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1.
Nucleic Acids Res ; 51(14): 7342-7356, 2023 08 11.
Article in English | MEDLINE | ID: mdl-37326017

ABSTRACT

Efficient repair of oxidized DNA is critical for genome-integrity maintenance. Cockayne syndrome protein B (CSB) is an ATP-dependent chromatin remodeler that collaborates with Poly(ADP-ribose) polymerase I (PARP1) in the repair of oxidative DNA lesions. How these proteins integrate during DNA repair remains largely unknown. Here, using chromatin co-fractionation studies, we demonstrate that PARP1 and PARP2 promote recruitment of CSB to oxidatively-damaged DNA. CSB, in turn, contributes to the recruitment of XRCC1, and histone PARylation factor 1 (HPF1), and promotes histone PARylation. Using alkaline comet assays to monitor DNA repair, we found that CSB regulates single-strand break repair (SSBR) mediated by PARP1 and PARP2. Strikingly, CSB's function in SSBR is largely bypassed when transcription is inhibited, suggesting CSB-mediated SSBR occurs primarily at actively transcribed DNA regions. While PARP1 repairs SSBs at sites regardless of the transcription status, we found that PARP2 predominantly functions in actively transcribed DNA regions. Therefore, our study raises the hypothesis that SSBR is executed by different mechanisms based on the transcription status.


Subject(s)
Chromatin , Humans , Carrier Proteins/genetics , Chromatin/genetics , DNA/genetics , DNA/metabolism , DNA Repair , Histones/metabolism , Nuclear Proteins/metabolism , Poly (ADP-Ribose) Polymerase-1/genetics , Poly (ADP-Ribose) Polymerase-1/metabolism , Poly(ADP-ribose) Polymerases/genetics , Poly(ADP-ribose) Polymerases/metabolism , X-ray Repair Cross Complementing Protein 1/genetics , X-ray Repair Cross Complementing Protein 1/metabolism
2.
Scand J Immunol ; 98(2): e13275, 2023 Aug.
Article in English | MEDLINE | ID: mdl-38441378

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic underlines a persistent threat of respiratory tract infectious diseases and warrants preparedness for a rapid response. At present, COVID-19 has had a serious social impact and imposed a heavy global burden on public health. The exact pathogenesis of COVID-19 has not been fully elucidated. Since the outbreak of COVID-19, a renewed attention has been brought to Toll-like receptors (TLRs). Available data and new findings have demonstrated that the interaction of human TLRs and SARS-CoV-2 is a vital mediator of COVID-19 immunopathogenesis. TLRs such as TLR2, 4, 7 and 8 are potentially important in viral combat and activation of immunity in patients with COVID-19. Therapeutics targeting TLRs are currently considered promising options against the pandemic. A number of TLR-targeting immunotherapeutics are now being investigated in preclinical studies and different phases of clinical trials. In addition, innovative vaccines based on TLRs under development could be a promising approach for building a new generation of vaccines to solve the current challenges. In this review, we summarize recent progress in the role of TLRs in COVID-19, focusing the new candidate drugs targeting TLRs, the current technology and potential paths forward for employing TLR agonists as vaccine adjuvants.


Subject(s)
COVID-19 , Vaccines , Humans , SARS-CoV-2 , Disease Outbreaks , Toll-Like Receptors
3.
Nutr Metab Cardiovasc Dis ; 32(8): 1917-1923, 2022 08.
Article in English | MEDLINE | ID: mdl-35680486

ABSTRACT

BACKGROUND AND AIMS: Growth arrest-specific 6 protein (Gas6) has been established to play important roles in various biological processes, but little is currently known on the role of Gas6 signaling in humans. This research explored the association between Gas6 expression and carotid atherosclerosis (AS) in type 2 diabetes mellitus (T2DM). METHODS AND RESULTS: As many as 126 T2DM patients were recruited in this study and classified into two groups based on their carotid intima-media thickness (CIMT). Meanwhile, 50 healthy individuals were recruited for the normal control group (NC). The subgroups were compared in terms of clinical data and Gas6 expression levels. Gas6 levels were decreased in T2DM patients with or without AS compared to NC subjects (9.64 ± 1.41 ng/ml, 11.38 ± 2.08 ng/ml, and 13.64 ± 2.61 ng/ml, respectively) (p < 0.001). The interaction between Gas6 and AS in T2DM was analyzed by logistic regression model and receiver operating characteristic (ROC) curve analysis. Decreased Gas6 expression was an independent risk factor relevant to AS in T2DM (p = 0.027). The area under the ROC curve to estimate the diagnostic value of low Gas6 expression for AS in T2DM was 0.750. The correlation between Gas6 and other parameters was evaluated by Pearson correlation analysis and linear regression model. Body mass index (BMI), hemoglobin A1c (HbA1c) and tumor necrosis factor-α(TNF-α) were independently correlated with Gas6. CONCLUSION: Low Gas6 expression is an independent risk factor for AS in T2DM. Gas6 expression is affected by BMI, HbA1c and TNF-α levels.


