1
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An MJ, Kim JY, Kim J, Kim DH, Shin GS, Lee HM, Jo AR, Park Y, Hwangbo Y, Kim CH, Kim MJ, Jung YS, Kim J, Rhee S, Seo SB, Kim JW. Reorganization of H3K9me heterochromatin leads to neuronal impairment via the cascading destruction of the KDM3B-centered epigenomic network. iScience 2024; 27:110380. [PMID: 39165843 PMCID: PMC11334829 DOI: 10.1016/j.isci.2024.110380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 03/14/2024] [Accepted: 06/24/2024] [Indexed: 08/22/2024] Open
Abstract
Histone H3K9 methylated heterochromatin silences repetitive non-coding sequences and lineage-specific genes during development, but how tissue-specific genes escape from heterochromatin in differentiated cells is unclear. Here, we examine age-dependent transcriptomic profiling of terminally differentiated mouse retina to identify epigenetic regulators involved in heterochromatin reorganization. The single-cell RNA sequencing analysis reveals a gradual downregulation of Kdm3b in cone photoreceptors during aging. Disruption of Kdm3b (Kdm3b +/- ) of 12-month-old mouse retina leads to the decreasing number of cones via apoptosis, and it changes the morphology of cone ribbon synapses. Integration of the transcriptome with epigenomic analysis in Kdm3b +/- retinas demonstrates gains of heterochromatin features in synapse assembly and vesicle transport genes that are downregulated via the accumulation of H3K9me1/2. Contrarily, losses of heterochromatin in apoptotic genes exacerbated retinal neurodegeneration. We propose that the KDM3B-centered epigenomic network is crucial for balancing of cone photoreceptor homeostasis via the modulation of gene set-specific heterochromatin features during aging.
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Affiliation(s)
- Mi-Jin An
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Ji-Young Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Jinho Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Dae-Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Geun-Seup Shin
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Hyun-Min Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Ah-Ra Jo
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Yuna Park
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Yujeong Hwangbo
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Chul-Hong Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Mi Jin Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Youn-Sang Jung
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Jeongkyu Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Sangmyung Rhee
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Sang-Beom Seo
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Jung-Woong Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
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2
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Yoo J, Kim GW, Jeon YH, Lee SW, Kwon SH. Epigenetic roles of KDM3B and KDM3C in tumorigenesis and their therapeutic implications. Cell Death Dis 2024; 15:451. [PMID: 38926399 PMCID: PMC11208531 DOI: 10.1038/s41419-024-06850-z] [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: 12/20/2023] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
Advances in functional studies on epigenetic regulators have disclosed the vital roles played by diverse histone lysine demethylases (KDMs), ranging from normal development to tumorigenesis. Most of the KDMs are Jumonji C domain-containing (JMJD) proteins. Many of these KDMs remove methyl groups from histone tails to regulate gene transcription. There are more than 30 known KDM proteins, which fall into different subfamilies. Of the many KDM subfamilies, KDM3 (JMJD1) proteins specifically remove dimethyl and monomethyl marks from lysine 9 on histone H3 and other non-histone proteins. Dysregulation of KDM3 proteins leads to infertility, obesity, metabolic syndromes, heart diseases, and cancers. Among the KDM3 proteins, KDM3A has been largely studied in cancers. However, despite a number of studies pointing out their importance in tumorigenesis, KDM3B and KDM3C are relatively overlooked. KDM3B and KDM3C show context-dependent functions, showing pro- or anti-tumorigenic abilities in different cancers. Thus, this review provides a thorough understanding of the involvement of KDM3B and KDMC in oncology that should be helpful in determining the role of KDM3 proteins in preclinical studies for development of novel pharmacological methods to overcome cancer.
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Affiliation(s)
- Jung Yoo
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983, Republic of Korea
| | - Go Woon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983, Republic of Korea
| | - Yu Hyun Jeon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983, Republic of Korea
| | - Sang Wu Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983, Republic of Korea
| | - So Hee Kwon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983, Republic of Korea.
