND). The TFND nodules with DICER1 mutations grew faster than those with wild-type DICER1. Organoid culture of a DICER1-mutant nodule revealed increased active follicular formation. Compared with the normal thyroid tissues, the DICER1-mutant nodules had comparable thyroid differentiation scores, significantly higher ERK scores (P=.0141) and lower epithelial‒mesenchymal transition scores (P=.0001). Moreover, the expression of genes related to follicular polarity, such as CDH16, SLC5A5, TSHR and TPO, was downregulated in the DICER1-mutant nodules. Somatic DICER1 two-hit mutations represent a notable percentage in adult TFND patients, and DICER1-mutant benign thyroid nodules were characterized by continuous growth.

PI 3-kinase/AKT/FOXO1 signaling in smooth muscle cells protects against abdominal aortic aneurysm

Abstract Background Abdominal aortic aneurysms (AAA) are characterized by loss of vascular smooth muscle cells (SMCs). Growth factors induce proliferation and cell survival of SMCs. PI 3-kinase (PI3K) is an important downstream mediator in growth factor signaling. Objective This project is based on the hypothesis that PI3K-mediated SMC proliferation can compensate for the loss of SMCs in AAA and thus inhibit AAA progression. Therefore, we determined effects of reduced PI3K activity in SMCs on AAA progression, cell proliferation as well as vascular remodeling. Methods To investigate the role of PI3K, we analyzed mice and aortic SMCs harboring a smooth muscle-specific deficiency of the PI3K catalytic subunit p110α (SM-p110α-/-). AAA development in SM-p110α-/- mice and wild-type (WT) littermates was induced by perfusion of the infrarenal aortic segment with porcine pancreatic elastase (PPE). AAA diameter was determined by echocardiography. Structural changes in the aorta were identified by (immuno)histochemical staining. SMC proliferation was measured in vitro by BrdU incorporation or real-time cell analysis. p110α induced signal transduction pathways were characterized by Western blot and transcriptome analysis. Results PPE treatment led to a massive loss of SMCs in the compromised aortic segment after 3 days in both SM-p110α-/- and WT mice. The aortic diameter was enlarged after 28 days in all PPE-treated mice. However, the increase was significantly higher in SM-p110α-/- mice (70.2±10.8%, n=9) compared to WT animals (42.4±6.0%, n=10) (p&amp;lt;0.05). A similar effect was obtained in aged (untreated) mice: In 24-month-old SM-p110α-/- mice, abdominal aortic lumen diameter was increased by 42% compared to 3-month-old animals, but only by 15% in corresponding WT mice. PPE-treated SM-p110α-/- mice were characterized by reduced vascular remodeling with less PCNA-positive proliferating cells compared to WT animals. In addition, proliferation of aortic p110α-/- SMCs in serum-containing medium was impaired. Mechanistic analyses showed that PDGF- and insulin-induced activation of AKT as well as AKT-dependent phosphorylation and inactivation of the transcription factors FOXO-1, -3 and -4 were significantly reduced in p110α-/- SMCs compared to WT cells. Further analyses revealed that specific inhibition of FOXO1 by AS1842856 rescued PDGF or serum stimulated proliferation of p110α-/- SMCs. In addition, expression analysis of FOXOs in patients revealed significantly increased FOXO1 expression in AAA compared to aortic samples from healthy individuals. Conclusion Deficiency of the catalytic PI3K isoform p110α in SMCs promotes the development and progression of AAA. p110α/AKT-dependent inactivation of FOXO1 induces SMC proliferation, which can ameliorate aortic wall damage. As FOXO1 inhibitors and a recently developed p110α activator are available, the PI3K/AKT/FOXO1 signaling cascade may provide a therapeutic target to influence the stability of the aortic wall in AAA.

