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Liu J, Fan H, Liang X, Chen Y. Polycomb repressor complex: Its function in human cancer and therapeutic target strategy. Biomed Pharmacother 2023; 169:115897. [PMID: 37981459 DOI: 10.1016/j.biopha.2023.115897] [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: 09/13/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/21/2023] Open
Abstract
The Polycomb Repressor Complex (PRC) plays a pivotal role in gene regulation during development and disease, with dysregulation contributing significantly to various human cancers. The intricate interplay between PRC and cellular signaling pathways sheds light on cancer complexity. PRC presents promising therapeutic opportunities, with inhibitors undergoing rigorous evaluation in preclinical and clinical studies. In this review, we emphasize the critical role of PRC complex in gene regulation, particularly PcG proteins mediated chromatin compaction through phase separation. We also highlight the pathological implications of PRC complex dysregulation in various tumors, elucidating underlying mechanisms driving cancer progression. The burgeoning field of therapeutic strategies targeting PRC complexes, notably EZH2 inhibitors, has advanced significantly. However, we explore the need for combination therapies to enhance PRC targeted treatments efficacy, providing a glimpse into the future of cancer therapeutics.
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Affiliation(s)
- Jingrong Liu
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
| | - Hongjie Fan
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
| | - Xinmiao Liang
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Yang Chen
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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2
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Nilles JD, Lim D, Boyer MP, Wilson BD, Betar RA, Showalter HA, Liu D, Ananieva EA. The occurrence of bone and joint cancers and their association with rural living and radon exposure in Iowa. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2023; 45:925-940. [PMID: 35381949 PMCID: PMC8983034 DOI: 10.1007/s10653-022-01261-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Primary bone and joint cancers are rare and understudied, yet these neoplasms are difficult to treat and impact all age groups. To explore the long-term changes in the occurrence of bone and joint cancers, patients diagnosed with these neoplasms between 1975 and 2016 were identified in the Surveillance Epidemiology and End Results of the National Cancer Institute of the USA. The age-adjusted incidence (AAIR) and mortality (AAMR) rates were calculated for three decades and compared to AAIR and AAMR in years 1975-1984. By using the population-based cancer registries of the USA, Iowa was identified as a state with increased cases of bone and joint malignancies. The bone and joint cancer cases in Iowa were correlated with the percentage of rural population, the average farmland size, or the residential radon levels. Results demonstrated that the mean AAIR of bone and joint cancers for US female and male patients (< 50 years of age) increased from 0.57 (95% C.I. 0.55-0.63) and 0.76 (95% C.I. 0.69-0.82) for years 1975-1984 to 0.71 (95% C.I. 0.66-0.76) and 0.94 (95% C.I. 0.87-1.07) for years 2005-2014, respectively. The increase in bone and joint cancer cases in Iowa positively correlated with the percentage rural population (R = 0.222, P < 0.02), and the average farmland size (R = 0.236, P < 0.02) but not the radon levels (R = - 0.038, P < 0.7). The findings revealed that patients younger than 50 years of age and those who resided in rural areas and engaged in farming were more likely to be diagnosed with primary bone and joint cancers.
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Affiliation(s)
- Jonathan D Nilles
- Department of Biochemistry and Nutrition, Des Moines University, 3200 Grand Avenue, Des Moines, IA, 50312, USA
| | - Dooyoung Lim
- Department of Public Health, Des Moines University, 3200 Grand Avenue, Des Moines, IA, 50312, USA
| | - Michael P Boyer
- Department of Biochemistry and Nutrition, Des Moines University, 3200 Grand Avenue, Des Moines, IA, 50312, USA
| | - Brittany D Wilson
- Department of Biochemistry and Nutrition, Des Moines University, 3200 Grand Avenue, Des Moines, IA, 50312, USA
| | - Rebekah A Betar
- Department of Biochemistry and Nutrition, Des Moines University, 3200 Grand Avenue, Des Moines, IA, 50312, USA
| | - Holly A Showalter
- Waukee Aspiring Professional Experience (APEX), 295 SE Ashworth Road, Waukee, IA, 50263, USA
| | - Darren Liu
- Department of Public Health, Des Moines University, 3200 Grand Avenue, Des Moines, IA, 50312, USA
| | - Elitsa A Ananieva
- Department of Biochemistry and Nutrition, Des Moines University, 3200 Grand Avenue, Des Moines, IA, 50312, USA.
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Critical Roles of Polycomb Repressive Complexes in Transcription and Cancer. Int J Mol Sci 2022; 23:ijms23179574. [PMID: 36076977 PMCID: PMC9455514 DOI: 10.3390/ijms23179574] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
Polycomp group (PcG) proteins are members of highly conserved multiprotein complexes, recognized as gene transcriptional repressors during development and shown to play a role in various physiological and pathological processes. PcG proteins consist of two Polycomb repressive complexes (PRCs) with different enzymatic activities: Polycomb repressive complexes 1 (PRC1), a ubiquitin ligase, and Polycomb repressive complexes 2 (PRC2), a histone methyltransferase. Traditionally, PRCs have been described to be associated with transcriptional repression of homeotic genes, as well as gene transcription activating effects. Particularly in cancer, PRCs have been found to misregulate gene expression, not only depending on the function of the whole PRCs, but also through their separate subunits. In this review, we focused especially on the recent findings in the transcriptional regulation of PRCs, the oncogenic and tumor-suppressive roles of PcG proteins, and the research progress of inhibitors targeting PRCs.
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Chen Y, Gong W, Dai W, Jiang H, Xu X. E2F1/2/4 mRNA is associated with immune infiltration and are potential biomarkers for the prognosis of human gastric carcinoma. Transl Cancer Res 2022; 10:2801-2811. [PMID: 35116590 PMCID: PMC8797903 DOI: 10.21037/tcr-21-45] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/27/2021] [Indexed: 12/19/2022]
Abstract
Background E2Fs are genes that regulate DNA synthesis and the cell cycle by encoding a family of transcription factors. Increasing experimental evidence has revealed that E2Fs play key roles in tumor progression in various types of cancer. Methods We investigated the survival, expression and transcriptional data of E2F1/2/4 in gastric cancer (GC) patients using the immunohistochemistry assay, Kaplan-Meier Plotter, cBioPortal, String, and GEPIA databases. The plasma of GC patients was analyzed using the real-time reverse transcription polymerase chain reaction (RT-PCR) assay. The correlation between E2F1/2/4 expression and clinical features was analyzed using the quartile method. As well, the correlation between E2F1/2/4 and GC immune infiltration was also investigated using the TIMER database. Database of Immune Cell Expression (DICE) was also used to analyze correlations between SOX4 and immune responses. Results RT-PCR and tissue immunohistochemistry confirmed that E2F1/2/4 was highly expressed in serum and GC tissue samples of GC patients, the expression of which was not affected by patient age and gender. Also, the survival analysis revealed that low levels of E2F1/2/4 expression were significantly associated with a longer overall survival (OS) in GC patients. E2F1/2/4 was correlated with patient prognosis and immune cell infiltration, including B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and DCs in GC. Our findings indicated that E2F1/2/4 could be used as a prognostic biomarker and indicator of immune infiltration in GC. Conclusions This study revealed that E2F1/2/4 could be a promising indicator for tumor-associated immune infiltration and prognosis in GC patients.