Subject(s)
Carotid Artery Diseases , Diabetes Mellitus, Type 2 , Intercellular Signaling Peptides and Proteins , Carotid Artery Diseases/blood , Carotid Artery Diseases/diagnostic imaging , Carotid Artery Diseases/pathology , Carotid Intima-Media Thickness , Diabetes Mellitus, Type 2/blood , Diabetes Mellitus, Type 2/diagnosis , Diabetes Mellitus, Type 2/pathology , Glycated Hemoglobin/metabolism , Humans , Intercellular Signaling Peptides and Proteins/blood , Risk Factors , Tumor Necrosis Factor-alpha/blood
4.
AAPS PharmSciTech ; 23(3): 85, 2022 Mar 14.
Article in English | MEDLINE | ID: mdl-35288801

ABSTRACT

Cannabidiol (CBD) has poor water solubility and is subjected to extensive first-pass metabolism. These absorption obstacles are responsible for low and variable oral bioavailability of CBD. This study endeavored to improve CBD bioavailability by intramuscular (IM) injection of CBD nanocrystals (CBD-NC). The nanocrystals were prepared by antisolvent precipitation method and were characterized in terms of the particle size, polydispersity index (PDI), zeta potential, morphology, and crystalline status. CBD-NC displayed a particle size of 141.7±1.5 nm, a PDI of 0.18±0.01, and a zeta potential of -25.73 mV. CBD-NC freeze-dried powder using bovine serum albumin (BSA) as cryoprotectant had good redispersibility, and the average particle size was 139.1±1.4 nm after reconstitution. Moreover, these freeze-dried powders were characterized for drug loading and pH and were evaluated for in vitro dissolution and in vivo studies in a rat model. The in vivo results showed that AUC0-24 h and Cmax of CBD by IM injection of CBD nanocrystals increased significantly compared with that of oral (P.O) administration of CBD nanocrystals and CBD oil solution. This underlines the nano-sized CBD could be suggested as a practical and simple nanosystem for IM delivery with improved bioavailability. More importantly, these results pave the way for future development of CBD-NC retentive dosage forms. Graphical abstract.


Subject(s)
Cannabidiol , Nanoparticles , Animals , Biological Availability , Nanoparticles/chemistry , Particle Size , Rats , Solubility
5.
Nucleic Acids Res ; 47(9): 4521-4538, 2019 05 21.
Article in English | MEDLINE | ID: mdl-30916347

ABSTRACT

Faithful propagation of transcription programs through cell division underlies cell-identity maintenance. Transcriptional regulators selectively bound on mitotic chromatin are emerging critical elements for mitotic transcriptional memory; however, mechanisms governing their site-selective binding remain elusive. By studying how protein-protein interactions impact mitotic chromatin binding of RBPJ, the major downstream effector of the Notch signaling pathway, we found that histone modifying enzymes HDAC1 and KDM5A play critical, regulatory roles in this process. We found that HDAC1 knockdown or inactivation leads to increased RBPJ occupancy on mitotic chromatin in a site-specific manner, with a concomitant increase of KDM5A occupancy at these sites. Strikingly, the presence of KDM5A is essential for increased RBPJ occupancy. Our results uncover a regulatory mechanism in which HDAC1 negatively regulates RBPJ binding on mitotic chromatin in a KDM5A-dependent manner. We propose that relative chromatin affinity of a minimal regulatory complex, reflecting a specific transcription program, renders selective RBPJ binding on mitotic chromatin.


Subject(s)
Chromatin/genetics , Histone Deacetylase 1/genetics , Immunoglobulin J Recombination Signal Sequence-Binding Protein/genetics , Retinoblastoma-Binding Protein 2/genetics , Animals , Binding Sites , CRISPR-Cas Systems/genetics , Cell Cycle/genetics , Cell Division/genetics , Gene Expression Regulation , Gene Knockout Techniques , Humans , Mice , Mitosis/genetics , Promoter Regions, Genetic , Protein Binding/genetics , Signal Transduction/genetics
6.
Nucleic Acids Res ; 46(15): 7471-7479, 2018 09 06.
Article in English | MEDLINE | ID: mdl-30032309

ABSTRACT

Cockayne syndrome protein B (CSB) is a member of the SNF2/SWI2 ATPase family and is essential for transcription-coupled nucleotide excision DNA repair (TC-NER). CSB also plays critical roles in transcription regulation. CSB can hydrolyze ATP in a DNA-dependent manner, alter protein-DNA contacts and anneal DNA strands. How the different biochemical activities of CSB are utilized in these cellular processes have only begun to become clear in recent years. Mutations in the gene encoding CSB account for majority of the Cockayne syndrome cases, which result in extreme sun sensitivity, premature aging features and/or abnormalities in neurology and development. Here, we summarize and integrate recent biochemical, structural, single-molecule and somatic cell genetic studies that have advanced our understanding of CSB. First, we review studies on the mechanisms that regulate the different biochemical activities of CSB. Next, we summarize how CSB is targeted to regulate transcription under different growth conditions. We then discuss recent advances in our understanding of how CSB regulates transcription mechanistically. Lastly, we summarize the various roles that CSB plays in the different steps of TC-NER, integrating the results of different studies and proposing a model as to how CSB facilitates TC-NER.


