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Sun SY, Lee DH, Liu HC, Yang Y, Han YH, Kwon T. Identifying competing endogenous RNA regulatory networks and hub genes in alcoholic liver disease for early diagnosis and potential therapeutic target insights. Aging (Albany NY) 2024; 16:9147-9167. [PMID: 38795390 PMCID: PMC11164510 DOI: 10.18632/aging.205861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/22/2024] [Indexed: 05/27/2024]
Abstract
Alcoholic liver disease (ALD) has a complex pathogenesis. Although early-stage ALD can be reversed by ceasing alcohol consumption, early symptoms are difficult to detect, and several factors contribute to making alcohol difficult to quit. Continued alcohol abuse worsens the condition, meaning it may gradually progress into alcoholic hepatitis and cirrhosis, ultimately, resulting in irreversible consequences. Therefore, effective treatments are urgently needed for early-stage ALD. Current research mainly focuses on preventing the progression of alcoholic fatty liver to alcoholic hepatitis and cirrhosis. However, challenges remain in identifying key therapeutic targets and understanding the molecular mechanisms that underlie the treatment of alcoholic hepatitis and cirrhosis, such as the limited discovery of effective therapeutic targets and treatments. Here, we downloaded ALD microarray data from Gene Expression Omnibus and used bioinformatics to compare and identify the hub genes involved in the progression of alcoholic fatty liver to alcoholic hepatitis and cirrhosis. We also predicted target miRNAs and long non-coding RNAs (lncRNAs) to elucidate the regulatory mechanisms (the mRNA-miRNA-lncRNA axis) underlying this progression, thereby building a competitive endogenous RNA (ceRNA) mechanism for lncRNA, miRNA, and mRNA. This study provides a theoretical basis for the early treatment of alcoholic hepatitis and cirrhosis and identifies potential therapeutic targets.
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Affiliation(s)
- Shuai-Yang Sun
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Dong Hun Lee
- Department of Biological Sciences, Research Center of Ecomimetics, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hao-Cheng Liu
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Yi Yang
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Ying-Hao Han
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Taeho Kwon
- Primate Resources Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeonbuk 56216, Republic of Korea
- Department of Applied Biological Engineering, KRIBB School of Biotechnology, Korea National University of Science and Technology, Daejeon 34113, Republic of Korea
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Feichtenschlager V, Chen L, Zheng YJ, Ho W, Sanlorenzo M, Vujic I, Fewings E, Lee A, Chen C, Callanan C, Lin K, Qu T, Hohlova D, Vujic M, Hwang Y, Lai K, Chen S, Nguyen T, Muñoz DP, Kohwi Y, Posch C, Daud A, Rappersberger K, Kohwi-Shigematsu T, Coppé JP, Ortiz-Urda S. The therapeutically actionable long non-coding RNA 'T-RECS' is essential to cancer cells' survival in NRAS/MAPK-driven melanoma. Mol Cancer 2024; 23:40. [PMID: 38383439 PMCID: PMC10882889 DOI: 10.1186/s12943-024-01955-7] [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: 01/02/2024] [Accepted: 02/05/2024] [Indexed: 02/23/2024] Open
Abstract
Finding effective therapeutic targets to treat NRAS-mutated melanoma remains a challenge. Long non-coding RNAs (lncRNAs) recently emerged as essential regulators of tumorigenesis. Using a discovery approach combining experimental models and unbiased computational analysis complemented by validation in patient biospecimens, we identified a nuclear-enriched lncRNA (AC004540.4) that is upregulated in NRAS/MAPK-dependent melanoma, and that we named T-RECS. Considering potential innovative treatment strategies, we designed antisense oligonucleotides (ASOs) to target T-RECS. T-RECS ASOs reduced the growth of melanoma cells and induced apoptotic cell death, while having minimal impact on normal primary melanocytes. Mechanistically, treatment with T-RECS ASOs downregulated the activity of pro-survival kinases and reduced the protein stability of hnRNPA2/B1, a pro-oncogenic regulator of MAPK signaling. Using patient- and cell line- derived tumor xenograft mouse models, we demonstrated that systemic treatment with T-RECS ASOs significantly suppressed the growth of melanoma tumors, with no noticeable toxicity. ASO-mediated T-RECS inhibition represents a promising RNA-targeting approach to improve the outcome of MAPK pathway-activated melanoma.
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Affiliation(s)
- Valentin Feichtenschlager
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA.
