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Lee SY, Park J, Seo SB. Negative regulation of HDAC3 transcription by histone acetyltransferase TIP60 in colon cancer. Genes Genomics 2024; 46:871-879. [PMID: 38805168 PMCID: PMC11208239 DOI: 10.1007/s13258-024-01524-8] [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: 04/05/2024] [Accepted: 05/12/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND Colon cancer is the third most common cancer globally. The expression of histone deacetylase 3 (HDAC3) is upregulated, whereas the expression of tat interactive protein, 60 kDa (TIP60) is downregulated in colon cancer. However, the relationship between HDAC3 and TIP60 in colon cancer has not been clearly elucidated. OBJECTIVE We investigated whether TIP60 could regulate the expression of HDAC3 and suppress colon cancer cell proliferation. METHODS RNA sequencing data (GSE108834) showed that HDAC3 expression was regulated by TIP60. Subsequently, we generated TIP60-knockdown HCT116 cells and examined the expression of HDAC3 by western blotting and reverse transcription-quantitative polymerase chain reaction (RT-qPCR). We examined the expression pattern of HDAC3 in various cancers using publicly available datasets. The promoter activity of HDAC3 was validated using a dual-luciferase assay, and transcription factors binding to HDAC3 were identified using GeneCards and Promo databases, followed by validation using chromatin immunoprecipitation-quantitative polymerase chain reaction. Cell proliferation and apoptosis were assessed using colony formation assays and fluorescence-activated cell sorting analysis of HCT116 cell lines. RESULTS In response to TIP60 knockdown, the expression level and promoter activity of HDAC3 increased. Conversely, when HDAC3 was downregulated by overexpression of TIP60, proliferation of HCT116 cells was inhibited and apoptosis was promoted. CONCLUSION TIP60 plays a crucial role in the regulation of HDAC3 transcription, thereby influencing cell proliferation and apoptosis in colon cancer. Consequently, TIP60 may function as a tumor suppressor by inhibiting HDAC3 expression in colon cancer cells.
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Affiliation(s)
- Seong Yun Lee
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Junyoung Park
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Sang Beom Seo
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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Jang J, Bentsen M, Kim YJ, Kim E, Garg V, Cai CL, Looso M, Li D. Endocardial HDAC3 is required for myocardial trabeculation. Nat Commun 2024; 15:4166. [PMID: 38755146 PMCID: PMC11099086 DOI: 10.1038/s41467-024-48362-6] [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: 04/16/2023] [Accepted: 04/25/2024] [Indexed: 05/18/2024] Open
Abstract
Failure of proper ventricular trabeculation is often associated with congenital heart disease. Support from endocardial cells, including the secretion of extracellular matrix and growth factors is critical for trabeculation. However, it is poorly understood how the secretion of extracellular matrix and growth factors is initiated and regulated by endocardial cells. We find that genetic knockout of histone deacetylase 3 in the endocardium in mice results in early embryo lethality and ventricular hypotrabeculation. Single cell RNA sequencing identifies significant downregulation of extracellular matrix components in histone deacetylase 3 knockout endocardial cells. Secretome from cultured histone deacetylase 3 knockout mouse cardiac endothelial cells lacks transforming growth factor ß3 and shows significantly reduced capacity in stimulating cultured cardiomyocyte proliferation, which is remarkably rescued by transforming growth factor ß3 supplementation. Mechanistically, we identify that histone deacetylase 3 knockout induces transforming growth factor ß3 expression through repressing microRNA-129-5p. Our findings provide insights into the pathogenesis of congenital heart disease and conceptual strategies to promote myocardial regeneration.
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Affiliation(s)
- Jihyun Jang
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43215, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43215, USA
| | - Mette Bentsen
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany
| | - Ye Jun Kim
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Erick Kim
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Vidu Garg
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43215, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43215, USA
| | - Chen-Leng Cai
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46201, USA
| | - Mario Looso
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany
| | - Deqiang Li
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43215, USA.
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43215, USA.
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Jha T, Jana R, Banerjee S, Baidya SK, Amin SA, Gayen S, Ghosh B, Adhikari N. Exploring different classification-dependent QSAR modelling strategies for HDAC3 inhibitors in search of meaningful structural contributors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2024; 35:367-389. [PMID: 38757181 DOI: 10.1080/1062936x.2024.2350504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 04/28/2024] [Indexed: 05/18/2024]
Abstract
Histone deacetylase 3 (HDAC3), a Zn2+-dependent class I HDACs, contributes to numerous disorders such as neurodegenerative disorders, diabetes, cardiovascular disease, kidney disease and several types of cancers. Therefore, the development of novel and selective HDAC3 inhibitors might be promising to combat such diseases. Here, different classification-based molecular modelling studies such as Bayesian classification, recursive partitioning (RP), SARpy and linear discriminant analysis (LDA) were conducted on a set of HDAC3 inhibitors to pinpoint essential structural requirements contributing to HDAC3 inhibition followed by molecular docking study and molecular dynamics (MD) simulation analyses. The current study revealed the importance of hydroxamate function for Zn2+ chelation as well as hydrogen bonding interaction with Tyr298 residue. The importance of hydroxamate function for higher HDAC3 inhibition was noticed in the case of Bayesian classification, recursive partitioning and SARpy models. Also, the importance of substituted thiazole ring was revealed, whereas the presence of linear alkyl groups with carboxylic acid function, any type of ester function, benzodiazepine moiety and methoxy group in the molecular structure can be detrimental to HDAC3 inhibition. Therefore, this study can aid in the design and discovery of effective novel HDAC3 inhibitors in the future.
