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Barrios-Camacho CM, Zunitch MJ, Louie JD, Jang W, Schwob JE. An in vitro model of acute horizontal basal cell activation reveals gene regulatory networks underlying the nascent activation phase. Stem Cell Reports 2024:S2213-6711(24)00191-7. [PMID: 39059377 DOI: 10.1016/j.stemcr.2024.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 06/21/2024] [Accepted: 06/23/2024] [Indexed: 07/28/2024] Open
Abstract
While horizontal basal cells (HBCs) make minor contributions to olfactory epithelium (OE) regeneration during homeostatic conditions, they possess a potent, latent capacity to activate and subsequently regenerate the OE following severe injury. Activation requires, and is mediated by, the downregulation of the transcription factor (TF) TP63. In this paper, we describe the cellular processes that drive the nascent stages of HBC activation. The compound phorbol 12-myristate 13-acetate (PMA) induces a rapid loss in TP63 protein and rapid enrichment of HOPX and the nuclear translocation of RELA, previously identified as components of HBC activation. Using bulk RNA sequencing (RNA-seq), we find that PMA-treated HBCs pass through various stages of activation identifiable by transcriptional regulatory signatures that mimic stages identified in vivo. These temporal stages are associated with varying degrees of engraftment and differentiation potential in transplantation assays. Together, these data show that our in vitro HBC activation system models physiologically relevant features of in vivo HBC activation and identifies new candidates for mechanistic testing.
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Affiliation(s)
- Camila M Barrios-Camacho
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA; Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Matthew J Zunitch
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA; Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Jonathan D Louie
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA; Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Woochan Jang
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - James E Schwob
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA.
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2
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Alenezi H, Parnell G, Schibeci S, Ozkan J, Willcox M, White AJR, Carnt N. Ocular surface immune transcriptome and tear cytokines in corneal infection patients. Front Cell Infect Microbiol 2024; 14:1346821. [PMID: 38694515 PMCID: PMC11061372 DOI: 10.3389/fcimb.2024.1346821] [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: 11/30/2023] [Accepted: 03/19/2024] [Indexed: 05/04/2024] Open
Abstract
Background Microbial keratitis is one of the leading causes of blindness globally. An overactive immune response during an infection can exacerbate damage, causing corneal opacities and vision loss. This study aimed to identify the differentially expressed genes between corneal infection patients and healthy volunteers within the cornea and conjunctiva and elucidate the contributing pathways to these conditions' pathogenesis. Moreover, it compared the corneal and conjunctival transcriptomes in corneal-infected patients to cytokine levels in tears. Methods Corneal and conjunctival swabs were collected from seven corneal infection patients and three healthy controls under topical anesthesia. RNA from seven corneal infection patients and three healthy volunteers were analyzed by RNA sequencing (RNA-Seq). Tear proteins were extracted from Schirmer strips via acetone precipitation from 38 cases of corneal infection and 14 healthy controls. The cytokines and chemokines IL-1β, IL-6, CXCL8 (IL-8), CX3CL1, IL-10, IL-12 (p70), IL-17A, and IL-23 were measured using an antibody bead assay. Results A total of 512 genes were found to be differentially expressed in infected corneas compared to healthy corneas, with 508 being upregulated and four downregulated (fold-change (FC) <-2 or > 2 and adjusted p <0.01). For the conjunctiva, 477 were upregulated, and 3 were downregulated (FC <-3 or ≥ 3 and adjusted p <0.01). There was a significant overlap in cornea and conjunctiva gene expression in patients with corneal infections. The genes were predominantly associated with immune response, regulation of angiogenesis, and apoptotic signaling pathways. The most highly upregulated gene was CXCL8 (which codes for IL-8 protein). In patients with corneal infections, the concentration of IL-8 protein in tears was relatively higher in patients compared to healthy controls but did not show statistical significance. Conclusions During corneal infection, many genes were upregulated, with most of them being associated with immune response, regulation of angiogenesis, and apoptotic signaling. The findings may facilitate the development of treatments for corneal infections that can dampen specific aspects of the immune response to reduce scarring and preserve sight.
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Affiliation(s)
- Heba Alenezi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
- School of Optometry and Vision Science, The University of New South Wales, Sydney, NSW, Australia
- Centre for Vision Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - Grant Parnell
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Stephen Schibeci
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - Jerome Ozkan
- School of Optometry and Vision Science, The University of New South Wales, Sydney, NSW, Australia
| | - Mark Willcox
- School of Optometry and Vision Science, The University of New South Wales, Sydney, NSW, Australia
| | - Andrew J. R. White
- School of Optometry and Vision Science, The University of New South Wales, Sydney, NSW, Australia
- Centre for Vision Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - Nicole Carnt
- School of Optometry and Vision Science, The University of New South Wales, Sydney, NSW, Australia
- Centre for Vision Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
- Institute of Ophthalmology, University College London, London, United Kingdom
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3
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Georgy SR, Rudiatmoko DR, Auden A, Partridge D, Butt T, Srivastava S, Wong N, Swaroop D, Carpinelli MR, Bogeski M, Jane SM. Identification of a Novel GRHL3/HOPX/Wnt/β-Catenin Proto-oncogenic Axis in Squamous Cell Carcinoma of the Esophagus. Cell Mol Gastroenterol Hepatol 2022; 15:1051-1069. [PMID: 36442813 PMCID: PMC10036738 DOI: 10.1016/j.jcmgh.2022.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND & AIMS Esophageal squamous cell carcinoma (ESCC) is an aggressive malignancy with a poor long-term prognosis. The molecular mechanisms underlying the initiation and progression of this tumor are largely unknown. The transcription factor GRHL3 functions as a potent tumor suppressor in SCC of skin, head, and neck. This study aims to determine whether GRHL3 also plays a role in the homeostasis of the esophageal epithelium and in the development of ESCC. METHODS The effects of Grhl3 deletion on squamous epithelial homeostasis in embryos and adult mice were examined using immunohistochemistry, transmission electron microscopy, and real-time polymerase chain reaction. The conditionally deleted mice were subsequently used to determine susceptibility to ESCC. Whole-transcriptome sequencing (RNA-seq) was performed on ESCC in wild-type and Grhl3 deleted animals. To decipher the signaling pathways, real-time polymerase chain reaction, immunohistochemistry, analysis of chromatin immunoprecipitation sequencing, chromatin immunoprecipitation-polymerase chain reaction, and RNA seq datasets were used. Primary human samples were used to validate the findings in the mouse model. RESULTS Loss of Grhl3 perturbs the proliferation-differentiation balance in the esophageal epithelium, thereby increasing the susceptibility to esophageal carcinogenesis in adult mice. Grhl3 imparts its tumor suppressor function by regulating the expression of HOPX. We have identified the Wnt/β-catenin pathway as the downstream effectors of GRHL3 and HOPX through our integrated approach using patient-derived ESCC samples and mouse models. CONCLUSIONS GRHL3 conveys its tumor suppressor function in ESCC through regulating its target gene HOPX, which limits Wnt/β-catenin signaling. Targeted therapies to inhibit this pathway could be a potential treatment strategy for ESCC patients with reduced GRHL3 expression.