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Affiliation(s)
- Yongyi Chen
- Department of Clinical Lab, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Wangang Gong
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China.,Zhejiang Cancer Research Institute, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
| | - Wumin Dai
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China.,Zhejiang Cancer Research Institute, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
| | - Huifen Jiang
- Department of Clinical Lab, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Xiaohong Xu
- Department of Clinical Lab, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
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Parreno V, Martinez AM, Cavalli G. Mechanisms of Polycomb group protein function in cancer. Cell Res 2022; 32:231-253. [PMID: 35046519 PMCID: PMC8888700 DOI: 10.1038/s41422-021-00606-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/10/2021] [Indexed: 02/01/2023] Open
Abstract
AbstractCancer arises from a multitude of disorders resulting in loss of differentiation and a stem cell-like phenotype characterized by uncontrolled growth. Polycomb Group (PcG) proteins are members of multiprotein complexes that are highly conserved throughout evolution. Historically, they have been described as essential for maintaining epigenetic cellular memory by locking homeotic genes in a transcriptionally repressed state. What was initially thought to be a function restricted to a few target genes, subsequently turned out to be of much broader relevance, since the main role of PcG complexes is to ensure a dynamically choregraphed spatio-temporal regulation of their numerous target genes during development. Their ability to modify chromatin landscapes and refine the expression of master genes controlling major switches in cellular decisions under physiological conditions is often misregulated in tumors. Surprisingly, their functional implication in the initiation and progression of cancer may be either dependent on Polycomb complexes, or specific for a subunit that acts independently of other PcG members. In this review, we describe how misregulated Polycomb proteins play a pleiotropic role in cancer by altering a broad spectrum of biological processes such as the proliferation-differentiation balance, metabolism and the immune response, all of which are crucial in tumor progression. We also illustrate how interfering with PcG functions can provide a powerful strategy to counter tumor progression.
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Tumorigenesis and cell competition in Drosophila in the absence of polyhomeotic function. Proc Natl Acad Sci U S A 2021; 118:2110062118. [PMID: 34702735 DOI: 10.1073/pnas.2110062118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2021] [Indexed: 12/12/2022] Open
Abstract
Cell competition is a homeostatic process that eliminates by apoptosis unfit or undesirable cells from animal tissues, including tumor cells that appear during the life of the organism. In Drosophila there is evidence that many types of oncogenic cells are eliminated by cell competition. One exception is cells mutant for polyhomeotic (ph), a member of the Polycomb family of genes; most of the isolated mutant ph clones survive and develop tumorous overgrowths in imaginal discs. To characterize the tumorigenic effect of the lack of ph, we first studied the growth of different regions of the wing disc deficient in ph activity and found that the effect is restricted to the proximal appendage. Moreover, we found that ph-deficient tissue is partially refractory to apoptosis. Second, we analyzed the behavior of clones lacking ph function and found that many suffer cell competition but are not completely eliminated. Unexpectedly, we found that nonmutant cells also undergo cell competition when surrounded by ph-deficient cells, indicating that within the same tissue cell competition may operate in opposite directions. We suggest two reasons for the incompleteness of cell competition in ph mutant cells: 1) These cells are partially refractory to apoptosis, and 2) the loss of ph function alters the identity of imaginal cells and subsequently their cell affinities. It compromises the winner/loser interaction, a prerequisite for cell competition.
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7
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Ren Y, Liu Y, Wang H. Identification of epigenetic regulators in the estrogen signaling pathway via siRNA screening. Mol Omics 2021; 17:596-606. [PMID: 34128034 DOI: 10.1039/d1mo00040c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Breast cancer is the most prevalent malignant disease among women across the globe. Notably, estrogen signaling plays a vital role in the progression of estrogen receptor-positive breast cancer. Therefore, targeting epigenetic regulators is a promising therapy for cancer. To identify epigenetic regulators, we conducted a siRNA screening targeting 140 epigenetic genes by which 32 positive and 15 negative regulators of estrogen signaling were obtained. The protein-protein interaction network of the candidate genes was constructed and the topological parameters of the network were calculated. As a result, the top 10 genes with higher MCC (Maximal Clique Centrality) scores were considered as hub genes. Notably, the hub genes all belong to polycomb group genes. The transcription levels of the above genes were compared between breast cancer and normal tissues using the UALCAN database. Then, the survival analysis of the hub genes was conducted using the Kaplan-Meier Plotter online database. Lastly, the effect of hub genes on MCF-7 cell proliferation and ER target gene expression were investigated. These results indicate that PcG genes regulate estrogen signaling and breast cancer development.
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Affiliation(s)
- Yun Ren
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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8
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Giaimo BD, Robert-Finestra T, Oswald F, Gribnau J, Borggrefe T. Chromatin Regulator SPEN/SHARP in X Inactivation and Disease. Cancers (Basel) 2021; 13:cancers13071665. [PMID: 33916248 PMCID: PMC8036811 DOI: 10.3390/cancers13071665] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Carcinogenesis is a multistep process involving not only the activation of oncogenes and disabling tumor suppressor genes, but also epigenetic modulation of gene expression. X chromosome inactivation (XCI) is a paradigm to study heterochromatin formation and maintenance. The double dosage of X chromosomal genes in female mammals is incompatible with early development. XCI is an excellent model system for understanding the establishment of facultative heterochromatin initiated by the expression of a 17,000 nt long non-coding RNA, known as Xinactivespecifictranscript (Xist), on the X chromosome. This review focuses on the molecular mechanisms of how epigenetic modulators act in a step-wise manner to establish facultative heterochromatin, and we put these in the context of cancer biology and disease. An in depth understanding of XCI will allow a better characterization of particular types of cancer and hopefully facilitate the development of novel epigenetic therapies. Abstract Enzymes, such as histone methyltransferases and demethylases, histone acetyltransferases and deacetylases, and DNA methyltransferases are known as epigenetic modifiers that are often implicated in tumorigenesis and disease. One of the best-studied chromatin-based mechanism is X chromosome inactivation (XCI), a process that establishes facultative heterochromatin on only one X chromosome in females and establishes the right dosage of gene expression. The specificity factor for this process is the long non-coding RNA Xinactivespecifictranscript (Xist), which is upregulated from one X chromosome in female cells. Subsequently, Xist is bound by the corepressor SHARP/SPEN, recruiting and/or activating histone deacetylases (HDACs), leading to the loss of active chromatin marks such as H3K27ac. In addition, polycomb complexes PRC1 and PRC2 establish wide-spread accumulation of H3K27me3 and H2AK119ub1 chromatin marks. The lack of active marks and establishment of repressive marks set the stage for DNA methyltransferases (DNMTs) to stably silence the X chromosome. Here, we will review the recent advances in understanding the molecular mechanisms of how heterochromatin formation is established and put this into the context of carcinogenesis and disease.
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Affiliation(s)
- Benedetto Daniele Giaimo
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
- Correspondence: (B.D.G.); (T.B.); Tel.: +49-641-9947-400 (T.B.)
| | - Teresa Robert-Finestra
- Department of Developmental Biology, Erasmus MC, Oncode Institute, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (T.R.-F.); (J.G.)
| | - Franz Oswald
- Center for Internal Medicine, Department of Internal Medicine I, University Medical Center Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany;
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, Oncode Institute, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (T.R.-F.); (J.G.)
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
- Correspondence: (B.D.G.); (T.B.); Tel.: +49-641-9947-400 (T.B.)
