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Chen W, Zhou L, Jiang J, Chen J, Geng D, Chen Y, Han X, Xie Q, Guo G, Chen X, Tang S, Zhong X. Induction of the p21/CDK6 pathway and alteration of the immune microenvironment by the stem cell marker CBX3 in melanoma. Stem Cell Res Ther 2025; 16:63. [PMID: 39934923 PMCID: PMC11816572 DOI: 10.1186/s13287-025-04179-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2024] [Accepted: 01/23/2025] [Indexed: 02/13/2025] Open
Abstract
BACKGROUND As one of the stem cell markers, chromobox protein homolog 3 (CBX3) participates in multiple signaling pathways that affect the progression of various tumors. However, the role of CBX3 in melanoma remains unclear, and the mechanisms by which CBX3 may regulate immunotherapy outcome remain largely unknown. METHODS We used the Cancer Genome Atlas, Genotype-Tissue Expression portal, and Gene Expression Omnibus database to estimate CBX3 expression and its prognostic effect in melanoma. The role of CBX3 in proliferation and migration of melanoma cells were examined using the CCK8, cloning, wound healing, and transwell assays. The effect of CBX3 on melanoma tumorigenesis was assessed using an in vivo animal model. The role of CBX3 in cell cycle was examined using flow cytometry, and expression levels of cell cycle-related genes and proteins in cells with altered CBX3 levels were analyzed using qPCR and western blotting. The function of CBX3 in the immune microenvironment of melanoma was studied using single-cell RNA sequencing and public databases. RESULTS We found that CBX3 was highly expressed in melanoma with poor prognosis. CBX3 promoted the proliferation and migration of melanoma cells in vivo and in vitro. Functional analysis revealed that CBX3 regulates cell cycle, as it accelerated the G1 to S transition, decreased p21 expression, and increased CDK6 expression. Finally, single-cell sequencing and immune-related assays showed that CBX3 is immunogenic and can change the immune microenvironment of melanoma. CONCLUSIONS We conclude that the stem cell marker, CBX3 activates the p21/CDK6 pathway and alters the immune microenvironment in melanoma.
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Affiliation(s)
- Wanxian Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, People's Republic of China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou, China
| | - Linsa Zhou
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, People's Republic of China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou, China
| | - Jingjing Jiang
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Jiasheng Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, People's Republic of China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou, China
| | - Deyi Geng
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, People's Republic of China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou, China
| | - Yaokun Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, People's Republic of China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou, China
| | - Xiaosha Han
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, People's Republic of China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou, China
| | - Qihu Xie
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, People's Republic of China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou, China
| | - Genghong Guo
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, People's Republic of China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou, China
| | - Xuefen Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, People's Republic of China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou, China
| | - Shijie Tang
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, People's Republic of China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou, China
| | - Xiaoping Zhong
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, People's Republic of China.
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou, China.
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Wang X, Meng P, Liu H, Tan J, Liu Y, Li X. CBX3 contributes to pancreatic adenocarcinoma progression via promoting KIF20A expression. Cytotechnology 2025; 77:25. [PMID: 39735331 PMCID: PMC11671669 DOI: 10.1007/s10616-024-00684-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Accepted: 12/16/2024] [Indexed: 12/31/2024] Open
Abstract
Pancreatic adenocarcinoma (PAAD) is one of the malignant tumors with poor prognosis. This study aims to inquiry the effects of Chromobox homologue 3 (CBX3) on PAAD progression. Pan-cancer analysis of CBX3 and its correlation with PAAD progression were investigated by informatics analysis. The role of CBX3 in PAAD was explored in vitro and in vivo. Cell viability, proliferation, migration and invasion were inspected by CCK-8 assay, EdU staining, scratch test and transwell assay, respectively. The morphology of tumors was observed by hematoxylin-eosin staining. Immunohistochemistry (Ki67) was performed to inspect the proliferation of tumor tissue. The protein levels were measured by western blot. Moreover, the downstream genes of CBX3 were screened, and the effects of target gene on PAAD was investigated in vitro. CBX3 was overexpressed in multi cancers, and high CBX3 expression indicated poor prognosis in PAAD. Through the in vitro assays, knockdown of CBX3 suppressed the viability, migration and invasion of PAAD cells, and restrained tumor growth in vivo. Subsequently, kinesin family member 20A (KIF20A) was screened as the downstream gene of CBX3, which was up-regulated in PAAD and related to low overall survival. Mechanistically, we discovered that CBX3 could regulate KIF20A expression. Knockdown of CBX3 promoted the oncogenic effects of KIF20A silencing on PAAD cells, and attenuated the pro-oncogenic effects of KIF20A overexpression on PPAD. Collectively, silencing CBX3 suppressed PAAD progression through regulating KIF20A expression, providing an underlying target for PAAD treatment.
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Affiliation(s)
- Xiaohui Wang
- Department of General Surgery, Bayinguoleng Mongolian Autonomous Prefecture People’s Hospital, No. 41. People’s East Road, Korla, 841000 Xinjiang Uygur Autonomous Region China
| | - Ping Meng
- Personnel Section, Bayinguoleng Mongolian Autonomous Prefecture People’s Hospital, No. 41. People’s East Road, Korla, 841000 Xinjiang Uygur Autonomous Region China
| | - Huili Liu
- Medical Department, Bayinguoleng Mongolian Autonomous Prefecture People’s Hospital, No. 41. People’s East Road, Korla, 841000 Xinjiang Uygur Autonomous Region China
| | - Jinhua Tan
- Department of Anesthesiology, Bayinguoleng Mongolian Autonomous Prefecture People’s Hospital, No. 41. People’s East Road, Korla, 841000 Xinjiang Uygur Autonomous Region China
| | - Yu Liu
- Gastroenterology, Bayinguoleng Mongolian Autonomous Prefecture People’s Hospital, No. 41. People’s East Road, Korla, 841000 Xinjiang Uygur Autonomous Region China
| | - Xu Li
- Department of General Surgery, Bayinguoleng Mongolian Autonomous Prefecture People’s Hospital, No. 41. People’s East Road, Korla, 841000 Xinjiang Uygur Autonomous Region China
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Liu H, Xiong W, Zhong W, Hu Y. NOVEL ACTIVE PROTEINS FOR SEPSIS PROGNOSIS REVEALED THROUGH ScRNA-seq AND QUANTITATIVE PROTEOMICS. Shock 2024; 62:738-745. [PMID: 38888471 DOI: 10.1097/shk.0000000000002408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
ABSTRACT Objective: To uncover critical active proteins influencing sepsis outcomes through multiomics analysis. Methods: This study collected peripheral blood from sepsis patients (NS = 26, SV = 27) and controls (Con = 16). Cellular heterogeneity was assessed using scRNA-seq. Cellular populations were identified through clustering and annotation. Gene set variation analysis was employed to detect pathway alterations in sepsis, while the Viper algorithm estimated protein activity at the single-cell level. Signaling networks were investigated via cell-cell communication analysis. Differentially expressed proteins were identified by DIA proteomics and confirmed through integrated analysis. Prognostic value was evaluated via meta and survival analyses. Results: scRNA-seq of 22,673 features within 34,228 cells identified five cellular clusters and 253 active proteins via Viper, validated by DIA (FC > 2, P < 0.05). Four proteins (SPI1, MEF2A, CBX3, UBTF) with prognostic significance were discovered and mapped onto the cellular landscape. Gene set variation analysis enrichment analysis revealed that the NS group exhibited significant alterations in pathways related to cellular apoptosis and inflammatory responses, while the SV group displayed increased activity in DNA repair and cellular survival pathways. Conclusion: The study's findings advance the understanding of sepsis pathophysiology by linking differentially active proteins to patient prognosis, paving the way for targeted therapeutic strategies.
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Affiliation(s)
- Hui Liu
- Department of Emergency Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Wei Xiong
- Department of Emergency Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | | | - Yingchun Hu
- Department of Emergency Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Sokolova V, Miratsky J, Svetlov V, Brenowitz M, Vant J, Lewis TS, Dryden K, Lee G, Sarkar S, Nudler E, Singharoy A, Tan D. Structural mechanism of HP1⍺-dependent transcriptional repression and chromatin compaction. Structure 2024; 32:2094-2106.e6. [PMID: 39383876 PMCID: PMC11560701 DOI: 10.1016/j.str.2024.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 08/12/2024] [Accepted: 09/12/2024] [Indexed: 10/11/2024]
Abstract
Heterochromatin protein 1 (HP1) plays a central role in establishing and maintaining constitutive heterochromatin. However, the mechanisms underlying HP1-nucleosome interactions and their contributions to heterochromatin functions remain elusive. Here, we present the cryoelectron microscopy (cryo-EM) structure of an HP1α dimer bound to an H2A.Z-nucleosome, revealing two distinct HP1α-nucleosome interfaces. The primary HP1α binding site is located at the N terminus of histone H3, specifically at the trimethylated lysine 9 (K9me3) region, while a secondary binding site is situated near histone H2B, close to nucleosome superhelical location 4 (SHL4). Our biochemical data further demonstrates that HP1α binding influences the dynamics of DNA on the nucleosome. It promotes DNA unwrapping near the nucleosome entry and exit sites while concurrently restricting DNA accessibility in the vicinity of SHL4. Our study offers a model for HP1α-mediated heterochromatin maintenance and gene silencing. It also sheds light on the H3K9me-independent role of HP1 in responding to DNA damage.
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Affiliation(s)
- Vladyslava Sokolova
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Jacob Miratsky
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Vladimir Svetlov
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Michael Brenowitz
- Departments of Biochemistry and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - John Vant
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Tyler S Lewis
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Kelly Dryden
- Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| | - Gahyun Lee
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Shayan Sarkar
- Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Dongyan Tan
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA.
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Porozhan Y, Carstensen M, Thouroude S, Costallat M, Rachez C, Batsché E, Petersen T, Christensen T, Muchardt C. Defective Integrator activity shapes the transcriptome of patients with multiple sclerosis. Life Sci Alliance 2024; 7:e202402586. [PMID: 39029934 PMCID: PMC11259605 DOI: 10.26508/lsa.202402586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/21/2024] Open
Abstract
HP1α/CBX5 is an epigenetic regulator with a suspected role in multiple sclerosis (MS). Here, using high-depth RNA sequencing on monocytes, we identified a subset of MS patients with reduced CBX5 expression, correlating with progressive stages of the disease and extensive transcriptomic alterations. Examination of rare non-coding RNA species in these patients revealed impaired maturation/degradation of U snRNAs and enhancer RNAs, indicative of reduced activity of the Integrator, a complex with suspected links to increased MS risk. At protein-coding genes, compromised Integrator activity manifested in reduced pre-mRNA splicing efficiency and altered expression of genes regulated by RNA polymerase II pause-release. Inactivation of Cbx5 in the mouse mirrored most of these transcriptional defects and resulted in hypersensitivity to experimental autoimmune encephalomyelitis. Collectively, our observations suggested a major contribution of the Integrator complex in safeguarding against transcriptional anomalies characteristic of MS, with HP1α/CBX5 emerging as an unexpected regulator of this complex's activity. These findings bring novel insights into the transcriptional aspects of MS and provide potential new criteria for patient stratification.
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Affiliation(s)
- Yevheniia Porozhan
- Institut de Biologie Paris-Seine (IBPS), CNRS UMR 8256, Biological Adaptation and Ageing, Sorbonne Université, Paris, France
| | - Mikkel Carstensen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Forum, Aarhus, Denmark
| | - Sandrine Thouroude
- Institut de Biologie Paris-Seine (IBPS), CNRS UMR 8256, Biological Adaptation and Ageing, Sorbonne Université, Paris, France
| | - Mickael Costallat
- Institut de Biologie Paris-Seine (IBPS), CNRS UMR 8256, Biological Adaptation and Ageing, Sorbonne Université, Paris, France
| | - Christophe Rachez
- Institut de Biologie Paris-Seine (IBPS), CNRS UMR 8256, Biological Adaptation and Ageing, Sorbonne Université, Paris, France
| | - Eric Batsché
- Institut de Biologie Paris-Seine (IBPS), CNRS UMR 8256, Biological Adaptation and Ageing, Sorbonne Université, Paris, France
| | - Thor Petersen
- Department of Neurology, Hospital of Southern Jutland and Research Unit in Neurology, Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | | | - Christian Muchardt
- Institut de Biologie Paris-Seine (IBPS), CNRS UMR 8256, Biological Adaptation and Ageing, Sorbonne Université, Paris, France
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Yang R, Wang R, Zhao D, Lian K, Shang B, Dong L, Yang X, Dang X, Sun D, Cheng Y. Integrative analysis of transcriptome-wide association study and mRNA expression profile identified risk genes for bipolar disorder. Neurosci Lett 2024; 839:137935. [PMID: 39151574 DOI: 10.1016/j.neulet.2024.137935] [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: 03/08/2024] [Revised: 08/05/2024] [Accepted: 08/09/2024] [Indexed: 08/19/2024]
Abstract
OBJECTIVE Bipolar disorder (BD) is a debilitating neuropsychiatric disorder, which is associated with genetic variation through "vast but mixed" Genome-Wide Association Studies (GWAS). Transcriptome-Wide Association Study (TWAS) is more effective in explaining genetic factors that influence complex diseases and can help identifying risk genes more reliably. So, this study aims to identify potential BD risk genes in pedigrees with TWAS. METHODS We conducted a TWAS analysis with expression quantitative trait loci (eQTL) analysis on extended BD pedigrees, and the BD genome-wide association study (GWAS) summary data acquired from the Psychiatric Genomics Consortium (PGC). Furthermore, the BD-associated genes identified by TWAS were validated by mRNA expression profiles from the Gene Expression Omnibus (GEO) Datasets (GSE23848 and GSE46416). Functional enrichment and annotation analysis were implemented by RStudio (version 4.2.0). RESULTS TWAS identified 362 genes with P value < 0.05, and 18 genes remain significant after Bonferroni correction, such as SEMA3G (PTWAS=1.07 × 10-11), ALOX5AP (PTWAS=3.12 × 10-8), and PLEC (PTWAS=1.27 × 10-7). Further 6 overlapped genes were detected in integrative analysis, such as UQCRB (PTWAS=0.0020, PmRNA=0.0000), TMPRSS9 (PTWAS=0.0405, PmRNA=0.0032), and SNX10 (PTWAS=0.0104, PmRNA=0.0015). Using genes identified by TWAS, Gene Ontology (GO) enrichment analysis identified 40 significant GO terms, such as mitochondrial ATP synthesis coupled electron transport, mitochondrial respiratory, aerobic electron transport chain, oxidative phosphorylation, mitochondrial membrane proteins, and ubiquinone activity. The Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway enrichment analysis identified significant 15 pathways for BD, such as Oxidative phosphorylation, endocannabinoids signaling, neurodegeneration, and reactive oxide species. CONCLUSIONS We found a set of BD-associated genes and pathways, validating the important role of neurodevelopmental abnormalities, inflammatory responses, and mitochondrial dysfunction in the pathology of BD, offering novel information for comprehending the genetic basis of BD.
