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Article: Genome-wide association study identified genes associated with ammonia nitrogen tolerance in

Fu, Shuo / Liu, Jianyong

2022 Volume 13, Page(s) 961009

Abstract: Ammonia nitrogen tolerance is an economically important trait of the farmed penaeid ... ...

Abstract	Ammonia nitrogen tolerance is an economically important trait of the farmed penaeid shrimp
Language	English
Publishing date	2022-08-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2022.961009
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Article ; Online: Nuclear factor interleukin 3 (NFIL3) participates in regulation of the NF-κB-mediated inflammation and antioxidant system in Litopenaeus vannamei under ammonia-N stress.

Zhuo, Hongbiao / Liu, Jianyong

Fish & shellfish immunology

2022 Volume 131, Page(s) 1192–1205

Abstract: Nuclear factor interleukin 3 (NFIL3) is a critical upstream regulator of the NF-κB pathway. Nevertheless, the detailed molecular mechanism of NFIL3 and its function in shrimp have not been well characterized. In the present study, NFIL3 was identified ... ...

Abstract	Nuclear factor interleukin 3 (NFIL3) is a critical upstream regulator of the NF-κB pathway. Nevertheless, the detailed molecular mechanism of NFIL3 and its function in shrimp have not been well characterized. In the present study, NFIL3 was identified and characterized from Litopenaeus vannamei. Molecular feature analysis revealed that the open reading frame (ORF) of LvNFIL3 was 2963 bp, which codes for a polypeptide of 516 amino acids with a conserved basic region leucine zipper (bZIP) domain. Sequence alignments and phylogenetic tree analysis showed that the amino acid sequence of LvNFIL3 shared 18.82%-98.07% identity with that of NFIL3 in other species, and was closely related to Penaeus monodon NFIL3. A core promoter in the 5' flanking region of LvNFIL3 was essential for regulation of transcription. LvNFIL3 mRNA was highly expressed in gills and hepatopancreas. Subcellular localization of the protein was observed almost exclusively in the nucleus. Amplification of mRNA by RT-qPCR showed that LvNFIL3 was induced in shrimp gills, hepatopancreas, and muscle after ammonia-N stress. Moreover, silencing of LvNFIL3 increased the mortality of shrimp exposed to ammonia-N. Furthermore, dual-luciferase reporter assay data suggested that LvNFIL3 was capable of activating the NF-κB pathway. Conversely, knockdown of LvNFIL3 decreased NF-κB homolog (Dorsal and Relish) and IkB homolog (Cactus) expression, as well as expression of anti-inflammatory cytokine (IL-16) and five antioxidant-related genes (HO-1, Mn-SOD, CAT, GPx, and GST), whereas NF-κB repressing factor (NKRF) and inflammation-related genes (TNFα and Spz) were upregulated. More importantly, LvNFIL3 knockdown exacerbated the pathology in hepatopancreas exposed to ammonia-N, and the total antioxidant capacity (T-AOC) and superoxide dismutase (T-SOD) were significantly decreased, resulting in a significant increased lipid peroxidation and protein carbonization. Taken together, these data suggest that LvNFIL3 was involved in ammonia-N tolerance in L. vannamei by regulating the inflammation and antioxidant system through the NF-κB pathway.
Language	English
Publishing date	2022-11-17
Publishing country	England
Document type	Journal Article
ZDB-ID	1067738-0
ISSN	1095-9947 ; 1050-4648
ISSN (online)	1095-9947
ISSN	1050-4648
DOI	10.1016/j.fsi.2022.11.028
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Article ; Online: A novel cholesterol metabolism-related ferroptosis pathway in hepatocellular carcinoma.

Fang, Weiwei / Liu, Jianyong / Zhang, Fanguo / Pang, Cheng / Li, Xiying

Discover. Oncology

2024 Volume 15, Issue 1, Page(s) 7

Abstract: Background: Emerging studies have reported the contribution of cholesterol to hepatocellular carcinoma (HCC) progression. However, the specific role and mechanism of cholesterol metabolism on spontaneous and progressive HCC development from the point of ...