Metabolome and Transcriptome Analyses Reveal Metabolomic Variations and Key Transcription Factors Involved in Lipid Biosynthesis During Seed Development in Carya illinoinensis

Plant oils are a large group of neutral lipids that play a vital role in the food and oleochemical industries. The pecan (Carya illinoinensis) is a promising woody oil crop known for its high-quality sources of essential fatty acids and various bioactive compounds that may aid in preventing heart diseases. However, there is still a lack of understanding regarding the accumulation of lipids and the molecular mechanism of lipid biosynthesis during seed development. This study aims to analyze the metabolite variations and molecular mechanisms of lipid biosynthesis by integrating untargeted metabolomics and transcriptomics during pecan seed development. A total of 293 differentially accumulated metabolites were identified and further categorized into 13 groups, with lipids and lipid-like molecules constituting the largest group. The oil content and fatty acid compositions of pecan embryos were assessed at three stages of seed development. Oleic acid (c18:1) and linoleic acid (c18:2n6) were found to be the most abundant unsaturated fatty acid components in pecan embryos. Additionally, a comprehensive analysis revealed 15,990 differentially expressed genes, with a focus on the key genes related to lipid metabolism. Furthermore, the study identified 1201 transcription factors from differentially expressed genes. These transcription factors were divided into 65 families, with different members in the same family exhibiting different expression patterns during seed development. The expression patterns of ten transcription factor genes during seed development were verified by qRT–PCR. Two key genes, CiABI3 and CiFUS3 were further cloned and found to be localized in the nucleus. This study used metabolome and transcriptome analysis during key periods of pecan seed development to identify the key genes associated with seed development and fatty acid biosynthesis.

CYP19A1 regulates chemoresistance in colorectal cancer through modulation of estrogen biosynthesis and mitochondrial function

Chemoresistance remains a major challenge in the effective treatment of colorectal cancer (CRC), contributing to poor patient outcomes. While the molecular mechanisms underlying chemoresistance are complex and multifaceted, emerging evidence suggests that altered mitochondrial function and hormone signaling play crucial roles. In this study, we investigated the role of CYP19A1, a key enzyme in estrogen biosynthesis, in regulating chemoresistance in CRC. Using a combination of in vitro functional assays, transcriptomic analysis, and clinical data mining, we demonstrate that CYP19A1 expression is significantly upregulated in CRC cells and patient-derived samples compared to normal controls. Mechanistically, we found that CYP19A1 regulates chemoresistance through modulation of mitochondrial function and complex I activity, which is mediated by CYP19A1-dependent estrogen biosynthesis. Notably, targeted inhibition of CYP19A1 and complex I using specific inhibitors effectively reversed the chemoresistance of CRC cells to chemotherapeutic drugs. Moreover, analysis of the TCGA CRC dataset revealed that high CYP19A1 expression correlates with poor overall survival in chemotherapy-treated patients. Taken together, our findings uncover a novel role for CYP19A1 in regulating chemoresistance in CRC through modulation of mitochondrial function and estrogen signaling, and highlight the potential of targeting the CYP19A1/estrogen/complex I axis as a therapeutic strategy to overcome chemoresistance and improve patient outcomes.

HECT domain containing-3 (HECTD3) E3 ubiquitin ligase attenuates cardiac ischemia and hypertrophy in mice

Abstract HECT domain containing 3 (HECTD3) is one of the E3 ubiquitin ligases, the cardiac function of which is not completely understood yet. We aimed here to understand the role of HECTD3 in cardiomyocytes using loss- and gain-of-function approaches in in vitro and in vivo models. Interestingly, we found that HECTD3 was significantly downregulated in cardiac tissue obtained from human patients suffering from cardiac hypertrophy and ischemia. We thus employed loss- and gain-of-function approaches in neonatal rat cardiomyocytes (NRVCMs) to get further insights into potential cardiac function of HECTD3. Overexpression of HECTD3 in NRVCMs attenuated cardiomyocyte hypertrophy and lipopolysaccharide (LPS) or interferon-γ (IFN- γ) induced cellular inflammation; its knockdown on the other hand aggravated these effects. Mechanistically, using Yeast two-hybrid screen, mass-spectrometry, and transcriptomics analyses, we identified Small Ubiquitin like Modifier 2 (SUMO2) Signal Transducer and Activator of Transcription-1 (STAT1) as novel substrates for HECTD3, regulation of which resulted into attenuation of hypertrophy and inflammation, respectively. To translate these in vitro results in vivo, we employed Adeno-associated virus-9 (AAV-9) mediated gene therapy approach to overexpress HECTD3 specifically in the heart of mouse models of cardiac ischemia due to permanent ligation of the left anterior descending artery (LAD), and cardiac hypertrophy due to transverse aortic constriction (TAC). Overexpression of HECTD3 in mice, though moderate but significantly improved cardiac function upon ischemic or hypertrophic stress compared to respective control groups. Importantly, in vitro findings were consistent in vivo, where AAV-9 mediated overexpression of HECTD3 substantially reduced cardiac hypertrophy and fibrosis, improved cardiac function as assessed by echocardiography, inhibited activation of STAT1-mediated downstream signaling, and attenuated infiltration of inflammatory cells to the heart after TAC or LAD ligation. This data indicates that HECTD3 is a novel modulator of cardiac ischemia, hypertrophy, and inflammation via regulation of SUMO2 and STAT1-signaling. In conclusion, we report here a novel cardioprotective mechanism involving the E3 ubiquitin ligase HECTD3, which exerts anti-hypertrophic and anti-inflammatory effects via dual regulation of SUMO2 and its SUMOylating target STAT1. We believe that this "dual pathway" inhibition exhibits translational importance and could further be exploited for the prevention and/or therapy of heart failure due to cardiac ischemia or hypertrophy.