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Affiliation(s)
- Runxu Yang
- Psychiatry Department, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Rui Wang
- Department of Prevention and Health Care, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Dongyan Zhao
- First Affiliated Hospital of Dali University, Dali, Yunnan, China
| | - Kun Lian
- Psychiatry Department, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Binli Shang
- Psychiatry Department, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Lei Dong
- Psychiatry Department, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Xuejuan Yang
- Lincang Psychiatric Hospital, Lincang, Yunnan, China
| | - Xinglun Dang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Duo Sun
- Psychiatry Department, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Yuqi Cheng
- Psychiatry Department, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China.
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Wahab MA, Del Gaudio N, Gargiulo B, Quagliariello V, Maurea N, Nebbioso A, Altucci L, Conte M. Exploring the Role of CBX3 as a Potential Therapeutic Target in Lung Cancer. Cancers (Basel) 2024; 16:3026. [PMID: 39272883 PMCID: PMC11394081 DOI: 10.3390/cancers16173026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 08/27/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024] Open
Abstract
Epigenetic changes regulate gene expression through histone modifications, chromatin remodeling, and protein translation of these modifications. The PRC1 and PRC2 complexes shape gene repression via histone modifications. Specifically, the CBX protein family aids PRC1 recruitment to chromatin, impacting the progressive multistep process driving chromatin silencing. Among family members, CBX3 is a complex protein involved in aberrant epigenetic mechanisms that drive lung cancer progression. CBX3 promotes lung tumorigenesis by interacting with key pathways such as PI3K/AKT, Ras/KRAS, Wnt/β-catenin, MAPK, Notch, and p53, leading to increased proliferation, inhibition of apoptosis, and enhanced resistance to therapy. Given our current lack of knowledge, additional research is required to uncover the intricate mechanisms underlying CBX3 activity, as well as its involvement in molecular pathways and its potential biomarker evaluation. Specifically, the dissimilar roles of CBX3 could be reexamined to gain a greater insight into lung cancer pathogenesis. This review aims to provide a clear overview of the context-related molecular profile of CBX3, which could be useful for addressing clinical challenges and developing novel targeted therapies based on personalized medicine.
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Affiliation(s)
- Muhammad Aamir Wahab
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Nunzio Del Gaudio
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Biagio Gargiulo
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Vincenzo Quagliariello
- Division of Cardiology, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Nicola Maurea
- Division of Cardiology, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Angela Nebbioso
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
- Program of Medical Epigenetics, Vanvitelli Hospital, 80138 Naples, Italy
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
- Program of Medical Epigenetics, Vanvitelli Hospital, 80138 Naples, Italy
- Institute of Endocrinology and Oncology "Gaetano Salvatore" (IEOS), 80131 Naples, Italy
- Biogem Institute of Molecular and Genetic Biology, 83031 Ariano Irpino, Italy
| | - Mariarosaria Conte
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
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Rodríguez TC, Yurkovetskiy L, Nagalekshmi K, Lam CHO, Jazbec E, Maitland SA, Wolfe SA, Sontheimer EJ, Luban J. PRC1.6 localizes on chromatin with the human silencing hub (HUSH) complex for promoter-specific silencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603173. [PMID: 39026796 PMCID: PMC11257501 DOI: 10.1101/2024.07.12.603173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
An obligate step in the life cycle of HIV-1 and other retroviruses is the establishment of the provirus in target cell chromosomes. Transcriptional regulation of proviruses is complex, and understanding the mechanisms underlying this regulation has ramifications for fundamental biology, human health, and gene therapy implementation. The three core components of the Human Silencing Hub (HUSH) complex, TASOR, MPHOSPH8 (MPP8), and PPHLN1 (Periphilin 1), were identified in forward genetic screens for host genes that repress provirus expression. Subsequent loss-of-function screens revealed accessory proteins that collaborate with the HUSH complex to silence proviruses in particular contexts. To identify proteins associated with a HUSH complex-repressed provirus in human cells, we developed a technique, Provirus Proximal Proteomics, based on proximity labeling with C-BERST (dCas9-APEX2 biotinylation at genomic elements by restricted spatial tagging). Our screen exploited a lentiviral reporter that is silenced by the HUSH complex in a manner that is independent of the integration site in chromatin. Our data reveal that proviruses silenced by the HUSH complex are associated with DNA repair, mRNA processing, and transcriptional silencing proteins, including L3MBTL2, a member of the non-canonical polycomb repressive complex 1.6 (PRC1.6). A forward genetic screen confirmed that PRC1.6 components L3MBTL2 and MGA contribute to HUSH complex-mediated silencing. PRC1.6 was then shown to silence HUSH-sensitive proviruses in a promoter-specific manner. Genome wide profiling showed striking colocalization of the PRC1.6 and HUSH complexes on chromatin, primarily at sites of active promoters. Finally, PRC1.6 binding at a subset of genes that are silenced by the HUSH complex was dependent on the core HUSH complex component MPP8. These studies offer new tools with great potential for studying the transcriptional regulation of proviruses and reveal crosstalk between the HUSH complex and PRC1.6.
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Affiliation(s)
- Tomás C. Rodríguez
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Leonid Yurkovetskiy
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Karthika Nagalekshmi
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Chin Hung Oscar Lam
- Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Eva Jazbec
- Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Stacy A. Maitland
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Scot A. Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Erik J. Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Jeremy Luban
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
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Hyder U, Challa A, Thornton M, Nandu T, Kraus WL, D'Orso I. KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription. Nat Commun 2024; 15:5859. [PMID: 38997286 PMCID: PMC11245487 DOI: 10.1038/s41467-024-49905-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
Signal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction remain poorly understood. By combining an acute depletion system with several genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. Acute KAP1 loss triggers an increase in RNA polymerase II elongation kinetics during early stimulation time points. This elongation defect derails the normal progression through the transcriptional cycle during late stimulation time points, ultimately leading to decreased recruitment of the transcription apparatus for re-initiation thereby dampening IEGs transcriptional output. Collectively, KAP1 plays a counterintuitive role by negatively regulating transcription elongation to support full activation across multiple transcription cycles of genes critical for cell physiology and organismal functions.
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Affiliation(s)
- Usman Hyder
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ashwini Challa
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Micah Thornton
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Iván D'Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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10
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Xiang Y, Mata-Garrido J, Fu Y, Desterke C, Batsché E, Hamaï A, Sedlik C, Sereme Y, Skurnik D, Jalil A, Onifarasoaniaina R, Frapy E, Beche JC, Alao R, Piaggio E, Arbibe L, Chang Y. CBX3 antagonizes IFNγ/STAT1/PD-L1 axis to modulate colon inflammation and CRC chemosensitivity. EMBO Mol Med 2024; 16:1404-1426. [PMID: 38684864 PMCID: PMC11178889 DOI: 10.1038/s44321-024-00066-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 03/27/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024] Open
Abstract
As an important immune stimulator and modulator, IFNγ is crucial for gut homeostasis and its dysregulation links to diverse colon pathologies, such as colitis and colorectal cancer (CRC). Here, we demonstrated that the epigenetic regulator, CBX3 (also known as HP1γ) antagonizes IFNγ signaling in the colon epithelium by transcriptionally repressing two critical IFNγ-responsive genes: STAT1 and CD274 (encoding Programmed death-ligand 1, PD-L1). Accordingly, CBX3 deletion resulted in chronic mouse colon inflammation, accompanied by upregulated STAT1 and CD274 expressions. Chromatin immunoprecipitation indicated that CBX3 tethers to STAT1 and CD274 promoters to inhibit their expression. Reversely, IFNγ significantly reduces CBX3 binding to these promoters and primes gene expression. This antagonist effect between CBX3 and IFNγ on STAT1/PD-L1 expression was also observed in CRC. Strikingly, CBX3 deletion heightened CRC cells sensitivity to IFNγ, which ultimately enhanced their chemosensitivity under IFNγ stimulation in vitro with CRC cells and in vivo with a syngeneic mouse tumor model. Overall, this work reveals that by negatively tuning IFNγ-stimulated immune genes' transcription, CBX3 participates in modulating colon inflammatory response and CRC chemo-resistance.
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Affiliation(s)
- Yao Xiang
- Université Paris Cité, INSERM, CNRS, Institut Necker Enfants Malades, F-75015, Paris, France
| | - Jorge Mata-Garrido
- Université Paris Cité, INSERM, CNRS, Institut Necker Enfants Malades, F-75015, Paris, France
| | - Yuanji Fu
- Université Paris Cité, INSERM, CNRS, Institut Necker Enfants Malades, F-75015, Paris, France
| | - Christophe Desterke
- Université Paris-Saclay, INSERM, Laboratory of Modèles de cellules souches malignes et thérapeutiques, Villejuif, F-94805, France
| | - Eric Batsché
- Sorbonne Université, Institut de Biologie Paris-Seine, CNRS UMR8256 Biological Adaptation and Aging (IBPS), Laboratory of Epigenetics and RNA Metabolism in Human Diseases, 75005, Paris, France
| | - Ahmed Hamaï
- Université Paris Cité, INSERM, CNRS, Institut Necker Enfants Malades, F-75015, Paris, France
| | - Christine Sedlik
- Institut Curie, PSL University, Department of Translational Research, Inserm U932, Laboratory of Immunity and Cancer, F-75005, Paris, France
| | - Youssouf Sereme
- Université Paris Cité, INSERM, CNRS, Institut Necker Enfants Malades, F-75015, Paris, France
| | - David Skurnik
- Université Paris Cité, INSERM, CNRS, Institut Necker Enfants Malades, F-75015, Paris, France
- Service de Bactériologie, virologie, parasitologie et hygiène, AP-HP, Hôpital Necker, F-75015, Paris, France
| | - Abdelali Jalil
- Université Paris Cité, CNRS, SPPIN - Saints-Pères Paris Institute for the Neurosciences, F-75006, Paris, France
| | | | - Eric Frapy
- Université Paris Cité, INSERM, CNRS, Institut Necker Enfants Malades, F-75015, Paris, France
| | - Jean-Christophe Beche
- Laboratory of Expérimentation Animale et Transgénèse SFR Necker-Inserm US 24, Paris, France
| | - Razack Alao
- Laboratory of Expérimentation Animale et Transgénèse SFR Necker-Inserm US 24, Paris, France
| | - Eliane Piaggio
- Institut Curie, PSL University, Department of Translational Research, Inserm U932, Laboratory of Immunity and Cancer, F-75005, Paris, France
| | - Laurence Arbibe
- Université Paris Cité, INSERM, CNRS, Institut Necker Enfants Malades, F-75015, Paris, France
| | - Yunhua Chang
- Université Paris Cité, INSERM, CNRS, Institut Necker Enfants Malades, F-75015, Paris, France.
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11
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Hyder U, Challa A, Thornton M, Nandu T, Kraus WL, D’Orso I. KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.05.592422. [PMID: 38746145 PMCID: PMC11092767 DOI: 10.1101/2024.05.05.592422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Signal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction remain poorly understood. By combining an acute depletion system with high resolution genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. Unexpectedly, acute KAP1 loss triggers an increase in RNA polymerase II elongation kinetics during early stimulation time points. This elongation defect derails the normal progression through the transcriptional cycle during late stimulation time points, ultimately leading to decreased recruitment of the transcription apparatus for re-initiation thereby dampening IEGs transcriptional output. Collectively, KAP1 plays a counterintuitive role by negatively regulating transcription elongation to support full activation across multiple transcription cycles of genes critical for cell physiology and organismal functions.
