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1.
J Cardiothorac Surg ; 19(1): 312, 2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38824570

ABSTRACT

OBJECTIVE: About 10% of patients after cardiopulmonary bypass (CPB) would undergo acute liver injury, which aggravated the mortality of patients. Ac2-26 has been demonstrated to ameliorate organic injury by inhibiting inflammation. The present study aims to evaluate the effect and mechanism of Ac2-26 on acute liver injury after CPB. METHODS: A total of 32 SD rats were randomized into sham, CPB, Ac, and Ac/AKT1 groups. The rats only received anesthesia, and rats in other groups received CPB. The rats in Ac/AKT1 were pre-injected with the shRNA to interfere with the expression of AKT1. The rats in CPB were injected with saline, and rats in Ac and Ac/AKT1 groups were injected with Ac2-26. After 12 h of CPB, all the rats were sacrificed and the peripheral blood and liver samples were collected to analyze. The inflammatory factors in serum and liver were detected. The liver function was tested, and the pathological injury of liver tissue was evaluated. RESULTS: Compared with the sham group, the inflammatory factors, liver function, and pathological injury were worsened after CPB. Compared with the CPB group, the Ac2-26 significantly decreased the pro-inflammatory factors and increased the anti-inflammatory factor, improved liver function, and ameliorated the pathological injury. All the therapeutic effects of Ac2-26 were notably attenuated by the shRNA of AKT1. The Ac2-26 increased the GSK3ß and eNOS, and this promotion was inhibited by the shRNA. CONCLUSION: The Ac2-26 significantly treated the liver injury, inhibited inflammation, and improved liver function. The effect of Ac2-26 on liver injury induced by CPB was partly associated with the promotion of AKT1/GSK3ß/eNOS.


Subject(s)
Cardiopulmonary Bypass , Glycogen Synthase Kinase 3 beta , Nitric Oxide Synthase Type III , Proto-Oncogene Proteins c-akt , Rats, Sprague-Dawley , Animals , Cardiopulmonary Bypass/adverse effects , Proto-Oncogene Proteins c-akt/metabolism , Glycogen Synthase Kinase 3 beta/metabolism , Rats , Nitric Oxide Synthase Type III/metabolism , Male , Disease Models, Animal , Liver/pathology , Signal Transduction
2.
CNS Neurosci Ther ; 30(5): e14744, 2024 05.
Article in English | MEDLINE | ID: mdl-38727249

ABSTRACT

BACKGROUND: Stroke is an acute cerebrovascular disease in which brain tissue is damaged due to sudden obstruction of blood flow to the brain or the rupture of blood vessels in the brain, which can prompt ischemic or hemorrhagic stroke. After stroke onset, ischemia, hypoxia, infiltration of blood components into the brain parenchyma, and lysed cell fragments, among other factors, invariably increase blood-brain barrier (BBB) permeability, the inflammatory response, and brain edema. These changes lead to neuronal cell death and synaptic dysfunction, the latter of which poses a significant challenge to stroke treatment. RESULTS: Synaptic dysfunction occurs in various ways after stroke and includes the following: damage to neuronal structures, accumulation of pathologic proteins in the cell body, decreased fluidity and release of synaptic vesicles, disruption of mitochondrial transport in synapses, activation of synaptic phagocytosis by microglia/macrophages and astrocytes, and a reduction in synapse formation. CONCLUSIONS: This review summarizes the cellular and molecular mechanisms related to synapses and the protective effects of drugs or compounds and rehabilitation therapy on synapses in stroke according to recent research. Such an exploration will help to elucidate the relationship between stroke and synaptic damage and provide new insights into protecting synapses and restoring neurologic function.