Subject(s)
Cockayne Syndrome/genetics , DNA Helicases/genetics , DNA Repair Enzymes/genetics , DNA Repair/genetics , Gene Expression Regulation/genetics , Poly-ADP-Ribose Binding Proteins/genetics , Adenosine Triphosphate/metabolism , DNA/genetics , Humans , Mutation/genetics , Schizosaccharomyces/genetics , Transcription, Genetic/genetics
7.
J Biol Chem ; 293(46): 17863-17874, 2018 11 16.
Article in English | MEDLINE | ID: mdl-30266807

ABSTRACT

Cockayne syndrome protein B (CSB) is an ATP-dependent chromatin remodeler that relieves oxidative stress by regulating DNA repair and transcription. CSB is proposed to participate in base-excision repair (BER), the primary pathway for repairing oxidative DNA damage, but exactly how CSB participates in this process is unknown. It is also unclear whether CSB contributes to other repair pathways during oxidative stress. Here, using a patient-derived CS1AN-sv cell line, we examined how CSB is targeted to chromatin in response to menadione-induced oxidative stress, both globally and locus-specifically. We found that menadione-induced, global CSB-chromatin association does not require CSB's ATPase activity and is, therefore, mechanistically distinct from UV-induced CSB-chromatin association. Importantly, poly(ADP-ribose) polymerase 1 (PARP1) enhanced the kinetics of global menadione-induced CSB-chromatin association. We found that the major BER enzymes, 8-oxoguanine DNA glycosylase (OGG1) and apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1), do not influence this association. Additionally, the level of γ-H2A histone family member X (γ-H2AX), a marker for dsDNA breaks, was not increased in menadione-treated cells. Therefore, our results support a model whereby PARP1 localizes to ssDNA breaks and recruits CSB to participate in DNA repair. Furthermore, this global CSB-chromatin association occurred independently of RNA polymerase II-mediated transcription elongation. However, unlike global CSB-chromatin association, both PARP1 knockdown and inhibition of transcription elongation interfered with menadione-induced CSB recruitment to specific genomic regions. This observation supports the hypothesis that CSB is also targeted to specific genomic loci to participate in transcriptional regulation in response to oxidative stress.


Subject(s)
Chromatin/metabolism , DNA Helicases/metabolism , DNA Repair Enzymes/metabolism , DNA/metabolism , Oxidative Stress/physiology , Poly (ADP-Ribose) Polymerase-1/metabolism , Poly-ADP-Ribose Binding Proteins/metabolism , CCCTC-Binding Factor/metabolism , DNA/radiation effects , DNA Damage , DNA Helicases/genetics , DNA Repair Enzymes/genetics , Genetic Loci , Humans , Mutation , Poly-ADP-Ribose Binding Proteins/genetics , Protein Binding , Ultraviolet Rays , Vitamin K 3/pharmacology
8.
Nucleic Acids Res ; 45(8): 4696-4707, 2017 05 05.
Article in English | MEDLINE | ID: mdl-28369616

ABSTRACT

Cockayne syndrome protein B (CSB) belongs to the SWI2/SNF2 ATP-dependent chromatin remodeler family, and CSB is the only ATP-dependent chromatin remodeler essential for transcription-coupled nucleotide excision DNA repair. CSB alone remodels nucleosomes ∼10-fold slower than the ACF remodeling complex. Strikingly, NAP1-like histone chaperones interact with CSB and greatly enhance CSB-mediated chromatin remodeling. While chromatin remodeling by CSB and NAP1-like proteins is crucial for efficient transcription-coupled DNA repair, the mechanism by which NAP1-like proteins enhance chromatin remodeling by CSB remains unknown. Here we studied CSB's DNA-binding and nucleosome-remodeling activities at the single molecule level in real time. We also determined how the NAP1L1 chaperone modulates these activities. We found that CSB interacts with DNA in two principle ways: by simple binding and a more complex association that involves gross DNA distortion. Remarkably, NAP1L1 suppresses both these interactions. Additionally, we demonstrate that nucleosome remodeling by CSB consists of three distinct phases: activation, translocation and pausing, similar to ACF. Importantly, we found that NAP1L1 promotes CSB-mediated remodeling by accelerating both activation and translocation. Additionally, NAP1L1 increases CSB processivity by decreasing the pausing probability during translocation. Our study, therefore, uncovers the different steps of CSB-mediated chromatin remodeling that can be regulated by NAP1L1.