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Affiliation(s)
- Usman Hyder
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ashwini Challa
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Micah Thornton
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W. Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Iván D’Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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12
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Ding Z, Peng L, Zeng J, Yuan K, Tang Y, Yi Q. Functions of HP1 in preventing chromosomal instability. Cell Biochem Funct 2024; 42:e4017. [PMID: 38603595 DOI: 10.1002/cbf.4017] [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: 12/14/2023] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/13/2024]
Abstract
Chromosomal instability (CIN), caused by errors in the segregation of chromosomes during mitosis, is a hallmark of many types of cancer. The fidelity of chromosome segregation is governed by a sophisticated cellular signaling network, one crucial orchestrator of which is Heterochromatin protein 1 (HP1). HP1 dynamically localizes to distinct sites at various stages of mitosis, where it regulates key mitotic events ranging from chromosome-microtubule attachment to sister chromatid cohesion to cytokinesis. Our evolving comprehension of HP1's multifaceted role has positioned it as a central protein in the orchestration of mitotic processes.
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Affiliation(s)
- Zexian Ding
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, Hunan, China
| | - Lei Peng
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, Hunan, China
| | - Jinghua Zeng
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, Hunan, China
| | - Kejia Yuan
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, Hunan, China
| | - Yan Tang
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, Hunan, China
| | - Qi Yi
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, Hunan, China
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13
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Jiang D, Zhu XL, An Y, Li YR. Clinical significance of small nuclear ribonucleoprotein U1 subunit 70 in patients with hepatocellular carcinoma. PeerJ 2024; 12:e16876. [PMID: 38500533 PMCID: PMC10946392 DOI: 10.7717/peerj.16876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 01/11/2024] [Indexed: 03/20/2024] Open
Abstract
Background & Aims Small nuclear ribonucleoprotein U1 subunit 70 (SNRNP70) as one of the components of the U1 small nuclear ribonucleoprotein (snRNP) is rarely reported in cancers. This study aims to estimate the application potential of SNRNP70 in hepatocellular carcinoma (HCC) clinical practice. Methods Based on the TCGA database and cohort of HCC patients, we investigated the expression patterns and prognostic value of SNRNP70 in HCC. Then, the combination of SNRNP70 and alpha-fetoprotein (AFP) in 278 HCC cases was analyzed. Next, western blotting and immunohistochemistry were used to detect the expression of SNRNP70 in nucleus and cytoplasm. Finally, Cell Counting Kit-8 (CCK-8) and scratch wound healing assays were used to detect the effect of SNRNP70 on the proliferation and migration of HCC cells. Results SNRNP70 was highly expressed in HCC. Its expression was increasingly high during the progression of HCC and was positively related to immune infiltration cells. Higher SNRNP70 expression indicated a poor outcome of HCC patients. In addition, nuclear SNRNP70/AFP combination could be a prognostic biomarker for overall survival and recurrence. Cell experiments confirmed that knockdown of SNRNP70 inhibited the proliferation and migration of HCC cells. Conclusion SNRNP70 may be a new biomarker for HCC progression and HCC diagnosis as well as prognosis. SNRNP70 combined with serum AFP may indicate the prognosis and recurrence status of HCC patients after operation.
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Affiliation(s)
- Dong Jiang
- Department of Ultrasound, Eastern Hepatobiliary Surgery Hospital, The Third Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Xia-Ling Zhu
- Department of Ultrasound, Eastern Hepatobiliary Surgery Hospital, The Third Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Yan An
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi-ran Li
- Department of Intensive Care Medicine, Eastern Hepatobiliary Surgery Hospital, The Third Affiliated Hospital of Naval Medical University, Shanghai, China
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14
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Sokolova V, Miratsky J, Svetlov V, Brenowitz M, Vant J, Lewis T, Dryden K, Lee G, Sarkar S, Nudler E, Singharoy A, Tan D. Structural mechanism of HP1α-dependent transcriptional repression and chromatin compaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569387. [PMID: 38076844 PMCID: PMC10705452 DOI: 10.1101/2023.11.30.569387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Heterochromatin protein 1 (HP1) plays a central role in establishing and maintaining constitutive heterochromatin. However, the mechanisms underlying HP1-nucleosome interactions and their contributions to heterochromatin functions remain elusive. In this study, we employed a multidisciplinary approach to unravel the interactions between human HP1α and nucleosomes. We have elucidated the cryo-EM structure of an HP1α dimer bound to an H2A.Z nucleosome, revealing that the HP1α dimer interfaces with nucleosomes at two distinct sites. The primary binding site is located at the N-terminus of histone H3, specifically at the trimethylated K9 (K9me3) region, while a novel secondary binding site is situated near histone H2B, close to nucleosome superhelical location 4 (SHL4). Our biochemical data further demonstrates that HP1α binding influences the dynamics of DNA on the nucleosome. It promotes DNA unwrapping near the nucleosome entry and exit sites while concurrently restricting DNA accessibility in the vicinity of SHL4. This study offers a model that explains how HP1α functions in heterochromatin maintenance and gene silencing, particularly in the context of H3K9me-dependent mechanisms. Additionally, it sheds light on the H3K9me-independent role of HP1 in responding to DNA damage.
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Affiliation(s)
- Vladyslava Sokolova
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY, USA
| | - Jacob Miratsky
- School of Molecular Sciences, Arizona State University; Tempe, AZ, USA
| | - Vladimir Svetlov
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Michael Brenowitz
- Departments of Biochemistry and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - John Vant
- School of Molecular Sciences, Arizona State University; Tempe, AZ, USA
| | - Tyler Lewis
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY, USA
| | - Kelly Dryden
- Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903 USA
| | - Gahyun Lee
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY, USA
| | - Shayan Sarkar
- Department of Pathology, Stony Brook University; Stony Brook, New York, 11794 USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Dongyan Tan
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY, USA
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15
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Stylianakis E, Chan JPK, Law PP, Jiang Y, Khadayate S, Karimi MM, Festenstein R, Vannier JB. Mouse HP1γ regulates TRF1 expression and telomere stability. Life Sci 2023; 331:122030. [PMID: 37598977 DOI: 10.1016/j.lfs.2023.122030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/22/2023]
Abstract
AIMS Telomeric repeat-containing RNAs are long non-coding RNAs generated from the telomeres. TERRAs are essential for the establishment of heterochromatin marks at telomeres, which serve for the binding of members of the heterochromatin protein 1 (HP1) protein family of epigenetic modifiers involved with chromatin compaction and gene silencing. While HP1γ is enriched on gene bodies of actively transcribed human and mouse genes, it is unclear if its transcriptional role is important for HP1γ function in telomere cohesion and telomere maintenance. We aimed to study the effect of mouse HP1γ on the transcription of telomere factors and molecules that can affect telomere maintenance. MAIN METHODS We investigated the telomere function of HP1γ by using HP1γ deficient mouse embryonic fibroblasts (MEFs). We used gene expression analysis of HP1γ deficient MEFs and validated the molecular and mechanistic consequences of HP1γ loss by telomere FISH, immunofluorescence, RT-qPCR and DNA-RNA immunoprecipitation (DRIP). KEY FINDINGS Loss of HP1γ in primary MEFs led to a downregulation of various telomere and telomere-accessory transcripts, including the shelterin protein TRF1. Its downregulation is associated with increased telomere replication stress and DNA damage (γH2AX), effects more profound in females. We suggest that the source for the impaired telomere maintenance is a consequence of increased telomeric DNA-RNA hybrids and TERRAs arising at and from mouse chromosomes 18 and X. SIGNIFICANCE Our results suggest an important transcriptional control by mouse HP1γ of various telomere factors including TRF1 protein and TERRAs that has profound consequences on telomere stability, with a potential sexually dimorphic nature.
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Affiliation(s)
- Emmanouil Stylianakis
- Telomere Replication & Stability group, Medical Research Council London Institute of Medical Sciences, London, United Kingdom; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom; Gene Control Mechanisms and Disease Group, Faculty of Medicine, Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - Jackson Ping Kei Chan
- Gene Control Mechanisms and Disease Group, Faculty of Medicine, Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - Pui Pik Law
- Gene Control Mechanisms and Disease Group, Faculty of Medicine, Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - Yi Jiang
- Gene Control Mechanisms and Disease Group, Faculty of Medicine, Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - Sanjay Khadayate
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Mohammad Mahdi Karimi
- Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Richard Festenstein
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom; Gene Control Mechanisms and Disease Group, Faculty of Medicine, Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - Jean-Baptiste Vannier
- Telomere Replication & Stability group, Medical Research Council London Institute of Medical Sciences, London, United Kingdom; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom.
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16
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Zukher I, Dujardin G, Sousa-Luís R, Proudfoot NJ. Elongation roadblocks mediated by dCas9 across human genes modulate transcription and nascent RNA processing. Nat Struct Mol Biol 2023; 30:1536-1548. [PMID: 37783853 PMCID: PMC10584677 DOI: 10.1038/s41594-023-01090-9] [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: 06/14/2022] [Accepted: 08/04/2023] [Indexed: 10/04/2023]
Abstract
Non-cleaving Cas9 (dCas9) is widely employed to manipulate specific gene loci, often with scant regard for unintended transcriptional effects. We demonstrate here that dCas9 mediates precise RNA polymerase II transcriptional pausing followed by transcription termination and potential alternative polyadenylation. By contrast, alternative splicing is unaffected, likely requiring more sustained alteration to elongation speed. The effect on transcription is orientation specific, with pausing only being induced when dCas9-associated guide RNA anneals to the non-template strand. Targeting the template strand induces minimal effects on transcription elongation and thus provides a neutral approach to recruit dCas9-linked effector domains to specific gene regions. In essence, we evaluate molecular effects of targeting dCas9 to mammalian transcription units. In so doing, we also provide new information on elongation by RNA polymerase II and coupled pre-mRNA processing.
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Affiliation(s)
- Inna Zukher
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
| | - Gwendal Dujardin
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rui Sousa-Luís
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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17
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Eguchi T, Csizmadia E, Kawai H, Sheta M, Yoshida K, Prince TL, Wegiel B, Calderwood SK. SCAND1 Reverses Epithelial-to-Mesenchymal Transition (EMT) and Suppresses Prostate Cancer Growth and Migration. Cells 2022; 11:cells11243993. [PMID: 36552758 PMCID: PMC9777339 DOI: 10.3390/cells11243993] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a reversible cellular program that transiently places epithelial (E) cells into pseudo-mesenchymal (M) cell states. The malignant progression and resistance of many carcinomas depend on EMT activation, partial EMT, or hybrid E/M status in neoplastic cells. EMT is activated by tumor microenvironmental TGFβ signal and EMT-inducing transcription factors, such as ZEB1/2, in tumor cells. However, reverse EMT factors are less studied. We demonstrate that prostate epithelial transcription factor SCAND1 can reverse the cancer cell mesenchymal and hybrid E/M phenotypes to a more epithelial, less invasive status and inhibit their proliferation and migration in DU-145 prostate cancer cells. SCAND1 is a SCAN domain-containing protein and hetero-oligomerizes with SCAN-zinc finger transcription factors, such as MZF1, for accessing DNA and the transcriptional co-repression of target genes. We found that SCAND1 expression correlated with maintaining epithelial features, whereas the loss of SCAND1 was associated with mesenchymal phenotypes of tumor cells. SCAND1 and MZF1 were mutually inducible and coordinately included in chromatin with hetero-chromatin protein HP1γ. The overexpression of SCAND1 reversed hybrid E/M status into an epithelial phenotype with E-cadherin and β-catenin relocation. Consistently, the co-expression analysis in TCGA PanCancer Atlas revealed that SCAND1 and MZF1 expression was negatively correlated with EMT driver genes, including CTNNB1, ZEB1, ZEB2 and TGFBRs, in prostate adenocarcinoma specimens. In addition, SCAND1 overexpression suppressed tumor cell proliferation by reducing the MAP3K-MEK-ERK signaling pathway. Of note, in a mouse tumor xenograft model, SCAND1 overexpression significantly reduced Ki-67(+) and Vimentin(+) tumor cells and inhibited migration and lymph node metastasis of prostate cancer. Kaplan-Meier analysis showed high expression of SCAND1 and MZF1 to correlate with better prognoses in pancreatic cancer and head and neck cancers, although with poorer prognosis in kidney cancer. Overall, these data suggest that SCAND1 induces expression and coordinated heterochromatin-binding of MZF1 to reverse the hybrid E/M status into an epithelial phenotype and, inhibits tumor cell proliferation, migration, and metastasis, potentially by repressing the gene expression of EMT drivers and the MAP3K-MEK-ERK signaling pathway.
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Affiliation(s)
- Takanori Eguchi
- Department of Dental Pharmacology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
- Correspondence: (T.E.); (S.K.C.); Tel.: +81-86-235-6661 (T.E.); +1-617-667-4240 (S.K.C.); Fax: +81-86-235-6664 (T.E.); +1-617-667-4245 (S.K.C.)
| | - Eva Csizmadia
- Division of Surgical Sciences, Department of Surgery, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Hotaka Kawai
- Department of Oral Pathology and Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
| | - Mona Sheta
- Department of Dental Pharmacology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
- Department of Cancer Biology, National Cancer Institute, Cairo University, Cairo 11796, Egypt
| | - Kunihiro Yoshida
- Department of Dental Pharmacology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
- Department of Oral and Craniofacial Surgery, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
| | | | - Barbara Wegiel
- Division of Surgical Sciences, Department of Surgery, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Stuart K. Calderwood
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
- Correspondence: (T.E.); (S.K.C.); Tel.: +81-86-235-6661 (T.E.); +1-617-667-4240 (S.K.C.); Fax: +81-86-235-6664 (T.E.); +1-617-667-4245 (S.K.C.)