Subject(s)
Stroke , Synapses , Humans , Animals , Synapses/pathology , Synapses/metabolism , Stroke/metabolism , Stroke/pathology , Stroke/complications , Stroke/physiopathology
3.
BMC Cardiovasc Disord ; 24(1): 266, 2024 May 21.
Article in English | MEDLINE | ID: mdl-38773462

ABSTRACT

BACKGROUND: Cardiopulmonary bypass (CPB) results in brain injury, which is primarily caused by inflammation. Ac2-26 protects against ischemic or hemorrhage brain injury. The present study was to explore the effect and mechanism of Ac2-26 on brain injury in CPB rats. METHODS: Forty-eight rats were randomized into sham, CPB, Ac, Ac/AKT1, Ac/GSK3ßi and Ac/AKT1/GSK3ßa groups. Rats in sham group only received anesthesia and in the other groups received standard CPB surgery. Rats in the sham and CPB groups received saline, and rats in the Ac, Ac/AKT1, Ac/GSK3ßi and Ac/AKT1/GSK3ßa groups received Ac2-26 immediately after CPB. Rats in the Ac/AKT1, Ac/GSK3ßi and Ac/AKT1/GSK3ßa groups were injected with shRNA, inhibitor and agonist of GSK3ß respectively. The neurological function score, brain edema and histological score were evaluated. The neuronal survival and hippocampal pyroptosis were assessed. The cytokines, activity of NF-κB, S100 calcium-binding protein ß(S100ß) and neuron-specific enolase (NSE), and oxidative were tested. The NLRP3, cleaved-caspase-1 and cleaved-gadermin D (GSDMD) in the brain were also detected. RESULTS: Compared to the sham group, all indicators were aggravated in rats that underwent CPB. Compared to the CPB group, Ac2-26 significantly improved neurological scores and brain edema and ameliorated pathological injury. Ac2-26 reduced the local and systemic inflammation, oxidative stress response and promoted neuronal survival. Ac2-26 reduced hippocampal pyroptosis and decreased pyroptotic proteins in brain tissue. The protection of Ac2-26 was notably lessened by shRNA and inhibitor of GSK3ß. The agonist of GSK3ß recovered the protection of Ac2-26 in presence of shRNA. CONCLUSIONS: Ac2-26 significantly improved neurological function, reduced brain injury via regulating inflammation, oxidative stress response and pyroptosis after CPB. The protective effect of Ac2-26 primarily depended on AKT1/ GSK3ß pathway.


Subject(s)
Cardiopulmonary Bypass , Disease Models, Animal , Glycogen Synthase Kinase 3 beta , Proto-Oncogene Proteins c-akt , Pyroptosis , Rats, Sprague-Dawley , Signal Transduction , Animals , Cardiopulmonary Bypass/adverse effects , Glycogen Synthase Kinase 3 beta/metabolism , Proto-Oncogene Proteins c-akt/metabolism , Pyroptosis/drug effects , Male , Neurons/drug effects , Neurons/pathology , Neurons/metabolism , Neurons/enzymology , Neuroprotective Agents/pharmacology , NLR Family, Pyrin Domain-Containing 3 Protein/metabolism , Brain Edema/prevention & control , Brain Edema/metabolism , Brain Edema/enzymology , Brain Edema/pathology , Anti-Inflammatory Agents/pharmacology , Rats , S100 Calcium Binding Protein beta Subunit/metabolism , Inflammation Mediators/metabolism
4.
Front Aging Neurosci ; 16: 1329357, 2024.
Article in English | MEDLINE | ID: mdl-38389559

ABSTRACT

Vascular dementia (VD) is a prevalent cognitive disorder among the elderly. Its pathological mechanism encompasses neuronal damage, synaptic dysfunction, vascular abnormalities, neuroinflammation, and oxidative stress, among others. In recent years, extracellular vesicles (EVs) derived from mesenchymal stem cells (MSCs) have garnered significant attention as an emerging therapeutic strategy. Current research indicates that MSC-derived extracellular vesicles (MSC-EVs) play a pivotal role in both the diagnosis and treatment of VD. Thus, this article delves into the recent advancements of MSC-EVs in VD, discussing the mechanisms by which EVs influence the pathophysiological processes of VD. These mechanisms form the theoretical foundation for their neuroprotective effect in VD treatment. Additionally, the article highlights the potential applications of EVs in VD diagnosis. In conclusion, MSC-EVs present a promising innovative treatment strategy for VD. With rigorous research and ongoing innovation, this concept can transition into practical clinical treatment, providing more effective options for VD patients.