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3
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Kim YY, Gryder BE, Sinniah R, Peach ML, Shern JF, Abdelmaksoud A, Pomella S, Woldemichael GM, Stanton BZ, Milewski D, Barchi JJ, Schneekloth JS, Chari R, Kowalczyk JT, Shenoy SR, Evans JR, Song YK, Wang C, Wen X, Chou HC, Gangalapudi V, Esposito D, Jones J, Procter L, O'Neill M, Jenkins LM, Tarasova NI, Wei JS, McMahon JB, O'Keefe BR, Hawley RG, Khan J. KDM3B inhibitors disrupt the oncogenic activity of PAX3-FOXO1 in fusion-positive rhabdomyosarcoma. Nat Commun 2024; 15:1703. [PMID: 38402212 PMCID: PMC10894237 DOI: 10.1038/s41467-024-45902-y] [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: 11/21/2022] [Accepted: 02/07/2024] [Indexed: 02/26/2024] Open
Abstract
Fusion-positive rhabdomyosarcoma (FP-RMS) is an aggressive pediatric sarcoma driven primarily by the PAX3-FOXO1 fusion oncogene, for which therapies targeting PAX3-FOXO1 are lacking. Here, we screen 62,643 compounds using an engineered cell line that monitors PAX3-FOXO1 transcriptional activity identifying a hitherto uncharacterized compound, P3FI-63. RNA-seq, ATAC-seq, and docking analyses implicate histone lysine demethylases (KDMs) as its targets. Enzymatic assays confirm the inhibition of multiple KDMs with the highest selectivity for KDM3B. Structural similarity search of P3FI-63 identifies P3FI-90 with improved solubility and potency. Biophysical binding of P3FI-90 to KDM3B is demonstrated using NMR and SPR. P3FI-90 suppresses the growth of FP-RMS in vitro and in vivo through downregulating PAX3-FOXO1 activity, and combined knockdown of KDM3B and KDM1A phenocopies P3FI-90 effects. Thus, we report KDM inhibitors P3FI-63 and P3FI-90 with the highest specificity for KDM3B. Their potent suppression of PAX3-FOXO1 activity indicates a possible therapeutic approach for FP-RMS and other transcriptionally addicted cancers.
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Affiliation(s)
| | - Berkley E Gryder
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | | | - Megan L Peach
- Basic Science Program, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD, USA
| | - Jack F Shern
- Pediatric Oncology Branch, NCI, NIH, Bethesda, MD, USA
| | | | - Silvia Pomella
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Department of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Girma M Woldemichael
- Leidos Biomed Res Inc, FNLCR, Basic Sci Program, Frederick, MD, USA
- Molecular Targets Program, NCI, NIH, Frederick, MD, USA
| | - Benjamin Z Stanton
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Nationwide Children's Hospital, Center for Childhood Cancer Research, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
- Department of Biological Chemistry & Pharmacology, The Ohio State University College of Medicine, Columbus, OH, USA
| | | | | | | | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program, FNLCR, Frederick, MD, USA
| | | | - Shilpa R Shenoy
- Leidos Biomed Res Inc, FNLCR, Basic Sci Program, Frederick, MD, USA
- Molecular Targets Program, NCI, NIH, Frederick, MD, USA
| | - Jason R Evans
- Natural Products Branch, NCI, NIH, Frederick, MD, USA
| | | | - Chaoyu Wang
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
| | - Xinyu Wen
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
| | | | | | | | - Jane Jones
- Protein Expression Laboratory, FNLCR, NIH, Frederick, MD, USA
| | - Lauren Procter
- Protein Expression Laboratory, FNLCR, NIH, Frederick, MD, USA
| | - Maura O'Neill
- Protein Characterization Laboratory, FNLCR, NIH, Frederick, MD, USA
| | | | | | - Jun S Wei
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
| | | | - Barry R O'Keefe
- Molecular Targets Program, NCI, NIH, Frederick, MD, USA
- Natural Products Branch, NCI, NIH, Frederick, MD, USA
| | - Robert G Hawley
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Department of Anatomy and Cell Biology, George Washington University, Washington, DC, USA
| | - Javed Khan
- Genetics Branch, NCI, NIH, Bethesda, MD, USA.
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4
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Wang Y, Pan H, Gong X, Wang Z, Qin X, Zhou S, Zhu C, Hu X, Chen S, Liu H, Jin H, Pang Q, Wu W. CDC123 promotes Hepatocellular Carcinoma malignant progression by regulating CDKAL1. Pathol Res Pract 2024; 254:154987. [PMID: 38237400 DOI: 10.1016/j.prp.2023.154987] [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: 06/29/2023] [Revised: 11/09/2023] [Accepted: 11/27/2023] [Indexed: 02/12/2024]
Abstract
The cell proliferation protein 123 (CDC123) is involved in the synthesis of the eukaryotic initiation factor 2 (eIF2), which regulates eukaryotic translation. Although CDC123 is considered a candidate oncogene in breast cancer, its expression and role in Hepatocellular Carcinoma (HCC) remain unknown. Herein, we obtained the CDC123 RNA-seq and clinical prognostic data from the TCGA database. The mRNA level revealed that CDC123 was highly expressed in HCC patients, and Kaplan-Meier analysis implied better prognoses in HCC patients with low CDC123 expression (P < 0.001). The multivariate Cox analysis revealed that the CDC123 level was an independent prognostic factor (P < 0.001). We further confirmed a high CDC123 expression in HCC cell lines. Additionally, we found that CDC123 knockdown in HCC cell lines significantly inhibited cellular proliferation, invasion, and migration. Moreover, CDC123 was co-expressed with the CDK5 Regulatory Subunit-Associated Protein 1 Like 1 (CDKAL1), whose mRNA level was decreased after silencing CDC123. Therefore, we hypothesized that CDC123 promotes HCC progression by regulating CDKAL1.