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Chen P, Li C, Huang H, Liang L, Zhang J, Li Q, Wang Q, Zhang S, Zeng K, Zhang X, Liang J. Circular RNA profiles and the potential involvement of down-expression of hsa_circ_0001360 in cutaneous squamous cell carcinogenesis. FEBS Open Bio 2021; 11:1209-1222. [PMID: 33569895 PMCID: PMC8016141 DOI: 10.1002/2211-5463.13114] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 12/27/2020] [Accepted: 02/08/2021] [Indexed: 12/13/2022] Open
Abstract
Circular RNAs (circRNAs) act as sponges of noncoding RNAs and have been implicated in many pathophysiological processes, including tumor development and progression. However, their roles in cutaneous squamous cell carcinoma (cSCC) are not yet well understood. This study aimed to identify differentially expressed circRNAs and their potential functions in cutaneous squamous cell carcinogenesis. The expression profiles of circRNAs in three paired cSCC and adjacent nontumorous tissues were detected with RNA sequencing and bioinformatics analysis. The candidate circRNAs were validated by PCR, Sanger sequencing and quantitative RT‐PCR in another five matched samples. The biological functions of circRNAs in SCL‐1 cells were assessed using circRNA silencing and overexpression, 3‐(4,5‐dimethylthiazol‐2‐yl)‐5‐(3‐carboxymethoxyphenyl)‐2‐(4‐sulfophenyl)‐2H‐tetrazolium inner salt (MTS), flow cytometry, transwell and colony formation assays. In addition, the circRNA–miRNA–mRNA interaction networks were predicted by bioinformatics. In summary, 1115 circRNAs, including 457 up‐regulated and 658 down‐regulated circRNAs (fold change ≥ 2 and P < 0.05), were differentially expressed in cSCC compared with adjacent nontumorous tissues. Of four selected circRNAs, two circRNAs (hsa_circ_0000932 and hsa_circ_0001360) were confirmed to be significantly decreased in cSCC using PCR, Sanger sequencing and quantitative RT‐PCR. Furthermore, hsa_circ_0001360 silencing was found to result in a significant increase of the proliferation, migration and invasion but a significant decrease of apoptosis in SCL‐1 cells in vitro, whereas hsa_circ_0001360 overexpression showed the opposite regulatory effects. hsa_circ_0001360 was predicted to interact with five miRNAs and their corresponding genes. In conclusion, circRNA dysregulation may play a critical role in carcinogenesis of cSCC, and hsa_circ_0001360 may have potential as a biomarker for cSCC.
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Affiliation(s)
- Pingjiao Chen
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Changxing Li
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | | | - Liuping Liang
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jing Zhang
- Institute of Dermatology, Guangzhou Medical University, China.,Department of Dermatology, Guangzhou Institute of Dermatology, China
| | - Qian Li
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qi Wang
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Sanquan Zhang
- Institute of Dermatology, Guangzhou Medical University, China.,Department of Dermatology, Guangzhou Institute of Dermatology, China
| | - Kang Zeng
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xibao Zhang
- Institute of Dermatology, Guangzhou Medical University, China.,Department of Dermatology, Guangzhou Institute of Dermatology, China
| | - Jingyao Liang
- Institute of Dermatology, Guangzhou Medical University, China.,Department of Dermatology, Guangzhou Institute of Dermatology, China
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Zheng Y, Chen Z, Zhou Z, Xu X, Yang H. Silencing of Long Non-Coding RNA LINC00607 Prevents Tumor Proliferation of Osteosarcoma by Acting as a Sponge of miR-607 to Downregulate E2F6. Front Oncol 2021; 10:584452. [PMID: 33585204 PMCID: PMC7877452 DOI: 10.3389/fonc.2020.584452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/10/2020] [Indexed: 01/06/2023] Open
Abstract
Osteosarcoma (OS), a type of malignant bone tumor, is commonly found in children and adolescents. Although previous studies have identified that long non-coding RNAs (lncRNAs) regulate OS, it is unclear whether lncRNAs impact the progression of OS. Here, we identified LINC00607, a lncRNA that facilitates OS proliferation, migration, and invasion. Based on the RNA-sequencing results, LINC00607 expression was significantly upregulated in pulmonary metastasis within OS. Functional experiments revealed that LINC00607 promoted migration and invasion of endothelial cells to exacerbate epithelial-mesenchymal transition (EMT). Furthermore, the results of RNA pull-down assay and invasion assay suggested that the binding between LINC00607 and miR-607 promoted OS invasion. Bioinformatic analysis and rescue experiments demonstrated that E2F6, a transcriptional factor, functioned downstream of LINC00607/miR-607. Finally, we found that LINC00607 promoted OS progression in vivo. This work revealed that LINC00607 worked as an miR-607 sponge to upregulate E2F6 expression, which promoted tumor proliferation in OS. These results identified a novel therapeutic target for treating OS.
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Affiliation(s)
- Yuehuan Zheng
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Department of Orthopedics, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhe Chen
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zezhu Zhou
- Department of Orthopedics, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, China
| | - Xiangyang Xu
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Department of Orthopedics, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Huilin Yang
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, China
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Polycomb group-mediated histone H2A monoubiquitination in epigenome regulation and nuclear processes. Nat Commun 2020; 11:5947. [PMID: 33230107 PMCID: PMC7683540 DOI: 10.1038/s41467-020-19722-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 10/12/2020] [Indexed: 12/19/2022] Open
Abstract
Histone posttranslational modifications are key regulators of chromatin-associated processes including gene expression, DNA replication and DNA repair. Monoubiquitinated histone H2A, H2Aub (K118 in Drosophila or K119 in vertebrates) is catalyzed by the Polycomb group (PcG) repressive complex 1 (PRC1) and reversed by the PcG-repressive deubiquitinase (PR-DUB)/BAP1 complex. Here we critically assess the current knowledge regarding H2Aub deposition and removal, its crosstalk with PcG repressive complex 2 (PRC2)-mediated histone H3K27 methylation, and the recent attempts toward discovering its readers and solving its enigmatic functions. We also discuss mounting evidence of the involvement of H2A ubiquitination in human pathologies including cancer, while highlighting some knowledge gaps that remain to be addressed. Histone H2A monoubiquitination on lysine 119 in vertebrate and lysine 118 in Drosophila (H2Aub) is an epigenomic mark usually associated with gene repression by Polycomb group factors. Here the authors review the current knowledge on the deposition and removal of H2Aub, its function in transcription and other DNA-associated processes as well as its relevance to human disease.
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12
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Li X. Epigenetics and cell cycle regulation in cystogenesis. Cell Signal 2019; 68:109509. [PMID: 31874209 DOI: 10.1016/j.cellsig.2019.109509] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 12/16/2022]
Abstract
The role of genetic mutations in the development of polycystic kidney disease (PKD), such as alterations in PKD1 and PKD2 genes in autosomal dominant PKD (ADPKD), is well understood. However, the significance of epigenetic mechanisms in the progression of PKD remains unclear and is increasingly being investigated. The term of epigenetics describes a range of mechanisms in genome function that do not solely result from the DNA sequence itself. Epigenetic information can be inherited during mammalian cell division to sustain phenotype specifically and physiologically responsive gene expression in the progeny cells. A multitude of functional studies of epigenetic modifiers and systematic genome-wide mapping of epigenetic marks reveal the importance of epigenomic mechanisms, including DNA methylation, histone/chromatin modifications and non-coding RNAs, in PKD pathologies. Deregulated proliferation is a characteristic feature of cystic renal epithelial cells. Moreover, defects in many of the molecules that regulate the cell cycle have been implicated in cyst formation and progression. Recent evidence suggests that alterations of DNA methylation and histone modifications on specific genes and the whole genome involved in cell cycle regulation and contribute to the pathogenesis of PKD. This review summarizes the recent advances of epigenetic mechanisms in PKD, which helps us to define the term of "PKD epigenetics" and group PKD epigenetic changes in three categories. In particularly, this review focuses on the interplay of epigenetic mechanisms with cell cycle regulation during normal cell cycle progression and cystic cell proliferation, and discusses the potential to detect and quantify DNA methylation from body fluids as diagnostic/prognostic biomarkers. Collectively, this review provides concepts and examples of epigenetics in cell cycle regulation to reveal a broad view of different aspects of epigenetics in biology and PKD, which may facilitate to identify possible novel therapeutic intervention points and to explore epigenetic biomarkers in PKD.