5.
Cancer Metab ; 12(1): 7, 2024 Feb 23.
Article in English | MEDLINE | ID: mdl-38395945

ABSTRACT

BACKGROUND: Hypoxia contributes to cancer progression through various molecular mechanisms and hepatocellular carcinoma (HCC) is one of the most hypoxic malignancies. Hypoxia-inducible gene domain protein-1a (HIGD1A) is typically induced via epigenetic regulation and promotes tumor cell survival during hypoxia. However, the role of HIGD1A in HCC remains unknown. METHODS: HIGD1A expression was determined in 24 pairs of human HCC samples and para-tumorous tissues. Loss-of-function experiments were conducted both in vivo and in vitro to explore the role of HIGD1A in HCC proliferation and metastasis. RESULTS: Increased HIGD1A expression was found in HCC tissues and cell lines, which was induced by hypoxia or low-glucose condition. Moreover, HIGD1A knockdown in HCC cells arrested the cell cycle at the G2/M phase and promoted hypoxia-induced cell apoptosis, resulting in great inhibition of cell proliferation, migration, and invasion, as well as tumor xenograft formation. Interestingly, these anti-tumor effects were not observed in normal hepatocyte cell line L02. Further, HIGD1A knockdown suppressed the expression of ornithine decarboxylase 1 (ODC1), a rate-limiting enzyme of polyamine metabolism under c-Myc regulation. HIGD1A was found to bind with the c-Myc promoter region, and its knockdown decreased the levels of polyamine metabolites. Consistently, the inhibitory effect on HCC phenotype by HIGD1A silencing could be reversed by overexpression of c-Myc or supplementation of polyamines. CONCLUSIONS: Our results demonstrated that HIGD1A activated c-Myc-ODC1 nexus to regulate polyamine synthesis and to promote HCC survival and malignant phenotype, implying that HIGD1A might represent a novel therapeutic target for HCC.

6.
Infect Immun ; 92(3): e0056022, 2024 Mar 12.
Article in English | MEDLINE | ID: mdl-38363133

ABSTRACT

The Gram-negative bacterium Coxiella burnetii is the causative agent of query fever in humans and coxiellosis in livestock. C. burnetii infects a variety of cell types, tissues, and animal species including mammals and arthropods, but there is much left to be understood about the molecular mechanisms at play during infection in distinct species. Human stimulator of interferon genes (STING) induces an innate immune response through the induction of type I interferons (IFNs), and IFN promotes or suppresses C. burnetii replication, depending on tissue type. Drosophila melanogaster contains a functional STING ortholog (Sting) which activates NF-κB signaling and autophagy. Here, we sought to address the role of D. melanogaster Sting during C. burnetii infection to uncover how Sting regulates C. burnetii infection in flies. We show that Sting-null flies exhibit higher mortality and reduced induction of antimicrobial peptides following C. burnetii infection compared to control flies. Additionally, Sting-null flies induce lower levels of oxidative stress genes during infection, but the provision of N-acetyl-cysteine (NAC) in food rescues Sting-null host survival. Lastly, we find that reactive oxygen species levels during C. burnetii infection are higher in Drosophila S2 cells knocked down for Sting compared to control cells. Our results show that at the host level, NAC provides protection against C. burnetii infection in the absence of Sting, thus establishing a role for Sting in protection against oxidative stress during C. burnetii infection.


Subject(s)
Coxiella burnetii , Q Fever , Animals , Drosophila melanogaster/genetics , Drosophila melanogaster/metabolism , NF-kappa B/metabolism , Q Fever/microbiology , Reactive Oxygen Species/metabolism
7.
J Am Heart Assoc ; 13(2): e030726, 2024 Jan 16.
Article in English | MEDLINE | ID: mdl-38214249