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Affiliation(s)
- Yong Wang
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China
| | - HongTao Pan
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China
| | - XuanKun Gong
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China; Department of Hepatobiliary Surgery, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui, China
| | - ZhiCheng Wang
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China; Department of Hepatobiliary Surgery, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui, China
| | - XiLiang Qin
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China; Department of Hepatobiliary Surgery, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui, China
| | - Shuai Zhou
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China
| | - Chao Zhu
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China
| | - XiaoSi Hu
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China
| | - ShiLei Chen
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China
| | - HuiChun Liu
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China
| | - Hao Jin
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China
| | - Qing Pang
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China; Department of Hepatobiliary Surgery, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui, China.
| | - WenYong Wu
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China; Department of Hepatobiliary Surgery, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui, China.
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5
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Song N, Deng L, Zeng L, He L, Liu C, Liu L, Fu R. USP9X deubiquitinates and stabilizes CDC123 to promote breast carcinogenesis through regulating cell cycle. Mol Carcinog 2023; 62:1487-1503. [PMID: 37314216 DOI: 10.1002/mc.23591] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/15/2023]
Abstract
Cell division cycle 123 (CDC123) has been implicated in a variety of human diseases. However, it remains unclear whether CDC123 plays a role in tumorigenesis and how its abundance is regulated. In this study, we found that CDC123 was highly expressed in breast cancer cells, and its high expression was positively correlated with a poor prognosis. Knowndown of CDC123 impaired the proliferation of breast cancer cells. Mechanistically, we identified a deubiquitinase, ubiquitin-specific peptidase 9, X-linked (USP9X), that could physically interact with and deubiquitinate K48-linked ubiquitinated CDC123 at the K308 site. Therefore, the expression of CDC123 was positively correlated with USP9X in breast cancer cells. In addition, we found that deletion of either USP9X or CDC123 led to altered expression of cell cycle-related genes and resulted in the accumulation of cells population in the G0/G1 phase, thereby suppressing cell proliferation. Treatment with the deubiquitinase inhibitor of USP9X, WP1130 (Degrasyn, a small molecule compound that USP9X deubiquitinase inhibitor), also led to the accumulation of breast cancer cells in the G0/G1 phase, but this effect could be rescued by overexpression of CDC123. Furthermore, our study revealed that the USP9X/CDC123 axis promotes the occurrence and development of breast cancer through regulating the cell cycle, and suggests that it may be a potential target for breast cancer intervention. In conclusion, our study demonstrates that USP9X is a key regulator of CDC123, providing a novel pathway for the maintenance of CDC123 abundance in cells, and supports USP9X/CDC123 as a potential target for breast cancer intervention through regulating the cell cycle.
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Affiliation(s)
- Nan Song
- Department of Hematology, Tianjin Medical University General Hospital, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ling Deng
- Department of Hematology, Tianjin Medical University General Hospital, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Lijie Zeng
- Department of Hematology, Tianjin Medical University General Hospital, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Li He
- Department of Hematology, Tianjin Medical University General Hospital, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Chunyan Liu
- Department of Hematology, Tianjin Medical University General Hospital, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ling Liu
- Department of Hematology, Tianjin Medical University General Hospital, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Rong Fu
- Department of Hematology, Tianjin Medical University General Hospital, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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6
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Song Y, Zhang J, Wang H, Wang H, Liu Y, Hu Z. Histone lysine demethylase 3B regulates autophagy via transcriptional regulation of GABARAPL1 in acute myeloid leukemia cells. Int J Oncol 2023; 63:87. [PMID: 37326062 PMCID: PMC10552699 DOI: 10.3892/ijo.2023.5535] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
Macroautophagy (hereafter referred to as autophagy) is a highly conserved self‑digestion process that is critical for maintaining homeostasis in response to various stresses. The autophagy‑related protein family, including the GABA type A receptor‑associated protein (GABARAP) and microtubule‑associated protein 1 light chain 3 subfamilies, is crucial for autophagosome biogenesis. Although the regulatory machinery of autophagy in the cytoplasm has been widely studied, its transcriptional and epigenetic regulatory mechanisms still require more targeted investigations. The present study identified histone lysine demethylase 3B (KDM3B) as a crucial component of autophagy on a panel of leukemia cell lines, including K562, THP1 and U937, resulting in transcriptional activation of the autophagy‑related gene GABA type A receptor‑associated protein like 1 (GABARAPL1). KDM3B expression promoted autophagosome formation and affected the autophagic flux in leukemia cells under the induction of external stimuli. Notably, RNA‑sequencing and reverse transcription‑quantitative PCR analysis showed that KDM3B knockout inhibited the expression of GABARAPL1. Chromatin immunoprecipitation‑quantitative PCR and luciferase assay showed that KDM3B was associated with the GABARAPL1 gene promoter under stimulation and enhanced its transcription. The present findings demonstrated that KDM3B was critical for regulating the GABARAPL1 gene and influencing the process of autophagy in leukemia cells. These results provide a new insight for exploring the association between autophagy and KDM3B epigenetic regulation in leukemia.