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Affiliation(s)
- Xiaogang Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, United States of America; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, United States of America.
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13
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Kanduc D. The comparative biochemistry of viruses and humans: an evolutionary path towards autoimmunity. Biol Chem 2019; 400:629-638. [PMID: 30504522 DOI: 10.1515/hsz-2018-0271] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 11/07/2018] [Indexed: 11/15/2022]
Abstract
Analyses of the peptide sharing between five common human viruses (Borna disease virus, influenza A virus, measles virus, mumps virus and rubella virus) and the human proteome highlight a massive viral vs. human peptide overlap that is mathematically unexpected. Evolutionarily, the data underscore a strict relationship between viruses and the origin of eukaryotic cells. Indeed, according to the viral eukaryogenesis hypothesis and in light of the endosymbiotic theory, the first eukaryotic cell (our lineage) originated as a consortium consisting of an archaeal ancestor of the eukaryotic cytoplasm, a bacterial ancestor of the mitochondria and a viral ancestor of the nucleus. From a pathologic point of view, the peptide sequence similarity between viruses and humans may provide a molecular platform for autoimmune crossreactions during immune responses following viral infections/immunizations.
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Affiliation(s)
- Darja Kanduc
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, I-70124 Bari, Italy
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Cell-Free, Embryo-Specific sncRNA as a Molecular Biological Bridge between Patient Fertility and IVF Efficiency. Int J Mol Sci 2019; 20:ijms20122912. [PMID: 31207900 PMCID: PMC6627040 DOI: 10.3390/ijms20122912] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/07/2019] [Accepted: 06/12/2019] [Indexed: 01/11/2023] Open
Abstract
Small noncoding RNAs (sncRNAs) are key regulators of the majority of human reproduction events. Understanding their function in the context of gametogenesis and embryogenesis will allow insight into the possible causes of in vitro fertilization (IVF) implantation failure. The aim of this study was to analyze the sncRNA expression profile of the spent culture media on day 4 after fertilization and to reveal a relationship with the morphofunctional characteristics of gametes and resultant embryos, in particular, with the embryo development and implantation potential. Thereto, cell-free, embryo-specific sncRNAs were identified by next generation sequencing (NGS) and quantified by reverse transcription coupled with polymerase chain reaction (RT-PCR) in real-time. Significant differences in the expression level of let-7b-5p, let-7i-5p, piR020401, piR16735, piR19675, piR20326, and piR17716 were revealed between embryo groups of various morphological gradings. Statistically significant correlations were found between the expression profiles of piR16735 and piR020401 with the oocyte-cumulus complex number, let-7b-5p and piR020401 with metaphase II oocyte and two pronuclei embryo numbers, let-7i-5p and piR20497 with the spermatozoid count per milliliter of ejaculate, piR19675 with the percentage of linearly motile spermatozoids, let-7b-5p with the embryo development grade, and let-7i-5p with embryo implantation. According to partial least squares discriminant analysis (PLS-DA), the expression levels of let-7i-5p (Variable Importance in Projection score (VIP) = 1.6262), piR020401 (VIP = 1.45281), and piR20497 (VIP = 1.42765) have the strongest influences on the implantation outcome.
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Yoshida K, Ishikawa A, Toyoda A, Shigenobu S, Fujiyama A, Kitano J. Functional divergence of a heterochromatin‐binding protein during stickleback speciation. Mol Ecol 2018; 28:1563-1578. [DOI: 10.1111/mec.14841] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/03/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Kohta Yoshida
- Division of Ecological Genetics National Institute of Genetics Mishima Shizuoka Japan
| | - Asano Ishikawa
- Division of Ecological Genetics National Institute of Genetics Mishima Shizuoka Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory National Institute of Genetics Mishima Shizuoka Japan
| | - Shuji Shigenobu
- NIBB Core Research Facilities National Institute for Basic Biology Okazaki Aichi Japan
| | - Asao Fujiyama
- Comparative Genomics Laboratory National Institute of Genetics Mishima Shizuoka Japan
| | - Jun Kitano
- Division of Ecological Genetics National Institute of Genetics Mishima Shizuoka Japan
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Jiang Y, Seimiya M, Schlumpf TB, Paro R. An intrinsic tumour eviction mechanism in Drosophila mediated by steroid hormone signalling. Nat Commun 2018; 9:3293. [PMID: 30120247 PMCID: PMC6098038 DOI: 10.1038/s41467-018-05794-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 07/11/2018] [Indexed: 12/02/2022] Open
Abstract
Polycomb group proteins are epigenetic regulators maintaining transcriptional memory during cellular proliferation. In Drosophila larvae, malfunction of Polyhomeotic (Ph), a member of the PRC1 silencing complex, results in neoplastic growth. Here, we report an intrinsic tumour suppression mechanism mediated by the steroid hormone ecdysone during metamorphosis. Ecdysone alters neoplastic growth into a nontumorigenic state of the mutant ph cells which then become eliminated during adult stage. We demonstrate that ecdysone exerts this function by inducing a heterochronic network encompassing the activation of the microRNA lethal-7, which suppresses its target gene chronologically inappropriate morphogenesis. This pathway can also promote remission of brain tumours formed in brain tumour mutants, revealing a restraining of neoplastic growth in different tumour types. Given the conserved role of let-7, the identification and molecular characterization of this innate tumour eviction mechanism in flies might provide important clues towards the exploitation of related pathways for human tumour therapy. Drosophila is an excellent model to study both development and tumorigenesis. Here the authors uncover an innate mechanism for a steroid hormone-induced block to tumorigenesis during metamorphosis of Drosophila.
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Affiliation(s)
- Yanrui Jiang
- D-BSSE, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Makiko Seimiya
- D-BSSE, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | | | - Renato Paro
- D-BSSE, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland. .,Faculty of Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland.
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17
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Josson S, Chung LWK, Gururajan M. microRNAs and Prostate Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 889:105-18. [PMID: 26658999 DOI: 10.1007/978-3-319-23730-5_7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
microRNAs are noncoding RNAs that are important for embryonic stem cell development and epithelial to mesenchymal transition (EMT). Tumor cells hijack EMT and stemness to grow and metastasize to distant organs including bone. In the tumor microenvironment, tumor cells interact with the stromal fibroblasts at the primary and metastatic sites and this interaction leads to tumor growth, EMT, and bone metastasis. Tumor-stromal interactions are a dynamic process that involves both cell-cell communications and extracellular vesicles and soluble factors. Growing body of evidence suggests that microRNAs are part of the payload that comprises the extracellular vesicles. microRNAs induce reactive stroma and thus convert normal stroma into tumor-associated stroma to promote aggressive tumorigenicity in vitro and in vivo. Landmark published studies demonstrate that expression of specific microRNAs of DLK1-DIO3 stem cell cluster correlates with patient survival in metastatic prostate cancer. Thus, microRNAs mediate tumor growth, EMT, and metastasis through cell intrinsic mechanisms and extracellular communications and could be novel biomarkers and therapeutic targets in bone metastatic prostate cancer.
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Affiliation(s)
- Sajni Josson
- Uro-Oncology Research Program, Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA. .,Neostrata Inc., Princeton, NJ, 08540, USA.
| | - Leland W K Chung
- Uro-Oncology Research Program, Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
| | - Murali Gururajan
- Uro-Oncology Research Program, Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA. .,Bristol-Myers Squibb Inc., Princeton, NJ, 08543, USA.