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Affiliation(s)
- T Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - R Jana
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S K Baidya
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S A Amin
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - B Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad, India
| | - N Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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Jang J, Bentsen M, Kim YJ, Kim E, Garg V, Cai CL, Looso M, Li D. Endocardial HDAC3 is required for myocardial trabeculation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.12.536668. [PMID: 37886504 PMCID: PMC10602027 DOI: 10.1101/2023.04.12.536668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
BACKGROUND Trabeculation, a key process in early heart development, is the formation of myocardial trabecular meshwork. The failure of trabeculation often leads to embryonic lethality. Support from endocardial cells, including the secretion of extracellular matrix (ECM) and growth factors is critical for trabeculation; however, it is unknown how the secretion of ECM and growth factors is initiated and regulated by endocardial cells. METHODS Various cellular and mouse models in conjunction with biochemical and molecular tools were employed to study the role of histone deacetylase 3 (HDAC3) in the developing endocardium. RESULTS We found that genetic deletion of Hdac3 in endocardial cells in mice resulted in early embryo lethality presenting as a hypotrabeculation cardiac phenotype. Single cell RNA sequencing identified several ECM components including collagens that were significantly downregulated in Hdac3 knockout (KO) endocardial cells. When cultured with supernatant from Hdac3 KO mouse cardiac endothelial cells (MCECs), wild-type mouse embryonic cardiomyocytes showed decreased proliferation, suggesting that growth signaling from Hdac3 KO MCECs is disrupted. Subsequent transcriptomic analysis revealed that transforming growth factor β3 (TGFβ3) was significantly downregulated in Hdac3 KO MCECs and Hdac3 cardiac endothelial KO hearts. Mechanistically, we identified that microRNA (miR)-129-5p was significantly upregulated in Hdac3 KO MCECs and Hdac3 cardiac endothelial KO hearts. Overexpression of miR-129-5p repressed Tgfβ3 expression in wild-type MCECs, whereas knockdown of miR-129-5p restored Tgfβ3 expression in Hdac3 KO MCECs. CONCLUSION Our findings reveal a critical signaling pathway in which endocardial HDAC3 promotes trabecular myocardium growth by stimulating TGFβ signaling through repressing miR-129-5p, providing novel insights into the etiology of congenital heart disease and conceptual strategies to promote myocardial regeneration.
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Saadh MJ, Allela OQB, Sattay ZJ, Al Zuhairi RAH, Ahmad H, Eldesoky GE, Adil M, Ali MS. Deciphering the functional landscape and therapeutic implications of noncoding RNAs in the TGF-β signaling pathway in colorectal cancer: A comprehensive review. Pathol Res Pract 2024; 255:155158. [PMID: 38320438 DOI: 10.1016/j.prp.2024.155158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 02/08/2024]
Abstract
Colorectal cancer (CRC) remains a major global health concern, necessitating an in-depth exploration of the intricate molecular mechanisms underlying its progression and potential therapeutic interventions. Transforming Growth Factor-β (TGF-β) signaling, a pivotal pathway implicated in CRC plays a dual role as a tumor suppressor in the early stages and a promoter of tumor progression in later stages. Recent research has shed light on the critical involvement of noncoding RNAs (ncRNAs) in modulating the TGF-β signaling pathway, introducing a new layer of complexity to our understanding of CRC pathogenesis. This comprehensive review synthesizes the current state of knowledge regarding the function and therapeutic potential of various classes of ncRNAs, including microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), in the context of TGF-β signaling in CRC. The intricate interplay between these ncRNAs and key components of the TGF-β pathway is dissected, revealing regulatory networks that contribute to the dynamic balance between tumor suppression and promotion. Emphasis is placed on how dysregulation of specific ncRNAs can disrupt this delicate equilibrium, fostering CRC initiation, progression, and metastasis. Moreover, the review provides a critical appraisal of the emerging therapeutic strategies targeting ncRNAs associated with TGF-β signaling in CRC. The potential of these ncRNAs as diagnostic and prognostic biomarkers is discussed, highlighting their clinical relevance. Additionally, the challenges and prospects of developing RNA-based therapeutics, such as RNA interference and CRISPR/Cas-based approaches, are explored in the context of modulating TGF-β signaling for CRC treatment. In conclusion, this review offers a comprehensive overview of the intricate interplay between ncRNAs and the TGF-β signaling pathway in CRC. By unraveling the functional significance of these regulatory elements, we gain valuable insights into the molecular landscape of CRC, paving the way for the development of novel and targeted therapeutic interventions aimed at modulating the TGF-β signaling cascade through the manipulation of ncRNAs.
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Affiliation(s)
- Mohamed J Saadh
- Faculty of Pharmacy, Middle East University, Amman 11831, Jordan
| | | | - Zahraa Jasim Sattay
- Department of Medical Laboratory Technology l, University of imam Jaafar Al-Sadiq, Iraq
| | | | - Hijaz Ahmad
- Section of Mathematics, International Telematic University Uninettuno, Corso Vittorio Emanuele II, 39, Rome 00186, Italy; Center for Applied Mathematics and Bioinformatics, Gulf University for Science and Technology, Kuwait; Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon
| | - Gaber E Eldesoky
- Chemistry Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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Wang Z, Lin W, Shi M, Hou Y, Liu J, Huang Z, Zhang X, Yang Y, Liu B, Yang Z, Ma W. Involucrasin B Inhibits the Proliferation of Caco-2 Cells by Regulating the TGFβ/SMAD2-3-4 Pathway. Molecules 2024; 29:686. [PMID: 38338430 PMCID: PMC10856266 DOI: 10.3390/molecules29030686] [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: 11/29/2023] [Revised: 01/19/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
(1) Background: Colorectal cancer (CRC) is the third most common malignant tumor worldwide and the second most common cause of cancer death. However, effective anti-CRC drugs are still lacking in clinical settings. This article investigated the anti-proliferative effect of involucrasin B on CRC Caco-2 cells. (2) Methods: This study employed a sulforhodamine B (SRB) method, colony formation experiments, flow cytometry, FastFUCCI assay, dual luciferase assay, and Western blot analysis for the investigation. (3) Results: The SRB method and colony formation experiments showed that involucrasin B exhibited an inhibitory effect on the Caco-2 cells cultured in vitro. Subsequently, the flow cytometry, FastFUCCI assay, and Western blotting results showed that involucrasin B induced cell cycle arrest in the G1 phase dose-dependently. Involucrasin B significantly enhanced the TGFβ RII protein level and SMAD3 phosphorylation, thus inhibiting the expression of CDK4 and cyclin D1 and causing G1 cell cycle arrest. (4) Conclusion: This study shows that involucrasin B exerts its anti-proliferative effect by regulating the TGFβ/SMAD2-3-4 pathway to cause G1 cycle arrest in Caco-2 cells.
