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Article ; Online: Integrative analysis of multi-omics data reveals inhibition of RB1 signaling promotes apatinib resistance of hepatocellular carcinoma.

He, Ke / An, Sanqi / Liu, Fei / Chen, Ye / Xiang, Guoan / Wang, Haihe

International journal of biological sciences

2023 Volume 19, Issue 14, Page(s) 4511–4524

Abstract: Although apatinib is a promising drug for the treatment of liver cancer, the underlying drug resistance mechanism is still unclear. Here, we constructed apatinib-resistant HepG2 cells. We then characterized the epigenomic, transcriptomic, and proteomic ... ...

Abstract	Although apatinib is a promising drug for the treatment of liver cancer, the underlying drug resistance mechanism is still unclear. Here, we constructed apatinib-resistant HepG2 cells. We then characterized the epigenomic, transcriptomic, and proteomic landscapes both in apatinib-resistant and non-resistant HepG2 cells. Differential expression, ATAC-seq, and proteomic data analyses were performed. We found that the cell cycle related protein RB1 may play an essential role in the process of apatinib resistant to hepatocarcinoma. Moreover, there were extensive variations at the transcriptome, epigenetic, and proteomic level. Finally, quantitative PCR (qPCR) and western blot analysis showed that expression level of RB1 in apatinib-resistant cell as well as the samples of patients in progressive disease were significantly lower than that in controls. Those results also showed that the RB1 pathway inhibitors CDK2-IN-73 and Palbociclib could relieve the resistance of apatinib resistant cells. Our results further enhance our understanding of the anti-tumorigenic and anti-angiogenic efficacy of apatinib in liver cancer and provide a novel perspective regarding apatinib resistance. Furthermore, we proved that CDKN2B inhibition of RB1 signaling promoted apatinib resistance in hepatocellular carcinoma. Those findings have greatly important biological significance for the resistance of apatinib and the treatment of liver cancer.
MeSH term(s)	Humans ; Carcinoma, Hepatocellular/drug therapy ; Carcinoma, Hepatocellular/genetics ; Carcinoma, Hepatocellular/pathology ; Cell Line, Tumor ; Liver Neoplasms/drug therapy ; Liver Neoplasms/genetics ; Liver Neoplasms/pathology ; Multiomics ; Proteomics ; Retinoblastoma Binding Proteins ; Ubiquitin-Protein Ligases ; Drug Resistance, Neoplasm
Chemical Substances	apatinib (5S371K6132) ; RB1 protein, human ; Retinoblastoma Binding Proteins ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
Language	English
Publishing date	2023-08-21
Publishing country	Australia
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2179208-2
ISSN	1449-2288 ; 1449-2288
ISSN (online)	1449-2288
ISSN	1449-2288
DOI	10.7150/ijbs.83862
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Potential Inhibitors of Monkeypox Virus Revealed by Molecular Modeling Approach to Viral DNA Topoisomerase I

Xiaopeng Hu / Sanqi An / Jiemei Chu / Bingyu Liang / Yanyan Liao / Junjun Jiang / Yao Lin / Li Ye / Hao Liang

Molecules, Vol 28, Iss 1444, p

2023 Volume 1444

Abstract: The monkeypox outbreak has become a global public health emergency. The lack of valid and safe medicine is a crucial obstacle hindering the extermination of orthopoxvirus infections. The identification of potential inhibitors from natural products, ... ...