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18
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Wang W, Qin JJ, Voruganti S, Nag S, Zhou J, Zhang R. Polycomb Group (PcG) Proteins and Human Cancers: Multifaceted Functions and Therapeutic Implications. Med Res Rev 2015; 35:1220-67. [PMID: 26227500 DOI: 10.1002/med.21358] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Polycomb group (PcG) proteins are transcriptional repressors that regulate several crucial developmental and physiological processes in the cell. More recently, they have been found to play important roles in human carcinogenesis and cancer development and progression. The deregulation and dysfunction of PcG proteins often lead to blocking or inappropriate activation of developmental pathways, enhancing cellular proliferation, inhibiting apoptosis, and increasing the cancer stem cell population. Genetic and molecular investigations of PcG proteins have long been focused on their PcG functions. However, PcG proteins have recently been shown to exert non-classical-Pc-functions, contributing to the regulation of diverse cellular functions. We and others have demonstrated that PcG proteins regulate the expression and function of several oncogenes and tumor suppressor genes in a PcG-independent manner, and PcG proteins are associated with the survival of patients with cancer. In this review, we summarize the recent advances in the research on PcG proteins, including both the Pc-repressive and non-classical-Pc-functions. We specifically focus on the mechanisms by which PcG proteins play roles in cancer initiation, development, and progression. Finally, we discuss the potential value of PcG proteins as molecular biomarkers for the diagnosis and prognosis of cancer, and as molecular targets for cancer therapy.
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Affiliation(s)
- Wei Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, 79106.,Center for Cancer Biology and Therapy, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, 79106
| | - Jiang-Jiang Qin
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, 79106
| | - Sukesh Voruganti
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, 79106
| | - Subhasree Nag
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, 79106
| | - Jianwei Zhou
- Department of Molecular Cell Biology and Toxicology, Cancer Center, School of Public Health, Nanjing Medical University, Nanjing, 210029, P. R. China
| | - Ruiwen Zhang
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, 79106.,Center for Cancer Biology and Therapy, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, 79106
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Glover J, Krailo M, Tello T, Marina N, Janeway K, Barkauskas D, Fan TM, Gorlick R, Khanna C. A summary of the osteosarcoma banking efforts: a report from the Children's Oncology Group and the QuadW Foundation. Pediatr Blood Cancer 2015; 62:450-5. [PMID: 25611047 PMCID: PMC4304398 DOI: 10.1002/pbc.25346] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 10/08/2014] [Indexed: 01/15/2023]
Abstract
BACKGROUND Survival rates of patients with osteosarcoma have remained stagnant over the last thirty years. Better understanding of biology, new therapeutics, and improved biomarkers are needed. The Children's Oncology Group (COG) addressed this need by developing one of the largest osteosarcoma biorepositories ever, containing over 15,000 tumor and tissue samples from over 1,500 patients. PROCEDURE The biology study P9851 and the banking study AOST06B1 has enrolled 1,787 patients (as of September, 2013). Clinical information was lacking on 510 patients on P9851, who were not enrolled on a concurrent therapeutic trial. The value of these specimens was diminished. The lack of statistical support available for biology projects slowed the analysis of several critical studies. The QuadW Foundation, CureSearch, and the COG formed the Childhood Sarcoma Biostatistics and Annotation Office (CSBAO) to provide the infrastructure and address these needs by linking clinically annotated patient data to archived tissue samples and to develop biostatistical support for childhood sarcoma research. RESULTS Originally 5.3% of samples from the 510 patients on P9851 not enrolled on a therapeutic study had full clinical annotation. The efforts of the CSBAO have linked clinical annotation to 90.8% of those specimens and provided statistical analyses to several studies that had used COG samples. As a result, 24 biology studies in osteosarcoma have been completed and published in peer-reviewed journals. CONCLUSIONS These samples and in-silico data are available to the research community for basic and translational science projects to improve the biological understanding and treatment of patients affected by osteosarcoma.
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Affiliation(s)
- Jason Glover
- Children’s Cancer and Blood Disorders Program, Randall Children’s Hospital, Portland OR USA
| | - Mark Krailo
- Children’s Oncology Group, Monrovia, CA, USA
| | - Tanya Tello
- Children’s Oncology Group, Monrovia, CA, USA
| | - Neyssa Marina
- Department of Pediatric Hematology/Oncology, Stanford University, Palo Alto, CA, USA
| | - Katherine Janeway
- Department of Pediatric Oncology, Dana Farber / Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Don Barkauskas
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Timothy M. Fan
- Department of Veterinary Clinical Medicine, University of Illinois, Urbana IL USA
| | - Richard Gorlick
- Division of Pediatric Hematology and Oncology, The Children’s Hospital at Montefiore, Bronx, New York, USA
| | - Chand Khanna
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda MD, USA
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20
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Nanyes DR, Junco SE, Taylor AB, Robinson AK, Patterson NL, Shivarajpur A, Halloran J, Hale SM, Kaur Y, Hart PJ, Kim CA. Multiple polymer architectures of human polyhomeotic homolog 3 sterile alpha motif. Proteins 2014; 82:2823-30. [PMID: 25044168 DOI: 10.1002/prot.24645] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/18/2014] [Accepted: 07/03/2014] [Indexed: 12/13/2022]
Abstract
The self-association of sterile alpha motifs (SAMs) into a helical polymer architecture is a critical functional component of many different and diverse array of proteins. For the Drosophila Polycomb group (PcG) protein Polyhomeotic (Ph), its SAM polymerization serves as the structural foundation to cluster multiple PcG complexes, helping to maintain a silenced chromatin state. Ph SAM shares 64% sequence identity with its human ortholog, PHC3 SAM, and both SAMs polymerize. However, in the context of their larger protein regions, PHC3 SAM forms longer polymers compared with Ph SAM. Motivated to establish the precise structural basis for the differences, if any, between Ph and PHC3 SAM, we determined the crystal structure of the PHC3 SAM polymer. PHC3 SAM uses the same SAM-SAM interaction as the Ph SAM sixfold repeat polymer. Yet, PHC3 SAM polymerizes using just five SAMs per turn of the helical polymer rather than the typical six per turn observed for all SAM polymers reported to date. Structural analysis suggested that malleability of the PHC3 SAM would allow formation of not just the fivefold repeat structure but also possibly others. Indeed, a second PHC3 SAM polymer in a different crystal form forms a sixfold repeat polymer. These results suggest that the polymers formed by PHC3 SAM, and likely others, are dynamic. The functional consequence of the variable PHC3 SAM polymers may be to create different chromatin architectures.
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Affiliation(s)
- David R Nanyes
- Department of Biochemistry, The University of Texas Health Science Center San Antonio, MSC 7760, 7703 Floyd Curl Dr., San Antonio, Texas, 78229
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21
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Wang X, Choi JH, Ding J, Yang L, Ngoka LC, Lee EJ, Zha Y, Mao L, Jin B, Ren M, Cowell J, Huang S, Shi H, Cui H, Ding HF. HOXC9 directly regulates distinct sets of genes to coordinate diverse cellular processes during neuronal differentiation. BMC Genomics 2013; 14:830. [PMID: 24274069 PMCID: PMC3906982 DOI: 10.1186/1471-2164-14-830] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 11/20/2013] [Indexed: 01/06/2023] Open
Abstract
Background Cellular differentiation is characterized by the acquisition of specialized structures and functions, cell cycle exit, and global attenuation of the DNA damage response. It is largely unknown how these diverse cellular events are coordinated at the molecular level during differentiation. We addressed this question in a model system of neuroblastoma cell differentiation induced by HOXC9. Results We conducted a genome-wide analysis of the HOXC9-induced neuronal differentiation program. Microarray gene expression profiling revealed that HOXC9-induced differentiation was associated with transcriptional regulation of 2,370 genes, characterized by global upregulation of neuronal genes and downregulation of cell cycle and DNA repair genes. Remarkably, genome-wide mapping by ChIP-seq demonstrated that HOXC9 bound to 40% of these genes, including a large number of genes involved in neuronal differentiation, cell cycle progression and the DNA damage response. Moreover, we showed that HOXC9 interacted with the transcriptional repressor E2F6 and recruited it to the promoters of cell cycle genes for repressing their expression. Conclusions Our results demonstrate that HOXC9 coordinates diverse cellular processes associated with differentiation by directly activating and repressing the transcription of distinct sets of genes.