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Affiliation(s)
- Zi Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China; (Z.W.); (W.L.); (M.S.); (Y.H.); (J.L.); (Z.H.); (X.Z.); (Y.Y.); (B.L.)
| | - Wanjun Lin
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China; (Z.W.); (W.L.); (M.S.); (Y.H.); (J.L.); (Z.H.); (X.Z.); (Y.Y.); (B.L.)
| | - Meina Shi
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China; (Z.W.); (W.L.); (M.S.); (Y.H.); (J.L.); (Z.H.); (X.Z.); (Y.Y.); (B.L.)
| | - Yu Hou
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China; (Z.W.); (W.L.); (M.S.); (Y.H.); (J.L.); (Z.H.); (X.Z.); (Y.Y.); (B.L.)
| | - Jiachen Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China; (Z.W.); (W.L.); (M.S.); (Y.H.); (J.L.); (Z.H.); (X.Z.); (Y.Y.); (B.L.)
| | - Zifeng Huang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China; (Z.W.); (W.L.); (M.S.); (Y.H.); (J.L.); (Z.H.); (X.Z.); (Y.Y.); (B.L.)
| | - Xuening Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China; (Z.W.); (W.L.); (M.S.); (Y.H.); (J.L.); (Z.H.); (X.Z.); (Y.Y.); (B.L.)
| | - Yanchao Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China; (Z.W.); (W.L.); (M.S.); (Y.H.); (J.L.); (Z.H.); (X.Z.); (Y.Y.); (B.L.)
| | - Beijia Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China; (Z.W.); (W.L.); (M.S.); (Y.H.); (J.L.); (Z.H.); (X.Z.); (Y.Y.); (B.L.)
| | - Zhuya Yang
- School of Traditional Chinese Medicine, Yunnan University of Traditional Chinese Medicine, Kunming 650500, China
| | - Wenzhe Ma
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China; (Z.W.); (W.L.); (M.S.); (Y.H.); (J.L.); (Z.H.); (X.Z.); (Y.Y.); (B.L.)
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Wu X, Yang C, Sun F, Zhang Y, Wang Y, Li X, Zheng F. Enterotoxigenic Bacteroides fragilis (ETBF) Enhances Colorectal Cancer Cell Proliferation and Metastasis Through HDAC3/miR-139-3p Pathway. Biochem Genet 2024:10.1007/s10528-023-10621-4. [PMID: 38244157 DOI: 10.1007/s10528-023-10621-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/03/2023] [Indexed: 01/22/2024]
Abstract
Enterotoxigenic Bacteroides fragilis (ETBF) is believed to promote the malignant process of colorectal cancer (CRC), but the underlying molecular mechanism still needs to be revealed. CRC cells (SW480 and HCT-116) were treated with ETBF strain. Cell proliferation, invasion and, migration were evaluated by cell counting kit 8 assay, EdU assay, colony formation assay, transwell assay, and wound healing assay. Protein expression was analyzed by western blot. MicroRNA (miR)-139-3p and histone deacetylase 3 (HDAC3) expression levels in tissues and cells were determined by qRT-PCR. Xenograft tumor model was conducted to evaluate the effect of miR-139-3p on CRC tumor growth. ETBF treatment could promote CRC cell proliferation, invasion and migration. MiR-139-3p expression was decreased by ETBF, and its overexpression reversed the effect of ETBF on CRC cell progression. HDAC3 negatively regulated miR-139-3p expression, and its overexpression facilitated CRC cell behaviors via reducing miR-139-3p expression. Moreover, HDAC3 expression was increased by ETBF, and its knockdown also abolished ETBF-mediated CRC cell progression. Additionally, miR-139-3p overexpression could reduce CRC tumor growth in vivo. ETBF aggravated CRC proliferation and metastasis via the regulation of HDAC3/miR-139-3p axis. The discovery of ETBF/HDAC3/miR-139-3p axis may provide a new direction for CRC treatment.
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Affiliation(s)
- Xiaoyong Wu
- Department of General Surgery, Affiliated Danzhou People's Hospital of Hainan Medical University, Danzhou City, Hainan, China
| | - Chengrui Yang
- Department of General Surgery, Affiliated Danzhou People's Hospital of Hainan Medical University, Danzhou City, Hainan, China
| | - Fangyuan Sun
- Department of General Surgery, Affiliated Danzhou People's Hospital of Hainan Medical University, Danzhou City, Hainan, China
| | - Yanzhong Zhang
- Department of General Surgery, Affiliated Danzhou People's Hospital of Hainan Medical University, Danzhou City, Hainan, China
| | - Yanliang Wang
- Department of General Surgery, Affiliated Danzhou People's Hospital of Hainan Medical University, Danzhou City, Hainan, China
| | - Xuzhao Li
- Department of Surgery, People's Hospital of Ningxia Hui Autonomous Region, Yinchuan, 750011, Ningxia, China
| | - Fengxian Zheng
- Department of Critical Care Medicine, Affiliated Danzhou People's Hospital of Hainan Medical University, No. 21-1, Datong Road, Nada Town, Danzhou City, 571747, Hainan, China.