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Affiliation(s)
- Ying Song
- Department of Hematology, Laboratory for Stem Cell and Regenerative Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261042
| | - Jiaqi Zhang
- Department of Hematology, Laboratory for Stem Cell and Regenerative Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261042
- Granduate School, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Haihua Wang
- Department of Hematology, Laboratory for Stem Cell and Regenerative Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261042
- Granduate School, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Haiying Wang
- Department of Hematology, Laboratory for Stem Cell and Regenerative Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261042
| | - Yong Liu
- Department of Hematology, Laboratory for Stem Cell and Regenerative Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261042
| | - Zhenbo Hu
- Department of Hematology, Laboratory for Stem Cell and Regenerative Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261042
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7
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Comprehensive analyses of prognostic biomarkers and immune infiltrates among histone lysine demethylases (KDMs) in hepatocellular carcinoma. Cancer Immunol Immunother 2022; 71:2449-2467. [DOI: 10.1007/s00262-022-03167-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/31/2022] [Indexed: 10/18/2022]
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8
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Diao W, Zheng J, Li Y, Wang J, Xu S. Targeting histone demethylases as a potential cancer therapy (Review). Int J Oncol 2022; 61:103. [PMID: 35801593 DOI: 10.3892/ijo.2022.5393] [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: 01/25/2022] [Accepted: 06/15/2022] [Indexed: 11/06/2022] Open
Abstract
Post‑translational modifications of histones by histone demethylases have an important role in the regulation of gene transcription and are implicated in cancers. Recently, the family of lysine (K)‑specific demethylase (KDM) proteins, referring to histone demethylases that dynamically regulate histone methylation, were indicated to be involved in various pathways related to cancer development. To date, numerous studies have been conducted to explore the effects of KDMs on cancer growth, metastasis and drug resistance, and a majority of KDMs have been indicated to be oncogenes in both leukemia and solid tumors. In addition, certain KDM inhibitors have been developed and have become the subject of clinical trials to explore their safety and efficacy in cancer therapy. However, most of them focus on hematopoietic malignancy. This review summarizes the effects of KDMs on tumor growth, drug resistance and the current status of KDM inhibitors in clinical trials.
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Affiliation(s)
- Wenfei Diao
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Jiabin Zheng
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Yong Li
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Junjiang Wang
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Songhui Xu
- Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
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9
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Gonzalez-Salinas F, Martinez-Amador C, Trevino V. Characterizing genes associated with cancer using the CRISPR/Cas9 system: A systematic review of genes and methodological approaches. Gene 2022; 833:146595. [PMID: 35598687 DOI: 10.1016/j.gene.2022.146595] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/22/2022] [Accepted: 05/16/2022] [Indexed: 12/24/2022]
Abstract
The CRISPR/Cas9 system enables a versatile set of genomes editing and genetic-based disease modeling tools due to its high specificity, efficiency, and accessible design and implementation. In cancer, the CRISPR/Cas9 system has been used to characterize genes and explore different mechanisms implicated in tumorigenesis. Different experimental strategies have been proposed in recent years, showing dependency on various intrinsic factors such as cancer type, gene function, mutation type, and technical approaches such as cell line, Cas9 expression, and transfection options. However, the successful methodological approaches, genes, and other experimental factors have not been analyzed. We, therefore, initially considered more than 1,300 research articles related to CRISPR/Cas9 in cancer to finally examine more than 400 full-text research publications. We summarize findings regarding target genes, RNA guide designs, cloning, Cas9 delivery systems, cell enrichment, and experimental validations. This analysis provides valuable information and guidance for future cancer gene validation experiments.
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Affiliation(s)
- Fernando Gonzalez-Salinas
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Morones Prieto avenue 3000, Monterrey, Nuevo Leon 64710, Mexico
| | - Claudia Martinez-Amador
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Morones Prieto avenue 3000, Monterrey, Nuevo Leon 64710, Mexico
| | - Victor Trevino
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Morones Prieto avenue 3000, Monterrey, Nuevo Leon 64710, Mexico; Tecnologico de Monterrey, The Institute for Obesity Research, Eugenio Garza Sada avenue 2501, Monterrey, Nuevo Leon 64849, México.