Subject(s)
DNA Helicases/genetics , DNA Repair Enzymes/genetics , Histone Chaperones/genetics , Nucleosome Assembly Protein 1/genetics , Transcription, Genetic , Adenosine Triphosphate/metabolism , Chromatin/genetics , Chromatin Assembly and Disassembly/genetics , DNA Repair/genetics , Humans , Nucleosomes/genetics , Poly-ADP-Ribose Binding Proteins
9.
Phytother Res ; 33(9): 2401-2408, 2019 Sep.
Article in English | MEDLINE | ID: mdl-31317585

ABSTRACT

Lupus nephritis (LN) is an autoimmune disease caused by systemic lupus erythematosus. Excessive proliferation of mesangial cells is one of the most serious pathological manifestations of LN. In addition, the expression of PTX3 is elevated in the serum of patients with LN. Quercetin has good anti-inflammatory effects and immunomodulatory activities. In this study, the result of MTT indicated that quercetin treatment alleviated the excessive proliferation of mesangial cells. ELISA and immunofluorescence experiments showed that quercetin treatment inhibited the expression of PTX3. Three doses of quercetin (20, 40, and 80 µM) were selected for the experiment. It is noteworthy that the efficacy of quercetin at 80 µM was significantly better than that of other dose groups. And the effect in inhibiting PTX3 expression was comparable with that of the PDTC (80 µM) positive control. Western blot and qRT-PCR analysis revealed that quercetin treatment reduced the expression of nuclear factor-κB p65 and IKKß, increased the expression of IκBα, and inhibited the expression of PTX3. In conclusion, through inhibiting the activation of nuclear factor-κB signaling pathway, quercetin treatment could reduce the expression of PTX3 and inhibit the excessive proliferation of mesangial cells, suggesting that quercetin is a potential therapeutic drug for LN.


Subject(s)
Antioxidants/therapeutic use , C-Reactive Protein/drug effects , NF-kappa B/metabolism , Quercetin/therapeutic use , Serum Amyloid P-Component/drug effects , Tumor Necrosis Factor-alpha/drug effects , Antioxidants/pharmacology , Cell Proliferation , Humans , Quercetin/pharmacology , Signal Transduction , Tumor Necrosis Factor-alpha/metabolism
10.
Mol Cell ; 37(2): 235-46, 2010 Jan 29.
Article in English | MEDLINE | ID: mdl-20122405

ABSTRACT

The ATP-dependent chromatin remodeler CSB is essential for transcription-coupled DNA repair, and mutations in CSB lead to Cockayne syndrome. Here, we examined the recruitment of CSB to chromatin after ultraviolet (UV) irradiation and uncovered a regulatory mechanism that ensures the specific association of this remodeler with chromatin. We demonstrate that ATP hydrolysis by CSB is essential for stable CSB-chromatin association after UV irradiation and that defects in this association underlie some forms of Cockayne syndrome. We also show that the N-terminal region of CSB negatively regulates chromatin association during normal cell growth. Of interest, in the absence of the negative regulatory region, ATP hydrolysis becomes dispensable for chromatin association, indicating that CSB uses energy from ATP hydrolysis to overcome the inhibitory effect imposed by its N-terminal region. Together, our results suggest that the recruitment of CSB to lesion-stalled transcription is an ATP-dependent process and involves a gross conformational change of CSB.


Subject(s)
Adenosine Triphosphate/metabolism , Chromatin/metabolism , DNA Helicases/physiology , DNA Repair Enzymes/physiology , Ultraviolet Rays , Adenosine Triphosphatases/physiology , Chromatin Assembly and Disassembly/physiology , Chromatin Assembly and Disassembly/radiation effects , Cockayne Syndrome/genetics , DNA Helicases/genetics , DNA Helicases/metabolism , DNA Repair Enzymes/genetics , DNA Repair Enzymes/metabolism , Humans , Models, Genetic , Poly-ADP-Ribose Binding Proteins
11.
Nucleic Acids Res ; 44(5): 2125-35, 2016 Mar 18.
Article in English | MEDLINE | ID: mdl-26578602

ABSTRACT

Cockayne syndrome is a premature aging disease associated with numerous developmental and neurological abnormalities, and elevated levels of reactive oxygen species have been found in cells derived from Cockayne syndrome patients. The majority of Cockayne syndrome cases contain mutations in the ATP-dependent chromatin remodeler CSB; however, how CSB protects cells from oxidative stress remains largely unclear. Here, we demonstrate that oxidative stress alters the genomic occupancy of the CSB protein and increases CSB occupancy at promoters. Additionally, we found that the long-range chromatin-structure regulator CTCF plays a pivotal role in regulating sites of genomic CSB occupancy upon oxidative stress. We show that CSB directly interacts with CTCF in vitro and that oxidative stress enhances the CSB-CTCF interaction in cells. Reciprocally, we demonstrate that CSB facilitates CTCF-DNA interactions in vitro and regulates CTCF-chromatin interactions in oxidatively stressed cells. Together, our results indicate that CSB and CTCF can regulate each other's chromatin association, thereby modulating chromatin structure and coordinating gene expression in response to oxidative stress.