Abstract	The monkeypox outbreak has become a global public health emergency. The lack of valid and safe medicine is a crucial obstacle hindering the extermination of orthopoxvirus infections. The identification of potential inhibitors from natural products, including Traditional Chinese Medicine (TCM), by molecular modeling could expand the arsenal of antiviral chemotherapeutic agents. Monkeypox DNA topoisomerase I (TOP1) is a highly conserved viral DNA repair enzyme with a small size and low homology to human proteins. The protein model of viral DNA TOP1 was obtained by homology modeling. The reliability of the TOP1 model was validated by analyzing its Ramachandran plot and by determining the compatibility of the 3D model with its sequence using the Verify 3D and PROCHECK services. In order to identify potential inhibitors of TOP1, an integrated library of 4103 natural products was screened via Glide docking. Surface Plasmon Resonance (SPR) was further implemented to assay the complex binding affinity. Molecular dynamics simulations (100 ns) were combined with molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) computations to reveal the binding mechanisms of the complex. As a result, three natural compounds were highlighted as potential inhibitors via docking-based virtual screening. Rosmarinic acid, myricitrin, quercitrin, and ofloxacin can bind TOP1 with KD values of 2.16 μM, 3.54 μM, 4.77 μM, and 5.46 μM, respectively, indicating a good inhibitory effect against MPXV. The MM/PBSA calculations revealed that rosmarinic acid had the lowest binding free energy at −16.18 kcal/mol. Myricitrin had a binding free energy of −13.87 kcal/mol, quercitrin had a binding free energy of −9.40 kcal/mol, and ofloxacin had a binding free energy of −9.64 kcal/mol. The outputs (RMSD/RMSF/Rg/SASA) also indicated that the systems were well-behaved towards the complex. The selected compounds formed several key hydrogen bonds with TOP1 residues (TYR274, LYS167, GLY132, LYS133, etc.) via the binding mode analysis. TYR274 was ...
Keywords	monkeypox virus ; DNA topoisomerase I (TOP1) ; natural products ; rosmarinic acid ; molecular dynamics simulation ; Surface Plasmon Resonance (SPR) ; Organic chemistry ; QD241-441
Subject code	540
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Integrative epigenomic profiling reveal AP-1 is a key regulator in intrahepatich cholangiocarcinoma.

He, Ke / Feng, Yuliang / An, Sanqi / Liu, Fei / Xiang, Guoan

Genomics

2021 Volume 114, Issue 1, Page(s) 241–252

Abstract: Intrahepatic cholangiocarcinoma (ICC) is a malignant tumor with poor prognosis while its mechanisms of pathogenesis remain elusive. In this study, we performed systemic epigenomic and transcriptomic profiling via MNase-seq, ChIP-seq and RNA-seq in normal ...

Abstract	Intrahepatic cholangiocarcinoma (ICC) is a malignant tumor with poor prognosis while its mechanisms of pathogenesis remain elusive. In this study, we performed systemic epigenomic and transcriptomic profiling via MNase-seq, ChIP-seq and RNA-seq in normal cholangiocyte and ICC cell lines. We showed that active histone modifications (H3K4me3, H3K4me1 and H3K27ac) were less enriched on cancer-related genes in ICC cell lines compared to control. The region of different histone modification patterns is enrichment in sites of AP-1 motif. Subsequent analysis showed that ICC had different nucleosome occupancy in differentially expressed genes compared to a normal cell line. Furthermore, we found that AP-1 plays a key role in ICC and regulates ICC-related genes through its AP-1 binding site. This study is the first report showing the global features of histone modification, transcript, and nucleosome profiles in ICC; we also show that the transcription factor AP-1 might be a key target gene in ICC.
MeSH term(s)	Bile Duct Neoplasms/genetics ; Bile Duct Neoplasms/metabolism ; Bile Duct Neoplasms/pathology ; Bile Ducts, Intrahepatic/metabolism ; Bile Ducts, Intrahepatic/pathology ; Cholangiocarcinoma/genetics ; Cholangiocarcinoma/metabolism ; Cholangiocarcinoma/pathology ; Epigenomics ; Humans ; Proto-Oncogene Proteins c-fos ; Proto-Oncogene Proteins c-jun ; Transcription Factor AP-1/genetics ; Transcription Factor AP-1/metabolism
Chemical Substances	Proto-Oncogene Proteins c-fos ; Proto-Oncogene Proteins c-jun ; Transcription Factor AP-1
Language	English
Publishing date	2021-12-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	356334-0
ISSN	1089-8646 ; 0888-7543
ISSN (online)	1089-8646
ISSN	0888-7543
DOI	10.1016/j.ygeno.2021.12.008
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Article ; Online: Dynamic m

Chu, Jiemei / Zheng, Ruili / Chen, Hubin / Chen, Yaxin / Lin, Yao / Li, Jingyi / Wei, Wudi / Chen, Rongfeng / Deng, Peixue / Su, Jinming / Jiang, Junjun / Ye, Li / Liang, Hao / An, Sanqi

Journal of medical virology

2023 Volume 96, Issue 2, Page(s) e29466

Abstract: Talaromyces marneffei (TM) immune evasion is an important factor leading to the high mortality rate of Penicilliosis marneffei. ... ...