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Affiliation(s)
- Smitha Rose Georgy
- Department of Anatomic Pathology, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Australia.
| | | | - Alana Auden
- Department of Medicine, Central Clinical School, Monash University, Melbourne, Australia
| | - Darren Partridge
- Department of Medicine, Central Clinical School, Monash University, Melbourne, Australia
| | - Tariq Butt
- Department of Medicine, Central Clinical School, Monash University, Melbourne, Australia
| | - Seema Srivastava
- Department of Medicine, Central Clinical School, Monash University, Melbourne, Australia
| | - Nick Wong
- Monash Bioinformatics Platform, Central Clinical School, Melbourne, Australia
| | - Dijina Swaroop
- Department of Medicine, Central Clinical School, Monash University, Melbourne, Australia
| | - Marina Rose Carpinelli
- Department of Medicine, Central Clinical School, Monash University, Melbourne, Australia
| | - Mirjana Bogeski
- Department of Anatomic Pathology, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Australia
| | - Stephen M Jane
- Department of Medicine, Central Clinical School, Monash University, Melbourne, Australia
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HOPX: A Unique Homeodomain Protein in Development and Tumor Suppression. Cancers (Basel) 2022; 14:cancers14112764. [PMID: 35681746 PMCID: PMC9179269 DOI: 10.3390/cancers14112764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 12/05/2022] Open
Abstract
Simple Summary Homeobox (HOX) genes encode homeodomain proteins that regulate a wide range of molecular pathways. The homeodomain is highly conserved and binds to DNA. One exception is homeodomain-only protein (HOPX) that lacks DNA-binding capacity. HOPX plays a crucial role in development and its functional impairment is associated with a variety of diseases, including cancer. Loss of HOPX function occurs in a wide range of cancer types, where it functions as a tumor suppressor gene. Understanding the molecular mechanisms by which HOPX regulates carcinogenesis will likely lead to the development of new therapeutic approaches. Abstract Homeobox genes are master regulators of morphogenesis and differentiation by acting at the top of genetic hierarchies and their deregulation is associated with a variety of human diseases. They usually contain a highly conserved sequence that codes for the homeodomain of the protein, a specialized motif with three α helices and an N-terminal arm that aids in DNA binding. However, one homeodomain protein, HOPX, is unique among its family members in that it lacks the capacity to bind DNA and instead functions by interacting with transcriptional regulators. HOPX plays crucial roles in organogenesis and is expressed in both embryonic and adult stem cells. Loss of HOPX expression is common in cancer, where it functions primarily as a tumor suppressor gene. In this review, we describe the function of HOPX in development and discuss its role in carcinogenesis.
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HOPX Exhibits Oncogenic Activity during Squamous Skin Carcinogenesis. J Invest Dermatol 2021; 141:2354-2368. [PMID: 33845078 DOI: 10.1016/j.jid.2020.04.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 04/27/2020] [Accepted: 04/27/2020] [Indexed: 11/23/2022]
Abstract
Cutaneous squamous cell carcinomas (SCCs) are frequent heterogeneous tumors arising from sun-exposed regions of the skin and characterized by complex pathogenesis. HOPX is a member of the homeodomain-containing superfamily of proteins holding an atypical homeodomain unable to bind to DNA. First discovered in the heart as a regulator of cardiac development, in the skin, HOPX modulates the terminal differentiation of keratinocytes. There is a particular interest in studying HOPX in squamous skin carcinogenesis because it has the atypical structure and the functional duality as an oncogene and a tumor suppressor gene, reported in different malignancies. In this study, we analyzed the effects of HOPX knockdown and overexpression on SCC tumorigenicity in vitro and in vivo. Our data show that HOPX knockdown in SCC cells inhibits their proliferative and invasive activity through the acceleration of apoptosis. We established that methylation of two alternative HOPX promoters leads to differential expression of HOPX transcripts in normal keratinocytes and SCC cells. Importantly, we report that HOPX acts as an oncogene in the pathogenesis of SCC probably through the activation of the second alternative promoter and the modulation of apoptosis.