Landscape transcriptomic analysis of bovine follicular cells during key phases of ovarian follicular development

BackgroundThere are many gaps in our understanding of the mechanisms involved in ovarian follicular development in cattle, particularly regarding follicular deviation, acquisition of ovulatory capacity, and preovulatory changes. Molecular evaluations of ovarian follicular cells during follicular development in cattle, especially serial transcriptomic analyses across key growth phases, have not been reported. This study aims to address this gap by analyzing gene expression using RNA-seq in granulosa and antral cells recovered from ovarian follicular fluid during critical phases of ovarian follicular development in Holstein cows.ResultsIntegrated analysis of gene ontology (GO), gene set enrichment (GSEA), protein–protein interaction (PPI), and gene topology identified that differentially expressed genes (DEGs) in the largest ovarian follicles at deviation (Dev) were primarily involved in FSH-negative feedback, steroidogenesis, cell proliferation, apoptosis, and the prevention of early follicle rupture. In contrast, DEGs in the second largest follicles (DevF2) were mainly related to loss of cell viability, apoptosis, and immune cell invasion. In the dominant (PostDev) and preovulatory (PreOv) follicles, DEGs were associated with vascular changes and inflammatory responses.ConclusionsThe transcriptome of ovarian follicular fluid cells had a predominance of granulosa cells in the dominant follicle at deviation, with upregulation of genes involved in cell viability, steroidogenesis, and apoptosis prevention, whereas in the non-selected follicle there was upregulation of cell death-related transcripts. Immune cell transcripts increased significantly after deviation, particularly in preovulatory follicles, indicating strong intrafollicular chemotactic activity. We inferred that immune cell invasion occurred despite an intact basal lamina, contributing to follicular maturation.Graphical

Conditional over-expression of heme-oxygenase 1 in myelomonocytic cells reduces AngII-induced hypertension and vascular inflammation in mice