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18
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Zhao Y, Huang S, Tan X, Long L, He Q, Liang X, Bai J, Li Q, Lin J, Li Y, Liu N, Ma J, Chen Y. N 6 -Methyladenosine-Modified CBX1 Regulates Nasopharyngeal Carcinoma Progression Through Heterochromatin Formation and STAT1 Activation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2205091. [PMID: 36310139 PMCID: PMC9798977 DOI: 10.1002/advs.202205091] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Indexed: 05/16/2023]
Abstract
Epitranscriptomic remodeling such as N6 -methyladenosine (m6 A) modification plays a critical role in tumor development. However, little is known about the underlying mechanisms connecting m6 A modification and nasopharyngeal carcinoma (NPC) progression. Here, CBX1 is identified, a histone methylation regulator, to be significantly upregulated with m6 A hypomethylation in metastatic NPC tissues. The m6 A-modified CBX1 mRNA transcript is recognized and destabilized by the m6 A reader YTHDF3. Furthermore, it is revealed that CBX1 promotes NPC cell migration, invasion, and proliferation through transcriptional repression of MAP7 via H3K9me3-mediated heterochromatin formation. In addition to its oncogenic effect, CBX1 can facilitate immune evasion through IFN-γ-STAT1 signaling-mediated PD-L1 upregulation. Clinically, CBX1 serves as an independent predictor for unfavorable prognosis in NPC patients. The results reveal a crosstalk between epitranscriptomic and epigenetic regulation in NPC progression, and shed light on the functions of CBX1 in tumorigenesis and immunomodulation, which may provide an appealing therapeutic target in NPC.
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Affiliation(s)
- Yin Zhao
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Shengyan Huang
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Xirong Tan
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Liufen Long
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Qingmei He
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Xiaoyu Liang
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Jiewen Bai
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Qingjie Li
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Jiayi Lin
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Yingqin Li
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Na Liu
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Jun Ma
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Yupei Chen
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
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19
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The Heterochromatin protein 1 is a regulator in RNA splicing precision deficient in ulcerative colitis. Nat Commun 2022; 13:6834. [PMID: 36400769 PMCID: PMC9674647 DOI: 10.1038/s41467-022-34556-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 10/27/2022] [Indexed: 11/19/2022] Open
Abstract
Defects in RNA splicing have been linked to human disorders, but remain poorly explored in inflammatory bowel disease (IBD). Here, we report that expression of the chromatin and alternative splicing regulator HP1γ is reduced in ulcerative colitis (UC). Accordingly, HP1γ gene inactivation in the mouse gut epithelium triggers IBD-like traits, including inflammation and dysbiosis. In parallel, we find that its loss of function broadly increases splicing noise, favoring the usage of cryptic splice sites at numerous genes with functions in gut biology. This results in the production of progerin, a toxic splice variant of prelamin A mRNA, responsible for the Hutchinson-Gilford Progeria Syndrome of premature aging. Splicing noise is also extensively detected in UC patients in association with inflammation, with progerin transcripts accumulating in the colon mucosa. We propose that monitoring HP1γ activity and RNA splicing precision can help in the management of IBD and, more generally, of accelerated aging.
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20
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Wang D, Li Y, Liu Y, Cheng S, Liu F, Zuo R, Ding C, Shi S, Liu G. NPM1 promotes cell proliferation by targeting PRDX6 in colorectal cancer. Int J Biochem Cell Biol 2022; 147:106233. [PMID: 35659568 DOI: 10.1016/j.biocel.2022.106233] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/29/2022] [Accepted: 05/29/2022] [Indexed: 10/18/2022]
Abstract
Colorectal cancer is a malignant tumor that begins in the colorectal mucosal epithelium. NPM1 is a nucleolar phosphoprotein that has been linked to tumor progression in humans. NPM1 is significantly overexpressed in a variety of tumors, including colorectal cancer, but its role and mechanism in colorectal cancer remain unknown. Therefore, the purpose of this study was to discover the role of NPM1 in promoting colorectal cancer proliferation via PRDX6 and its molecular mechanism. NPM1 knockdown or overexpression inhibited or promoted the proliferation and cell cycle progression of HCT-116 and HT-29 colorectal cancer cells, respectively, according to our findings. Furthermore, NPM1 knockdown or overexpression increased or decreased intracellular ROS levels. Animal experiments revealed that NPM1 knockdown or overexpression inhibited or promoted the growth of colorectal cancer cells transplanted subcutaneously. NPM1 knockdown or overexpression reduced or increased PRDX6 expression and related enzyme activities, respectively, according to our findings. NPM1 formed a complex with CBX3 as evidenced by immunoprecipitation, and the double luciferase reporter gene assay confirmed that the CBX3-NPM1 complex promoted PRDX6 transcription. Our data support the role of NPM1 in promoting the proliferation of colorectal cancer, which may be accomplished by CBX3 promoting the expression of the antioxidant protein PRDX6 and thus inhibiting intracellular ROS levels. NPM1 and PRDX6 are potential colorectal cancer therapeutic targets.
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Affiliation(s)
- Dan Wang
- Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Yin Li
- Department of Medical Examination, Xiamen International Travel Healthcare Center, Xiamen 361000, Fujian, China
| | - Yanling Liu
- School of Pharmaceutical Sciences Xiamen University, Xiamen, Fujian 361102, China
| | - Shuyu Cheng
- Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Fan Liu
- Department of Basic Medicine, Medical College of Xiamen University, Xiamen, Fujian 361002, China
| | - Renjie Zuo
- Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Chenchun Ding
- Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Songlin Shi
- Department of Basic Medicine, Medical College of Xiamen University, Xiamen, Fujian 361002, China.
| | - Guoyan Liu
- Department of Gastrointestinal Surgery, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361002, China; Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China; School of Pharmaceutical Sciences Xiamen University, Xiamen, Fujian 361102, China.
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21
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Schoelz JM, Riddle NC. Functions of HP1 proteins in transcriptional regulation. Epigenetics Chromatin 2022; 15:14. [PMID: 35526078 PMCID: PMC9078007 DOI: 10.1186/s13072-022-00453-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/18/2022] [Indexed: 01/24/2023] Open
Abstract
In eukaryotes, DNA is packaged into chromatin, which presents significant barriers to transcription. Non-histone chromatin proteins such as the Heterochromatin Protein 1 (HP1) proteins are critical regulators of transcription, contributing to gene regulation through a variety of molecular mechanisms. HP1 proteins are highly conserved, and many eukaryotic genomes contain multiple HP1 genes. Given the presence of multiple HP1 family members within a genome, HP1 proteins can have unique as well as shared functions. Here, we review the mechanisms by which HP1 proteins contribute to the regulation of transcription. Focusing on the Drosophila melanogaster HP1 proteins, we examine the role of these proteins in regulating the transcription of genes, transposable elements, and piRNA clusters. In D. melanogaster, as in other species, HP1 proteins can act as transcriptional repressors and activators. The available data reveal that the precise impact of HP1 proteins on gene expression is highly context dependent, on the specific HP1 protein involved, on its protein partners present, and on the specific chromatin context the interaction occurs in. As a group, HP1 proteins utilize a variety of mechanisms to contribute to transcriptional regulation, including both transcriptional (i.e. chromatin-based) and post-transcriptional (i.e. RNA-based) processes. Despite extensive studies of this important protein family, open questions regarding their functions in gene regulation remain, specifically regarding the role of hetero- versus homodimerization and post-translational modifications of HP1 proteins.
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Affiliation(s)
- John M Schoelz
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nicole C Riddle
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
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22
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Zhang P, Yang X, Zha Z, Zhu Y, Zhang G, Li G. CBX3 regulated by miR-139 promotes the development of HCC by regulating cell cycle progression. Cell Cycle 2022; 21:1740-1752. [PMID: 35471148 PMCID: PMC9302499 DOI: 10.1080/15384101.2022.2068329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Hepatocellular carcinoma (HCC), a major primary liver cancer, is one of the most lethal malignancies worldwide. Increasing evidence has demonstrated that chromobox protein homolog 3 (CBX3) functions as an oncogene in different cancers. However, its expression profiles and biological functions in HCC remain unknown. Data on CBX3 expression in HCC acquired from the GEO and TCGA databases were analyzed. The biological functions of CBX3 in HCC were examined by in vitro experiments. Bioinformatics analysis, qRT-PCR and western blotting were performed to explore the mechanism of CBX3 in HCC. CBX3 mRNA was upregulated in HCC tissues, and overexpression of CBX3 mRNA was negatively correlated with malignancies and poor prognosis in HCC patients. CBX3 knockdown decreased growth, migration and invasion of HCC cells in vitro. Moreover, bioinformatics analysis and experimental observation indicated that CBX3 expression was correlated with cell cycle regulatory proteins in HCC cells. Finally, starBase predicted that miR-139 could directly target CBX3 in HCC. Confirmatory experiments verified that miR-139 overexpression attenuated HCC cell proliferation and migration, and these effects could be reversed by overexpressing CBX3. Our results showed that the miR-139/CBX3 axis may be involved in HCC development by regulating cell cycle progression and may be a promising target in the treatment of HCC.
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Affiliation(s)
- Pan Zhang
- Department of Infectious Diseases, Luoyang Central Hospital Affiliated to Zhengzhou University, Henan, Zhengzhou, China
| | - Xiaoyan Yang
- Department of Infectious Diseases, Luoyang Central Hospital Affiliated to Zhengzhou University, Henan, Zhengzhou, China
| | - Zhongming Zha
- Department of Hepatobiliary Surgery, Luoyang Central Hospital Affiliated to Zhengzhou University, Henan, Zhengzhou, China
| | - Yumeng Zhu
- Department of Infectious Diseases, Luoyang Central Hospital Affiliated to Zhengzhou University, Henan, Zhengzhou, China
| | - Guoqiang Zhang
- Department of Infectious Diseases, Luoyang Central Hospital Affiliated to Zhengzhou University, Henan, Zhengzhou, China.,Department of Luoyang, Digestive Diseases Institute, Digestive Disease Center of Luoyang City, Henan, Zhengzhou, China
| | - Guotao Li
- Department of Infectious Diseases, Luoyang Central Hospital Affiliated to Zhengzhou University, Henan, Zhengzhou, China
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23
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Molecular and cytological profiling of biological aging of mouse cochlear inner and outer hair cells. Cell Rep 2022; 39:110665. [PMID: 35417713 PMCID: PMC9069708 DOI: 10.1016/j.celrep.2022.110665] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/08/2022] [Accepted: 03/21/2022] [Indexed: 12/12/2022] Open
Abstract
Age-related hearing loss (ARHL) negatively impacts quality of life in the elderly population. The prevalent cause of ARHL is loss of mechanosensitive cochlear hair cells (HCs). The molecular and cellular mechanisms of HC degeneration remain poorly understood. Using RNA-seq transcriptomic analyses of inner and outer HCs isolated from young and aged mice, we show that HC aging is associated with changes in key molecular processes, including transcription, DNA damage, autophagy, and oxidative stress, as well as genes related to HC specialization. At the cellular level, HC aging is characterized by loss of stereocilia, shrinkage of HC soma, and reduction in outer HC mechanical properties, suggesting that functional decline in mechanotransduction and cochlear amplification precedes HC loss and contributes to ARHL. Our study reveals molecular and cytological profiles of aging HCs and identifies genes such as Sod1, Sirt6, Jund, and Cbx3 as biomarkers and potential therapeutic targets for ameliorating ARHL. Using RNA-seq, advanced imaging, and electrophysiology, Liu et al. reveal molecular and cytological profiles of aging cochlear hair cells. Their study also suggests that a functional decline in mechanotransduction and cochlear amplification precedes hair cell loss and contributes to age-related hearing loss.
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24
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Lu M, Yuan B, Yan X, Sun Z, Lillehoj HS, Lee Y, Baldwin-Bott C, Li C. Clostridium perfringens-Induced Host-Pathogen Transcriptional Changes in the Small Intestine of Broiler Chickens. Pathogens 2021; 10:pathogens10121607. [PMID: 34959561 PMCID: PMC8705629 DOI: 10.3390/pathogens10121607] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/26/2021] [Accepted: 12/04/2021] [Indexed: 11/16/2022] Open
Abstract
Clostridium perfringens is an important opportunistic pathogen that may result in toxin-mediated diseases involving food poisoning/tissue gangrene in humans and various enterotoxaemia in animal species. It is a main etiological agent for necrotic enteritis (NE), the most financially devastating bacterial disease in broiler chickens, especially if raised under antibiotic-free conditions. Importantly, NE is responsible for losses of six billion US dollars annually in the global poultry industry. To investigate the molecular mechanisms of C. perfringens-induced pathogenesis in the gut and its microbiome mRNA levels in C. perfringens-infected and non-infected hosts, we used RNA sequencing technology to perform transcriptional analysis of both host intestine and microbiome using our NE model. The growth rate was significantly impaired in chickens infected by C. perfringens. In total, 13,473 annotated chicken genes were differentially expressed between these two groups, with ninety-six genes showing statistical significance (|absolute fold changes| > 2.0, adjusted p value < 0.05). Genes involved in energy production, MHC Class I antigen, translation, ribosomal structures, and amino acid, nucleotide and carbohydrate metabolism from infected gut tissues were significantly down-regulated. The upregulated genes were mainly engaged in innate and adaptive immunity, cellular processes, genetic information processing, and organismal systems. Additionally, the transcriptional levels of four crucial foodborne pathogens were significantly elevated in a synergic relationship with pathogenic C. perfringens infection. This study presents the profiling data that would likely be a relevant reference for NE pathogenesis and may provide new insights into the mechanism of host-pathogen interaction in C. perfringens-induced NE infection in broiler chickens.