- Department of Dermatology, Academic Teaching Hospital, Clinic Landstrasse Vienna, Medical University Vienna, Vienna, Austria.
| | - Linan Chen
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Yixuan James Zheng
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
- School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Wilson Ho
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Martina Sanlorenzo
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Igor Vujic
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
- Department of Dermatology, Academic Teaching Hospital, Clinic Landstrasse Vienna, Medical University Vienna, Vienna, Austria
- Faculty of Medicine, Sigmund Freud Private University, Vienna, Austria
| | - Eleanor Fewings
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Albert Lee
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Christopher Chen
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Ciara Callanan
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Kevin Lin
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Tiange Qu
- Department of Orofacial Science, Health Science West, University of California San Francisco School of Dentistry, San Francisco, CA, USA
| | - Dasha Hohlova
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
- Department of Biology, University of San Francisco, San Francisco, CA, USA
| | - Marin Vujic
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
- Department of Dermatology, Academic Teaching Hospital, Clinic Landstrasse Vienna, Medical University Vienna, Vienna, Austria
| | - Yeonjoo Hwang
- Department of Hematology-Oncology, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Kevin Lai
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Stephanie Chen
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Thuan Nguyen
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Denise P Muñoz
- Department of Hematology-Oncology, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Yoshinori Kohwi
- Department of Orofacial Science, Health Science West, University of California San Francisco School of Dentistry, San Francisco, CA, USA
| | - Christian Posch
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
- Department of Dermatology, Academic Teaching Hospital, Clinic Landstrasse Vienna, Medical University Vienna, Vienna, Austria
- Faculty of Medicine, Sigmund Freud Private University, Vienna, Austria
- Department of Dermatology and Allergy, School of Medicine, German Cancer Consortium (DKTK), Technical University of Munich, Munich, Germany
| | - Adil Daud
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Klemens Rappersberger
- Department of Dermatology, Academic Teaching Hospital, Clinic Landstrasse Vienna, Medical University Vienna, Vienna, Austria
| | - Terumi Kohwi-Shigematsu
- Department of Orofacial Science, Health Science West, University of California San Francisco School of Dentistry, San Francisco, CA, USA
| | - Jean-Philippe Coppé
- Department of Radiation Oncology, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Susana Ortiz-Urda
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
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3
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Feichtenschlager V, Chen L, Zheng YJ, Ho W, Sanlorenzo M, Vujic I, Fewings E, Lee A, Chen C, Callanan C, Lin K, Qu T, Hohlova D, Vujic M, Hwang Y, Lai K, Chen S, Nguyen T, Muñoz DP, Kohwi Y, Posch C, Daud A, Rappersberger K, Kohwi-Shigematsu T, Coppé JP, Ortiz-Urda S. The therapeutically actionable long non-coding RNA ' T-RECS' is essential to cancer cells' survival in NRAS/MAPK-driven melanoma. RESEARCH SQUARE 2023:rs.3.rs-1297358. [PMID: 38077055 PMCID: PMC10705697 DOI: 10.21203/rs.3.rs-1297358/v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Finding effective therapeutic targets to treat NRAS-mutated melanoma remains a challenge. Long non-coding RNAs (lncRNAs) recently emerged as essential regulators of tumorigenesis. Using a discovery approach combining experimental models and unbiased computational analysis complemented by validation in patient biospecimens, we identified a nuclear-enriched lncRNA (AC004540.4) that is upregulated in NRAS/MAPK-dependent melanoma, and that we named T-RECS. Considering potential innovative treatment strategies, we designed antisense oligonucleotides (ASOs) to target T-RECS. T-RECS ASOs reduced the growth of melanoma cells and induced apoptotic cell death, while having minimal impacton normal primary melanocytes. Mechanistically, treatment with T-RECS ASOs downregulated the activity of pro-survival kinases and reduced the protein stability of hnRNPA2/B1, a pro-oncogenic regulator of MAPK signaling. Using patient- and cell line- derived tumor xenograft mouse models, we demonstrated that systemic treatment with T-RECS ASOs significantly suppressed the growth of melanoma tumors, with no noticeable toxicity. ASO-mediated T-RECS inhibition represents a promising RNA-targeting approach to improve the outcome of MAPK pathway-activated melanoma.