Subject(s)
Chromatin/chemistry , DNA Helicases/genetics , DNA Repair Enzymes/genetics , DNA/genetics , Fibroblasts/metabolism , Repressor Proteins/genetics , Base Sequence , Binding Sites , CCCTC-Binding Factor , Cell Line, Transformed , Chromatin/drug effects , Chromatin/metabolism , Chromatin Assembly and Disassembly/drug effects , DNA/metabolism , DNA Helicases/metabolism , DNA Repair Enzymes/metabolism , Fibroblasts/cytology , Fibroblasts/drug effects , Gene Expression Regulation , Humans , Molecular Sequence Data , Oxidative Stress , Poly-ADP-Ribose Binding Proteins , Protein Binding , RNA, Small Interfering/genetics , RNA, Small Interfering/metabolism , Repressor Proteins/antagonists & inhibitors , Repressor Proteins/metabolism , Signal Transduction , Vitamin K 3/pharmacology
12.
Phytother Res ; 32(1): 103-114, 2018 Jan.
Article in English | MEDLINE | ID: mdl-29071768

ABSTRACT

Renal ischaemia-reperfusion (I/R) injury is the most common cause of acute kidney injury (AKI). Peritubular capillary (PTC) endothelium damages are an important pathogenesis during I/R AKI. Salvianolic acid A (SAA) possesses various pharmacological activities. The study investigated whether SAA ameliorated I/R AKI through protecting against PTC endothelium damages. Male Sprague-Dawley rats were divided into 6 groups: control, sham, I/R, and I/R plus SAA (2.5, 5, 10 mg/kg) groups. Rats were subjected to bilateral renal pedicle clamping for 60 min, and killed at 24 hr after reperfusion. Kidney injury, PTC endothelium damages and factors affecting PTC endothelium were evaluated. SAA significantly decreased blood urea nitrogen and serum creatinine levels, and reduced urine kidney injury molecule-1 concentration. Simultaneously, SAA alleviated histological damages, prevented PTC endothelium damages, preserved the density of PTC and improved renal hypoxia. Furthermore, SAA inhibited platelet activation, elevated Klotho protein expression and up-regulated vascular endothelial growth factor A expression. Overall, SAA has protective effects on AKI induced by I/R. Preventing PTC endothelium damages and preserving PTC integrity to improve the renal hypoxia may be the ways for SAA to ameliorate AKI. All these indicate that SAA is likely to be a promising agent for AKI.


Subject(s)
Acute Kidney Injury/drug therapy , Caffeic Acids/chemistry , Drugs, Chinese Herbal/chemistry , Endothelium, Vascular/drug effects , Kidney/pathology , Lactates/chemistry , Reperfusion Injury/drug therapy , Acute Kidney Injury/pathology , Animals , Endothelium, Vascular/metabolism , Endothelium, Vascular/pathology , Flow Cytometry , Male , Rats , Rats, Sprague-Dawley , Reperfusion Injury/pathology
13.
RNA ; 21(12): 2053-66, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26437669

ABSTRACT

HnRNP L is a ubiquitous splicing-regulatory protein that is critical for the development and function of mammalian T cells. Previous work has identified a few targets of hnRNP L-dependent alternative splicing in T cells and has described transcriptome-wide association of hnRNP L with RNA. However, a comprehensive analysis of the impact of hnRNP L on mRNA expression remains lacking. Here we use next-generation sequencing to identify transcriptome changes upon depletion of hnRNP L in a model T-cell line. We demonstrate that hnRNP L primarily regulates cassette-type alternative splicing, with minimal impact of hnRNP L depletion on transcript abundance, intron retention, or other modes of alternative splicing. Strikingly, we find that binding of hnRNP L within or flanking an exon largely correlates with exon repression by hnRNP L. In contrast, exons that are enhanced by hnRNP L generally lack proximal hnRNP L binding. Notably, these hnRNP L-enhanced exons share sequence and context features that correlate with poor nucleosome positioning, suggesting that hnRNP may enhance inclusion of a subset of exons via a cotranscriptional or epigenetic mechanism. Our data demonstrate that hnRNP L controls inclusion of a broad spectrum of alternative cassette exons in T cells and suggest both direct RNA regulation as well as indirect mechanisms sensitive to the epigenetic landscape.


Subject(s)
Epigenesis, Genetic , RNA, Messenger/metabolism , Ribonucleoproteins/physiology , Alternative Splicing , Exons , Humans , Jurkat Cells , Nucleosomes/metabolism , RNA, Messenger/genetics , Transcriptome
14.
PLoS Genet ; 10(3): e1004204, 2014 Mar.
Article in English | MEDLINE | ID: mdl-24603501