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PKCα/ERK/C7ORF41 axis regulates epidermal keratinocyte differentiation through the IKKα nuclear translocation. Biochem J 2021; 478:839-854. [PMID: 33528492 DOI: 10.1042/bcj20200879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 11/17/2022]
Abstract
Aberrant differentiation of keratinocytes disrupts the skin barrier and causes a series of skin diseases. However, the molecular basis of keratinocyte differentiation is still poorly understood. In the present study, we examined the expression of C7ORF41 using tissue microarrays by immunohistochemistry and found that C7ORF41 is specifically expressed in the basal layers of skin epithelium and its expression is gradually decreased during keratinocytes differentiation. Importantly, we corroborated the pivotal role of C7ORF41 during keratinocyte differentiation by C7ORF41 knockdown or overexpression in TPA-induced Hacat keratinocytes. Mechanismly, we first demonstrated that C7ORF41 inhibited keratinocyte differentiation mainly through formatting a complex with IKKα in the cytoplasm, which thus blocked the nuclear translocation of IKKα. Furthermore, we also demonstrated that inhibiting the PKCα/ERK signaling pathway reversed the reduction in C7ORF41 in TPA-induced keratinocytes, indicating that C7ORF41 expression could be regulated by upstream PKCα/ERK signaling pathway during keratinocyte differentiation. Collectively, our study uncovers a novel regulatory network PKCα/ERK/C7ORF41/IKKα during keratinocyte differentiation, which provides potential therapeutic targets for skin diseases.
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The role of HOPX in normal tissues and tumor progression. Biosci Rep 2020; 40:221873. [PMID: 31934721 PMCID: PMC6997107 DOI: 10.1042/bsr20191953] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 12/03/2019] [Accepted: 12/23/2019] [Indexed: 02/06/2023] Open
Abstract
The homeodomain-only protein homeobox (HOPX) as the smallest homeodomain protein, lacks certain conserved residues required for DNA binding. Through our literature search, we reviewed the current understandings of HOPX in normal tissues and tumor progression. HOPX was initially identified as a critical transcription factor in various normal tissues, which interacted with serum response factor (SRF) or other substance to regulate normal physiological function. However, HOPX is at a low expression or methylation level in tumors. These data indicated that HOPX may play a very important role in regulating differentiation phenotype and tumor suppressive function. We predicted the prognosis of HOPX in tumors from TCGA database and discussed the downstream genes of HOPX. To understand how HOPX is involved in the mechanisms between physical and pathological conditions could lead to novel therapeutic strategies for treatment.
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8
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HOPX regulates bone marrow-derived mesenchymal stromal cell fate determination via suppression of adipogenic gene pathways. Sci Rep 2020; 10:11345. [PMID: 32647304 PMCID: PMC7347885 DOI: 10.1038/s41598-020-68261-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/22/2020] [Indexed: 01/08/2023] Open
Abstract
Previous studies of global binding patterns identified the epigenetic factor, EZH2, as a regulator of the homeodomain-only protein homeobox (HOPX) gene expression during bone marrow stromal cell (BMSC) differentiation, suggesting a potential role for HOPX in regulating BMSC lineage specification. In the present study, we confirmed that EZH2 direct binds to the HOPX promoter region, during normal growth and osteogenic differentiation but not under adipogenic inductive conditions. HOPX gene knockdown and overexpression studies demonstrated that HOPX is a promoter of BMSC proliferation and an inhibitor of adipogenesis. However, functional studies failed to observe any affect by HOPX on BMSC osteogenic differentiation. RNA-seq analysis of HOPX overexpressing BMSC during adipogenesis, found HOPX function to be acting through suppression of adipogenic pathways associated genes such as ADIPOQ, FABP4, PLIN1 and PLIN4. These findings suggest that HOPX gene target pathways are critical factors in the regulation of fat metabolism.
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9
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Phillips MA, Cánovas A, Rea MA, Islas-Trejo A, Medrano JF, Durbin-Johnson B, Rocke DM, Rice RH. Deducing signaling pathways from parallel actions of arsenite and antimonite in human epidermal keratinocytes. Sci Rep 2020; 10:2890. [PMID: 32076005 PMCID: PMC7031270 DOI: 10.1038/s41598-020-59577-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/29/2020] [Indexed: 11/09/2022] Open
Abstract
Inorganic arsenic oxides have been identified as carcinogens in several human tissues, including epidermis. Due to the chemical similarity between trivalent inorganic arsenic (arsenite) and antimony (antimonite), we hypothesized that common intracellular targets lead to similarities in cellular responses. Indeed, transcriptional and proteomic profiling revealed remarkable similarities in differentially expressed genes and proteins resulting from exposure of cultured human epidermal keratinocytes to arsenite and antimonite in contrast to comparisons of arsenite with other metal compounds. These data were analyzed to predict upstream regulators and affected signaling pathways following arsenite and antimonite treatments. A majority of the top findings in each category were identical after treatment with either compound. Inspection of the predicted upstream regulators led to previously unsuspected roles for oncostatin M, corticosteroids and ephrins in mediating cellular response. The influence of these predicted mediators was then experimentally verified. Together with predictions of transcription factor effects more generally, the analysis has led to model signaling networks largely accounting for arsenite and antimonite action. The striking parallels between responses to arsenite and antimonite indicate the skin carcinogenic risk of exposure to antimonite merits close scrutiny.
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Affiliation(s)
- Marjorie A Phillips
- Department of Environmental Toxicology, University of California, Davis, CA, USA
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Miguel A Rea
- Department of Chemistry, Universidad Autónoma Querétaro, Querétaro, Mexico
| | - Alma Islas-Trejo
- Department of Animal Science, University of California, Davis, CA, USA
| | - Juan F Medrano
- Department of Animal Science, University of California, Davis, CA, USA
| | - Blythe Durbin-Johnson
- Division of Biostatistics, Department of Public Health Sciences, Clinical and Translational Science Center Biostatistics Core, University of California, Davis, CA, USA
| | - David M Rocke
- Division of Biostatistics, Department of Public Health Sciences, Clinical and Translational Science Center Biostatistics Core, University of California, Davis, CA, USA
| | - Robert H Rice
- Department of Environmental Toxicology, University of California, Davis, CA, USA.