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10
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Inhibition of histone demethylase KDM4 by ML324 induces apoptosis through the unfolded protein response and Bim upregulation in hepatocellular carcinoma cells. Chem Biol Interact 2022; 353:109806. [PMID: 34999051 DOI: 10.1016/j.cbi.2022.109806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/30/2021] [Accepted: 01/05/2022] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) is an extremely aggressive malignancy that ranks as the sixth-leading cause of cancer-associated death worldwide. Recently, various epigenetic mechanisms including gene methylation were reported to be potential next era HCC therapeutics and biomarkers. Although inhibition of epigenetic enzymes including histone lysine demethylase 4 (KDM4) enhanced cell death in HCC cells, the detailed mechanism of cell death machinery is poorly understood. In this study, we found that ML324, a small molecule KDM4-specific inhibitor, induced the death of HCC cells in a general cell culture system and 3D spheroid culture with increased cleavage of caspase-3. Mechanistically, we identified that unfolded protein responses (UPR) were involved in ML324-induced HCC cell death. Incubation of HCC cells with ML324 upregulated death receptor 5 (DR5) expression through the activation transcription factor 3 (ATF3)-C/EBP homologous protein (CHOP)-dependent pathway. Moreover, we identified BIM protein as a mediator of ML324-induced apoptosis using CRISPR/Cas9 knockout analysis. We showed that the loss of Bim suppressed ML324-induced apoptosis by flow cytometry analysis, colony formation assay, and caspase-3 activation assay. Interestingly, BIM protein expression by ML324 was regulated by ATF3, CHOP, and DR5 which are factors involved in UPR. Specifically, we confirmed the regulating roles of KDM4E in Bim and CHOP expression using a chromatin immune precipitation (ChIP) assay. Physical binding of KDM4E to Bim and CHOP promoters decreased the response to ML324. Our findings suggest that KDM4 inhibition is a potent anti-tumor therapeutic strategy for human HCC, and further studies of UPR-induced apoptosis and the associated epigenetic functional mechanisms may lead to the discovery of novel target for future cancer therapy.
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11
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Xie S, Jiang X, Qin R, Song S, Lu Y, Wang L, Chen Y, Lu D. miR-1307 promotes hepatocarcinogenesis by CALR-OSTC-endoplasmic reticulum protein folding pathway. iScience 2021; 24:103271. [PMID: 34761190 PMCID: PMC8567365 DOI: 10.1016/j.isci.2021.103271] [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: 05/17/2021] [Revised: 08/27/2021] [Accepted: 10/12/2021] [Indexed: 12/20/2022] Open
Abstract
miR-1307 is highly expressed in liver cancer and inhibits methyltransferase protein8. Thereby, miR-1307 inhibits the expression of KDM3A and KDM3B and increases the methylation modification of histone H3 lysine 9, which enhances the expression of endoplasmic-reticulum-related gene CALR. Of note, miR-1307 weakens the binding ability of OSTC to CDK2, CDK4, CyclinD1, and cyclinE and enhances the binding ability of CALR to CDK2, CDK4, CyclinD1, and cyclinE, decreasing of p21WAF1/CIP1, GADD45, pRB, and p18, and decreasing of ppRB. Furthermore, miR-1307 increases the activity of H-Ras, PKM2, and PLK1. Strikingly, miR-1307 reduces the binding ability of OSTC to ATG4 and enhances the binding ability of CALR to ATG4. Therefore, miR-1307 reduces the occurrence of autophagy based on ATG4-LC3-ATG3-ATG7-ATG5-ATG16L1-ATG12-ATG9- Beclin1. In particular, miR-1307 enhances the expression of PAK2, PLK1, PRKAR2A, MYBL1, and Trim44 and inhibits the expression of Sash1 and Smad5 via autophagy. Our observations suggest that miR-1307 promotes hepatocarcinogenesis by CALR-OSTC-endoplasmic reticulum protein folding pathway.