ABSTRACT

BACKGROUND: Observational studies have suggested the potential role of inflammatory factors in the risk of coronary artery disease (CAD). We aimed to perform 2-sample Mendelian randomization (MR) analyses to assess the causal association between circulating cytokines/growth factors and CAD. METHODS AND RESULTS: The instrumental variables for 28 circulating cytokines and growth factors were identified from a genome-wide association study of 8293 European participants. Summary-level data on CAD were derived from a large genome-wide association study (71 602 cases and 260 875 controls). We used the inverse-variance-weighted and Wald ratio methods as our main MR methods. The weighted median, simple median, maximum likelihood, MR pleiotropy residual sum and outlier, and MR-Egger methods were performed as sensitivity analyses. Genetic colocalization analyses were conducted to validate the robustness of our MR findings. We found that genetically predicted circulating levels of macrophage migration inhibitory factor were associated with an increased risk of CAD at the Bonferroni-adjusted level of significance (P<1.79×10-3). The odds ratio was 1.20 (95% CI, 1.08-1.33; P=6.83×10-4) per 1-SD increase in macrophage migration inhibitory factor. Colocalization analyses supported our MR findings. Additionally, we found suggestive evidence between the genetic effects of stem cell growth factor-ß and the risk of CAD (odds ratio, 0.95 [95% CI, 0.91-0.98]; P=0.007). CONCLUSIONS: Our findings suggested a risk-increasing effect of macrophage migration inhibitory factor level on the development of CAD. The roles of these inflammatory factors for CAD warrant further investigation.


Subject(s)
Coronary Artery Disease , Macrophage Migration-Inhibitory Factors , Humans , Coronary Artery Disease/genetics , Genome-Wide Association Study , Intercellular Signaling Peptides and Proteins/genetics , Causality
8.
Int J Biol Macromol ; 256(Pt 1): 128400, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38007015

ABSTRACT

Fe/Mn bimetallic carbon materials were synthesized by combining oat and urea, followed by and carbonization processes, the activity and mechanism of the obtained materials in activating peroxymonosulfate (PMS) for sulfamethoxazole (SMX) degradation were determined. Data suggested that the obtained material (CN@FeMn-10-800) showed the optimal performance for SMX degradation under the1:8:0.05:0.05 mass ratios of oat/urea/Fe/Mn. Around 91.2 % SMX (10 mg L-1) was removed under the conditions of 0.15 g L-1 CN@FeMn-10-800 and 0.20 g L-1 PMS. The CN@FeMn-10-800 showed great adaptability under different conditions, satisfactory activation repeatability and versatility. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) demonstrated that core-shell structure with rich porous of CN@FeMn-10-800 was achieved. Quenching test and electron paramagnetic resonance (EPR) indicated that surface bound oxygen and singlet oxygen (1O2) were the dominate reactive groups in this system. X-ray photoelectron spectroscopy (XPS) suggested that graphite N, Fe0, Fe3C and Mn(II) were the dominant active sites. Through the work, a simple strategy could be found to make high-value use of biomass and use it to effectively purified wastewater.


Subject(s)
Carbon , Peroxides , Sulfamethoxazole , Sulfamethoxazole/chemistry , Avena , Starch , Oxygen , Urea
9.
Gene ; 898: 148118, 2024 Mar 10.
Article in English | MEDLINE | ID: mdl-38159618

ABSTRACT

FRS2 has demonstrated oncogenic roles in various malignancies, including liposarcoma and giant cell tumor of bone. However, its role in osteosarcoma remains less understood, and the upstream regulatory molecules influencing FRS2 remain unclear. This study aims to explore the clinical implications and biological function of FRS2 in osteosarcoma, and the potential regulatory microRNAs (miRNAs) governing its expression. Our study indicated significant upregulation of FRS2 in osteosarcoma cells and tissues by Western blotting and immunohistochemical staining. Elevated FRS2 expression correlated positively with increased angiogenesis and poor prognosis, possibly serving as an independent prognostic indicator for osteosarcoma patients. Functional assays revealed that attenuating FRS2 in osteosarcoma cells could mitigate proliferation, migration, and angiogenesis of vascular endothelial cells. Further investigations revealed that miR-429 and miR-206 directly targeted FRS2, exerting a negative regulation on its expression. Furthermore, FRS2 played a role in repressing osteosarcoma advancement influenced by miR-429 or miR-206. In summary, FRS2, influenced by miR-429 and miR-206, emerges as a promising therapeutic candidate for antiangiogenic osteosarcoma treatments.