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10
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Chen SY, Ishii MA, Cheng B, Otten ABC, Sun BK. HOPX Is a ZNF750 Target that Promotes Late Epidermal Differentiation. J Invest Dermatol 2019; 139:2039-2042.e2. [PMID: 30959041 DOI: 10.1016/j.jid.2019.03.1141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 02/08/2019] [Accepted: 03/05/2019] [Indexed: 11/25/2022]
Affiliation(s)
- Selena Y Chen
- Department of Dermatology, University of California-San Diego, La Jolla, California, USA
| | - Mitsuhiro A Ishii
- Department of Dermatology, University of California-San Diego, La Jolla, California, USA
| | - Binbin Cheng
- Department of Dermatology, University of California-San Diego, La Jolla, California, USA
| | - Auke B C Otten
- Department of Dermatology, University of California-San Diego, La Jolla, California, USA
| | - Bryan K Sun
- Department of Dermatology, University of California-San Diego, La Jolla, California, USA.
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Li J, Zheng L, Uchiyama A, Bin L, Mauro TM, Elias PM, Pawelczyk T, Sakowicz-Burkiewicz M, Trzeciak M, Leung DYM, Morasso MI, Yu P. A data mining paradigm for identifying key factors in biological processes using gene expression data. Sci Rep 2018; 8:9083. [PMID: 29899432 PMCID: PMC5998123 DOI: 10.1038/s41598-018-27258-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 05/21/2018] [Indexed: 12/15/2022] Open
Abstract
A large volume of biological data is being generated for studying mechanisms of various biological processes. These precious data enable large-scale computational analyses to gain biological insights. However, it remains a challenge to mine the data efficiently for knowledge discovery. The heterogeneity of these data makes it difficult to consistently integrate them, slowing down the process of biological discovery. We introduce a data processing paradigm to identify key factors in biological processes via systematic collection of gene expression datasets, primary analysis of data, and evaluation of consistent signals. To demonstrate its effectiveness, our paradigm was applied to epidermal development and identified many genes that play a potential role in this process. Besides the known epidermal development genes, a substantial proportion of the identified genes are still not supported by gain- or loss-of-function studies, yielding many novel genes for future studies. Among them, we selected a top gene for loss-of-function experimental validation and confirmed its function in epidermal differentiation, proving the ability of this paradigm to identify new factors in biological processes. In addition, this paradigm revealed many key genes in cold-induced thermogenesis using data from cold-challenged tissues, demonstrating its generalizability. This paradigm can lead to fruitful results for studying molecular mechanisms in an era of explosive accumulation of publicly available biological data.
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Affiliation(s)
- Jin Li
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77843, USA
- TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Le Zheng
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Akihiko Uchiyama
- Laboratory of Skin Biology, National Institute for Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lianghua Bin
- Department of Pediatrics, National Jewish Health, Denver, Colorado, USA
| | - Theodora M Mauro
- Dermatology Service, Veterans Affairs Medical Center, and Department of Dermatology, UCSF, San Francisco, California, USA
| | - Peter M Elias
- Dermatology Service, Veterans Affairs Medical Center, and Department of Dermatology, UCSF, San Francisco, California, USA
| | - Tadeusz Pawelczyk
- Department of Molecular Medicine, Medical University of Gdansk, Gdansk, Poland
| | | | - Magdalena Trzeciak
- Department of Dermatology, Venerology and Allergology, Medical University of Gdansk, Gdansk, Poland
| | - Donald Y M Leung
- Department of Pediatrics, National Jewish Health, Denver, Colorado, USA
| | - Maria I Morasso
- Laboratory of Skin Biology, National Institute for Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Peng Yu
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77843, USA.
- TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX, 77843, USA.
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12
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Ren X, Yang X, Cheng B, Chen X, Zhang T, He Q, Li B, Li Y, Tang X, Wen X, Zhong Q, Kang T, Zeng M, Liu N, Ma J. HOPX hypermethylation promotes metastasis via activating SNAIL transcription in nasopharyngeal carcinoma. Nat Commun 2017; 8:14053. [PMID: 28146149 PMCID: PMC5296651 DOI: 10.1038/ncomms14053] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 11/22/2016] [Indexed: 12/24/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is characterized by a high rate of local invasion and early distant metastasis. Increasing evidence indicates that epigenetic abnormalities play important roles in NPC development. However, the epigenetic mechanisms underlying NPC metastasis remain unclear. Here we investigate aberrantly methylated transcription factors in NPC tissues, and we identify the HOP homeobox HOPX as the most significantly hypermethylated gene. Consistently, we find that HOXP expression is downregulated in NPC tissues and NPC cell lines. Restoring HOPX expression suppresses metastasis and enhances chemosensitivity of NPC cells. These effects are mediated by HOPX-mediated epigenetic silencing of SNAIL transcription through the enhancement of histone H3K9 deacetylation in the SNAIL promoter. Moreover, we find that patients with high methylation levels of HOPX exhibit poor clinical outcomes in both the training and validation cohorts. In summary, HOPX acts as a tumour suppressor via the epigenetic regulation of SNAIL transcription, which provides a novel prognostic biomarker for NPC metastasis and therapeutic target for NPC treatment.