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Affiliation(s)
- Mingmin Lu
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service-US Department of Agriculture, Beltsville, MD 20705, USA; (M.L.); (B.Y.); (Z.S.); (H.S.L.); (Y.L.); (C.B.-B.)
| | - Baohong Yuan
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service-US Department of Agriculture, Beltsville, MD 20705, USA; (M.L.); (B.Y.); (Z.S.); (H.S.L.); (Y.L.); (C.B.-B.)
- School of Basic Medicine Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Xianghe Yan
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service-US Department of Agriculture, Beltsville, MD 20705, USA
- Correspondence: (X.Y.); (C.L.)
| | - Zhifeng Sun
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service-US Department of Agriculture, Beltsville, MD 20705, USA; (M.L.); (B.Y.); (Z.S.); (H.S.L.); (Y.L.); (C.B.-B.)
| | - Hyun S. Lillehoj
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service-US Department of Agriculture, Beltsville, MD 20705, USA; (M.L.); (B.Y.); (Z.S.); (H.S.L.); (Y.L.); (C.B.-B.)
| | - Youngsub Lee
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service-US Department of Agriculture, Beltsville, MD 20705, USA; (M.L.); (B.Y.); (Z.S.); (H.S.L.); (Y.L.); (C.B.-B.)
| | - Calder Baldwin-Bott
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service-US Department of Agriculture, Beltsville, MD 20705, USA; (M.L.); (B.Y.); (Z.S.); (H.S.L.); (Y.L.); (C.B.-B.)
- Eleanor Roosevelt High School, Greenbelt, MD 20770, USA
| | - Charles Li
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service-US Department of Agriculture, Beltsville, MD 20705, USA; (M.L.); (B.Y.); (Z.S.); (H.S.L.); (Y.L.); (C.B.-B.)
- Correspondence: (X.Y.); (C.L.)
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25
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Kleene R, Loers G, Castillo G, Schachner M. Cell adhesion molecule L1 interacts with the chromo shadow domain of heterochromatin protein 1 isoforms α, β, and ɣ via its intracellular domain. FASEB J 2021; 36:e22074. [PMID: 34859928 DOI: 10.1096/fj.202100816r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 11/01/2021] [Accepted: 11/15/2021] [Indexed: 11/11/2022]
Abstract
Cell adhesion molecule L1 regulates multiple cell functions and L1 deficiency is linked to several neural diseases. Proteolytic processing generates functionally decisive L1 fragments, which are imported into the nucleus. By computational analysis, we found at L1's C-terminal end the chromo shadow domain-binding motif PxVxL, which directs the binding of nuclear proteins to the heterochromatin protein 1 (HP1) isoforms α, β, and ɣ. By enzyme-linked immunosorbent assay, we show that the intracellular L1 domain binds to all HP1 isoforms. These interactions involve the HP1 chromo shadow domain and are mediated via the sequence 1158 KDET1161 in the intracellular domain of murine L1, but not by L1's C-terminal PxVxL motif. Immunoprecipitation using nuclear extracts from the brain and from cultured cerebellar and cortical neurons indicates that HP1 isoforms interact with a yet unknown nuclear L1 fragment of approximately 55 kDa (L1-55), which carries ubiquitin residues. Proximity ligation indicates a close association between L1-55 and the HP1 isoforms in neuronal nuclei. This association is reduced after the treatment of neurons with inhibitors of metalloproteases, β-site of amyloid precursor protein cleaving enzyme (BACE1), or ɣ-secretase, suggesting that cleavage of full-length L1 by these proteases generates L1-55. Reduction of HP1α, -β, or -ɣ expression by siRNA decreases L1-dependent neurite outgrowth from cultured cortical neurons and decreases the L1-dependent migration of L1-transfected HEK293 cells in a scratch assay. These findings indicate that the interaction of the novel fragment L1-55 with HP1 isoforms in nuclei affects L1-dependent functions, such as neurite outgrowth and neuronal migration.
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Affiliation(s)
- Ralf Kleene
- Research Group Biosynthesis of Neural Structures, Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Gabriele Loers
- Research Group Biosynthesis of Neural Structures, Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Gaston Castillo
- Research Group Biosynthesis of Neural Structures, Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Melitta Schachner
- Department of Cell Biology and Neuroscience, Keck Center for Collaborative Neuroscience, Rutgers University, Piscataway, New Jersey, USA
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26
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Le PT, Ha N, Tran NK, Newman AG, Esselen KM, Dalrymple JL, Schmelz EM, Bhandoola A, Xue HH, Singh PB, Thai TH. Targeting Cbx3/HP1γ Induces LEF-1 and IL-21R to Promote Tumor-Infiltrating CD8 T-Cell Persistence. Front Immunol 2021; 12:738958. [PMID: 34721405 PMCID: PMC8549513 DOI: 10.3389/fimmu.2021.738958] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/08/2021] [Indexed: 11/13/2022] Open
Abstract
Immune checkpoint blockade (ICB) relieves CD8+ T-cell exhaustion in most mutated tumors, and TCF-1 is implicated in converting progenitor exhausted cells to functional effector cells. However, identifying mechanisms that can prevent functional senescence and potentiate CD8+ T-cell persistence for ICB non-responsive and resistant tumors remains elusive. We demonstrate that targeting Cbx3/HP1γ in CD8+ T cells augments transcription initiation and chromatin remodeling leading to increased transcriptional activity at Lef1 and Il21r. LEF-1 and IL-21R are necessary for Cbx3/HP1γ-deficient CD8+ effector T cells to persist and control ovarian cancer, melanoma, and neuroblastoma in preclinical models. The enhanced persistence of Cbx3/HP1γ-deficient CD8+ T cells facilitates remodeling of the tumor chemokine/receptor landscape ensuring their optimal invasion at the expense of CD4+ Tregs. Thus, CD8+ T cells heightened effector function consequent to Cbx3/HP1γ deficiency may be distinct from functional reactivation by ICB, implicating Cbx3/HP1γ as a viable cancer T-cell-based therapy target for ICB resistant, non-responsive solid tumors.
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Affiliation(s)
- Phuong T Le
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Ngoc Ha
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Ngan K Tran
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Andrew G Newman
- Institute of Cell and Neurobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Katharine M Esselen
- Division of Gynecologic Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - John L Dalrymple
- Division of Gynecologic Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Eva M Schmelz
- Department of Human Nutrition, Food, and Exercise, Virginia Tech, Blacksburg, VA, United States
| | - Avinash Bhandoola
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Hai-Hui Xue
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ, United States
| | - Prim B Singh
- Nazarbayev University School of Medicine, Nur-Sultan, Kazakhstan
| | - To-Ha Thai
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States.,Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
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27
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Long J, Long T, Li Y, Yuan P, Liu K, Li J, Cheng L. A Functional Polymorphism in Accessible Chromatin Region Confers Risk of Non-Small Cell Lung Cancer in Chinese Population. Front Oncol 2021; 11:698993. [PMID: 34552866 PMCID: PMC8450516 DOI: 10.3389/fonc.2021.698993] [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: 04/22/2021] [Accepted: 08/17/2021] [Indexed: 11/21/2022] Open
Abstract
Background The disease-associated non-coding variants identified by genome-wide association studies (GWASs) were enriched in open chromatin regions (OCRs) and implicated in gene regulation. Genetic variants in OCRs thus may exert regulatory functions and contribute to non-small cell lung cancer (NSCLC) susceptibility. Objective To fine map potential functional variants in GWAS loci that contribute to NSCLC predisposition using chromatin accessibility and histone modification data and explore their functions by population study and biochemical experimental analyses. Methods We mapped the chromatin accessible regions of lung tissues using data of assay for transposase-accessible chromatin using sequencing (ATAC-seq) in The Cancer Genome Atlas (TCGA) and prioritized potential regulatory variants within lung cancer GWAS loci by aligning with histone signatures using data of chromatin immunoprecipitation assays followed by sequencing (ChIP-seq) in the Encyclopedia of DNA Elements (ENCODE). A two-stage case–control study with 1,830 cases and 2,001 controls was conducted to explore the associations between candidate variants and NSCLC risk in Chinese population. Bioinformatic annotations and biochemical experiments were performed to further reveal the potential functions of significant variants. Results Sixteen potential functional single-nucleotide polymorphisms (SNPs) were selected as candidates from bioinformatics analyses. Three variants out of the 16 candidate SNPs survived after genotyping in stage 1 case–control study, and only the results of SNP rs13064999 were successfully validated in the analyses of stage 2 case–control study. In combined analyses, rs13064999 was significantly associated with NSCLC risk [additive model; odds ratio (OR) = 1.17; 95%CI, 1.07–1.29; p = 0.001]. Functional annotations indicated its potential enhancer bioactivity, and dual-luciferase reporter assays revealed a significant increase in luciferase activity for the reconstructed plasmid with rs13064999 A allele, when compared to the one with wild-type G allele (pA549 < 0.001, pSK-MES-1 = 0.004). Further electrophoretic mobility shift assays (EMSA) and super-shift assays confirmed a stronger affinity of HP1γ for the binding motif containing SNP rs13064999 A allele. Conclusion These findings suggested that the functional variant rs13064999, identified by the integration of ATAC-seq and ChIP-seq data, contributes to the susceptibility of NSCLC by affecting HP1γ binding, while the exact biological mechanism awaits further exploration.
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Affiliation(s)
- Jieyi Long
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tingting Long
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peihong Yuan
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ke Liu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiaoyuan Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liming Cheng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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28
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Rachez C, Legendre R, Costallat M, Varet H, Yi J, Kornobis E, Muchardt C. HP1γ binding pre-mRNA intronic repeats modulates RNA splicing decisions. EMBO Rep 2021; 22:e52320. [PMID: 34312949 DOI: 10.15252/embr.202052320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 06/17/2021] [Accepted: 06/22/2021] [Indexed: 12/30/2022] Open
Abstract
HP1 proteins are best known as markers of heterochromatin and gene silencing. Yet, they are also RNA-binding proteins and the HP1γ/CBX3 family member is present on transcribed genes together with RNA polymerase II, where it regulates co-transcriptional processes such as alternative splicing. To gain insight in the role of the RNA-binding activity of HP1γ in transcriptionally active chromatin, we have captured and analysed RNAs associated with this protein. We find that HP1γ is specifically targeted to hexameric RNA motifs and coincidentally transposable elements of the SINE family. As these elements are abundant in introns, while essentially absent from exons, the HP1γ RNA association tethers unspliced pre-mRNA to chromatin via the intronic regions and limits the usage of intronic cryptic splice sites. Thus, our data unveil novel determinants in the relationship between chromatin and co-transcriptional splicing.
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Affiliation(s)
- Christophe Rachez
- Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France.,CNRS UMR 8256, Biological Adaptation and Aging, Paris, France.,Epigenetic Regulation Unit, Institut Pasteur, CNRS UMR 3738, Paris, France
| | - Rachel Legendre
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, USR 3756 CNRS, Paris, France.,Biomics Technological Platform, Center for Technological Resources and Research, Institut Pasteur, Paris, France
| | - Mickaël Costallat
- Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France.,CNRS UMR 8256, Biological Adaptation and Aging, Paris, France.,Epigenetic Regulation Unit, Institut Pasteur, CNRS UMR 3738, Paris, France
| | - Hugo Varet
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, USR 3756 CNRS, Paris, France.,Biomics Technological Platform, Center for Technological Resources and Research, Institut Pasteur, Paris, France
| | - Jia Yi
- Epigenetic Regulation Unit, Institut Pasteur, CNRS UMR 3738, Paris, France.,Sorbonne Université, Ecole Doctorale Complexité du Vivant (ED515), Paris, France
| | - Etienne Kornobis
- Epigenetic Regulation Unit, Institut Pasteur, CNRS UMR 3738, Paris, France
| | - Christian Muchardt
- Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France.,CNRS UMR 8256, Biological Adaptation and Aging, Paris, France.,Epigenetic Regulation Unit, Institut Pasteur, CNRS UMR 3738, Paris, France
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29
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Vodnala M, Choi EB, Fong YW. Low complexity domains, condensates, and stem cell pluripotency. World J Stem Cells 2021; 13:416-438. [PMID: 34136073 PMCID: PMC8176841 DOI: 10.4252/wjsc.v13.i5.416] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 02/06/2023] Open
Abstract
Biological reactions require self-assembly of factors in the complex cellular milieu. Recent evidence indicates that intrinsically disordered, low-complexity sequence domains (LCDs) found in regulatory factors mediate diverse cellular processes from gene expression to DNA repair to signal transduction, by enriching specific biomolecules in membraneless compartments or hubs that may undergo liquid-liquid phase separation (LLPS). In this review, we discuss how embryonic stem cells take advantage of LCD-driven interactions to promote cell-specific transcription, DNA damage response, and DNA repair. We propose that LCD-mediated interactions play key roles in stem cell maintenance and safeguarding genome integrity.
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Affiliation(s)
- Munender Vodnala
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
| | - Eun-Bee Choi
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
| | - Yick W Fong
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
- Harvard Stem Cell Institute, Cambridge, MA 02138, United States.