Abstract	Background: Emerging studies have reported the contribution of cholesterol to hepatocellular carcinoma (HCC) progression. However, the specific role and mechanism of cholesterol metabolism on spontaneous and progressive HCC development from the point of view of ferroptosis are still worth exploring. The present study aimed to reveal a novel mechanism of cholesterol metabolism-related ferroptosis in hepatocellular carcinoma cells. Methods: Two microarray datasets (GSE25097, GSE22058) related to HCC were downloaded from Gene Expression Omnibus (GEO) datasets. Metabolomics analysis was performed by ultra performance liquid chromatography - tandem mass spectrometer (UPLC-MS/MS). The cholesterol-related proteins were downloaded from HMBD. Ferroptosis-related genes were extracted from FerrDb database. Data sets were separated into two groups. GSE25097 was used to identify ferroptosis-related genes, and GSE22058 was used to verify results. During these processes, chemical-protein interaction (CPI), protein-protein interaction (PPI), the Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted. Multivariate logistic regression analysis was used to test the associated pathway. Results: We identified 8 differentially expressed ferroptosis-related genes (HAMP, PTGS2, IL1B, ALOX15B, CDKN2A, RRM2, NQO1 and KIF20A) and 4 differentially expressed cholesterol-related genes (LCAT, CH25H, CEL and CYP7A1). Furthermore, based on the predicted results with STITCH, we identified indomethacin and IL1B as the essential node for cholesterol-mediated ferroptosis in hepatocellular carcinoma cell. Multivariate logistic regression analysis showed the activities of plasma IL1B in liver cancer patients enrolled have been significantly affected by the level of plasma cholesterol (P < 0.001) and the test result of IL1B is a predictor variable causing the changes of serum Fe levels (P < 0.001). Conclusions: Our findings shed new light on the association between cholesterol metabolism and ferroptosis in HCC, and suggest that IL1B is the necessary node for cholesterol to lead to ferroptosis process in HCC. Also, we identified the potential role of indomethacin in adjuvant therapy of HCC with complications of abnormal cholesterol metabolism.
Language	English
Publishing date	2024-01-08
Publishing country	United States
Document type	Journal Article
ISSN	2730-6011
ISSN (online)	2730-6011
DOI	10.1007/s12672-023-00822-z
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Article ; Online: Role of Nrf2-Keap1 signaling in the antioxidant defense response induced by low salinity in the kuruma shrimp (Marsupenaeus japonicus)

Ou, Haixin / Liu, Jianyong

Aquacult Int. 2022 Dec., v. 30, no. 6 p.2793-2811

2022

Abstract: Salinity is an important environmental factor that induces oxidative stress in shrimp. This study evaluated the effects of abrupt low-salinity stress (23, 17, and 11) on histological structure, lipid peroxidation, mRNA levels and activities of ... ...

Abstract	Salinity is an important environmental factor that induces oxidative stress in shrimp. This study evaluated the effects of abrupt low-salinity stress (23, 17, and 11) on histological structure, lipid peroxidation, mRNA levels and activities of antioxidant enzymes, and gene expression of Nrf2-Keap1 signaling molecules at different times (6, 12, 24, 48, and 96 h) in the gills and hepatopancreas of Marsupenaeus japonicus. Mild or strong increase in the levels of nuclear factor erythroid 2-related factor-2 (Nrf2) and antioxidant genes and enzymes such as superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPX) were observed after short-term exposure (6 and 12 h). After 48 and/or 96 h of exposure to low salinity, Nrf2 was significantly downregulated (P < 0.05), which was accompanied by downregulation of the levels of Nrf2-Keap1 pathway-related genes and enzymes such as SOD, CAT, and GPX, along with upregulation of Kelch-like-ECH-associated protein 1 (Keap1) and malondialdehyde (MDA). Pathological alterations were also observed in the gills and hepatopancreas of M. japonicus after 96 h of exposure to different salinities. The observed changes in antioxidant gene expression are consistent with a requirement for Nrf2 in the induction of antioxidant genes. Furthermore, there was a negative correlation between the mRNA levels of Nrf2 and Keap1, indicating that Keap1 is important for inhibition of the Nrf2 response. Negative relationships were observed between lipid peroxidation and antioxidant enzyme activities, while positive relationships were observed between activities and gene expression levels of antioxidant enzymes, suggesting the changes in molecular and enzyme activity levels may provide protection against damage from low-salinity stress. In conclusion, our data demonstrated that Nrf2-Keap1 signaling is important for modulating the gene expression levels of antioxidant enzymes. This is the first study to elucidate the effects of low-salinity stress on antioxidant responses in M. japonicus through the Nrf2-Keap1 pathway. The results provide insights into the mechanisms by which crustaceans resist salinity stress.
Keywords	Marsupenaeus japonicus ; acute exposure ; antioxidant activity ; antioxidant enzymes ; antioxidant genes ; catalase ; environmental factors ; enzyme activity ; gene expression ; glutathione peroxidase ; hepatopancreas ; histology ; lipid peroxidation ; malondialdehyde ; oxidative stress ; salinity ; salt stress ; shrimp ; superoxide dismutase
Language	English
Dates of publication	2022-12
Size	p. 2793-2811.
Publishing place	Springer International Publishing
Document type	Article ; Online
ZDB-ID	1176356-5
ISSN	1573-143X ; 0967-6120
ISSN (online)	1573-143X
ISSN	0967-6120
DOI	10.1007/s10499-022-00941-4
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Unraveling the Mechanism of ACQ-to-AIE Transformation of Fluorescein Derivatives.