Subject(s)
Bone Neoplasms , MicroRNAs , Osteosarcoma , Humans , Endothelial Cells/metabolism , Angiogenesis , Cell Line, Tumor , MicroRNAs/genetics , MicroRNAs/metabolism , Osteosarcoma/metabolism , Bone Neoplasms/metabolism , Cell Proliferation/genetics , Cell Movement/genetics , Gene Expression Regulation, Neoplastic , Membrane Proteins/genetics , Membrane Proteins/metabolism , Adaptor Proteins, Signal Transducing/genetics
10.
Bioresour Technol ; 394: 130233, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38141883

ABSTRACT

Squalene is an important triterpene with a wide range of applications. Given the growing market demand for squalene, the development of microbial cell factories capable of squalene production is considered a sustainable method. This study aimed to investigate the squalene production potential of Yarrowia lipolytica. First, HMG-CoA reductase from Saccharomyces cerevisiae and squalene synthase from Y. lipolytica was co-overexpressed in Y. lipolytica. Second, by enhancing the supply of NADPH in the squalene synthesis pathway, the production of squalene in Y. lipolytica was effectively increased. Furthermore, by constructing an isoprenol utilization pathway and overexpressing YlDGA1, the strain YLSQ9, capable of producing 868.1 mg/L squalene, was obtained. Finally, by optimizing the fermentation conditions, the highest squalene concentration of 1628.2 mg/L (81.0 mg/g DCW) in Y. lipolytica to date was achieved. This study demonstrated the potential for achieving high squalene production using Y. lipolytica.


Subject(s)
Triterpenes , Yarrowia , Squalene/metabolism , Yarrowia/genetics , Yarrowia/metabolism , Metabolic Engineering/methods , Triterpenes/metabolism , Fermentation , Saccharomyces cerevisiae/metabolism
12.
Nat Commun ; 14(1): 4965, 2023 08 16.
Article in English | MEDLINE | ID: mdl-37587100

ABSTRACT

Astrocytes are intimately linked with brain blood vessels, an essential relationship for neuronal function. However, astroglial factors driving these physical and functional associations during postnatal brain development have yet to be identified. By characterizing structural and transcriptional changes in mouse cortical astrocytes during the first two postnatal weeks, we find that high-mobility group box 1 (Hmgb1), normally upregulated with injury and involved in adult cerebrovascular repair, is highly expressed in astrocytes at birth and then decreases rapidly. Astrocyte-selective ablation of Hmgb1 at birth affects astrocyte morphology and endfoot placement, alters distribution of endfoot proteins connexin43 and aquaporin-4, induces transcriptional changes in astrocytes related to cytoskeleton remodeling, and profoundly disrupts endothelial ultrastructure. While lack of astroglial Hmgb1 does not affect the blood-brain barrier or angiogenesis postnatally, it impairs neurovascular coupling and behavior in adult mice. These findings identify astroglial Hmgb1 as an important player in postnatal gliovascular maturation.


Subject(s)
Astrocytes , Blood-Brain Barrier , HMGB1 Protein , Animals , Mice , Aquaporin 4 , Brain , Morphogenesis , HMGB1 Protein/metabolism
13.
Bio Protoc ; 13(13): e4711, 2023 Jul 05.
Article in English | MEDLINE | ID: mdl-37449041

ABSTRACT

The trachea tube is the exclusive route to allow gas exchange between the external environment and the lungs. Recent studies have shown the critical role of mesenchymal cells in tracheal tubulogenesis. Improved methods for studying the dynamics of the tracheal mesenchyme development are needed to investigate the cellular and molecular mechanisms during tracheal tubulogenesis. Here, we describe a detailed protocol for a systematic analysis of tracheal tube development to enable observing tracheal smooth muscle (SM) and cartilage ring formation. We describe immunostaining, confocal and stereomicroscopy imaging, and quantitative methods to study the process of tracheal SM and cartilage ring development, including SM cell alignment, polarization, and changes in cell shape as well as mesenchymal condensation. The technologies and approaches described here not only improve analysis of the patterning of the developing trachea but also help uncover the mechanisms underlying airway disease. This protocol also provides a useful technique to analyze cell organization, polarity, and nuclear shape in other organ systems.