ABSTRACT

Mechanisms that maintain transcriptional memory through cell division are important to maintain cell identity, and sequence-specific transcription factors that remain associated with mitotic chromatin are emerging as key players in transcriptional memory propagation. Here, we show that the major transcriptional effector of Notch signaling, RBPJ, is retained on mitotic chromatin, and that this mitotic chromatin association is mediated through the direct association of RBPJ with DNA. We further demonstrate that RBPJ binds directly to nucleosomal DNA in vitro, with a preference for sites close to the entry/exit position of the nucleosomal DNA. Genome-wide analysis in the murine embryonal-carcinoma cell line F9 revealed that roughly 60% of the sites occupied by RBPJ in asynchronous cells were also occupied in mitotic cells. Among them, we found that a fraction of RBPJ occupancy sites shifted between interphase and mitosis, suggesting that RBPJ can be retained on mitotic chromatin by sliding on DNA rather than disengaging from chromatin during mitotic chromatin condensation. We propose that RBPJ can function as a mitotic bookmark, marking genes for efficient transcriptional activation or repression upon mitotic exit. Strikingly, we found that sites of RBPJ occupancy were enriched for CTCF-binding motifs in addition to RBPJ-binding motifs, and that RBPJ and CTCF interact. Given that CTCF regulates transcription and bridges long-range chromatin interactions, our results raise the intriguing hypothesis that by collaborating with CTCF, RBPJ may participate in establishing chromatin domains and/or long-range chromatin interactions that could be propagated through cell division to maintain gene expression programs.


Subject(s)
Chromatin/genetics , DNA/genetics , Immunoglobulin J Recombination Signal Sequence-Binding Protein/genetics , Mitosis/genetics , Animals , CCCTC-Binding Factor , Humans , Immunoglobulin J Recombination Signal Sequence-Binding Protein/metabolism , Interphase/genetics , Mice , Nucleosomes/genetics , Nucleosomes/metabolism , Receptors, Notch/genetics , Receptors, Notch/metabolism , Repressor Proteins/metabolism , Signal Transduction , Transcription Factors/genetics
15.
PLoS Genet ; 10(4): e1004284, 2014 Apr.
Article in English | MEDLINE | ID: mdl-24743307

ABSTRACT

Cockayne syndrome is an inherited premature aging disease associated with numerous developmental and neurological defects, and mutations in the gene encoding the CSB protein account for the majority of Cockayne syndrome cases. Accumulating evidence suggests that CSB functions in transcription regulation, in addition to its roles in DNA repair, and those defects in this transcriptional activity might contribute to the clinical features of Cockayne syndrome. Transcription profiling studies have so far uncovered CSB-dependent effects on gene expression; however, the direct targets of CSB's transcriptional activity remain largely unknown. In this paper, we report the first comprehensive analysis of CSB genomic occupancy during replicative cell growth. We found that CSB occupancy sites display a high correlation to regions with epigenetic features of promoters and enhancers. Furthermore, we found that CSB occupancy is enriched at sites containing the TPA-response element. Consistent with this binding site preference, we show that CSB and the transcription factor c-Jun can be found in the same protein-DNA complex, suggesting that c-Jun can target CSB to specific genomic regions. In support of this notion, we observed decreased CSB occupancy of TPA-response elements when c-Jun levels were diminished. By modulating CSB abundance, we found that CSB can influence the expression of nearby genes and impact nucleosome positioning in the vicinity of its binding site. These results indicate that CSB can be targeted to specific genomic loci by sequence-specific transcription factors to regulate transcription and local chromatin structure. Additionally, comparison of CSB occupancy sites with the MSigDB Pathways database suggests that CSB might function in peroxisome proliferation, EGF receptor transactivation, G protein signaling and NF-κB activation, shedding new light on the possible causes and mechanisms of Cockayne syndrome.


Subject(s)
Chromatin/genetics , DNA Helicases/genetics , DNA Repair Enzymes/genetics , Proto-Oncogene Proteins c-jun/genetics , Proto-Oncogene Proteins c-jun/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Transcription, Genetic/genetics , Cell Line , Chromatin/metabolism , ErbB Receptors/genetics , ErbB Receptors/metabolism , GTP-Binding Proteins/genetics , GTP-Binding Proteins/metabolism , Humans , NF-kappa B/genetics , NF-kappa B/metabolism , Poly-ADP-Ribose Binding Proteins , Promoter Regions, Genetic/genetics
16.
Gastroenterology ; 149(7): 1872-1883.e9, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26344056

ABSTRACT

BACKGROUND & AIMS: DNA structural lesions are prevalent in sporadic colorectal cancer. Therefore, we proposed that gene variants that predispose to DNA double-strand breaks (DSBs) would be found in patients with familial colorectal carcinomas of an undefined genetic basis (UFCRC). METHODS: We collected primary T cells from 25 patients with UFCRC and matched patients without colorectal cancer (controls) and assayed for DSBs. We performed exome sequence analyses of germline DNA from 20 patients with UFCRC and 5 undiagnosed patients with polyposis. The prevalence of identified variants in genes linked to DNA integrity was compared with that of individuals without a family history of cancer. The effects of representative variants found to be associated with UFCRC was confirmed in functional assays with HCT116 cells. RESULTS: Primary T cells from most patients with UFCRC had increased levels of the DSB marker γ(phosphorylated)histone2AX (γH2AX) after treatment with DNA damaging agents, compared with T cells from controls (P < .001). Exome sequence analysis identified a mean 1.4 rare variants per patient that were predicted to disrupt functions of genes relevant to DSBs. Controls (from public databases) had a much lower frequency of variants in the same genes (P < .001). Knockdown of representative variant genes in HCT116 CRC cells increased γH2AX. A detailed analysis of immortalized patient-derived B cells that contained variants in the Werner syndrome, RecQ helicase-like gene (WRN, encoding T705I), and excision repair cross-complementation group 6 (ERCC6, encoding N180Y) showed reduced levels of these proteins and increased DSBs, compared with B cells from controls. This phenotype was rescued by exogenous expression of WRN or ERCC6. Direct analysis of the recombinant variant proteins confirmed defective enzymatic activities. CONCLUSIONS: These results provide evidence that defects in suppression of DSBs underlie some cases of UFCRC; these can be identified by assays of circulating lymphocytes. We specifically associated UFCRC with variants in WRN and ERCC6 that reduce the capacity for repair of DNA DSBs. These observations could lead to a simple screening strategy for UFCRC, and provide insight into the pathogenic mechanisms of colorectal carcinogenesis.


