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Guo R, Wang S, Guo S, Fan X, Zang H, Gao X, Jing X, Liu Z, Na Z, Zou P, Chen D. Regulatory Roles of Long Non-Coding RNAs Relevant to Antioxidant Enzymes and Immune Responses of Apis cerana Larvae Following Ascosphaera apis Invasion. Int J Mol Sci 2023; 24:14175. [PMID: 37762477 PMCID: PMC10532054 DOI: 10.3390/ijms241814175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/06/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play an essential part in controlling gene expression and a variety of biological processes such as immune defense and stress-response. However, whether and how lncRNAs regulate responses of Apis cerana larvae to Ascosphaera apis invasion has remained unclear until now. Here, the identification and structural analysis of lncRNAs in the guts of A. cerana worker larvae were conducted, and the expression profile of larval lncRNAs during the A. apis infection process was then analyzed, followed by an investigation of the regulatory roles of differentially expressed lncRNAs (DElncRNAs) in the host response. In total, 76 sense lncRNAs, 836 antisense lncRNAs, 184 intron lncRNAs, 362 bidirectional lncRNAs, and 2181 intron lncRNAs were discovered in the larval guts. Additionally, 30 known and 9 novel lncRNAs were potential precursors for 36 and 11 miRNAs, respectively. In the three comparison groups, 386, 351, and 272 DElncRNAs were respectively identified, indicating the change in the overall expression pattern of host lncRNAs following the A. apis invasion. Analysis of cis-acting effect showed that DElncRNAs in the 4-, 5-, and 6-day-old comparison groups putatively regulated 55, 30, and 20 up- and down-stream genes, respectively, which were involved in a series of crucial functional terms and pathways, such as MAPK signaling pathway, and cell process. Analysis showed that 31, 8, and 11 DElncRNAs as potential antisense lncRNAs may interact with 26, 8, and 9 sense-strand mRNAs. Moreover, investigation of the competing endogenous RNA (ceRNA) network indicated that 148, 283, and 257 DElncRNAs were putatively regulated. The expression of target genes by targeting corresponding DEmiRNAs included those associated with antioxidant enzymes and immune responses. These results suggested that DElncRNAs played a potential part in the larval guts responding to the A. apis infection through a cis-acting manner and ceRNA mechanisms. Our findings deepen our understanding of interactions between A. cerana larvae and A. apis and offer a basis for clarifying the DElncRNA-mediated mechanisms underlying the host response to fungal invasion.
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Affiliation(s)
- Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.G.); (S.W.); (S.G.); (X.F.); (H.Z.); (X.G.); (X.J.); (Z.L.); (Z.N.); (P.Z.)
- Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siyi Wang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.G.); (S.W.); (S.G.); (X.F.); (H.Z.); (X.G.); (X.J.); (Z.L.); (Z.N.); (P.Z.)
| | - Sijia Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.G.); (S.W.); (S.G.); (X.F.); (H.Z.); (X.G.); (X.J.); (Z.L.); (Z.N.); (P.Z.)
| | - Xiaoxue Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.G.); (S.W.); (S.G.); (X.F.); (H.Z.); (X.G.); (X.J.); (Z.L.); (Z.N.); (P.Z.)
| | - He Zang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.G.); (S.W.); (S.G.); (X.F.); (H.Z.); (X.G.); (X.J.); (Z.L.); (Z.N.); (P.Z.)
| | - Xuze Gao
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.G.); (S.W.); (S.G.); (X.F.); (H.Z.); (X.G.); (X.J.); (Z.L.); (Z.N.); (P.Z.)
| | - Xin Jing
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.G.); (S.W.); (S.G.); (X.F.); (H.Z.); (X.G.); (X.J.); (Z.L.); (Z.N.); (P.Z.)
| | - Zhitan Liu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.G.); (S.W.); (S.G.); (X.F.); (H.Z.); (X.G.); (X.J.); (Z.L.); (Z.N.); (P.Z.)
| | - Zhihao Na
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.G.); (S.W.); (S.G.); (X.F.); (H.Z.); (X.G.); (X.J.); (Z.L.); (Z.N.); (P.Z.)
| | - Peiyuan Zou
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.G.); (S.W.); (S.G.); (X.F.); (H.Z.); (X.G.); (X.J.); (Z.L.); (Z.N.); (P.Z.)
| | - Dafu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.G.); (S.W.); (S.G.); (X.F.); (H.Z.); (X.G.); (X.J.); (Z.L.); (Z.N.); (P.Z.)
- Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Lin S, Huang L, Wu Y, Huang L, Wu P, Huang T, Li Z, Hu Y. Uncovering the protective mechanism of Pien-Tze-Huang in rat with alcoholic liver injury based on cytokines analysis and untargeted metabonomics. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1217:123626. [PMID: 36753840 DOI: 10.1016/j.jchromb.2023.123626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 12/17/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
Pien-Tze-Huang (PTH) is a well-known traditional Chinese patent medicine with excellent liver-protection effect. However, the mechanism of hepatoprotective action has not yet been entirely elucidated. The aim of this study was to investigate the mechanism of protective effect of PTH on alcohol-induced liver injury in rats using cytokine analysis and untargeted metabolomics approaches. An alcoholic liver disease (ALD) model with SD rats was established, and PTH was administered according to the prescribed dose. The hepatoprotective effect of PTH was evaluated by pathological observation of liver tissue and changes in biochemical index activity and cytokines in serum. Serum samples were analyzed by ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UHPLC-QTOF/MS), and differentially expressed metabolites were screened by multivariate statistical analysis. KEGG combined with metabolic pathway analysis were used to evaluate the underlying metabolic pathways. Results showed liver histopathology injury was attenuated. The levels of IL-6, TNF-α and NF-κB were significantly decreased in rats intervened with PTH groups, suggesting that it may alleviate inflammation via suppressing the inflammatory cytokines signaling pathway. Eighty differentially expressed metabolites were found and identified. Pathway analysis indicated that the hepatoprotective effects of PTH occurred through the regulation of inflammatory cytokines signaling pathway, primary bile acid biosynthesis, vitamin B6 metabolism pathway, cholesterol metabolism, and tyrosine metabolism. PTH showed favorable hepatoprotective effect through multiple pathways. This study has great importance in fully revealing the mechanism of hepatoprotective action and can help improve the clinical application of PTH.
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Affiliation(s)
- Shouer Lin
- School of Pharmacy, Fujian Medical university, Fuzhou, Fujian, 350122, China; Physical and Chemical Analysis Department, Fujian Provincial Center For Disease Control and Prevention, Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou, Fujian, 350001, China
| | - Lingyi Huang
- School of Pharmacy, Fujian Medical university, Fuzhou, Fujian, 350122, China
| | - Youjia Wu
- School of Pharmacy, Fujian Medical university, Fuzhou, Fujian, 350122, China
| | - Liying Huang
- School of Pharmacy, Fujian Medical university, Fuzhou, Fujian, 350122, China.
| | - Pingping Wu
- School of Pharmacy, Fujian Medical university, Fuzhou, Fujian, 350122, China
| | - Tingxuan Huang
- School of Pharmacy, Fujian Medical university, Fuzhou, Fujian, 350122, China
| | - Zhenyue Li
- School of Pharmacy, Fujian Medical university, Fuzhou, Fujian, 350122, China
| | - Yuhan Hu
- School of Pharmacy, Fujian Medical university, Fuzhou, Fujian, 350122, China
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Yang W, Guo R, Pi A, Ding Q, Hao L, Song Q, Chen L, Dou X, Na L, Li S. Long non-coding RNA-EN_181 potentially contributes to the protective effects of N-acetylcysteine against non-alcoholic fatty liver disease in mice. Br J Nutr 2022; 129:1-15. [PMID: 35710106 DOI: 10.1017/s0007114522001829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
N-acetylcysteine (NAC) possesses a strong capability to ameliorate high-fat diet (HFD)-induced non-alcoholic fatty liver disease (NAFLD) in mice, but the underlying mechanism is still unknown. Our study aimed to clarify the involvement of long non-coding RNA (lncRNA) in the beneficial effects of NAC on HFD-induced NAFLD. C57BL/6J mice were fed a normal-fat diet (10 % fat), a HFD (45 % fat) or a HFD plus NAC (2 g/l). After 14-week of intervention, NAC rescued the deleterious alterations induced by HFD, including the changes in body and liver weights, hepatic TAG, plasma alanine aminotransferase, plasma aspartate transaminase and liver histomorphology (haematoxylin and eosin and Oil red O staining). Through whole-transcriptome sequencing, 52 167 (50 758 known and 1409 novel) hepatic lncRNA were detected. Our cross-comparison data revealed the expression of 175 lncRNA was changed by HFD but reversed by NAC. Five of those lncRNA, lncRNA-NONMMUT148902·1 (NO_902·1), lncRNA-XR_001781798·1 (XR_798·1), lncRNA-NONMMUT141720·1 (NO_720·1), lncRNA-XR_869907·1 (XR_907·1), and lncRNA-ENSMUST00000132181 (EN_181), were selected based on an absolute log2 fold change value of greater than 4, P-value < 0·01 and P-adjusted value < 0·01. Further qRT-PCR analysis showed the levels of lncRNA-NO_902·1, lncRNA-XR_798·1, and lncRNA-EN_181 were decreased by HFD but restored by NAC, consistent with the RNA sequencing. Finally, we constructed a ceRNA network containing lncRNA-EN_181, 3 miRNA, and 13 mRNA, which was associated with the NAC-ameliorated NAFLD. Overall, lncRNA-EN_181 might be a potential target in NAC-ameliorated NAFLD. This finding enhanced our understanding of the biological mechanisms underlying the beneficial role of NAC.