Abstract	Talaromyces marneffei (TM) immune evasion is an important factor leading to the high mortality rate of Penicilliosis marneffei. N
MeSH term(s)	Humans ; Toll-Like Receptor 2/genetics ; Coinfection ; Mycoses ; HIV Infections ; RNA Helicases
Chemical Substances	Toll-Like Receptor 2 ; TLR2 protein, human ; YTHDC2 protein, human (EC 3.6.4.13) ; RNA Helicases (EC 3.6.4.13)
Language	English
Publishing date	2023-10-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.29466
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Article ; Online: Systematic analysis of clinical relevance and molecular characterization of m

An, Sanqi / Xie, Zhouhua / Liao, Yanyan / Jiang, Junjun / Dong, Wenyi / Yin, Fuqiang / Li, Wen-Xing / Ye, Li / Lin, Jianyan / Liang, Hao

Genes & diseases

2022 Volume 9, Issue 5, Page(s) 1170–1173

Language	English
Publishing date	2022-01-05
Publishing country	China
Document type	Journal Article
ZDB-ID	2821806-1
ISSN	2352-3042 ; 2352-3042
ISSN (online)	2352-3042
ISSN	2352-3042
DOI	10.1016/j.gendis.2021.12.005
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Article ; Online: Integrative epigenomic profiling reveal AP-1 is a key regulator in intrahepatic cholangiocarcinoma

He, Ke / Feng, Yuliang / An, Sanqi / Liu, Fei / Xiang, Guoan

Genomics. 2022 Jan., v. 114, no. 1 p.241-252

2022

Abstract	Intrahepatic cholangiocarcinoma (ICC) is a malignant tumor with poor prognosis while its mechanisms of pathogenesis remain elusive. In this study, we performed systemic epigenomic and transcriptomic profiling via MNase-seq, ChIP-seq and RNA-seq in normal cholangiocyte and ICC cell lines. We showed that active histone modifications (H3K4me3, H3K4me1 and H3K27ac) were less enriched on cancer-related genes in ICC cell lines compared to control. The region of different histone modification patterns is enrichment in sites of AP-1 motif. Subsequent analysis showed that ICC had different nucleosome occupancy in differentially expressed genes compared to a normal cell line. Furthermore, we found that AP-1 plays a key role in ICC and regulates ICC-related genes through its AP-1 binding site. This study is the first report showing the global features of histone modification, transcript, and nucleosome profiles in ICC; we also show that the transcription factor AP-1 might be a key target gene in ICC.
Keywords	cell lines ; chromatin immunoprecipitation ; epigenome ; gene expression regulation ; genes ; genomics ; histone code ; histones ; neoplasms ; nucleosomes ; pathogenesis ; prognosis ; sequence analysis ; transcription factors ; transcriptomics ; Intrahepatic cholangiocarcinoma ; Histone modification ; Nucleosome positioning ; Data analysis ; AP-1
Language	English
Dates of publication	2022-01
Size	p. 241-252.
Publishing place	Elsevier Inc.
Document type	Article ; Online
Note	Use and reproduction
ZDB-ID	356334-0
ISSN	1089-8646 ; 0888-7543
ISSN (online)	1089-8646
ISSN	0888-7543
DOI	10.1016/j.ygeno.2021.12.008
Database	NAL-Catalogue (AGRICOLA)

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ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Potential Inhibitors of Monkeypox Virus Revealed by Molecular Modeling Approach to Viral DNA Topoisomerase I.

Hu, Xiaopeng / An, Sanqi / Chu, Jiemei / Liang, Bingyu / Liao, Yanyan / Jiang, Junjun / Lin, Yao / Ye, Li / Liang, Hao

Molecules (Basel, Switzerland)