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Affiliation(s)
- Xianyue Ren
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, Guangdong 510060, China.,Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, 56 Lingyuan Road west, Guangzhou, Guangdong 510055, China
| | - Xiaojing Yang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, Guangdong 510060, China
| | - Bin Cheng
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, 56 Lingyuan Road west, Guangzhou, Guangdong 510055, China
| | - Xiaozhong Chen
- Department of Radiation Oncology, Zhejiang Cancer Hospital, 38 Guangji Road, Hangzhou, Zhejiang 310022, China
| | - Tianpeng Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, 132 Waihuan Road East, Guangzhou, Guangdong 510006, China
| | - Qingmei He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, Guangdong 510060, China
| | - Bin Li
- Department of Radiation Oncology, Zhejiang Cancer Hospital, 38 Guangji Road, Hangzhou, Zhejiang 310022, China
| | - Yingqin Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, Guangdong 510060, China
| | - Xinran Tang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, Guangdong 510060, China
| | - Xin Wen
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, Guangdong 510060, China
| | - Qian Zhong
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, Guangdong 510060, China
| | - Tiebang Kang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, Guangdong 510060, China
| | - Musheng Zeng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, Guangdong 510060, China
| | - Na Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, Guangdong 510060, China
| | - Jun Ma
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, Guangdong 510060, China
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Homeobox-Only Protein Expression Is a Critical Prognostic Indicator of Pancreatic Neuroendocrine Tumor and Is Regulated by Promoter DNA Hypermethylation. Pancreas 2016; 45:1255-1262. [PMID: 27776044 DOI: 10.1097/mpa.0000000000000646] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVES We have identified homeobox-only protein (HOPX) as a tumor suppressor gene in various human cancer, and its expression was reduced by promoter DNA hypermethylation. Homeobox-only protein is strongly expressed on pancreatic islet cells; however, clinical relevance of HOPX expression has remained elusive in pancreatic neuroendocrine tumor (pNET). METHODS We investigated 36 patients with pNET who undertook surgical resection between 1988 and 2012 for HOPX expression and DNA methylation to reveal its clinical significance. RESULTS (1) Homeobox-only protein is strongly expressed on pancreatic islet cells by immunohistochemistry (IHC). Homeobox-only protein expression was recognized on pNET tumor cells for 1+ in 15, for 2+ in 16, and for 3+ in 5. (2) Homeobox-only protein IHC expression was significantly associated with prognosis (P = 0.03), and survival rate was 37.5%, 70.3%, and 100% in HOPX 1+, 2+, and 3+, respectively. (3) Promoter DNA methylation was quantitatively assessed, and HOPX hypermethylation is found in 6.3%, 11.8%, and 66.7% of G1/G2/G3 pNET, respectively (P = 0.02). (4) Multivariate Cox proportional hazards model identified HOPX IHC expression and HOPX promoter DNA hypermethylation as independent prognostic factors in pNET. CONCLUSIONS Homeobox-only protein expression is a critical prognostic indicator of pNET, and its regulation may be made through promoter DNA methylation.
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Mariotto A, Pavlova O, Park HS, Huber M, Hohl D. HOPX: The Unusual Homeodomain-Containing Protein. J Invest Dermatol 2016; 136:905-911. [PMID: 27017330 DOI: 10.1016/j.jid.2016.01.032] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 12/23/2015] [Accepted: 01/04/2016] [Indexed: 01/15/2023]
Abstract
The homeodomain-only protein homeobox (HOPX) is the smallest known member of the homeodomain-containing protein family, atypically unable to bind DNA. HOPX is widely expressed in diverse tissues, where it is critically involved in the regulation of proliferation and differentiation. In human skin, HOPX controls epidermal formation through the regulation of late differentiation markers, and HOPX expression correlates with the level of differentiation in cutaneous pathologies. In mouse skin, Hopx was additionally identified as a lineage tracing marker of quiescent hair follicle stem cells. This review discusses current knowledge of HOPX structure and function in normal and pathological conditions.
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Affiliation(s)
- Anita Mariotto
- Laboratory of Cutaneous Biology, Service of Dermatology and Venereology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Olesya Pavlova
- Laboratory of Cutaneous Biology, Service of Dermatology and Venereology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Hyun-Sook Park
- Laboratory of Cutaneous Biology, Service of Dermatology and Venereology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Marcel Huber
- Laboratory of Cutaneous Biology, Service of Dermatology and Venereology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Daniel Hohl
- Laboratory of Cutaneous Biology, Service of Dermatology and Venereology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland.
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15
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Abstract
PURPOSE A distinct subset of genes, so-called "late fiber genes," is expressed in cells bordering the central, organelle-free zone (OFZ) of the lens. The purpose of this study was to identify additional members of this group. METHODS Fiber cells were harvested from various layers of the lens by laser micro-dissection and subjected to microarray, in situ hybridization, and Western blot analysis. RESULTS Expression of Livin, a member of the inhibitor of apoptosis protein (IAP) family encoded by Birc7, was strongly upregulated in deep cortical fiber cells. The depth-dependent distribution of Livin mRNA was confirmed by quantitative PCR and in situ hybridization. The onset of Livin expression coincided with loss of organelles from primary fiber cells. Livin expression peaked at 1 month but was sustained even in aged lenses. Antibodies raised against mouse Livin labeled multiple bands on immunoblots, reflecting progressive proteolysis of the parent molecule during differentiation. Mice harboring a floxed Birc7 allele were generated and used to conditionally delete Birc7 in lens. Lenses from knockout mice grew normally and retained their transparency, suggesting that Livin does not have an indispensable role in fiber cell differentiation. CONCLUSIONS Birc7 is a late fiber gene of the mouse lens. In tumor cells, Livin acts as an antiapoptotic protein, but its function in the lens is enigmatic. Livin is a RING domain protein with putative E3 ubiquitin ligase activity. Its expression in cells bordering the OFZ is consistent with a role in organelle degradation, a process in which the ubiquitin proteasome pathway has been implicated previously.