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Guo F, Yang H, Bai X, Li J, Han W, Li W. Probing the mechanisms of hydrazide-based HDAC inhibitors binding to HDAC3 using Gaussian accelerated molecular dynamics (GaMD) simulations. J Biomol Struct Dyn 2023:1-14. [PMID: 37937774 DOI: 10.1080/07391102.2023.2278085] [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: 09/19/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023]
Abstract
Histone deacetylases (HDACs) have emerged as promising targets for anticancer drug development. They regulate gene expression by removing acetyl groups from lysine residues on histone tails, leading to chromatin condensation. A hydrazide-based HDAC inhibitor, N-(4-(2-Propylhydrazine-1-carbonyl)benzyl)-1H-indole-2-carboxamide (11h), has been reported to exhibit significant in vivo antitumor activity. In comparison to the lead compound N-(4-(2-Propylhydrazine-1-carbonyl)benzyl)cinnamamide (17), compound 11h demonstrates 2- to 5-fold higher HDAC inhibition and cell-based antitumor activity. However, the inhibitory mechanism of 11h remains insufficiently explored. In this study, we conducted 500 ns Gaussian Accelerated Molecular Dynamics (GaMD) simulations on Histone deacetylase 3 (HDAC3) and two complex systems (HDAC3-17 and HDAC3-11h). Our findings revealed that upon inhibitor binding, the active pocket volume of HDAC3 undergone alterations, and the movement of the L6-loop toward the active site impeded substrate entry. Moreover, we observed a destabilization of the α-helix in the aa75-89 region of HDAC3 compared to the two complex systems, indicating partial unwinding. Notably, 11h exhibited a closer proximity of its carbonyl oxygen to the active pocket's Zn2+ metal compared to 17, increasing the likelihood of coordination with the Zn2+ metal. The analysis of protein-ligand interactions highlighted a greater number of hydrogen bonds and other interactions between 11h and the receptor protein when compared to 17, underscoring the stronger binding of 11h to HDAC3. In conclusion, our study provided theoretical insights into the inhibitory mechanism of hydrazide-based HDAC inhibitors on HDAC3, thereby contributing to the development of improved drug targets for cancer therapy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fangfang Guo
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun, China
| | - Hengzheng Yang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Xue Bai
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Jiaying Li
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun, China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Wannan Li
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun, China
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Gong T, Li Y, Feng L, Xu Q, Dai G, Li M, Wang Y, Liu S. SNHG25 promotes colorectal cancer metastasis by regulating MMP2. Aging (Albany NY) 2023; 15:10105-10116. [PMID: 37751586 PMCID: PMC10599716 DOI: 10.18632/aging.205060] [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: 05/24/2023] [Accepted: 09/02/2023] [Indexed: 09/28/2023]
Abstract
LncRNA has been shown to play an important role in tumors, but the functions of most lncRNAs in colorectal cancer is not clear. By analyzing the transcriptome data of tumor tissues and adjacent tissues, we identified the lncRNA profiles that were abnormally expressed in colorectal cancer and selected the abnormally highly expressed lncRNA SNHG25 for further study. The functional assays showed that after knocking down SNHG25, the metastatic ability of colorectal cancer cells was significantly reduced. Western blot and immunofluorescence assays showed that inhibiting SNHG25 would affect the expression of Vimentin and E-Cadherin. In terms of mechanism, the results of RNA pull down assays, RNA immunoprecipitation (RIP) assays and dual luciferase reporter assays showed that SNHG25 could promote MMP2 expression by adsorbing miR-296-3p. In addition, chromatin immunoprecipitation (ChIP) assays and promoter luciferase reporter assays revealed that PAX5 could activate the transcription of SNHG25 in colorectal cancer cells. Our study proved that SNHG25 acts a pro-metastasis role in colorectal cancer, enriching the theory of the functions of lncRNA in colorectal cancer.
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Affiliation(s)
- Tao Gong
- Oncology, Nanjing Hospital of Chinese Medicine, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yu Li
- Oncology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
| | - Liang Feng
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Qingyu Xu
- Interventional Radiology Department, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and the Affiliated Cancer Hospital of Nanjing Medical University, Nanjing 210000, China
| | - Guoliang Dai
- Department of Clinical Pharmacology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
| | - Min Li
- Oncology, Nanjing Hospital of Chinese Medicine, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yi Wang
- Colorectal Surgery, Nanjing Hospital of Chinese Medicine, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Shenlin Liu
- Oncology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
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Li Z, Bu D, Wang X, Zhu L, Lei D, Tang F, Sun X, Chen C, Ji X, Bai S. Chidamide and Oxaliplatin Synergistically Inhibit Colorectal Cancer Growth by Regulating the RPS27A-MDM2-P53 Axis. Onco Targets Ther 2023; 16:703-721. [PMID: 37667747 PMCID: PMC10475304 DOI: 10.2147/ott.s416824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/13/2023] [Indexed: 09/06/2023] Open
Abstract
Purpose The present study explored the anti-tumor effects of chidamide plus oxaliplatin on colorectal cancer (CRC) and examined its underlying mechanism. Material and Methods First, the Combination Index (CI) of chidamide and oxaliplatin was evaluated via CCK-8 assay. Second, the effects of chidamide and oxaliplatin monotherapy and the combined treatment on cell proliferation, invasion, migration, and apoptosis were detected. Third, whole-transcriptome RNA sequencing (RNA-seq) was performed to seek the potential targeted gene by which chidamide plus oxaliplatin exerted anti-tumor effects. Fourth, the validation of the targeted gene and the signal pathway it regulated were performed. Finally, the anti-tumor effect of chidamide plus oxaliplatin on mice xenograft was examined. Results Chidamide and oxaliplatin acted synergistically to inhibit CRC growth in vitro and in vivo (CI<1). Besides, compared with oxaliplatin monotherapy, chidamide could significantly enhance oxaliplatin-induced inhibition in cell proliferation, invasion, and migration, and promotion in HCT-116 and RKO cell apoptosis (P<0.05). The RNA-seq displayed that, compared to oxaliplatin monotherapy, RPS27A mRNA was evidently decreased in HCT-116 cells treated with chidamide plus oxaliplatin (P<0.001). Then, we found RPS27A was highly expressed in CRC tissues and CRC cell lines (P<0.001). Silence of RPS27A attenuated proliferation and induced apoptosis in HCT-116 and RKO cells via downregulation of MDM2 expression and upregulation of P53. Next, RPS27A overexpression could partially reverse chidamide plus oxaliplatin induced growth inhibition and apoptosis in HCT-116 and RKO cells (P<0.01). RPS27A overexpression could promote the upregulation of MDM2 and downregulation of P53 after the combined treatment of chidamide with oxaliplatin. Conclusion Chidamide and oxaliplatin acted synergistically to suppress CRC growth by the inhibition of the RPS27A-MDM2-p53 axis.