Subject(s)
Biomarkers, Tumor/genetics , Colorectal Neoplasms/genetics , DNA Breaks, Double-Stranded , Genetic Variation , T-Lymphocytes/pathology , Adult , Aged , Aged, 80 and over , Biomarkers, Tumor/metabolism , Case-Control Studies , Colorectal Neoplasms/immunology , Colorectal Neoplasms/metabolism , Colorectal Neoplasms/pathology , Computational Biology , DNA Helicases/genetics , DNA Helicases/metabolism , DNA Repair , DNA Repair Enzymes/genetics , DNA Repair Enzymes/metabolism , Databases, Genetic , Exodeoxyribonucleases/genetics , Exodeoxyribonucleases/metabolism , Exome , Female , Gene Frequency , Gene Knockdown Techniques , Genetic Predisposition to Disease , Genomic Instability , HCT116 Cells , Heredity , Histones/metabolism , Humans , Male , Middle Aged , Mutagens/pharmacology , Phenotype , Phosphorylation , Poly-ADP-Ribose Binding Proteins , RecQ Helicases/genetics , RecQ Helicases/metabolism , Sequence Analysis, DNA , T-Lymphocytes/drug effects , T-Lymphocytes/immunology , T-Lymphocytes/metabolism , Transfection , Up-Regulation , Werner Syndrome Helicase
17.
PLoS Genet ; 9(4): e1003407, 2013 Apr.
Article in English | MEDLINE | ID: mdl-23637612

ABSTRACT

The Cockayne syndrome complementation group B (CSB) protein is essential for transcription-coupled DNA repair, and mutations in CSB are associated with Cockayne syndrome--a devastating disease with complex clinical features, including the appearance of premature aging, sun sensitivity, and numerous neurological and developmental defects. CSB belongs to the SWI2/SNF2 ATP-dependent chromatin remodeler family, but the extent to which CSB remodels chromatin and whether this activity is utilized in DNA repair is unknown. Here, we show that CSB repositions nucleosomes in an ATP-dependent manner in vitro and that this activity is greatly enhanced by the NAP1-like histone chaperones, which we identify as new CSB-binding partners. By mapping functional domains and analyzing CSB derivatives, we demonstrate that chromatin remodeling by the combined activities of CSB and the NAP1-like chaperones is required for efficient transcription-coupled DNA repair. Moreover, we show that chromatin remodeling and repair protein recruitment mediated by CSB are separable activities. The collaboration that we observed between CSB and the NAP1-like histone chaperones adds a new dimension to our understanding of the ways in which ATP-dependent chromatin remodelers and histone chaperones can regulate chromatin structure. Taken together, the results of this study offer new insights into the functions of chromatin remodeling by CSB in transcription-coupled DNA repair as well as the underlying mechanisms of Cockayne syndrome.


Subject(s)
Chromatin Assembly and Disassembly , Cockayne Syndrome , Adenosine Triphosphate/metabolism , Cockayne Syndrome/genetics , DNA Helicases/genetics , DNA Repair , DNA Repair Enzymes/genetics , Histone Chaperones/genetics , Humans , Transcription, Genetic
18.
Molecules ; 21(7)2016 Jul 16.
Article in English | MEDLINE | ID: mdl-27438811

ABSTRACT

Geniposide (GE) is the main bioactive component of Gardeniae Fructus. The hepatotoxicity of geniposide limited clinical application. In order to get a new geniposide derivative that has less hepatotoxicity and still possesses the antidepressant activity, a new C-1 hydroxyl methylation derivative named methyl genipin (MG) was synthesized from geniposide. In the present study, we demonstrated that MG did not increase the liver index, alanine aminotransferase (ALT) and aspirate aminotransferase (AST). Histopathological examination suggested that no toxic damages were observed in rats treated orally with MG (0.72 mmol/kg). More importantly, a 7-day treatment with MG at 0.13, 0.26, and 0.52 mmol/kg/day could reduce the duration of immobility. It showed that the antidepressant-like effects of MG were similar to GE in the tail suspension test and the forced swim test. Furthermore, we found MG could be detected in the brain homogenate of mice treated orally with MG 0.52 mmol/kg/day for 1 day by HPLC. The area under the curve (AUC) of MG in the brain homogenate was enhanced to 21.7 times that of GE. The brain amount and distribution speed of MG were improved significantly after oral administration. This study demonstrated that MG possessed the antidepressant effects and could cross the blood-brain barrier, but had less hepatotoxicity.