2023 Volume 28, Issue 3

Abstract	The monkeypox outbreak has become a global public health emergency. The lack of valid and safe medicine is a crucial obstacle hindering the extermination of orthopoxvirus infections. The identification of potential inhibitors from natural products, including Traditional Chinese Medicine (TCM), by molecular modeling could expand the arsenal of antiviral chemotherapeutic agents. Monkeypox DNA topoisomerase I (TOP1) is a highly conserved viral DNA repair enzyme with a small size and low homology to human proteins. The protein model of viral DNA TOP1 was obtained by homology modeling. The reliability of the TOP1 model was validated by analyzing its Ramachandran plot and by determining the compatibility of the 3D model with its sequence using the Verify 3D and PROCHECK services. In order to identify potential inhibitors of TOP1, an integrated library of 4103 natural products was screened via Glide docking. Surface Plasmon Resonance (SPR) was further implemented to assay the complex binding affinity. Molecular dynamics simulations (100 ns) were combined with molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) computations to reveal the binding mechanisms of the complex. As a result, three natural compounds were highlighted as potential inhibitors via docking-based virtual screening. Rosmarinic acid, myricitrin, quercitrin, and ofloxacin can bind TOP1 with KD values of 2.16 μM, 3.54 μM, 4.77 μM, and 5.46 μM, respectively, indicating a good inhibitory effect against MPXV. The MM/PBSA calculations revealed that rosmarinic acid had the lowest binding free energy at -16.18 kcal/mol. Myricitrin had a binding free energy of -13.87 kcal/mol, quercitrin had a binding free energy of -9.40 kcal/mol, and ofloxacin had a binding free energy of -9.64 kcal/mol. The outputs (RMSD/RMSF/Rg/SASA) also indicated that the systems were well-behaved towards the complex. The selected compounds formed several key hydrogen bonds with TOP1 residues (TYR274, LYS167, GLY132, LYS133, etc.) via the binding mode analysis. TYR274 was predicted to be a pivotal residue for compound interactions in the binding pocket of TOP1. The results of the enrichment analyses illustrated the potential pharmacological networks of rosmarinic acid. The molecular modeling approach may be acceptable for the identification and design of novel poxvirus inhibitors; however, further studies are warranted to evaluate their therapeutic potential.
MeSH term(s)	Biological Products ; DNA Topoisomerases, Type I ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Monkeypox virus/drug effects ; Ofloxacin ; Reproducibility of Results ; Antiviral Agents/chemistry ; Rosmarinic Acid
Chemical Substances	Biological Products ; DNA Topoisomerases, Type I (EC 5.99.1.2) ; Ofloxacin (A4P49JAZ9H) ; Antiviral Agents
Language	English
Publishing date	2023-02-02
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules28031444
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Article ; Online: Willingness to accept monkeypox vaccine and its correlates among men who have sex with men in Southern China: a web-based online cross-sectional study.

Huang, Xinju / Lin, Zhifeng / Qin, Jiao / Yu, Dee / Zhang, Fei / Fang, Ganggang / Chen, Xi / He, Jinfeng / Cen, Ping / Li, Mu / Zhang, Rongjing / Luo, Tong / Jiang, Junjun / An, Sanqi / Liang, Hao / Ye, Li / Liang, Bingyu

Frontiers in public health

2024 Volume 12, Page(s) 1289918

Abstract: Background: The May 2022 global outbreak of monkeypox (MPX) poses a threat to the health of men who have sex with men. However, there is limited data on the willingness of MSM to receive monkeypox vaccination in Southern China. This study aimed to ... ...

Abstract	Background: The May 2022 global outbreak of monkeypox (MPX) poses a threat to the health of men who have sex with men. However, there is limited data on the willingness of MSM to receive monkeypox vaccination in Southern China. This study aimed to assess the knowledge of MPX, concerns regarding MPX, and willingness to receive monkeypox vaccination, as well as their correlates, among MSM in China. Methods: We conducted a Web-based online survey of MSM in Southern China from August to September 2022. Data were collected on the socio-demographic characteristics, knowledge, worries, concerns regarding MPX and willingness to receive monkeypox vaccination. Multivariate logistic regression was employed to explore the factors associated with willingness to receive monkeypox vaccination. Results: A total of 1903 participants completed the survey. Among them, approximately 69.9% reported being aware of MPX awareness, 94.1% of the participants supported the promotion of monkeypox vaccination. The majority of participants (91.4%) expressed their willingness to receive monkeypox vaccination. Participants who considered monkeypox vaccination safe [adjusted odds ratio (aOR) = 4.82, 95% CI: 1.35-17.18], agreed on the necessity of government promotion of monkeypox vaccination in China (aOR = 6.03, 95% CI: 1.07-33.93), believed in prioritizing monkeypox vaccination for MSM (aOR = 5.01, 95% CI: 1.10-22.71), and had friends or sexual partners who had already received the monkeypox or smallpox vaccination (aOR = 10.37, 95% CI: 2.11-50.99) are more likely to be vaccinated. Conversely, married individuals (aOR = 0.13, 95% CI: 0.03-0.47), those engaging in anal sex 4-6 times per week in the past 3 months (aOR = 0.26, 95% CI: 0.09-0.77) expressed hesitancy toward monkeypox vaccination. Conclusion: There was a high willingness to receive monkeypox vaccination among MSM in China. The hesitancy toward the monkeypox vaccine can be effectively mitigated by addressing concerns about its safety and potential adverse reactions. Moreover, increasing acceptance of the monkeypox vaccination among MSM and their peers is crucial, as social influence significantly impacts vaccine attitudes and behaviors.
MeSH term(s)	Male ; Humans ; Homosexuality, Male ; Smallpox Vaccine ; Cross-Sectional Studies ; HIV Infections/epidemiology ; Mpox (monkeypox) ; Sexual and Gender Minorities ; China/epidemiology ; Internet
Chemical Substances	Smallpox Vaccine
Language	English
Publishing date	2024-02-07
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2711781-9
ISSN	2296-2565 ; 2296-2565
ISSN (online)	2296-2565
ISSN	2296-2565
DOI	10.3389/fpubh.2024.1289918
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Article ; Online: Weighted gene co-expression network analysis revealed T cell differentiation associated with the age-related phenotypes in COVID-19 patients