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Affiliation(s)
- Sijie Xie
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
| | - Xiaoxue Jiang
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
| | - Rushi Qin
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
| | - Shuting Song
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
| | - Yanan Lu
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
| | - Liyan Wang
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
| | - Yingjie Chen
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
| | - Dongdong Lu
- Shanghai Putuo People's Hospital, School of Life Science and Technology, Tongji University, 200092 Shanghai, China
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12
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Li Y, Liu M, Zhang Z, Deng L, Zhai Z, Liu H, Wang Y, Zhang C, Xiong J, Shi C. QSOX2 Is an E2F1 Target Gene and a Novel Serum Biomarker for Monitoring Tumor Growth and Predicting Survival in Advanced NSCLC. Front Cell Dev Biol 2021; 9:688798. [PMID: 34350181 PMCID: PMC8326667 DOI: 10.3389/fcell.2021.688798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/29/2021] [Indexed: 11/13/2022] Open
Abstract
Background Quiescin Q6 sulfhydryl oxidase 2 (QSOX2), an enzyme that can be directly secreted into the extracellular space, is known to be associated with oxidative protein folding. However, whether QSOX2 is abnormally expressed in non-small cell lung cancer (NSCLC) and its role in tumor growth remains unclear. Methods Real-time quantitative PCR (qPCR), immunohistochemistry (IHC), bioinformatics analyses were applied to analyze the expression pattern and prognostic significance of QSOX2 in NSCLC. Xenografts model, enzyme-linked immunosorbent assays (ELISA), western blot analysis (WB), and IHC were preformed to examine in vivo tumor suppression and intracellular and extracellular expression of QSOX2. Flow cytometry, WB and qPCR analyses were used to elucidate the role of QSOX2 in cell cycle regulation. Chromatin immunoprecipitation assay (ChIP) assay and Dual-Luciferase reporter assay were employed to investigate transcriptional regulation of QSOX2 by E2F Transcription Factor 1 (E2F1). Results Quiescin sulfhydryl oxidase 2 was significantly overexpressed in NSCLC and associated with poor survival in advanced-stage patients. The intracellular and extracellular expression of QSOX2 by tumor cells markedly decreased after anti-cancer therapy in vitro, in vivo and in the clinic. Moreover, QSOX2 silencing in NSCLC cell lines resulted in inhibition of cancer cell proliferation, induction of apoptosis, and decreased expression of cell division-related genes (CENPF and NUSAP1) and Wnt pathway activators (PRRX2 and Nuc-β-catenin). Mechanistically, QSOX2 was expressed periodically during cell cycle and directly regulated by E2F1. Conclusions Our findings demonstrate that QSOX2 is directly regulated by E2F1 in the cell cycle, which is essential for the proliferation of NSCLC cells. Furthermore, QSOX2 is a prognostic indicator for NSCLC and may be developed into a biomarker for monitoring tumor burden and therapeutic progress.
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Affiliation(s)
- Yaqi Li
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Mei Liu
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhuoxian Zhang
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Libin Deng
- Institute of Translational Medicine, Nanchang University, Nanchang, China
| | - ZhenYu Zhai
- Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hua Liu
- Department of Clinical Laboratory, The Fourth Affiliated Hospital, Nanchang University, Nanchang, China
| | - Yiting Wang
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Cheng Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang, China
| | - Jianping Xiong
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chao Shi
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
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KDM3B-ETF1 fusion gene downregulates LMO2 via the WNT/β-catenin signaling pathway, promoting metastasis of invasive ductal carcinoma. Cancer Gene Ther 2021; 29:215-224. [PMID: 33828234 DOI: 10.1038/s41417-021-00301-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 01/11/2021] [Accepted: 01/25/2021] [Indexed: 11/08/2022]
Abstract
Breast cancer is the most common malignancy for women, with invasive ductal carcinoma being the largest subtype of breast cancers, accounting for 75-80% of cases. However, the underlying mechanism of invasive ductal carcinoma remains unclear. In this study, we investigate the possible effects KDM3B-ETF1 fusion gene has on breast cancer cell metastasis, invasion and its downstream signaling mediators as revealed from RNA sequence data analysis. As predicted, KDM3B-ETF1 expression was increased in breast cancer tissues and cells. Overexpression of KDM3B-ETF1 in cancer cell lines promoted the growth and invasion of breast cancer cells, while KDM3B-ETF1 knockdown showed the opposite effects on malignant cell growth and invasion both in vivo and in vitro as evidenced by cell counting kit-8, Transwell assay and tumor xenograft in nude mice. On the contrary, LIM Domain Only 2 (LMO2) expression was significantly reduced in breast cancer tissues and cells. According to chromatin immunoprecipitation and Western blot analysis, KDM3B-ETF1 targets LMO2 and reduced the expression of LMO2, leading to an increase in WNT/β-catenin signaling pathway and thus promoting invasion. In conclusion, fusion gene KDM3B-ETF1 inhibits LMO2, activates the Wnt/β-catenin signaling pathway that leads to increased breast cancer cell invasion and metastasis, providing a novel insight into developing therapeutic strategies. These results provide novel insights into the molecular mechanism of invasive ductal carcinomas, which may lead to potential therapeutic targets.