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Abstract
PURPOSE OF REVIEW Myocardial injury and disease often result in heart failure, a major cause of death worldwide. To achieve myocardial regeneration and foster development of efficient therapeutics for cardiac injury, it is essential to uncover molecular mechanisms that will promote myocardial regeneration. In this review, we examine the latest progress made in elucidation of the roles of small non-coding RNAs called microRNAs (miRs) in myocardial regeneration. RECENT FINDINGS Promising progress has been made in studying cardiac regeneration. Several miRs, which include miR-590, miR-199a, miR-17-92 cluster, miR-199a-214 cluster, miR-34a, and miR-15 family, have been recently shown to play an essential role in myocardial regeneration by regulating different processes during cardiac repair, including cell death, proliferation, and metabolism. For example, miR-590 promotes cardiac regeneration through activating cardiomyocyte proliferation, whereas miR-34a inhibits cardiac repair through inducing apoptosis. SUMMARY These recent findings shed new light on our understanding of myocardial regeneration and suggest potential novel therapeutic targets to treat cardiac disease.
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17
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Edqvist PHD, Fagerberg L, Hallström BM, Danielsson A, Edlund K, Uhlén M, Pontén F. Expression of human skin-specific genes defined by transcriptomics and antibody-based profiling. J Histochem Cytochem 2014; 63:129-41. [PMID: 25411189 DOI: 10.1369/0022155414562646] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
To increase our understanding of skin, it is important to define the molecular constituents of the cell types and epidermal layers that signify normal skin. We have combined a genome-wide transcriptomics analysis, using deep sequencing of mRNA from skin biopsies, with immunohistochemistry-based protein profiling to characterize the landscape of gene and protein expression in normal human skin. The transcriptomics and protein expression data of skin were compared to 26 (RNA) and 44 (protein) other normal tissue types. All 20,050 putative protein-coding genes were classified into categories based on patterns of expression. We found that 417 genes showed elevated expression in skin, with 106 genes expressed at least five-fold higher than that in other tissues. The 106 genes categorized as skin enriched encoded for well-known proteins involved in epidermal differentiation and proteins with unknown functions and expression patterns in skin, including the C1orf68 protein, which showed the highest relative enrichment in skin. In conclusion, we have applied a genome-wide analysis to identify the human skin-specific proteome and map the precise localization of the corresponding proteins in different compartments of the skin, to facilitate further functional studies to explore the molecular repertoire of normal skin and to identify biomarkers related to various skin diseases.
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Affiliation(s)
- Per-Henrik D Edqvist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden (PHDE, AD, KE, FP)
| | - Linn Fagerberg
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden (LF, BMH, MU)
| | - Björn M Hallström
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden (LF, BMH, MU)
| | - Angelika Danielsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden (PHDE, AD, KE, FP)
| | - Karolina Edlund
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden (PHDE, AD, KE, FP)
| | - Mathias Uhlén
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden (LF, BMH, MU)
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden (PHDE, AD, KE, FP)
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18
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Gordon WM, Zeller MD, Klein RH, Swindell WR, Ho H, Espetia F, Gudjonsson JE, Baldi PF, Andersen B. A GRHL3-regulated repair pathway suppresses immune-mediated epidermal hyperplasia. J Clin Invest 2014; 124:5205-18. [PMID: 25347468 DOI: 10.1172/jci77138] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 09/18/2014] [Indexed: 12/27/2022] Open
Abstract
Dermal infiltration of T cells is an important step in the onset and progression of immune-mediated skin diseases such as psoriasis; however, it is not known whether epidermal factors play a primary role in the development of these diseases. Here, we determined that the prodifferentiation transcription factor grainyhead-like 3 (GRHL3), which is essential during epidermal development, is dispensable for adult skin homeostasis, but required for barrier repair after adult epidermal injury. Consistent with activation of a GRHL3-regulated repair pathway in psoriasis, we found that GRHL3 is upregulated in lesional skin and binds known epidermal differentiation gene targets. Using an imiquimod-induced model of immune-mediated epidermal hyperplasia, we found that mice lacking GRHL3 have an exacerbated epidermal damage response, greater sensitivity to disease induction, delayed resolution of epidermal lesions, and resistance to anti-IL-22 therapy compared with WT animals. ChIP-Seq and gene expression profiling of murine skin revealed that while GRHL3 regulates differentiation pathways both during development and during repair from immune-mediated damage, it targets distinct sets of genes in the 2 processes. In particular, GRHL3 suppressed a number of alarmin and other proinflammatory genes after immune injury. This study identifies a GRHL3-regulated epidermal barrier repair pathway that suppresses disease initiation and helps resolve existing lesions in immune-mediated epidermal hyperplasia.
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Tao H, Yang JJ, Shi KH, Deng ZY, Li J. DNA methylation in cardiac fibrosis: new advances and perspectives. Toxicology 2014; 323:125-9. [PMID: 25017140 DOI: 10.1016/j.tox.2014.07.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 07/08/2014] [Accepted: 07/09/2014] [Indexed: 01/22/2023]
Abstract
Cardiac fibrosis is characterized by net accumulation of extracellular matrix (ECM) proteins in the cardiac interstitium, and contributes to both systolic and diastolic dysfunction in many cardiac pathophysiologic conditions. More specifically, cardiac fibroblasts are activated by a variety of pathological stimuli, thereby undergoing proliferation, differentiation to myofibroblasts, and production of various cytokines and ECM proteins. Thus, understanding the biological processes of cardiac fibroblasts will provide novel insights into the underlying mechanisms of cardiac fibrosis. DNA methylation is an important epigenetic mechanism, which often occurs in response to environmental stimuli and is crucial in regulating gene expression. The aberrant methylation of CpG island promoters of selected genes is the prominent epigenetic mechanism by which gene transcription can be effectively silenced. Aberrant hypermethylation of a few selected genes such as RASSF1A plays an important role in facilitating fibrotic fibroblast activation and in driving fibrosis. In this review we will discuss the mechanisms of DNA methylation and their implications for cardiac fibroblasts activation and fibrosis. Control of DNA methylation may serve as a new strategy for anti-fibrotic therapy.