14.
J Am Soc Mass Spectrom ; 34(9): 1998-2005, 2023 Sep 06.
Article in English | MEDLINE | ID: mdl-37523498

ABSTRACT

Characterization of nonpolar lipids is crucial due to their essential biological functions and ability to exist in various isomeric forms. In this study, we introduce the N-H aziridination method to target carbon-carbon double bonds (C═C bonds) in nonpolar sterol lipids. The resulting fragments are readily dissociated upon collision-induced dissociation, generating specific fragment ions for C═C bond position determination and fingerprint fragments for backbone characterization. This method significantly enhances lipid ionization efficiency, thereby improving the sensitivity and accuracy of nonpolar lipid analysis. We demonstrated that aziridination of sterols leads to distinctive fragmentation pathways for chain and ring C═C bonds, enabling the identification of sterol isomers such as desmosterol and 7-dehydrocholesterol. Furthermore, aziridination can assist in identifying the sterol backbone by providing fingerprint tandem mass spectra. We also demonstrated the quantitative capacity of this approach with a limit of detection of 10 nM in the solvent mixture of methanol and water. To test the feasibility of this method in complex biological samples, we used mouse prostate cancerous tissues and found significant differences in nonpolar lipid profiles between healthy and cancerous samples. The high efficiency and specificity of aziridination-assisted mass spectrometric analysis, as well as its quantitative analysis ability, make it highly suitable for broad applications in nonpolar lipid research.


Subject(s)
Phytosterols , Sterols , Male , Mice , Animals , Isomerism , Tandem Mass Spectrometry/methods , Carbon , Spectrometry, Mass, Electrospray Ionization/methods
15.
Pharmaceutics ; 15(5)2023 May 22.
Article in English | MEDLINE | ID: mdl-37242805

ABSTRACT

BACKGROUND: ATP-binding cassette (ABC) transporters comprise a superfamily of genes encoding membrane proteins with nucleotide-binding domains (NBD). These transporters, including drug efflux across the blood-brain barrier (BBB), carry a variety of substrates through plasma membranes against substrate gradients, fueled by hydrolyzing ATP. The expression patterns/enrichment of ABC transporter genes in brain microvessels compared to peripheral vessels and tissues are largely uncharacterized. METHODS: In this study, the expression patterns of ABC transporter genes in brain microvessels, peripheral tissues (lung, liver and spleen) and lung vessels were investigated using RNA-seq and WesTM analyses in three species: human, mouse and rat. RESULTS: The study demonstrated that ABC drug efflux transporter genes (including ABCB1, ABCG2, ABCC4 and ABCC5) were highly expressed in isolated brain microvessels in all three species studied; the expression of ABCB1, ABCG2, ABCC1, ABCC4 and ABCC5 was generally higher in rodent brain microvessels compared to those of humans. In contrast, ABCC2 and ABCC3 expression was low in brain microvessels, but high in rodent liver and lung vessels. Overall, most ABC transporters (with the exception of drug efflux transporters) were enriched in peripheral tissues compared to brain microvessels in humans, while in rodent species, additional ABC transporters were found to be enriched in brain microvessels. CONCLUSIONS: This study furthers the understanding of species similarities and differences in the expression patterns of ABC transporter genes; this is important for translational studies in drug development. In particular, CNS drug delivery and toxicity may vary among species depending on their unique profiles of ABC transporter expression in brain microvessels and BBB.