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Affiliation(s)
- Zhaopeng Li
- Department of Geriatric General Surgery, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650000, People’s Republic of China
| | - Deyong Bu
- Department of Geriatric General Surgery, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650000, People’s Republic of China
| | - Xiaobin Wang
- Department of Geriatric General Surgery, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650000, People’s Republic of China
| | - Lin Zhu
- Department of Ultrasound, the Affiliated Nanchong Central Hospital of North Sichuan Medical College, Nanchong, Sichuan, 637000, People’s Republic of China
| | - Daoyan Lei
- Department of Ultrasound, Jiangchuan District People’s Hospital, Yuxi, Yunnan, 652600, People’s Republic of China
| | - Fengling Tang
- Department of Geriatric General Surgery, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650000, People’s Republic of China
| | - Xianghua Sun
- Department of Geriatric General Surgery, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650000, People’s Republic of China
| | - Cheng Chen
- Department of Breast Surgery, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650000, People’s Republic of China
| | - Xiang Ji
- Department of Day Surgery, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650000, People’s Republic of China
| | - Song Bai
- Department of Geriatric General Surgery, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650000, People’s Republic of China
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11
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Banerjee S, Dumawat S, Jha T, Lanka G, Adhikari N, Ghosh B. Fragment-based structural exploration and chemico-biological interaction study of HDAC3 inhibitors through non-linear pattern recognition, chemical space, and binding mode of interaction analysis. J Biomol Struct Dyn 2023:1-23. [PMID: 37608752 DOI: 10.1080/07391102.2023.2248509] [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: 02/27/2023] [Accepted: 08/10/2023] [Indexed: 08/24/2023]
Abstract
HDAC3 is an emerging target for the identification and discovery of novel drug candidates against several disease conditions including cancer. Here, a fragment-based non-linear machine learning (ML) method along with chemical space exploration followed by a structure-based binding mode of interaction analysis study was carried out on some HDAC3 inhibitors to obtain the key structural features modulating HDAC3 inhibition. Both the ML and chemical space analysis identified several physicochemical and structural properties namely lipophilicity, polar and relative polar surface area, arylcarboxamide moiety, bulky fused aromatic group, n-alkyl, and cinnamoyl moieties, the higher number of oxygen atoms, π-electrons for the substituted tetrahydrofuronaphthodioxolone moiety favorable for higher HDAC3 inhibition. Moreover, hydrogen bond forming capabilities, the length and substitution position of the linker moiety, the importance of phenyl ring in the linker motif, the contribution of heterocyclic cap moieties for effective inhibitor binding at the HDAC3 catalytic site that correspondingly affects the HDAC3 inhibitory potency. Again, macrocyclic ring structure and cyclohexyl cap moiety are responsible for lower HDAC3 inhibition. The MD simulation study of selected compounds explained strong binding patterns at the HDAC3 active site as evidenced by the lower RMSD and RMSF values. Nevertheless, it also explained the importance of the crucial structural fragments derived from the fragment-based analysis during ligand-enzyme interactions. Therefore, the outcomes of this current structural analysis will be a useful tool for fragment-based drug discovery of effective HDAC3 inhibitors for clinical therapeutics in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Shraddha Dumawat
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Goverdhan Lanka
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, India
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12
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Xiao W, Li P. Circ_0087862 promotes tumorigenesis and glycolysis in colorectal cancer by sponging miR-296-3p to regulate PGK1 expression. Pathol Res Pract 2023; 248:154695. [PMID: 37494801 DOI: 10.1016/j.prp.2023.154695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 06/13/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023]
Abstract
BACKGROUND Circular RNAs (circRNAs) exert crucial roles in tumor progression of multiple cancers, including colorectal cancer (CRC). However, the functions of most circRNAs are not been fully elucidated. In this study, the role and mechanism of circ_0087862 in CRC were investigated. METHODS The expression of circ_0087862, microRNA-296-3p (miR-296-3p) and phosphoglycerate kinase 1 (PGK1) was detected by quantitative real-time PCR (qRT-PCR). Cell Counting Kit-8 (CCK-8) assay and 5-ethynyl-2'-deoxyuridine (EdU) assay were used to assess cell proliferation. Flow cytometry was employed to analyze cell apoptosis. Transwell assay was employed to evaluate cell invasion. Western blot assay was employed to detect the level of related protein markers and PGK1. The glucose consumption, lactate production were tested by corresponding kits. The relationship between miR-296-3p and circ_0087862 or PGK1 was verified by dual-luciferase reporter assay or RNA immunoprecipitation (RIP) assay. The in vivo function of circ_0087862 was examined by xenograft mice model. RESULTS The expression levels of circ_0087862 and PGK1 were up-regulated in CRC tissues and cells, while miR-296-3p was down-regulated. Circ_0087862 silencing suppressed cell proliferation, invasion and glycolysis and promoted cell apoptosis in CRC cells. Circ_0087862 targeted miR-296-3p in CRC cells. MiR-296-3p inhibition reversed circ_0087862 silencing-mediated inhibition effect on cell proliferation, invasion and glycolysis, as well as the promotion effect on cell apoptosis. PGK1 was a target of miR-296-3p, and the overexpression of PGK1 attenuated miR-296-3p-mediated tumor suppression effect on CRC progression. Moreover, knockdown of circ_0087862 inhibited tumorigenesis in vivo. CONCLUSION Circ_0087862 promoted CRC progression via miR-296-3p/PGK1 axis and might act as a potential target for CRC therapy.
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Affiliation(s)
- Weisheng Xiao
- Department of Gastroenterology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Peiyuan Li
- Department of Gastroenterology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China.
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13
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He F, Liu Q, Liu H, Pei Q, Zhu H. Circular RNA ACACA negatively regulated p53-modulated mevalonate pathway to promote colorectal tumorigenesis via regulating miR-193a/b-3p/HDAC3 axis. Mol Carcinog 2023; 62:754-770. [PMID: 36920044 DOI: 10.1002/mc.23522] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 03/16/2023]
Abstract
This study aimed to explore the biological functions and underlying mechanism of circRNA acetyl-CoA carboxylase alpha (circACACA) in colorectal cancer (CRC). The RNA and protein levels were detected by qRT-PCR and western blot assays. The malignant capacities of CRC cells were analyzed by cell counting kit-8 (CCK-8), colony formation, flow cytometry, and transwell assays. The target relationship between miR-193a/b-3p and circACACA/histone deacetylase 3 (HDAC3) was determined by luciferase reporter assay and RNA immunoprecipitation. The binding of HDAC3 to the p53 promoter was validated by chromatin immunoprecipitation (ChIP). CRC cell growth and lung metastasis were evaluated in nude mice in vivo. High expression of circACACA was found in CRC tissues and cells, which was closely associated with the advanced tumor, lymph node, metastasis (TNM) stage, metastasis, and low overall survival rate. circACACA downregulation effectively delayed CRC cell proliferation and metastasis, but triggered apoptosis via inactivating the mevalonic acid (MVA) pathway. However, circACACA overexpression resulted in the opposite effects. Mechanistically, circACACA enhanced HDAC3 expression through sponging miR-193a/b-3p, which activated the MVA pathway via inhibiting the acetylation and transcription of p53. Moreover, rescue experiments confirmed that miR-193a/b-3p inhibition reversed the inhibitory effect of circACACA deficiency on CRC growth and metastasis. Moreover, circACACA overexpression-mediated malignant phenotypes of CRC cells were abrogated by HDAC3 knockdown. circACACA promoted CRC progression via regulating the miR-193a/b-3p/HDAC3/p53 axis to activate the MVA pathway, providing evidence for circACACA as a promising therapeutic target for CRC.