Subject(s)
Antidepressive Agents/pharmacology , Blood-Brain Barrier/drug effects , Blood-Brain Barrier/metabolism , Iridoids/pharmacology , Liver/drug effects , Animals , Antidepressive Agents/adverse effects , Antidepressive Agents/chemistry , Body Weight/drug effects , Brain/drug effects , Brain/metabolism , Chromatography, High Pressure Liquid , Iridoids/administration & dosage , Iridoids/adverse effects , Iridoids/chemistry , Liver/pathology , Molecular Structure , Permeability , Rats , Tissue Distribution
19.
Drug Metab Dispos ; 42(2): 274-81, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24277725

ABSTRACT

This study investigated the metabolism of salvianolic acid A (SAA) both in vivo and in vitro. Liquid chromatography-mass spectrometry analysis of drug-containing rat bile samples and bile samples hydrolyzed by glucuronidase revealed a series of methylated conjugates of SAA and its glucuronides, as well as the predominance of the methylation pathway of SAA in rats. For the first time, four major methylated metabolites present in vivo were prepared for structure characterization and bioactivity evaluation using in vitro coincubation systems with rat hepatic cytosol protein as the enzyme donor. By using nuclear magnetic resonance imaging and other spectroscopic methods, these metabolites were unambiguously elucidated as 3-O-methyl-SAA (M1), 3'-O-methyl-SAA (M2), 3,3″-O-dimethyl-SAA (M3), and 3',3″-O-dimethyl-SAA (M4), respectively. Along with results from the enzyme inhibition study, selective formation of these meta-O-methylated derivatives indicated that catechol O-methyltransferase (COMT) is responsible for methylated transformation of SAA. All of these metabolites displayed fairly high antioxidant potency against in vitro rat liver lipid peroxidation with half-maximal inhibitory concentrations that were much lower than those of the positive controls and even SAA. Overall, the results from this study demonstrate that SAA is a metabolically unstable compound that undergoes rapid methylation metabolism catalyzed by COMT, and these generated O-methylated metabolites may be largely responsible for its in vivo pharmacological effects.


Subject(s)
Alkenes/metabolism , Antioxidants/metabolism , Polyphenols/metabolism , Alkenes/pharmacology , Animals , Antioxidants/pharmacology , Bile/metabolism , Biotransformation , Catechol O-Methyltransferase/metabolism , Catechol O-Methyltransferase Inhibitors , Dose-Response Relationship, Drug , Enzyme Inhibitors/pharmacology , Glucuronides/metabolism , Lipid Peroxidation/drug effects , Male , Methylation , Polyphenols/pharmacology , Rats , Rats, Sprague-Dawley
20.
Neurotherapeutics ; 21(3): e00342, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38493057

ABSTRACT

Novel therapeutics for the treatment of ischemic stroke remains to be the unmet clinical needs. Previous studies have indicated that salvianolic acid A (SAA) is a promising candidate for the treatment of the brain diseases. However, SAA has poor absolute bioavailability and does not efficiently cross the intact blood-brain barrier (BBB), which limit its efficacy. To this end we developed a brain-targeted liposomes for transporting SAA via the BBB by incorporating the liposomes to a transport receptor, insulin-like growth factor-1 receptor (IGF1R). The liposomes were prepared by ammonium sulfate gradients loading method. The prepared SAA-loaded liposomes (Lipo/SAA) were modified with IGF1R monoclonal antibody to generate IGF1R antibody-conjugated Lipo/SAA (IGF1R-targeted Lipo/SAA). The penetration of IGF1R-targeted Lipo/SAA into the brain was confirmed by labeling with Texas Red, and their efficacy were evaluate using middle cerebral artery occlusion (MCAO) model. The results showed that IGF1R-targeted Lipo/SAA are capable of transporting SAA across the BBB into the brain, accumulation in brain tissue, and sustained releasing SAA for several hours. Administration o IGF1R-targeted Lipo/SAA notably reduced infarct size and neuronal damage, improved neurological function and inhibited cerebral inflammation, which had much higher efficiency than no-targeted SAA.


Subject(s)
Ischemic Stroke , Liposomes , Animals , Ischemic Stroke/drug therapy , Male , Caffeic Acids/administration & dosage , Caffeic Acids/chemistry , Caffeic Acids/pharmacology , Blood-Brain Barrier/drug effects , Blood-Brain Barrier/metabolism , Receptor, IGF Type 1/metabolism , Mice , Lactates/administration & dosage , Lactates/chemistry , Infarction, Middle Cerebral Artery/drug therapy , Drug Delivery Systems/methods , Rats, Sprague-Dawley , Rats , Brain/metabolism , Brain/drug effects
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