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Affiliation(s)
- Hui Tao
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei 230601, China; Cardiovascular Research Center, Anhui Medical University, Hefei 230601, China
| | - Jing-Jing Yang
- Department of Pharmacology, The Second Hospital of Anhui Medical University, Hefei 230601, China; School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Kai-Hu Shi
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei 230601, China; Cardiovascular Research Center, Anhui Medical University, Hefei 230601, China.
| | - Zi-Yu Deng
- Department of Scientific and Educational, The Second Hospital of Anhui Medical University, Hefei 230032, China.
| | - Jun Li
- School of Pharmacy, Anhui Medical University, Hefei 230032, China.
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The homeobox only protein homeobox (HOPX) and colorectal cancer. Int J Mol Sci 2013; 14:23231-43. [PMID: 24287901 PMCID: PMC3876040 DOI: 10.3390/ijms141223231] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/31/2013] [Accepted: 11/01/2013] [Indexed: 12/13/2022] Open
Abstract
The HOP (homeobox only protein) homeobox (HOPX) is most closely related to the homeobox protein that contains a homeobox-like domain but lacks certain conserved residues required for DNA binding. Here, we review the current understanding of HOPX in the progression of colorectal cancer (CRC). HOPX was initially reported as a differentiation marker and is expressed in various normal tissues. In the colon, HOPX is expressed uniquely in the quiescent stem cell, +4, and in differentiated mucosal cells of the colon. HOPX expression is markedly suppressed in a subset of cancers, mainly in an epigenetic manner. CRC may include separate entities which are differentially characterized by HOPX expression from a prognostic point of view. HOPX itself can regulate epigenetics, and defective expression of HOPX can result in loss of tumor suppressive function and differentiation phenotype. These findings indicate that HOPX may be both a central regulator of epigenetic dynamics and a critical determinant for differentiation in human cells. HOPX downstream targets were identified in CRC cell lines and hold promise as candidates for therapeutic targets of CRC, such as EphA2 or AP-1. Further analysis will elucidate and confirm the precise role of such proteins in CRC progression.
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21
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Marcinkiewicz KM, Gudas LJ. Altered epigenetic regulation of homeobox genes in human oral squamous cell carcinoma cells. Exp Cell Res 2013; 320:128-43. [PMID: 24076275 DOI: 10.1016/j.yexcr.2013.09.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 09/11/2013] [Accepted: 09/17/2013] [Indexed: 12/18/2022]
Abstract
To gain insight into oral squamous cell carcinogenesis, we performed deep sequencing (RNAseq) of non-tumorigenic human OKF6-TERT1R and tumorigenic SCC-9 cells. Numerous homeobox genes are differentially expressed between OKF6-TERT1R and SCC-9 cells. Data from Oncomine, a cancer microarray database, also show that homeobox (HOX) genes are dysregulated in oral SCC patients. The activity of Polycomb repressive complexes (PRC), which causes epigenetic modifications, and retinoic acid (RA) signaling can control HOX gene transcription. HOXB7, HOXC10, HOXC13, and HOXD8 transcripts are higher in SCC-9 than in OKF6-TERT1R cells; using ChIP (chromatin immunoprecipitation) we detected PRC2 protein SUZ12 and the epigenetic H3K27me3 mark on histone H3 at these genes in OKF6-TERT1R, but not in SCC-9 cells. In contrast, IRX1, IRX4, SIX2 and TSHZ3 transcripts are lower in SCC-9 than in OKF6-TERT1R cells. We detected SUZ12 and the H3K27me3 mark at these genes in SCC-9, but not in OKF6-TERT1R cells. SUZ12 depletion increased HOXB7, HOXC10, HOXC13, and HOXD8 transcript levels and decreased the proliferation of OKF6-TERT1R cells. Transcriptional responses to RA are attenuated in SCC-9 versus OKF6-TERT1R cells. SUZ12 and H3K27me3 levels were not altered by RA at these HOX genes in SCC-9 and OKF6-TERT1R cells. We conclude that altered activity of PRC2 is associated with dysregulation of homeobox gene expression in human SCC cells, and that this dysregulation potentially plays a role in the neoplastic transformation of oral keratinocytes.
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Affiliation(s)
- Katarzyna M Marcinkiewicz
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, USA; Department of Pharmacology, Weill Cornell Graduate School of Medical Sciences of Cornell University, 1300 York Avenue, New York, NY 10065, USA
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22
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Bao X, Tang J, Lopez-Pajares V, Tao S, Qu K, Crabtree GR, Khavari PA. ACTL6a enforces the epidermal progenitor state by suppressing SWI/SNF-dependent induction of KLF4. Cell Stem Cell 2013; 12:193-203. [PMID: 23395444 DOI: 10.1016/j.stem.2012.12.014] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 10/05/2012] [Accepted: 12/04/2012] [Indexed: 10/27/2022]
Abstract
Somatic progenitors suppress differentiation to maintain tissue self-renewal. The mammalian SWI/SNF chromatin-remodeling complex regulates nucleosome packaging to control differentiation in embryonic and adult stem cells. Catalytic Brg1 and Brm subunits are required for these processes; however, the roles of SWI/SNF regulatory subunits are not fully understood. Here, we show that ACTL6a/BAF53A modulates the SWI/SNF complex to suppress differentiation in epidermis. Conditional loss of ACTL6a resulted in terminal differentiation, cell-cycle exit, and hypoplasia, whereas ectopic expression of ACTL6a promoted the progenitor state. A significant portion of genes regulated by ACTL6a were found to also be targets of KLF4, a known activator of epidermal differentiation. Mechanistically, we show that ACTL6a prevents SWI/SNF complex binding to promoters of KLF4 and other differentiation genes and that SWI/SNF catalytic subunits are required for full induction of KLF4 targets. Thus, ACTL6a controls the epidermal progenitor state by sequestering SWI/SNF to prevent activation of differentiation programs.