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Affiliation(s)
- Wenwen Yang
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou310053, People's Republic of China
- School of Life Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang310053, People's Republic of China
| | - Rui Guo
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou310053, People's Republic of China
- Institute of Nutrition and Health, School of Public Health, Zhejiang Chinese Medical University, Hangzhou310053, People's Republic of China
- Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang310053, People's Republic of China
| | - Aiwen Pi
- School of Life Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang310053, People's Republic of China
| | - Qinchao Ding
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou310053, People's Republic of China
- Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang310053, People's Republic of China
| | - Liuyi Hao
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou310053, People's Republic of China
- Institute of Nutrition and Health, School of Public Health, Zhejiang Chinese Medical University, Hangzhou310053, People's Republic of China
- Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang310053, People's Republic of China
| | - Qing Song
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou310053, People's Republic of China
- School of Life Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang310053, People's Republic of China
| | - Lin Chen
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou310053, People's Republic of China
- Institute of Nutrition and Health, School of Public Health, Zhejiang Chinese Medical University, Hangzhou310053, People's Republic of China
| | - Xiaobing Dou
- School of Life Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang310053, People's Republic of China
| | - Lixin Na
- Public Health College, Shanghai University of Medicine & Health Sciences, Shanghai201318, People's Republic of China
| | - Songtao Li
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou310053, People's Republic of China
- Institute of Nutrition and Health, School of Public Health, Zhejiang Chinese Medical University, Hangzhou310053, People's Republic of China
- Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang310053, People's Republic of China
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Habash NW, Sehrawat TS, Shah VH, Cao S. Epigenetics of alcohol-related liver diseases. JHEP REPORTS : INNOVATION IN HEPATOLOGY 2022; 4:100466. [PMID: 35462859 PMCID: PMC9018389 DOI: 10.1016/j.jhepr.2022.100466] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/14/2022] [Accepted: 02/22/2022] [Indexed: 02/07/2023]
Abstract
Alcohol-related liver disease (ARLD) is a primary cause of chronic liver disease in the United States. Despite advances in the diagnosis and management of ARLD, it remains a major public health problem associated with significant morbidity and mortality, emphasising the need to adopt novel approaches to the study of ARLD and its complications. Epigenetic changes are increasingly being recognised as contributing to the pathogenesis of multiple disease states. Harnessing the power of innovative technologies for the study of epigenetics (e.g., next-generation sequencing, DNA methylation assays, histone modification profiling and computational techniques like machine learning) has resulted in a seismic shift in our understanding of the pathophysiology of ARLD. Knowledge of these techniques and advances is of paramount importance for the practicing hepatologist and researchers alike. Accordingly, in this review article we will summarise the current knowledge about alcohol-induced epigenetic alterations in the context of ARLD, including but not limited to, DNA hyper/hypo methylation, histone modifications, changes in non-coding RNA, 3D chromatin architecture and enhancer-promoter interactions. Additionally, we will discuss the state-of-the-art techniques used in the study of ARLD (e.g. single-cell sequencing). We will also highlight the epigenetic regulation of chemokines and their proinflammatory role in the context of ARLD. Lastly, we will examine the clinical applications of epigenetics in the diagnosis and management of ARLD.