Jiang, Gaoshang / Liu, Jianyong / Zhou, Panwang

The journal of physical chemistry. A

2023 Volume 127, Issue 24, Page(s) 5193–5201

Abstract: Although fluorescein derivatives have excellent properties and strong practicability, they are typical aggregation-induced quenching (ACQ) molecules, which are not conducive to working in the solid state. Recently, the fluorescein derivative Fl-Me with ... ...

Abstract	Although fluorescein derivatives have excellent properties and strong practicability, they are typical aggregation-induced quenching (ACQ) molecules, which are not conducive to working in the solid state. Recently, the fluorescein derivative Fl-Me with aggregation-induced emission (AIE) property was synthesized, which brought a new dawn for the research and development of fluorescein-based materials. In this study, the AIE mechanism of Fl-Me was investigated based on time-dependent density functional theory and the ONIOM method. The results revealed that an effective dark-state deactivation pathway leads to the fluorescence quenching of Fl-Me in a solution environment. Accordingly, the AIE phenomenon originates from the closure of the dark-state quenching channel. It is worth emphasizing that we found that the carbonyl group of molecular Fl-Me has intermolecular hydrogen bonding interaction with the adjacent molecules, which caused the increase of the dark-state energy in the crystalline state. Moreover, the restriction of the rotational motion and the nonexistence of the π-π stacking interaction are beneficial to the enhancement of fluorescence upon aggregation. Finally, the ACQ-to-AIE transformation mechanisms of fluorescein derivatives have been discussed. This work provides deeper insight into the photophysical mechanism for the fluorescein derivatives Fl-Me with AIE feature and eventually is expected to help researchers to develop more fluorescein-based AIE materials with remarkable properties for various fields.
Language	English
Publishing date	2023-06-09
Publishing country	United States
Document type	Journal Article
ISSN	1520-5215
ISSN (online)	1520-5215
DOI	10.1021/acs.jpca.3c02244
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Article ; Online: A 9 mRNAs-based diagnostic signature for rheumatoid arthritis by integrating bioinformatic analysis and machine-learning.

Liu, Jianyong / Chen, Ningjie

Journal of orthopaedic surgery and research

2021 Volume 16, Issue 1, Page(s) 44

Abstract: Background: Rheumatoid arthritis (RA) is an autoimmune rheumatic disease that carries a substantial burden for both patients and society. Early diagnosis of RA is essential to prevent disease progression and select an optimal therapeutic strategy. ... ...

Abstract	Background: Rheumatoid arthritis (RA) is an autoimmune rheumatic disease that carries a substantial burden for both patients and society. Early diagnosis of RA is essential to prevent disease progression and select an optimal therapeutic strategy. However, RA diagnosis is challenging, partly due to a lack of reliable biomarkers. Here, we aimed to explore the diagnostic signature and establish a predictive model of RA. Methods: The mRNA expression profiling data of GSE17755, containing blood samples of 112 RA patients and 53 healthy control patients, were obtained from the Gene Expression Omnibus (GEO) database, followed by differential expression, GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis. A PPI network was constructed to select candidate hub genes, then logistic regression and random forest models were established based on the identified genes. Results: Significantly, we identified 52 differentially expressed genes (DEGs), including 16 upregulated genes and 36 downregulated genes in RA samples compared with control samples. GO and KEGG analysis showed that several immune-related cellular processes were particularly enriched. We identified nine hub genes in the PPI network, including CFL1, COTL1, ACTG1, PFN1, LCP1, LCK, HLA-E, FYN, and HLA-DRA. The logistic regression and random forest models based on the nine identified genes reliably distinguished the RA samples from the healthy samples with substantially high AUC. Conclusion: The diagnostic logistic regression and random forest models based on nine hub genes reliably predicted the occurrence of RA. Our findings could provide new insights into RA diagnostics.
Language	English
Publishing date	2021-01-11
Publishing country	England
Document type	Journal Article
ISSN	1749-799X
ISSN (online)	1749-799X
DOI	10.1186/s13018-020-02180-w
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Article ; Online: Strategies for maximizing photothermal conversion efficiency based on organic dyes.