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30
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Sena RM, Twiss JL, Gardiner AS, Dell’Orco M, Linsenbardt DN, Perrone-Bizzozero NI. The RNA-Binding Protein HuD Regulates Alternative Splicing and Alternative Polyadenylation in the Mouse Neocortex. Molecules 2021; 26:2836. [PMID: 34064652 PMCID: PMC8151252 DOI: 10.3390/molecules26102836] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 11/18/2022] Open
Abstract
The neuronal Hu/ELAV-like proteins HuB, HuC and HuD are a class of RNA-binding proteins that are crucial for proper development and maintenance of the nervous system. These proteins bind to AU-rich elements (AREs) in the untranslated regions (3'-UTRs) of target mRNAs regulating mRNA stability, transport and translation. In addition to these cytoplasmic functions, Hu proteins have been implicated in alternative splicing and alternative polyadenylation in the nucleus. The purpose of this study was to identify transcriptome-wide effects of HuD deletion on both of these nuclear events using RNA sequencing data obtained from the neocortex of Elavl4-/- (HuD KO) mice. HuD KO affected alternative splicing of 310 genes, including 17 validated HuD targets such as Cbx3, Cspp1, Snap25 and Gria2. In addition, deletion of HuD affected polyadenylation of 53 genes, with the majority of significantly altered mRNAs shifting towards usage of proximal polyadenylation signals (PAS), resulting in shorter 3'-UTRs. None of these genes overlapped with those showing alternative splicing events. Overall, HuD KO had a greater effect on alternative splicing than polyadenylation, with many of the affected genes implicated in several neuronal functions and neuropsychiatric disorders.
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Affiliation(s)
- Rebecca M. Sena
- Department Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; (R.M.S.); (A.S.G.); (M.D.)
| | - Jeffery L. Twiss
- Department Biological Sciences, University of South Carolina, Columbia, SC 29208, USA;
| | - Amy S. Gardiner
- Department Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; (R.M.S.); (A.S.G.); (M.D.)
- Department Cell Biology and Physiology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
| | - Michela Dell’Orco
- Department Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; (R.M.S.); (A.S.G.); (M.D.)
| | - David N. Linsenbardt
- Department Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; (R.M.S.); (A.S.G.); (M.D.)
| | - Nora I. Perrone-Bizzozero
- Department Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; (R.M.S.); (A.S.G.); (M.D.)
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31
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Alphonse N, Dickenson RE, Odendall C. Interferons: Tug of War Between Bacteria and Their Host. Front Cell Infect Microbiol 2021; 11:624094. [PMID: 33777837 PMCID: PMC7988231 DOI: 10.3389/fcimb.2021.624094] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/05/2021] [Indexed: 12/30/2022] Open
Abstract
Type I and III interferons (IFNs) are archetypally antiviral cytokines that are induced in response to recognition of foreign material by pattern recognition receptors (PRRs). Though their roles in anti-viral immunity are well established, recent evidence suggests that they are also crucial mediators of inflammatory processes during bacterial infections. Type I and III IFNs restrict bacterial infection in vitro and in some in vivo contexts. IFNs mainly function through the induction of hundreds of IFN-stimulated genes (ISGs). These include PRRs and regulators of antimicrobial signaling pathways. Other ISGs directly restrict bacterial invasion or multiplication within host cells. As they regulate a diverse range of anti-bacterial host responses, IFNs are an attractive virulence target for bacterial pathogens. This review will discuss the current understanding of the bacterial effectors that manipulate the different stages of the host IFN response: IFN induction, downstream signaling pathways, and target ISGs.
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Affiliation(s)
- Noémie Alphonse
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
- Immunoregulation Laboratory, Francis Crick Institute, London, United Kingdom
| | - Ruth E. Dickenson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Charlotte Odendall
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
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32
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Puri D, Swamy CVB, Dhawan J, Mishra RK. Comparative nuclear matrix proteome analysis of skeletal muscle cells in different cellular states. Cell Biol Int 2021; 45:580-598. [PMID: 33200434 DOI: 10.1002/cbin.11499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/01/2020] [Accepted: 11/11/2020] [Indexed: 12/20/2022]
Abstract
The nuclear matrix (NuMat) serves as the structural framework for organizing and maintaining nuclear architecture, however, the mechanisms by which this non-chromatin compartment is constructed and regulated are poorly understood. This study presents a proteomic analysis of the NuMat isolated from cultured skeletal muscle cells in three distinct cellular states- proliferating myoblasts (MBs), terminally differentiated myotubes (MTs), and mitotically quiescent (G0) myoblasts. About 40% of the proteins identified were found to be common in the NuMat proteome of these morphologically and functionally distinct cell states. These proteins, termed as the "core NuMat," define the stable, conserved, structural constituent of the nucleus, with functions such as RNA splicing, cytoskeletal organization, and chromatin modification, while the remaining NuMat proteins showed cell-state specificity, consistent with a more dynamic and potentially regulatory function. Specifically, myoblast NuMat was enriched in cell cycle, DNA replication and repair proteins, myotube NuMat in muscle differentiation and muscle function proteins, while G0 NuMat was enriched in metabolic, transcription, and transport proteins. These findings offer a new perspective for a cell-state-specific role of nuclear architecture and spatial organization, integrated with diverse cellular processes, and implicate NuMat proteins in the control of the cell cycle, lineage commitment, and differentiation.
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Affiliation(s)
- Deepika Puri
- Centre for Cellular and Molecular Biology, Council for Scientific and Industrial Research, Hyderabad, India
| | - Ch V B Swamy
- Centre for Cellular and Molecular Biology, Council for Scientific and Industrial Research, Hyderabad, India
| | - Jyotsna Dhawan
- Centre for Cellular and Molecular Biology, Council for Scientific and Industrial Research, Hyderabad, India
| | - Rakesh K Mishra
- Centre for Cellular and Molecular Biology, Council for Scientific and Industrial Research, Hyderabad, India
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33
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Zaidan NZ, Sridharan R. HP1γ regulates H3K36 methylation and pluripotency in embryonic stem cells. Nucleic Acids Res 2020; 48:12660-12674. [PMID: 33237287 PMCID: PMC7736818 DOI: 10.1093/nar/gkaa1091] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 10/12/2020] [Accepted: 10/27/2020] [Indexed: 01/01/2023] Open
Abstract
The heterochromatin protein 1 (HP1) family members are canonical effectors and propagators of gene repression mediated by histone H3 lysine 9 (H3K9) methylation. HP1γ exhibits an increased interaction with active transcription elongation-associated factors in embryonic stem cells (ESCs) compared to somatic cells. However, whether this association has a functional consequence remains elusive. Here we find that genic HP1γ colocalizes and enhances enrichment of transcription elongation-associated H3K36me3 rather than H3K9me3. Unexpectedly, sustained H3K36me3 deposition is dependent on HP1γ. HP1γ-deleted ESCs display reduced H3K36me3 enrichment, concomitant with decreased expression at shared genes which function to maintain cellular homeostasis. Both the H3K9me3-binding chromodomain and histone binding ability of HP1γ are dispensable for maintaining H3K36me3 levels. Instead, the chromoshadow together with the hinge domain of HP1γ that confer protein and nucleic acid-binding ability are sufficient because they retain the ability to interact with NSD1, an H3K36 methyltransferase. HP1γ-deleted ESCs have a slower self-renewal rate and an impaired ability to differentiate towards cardiac mesoderm. Our findings reveal a requirement for HP1γ in faithful establishment of transcription elongation in ESCs, which regulates pluripotency.
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Affiliation(s)
- Nur Zafirah Zaidan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA.,Genetics Training Program, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA.,Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53715, USA
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34
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Lin H, Lian J, Xia L, Guan G, You J. CBX3 Promotes Gastric Cancer Progression and Affects Factors Related to Immunotherapeutic Responses. Cancer Manag Res 2020; 12:10113-10125. [PMID: 33116867 PMCID: PMC7569062 DOI: 10.2147/cmar.s271807] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/16/2020] [Indexed: 12/13/2022] Open
Abstract
Background Chromobox 3 (CBX3) is a member of the chromobox family proteins, which plays a critical role in tumor progression, but the exact function of CBX3 in gastric cancer remains unknown. The current research mainly investigates the underlying mechanisms and clinical value of CBX3 in gastric cancer. Methods Gene expression cohorts from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were analyzed to assess the effect of CBX3 in gastric cancer. CBX3 expression was further determined by immunohistochemistry (IHC). The function of CBX3 on proliferation, migration and the cell cycle was explored via colony-forming, cell cycle and transwell assays, respectively. Moreover, RNA sequencing (RNA-seq) in AGS cells and two cohorts was utilized to explore the specific mechanism of CBX3. Results CBX3 expression was upregulated in human gastric cancer tissues and the expression level was closely associated with adverse signs. Knockdown of CBX3 in gastric cancer cells significantly inhibited the malignant phenotype. In addition, RNA-seq analysis revealed that CBX3 regulates genes related to the cell cycle, mismatch repair and immune-related pathways. Furthermore, the expression of CBX3 was significantly and inversely related to the abundance of tumor-infiltrating lymphocytes (TILs), PDCD1 and PDCD1LG2 expression and immunotherapy responses. Moreover, CBX3 influences the effectiveness of chemotherapy, thereby impacting the prognosis of gastric cancer patients. Conclusion CBX3 contributes to gastric cancer progression and is associated with chemotherapy and immunotherapy response. CBX3 may serve as a new diagnostic biomarker and potential target for immunotherapy and chemotherapy in gastric cancer.
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Affiliation(s)
- Hexin Lin
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, People's Republic of China.,Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Jiabian Lian
- Department of Laboratory Medicine, Xiamen Key Laboratory of Genetic Testing, The First Affiliated Hospital of Xiamen University, Xiamen, People's Republic of China.,School of Clinical Medicine, Fujian Medical University, Fuzhou, People's Republic of China
| | - Lu Xia
- School of Clinical Medicine, Fujian Medical University, Fuzhou, People's Republic of China.,Laboratory of Cancer Center, The First Affiliated Hospital of Xiamen University, Xiamen, People's Republic of China
| | - Guoxian Guan
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Jun You
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, People's Republic of China.,School of Clinical Medicine, Fujian Medical University, Fuzhou, People's Republic of China
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35
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He Z, Chen J, Chen X, Wang H, Tang L, Han C. microRNA-377 acts as a suppressor in esophageal squamous cell carcinoma through CBX3-dependent P53/P21 pathway. J Cell Physiol 2020; 236:107-120. [PMID: 33459391 DOI: 10.1002/jcp.29631] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 01/30/2020] [Indexed: 12/19/2022]
Abstract
Stem cells play pivotal roles in esophageal squamous cell carcinoma (ESCC) recurrence and metastasis. The self-renewal ability of stem cells was associated with specific microRNAs (miRs). Herein, we identified the effects of miR-377 on ESCC stem cell activities. First, the expression of miR-377 in ESCC and adjacent normal tissues was determined. The relationship between miR-377 and chromobox protein homolog 3 (CBX3) was assessed by a dual-luciferase reporter gene assay. miR-377 was overexpressed or inhibited in ESCC stem cells to explore its role in ESCC. To further investigate the mechanism of miR-377 in ESCC, cells were introduced with short hairpin RNA against CBX3 or pifithrin-α (inhibitor of P53 pathway). Besides, the expression of P21, P53, CD133, CD13, Nanog, sex determining region Y-Box 2 (Sox2), and octamer-binding transcription factor 4 (Oct4), cell sphere formation, colony formation, and proliferation were evaluated respectively. Finally, limiting dilution assay in vivo and tumor xenograft in nude mice were conducted to confirm the roles of miR-377 in vivo. miR-377 was poorly expressed in ESCC. Overexpression of miR-377 could suppress the stem-like trait of ESCC as well as the tumor growth in vivo. miR-377 targeted CBX3 to activate the P53/P21 pathway. Besides, the expression of stem-like markers including CD133, CD13, Oct4, Sox2, and Nanog was decreased, and the abilities of cell sphere formation, colony formation, proliferation, and tumorigenicity were significantly reduced by overexpressing miR-377 or silencing CBX3. The results were reversed after inactivating the P53/P21 pathway. In summary, upregulation of miR-377 inhibits the self-renewal of ESCC stem cells by inhibiting CBX3 expression and promoting activation of the P53/P21 pathway.
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Affiliation(s)
- Zhisheng He
- Department of Thoracic Surgery Oncology, Jiangxi Cancer Hospital, Nanchang, China
| | - Junjing Chen
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang, China
| | - Xiaoliang Chen
- Department of Thoracic Surgery Oncology, Jiangxi Cancer Hospital, Nanchang, China
| | - Huanyuan Wang
- Department of Thoracic Surgery Oncology, Jiangxi Cancer Hospital, Nanchang, China
| | - Lang Tang
- Department of Thoracic Surgery Oncology, Jiangxi Cancer Hospital, Nanchang, China
| | - Chunbin Han
- Department of Thoracic Surgery Oncology, Jiangxi Cancer Hospital, Nanchang, China
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36
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Singh PB, Belyakin SN, Laktionov PP. Biology and Physics of Heterochromatin- Like Domains/Complexes. Cells 2020; 9:E1881. [PMID: 32796726 PMCID: PMC7465696 DOI: 10.3390/cells9081881] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 07/29/2020] [Accepted: 08/04/2020] [Indexed: 11/17/2022] Open
Abstract
The hallmarks of constitutive heterochromatin, HP1 and H3K9me2/3, assemble heterochromatin-like domains/complexes outside canonical constitutively heterochromatic territories where they regulate chromatin template-dependent processes. Domains are more than 100 kb in size; complexes less than 100 kb. They are present in the genomes of organisms ranging from fission yeast to human, with an expansion in size and number in mammals. Some of the likely functions of domains/complexes include silencing of the donor mating type region in fission yeast, preservation of DNA methylation at imprinted germline differentially methylated regions (gDMRs) and regulation of the phylotypic progression during vertebrate development. Far cis- and trans-contacts between micro-phase separated domains/complexes in mammalian nuclei contribute to the emergence of epigenetic compartmental domains (ECDs) detected in Hi-C maps. A thermodynamic description of micro-phase separation of heterochromatin-like domains/complexes may require a gestalt shift away from the monomer as the "unit of incompatibility" that determines the sign and magnitude of the Flory-Huggins parameter, χ. Instead, a more dynamic structure, the oligo-nucleosomal "clutch", consisting of between 2 and 10 nucleosomes is both the long sought-after secondary structure of chromatin and its unit of incompatibility. Based on this assumption we present a simple theoretical framework that enables an estimation of χ for domains/complexes flanked by euchromatin and thereby an indication of their tendency to phase separate. The degree of phase separation is specified by χN, where N is the number of "clutches" in a domain/complex. Our approach could provide an additional tool for understanding the biophysics of the 3D genome.