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Affiliation(s)
- Xiangwei Wang
- Cancer Center, Georgia Regents University, Augusta, GA 30912, USA.
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22
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Mutational analysis of Polycomb genes in solid tumours identifies PHC3 amplification as a possible cancer-driving genetic alteration. Br J Cancer 2013; 109:1699-702. [PMID: 23942079 PMCID: PMC3776977 DOI: 10.1038/bjc.2013.454] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 07/15/2013] [Accepted: 07/19/2013] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Polycomb group genes (PcGs) are epigenetic effectors implicated in most cancer hallmarks. The mutational status of all PcGs has never been systematically assessed in solid tumours. METHODS We conducted a multi-step analysis on publically available databases and patient samples to identify somatic aberrations of PcGs. RESULTS Data from more than 1000 cancer patients show for the first time that the PcG member PHC3 is amplified in three epithelial neoplasms (rate: 8-35%). This aberration predicts poorer prognosis in lung and uterine carcinomas (P<0.01). Gene amplification correlates with mRNA overexpression (P<0.01), suggesting a functional role of this aberration. CONCLUSION PHC3 amplification may emerge as a biomarker and potential therapeutic target in a relevant fraction of epithelial tumours.
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23
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Biochemical and functional interactions of human papillomavirus proteins with polycomb group proteins. Viruses 2013; 5:1231-49. [PMID: 23673719 PMCID: PMC3712305 DOI: 10.3390/v5051231] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 04/23/2013] [Accepted: 04/27/2013] [Indexed: 12/22/2022] Open
Abstract
The role of enzymes involved in polycomb repression of gene transcription has been studied extensively in human cancer. Polycomb repressive complexes mediate oncogene-induced senescence, a principal innate cell-intrinsic tumor suppressor pathway that thwarts expansion of cells that have suffered oncogenic hits. Infections with human cancer viruses including human papillomaviruses (HPVs) and Epstein-Barr virus can trigger oncogene-induced senescence, and the viruses have evolved strategies to abrogate this response in order to establish an infection and reprogram their host cells to establish a long-term persistent infection. As a consequence of inhibiting polycomb repression and evading oncogene induced-senescence, HPV infected cells have an altered epigenetic program as evidenced by aberrant homeobox gene expression. Similar alterations are frequently observed in non-virus associated human cancers and may be harnessed for diagnosis and therapy.
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24
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Valenzuela CD, Allori AC, Reformat DD, Sailon AM, Allen RJ, Davidson EH, Alikhani M, Bromage TG, Ricci JL, Warren SM. Characterization of adipose-derived mesenchymal stem cell combinations for vascularized bone engineering. Tissue Eng Part A 2013; 19:1373-85. [PMID: 23343199 DOI: 10.1089/ten.tea.2012.0323] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Since bone repair and regeneration depend on vasculogenesis and osteogenesis, both of these processes are essential for successful vascularized bone engineering. Using adipose-derived stem cells (ASCs), we investigated temporal gene expression profiles, as well as bone nodule and endothelial tubule formation capacities, during osteogenic and vasculogenic ASC lineage commitment. Osteoprogenitor-enriched cell populations were found to express RUNX2, MSX2, SP7 (osterix), BGLAP (osteocalcin), SPARC (osteonectin), and SPP1 (osteopontin) in a temporally specific sequence. Irreversible commitment of ASCs to the osteogenic lineage occurred between days 6 and 9 of differentiation. Endothelioprogenitor-enriched cell populations expressed CD34, PECAM1 (CD31), ENG (CD105), FLT1 (Vascular endothelial growth factor [VEGFR1]), and KDR (VEGFR2). Capacity for microtubule formation was evident in as early as 3 days. Functional capacity was assessed in eight coculture combinations for both bone nodule and endothelial tubule formation, and the greatest expression of these end-differentiation phenotypes was observed in the combination of well-differentiated endothelial cells with less-differentiated osteoblastic cells. Taken together, our results demonstrate vascularized bone engineering utilizing ASCs is a promising enterprise, and that coculture strategies should focus on developing a more mature vascular network in combination with a less mature osteoblastic stromal cell.
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Affiliation(s)
- Cristian D Valenzuela
- Institute of Reconstructive Plastic Surgery Laboratories, New York University Langone Medical Center, New York, New York 10016, USA
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25
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Gonzalez-Perez A, Jene-Sanz A, Lopez-Bigas N. The mutational landscape of chromatin regulatory factors across 4,623 tumor samples. Genome Biol 2013; 14:r106. [PMID: 24063517 PMCID: PMC4054018 DOI: 10.1186/gb-2013-14-9-r106] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 09/24/2013] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Chromatin regulatory factors are emerging as important genes in cancer development and are regarded as interesting candidates for novel targets for cancer treatment. However, we lack a comprehensive understanding of the role of this group of genes in different cancer types. RESULTS We have analyzed 4,623 tumor samples from thirteen anatomical sites to determine which chromatin regulatory factors are candidate drivers in these different sites. We identify 34 chromatin regulatory factors that are likely drivers in tumors from at least one site, all with relatively low mutational frequency. We also analyze the relative importance of mutations in this group of genes for the development of tumorigenesis in each site, and indifferent tumor types from the same site. CONCLUSIONS We find that, although tumors from all thirteen sites show mutations in likely driver chromatin regulatory factors, these are more prevalent in tumors arising from certain tissues. With the exception of hematopoietic, liver and kidney tumors, as a median, the mutated factors are less than one fifth of all mutated drivers across all sites analyzed. We also show that mutations in two of these genes, MLL and EP300, correlate with broad expression changes across cancer cell lines, thus presenting at least one mechanism through which these mutations could contribute to tumorigenesis in cells of the corresponding tissues.
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Affiliation(s)
- Abel Gonzalez-Perez
- Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, Barcelona, Spain
| | - Alba Jene-Sanz
- Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, Barcelona, Spain
| | - Nuria Lopez-Bigas
- Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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26
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Robinson AK, Leal BZ, Nanyes DR, Kaur Y, Ilangovan U, Schirf V, Hinck AP, Demeler B, Kim CA. Human polyhomeotic homolog 3 (PHC3) sterile alpha motif (SAM) linker allows open-ended polymerization of PHC3 SAM. Biochemistry 2012; 51:5379-86. [PMID: 22724443 DOI: 10.1021/bi3004318] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Sterile alpha motifs (SAMs) are frequently found in eukaryotic genomes. An intriguing property of many SAMs is their ability to self-associate, forming an open-ended polymer structure whose formation has been shown to be essential for the function of the protein. What remains largely unresolved is how polymerization is controlled. Previously, we had determined that the stretch of unstructured residues N-terminal to the SAM of a Drosophila protein called polyhomeotic (Ph), a member of the polycomb group (PcG) of gene silencers, plays a key role in controlling Ph SAM polymerization. Ph SAM with its native linker created shorter polymers compared to Ph SAM attached to either a random linker or no linker. Here, we show that the SAM linker for the human Ph ortholog, polyhomeotic homolog 3 (PHC3), also controls PHC3 SAM polymerization but does so in the opposite fashion. PHC3 SAM with its native linker allows longer polymers to form compared to when attached to a random linker. Attaching the PHC3 SAM linker to Ph SAM also resulted in extending Ph SAM polymerization. Moreover, in the context of full-length Ph protein, replacing the SAM linker with PHC3 SAM linker, intended to create longer polymers, resulted in greater repressive ability for the chimera compared to wild-type Ph. These findings show that polymeric SAM linkers evolved to modulate a wide dynamic range of SAM polymerization abilities and suggest that rationally manipulating the function of SAM containing proteins through controlling their SAM polymerization may be possible.