Weng, Xiao-Lu / Liu, Jian-Yong

Drug discovery today

2021 Volume 26, Issue 8, Page(s) 2045–2052

Abstract: Photothermal therapy (PTT) has emerged as a promising therapeutic approach for tumor control and ablation. Attention has focused on exploring advanced organic photothermal agents (OPTAs), with advantages of easy modification, adjustable photophysical and ...

Abstract	Photothermal therapy (PTT) has emerged as a promising therapeutic approach for tumor control and ablation. Attention has focused on exploring advanced organic photothermal agents (OPTAs), with advantages of easy modification, adjustable photophysical and photochemical properties, good compatibility, and inherent biodegradability. However, few detailed studies on how to maximally channelize nonradiative heat generation from the viewpoint of the photothermal conversion mechanism have been reported. Thus, here we assimilate and elaborate on several available action mechanisms to maximize the photothermal conversion efficiency (PCE) of organic dyes. Moreover, we also propose several potential challenges that require substantial future work to address.
MeSH term(s)	Coloring Agents/chemistry ; Humans ; Hyperthermia, Induced/methods ; Neoplasms/therapy ; Phototherapy/methods
Chemical Substances	Coloring Agents
Language	English
Publishing date	2021-03-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1324988-5
ISSN	1878-5832 ; 1359-6446
ISSN (online)	1878-5832
ISSN	1359-6446
DOI	10.1016/j.drudis.2021.03.009
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Article ; Online: Uncovering the Effect of A-Site Cations on Localized Excitons Photoluminescence of Manganese-Doped Zinc Chloride Nanocrystals.

Hou, Jie / Chen, Jun / Liu, Huaxin / Luo, Cheng / Li, Juntao / Liu, Jianyong / Yang, Bin

The journal of physical chemistry letters

2024 Volume 15, Issue 15, Page(s) 4076–4081

Abstract: Elucidating the key factors that affect the localized excitons (LEs) photoluminescence (PL) in lead-free metal halide nanocrystals (NCs) is important for their optoelectronic applications. However, the effect of A-site cations on LEs based PL is not well ...

Abstract	Elucidating the key factors that affect the localized excitons (LEs) photoluminescence (PL) in lead-free metal halide nanocrystals (NCs) is important for their optoelectronic applications. However, the effect of A-site cations on LEs based PL is not well understood. Herein, we varied the A-site cation ratio (Rb/Cs) to investigate the influence on LEs based PL in manganese-doped zinc chloride NCs. Through time-resolved photoluminescence (TR-PL) spectra and density functional theory (DFT) calculations, we discovered that Cl vacancy is energetically more favorable in Mn
Language	English
Publishing date	2024-04-08
Publishing country	United States
Document type	Journal Article
ISSN	1948-7185
ISSN (online)	1948-7185
DOI	10.1021/acs.jpclett.4c00610
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Article ; Online: Clinical effects of comprehensive treatment and liver transplantation for hepatocellular carcinoma exceeding Milan criteria

LIU Jianyong

Journal of Clinical Hepatology, Vol 30, Iss 9, Pp 913-

a comparative study

2014 Volume 916

Abstract: ObjectiveTo analyze and compare the clinical effects of comprehensive treatment and liver transplantation for hepatocellular carcinomas (HCC) exceeding Milan criteria. MethodsA retrospective analysis was performed on the clinical data of 157 patients ... ...