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Affiliation(s)
- Fengjiao He
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan Province, P.R. China.,Department of Oncology, Hunan Academy of Traditional Chinese Medicine Affiliated Hospital, Changsha, Hunan Province, P.R. China
| | - Qiong Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan Province, P.R. China
| | - Huan Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan Province, P.R. China
| | - Qian Pei
- Department of Gastrointestinal Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, P.R. China
| | - Hong Zhu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan Province, P.R. China
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14
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Liu X, Wang A, Shi Y, Dai M, Liu M, Cai HB. PROTACs in Epigenetic Cancer Therapy: Current Status and Future Opportunities. Molecules 2023; 28:molecules28031217. [PMID: 36770884 PMCID: PMC9919707 DOI: 10.3390/molecules28031217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/24/2022] [Accepted: 01/06/2023] [Indexed: 01/28/2023] Open
Abstract
The epigenetic regulation of gene functions has been proven to be strongly associated with the development and progression of cancer. Reprogramming the cancer epigenome landscape is one of the most promising target therapies in both treatments and in reversing drug resistance. Proteolytic targeted chimeras (PROTACs) are an emerging therapeutic modality for selective degradation via the native ubiquitin-proteasome system. Rapid advances in PROTACs have facilitated the exploration of targeting epigenetic proteins, a lot of PROTAC degraders have already been designed in the field of epigenetic cancer therapy, and PROTACs targeting epigenetic proteins can better exploit target druggability and improve the mechanistic understanding of the epigenetic regulation of cancer. Thus, this review focuses on the progress made in the development of PROTAC degraders and PROTAC drugs targeting epigenetics in cancer and discusses challenges and future opportunities for the field.
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Affiliation(s)
- Xuelian Liu
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Cancer Clinical Study Center, Wuhan 430071, China
| | - Anjin Wang
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Cancer Clinical Study Center, Wuhan 430071, China
| | - Yuying Shi
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Cancer Clinical Study Center, Wuhan 430071, China
| | - Mengyuan Dai
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Cancer Clinical Study Center, Wuhan 430071, China
- Correspondence: (M.D.); (H.-B.C.)
| | - Miao Liu
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hong-Bing Cai
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Cancer Clinical Study Center, Wuhan 430071, China
- Correspondence: (M.D.); (H.-B.C.)
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15
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Mao D, Zhang X, Wang Z, Xu G, Zhang Y. TMEM97 is transcriptionally activated by YY1 and promotes colorectal cancer progression via the GSK-3β/β-catenin signaling pathway. Hum Cell 2022; 35:1535-1546. [PMID: 35907137 DOI: 10.1007/s13577-022-00759-5] [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: 04/29/2022] [Accepted: 07/21/2022] [Indexed: 11/25/2022]
Abstract
Transmembrane protein 97 (TMEM97) is a conserved integral membrane protein highly expressed in various human cancers, including colorectal cancer (CRC), and it exhibits pro-tumor roles in breast cancer, gastric cancer, and glioma. However, whether TMEM97 participates in CRC progression is not fully understood. The expression of mRNA and protein was evaluated by real-time qPCR, western blotting, immunofluorescent, and immunohistochemical staining. TMEM97 functions in cell proliferation, apoptosis, migration, and invasion were assessed by CCK-8, flow cytometry, and transwell assays. The roles of TMEM97 in CRC cells in vivo was investigated using a subcutaneous xenograft model. The transcriptional regulation of TMEM97 was explored by luciferase reporter and ChIP assays. The silencing of TMEM97 inhibited migration and invasion of CRC cells in vitro and led to suppressed growth and enhanced apoptosis in CRC cells and xenografts, whereas overexpression of TMEM97 displayed opposite effects. Mechanistically, TMEM97 knockdown caused a reduction of the proliferating marker PCNA and an increase of pro-apoptotic proteins (cleaved caspase 8/3/7 and cleaved PARP) in CRC cells. TMEM97 also positively regulated the β-catenin signaling pathway in CRC cells and xenografts by modulating the phosphorylated-GSK-3β and active (non-phospho) β-catenin levels. Interestingly, YY1, a well-recognized oncogenic transcription factor, was identified to bind to the TMEM97 promoter and enhance its transcriptional activity, and silencing of TMEM97 abolished YY1-mediated pro-tumor effects on CRC cells. Our results suggest that TMEM97 is transcriptionally activated by YY1 and promotes CRC progression via the GSK-3β/β-catenin signaling pathway, providing that TMEM97 might be a novel therapeutic target for preventing CRC development.
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Affiliation(s)
- Dong Mao
- Department of General Surgery, The First Affiliated Hospital of Jinzhou Medical University, No. 2, The Fifth Section of Renmin Street, Jinzhou, Liaoning Province, China
| | - Xiaowei Zhang
- Department of General Surgery, The First Affiliated Hospital of Jinzhou Medical University, No. 2, The Fifth Section of Renmin Street, Jinzhou, Liaoning Province, China
| | - Zhaoping Wang
- Department of General Surgery, The First Affiliated Hospital of Jinzhou Medical University, No. 2, The Fifth Section of Renmin Street, Jinzhou, Liaoning Province, China
| | - Guannan Xu
- Department of General Surgery, The First Affiliated Hospital of Jinzhou Medical University, No. 2, The Fifth Section of Renmin Street, Jinzhou, Liaoning Province, China
| | - Yun Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinzhou Medical University, No. 2, The Fifth Section of Renmin Street, Jinzhou, Liaoning Province, China.