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Affiliation(s)
- Angela K Robinson
- Department of Biochemistry and CTRC, University of Texas Health Science Center at San Antonio, 78229-3990, United States
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27
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Piunti A, Pasini D. Epigenetic factors in cancer development: polycomb group proteins. Future Oncol 2011; 7:57-75. [PMID: 21174538 DOI: 10.2217/fon.10.157] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The role of chromatin-modifying factors in cancer biology emerged exponentially in the last 10 years, and increased attention has been focused on Polycomb group (PcG) proteins and their enzymatic activities. PcG proteins are repressive chromatin modifiers required for proliferation and development. The frequent deregulation of PcG activities in human tumors has direct oncogenic effects and results, essential for cancer cell proliferation. Here we will review the recent findings regarding PcG proteins in prospective tumor development, focusing on the molecular mechanisms that deregulate PcG expression in different tumors, at the downstream pathways to PcG expression (that contribute to cancer development) and at the mechanisms that regulate PcG recruitment to specific targets. Finally, we will speculate on the benefit of PcG inhibition for cancer treatment, reviewing potential pharmacological strategies.
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Affiliation(s)
- Andrea Piunti
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, Milan, Italy
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L3MBTL2 protein acts in concert with PcG protein-mediated monoubiquitination of H2A to establish a repressive chromatin structure. Mol Cell 2011; 42:438-50. [PMID: 21596310 DOI: 10.1016/j.molcel.2011.04.004] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Revised: 02/01/2011] [Accepted: 03/31/2011] [Indexed: 01/15/2023]
Abstract
We have identified human MBT domain-containing protein L3MBTL2 as an integral component of a protein complex that we termed Polycomb repressive complex 1 (PRC1)-like 4 (PRC1L4), given the copresence of PcG proteins RING1, RING2, and PCGF6/MBLR. PRC1L4 also contained E2F6 and CBX3/HP1γ, known to function in transcriptional repression. PRC1L4-mediated repression necessitated L3MBTL2 that compacted chromatin in a histone modification-independent manner. Genome-wide location analyses identified several hundred genes simultaneously bound by L3MBTL2 and E2F6, preferentially around transcriptional start sites that exhibited little overlap with those targeted by other E2Fs or by L3MBTL1, another MBT domain-containing protein that interacts with RB1. L3MBTL2-specific RNAi resulted in increased expression of target genes that exhibited a significant reduction in H2A lysine 119 monoubiquitination. Our findings highlight a PcG/MBT collaboration that attains repressive chromatin without entailing histone lysine methylation marks.
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29
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Polycomb group proteins: multi-faceted regulators of somatic stem cells and cancer. Cell Stem Cell 2010; 7:299-313. [PMID: 20804967 DOI: 10.1016/j.stem.2010.08.002] [Citation(s) in RCA: 526] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 07/30/2010] [Accepted: 08/06/2010] [Indexed: 02/06/2023]
Abstract
Polycomb Group (PcG) proteins are transcriptional repressors that epigenetically modify chromatin and participate in the establishment and maintenance of cell fates. These proteins play important roles in both stem cell self-renewal and in cancer development. Our understanding of their mechanism of action has greatly advanced over the past 10 years, but many unanswered questions remain. In this review, we present the currently available experimental data that connect PcG protein function with some of the key processes which govern somatic stem cell activity. We also highlight recent studies suggesting that a delicate balance in PcG gene dosage is crucial for proper stem cell homeostasis and prevention of cancer stem cell development.
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Loss of the Polycomb group gene polyhomeotic induces non-autonomous cell overproliferation. EMBO Rep 2010; 12:157-63. [PMID: 21164514 DOI: 10.1038/embor.2010.188] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 10/27/2010] [Accepted: 11/03/2010] [Indexed: 11/09/2022] Open
Abstract
Polycomb group (PcG) proteins are conserved epigenetic regulators that are linked to cancer in humans. However, little is known about how they control cell proliferation. Here, we report that mutant clones of the PcG gene polyhomeotic (ph) form unique single-cell-layer cavities that secrete three JAK/STAT pathway ligands, which in turn act redundantly to stimulate overproliferation of surrounding wild-type cells. Notably, different ph alleles cause different phenotypes at the cellular level. Although the ph-null allele induces non-autonomous overgrowth, an allele encoding truncated Ph induces both autonomous and non-autonomous overgrowth. We propose that PcG misregulation promotes tumorigenesis through several cellular mechanisms.
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Abstract
Progression of the mammalian cell cycle depends on correct timing and co-ordination of a series of events, which are managed by the cellular transcriptional machinery and epigenetic mechanisms governing genome accessibility. Epigenetic chromatin modifications are dynamic across the cell cycle, and are shown to influence and be influenced by cell-cycle progression. Chromatin modifiers regulate cell-cycle progression locally by controlling the expression of individual genes and globally by controlling chromatin condensation and chromosome segregation. The cell cycle, on the other hand, ensures a correct inheritance of epigenetic chromatin modifications to daughter cells. In this chapter, we summarize the current knowledge on the dynamics of epigenetic chromatin modifications during progression of the cell cycle.
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Iwata S, Takenobu H, Kageyama H, Koseki H, Ishii T, Nakazawa A, Tatezaki SI, Nakagawara A, Kamijo T. Polycomb group molecule PHC3 regulates polycomb complex composition and prognosis of osteosarcoma. Cancer Sci 2010; 101:1646-52. [PMID: 20491773 DOI: 10.1111/j.1349-7006.2010.01586.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Polyhomeotic homolog 3 (PHC 3) is a member of the human polycomb complex and has been regarded as a candidate tumor suppressor of osteosarcoma. In the present paper, we performed a mutation survey and PHC3 expression analysis by quantitative real-time PCR using 10 osteosarcoma cell lines and 42 primary osteosarcoma samples. Relative PHC3 expression values of clinical samples were analyzed with clinical outcomes, and it was suggested that lower PHC3-expressing patients had significantly worse overall survival. Relative PHC3 values of clinical samples were less than those of normal bone tissues, whereas they were greater than those of cell lines. By denaturing high performance liquid chromatography analysis and direct sequencing, we found a PHC3 missense mutation in U2OS cells, which resulted in arginine56 to proline substitution. The same point mutation existed in four of 42 primary osteosarcoma samples. Regarding functional analysis, PHC3 expression significantly suppressed the colony formation of tumor cells. Intriguingly, polycomb repressive complex 1 members, Bmi1 and Ring1b proteins, were reduced in PHC3-expressing osteosarcoma cells. Deletion mutant PHC3 expression suggested that the carboxyl terminus of PHC3 has a role in suppression; the above-mentioned point mutation of PHC3 also lost inhibitory activities. Conversely, Bmi1 expression reduced PHC3 at the mRNA level and induced the proliferation of osteosarcoma cells. Taken together, we confirmed the role of PHC3 as a tumor suppressor in osteosarcoma cells and found that PHC3-dependent tumor suppression may be caused by modification of the composition of polycomb repressive complex 1 in cancer cells.