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Affiliation(s)
- Prim B. Singh
- Nazarbayev University School of Medicine, Nur-Sultan City 010000, Kazakhstan
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Stepan N. Belyakin
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Genomics laboratory, Institute of molecular and cellular biology SD RAS, Lavrentyev ave, 8/2, 630090 Novosibirsk, Russia; (S.N.B.); (P.P.L.)
| | - Petr P. Laktionov
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Genomics laboratory, Institute of molecular and cellular biology SD RAS, Lavrentyev ave, 8/2, 630090 Novosibirsk, Russia; (S.N.B.); (P.P.L.)
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Xu Y, Pan S, Song Y, Pan C, Chen C, Zhu X. The Prognostic Value of the Chromobox Family in Human Ovarian Cancer. J Cancer 2020; 11:5198-5209. [PMID: 32742466 PMCID: PMC7378907 DOI: 10.7150/jca.44475] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 06/15/2020] [Indexed: 12/18/2022] Open
Abstract
Ovarian cancer is one of the most lethal gynecologic tumors in women and has a poor prognosis. The purpose of our study was to identify new prognostic markers in ovarian cancer. We examined the prognostic roles of mRNA expression of the chromobox (CBX) family in patients with ovarian cancer utilizing the Kaplan-Meier plotter database. The prognostic values and expression levels of CBX members associated with prognosis were further evaluated using KM plotter in diverse subgroups and immunohistochemistry (IHC) analysis in ovarian carcinoma. The results revealed that elevated CBX1-3 mRNA expression may predict poor overall survival (OS) and progression-free survival (PFS) outcomes in patients with ovarian cancer. Notably, in women with ovarian cancer, increased CBX1 mRNA expression was linked to a short OS in all stages and in the grade II and grade III subgroups. Additionally, CBX2 and CBX3 were strongly related to short OS in stage III+IV patients, and a link between high CBX3 mRNA expression and unfavorable OS in grade II patients was observed. High expression levels of CBX1 and CBX3 were significantly associated with chemotherapy resistance in ovarian cancer patients. IHC staining showed that the CBX1-3 proteins were upregulated in serous ovarian carcinoma tissues compared with normal ovarian tissues. Therefore, our results indicated that CBX1-3 could be attractive biomarkers for predicting poor prognosis of ovarian cancer.
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Affiliation(s)
| | | | | | | | | | - Xueqiong Zhu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Cytotoxic potential of Artemisia absinthium extract loaded polymeric nanoparticles against breast cancer cells: Insight into the protein targets. Int J Pharm 2020; 586:119583. [PMID: 32603837 DOI: 10.1016/j.ijpharm.2020.119583] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 06/18/2020] [Accepted: 06/23/2020] [Indexed: 12/26/2022]
Abstract
Targeted drug delivery system in the form of herbal based nano-formulations is the new ray of hope for minimizing the side effects related to the anti-cancer drugs as well as conventional drug delivery system. In view of this, the present study was designed to evaluate the cytotoxic potential of A. absinthium extract loaded polymeric nanoparticles (NVA-AA) against the breast cancer cell lines (MCF-7 and MDA MB-231) and to identify the protein targets for the caused cytotoxicity. The polymeric nanoparticles (PNPs) were prepared by free radical mechanism and loaded with the whole plant extract. The cytotoxicity of these NVA-AA were evaluated on the breast cancer cell lines via different cytotoxic parameters viz. MTT assay, CFSE proliferation assay, apoptosis assay, cell cycle study. The protein targets and the interaction among them were identified by nano-LCMS/MS analysis and STRING online tool respectively, which were further validated by qPCR and BLI. The LCMS/MS analysis suggests that the caused cytotoxicity was due to the alteration of proteins involved in vesicular trafficking, apoptosis, proliferation and metastasis. Further, interactome analysis identified UBA52 in MCF-7 and TIAL1, PPP1CC in MDA MB-231 cells as the central molecule in the vesicular trafficking and apoptosis networking connection.
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Zhong X, Kan A, Zhang W, Zhou J, Zhang H, Chen J, Tang S. CBX3/HP1γ promotes tumor proliferation and predicts poor survival in hepatocellular carcinoma. Aging (Albany NY) 2019; 11:5483-5497. [PMID: 31375643 PMCID: PMC6710055 DOI: 10.18632/aging.102132] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/26/2019] [Indexed: 02/05/2023]
Abstract
HP1γ, encoded by CBX3, is associated with cancer progression and patient prognosis. However, the prognostic value and functions of CBX3/HP1γ in hepatocellular carcinoma (HCC) remain unclear. Here, we performed a bioinformatics analysis using the Oncomine, TCGA and Human Protein Atlas databases, the Kaplan-Meier plotter, and the UALCAN web-portal to explore the expression and prognostic significance of CBX3/HP1γ in patients with different cancers, including liver cancer. HCC tissues and microarrays containing 354 samples were examined using immunohistochemical staining, quantitative real-time polymerase chain reaction, and Western blotting. CBX3-overexpression HCC cell lines were tested in proliferation assays to determine the function of CBX3/HP1γ. We found that CBX3/HP1γ was upregulated in many cancers and was associated with poor prognosis. Our results also revealed that CBX3/HP1γ is elevated in HCC tissues and is associated with malignant clinicopathological characteristics. Kaplan-Meier and Cox regression analyses verified that high CBX3/HP1γ expression is an independent and significant prognostic factor for reduced overall survival in HCC patients. Moreover, invitro functional assays showed that CBX3/HP1γ overexpression promotes HCC cell proliferation. These findings suggest that CBX3/HP1γ is an important oncogene in HCC that might act as a useful biomarker for prognosis and targeted therapy.
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MESH Headings
- Adult
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/pathology
- Cell Line, Tumor
- Cell Proliferation
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Kaplan-Meier Estimate
- Liver Neoplasms/genetics
- Liver Neoplasms/metabolism
- Liver Neoplasms/pathology
- Male
- Middle Aged
- Prognosis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Up-Regulation
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Affiliation(s)
- Xiaoping Zhong
- Department of Burns and Plastic Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, P.R. China
- The Department of Hepatobiliary Oncology of Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, Guangdong 510060, P.R. China
| | - Anna Kan
- The Department of Hepatobiliary Oncology of Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, Guangdong 510060, P.R. China
| | - Wancong Zhang
- Department of Burns and Plastic Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, P.R. China
| | - Jianda Zhou
- Department of Plastic Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P.R. China
| | - Huayong Zhang
- The Department of Hepatobiliary Oncology of Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, Guangdong 510060, P.R. China
- Department of Thyroid and Breast Surgery, The Fifth Affiliated Hospital of Sun Yat sen University, Zhuhai, Guangdong 519000, P.R. China
| | - Jiasheng Chen
- Department of Burns and Plastic Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, P.R. China
| | - Shijie Tang
- Department of Burns and Plastic Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, P.R. China
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BET bromodomain inhibition blocks the function of a critical AR-independent master regulator network in lethal prostate cancer. Oncogene 2019; 38:5658-5669. [PMID: 30996246 DOI: 10.1038/s41388-019-0815-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/15/2019] [Accepted: 03/19/2019] [Indexed: 12/14/2022]
Abstract
BET bromodomain inhibitors block prostate cancer cell growth at least in part through c-Myc and androgen receptor (AR) suppression. However, little is known about other transcriptional regulators whose suppression contributes to BET bromodomain inhibitor anti-tumor activity. Moreover, the anti-tumor activity of BET bromodomain inhibition in AR-independent castration-resistant prostate cancers (CRPC), whose frequency is increasing, is also unknown. Herein, we demonstrate that BET bromodomain inhibition blocks growth of a diverse set of CRPC cell models, including those that are AR-independent or in which c-Myc is not suppressed. To identify transcriptional regulators whose suppression accounts for these effects, we treated multiple CRPC cell lines with the BET bromodomain inhibitor JQ1 and then performed RNA-sequencing followed by Master Regulator computational analysis. This approach identified several previously unappreciated transcriptional regulators that are highly expressed in CRPC and whose suppression, via both transcriptional or post-translational mechanisms, contributes to the anti-tumor activity of BET bromodomain inhibitors.
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Wiese M, Bannister AJ, Basu S, Boucher W, Wohlfahrt K, Christophorou MA, Nielsen ML, Klenerman D, Laue ED, Kouzarides T. Citrullination of HP1γ chromodomain affects association with chromatin. Epigenetics Chromatin 2019; 12:21. [PMID: 30940194 PMCID: PMC6444592 DOI: 10.1186/s13072-019-0265-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/19/2019] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Stem cell differentiation involves major chromatin reorganisation, heterochromatin formation and genomic relocalisation of structural proteins, including heterochromatin protein 1 gamma (HP1γ). As the principal reader of the repressive histone marks H3K9me2/3, HP1 plays a key role in numerous processes including heterochromatin formation and maintenance. RESULTS We find that HP1γ is citrullinated in mouse embryonic stem cells (mESCs) and this diminishes when cells differentiate, indicating that it is a dynamically regulated post-translational modification during stem cell differentiation. Peptidylarginine deiminase 4, a known regulator of pluripotency, citrullinates HP1γ in vitro. This requires R38 and R39 within the HP1γ chromodomain, and the catalytic activity is enhanced by trimethylated H3K9 (H3K9me3) peptides. Mutation of R38 and R39, designed to mimic citrullination, affects HP1γ binding to H3K9me3-containing peptides. Using live-cell single-particle tracking, we demonstrate that R38 and R39 are important for HP1γ binding to chromatin in vivo. Furthermore, their mutation reduces the residence time of HP1γ on chromatin in differentiating mESCs. CONCLUSION Citrullination is a novel post-translational modification of the structural heterochromatin protein HP1γ in mESCs that is dynamically regulated during mESC differentiation. The citrullinated residues lie within the HP1γ chromodomain and are important for H3K9me3 binding in vitro and chromatin association in vivo.
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Affiliation(s)
- Meike Wiese
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP UK
- Max Planck Institute for Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Andrew J. Bannister
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP UK
| | - Srinjan Basu
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, CB2 1QR UK
| | - Wayne Boucher
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - Kai Wohlfahrt
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - Maria A. Christophorou
- Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU UK
| | - Michael L. Nielsen
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Ernest D. Laue
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - Tony Kouzarides
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP UK
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Zaidan NZ, Walker KJ, Brown JE, Schaffer LV, Scalf M, Shortreed MR, Iyer G, Smith LM, Sridharan R. Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance. Stem Cell Reports 2019; 10:627-641. [PMID: 29358085 PMCID: PMC5830946 DOI: 10.1016/j.stemcr.2017.12.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 12/31/2022] Open
Abstract
The heterochromatin protein 1 (HP1) family is involved in various functions with maintenance of chromatin structure. During murine somatic cell reprogramming, we find that early depletion of HP1γ reduces the generation of induced pluripotent stem cells, while late depletion enhances the process, with a concomitant change from a centromeric to nucleoplasmic localization and elongation-associated histone H3.3 enrichment. Depletion of heterochromatin anchoring protein SENP7 increased reprogramming efficiency to a similar extent as HP1γ, indicating the importance of HP1γ release from chromatin for pluripotency acquisition. HP1γ interacted with OCT4 and DPPA4 in HP1α and HP1β knockouts and in H3K9 methylation depleted H3K9M embryonic stem cell (ESC) lines. HP1α and HP1γ complexes in ESCs differed in association with histones, the histone chaperone CAF1 complex, and specific components of chromatin-modifying complexes such as DPY30, implying distinct functional contributions. Taken together, our results reveal the complex contribution of the HP1 proteins to pluripotency. Release of HP1γ from anchoring by Senp7 increases reprogramming efficiency HP1γ switches enrichment from histone H1 to histone H3.3 in pluripotent cells HP1γ interacts with OCT4 and DPPA4 independent of HP1α, HP1β, and H3K9 methylation Proteomic characterization of HP1 protein family in pluripotent cells
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Affiliation(s)
- Nur Zafirah Zaidan
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; Genetics Training Program, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Kolin J Walker
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Jaime E Brown
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Leah V Schaffer
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Gopal Iyer
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Rupa Sridharan
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53715, USA.