Abstract	ObjectiveTo analyze and compare the clinical effects of comprehensive treatment and liver transplantation for hepatocellular carcinomas (HCC) exceeding Milan criteria. MethodsA retrospective analysis was performed on the clinical data of 157 patients with HCC (exceeding Milan criteria) who received comprehensive treatment (99 patients, including 48 cases meeting Shanghai criteria) and liver transplantation (58 patients, including 26 cases meeting Shanghai criteria) in our hospital from January 2006 to January 2010. The median survival times and 1-, 2-, and 3-year survival rates were calculated by the Kaplan-Meier method, and the log-rank test was used for survival difference analysis. ResultsFor all patients, the median survival times of the comprehensive treatment group and liver transplantation group were 1800±1.15 and 23.40±4.44 months, respectively, and their 3-year survival rates were(18.2±3.9)% and (397±6.4)%, respectively; the survival was significantly improved by the treatment of liver transplantation (P=0.009). For patients meeting Shanghai criteria, the median survival times of the comprehensive treatment group and liver transplantation group were 20.00±1.17 and 3600±0.00 months, respectively, and their 3-year survival rates were (25.0±6.3)% and (57.7±9.7)%, respectively; there was significant survival difference between the two groups (P=0.008). For patients exceeding Shanghai criteria, the median survival times of the comprehensive treatment group and liver transplantation group were 16.00±1.78 and 16.00±1.69 months, respectively, and their 3-year survival rates were (11.8±4.5)% and (25.0±7.7)%, respectively; there was no significant survival difference between the two groups (P=0.221). ConclusionCompared with comprehensive treatment, liver transplantation leads to a significant higher long-term survival rate in HCC patients exceeding Milan criteria but meeting Shanghai criteria. However, the two therapies cause no significant survival difference in HCC patients exceeding Shanghai criteria.
Keywords	liver neoplasms; combined modality therapy; liver transplantation ; Medicine (General) ; R5-920 ; Medicine ; R
Subject code	610
Language	Chinese
Publishing date	2014-09-01T00:00:00Z
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Causal effects of modifiable risk factors on kidney stones: a bidirectional mendelian randomization study.

Liu, Wen / Wang, Miaomiao / Liu, Jianyong / Yan, Qiuxia / Liu, Ming

BMC medical genomics

2023 Volume 16, Issue 1, Page(s) 82

Abstract: Background: Increasing epidemiological studies demonstrated that modifiable risk factors affected the risk of kidney stones. We aimed to systemically assess these causal associations using a bidirectional Mendelian randomization study.: Methods: We ... ...

Abstract	Background: Increasing epidemiological studies demonstrated that modifiable risk factors affected the risk of kidney stones. We aimed to systemically assess these causal associations using a bidirectional Mendelian randomization study. Methods: We obtained instrumental variables related to each exposure at the genome-wide significant threshold (P < 5 × 10 Results: Among 46 risk factors, five were significantly associated with nephrolithiasis risk in the FinnGen consortium, UK Biobank, and meta-analyses collectively. The odds ratios (ORs) (95% confidence intervals [95%CIs]) of kidney stones were 1.21 (1.13, 1.29) per standard deviation (SD) increase in serum calcium, 1.55 (1.01, 2.36) per SD increase in serum 25(OH)D, 1.14 (1.00, 1.29) per SD increase in total triglycerides, 2.38 (1.34, 4.22) per SD increase in fasting insulin, and 0.28 (0.23, 0.35) per unit increase in log OR of urine pH. In addition, genetically predicted serum phosphorus, urinary sodium, tea consumption, and income affected the risk of kidney stones (false discovery rate [FDR] P < 0.05) based on the outcome data from the FinnGen consortium, and the significant associations of education and waist-to-hip ratio with nephrolithiasis risks were found after FDR correction (FDR P < 0.05) based on the outcome data from UK Biobank. Conclusions: Our findings comprehensively provide modifiable risk factors for the prevention of nephrolithiasis. Genome-wide association studies with larger sample sizes are needed to verify these causal associations in the future further.
MeSH term(s)	Humans ; Genome-Wide Association Study ; Mendelian Randomization Analysis ; Kidney Calculi/epidemiology ; Kidney Calculi/genetics ; Risk Factors ; Educational Status ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2023-04-20
Publishing country	England
Document type	Meta-Analysis ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2411865-5
ISSN	1755-8794 ; 1755-8794
ISSN (online)	1755-8794
ISSN	1755-8794
DOI	10.1186/s12920-023-01520-z
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