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Affiliation(s)
| | | | | | - Wilson Ho
- University of California San Francisco
| | | | - Igor Vujic
- Department of Dermatology and Venerology, Medical Institution Rudolfstiftung, Vienna, Austria
| | | | | | | | | | - Kevin Lin
- University of California San Francisco
| | - Tiange Qu
- University of California San Francisco
| | | | | | | | - Kevin Lai
- University of California San Francisco
| | | | | | | | | | | | - Adil Daud
- University of California at San Francisco
| | - Klemens Rappersberger
- Department of Dermatology, Clinic Landstrasse Vienna, Academic Teaching Hospital, Medical University Vienna, Vienna, Austria
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4
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Xiang R, Liu Y, Fan L, Jiang B, Wang F. RNA adenosine deaminase (ADAR1) alleviates high-fat diet-induced nonalcoholic fatty liver disease by inhibiting NLRP3 inflammasome. J Transl Med 2022; 102:1088-1100. [PMID: 36775349 DOI: 10.1038/s41374-022-00805-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 04/13/2022] [Accepted: 05/06/2022] [Indexed: 12/26/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a chronic inflammatory disease in which nucleotide-binding domain of leucine-rich repeat protein 3 (NLRP3) inflammasome plays an important role. The present research was aimed to explore the protective function of ADAR1, an RNA editing enzyme, against inflammatory damages in high-fat diet (HFD)-induced NAFLD through inhibiting NLRP3 inflammasome and subsequent inflammation. A total of 30 patients with NAFLD were investigated, and ADAR1 mRNA expression in peripheral blood monocytes surveyed. The in vivo study used lentivirus to explore the function of ADAR1 overexpression in the HFD-induced mouse model of NAFLD. The in vitro study used lentivirus and siRNA to explore the function of ADAR1 on the NLRP3 inflammasome activation in THP-1 cells. Results shown that the ADAR1 expression was upregulated in NAFLD patients in comparison to healthy controls. In vivo, the upregulation of ADAR1 impaired NLRP3 inflammasome activation and alleviated liver disease in HFD mice in comparison to the control group. Moreover, ADAR1 overexpression attenuated NLRP3 inflammasome in lipopolysaccharide (LPS)+ palmitic acid (PA)-induced THP-1 cells, while ADAR1 knockdown increased the NLRP3 inflammasome activation. Furthermore, we speculated that c-Jun may participate in ADAR1's inhibition of NLRP3 inflammasome. Our results suggested that ADAR1 is a potential treatment target for NAFLD via regulating the activation of NLRP3 inflammasome.
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Affiliation(s)
- Rong Xiang
- The Endocrinology Department of the Third Xiangya Hospital, Central South University, Changsha, Hunan Province, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410013, China.,Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, 410078, China.,Hunan Key Laboratory of Animal for Human Disease, School of Life Sciences, Central South University, Changsha, China
| | - Yuxing Liu
- The Endocrinology Department of the Third Xiangya Hospital, Central South University, Changsha, Hunan Province, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410013, China
| | - Liangliang Fan
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410013, China.,Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, 410078, China.,Hunan Key Laboratory of Animal for Human Disease, School of Life Sciences, Central South University, Changsha, China
| | - Boyue Jiang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410013, China
| | - Fang Wang
- The Endocrinology Department of the Third Xiangya Hospital, Central South University, Changsha, Hunan Province, China. .,Hunan Key Laboratory of Animal for Human Disease, School of Life Sciences, Central South University, Changsha, China.
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6
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Matboli M, Gadallah SH, Rashed WM, Hasanin AH, Essawy N, Ghanem HM, Eissa S. mRNA-miRNA-lncRNA Regulatory Network in Nonalcoholic Fatty Liver Disease. Int J Mol Sci 2021; 22:ijms22136770. [PMID: 34202571 PMCID: PMC8269036 DOI: 10.3390/ijms22136770] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
AIM we aimed to construct a bioinformatics-based co-regulatory network of mRNAs and non coding RNAs (ncRNAs), which is implicated in the pathogenesis of non-alcoholic fatty liver disease (NAFLD), followed by its validation in a NAFLD animal model. MATERIALS AND METHODS The mRNAs-miRNAs-lncRNAs regulatory network involved in NAFLD was retrieved and constructed utilizing bioinformatics tools. Then, we validated this network using an NAFLD animal model, high sucrose and high fat diet (HSHF)-fed rats. Finally, the expression level of the network players was assessed in the liver tissues using reverse transcriptase real-time polymerase chain reaction. RESULTS in-silico constructed network revealed six mRNAs (YAP1, FOXA2, AMOTL2, TEAD2, SMAD4 and NF2), two miRNAs (miR-650 and miR-1205), and two lncRNAs (RPARP-AS1 and SRD5A3-AS1) that play important roles as a co-regulatory network in NAFLD pathogenesis. Moreover, the expression level of these constructed network-players was significantly different between NAFLD and normal control. Conclusion and future perspectives: this study provides new insight into the molecular mechanism of NAFLD pathogenesis and valuable clues for the potential use of the constructed RNA network in effective diagnostic or management strategies of NAFLD.
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Affiliation(s)
- Marwa Matboli
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Cairo 11382, Egypt
- Correspondence: (M.M.); (S.E.)
| | - Shaimaa H. Gadallah
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo 11382, Egypt; (S.H.G.); (H.M.G.)
| | - Wafaa M. Rashed
- Department of Research, Children’s Cancer Hospital-57357, Cairo 11382, Egypt;
| | - Amany Helmy Hasanin
- Department of Clinical Pharmacology, Faculty of Medicine, Ain Shams University, Cairo 11382, Egypt;
| | - Nada Essawy
- Institut Pasteur, CEDEX 15, 75724 Paris, France;
| | - Hala M. Ghanem
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo 11382, Egypt; (S.H.G.); (H.M.G.)
| | - Sanaa Eissa
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Cairo 11382, Egypt
- Correspondence: (M.M.); (S.E.)
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