16.
Fluids Barriers CNS ; 20(1): 36, 2023 May 26.
Article in English | MEDLINE | ID: mdl-37237379

ABSTRACT

Blood brain barrier (BBB) models in vitro are an important tool to aid in the pre-clinical evaluation and selection of BBB-crossing therapeutics. Stem cell derived BBB models have recently demonstrated a substantial advantage over primary and immortalized brain endothelial cells (BECs) for BBB modeling. Coupled with recent discoveries highlighting significant species differences in the expression and function of key BBB transporters, the field is in need of robust, species-specific BBB models for improved translational predictability. We have developed a mouse BBB model, composed of mouse embryonic stem cell (mESC-D3)-derived brain endothelial-like cells (mBECs), employing a directed monolayer differentiation strategy. Although the mBECs showed a mixed endothelial-epithelial phenotype, they exhibited high transendothelial electrical resistance, inducible by retinoic acid treatment up to 400 Ω cm2. This tight cell barrier resulted in restricted sodium fluorescein permeability (1.7 × 10-5 cm/min), significantly lower than that of bEnd.3 cells (1.02 × 10-3 cm/min) and comparable to human induced pluripotent stem cell (iPSC)-derived BECs (2.0 × 10-5 cm/min). The mBECs expressed tight junction proteins, polarized and functional P-gp efflux transporter and receptor mediated transcytosis (RMT) receptors; collectively important criteria for studying barrier regulation and drug delivery applications in the CNS. In this study, we compared transport of a panel of antibodies binding species selective or cross-reactive epitopes on BBB RMT receptors in both the mBEC and human iPSC-derived BEC model, to demonstrate discrimination of species-specific BBB transport mechanisms.


Subject(s)
Blood-Brain Barrier , Induced Pluripotent Stem Cells , Humans , Animals , Mice , Blood-Brain Barrier/metabolism , Endothelial Cells/metabolism , Mouse Embryonic Stem Cells/metabolism , Induced Pluripotent Stem Cells/physiology , Antibodies/metabolism , Transcytosis
17.
Methods Mol Biol ; 2659: 119-135, 2023.
Article in English | MEDLINE | ID: mdl-37249890

ABSTRACT

In RNA-seq data processing, short reads are usually aligned from one species against its own genome sequence; however, in plant-pathogen interaction systems, reads from both host and pathogen samples are blended together. In contrast with single-genome analyses, both pathogen and host reference genomes are involved in the alignment process. In such circumstances, the order in which the alignment is carried out, whether the host or pathogen is aligned first, or if both genomes are aligned simultaneously, influences the read counts of certain genes. This is a problem, especially at advanced infection stages. It is crucial to have an appropriate strategy for aligning the reads to their respective genomes, yet the existing strategies of either sequential or parallel alignment become problematic when mapping mixed reads to their corresponding reference genomes. The challenge lies in the determination of which reads belong to which species, especially when homology exists between the host and pathogen genomes. This chapter proposes a combo-genome alignment strategy, which was compared with existing alignment scenarios. Simulation results demonstrated that the degree of discrepancy in the results is correlated with phylogenetic distance of the two species in the mixture which was attributable to the extent of homology between the two genomes involved. This correlation was also found in the analysis using two real RNA-seq datasets of Fusarium-challenged wheat plants. Comparisons of the three RNA-seq processing strategies on three simulation datasets and two real Fusarium-infected wheat datasets showed that an alignment to a combo-genome, consisting of both host and pathogen genomes, improves mapping quality as compared to sequential alignment procedures.


Subject(s)
Genome , Software , RNA-Seq , Phylogeny , Computer Simulation
18.
Methods Mol Biol ; 2659: 137-159, 2023.
Article in English | MEDLINE | ID: mdl-37249891

ABSTRACT

In differential gene expression data analysis, one objective is to identify groups of co-expressed genes from a large dataset in order to detect the association between such a group of genes and an experimental condition. This is often done through a clustering approach, such as k-means or bipartition hierarchical clustering, based on particular similarity measures in the grouping process. In such a dataset, the gene differential expression itself is an innate attribute that can be used in the feature extraction process. For example, in a dataset consisting of multiple treatments versus their controls, the expression of a gene in each treatment would have three possible behaviors, upregulated, downregulated, or unchanged. We present in this chapter, a differential expression feature extraction (DEFE) method by using a string consisting of three numerical values at each character to denote such behavior, i.e., 1 = up, 2 = down, and 0 = unchanged, which results in up to 3B differential expression patterns across all B comparisons. This approach has been successfully applied in many research projects, and among these, we demonstrate the strength of DEFE in a case study on RNA-sequencing (RNA-seq) data analysis of wheat challenged with the phytopathogenic fungus, Fusarium graminearum. Combinations of multiple schemes of DEFE patterns revealed groups of genes putatively associated with resistance or susceptibility to FHB.