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Key Words
- 3C, chromosome conformation capture
- 4C, chromosome conformation capture-on-chip
- AH, alcohol-related hepatitis
- ARLD, alcohol-related liver disease
- ASH, alcohol-related steatohepatitis
- ATAC, assay for transposase-accessible chromatin
- Acetylation
- Alcohol liver disease
- BET, bromodomain and extraterminal motif
- BETi, BET inhibitor
- BRD, bromodomain
- CCL2, C-C motif chemokine ligand 2
- CTCF, CCCTC-binding factor
- CXCL, C-X-C motif chemokine ligand
- Chromatin architecture
- Computational biology
- DNA methylation
- DNMT, DNA methyltransferase
- E-P, enhancer-promoter
- Epidrugs
- Epigenetics
- FKBP5, FK506-binding protein 5
- HCC, hepatocellular carcinoma
- HDAC, histone deacetylase
- HIF1α, hypoxia inducible factor-1α
- HMGB1, high-mobility group box protein 1
- HNF4α, hepatocyte nuclear factor 4α
- HSC, hepatic stellate cell
- Hi-C, chromosome capture followed by high-throughput sequencing
- Histones
- IL, interleukin
- LPS, lipopolysaccharide
- MALAT1, metastasis-associated lung adenocarcinoma transcript 1
- MECP2, methyl-CpG binding protein 2
- NAFLD, non-alcohol-related fatty liver disease
- PPARG, peroxisome proliferator activated receptor-γ
- SAA, salvianolic acid A
- SIRT, sirtuin
- SREBPs, sterol regulatory element-binding proteins
- Single cell epigenome
- TAD, topologically associating domain
- TEAD, TEA domain transcription factor
- TLR, Toll-like receptor
- TNF, tumour necrosis factor
- YAP, Yes-associated protein
- lncRNA, long non-coding RNA
- miRNA, microRNA
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Affiliation(s)
| | | | - Vijay H. Shah
- Corresponding authors. Address: Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA. Tel. 507-255-6028, fax: 507-255-6318.
| | - Sheng Cao
- Corresponding authors. Address: Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA. Tel. 507-255-6028, fax: 507-255-6318.
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Li S, Song Z, Yao P, Qin J. Editorial: Alcohol Consumption and Liver Diseases: From Pathology to Phytotherapy. Front Pharmacol 2022; 13:848334. [PMID: 35250600 PMCID: PMC8889066 DOI: 10.3389/fphar.2022.848334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Songtao Li
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China
- *Correspondence: Songtao Li,
| | - Zhenyuan Song
- Department of Kinesiology and Nutrition, University of Illinois at Chicago, Chicago, IL, United States
| | - Ping Yao
- School of Public Health, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Jiangjiang Qin
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
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Regulatory Networks of Prognostic mRNAs in Pediatric Acute Myeloid Leukemia. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:2691997. [PMID: 35035819 PMCID: PMC8754609 DOI: 10.1155/2022/2691997] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 11/27/2021] [Accepted: 12/09/2021] [Indexed: 12/24/2022]
Abstract
Acute myeloid leukemia (AML) in children refers to a malignant tumor caused by the abnormal proliferation of immature myeloid cells in the bone marrow and peripheral blood. The prognosis of patients with pediatric acute myeloid leukemia (AML) remains poor, highlighting the need for improved targeted therapy. The expression data of lncRNAs, mRNAs, and miRNAs and survival information of pediatric AML patients were collected from The Cancer Genome Atlas (TCGA) database. Cox regression analysis was used to screen the lncRNAs, mRNAs, and miRNAs that significantly affect the overall survival (OS) of patients as OS-related genes (included lncRNAs, mRNAs, and miRNAs). Enrichment analysis and protein-protein interaction (PPI) network construction were performed for the OS-related mRNAs. We further established a ceRNAs regulatory network. In addition, the potential prognostic role of genes was further evaluated by risk score. We have identified 5275 lncRNAs, 176 miRNAs, and 6221 mRNAs that significantly affect the prognosis of pediatric AML patients. It is worth noting that OS-related mRNAs are mainly involved in ribosome, RNA transport, and spliceosome. We identified the top 10 most connected mRNAs in the PPI network as important mRNAs and constructed a ceRNAs regulatory network (including NCBP2, RPLP0, UBC, RPS2, and RPS9). The risk score and nomogram results suggest that NCBP2 may be a risk factor for pediatric AML, while RPLP0, UBC, RPS2, and RPS9 may be protective factors. Our results construct 5 gene signals as new prognostic indicators for predicting the survival of pediatric AML patients. Our research has demonstrated the ceRNAs regulatory network may become a new target for pediatric AML treatment.
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