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14
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The Histone Demethylase KDM3B Promotes Osteo-/Odontogenic Differentiation, Cell Proliferation, and Migration Potential of Stem Cells from the Apical Papilla. Stem Cells Int 2020; 2020:8881021. [PMID: 33082788 PMCID: PMC7563049 DOI: 10.1155/2020/8881021] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/11/2020] [Accepted: 09/20/2020] [Indexed: 02/07/2023] Open
Abstract
Understanding the regulation mechanisms of mesenchymal stem cells (MSCs) can assist in tissue regeneration. The histone demethylase (KDM) family has a crucial role in differentiation and cell proliferation of MSCs, while the function of KDM3B in MSCs is not well understood. In this study, we used the stem cells from the apical papilla (SCAPs) to test whether KDM3B could regulate the function of MSCs. By an alkaline phosphatase (ALP) activity assay, Alizarin red staining, real-time RT-PCR, and western blot analysis, we found that KDM3B enhanced the ALP activity and mineralization of SCAPs and promoted the expression of runt-related transcription factor 2 (RUNX2), osterix (OSX), dentin sialophosphoprotein (DSPP), and osteocalcin (OCN). Additionally, the CFSE, CCK-8, and flow cytometry assays revealed that KDM3B improved cell proliferation by accelerating cell cycle transition from the G1 to S phase. Scratch and transwell migration assays displayed that KDM3B promoted the migration potential of SCAPs. Mechanically, microarray results displayed that 98 genes were upregulated, including STAT1, CCND1, and FGF5, and 48 genes were downregulated after KDM3B overexpression. Besides, we found that the Toll-like receptor and JAK-STAT signaling pathway may be involved in the regulating function of KDM3B in SCAPs. In brief, we discovered that KDM3B promoted the osteo-/odontogenic differentiation, cell proliferation, and migration potential of SCAPs and provided a novel target and theoretical basis for regenerative medicine.
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15
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Martínez-Jiménez F, Muiños F, Sentís I, Deu-Pons J, Reyes-Salazar I, Arnedo-Pac C, Mularoni L, Pich O, Bonet J, Kranas H, Gonzalez-Perez A, Lopez-Bigas N. A compendium of mutational cancer driver genes. Nat Rev Cancer 2020; 20:555-572. [PMID: 32778778 DOI: 10.1038/s41568-020-0290-x] [Citation(s) in RCA: 534] [Impact Index Per Article: 133.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/02/2020] [Indexed: 12/11/2022]
Abstract
A fundamental goal in cancer research is to understand the mechanisms of cell transformation. This is key to developing more efficient cancer detection methods and therapeutic approaches. One milestone towards this objective is the identification of all the genes with mutations capable of driving tumours. Since the 1970s, the list of cancer genes has been growing steadily. Because cancer driver genes are under positive selection in tumorigenesis, their observed patterns of somatic mutations across tumours in a cohort deviate from those expected from neutral mutagenesis. These deviations, which constitute signals of positive selection, may be detected by carefully designed bioinformatics methods, which have become the state of the art in the identification of driver genes. A systematic approach combining several of these signals could lead to a compendium of mutational cancer genes. In this Review, we present the Integrative OncoGenomics (IntOGen) pipeline, an implementation of such an approach to obtain the compendium of mutational cancer drivers. Its application to somatic mutations of more than 28,000 tumours of 66 cancer types reveals 568 cancer genes and points towards their mechanisms of tumorigenesis. The application of this approach to the ever-growing datasets of somatic tumour mutations will support the continuous refinement of our knowledge of the genetic basis of cancer.
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Affiliation(s)
- Francisco Martínez-Jiménez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ferran Muiños
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Inés Sentís
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jordi Deu-Pons
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Iker Reyes-Salazar
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Claudia Arnedo-Pac
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Loris Mularoni
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Oriol Pich
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jose Bonet
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Hanna Kranas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Abel Gonzalez-Perez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain.
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
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16
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Jung H, Seo SB. Histone lysine demethylase 3B (KDM3B) regulates the propagation of autophagy via transcriptional activation of autophagy-related genes. PLoS One 2020; 15:e0236403. [PMID: 32716961 PMCID: PMC7384621 DOI: 10.1371/journal.pone.0236403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 07/05/2020] [Indexed: 12/14/2022] Open
Abstract
Autophagy, a self-degradative physiological process, is critical for homeostasis maintenance and energy source balancing in response to various stresses, including nutrient deprivation. It is a highly conserved catabolic process in eukaryotes and is indispensable for cell survival as it involves degradation of unessential or excessive components and their subsequent recycling as building blocks for the synthesis of necessary molecules. Although the dysregulation of autophagy has been reported to broadly contribute to various diseases, including cancers and neurodegenerative diseases, the molecular mechanisms underlying the epigenetic regulation of autophagy are poorly elucidated. Here, we report that the level of lysine demethylase 3B (KDM3B) increases in nutrient-deprived HCT116 cells, a colorectal carcinoma cell line, resulting in transcriptional activation of the autophagy-inducing genes. KDM3B was found to enhance the transcription by demethylating H3K9me2 on the promoter of these genes. Furthermore, we observed that the depletion of KDM3B inhibited the autophagic flux in HCT116 cells. Collectively, these data suggested the critical role of KDM3B in the regulation of autophagy-related genes via H3K9me2 demethylation and induction of autophagy in nutrient-starved HCT116 cells.