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16
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Abstract
In mammalian cells, genomic DNA is packaged with histone proteins and condensed into chromatin. To gain access to the DNA, chromatin remodelling is required that is enhanced through histone post-translational modifications, which subsequently stimulate processes including DNA repair and transcription. Histone acetylation is one of the most well understood modifications and is controlled by histone acetyltransferases (HATs) and histone deacetylases (HDACs). These enzymes play critical roles in normal cellular functioning, and the dysregulation of HDAC expression in particular has been linked with the development of a number of different cancer types. Conversely, tumour cell killing following radiotherapy is triggered through DNA damage and HDACs can help co-ordinate the cellular DNA damage response which promotes radioresistance. Consequently, HDAC inhibitors have been investigated as potential radiosensitizers in vitro and in vivo to improve the efficacy or radiotherapy in specific tumour types. In this review, we provide an up-to-date summary of HDACs and their cellular functions, including in DNA damage repair. We also review evidence demonstrating that HDAC inhibitors can effectively enhance tumour radiosensitisation, and which therefore show potential for translation into the clinic for cancer patient benefit.
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17
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Identification of novel leads as potent inhibitors of HDAC3 using ligand-based pharmacophore modeling and MD simulation. Sci Rep 2022; 12:1712. [PMID: 35110603 PMCID: PMC8810932 DOI: 10.1038/s41598-022-05698-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/03/2022] [Indexed: 02/08/2023] Open
Abstract
In the landscape of epigenetic regulation, histone deacetylase 3 (HDAC3) has emerged as a prominent therapeutic target for the design and development of candidate drugs against various types of cancers and other human disorders. Herein, we have performed ligand-based pharmacophore modeling, virtual screening, molecular docking, and MD simulations to design potent and selective inhibitors against HDAC3. The predicted best pharmacophore model ‘Hypo 1’ showed excellent correlation (R2 = 0.994), lowest RMSD (0.373), lowest total cost value (102.519), and highest cost difference (124.08). Hypo 1 consists of four salient pharmacophore features viz. one hydrogen bond acceptor (HBA), one ring aromatic (RA), and two hydrophobic (HYP). Hypo 1 was validated by Fischer's randomization with a 95% of confidence level and the external test set of 60 compounds with a good correlation coefficient (R2 = 0.970). The virtual screening of chemical databases, drug-like properties calculations followed by molecular docking resulted in identifying 22 representative hit compounds. Performed 50 ns of MD simulations on top three hits were retained the salient π-stacking, Zn2+ coordination, hydrogen bonding, and hydrophobic interactions with catalytic residues from the active site pocket of HDAC3. Total binding energy calculated by MM-PBSA showed that the Hit 1 and Hit 2 formed stable complexes with HDAC3 as compared to reference TSA. Further, the PLIP analysis showed a close resemblance between the salient pharmacophore features of Hypo 1 and the presence of molecular interactions in co-crystallized FDA-approved drugs. We conclude that the screened hit compounds may act as potent inhibitors of HDAC3 and further preclinical and clinical studies may pave the way for developing them as effective therapeutic agents for the treatment of different cancers and neurodegenerative disorders.
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18
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Li J, Hu M, Liu N, Li H, Yu Z, Yan Q, Zhou M, Wang Y, Song Y, Pan G, Liang F, Chen R. Correction to: HDAC3 deteriorates colorectal cancer progression via microRNA-296-3p/TGIF1/TGFβ axis. J Exp Clin Cancer Res 2021; 40:404. [PMID: 34972530 PMCID: PMC8719399 DOI: 10.1186/s13046-021-02232-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- Jinxiao Li
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1227 Jiefang Avenue, Wuhan City, 430022, Hubei Province, China
| | - Man Hu
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1227 Jiefang Avenue, Wuhan City, 430022, Hubei Province, China
| | - Na Liu
- Rehabilitation Department of traditional Chinese Medicine, Union Red Cross Hospital, Wuhan, 430015, China
| | - Huarong Li
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1227 Jiefang Avenue, Wuhan City, 430022, Hubei Province, China
| | - Zhaomin Yu
- Department of Oncology, Hubei Provincial Hospital of Integrated Chinese and Western Medicine, Wuhan, 430071, China
| | - Qian Yan
- First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510405, China
| | - Minfeng Zhou
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1227 Jiefang Avenue, Wuhan City, 430022, Hubei Province, China
| | - Yayuan Wang
- College of Acupuncture & Moxibustion and Orthopaedics, Hubei University of Chinese Medicine, Wuhan, 430060, China
| | - Yanjuan Song
- College of Acupuncture & Moxibustion and Orthopaedics, Hubei University of Chinese Medicine, Wuhan, 430060, China
| | - Guangtao Pan
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1227 Jiefang Avenue, Wuhan City, 430022, Hubei Province, China
| | - Fengxia Liang
- College of Acupuncture & Moxibustion and Orthopaedics, Hubei University of Chinese Medicine, Wuhan, 430060, China.
| | - Rui Chen
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1227 Jiefang Avenue, Wuhan City, 430022, Hubei Province, China.
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19
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Hu F, Wang J, Zhang M, Wang S, Zhao L, Yang H, Wu J, Cui B. Comprehensive Analysis of Subtype-Specific Molecular Characteristics of Colon Cancer: Specific Genes, Driver Genes, Signaling Pathways, and Immunotherapy Responses. Front Cell Dev Biol 2021; 9:758776. [PMID: 34912802 PMCID: PMC8667669 DOI: 10.3389/fcell.2021.758776] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Colon cancer is a complex, heterogeneous disease. The Colorectal Cancer Subtyping Consortium reported a novel classification system for colon cancer in 2015 to better understand its heterogeneity. This molecular classification system divided colon cancer into four distinct consensus molecular subtypes (CMS 1, 2, 3, and 4). However, the characteristics of different colon cancer molecular subtypes have not been fully elucidated. This study comprehensively analyzed the molecular characteristics of varying colon cancer subtypes using multiple databases and algorithms, including The Cancer Genome Atlas (TCGA) database, DriverDBv3 database, CIBERSORT, and MCP-counter algorithms. We analyzed the alterations in the subtype-specific genes of different colon cancer subtypes, such as the RNA levels and DNA alterations, and showed that specific subtype-specific genes significantly affected prognosis. We also explored the changes in colon cancer driver genes and representative genes of 10 signaling pathways in different subtypes. We identified genes that were altered in specific subtypes. We further detected the infiltration of 22 immune cell types in four colon cancer subtypes and the infiltration level of primary immune cells among these subtypes. Additionally, we explored changes in immune checkpoint genes (ICGs) and immunotherapy responses among different colon cancer subtypes. This study may provide clues for the molecular mechanism of tumorigenesis and progression in colon cancer. It also offers potential biomarkers and targets for the clinical diagnosis and treatment of different colon cancer subtypes.