Subject(s)
Fusarium , Triticum , RNA-Seq , Triticum/microbiology , Fusarium/genetics , Fusarium/metabolism , Plant Diseases/genetics , Plant Diseases/microbiology
19.
J Med Virol ; 95(4): e28749, 2023 04.
Article in English | MEDLINE | ID: mdl-37185850

ABSTRACT

Hepatitis B Virus (HBV) replication has been reported to be restricted by the intrahepatic host restriction factors and antiviral signaling pathways. The intracellular mechanisms underlying the significant viremia difference among different phases of the natural history chronic HBV infection remain elusive. We herein report that the hypoxia-induced gene domain protein-1a (HIGD1A) was highly expressed in the liver of inactive HBV carriers with low viremia. Ectopic expression of HIGD1A in hepatocyte-derived cells significantly inhibited HBV transcription and replication in a dose-dependent manner, while silence of HIGD1A promoted HBV gene expression and replication. Similar results were also observed in both de novo HBV-infected cell culture model and HBV persistence mouse model. Mechanistically, HIGD1A is located on the mitochondrial inner membrane and activates nuclear factor kappa B (NF-κB) signaling pathway through binding to paroxysmal nonkinesigenic dyskinesia (PNKD), which further enhances the expression of a transcription factor NR2F1 to inhibit HBV transcription and replication. Consistently, knockdown of PNKD or NR2F1 and blockage of NF-κB signaling pathway abrogated the inhibitory effect of HIGD1A on HBV replication. Mitochondrial HIGD1A exploits the PNKD-NF-κB-NR2F1 nexus to act as a host restriction factor of HBV infection. Our study thus shed new lights on the regulation of HBV by hypoxia-related genes and related antiviral strategies.


Subject(s)
Hepatitis B virus , Hepatitis B , Animals , Mice , Antiviral Agents/pharmacology , Hepatitis B virus/physiology , NF-kappa B/genetics , NF-kappa B/metabolism , Viral Transcription , Viremia , Virus Replication , Humans
20.
J Transl Med ; 21(1): 253, 2023 04 12.
Article in English | MEDLINE | ID: mdl-37041638

ABSTRACT

BACKGROUND: The Hypoxia inducible gene domain family member 2A (HIGD2A) protein is indispensable for the assembly of the mitochondrial respiratory supercomplex, which has been implicated in cell proliferation and cell survival under hypoxic conditions. Because the liver has a naturally low oxygen microenvironment, the role of HIGD2A in the development of hepatocellular carcinoma (HCC) remains largely unknown. METHODS: Gene expression data and clinical information were obtained from multiple public databases. A lentivirus-mediated gene knockdown approach was conducted to explore the function and mechanism of HIGD2A activity in HCC cells. In vivo and in vitro assays were performed to investigate the biological roles of HIGD2A. RESULTS: HIGD2A was overexpressed in HCC tissues and cell lines and was associated with a worse prognosis. Silencing HIGD2A expression significantly attenuated cell proliferation and migration, caused S-phase cell cycle arrest, and decreased tumor formation in nude mice. Mechanistically, HIGD2A depletion greatly decreased cellular ATP levels by disrupting mitochondrial ATP production. Moreover, HIGD2A knockdown cells displayed impaired mitochondrial function, such as mitochondrial fusion, increased expression of the mitochondrial stress response protein, and decreased oxygen consumption. Furthermore, knockdown of HIGD2A markedly attenuated the activation of the MAPK/ERK pathway. CONCLUSIONS: HIGD2A promoted liver cancer cell growth by fueling mitochondrial ATP synthesis and activating the MAPK/ERK pathway, suggested that targeting HIGD2A may represent a new strategy for HCC therapy.


Subject(s)
Carcinoma, Hepatocellular , Liver Neoplasms , Animals , Mice , Adenosine Triphosphate/metabolism , Carcinoma, Hepatocellular/genetics , Cell Line, Tumor , Liver Neoplasms/genetics , MAP Kinase Signaling System , Mice, Nude , Mitochondria/metabolism , Tumor Microenvironment
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