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Affiliation(s)
- Hyeonsoo Jung
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul, Republic of Korea
| | - Sang-Beom Seo
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul, Republic of Korea
- * E-mail:
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Sui Y, Gu R, Janknecht R. Crucial Functions of the JMJD1/KDM3 Epigenetic Regulators in Cancer. Mol Cancer Res 2020; 19:3-13. [PMID: 32605929 DOI: 10.1158/1541-7786.mcr-20-0404] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 11/16/2022]
Abstract
Epigenetic changes are one underlying cause for cancer development and often due to dysregulation of enzymes modifying DNA or histones. Most Jumonji C domain-containing (JMJD) proteins are histone lysine demethylases (KDM) and therefore epigenetic regulators. One JMJD subfamily consists of JMJD1A/KDM3A, JMJD1B/KDM3B, and JMJD1C/KDM3C that are roughly 50% identical at the amino acid level. All three JMJD1 proteins are capable of removing dimethyl and monomethyl marks from lysine 9 on histone H3 and might also demethylate histone H4 on arginine 3 and nonhistone proteins. Analysis of knockout mice revealed critical roles for JMJD1 proteins in fertility, obesity, metabolic syndrome, and heart disease. Importantly, a plethora of studies demonstrated that especially JMJD1A and JMJD1C are overexpressed in various tumors, stimulate cancer cell proliferation and invasion, and facilitate efficient tumor growth. However, JMJD1A may also inhibit the formation of germ cell tumors. Likewise, JMJD1B appears to be a tumor suppressor in acute myeloid leukemia, but a tumor promoter in other cancers. Notably, by reducing methylation levels on histone H3 lysine 9, JMJD1 proteins can profoundly alter the transcriptome and thereby affect tumorigenesis, including through upregulating oncogenes such as CCND1, JUN, and MYC This epigenetic activity of JMJD1 proteins is sensitive to heavy metals, oncometabolites, oxygen, and reactive oxygen species, whose levels are frequently altered within cancer cells. In conclusion, inhibition of JMJD1 enzymatic activity through small molecules is predicted to be beneficial in many different cancers, but not in the few malignancies where JMJD1 proteins apparently exert tumor-suppressive functions.
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Affiliation(s)
- Yuan Sui
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Ruicai Gu
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Ralf Janknecht
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma. .,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
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Liao Y, Yin G, Wang X, Zhong P, Fan X, Huang C. Identification of candidate genes associated with the pathogenesis of small cell lung cancer via integrated bioinformatics analysis. Oncol Lett 2019; 18:3723-3733. [PMID: 31516585 PMCID: PMC6732946 DOI: 10.3892/ol.2019.10685] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 07/05/2019] [Indexed: 02/06/2023] Open
Abstract
The pathogenesis of small cell lung cancer (SCLC), a highly metastatic malignant tumor, remains unclear. In the present study, important genes and pathways that are involved in the pathogenesis of SCLC were identified. The following four datasets were downloaded from the Gene Expression Omnibus: GSE60052, GSE43346, GSE15240 and GSE6044. The differentially expressed genes (DEGs) between the SCLC samples and the normal samples were analyzed using R software. The limma package was used for every dataset. The RobustRankAggreg package was used to integrate the DEGs from the four datasets. Functional and pathway enrichment analyses were conducted using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases with FunRich software and R software, respectively. In addition, the protein-protein interaction (PPI) network of the DEGs was constructed using the STRING database and Cytoscape software. Hub genes and significant modules were identified using Molecular Complex Detection in Cytoscape software. Finally, the expression values of hub genes were determined using the Oncomine online database. In total, 412 DEGs were identified following the integration of the four datasets, with 146 upregulated genes and 266 downregulated genes. The upregulated DEGs were primarily enriched in the cell cycle, cell division and microtubule binding. The downregulated DEGs were primarily enriched in the complement and coagulation cascades, the cytokine-mediated signaling pathway and protein binding. Eight hub genes and 1 significant module correlated to the cell cycle pathway were identified based on a subset of the PPI network. Finally, five hub genes were identified as highly expressed in SCLC tissue compared with normal tissue. The cell cycle pathway may be the pathway most closely associated with the pathogenesis of SCLC. NDC80, BUB1B, PLK1, CDC20 and MAD2L1 should be the focus of follow-up studies regarding the diagnosis and treatment of SCLC.
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Affiliation(s)
- Yi Liao
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhuo, Sichuan 646000, P.R. China
| | - Guofang Yin
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhuo, Sichuan 646000, P.R. China
| | - Xue Wang
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhuo, Sichuan 646000, P.R. China
| | - Ping Zhong
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhuo, Sichuan 646000, P.R. China
| | - Xianming Fan
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhuo, Sichuan 646000, P.R. China
| | - Chengliang Huang
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhuo, Sichuan 646000, P.R. China
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