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Yang Y, Meng Q, Wang C, Li X, Lu Y, Xin X, Zheng Q, Lu D. MicroRNA 675 cooperates PKM2 to aggravate progression of human liver cancer stem cells induced from embryonic stem cells. J Mol Med (Berl) 2018; 96:1119-1130. [PMID: 30140938 DOI: 10.1007/s00109-018-1687-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 08/08/2018] [Accepted: 08/13/2018] [Indexed: 01/17/2023]
Abstract
Both miR675 and pyruvate kinase M2 (PKM2) contribute to malignant progression of tumor, but its functions in liver cancer stem cells remain unclear. Herein, our findings indicate that miR675 plus PKM2 strongly promotes the growth of liver cancer stem cells. Mechanistically, miR675 plus PKM2 enhances the transcriptional activity of SUV39h2. On the other hand, the excessive SUV39h2 binds to more substrate histone H3, triggering an increase of tri-methylation of histone H3 on the ninth lysine. Furthermore, the tri-methylation of histone 3 on the ninth lysine (H3K9me3)-heterochromatin protein 1 alpha (HP1α) complex is increased when the complex occupancy ability on the C-myc promoter region is raised, recruiting CREB, P300, and RNApolII to the special position that results in C-myc high abundance. Therefore, miR675 plus PKM2 triggered the upregulation of C-myc by increasing the interaction between H3K9me3 and HP1α. Understanding the signaling pathways that miR675 plus PKM2 epigenetically possesses during the malignant transformation of liver cancer stem cells will contribute to more effective liver cancer therapies.
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Affiliation(s)
- Yuxin Yang
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Qiuyu Meng
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Chen Wang
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Xiaonan Li
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Yanan Lu
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Xiaoru Xin
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Qidi Zheng
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Dongdong Lu
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China.
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Analysis of new therapeutic strategies for diabetes mellitus based on traditional Chinese medicine “xiaoke” formulae. JOURNAL OF TRADITIONAL CHINESE MEDICAL SCIENCES 2018. [DOI: 10.1016/j.jtcms.2018.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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45
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Saldi TK, Gonzales P, Garrido-Lecca A, Dostal V, Roberts CM, Petrucelli L, Link CD. The Caenorhabditis elegans Ortholog of TDP-43 Regulates the Chromatin Localization of the Heterochromatin Protein 1 Homolog HPL-2. Mol Cell Biol 2018; 38:e00668-17. [PMID: 29760282 PMCID: PMC6048318 DOI: 10.1128/mcb.00668-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/04/2018] [Accepted: 05/01/2018] [Indexed: 12/13/2022] Open
Abstract
TDP-1 is the Caenorhabditis elegans ortholog of mammalian TDP-43, which is strongly implicated in the etiology of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). We discovered that deletion of the tdp-1 gene results in enhanced nuclear RNA interference (RNAi). As nuclear RNAi in C. elegans involves chromatin changes moderated by HPL-2, a homolog of heterochromatin protein 1 (HP1), we investigated the interaction of TDP-1 and HPL-2. We found that TDP-1 and HPL-2 interact directly and that loss of TDP-1 dramatically alters the chromatin association of HPL-2. We showed previously that deletion of the tdp-1 gene results in transcriptional alterations and the accumulation of double-stranded RNA (dsRNA). These molecular changes are replicated in an hpl-2 deletion strain, consistent with HPL-2 acting in consort with TDP-1 to modulate these aspects of RNA metabolism. Our observations identify novel mechanisms by which HP1 homologs can be recruited to chromatin and by which nuclear depletion of human TDP-43 may lead to changes in RNA metabolism that are relevant to disease.
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Affiliation(s)
- Tassa K Saldi
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Patrick Gonzales
- Integrative Physiology, University of Colorado, Boulder, Colorado, USA
| | - Alfonso Garrido-Lecca
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Vishantie Dostal
- Integrative Physiology, University of Colorado, Boulder, Colorado, USA
| | | | | | - Christopher D Link
- Integrative Physiology, University of Colorado, Boulder, Colorado, USA
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, USA
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46
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Overexpression of CBX3 in Pancreatic Adenocarcinoma Promotes Cell Cycle Transition-Associated Tumor Progression. Int J Mol Sci 2018; 19:ijms19061768. [PMID: 29903985 PMCID: PMC6032220 DOI: 10.3390/ijms19061768] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 05/28/2018] [Accepted: 06/12/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Previous studies showed that Chromobox protein homolog 3 (CBX3) was overexpressed in several types of human cancers, however its pattern and role in pancreatic adenocarcinoma (PAAD) has not yet been understood. The aim of this study was to identify the expression and function of CBX3 in PAAD. METHODS Data of transcriptomic and protein expression of CBX3 in PAAD were collected from different databases and analyzed. The in vitro and in vivo role of CBX3 in PAAD was examined. RESULTS CBX3 was overexpressed in human PAAD tissues, which was associated with poor prognosis of overall and disease-free survival of the patients. Overexpression of CBX3 induced the in vitro proliferation, anchorage-free growth, migration and invasion of the PAAD cells, and led to in vivo growth of orthotoptic PAAD tumors in mice. GO and KEGG pathway analysis, as well as experimental observation showed that CBX3 may be associated with cell cycle transition of PAAD cells, and cyclin-dependent kinase 1 (CDK1) and proliferating cell nuclear antigen (PCNA) may mediate the tumor-promoting action of CBX3. CDK1 knockdown attenuated the cell cycle transition, proliferation and invasion of CBX3-overexpressing PAAD cells. CONCLUSION Our findings suggest the tumor-promoting role of CBX3 in PAAD to be targeted by novel therapeutic strategies.
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Alam H, Li N, Dhar SS, Wu SJ, Lv J, Chen K, Flores ER, Baseler L, Lee MG. HP1γ Promotes Lung Adenocarcinoma by Downregulating the Transcription-Repressive Regulators NCOR2 and ZBTB7A. Cancer Res 2018; 78:3834-3848. [PMID: 29764865 DOI: 10.1158/0008-5472.can-17-3571] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 03/09/2018] [Accepted: 05/11/2018] [Indexed: 12/16/2022]
Abstract
Lung adenocarcinoma is a major form of lung cancer, which is the leading cause of cancer death. Histone methylation reader proteins mediate the effect of histone methylation, a hallmark of epigenetic and transcriptional regulation of gene expression. However, their roles in lung adenocarcinoma are poorly understood. Here, our bioinformatic screening and analysis in search of a lung adenocarcinoma-promoting histone methylation reader protein show that heterochromatin protein 1γ (HP1γ; also called CBX3) is among the most frequently overexpressed and amplified histone reader proteins in human lung adenocarcinoma, and that high HP1γ mRNA levels are associated with poor prognosis in patients with lung adenocarcinoma. In vivo depletion of HP1γ reduced K-RasG12D-driven lung adenocarcinoma and lengthened survival of mice bearing K-RasG12D-induced lung adenocarcinoma. HP1γ and its binding activity to methylated histone H3 lysine 9 were required for the proliferation, colony formation, and migration of lung adenocarcinoma cells. HP1γ directly repressed expression of the transcription-repressive regulators NCOR2 and ZBTB7A. Knockdown of NCOR2 or ZBTB7A significantly restored defects in proliferation, colony formation, and migration in HP1γ-depleted lung adenocarcinoma cells. Low NCOR2 or ZBTB7A mRNA levels were associated with poor prognosis in patients with lung adenocarcinoma and correlated with high HP1γ mRNA levels in lung adenocarcinoma samples. NCOR2 and ZBTB7A downregulated expression of tumor-promoting factors such as ELK1 and AXL, respectively. These findings highlight the importance of HP1γ and its reader activity in lung adenocarcinoma tumorigenesis and reveal a unique lung adenocarcinoma-promoting mechanism in which HP1γ downregulates NCOR2 and ZBTB7A to enhance expression of protumorigenic genes.Significance: Direct epigenetic repression of the transcription-repressive regulators NCOR2 and ZBTB7A by the histone reader protein HP1γ leads to activation of protumorigenic genes in lung adenocarcinoma. Cancer Res; 78(14); 3834-48. ©2018 AACR.
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Affiliation(s)
- Hunain Alam
- Department of Molecular and Cellular Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Na Li
- Department of Molecular and Cellular Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shilpa S Dhar
- Department of Molecular and Cellular Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sarah J Wu
- Department of Molecular and Cellular Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas.,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas
| | - Jie Lv
- Institute for Academic Medicine, the Methodist Hospital Research Institute, Houston, Texas.,Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, the Methodist Hospital Research Institute, Houston, Texas.,Weill Cornell Medical College, Cornell University, New York, New York
| | - Kaifu Chen
- Institute for Academic Medicine, the Methodist Hospital Research Institute, Houston, Texas.,Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, the Methodist Hospital Research Institute, Houston, Texas.,Weill Cornell Medical College, Cornell University, New York, New York
| | - Elsa R Flores
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Laura Baseler
- Department of Veterinary Medicine and Surgery, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Min Gyu Lee
- Department of Molecular and Cellular Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas. .,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas
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48
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CBX3 promotes tumor proliferation by regulating G1/S phase via p21 downregulation and associates with poor prognosis in tongue squamous cell carcinoma. Gene 2018; 654:49-56. [PMID: 29462646 DOI: 10.1016/j.gene.2018.02.043] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 02/13/2018] [Accepted: 02/14/2018] [Indexed: 01/14/2023]
Abstract
Chromobox protein homolog 3 (CBX3), a core component of the heterochromatin proteins 1, is recently proved to be involved in human cancerogenesis and associated with the prognosis of patient. However, the role of CBX3 in Tongue squamous cell carcinoma (TSCC) remains unclear. In the present study we found that CBX3 was upregulated in TSCC tissues when compared to adjacent non-tumor tissues, and multivariable analysis showed that high CBX3 expression was associated with clinical stage and cervical node metastasis, which was an independent prognostic indicator of TSCC. Furthermore, Kaplan-Meier survival analysis and log-rank test showed that TSCC patients with high CBX3 expression had a poorer rate of OS compared to patients with low CBX3 expression. Moreover, knocking down CBX3 inhibited TSCC cells proliferation both in vitro and in vivo, while overexpressing CBX3 promoted TSCC cells proliferation. In addition, CBX3 depletion resulted in cell cycle delay at the G1/S phase via the p21 pathway. In summary, we identifies CBX3 as a potential novel oncogene in TSCC, which may act as a biomarker and target in the diagnosis and treatment of this killer disease.
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49
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Nanan KK, Ocheltree C, Sturgill D, Mandler MD, Prigge M, Varma G, Oberdoerffer S. Independence between pre-mRNA splicing and DNA methylation in an isogenic minigene resource. Nucleic Acids Res 2017; 45:12780-12797. [PMID: 29244186 PMCID: PMC5727405 DOI: 10.1093/nar/gkx900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 09/13/2017] [Accepted: 09/25/2017] [Indexed: 12/27/2022] Open
Abstract
Actively transcribed genes adopt a unique chromatin environment with characteristic patterns of enrichment. Within gene bodies, H3K36me3 and cytosine DNA methylation are elevated at exons of spliced genes and have been implicated in the regulation of pre-mRNA splicing. H3K36me3 is further responsive to splicing, wherein splicing inhibition led to a redistribution and general reduction over gene bodies. In contrast, little is known of the mechanisms supporting elevated DNA methylation at actively spliced genic locations. Recent evidence associating the de novo DNA methyltransferase Dnmt3b with H3K36me3-rich chromatin raises the possibility that genic DNA methylation is influenced by splicing-associated H3K36me3. Here, we report the generation of an isogenic resource to test the direct impact of splicing on chromatin. A panel of minigenes of varying splicing potential were integrated into a single FRT site for inducible expression. Profiling of H3K36me3 confirmed the established relationship to splicing, wherein levels were directly correlated with splicing efficiency. In contrast, DNA methylation was equivalently detected across the minigene panel, irrespective of splicing and H3K36me3 status. In addition to revealing a degree of independence between genic H3K36me3 and DNA methylation, these findings highlight the generated minigene panel as a flexible platform for the query of splicing-dependent chromatin modifications.
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Affiliation(s)
- Kyster K. Nanan
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cody Ocheltree
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mariana D. Mandler
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria Prigge
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Garima Varma
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shalini Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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50
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Zhang C, Chen D, Maguire EM, He S, Chen J, An W, Yang M, Afzal TA, Luong LA, Zhang L, Lei H, Wu Q, Xiao Q. Cbx3 inhibits vascular smooth muscle cell proliferation, migration, and neointima formation. Cardiovasc Res 2017; 114:443-455. [DOI: 10.1093/cvr/cvx236] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 11/29/2017] [Indexed: 12/14/2022] Open
Affiliation(s)
- Cheng Zhang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Chongqing 400016, Yuzhong District, China
| | - Dan Chen
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Chongqing 400016, Yuzhong District, China
| | - Eithne Margaret Maguire
- Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Shiping He
- Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Jiangyong Chen
- Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
- Department of Cardiothoracic Surgery, Yongchuan Hospital of Chongqing Medical University, Chongqing 402160, China
| | - Weiwei An
- Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Mei Yang
- Department of Cardiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang, China
| | - Tayyab Adeel Afzal
- Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Le Anh Luong
- Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Li Zhang
- Department of Cardiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang, China
| | - Han Lei
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Chongqing 400016, Yuzhong District, China
| | - Qingchen Wu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Chongqing 400016, Yuzhong District, China
| | - Qingzhong Xiao
- Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
- Key Laboratory of Cardiovascular Diseases, The Second Affiliated Hospital, School of Basic Medical Sciences, Guangzhou Medical University, Xinzao Town, Guangzhou, Guangdong 511436, Panyu District, China
- Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Xinzao Town, Guangzhou, Guangdong 511436, Panyu District, China
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