Yao Lin / Yueqi Li / Hubin Chen / Jun Meng / Jingyi Li / Jiemei Chu / Ruili Zheng / Hailong Wang / Peijiang Pan / Jinming Su / Junjun Jiang / Li Ye / Hao Liang / Sanqi An

BMC Medical Genomics, Vol 16, Iss 1, Pp 1-

2023 Volume 14

Abstract: Abstract The risk of severe condition caused by Corona Virus Disease 2019 (COVID-19) increases with age. However, the underlying mechanisms have not been clearly understood. The dataset GSE157103 was used to perform weighted gene co-expression network ... ...

Abstract	Abstract The risk of severe condition caused by Corona Virus Disease 2019 (COVID-19) increases with age. However, the underlying mechanisms have not been clearly understood. The dataset GSE157103 was used to perform weighted gene co-expression network analysis on 100 COVID-19 patients in our analysis. Through weighted gene co-expression network analysis, we identified a key module which was significantly related with age. This age-related module could predict Intensive Care Unit status and mechanical-ventilation usage, and enriched with positive regulation of T cell receptor signaling pathway biological progress. Moreover, 10 hub genes were identified as crucial gene of the age-related module. Protein–protein interaction network and transcription factors-gene interactions were established. Lastly, independent data sets and RT-qPCR were used to validate the key module and hub genes. Our conclusion revealed that key genes were associated with the age-related phenotypes in COVID-19 patients, and it would be beneficial for clinical doctors to develop reasonable therapeutic strategies in elderly COVID-19 patients.
Keywords	COVID-19 ; Weighted gene ; Aging ; T-cell immunity ; Internal medicine ; RC31-1245 ; Genetics ; QH426-470
Subject code	610
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Talaromyces marneffei suppresses macrophage inflammation by regulating host alternative splicing.

Wei, Wudi / Wang, Gang / Zhang, Hong / Bao, Xiuli / An, Sanqi / Luo, Qiang / He, Jinhao / Chen, Lixiang / Ning, Chuanyi / Lai, Jingzhen / Yuan, Zongxiang / Chen, Rongfeng / Jiang, Junjun / Ye, Li / Liang, Hao

Communications biology

2023 Volume 6, Issue 1, Page(s) 1046

Abstract: Talaromyces marneffei (T. marneffei) immune escape is essential in the pathogenesis of talaromycosis. It is currently known that T. marneffei achieves immune escape through various strategies. However, the role of cellular alternative splicing (AS) in ... ...

Abstract	Talaromyces marneffei (T. marneffei) immune escape is essential in the pathogenesis of talaromycosis. It is currently known that T. marneffei achieves immune escape through various strategies. However, the role of cellular alternative splicing (AS) in immune escape remains unclear. Here, we depict the AS landscape in macrophages upon T. marneffei infection via high-throughput RNA sequencing and detect a truncated protein of NCOR2 / SMRT, named NCOR2-013, which is significantly upregulated after T. marneffei infection. Mechanistic analysis indicates that NCOR2-013 forms a co-repression complex with TBL1XR1 / TBLR1 and HDAC3, thereby inhibiting JunB-mediated transcriptional activation of pro-inflammatory cytokines via the inhibition of histone acetylation. Furthermore, we identify TUT1 as the AS regulator that regulates NCOR2-013 production and promotes T. marneffei immune evasion. Collectively, these findings indicate that T. marneffei escapes macrophage killing through TUT1-mediated alternative splicing of NCOR2 / SMRT, providing insight into the molecular mechanisms of T. marneffei immune evasion and potential targets for talaromycosis therapy.
MeSH term(s)	Humans ; Alternative Splicing ; Macrophages ; Inflammation/genetics
Language	English
Publishing date	2023-10-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-023-05409-6
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