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Affiliation(s)
- Shintaro Iwata
- Division of Biochemistry and Molecular Carcinogenesis, Chiba Cancer Center Research Institute, Chiba, Japan
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Chang SJ, Wang TY, Tsai CY, Hu TF, Chang MDT, Wang HW. Increased epithelial stem cell traits in advanced endometrial endometrioid carcinoma. BMC Genomics 2009; 10:613. [PMID: 20015385 PMCID: PMC2810306 DOI: 10.1186/1471-2164-10-613] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Accepted: 12/16/2009] [Indexed: 11/11/2022] Open
Abstract
Background It has been recognized cancer cells acquire characters reminiscent of those of normal stem cells, and the degree of stem cell gene expression correlates with patient prognosis. Lgr5(+) or CD133(+) epithelial stem cells (EpiSCs) have recently been identified and these cells are susceptible to neoplastic transformation. It is unclear, however, whether genes enriched in EpiSCs also contribute in tumor malignancy. Endometrial endometrioid carcinoma (EEC) is a dominant type of the endometrial cancers and is still among the most common female cancers. Clinically endometrial carcinoma is classified into 4 FIGO stages by the degree of tumor invasion and metastasis, and the survival rate is low in patients with higher stages of tumors. Identifying genes shared between advanced tumors and stem cells will not only unmask the mechanisms of tumor malignancy but also provide novel therapeutic targets. Results To identify EpiSC genes in late (stages III-IV) EECs, a molecular signature distinguishing early (stages I-II) and late EECs was first identified to delineate late EECs at the genomics level. ERBB2 and CCR1 were genes activated in late EECs, while APBA2 (MINT2) and CDK inhibitor p16 tumor suppressors in early EECs. MAPK pathway was significantly up in late EECs, indicating drugs targeting this canonical pathway might be useful for treating advanced EECs. A six-gene mini-signature was further identified to differentiate early from advanced EECs in both the training and testing datasets. Advanced, invasive EECs possessed a clear EpiSC gene expression pattern, explaining partly why these tumors are more malignant. Conclusions Our work provides new insights into the pathogenesis of EECs and reveals a previously unknown link between adult stem cells and the histopathological traits of EECs. Shared EpiSC genes in late EECs may contribute to the stem cell-like phenotypes shown by advanced tumors and hold the potential of being candidate therapeutic targets and novel prognosis biomarkers.
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Affiliation(s)
- Shing-Jyh Chang
- Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, Taiwan.
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Polyhomeotic has a tumor suppressor activity mediated by repression of Notch signaling. Nat Genet 2009; 41:1076-82. [DOI: 10.1038/ng.414] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Accepted: 06/05/2009] [Indexed: 01/26/2023]
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Lechtenberg BC, Allen MD, Rutherford TJ, Freund SMV, Bycroft M. Solution structure of the FCS zinc finger domain of the human polycomb group protein L(3)mbt-like 2. Protein Sci 2009; 18:657-61. [PMID: 19241375 DOI: 10.1002/pro.51] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Polycomb group proteins are epigenetic regulators that maintain patterns of gene expression over multiple rounds of cell division. Many of these proteins, including polyhomeotic and the MBT repeat containing proteins SCM and dSfmbt, contain an atypical C2C2 zinc finger with a characteristic phenylalanine-cysteine-serine sequence motif. The reoccurrence of this so-called FCS zinc finger in a variety of polycomb group proteins suggests that it has an important regulatory function. We have determined the solution structure of the FCS zinc finger of the human dSfmbt homologue L(3)mbt-like 2 (L3MBTL2). The structure consists of a beta-hairpin followed by an alpha-helix. The zinc ligands are situated in the beta-hairpin and at the N-terminus of the alpha-helix an arrangement typical of the treble clef class of zinc fingers. The structure is consistent with the proposal that FCS zinc fingers bind to regulatory RNAs.
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Identification of protein O-GlcNAcylation sites using electron transfer dissociation mass spectrometry on native peptides. Proc Natl Acad Sci U S A 2009; 106:8894-9. [PMID: 19458039 DOI: 10.1073/pnas.0900288106] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein O-GlcNAcylation occurs in all animals and plants and is implicated in modulation of a wide range of cytosolic and nuclear protein functions, including gene silencing, nutrient and stress sensing, phosphorylation signaling, and diseases such as diabetes and Alzheimer's. The limiting factor impeding rapid progress in deciphering the biological functions of protein O-GlcNAcylation has been the inability to easily identify exact residues of modification. We describe a robust, high-sensitivity strategy able to assign O-GlcNAcylation sites of native modified peptides using electron transfer dissociation mass spectrometry. We have studied the murine postsynaptic density pseudoorganelle and report the assignment of 58 modification sites from a single experiment--significantly increasing the number of sites known in the literature. Components of several repressor complexes, such as NCoR1, polyhomeotic-like protein3, and EMSY, are modified. In addition, 28 O-GlcNAc sites were found on the protein Bassoon, effectively matching the number of phosphorylation sites reported previously on this protein. This finding suggests that on certain proteins, O-GlcNAcylation may be as extensive and important as phosphorylation in regulating protein function. Three of the newly discovered O-GlcNAc sites on Bassoon have previously been reported as phosphorylation sites, highlighting the interplay of the modifications. Surprisingly, several peptides with GlcNAc modifications on asparagines within the N-X-S/T consensus sequence were also observed from membrane protein extracellular domains. This powerful strategy fulfills a long-standing need in the biological community by facilitating modification site identifications that will accelerate understanding of the biological significance of this elusive regulatory posttranslational modification.
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Xu X, Bieda M, Jin VX, Rabinovich A, Oberley MJ, Green R, Farnham PJ. A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. Genome Res 2007; 17:1550-61. [PMID: 17908821 PMCID: PMC2045138 DOI: 10.1101/gr.6783507] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Using ChIP-chip assays (employing ENCODE arrays and core promoter arrays), we examined the binding patterns of three members of the E2F family in five cell types. We determined that most E2F1, E2F4, and E2F6 binding sites are located within 2 kb of a transcription start site, in both normal and tumor cells. In fact, the majority of promoters that are active (as defined by TAF1 or POLR2A binding) in GM06990 B lymphocytes and Ntera2 carcinoma cells were also bound by an E2F. This very close relationship between E2F binding sites and binding sites for general transcription factors in both normal and tumor cells suggests that a chromatin-bound E2F may be a signpost for active transcription initiation complexes. In general, we found that several E2Fs bind to a given promoter and that there is only modest cell type specificity of the E2F family. Thus, it is difficult to assess the role of any particular E2F in transcriptional regulation, due to extreme redundancy of target promoters. However, Ntera2 carcinoma cells were exceptional in that a large set of promoters were bound by E2F6, but not by E2F1 or E2F4. It has been proposed that E2F6 contributes to gene silencing by recruiting enzymes involved in methylating histone H3. To test this hypothesis, we created Ntera2 cell lines harboring shRNAs to E2F6. We found that reduction of E2F6 only induced minimal alteration of the transcriptome of Ntera2 transcriptome. Our results support the concept of functional redundancy in the E2F family and suggest that E2F6 is not critical for histone methylation.
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Affiliation(s)
- Xiaoqin Xu
- Department of Pharmacology and the Genome Center, University of California-Davis, Davis, California 95616, USA
| | - Mark Bieda
- Department of Pharmacology and the Genome Center, University of California-Davis, Davis, California 95616, USA
| | - Victor X. Jin
- Department of Pharmacology and the Genome Center, University of California-Davis, Davis, California 95616, USA
| | - Alina Rabinovich
- Department of Pharmacology and the Genome Center, University of California-Davis, Davis, California 95616, USA
| | - Mathew J. Oberley
- University of Wisconsin Medical School, Madison, Wisconsin, 53705 USA
| | - Roland Green
- NimbleGen Systems Inc., Madison, Wisconsin, 53711 USA
| | - Peggy J. Farnham
- Department of Pharmacology and the Genome Center, University of California-Davis, Davis, California 95616, USA
- Corresponding author.E-mail ; fax (530) 754-9658
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