Abstract Background Systemic arterial Hypertension is one of the most important risk factor responsible for morbidity and mortality world-wide. Angiotensin II (Ang II), a potent vasoconstrictor and key player in the renin-angiotensin-aldosterone system (RAAS) is responsible for vascular dysfunction, inflammation, and tissue damage. Heme oxygenase-1 (HO-1) overexpression may confer antioxidant and anti-inflammatory properties in Ang II-induced hypertension through its action on heme catabolism, generating carbon monoxide (CO), ferritin and biliverdin/bilirubin by the action of biliverdin reductase A (BLVRA). Methods and results Male 9–12-weeks-old HO-1indxLySMCre/wt and LySMCre/wt mice were infused with AngII (1mgAngII/Day/Kg) for 7 days to induce hypertension and compared to sham treatment. Blood pressure monitoring by tail-cuff method, and endothelium-dependent vasodilator studies via organ chamber system using acetylcholine (ACh) in isolated aortic segments (~4 mm), revealed that overexpression of HO-1 in myeloid cells resulted in decreased systolic blood pressure and improved endothelial function in AngII-infused HO-1indxLySMCre/wt mice compared to controls. Concurrently, increased BLVRA expression in liver tissue and elevated plasma bilirubin levels were detected by transcriptome analysis and high-performance liquid chromatography, respectively. These results were supported by a reduction in the expression of inducible cytokines and cell adhesion molecules (CAMs) in the aorta, assessed using qPCR. Bone marrow transplant experiments demonstrated that bone marrow from LysMcre mice in HO-1indxLySMCre/wt mice abrogated the protective effect of HO-1, resulting in endothelial damage and increased blood pressure, potentially due to decreased liver BLVRA expression and the accumulation of bone marrow-derived cells in the vessel wall in response to AngII. Additionally, adeno-associated viral vector (AAV) transfection targeting specifically BLVRA activity in liver lead to an increase in blood pressure values and worse endothelium relaxation, in parallel with higher oxidative stress and the blood neutrophils concentration, as assessed in whole blood by using oxidative burst method and blood count system respectively. Conclusion The overexpression of HO-1 in myeloid cells confers anti-inflammatory protection in AngII-induced arterial hypertension in mice. Myeloid cells bone marrow-derived overexpressing HO-1 regulate the differentiation and infiltration of pro-inflammatory immune cells in the vasculature. BLVRA expression and bilirubin levels downstream of HO-1 play a critical role in protecting against vascular damage by reducing leukocyte infiltration.

Investigating the role of WT1 in Brugada syndrome pathophysiology

Abstract Background Brugada syndrome (BrS) is a heritable arrhythmic disorder presumably caused by conduction slowing in the right ventricular (RV) outflow tract (RVOT). A recent genome-wide association study found an association between common variants on chromosome 11 near WT1, tagged by the SNP rs72905083, and BrS susceptibility. Purpose To study whether WT1 affects cardiac conduction and could therefore represents the underlying association of the chr11 locus with BrS susceptibility. Methods We conducted in silico analyses of omics datasets to identify the likely causal gene at the chr11 BrS locus. Next, we conducted electrophysiological studies in heterozygous young adult (4 months old) Wt1-deficient (Wt1+/-) mice and wild-type littermates to explore the effect of Wt1 on cardiac conduction. To study the potential role of Wt1 in the setting of reduced conduction reserve, we compared aged Scn5a haploinsufficient mice (Scn5a+/-;Wt1+/+, 17 months) with littermates haploinsufficient for both Wt1 and Scn5a (Scn5a+/-;Wt1+/-). Optical mapping was performed in Langendorff-perfused hearts, where conduction was further challenged by acute ajmaline administration or by pacing at the effective refractory period (ERP). Transcriptomic analyses were conducted in Wt1+/- and wild-type mice by RNAseq of PCM1-sorted cardiomyocytes. Results Analysis of omics datasets uncovered WT1 as the likely causal gene since WT1 was the closest gene to, and in fact overlapped, the BrS-associated region; promoter capture Hi-C data in human tissue showed chromatin contact between the promoter of WT1 and the associated region; and H3K27ac ChIP-seq signals (i.e. enhancer activity) of putative cardiac enhancers located within the associated region were correlated with WT1 transcript abundance across multiple tissues (Z-score = 4.32, p=1.57e-05). No differences were observed in ECG parameters or optically mapped epicardial conduction between Wt1+/- mice and wild-type littermates. However, comparison of aged Scn5a+/-;Wt1+/- and Scn5a+/-; Wt1+/+ hearts, in the setting of acute ajmaline challenge or pacing at the ERP, showed faster conduction in RV/RVOT in the presence of Wt1 haploinsufficiency (genotype effect: p=0.057 and p=0.041 for RV and RVOT epicardial conduction, respectively, during ajmaline challenge; p=0.034 for RV epicardial conduction during pacing at ERP). RNAseq of RV/RVOT cardiomyocytes revealed higher Scn5a expression in Wt1+/- vs wild-type (p=0.006). Conclusion We identified WT1 as the gene that most likely underlies the effect of the chr11 BrS susceptibility locus. Functional data revealed protective effects of reduced Wt1 expression in the setting of reduced conduction reserve. Transcriptomic data suggest that this occurs through a transcriptional effect on Scn5a expression.