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Affiliation(s)
- Fangjie Hu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
| | - Jianyi Wang
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Minghui Zhang
- Department of Oncology, Chifeng City Hospital, Chifeng, China
| | - Shuoshuo Wang
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Lingyu Zhao
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Hao Yang
- Department of Radiation Oncology, Inner Mongolia Cancer Hospital & Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Jinrong Wu
- Department of Anaesthesiology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Binbin Cui
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
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Zhang S, Sun J, Gu M, Wang G, Wang X. Circular RNA: A promising new star for the diagnosis and treatment of colorectal cancer. Cancer Med 2021; 10:8725-8740. [PMID: 34796685 PMCID: PMC8683543 DOI: 10.1002/cam4.4398] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/18/2021] [Accepted: 10/19/2021] [Indexed: 12/11/2022] Open
Abstract
Background Colorectal cancer (CRC) is one of the most common malignant tumors of the digestive tract. According to the research of circular RNAs in the CRC field, compared with linear RNAs, circular RNAs are a special type of noncoding RNA that are covalently closed circular structures, which have no 5' cap structure and 3' polyA tail and are not affected by RNA exonuclease and actinomycin D. Biological functions Notably, circular RNAs have a high degree of stability and potential effect on gene regulation. Meanwhile, circular RNAs are involved in the sponge action of microRNAs and mediate protein translation and direct binding, alternative splicing, and histone modification. Relationships with CRC Studies have shown that circular RNAs are related to the proliferation, invasion, recurrence, metastasis, ferroptosis, apoptosis, and chemotherapy resistance of CRC. Conclusions This article provides a brief review based on the source, structural characteristics, mechanisms, biological functions of circular RNAs, and the relationships between CRC.
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Affiliation(s)
- Shunhao Zhang
- Graduate School of Nantong University, Nantong, China
| | - Jing Sun
- Graduate School of Nantong University, Nantong, China
| | - Minqi Gu
- Graduate School of Nantong University, Nantong, China
| | - Guihua Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Xudong Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
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21
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Dong L, Huang J, Zu P, Liu J, Gao X, Du J, Li Y. Transcription factor 3 (TCF3) combined with histone deacetylase 3 (HDAC3) down-regulates microRNA-101 to promote Burkitt lymphoma cell proliferation and inhibit apoptosis. Bioengineered 2021; 12:7995-8005. [PMID: 34658308 PMCID: PMC8806859 DOI: 10.1080/21655979.2021.1977557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
To explore the function of transcription factor 3 (TCF3) on the proliferation and apoptosis of Burkitt lymphoma cells and its mechanism. qRT-PCR was performed to determine the expression of TCF3, histone deacetylase 3 (HDAC3), and microRNA-101 (miR-101) in the Burkitt lymphoma (BL) tumor tissues and lymph node tissues with reactive lymph node hyperplasia (RLNH). We found that the expression of TCF3 and HDAC3 was up-regulated in BL tumor tissues and lymphoma cells, and the miR-101 expression was down-regulated. And TCF3 and HDAC3 were negatively correlated with the expression of miR-101, respectively. In addition, knockdown of TCF3 can inhibit BL cell proliferation, reduce cell viability and promote cell apoptosis, retain the cell cycle in the G0/G1 phase, and inhibit the expression of Akt/mTOR pathway-related proteins (p-Akt and p-mTOR). When miR-101 was overexpressed, the results were the same as when TCF3 was knocked down. Moreover, we used Co-immunoprecipitation (Co-IP) to detect the interaction between TCF3 and HDAC3, and performed the Chromatin immunoprecipitation (ChIP) experiment to detect the enrichment of TCF3 and HDAC3 in the promoter region of miR-101. We found that TCF3 can interact with HDAC3 and is enriched in the miR-101 promoter region. In conclusion, TCF3 combined with HDAC3 down-regulates the expression of miR-101, thereby promoting the proliferation of BL cells and inhibiting their apoptosis.
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Affiliation(s)
- Lihua Dong
- Department of Hematology, Henan Institute of Hematology, the Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Jingjing Huang
- Department of Hematology, Henan Institute of Hematology, the Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Peng Zu
- Department of Hematology, Henan Institute of Hematology, the Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Jing Liu
- Department of Hematology, Henan Institute of Hematology, the Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Xue Gao
- Department of Hematology, Henan Institute of Hematology, the Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Jianwei Du
- Department of Hematology, Henan Institute of Hematology, the Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Yufu Li
- Department of Hematology, Henan Institute of Hematology, the Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
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22
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Lu Q, Lou J, Cai R, Han W, Pan H. Emerging roles of a pivotal lncRNA SBF2-AS1 in cancers. Cancer Cell Int 2021; 21:417. [PMID: 34372871 PMCID: PMC8351094 DOI: 10.1186/s12935-021-02123-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/29/2021] [Indexed: 12/25/2022] Open
Abstract
Long non-coding RNAs refer to transcripts over 200 nt in length that lack the ability to encode proteins, which occupy the majority of the genome and play a crucial role in the occurrence and development of human diseases, especially cancers. SBF2-AS1, a newly identified long non-coding RNA, has been verified to be highly expressed in diversiform cancers, and is involved in processes promoting tumorigenesis, tumor progression and tumor metastasis. Moreover, upregulation of SBF2-AS1 expression was significantly related to disadvantageous clinicopathologic characteristics and indicated poor prognosis. In this review, we comprehensively summarize the up-to-date knowledge of the detailed mechanisms and underlying functions of SBF2-AS1 in diverse cancer types, highlighting the potential of SBF2-AS1 as a diagnostic and prognostic biomarker and even a therapeutic target.
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Affiliation(s)
- Qian Lu
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jun Lou
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ruyun Cai
- Department of Colorectal Surgery, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Weidong Han
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
| | - Hongming Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
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