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Affiliation(s)
- Xiaomin Bao
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
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23
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Berletch JB, Deng X, Nguyen DK, Disteche CM. Female bias in Rhox6 and 9 regulation by the histone demethylase KDM6A. PLoS Genet 2013; 9:e1003489. [PMID: 23658530 PMCID: PMC3642083 DOI: 10.1371/journal.pgen.1003489] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 03/18/2013] [Indexed: 12/20/2022] Open
Abstract
The Rhox cluster on the mouse X chromosome contains reproduction-related homeobox genes expressed in a sexually dimorphic manner. We report that two members of the Rhox cluster, Rhox6 and 9, are regulated by de-methylation of histone H3 at lysine 27 by KDM6A, a histone demethylase with female-biased expression. Consistent with other homeobox genes, Rhox6 and 9 are in bivalent domains prior to embryonic stem cell differentiation and thus poised for activation. In female mouse ES cells, KDM6A is specifically recruited to Rhox6 and 9 for gene activation, a process inhibited by Kdm6a knockdown in a dose-dependent manner. In contrast, KDM6A occupancy at Rhox6 and 9 is low in male ES cells and knockdown has no effect on expression. In mouse ovary where Rhox6 and 9 remain highly expressed, KDM6A occupancy strongly correlates with expression. Our study implicates Kdm6a, a gene that escapes X inactivation, in the regulation of genes important in reproduction, suggesting that KDM6A may play a role in the etiology of developmental and reproduction-related effects of X chromosome anomalies.
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Affiliation(s)
- Joel B. Berletch
- Department of Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Xinxian Deng
- Department of Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Di Kim Nguyen
- Department of Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Christine M. Disteche
- Department of Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, School of Medicine, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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24
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Kretz M, Webster DE, Flockhart RJ, Lee CS, Zehnder A, Lopez-Pajares V, Qu K, Zheng GXY, Chow J, Kim GE, Rinn JL, Chang HY, Siprashvili Z, Khavari PA. Suppression of progenitor differentiation requires the long noncoding RNA ANCR. Genes Dev 2012; 26:338-43. [PMID: 22302877 DOI: 10.1101/gad.182121.111] [Citation(s) in RCA: 355] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) regulate diverse processes, yet a potential role for lncRNAs in maintaining the undifferentiated state in somatic tissue progenitor cells remains uncharacterized. We used transcriptome sequencing and tiling arrays to compare lncRNA expression in epidermal progenitor populations versus differentiating cells. We identified ANCR (anti-differentiation ncRNA) as an 855-base-pair lncRNA down-regulated during differentiation. Depleting ANCR in progenitor-containing populations, without any other stimuli, led to rapid differentiation gene induction. In epidermis, ANCR loss abolished the normal exclusion of differentiation from the progenitor-containing compartment. The ANCR lncRNA is thus required to enforce the undifferentiated cell state within epidermis.
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Affiliation(s)
- Markus Kretz
- Veterans Affairs Palo Alto Healthcare System, California 94304, USA
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Mattiuzzo NR, Toulza E, Jonca N, Serre G, Guerrin M. A large-scale multi-technique approach identifies forty-nine new players of keratinocyte terminal differentiation in human epidermis. Exp Dermatol 2011; 20:113-8. [PMID: 21255089 DOI: 10.1111/j.1600-0625.2010.01188.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
At the latest stage of terminal differentiation in the epidermis, granular keratinocytes (GKs) undergo cornification, a programmed cell death required for the establishment of a functional skin barrier. A complex genetic regulatory network orchestrates the underlying biochemical modifications, but very few transcription factors specific to this programme have been identified to date. Here, we describe a large-scale, multi-technique approach performed on cells purified from normal human epidermis, primarily focusing on the identification of regulators. We combined data from microarray analysis of cell fractions enriched in GKs or basal keratinocytes, from an expressed sequence tag (EST) library built from GKs and from an in silico promoter analysis of 52 differentiation-associated genes. Among 3576 genes potentially expressed in GK, 298 candidates were selected, and half were directly profiled for the first time in the different layers of the epidermis by quantitative real-time PCR. Forty-nine genes upregulated during terminal differentiation, associated with numerous function of GK including lipid synthesis and secretion, were identified. Of 94 transcription factors detected, 37 were found to be either positively or negatively regulated, suggesting their involvement as regulators of gene expression in the GKs. These results largely extend the number of genes known as involved in the latest step of the terminal differentiation of human epidermis as well as the number of transcription factors known to control the expression of these genes.
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Affiliation(s)
- Nicolas R Mattiuzzo
- UMR 5165 Epidermis Differentiation and Rheumatoid Autoimmunity, CNRS - University of Toulouse, Toulouse, France
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26
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Obarzanek-Fojt M, Favre B, Kypriotou M, Ryser S, Huber M, Hohl D. Homeodomain-only protein HOP is a novel modulator of late differentiation in keratinocytes. Eur J Cell Biol 2011; 90:279-90. [PMID: 21256618 DOI: 10.1016/j.ejcb.2010.11.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2010] [Revised: 11/03/2010] [Accepted: 11/03/2010] [Indexed: 02/03/2023] Open
Abstract
The homeodomain-only protein (HOP) contains an atypical homeodomain which is unable to bind to DNA due to mutations in residues important for DNA binding. Recently, HOP was reported to regulate proliferation/differentiation homeostasis in different cell types. In the present study, we performed transcriptional profiling of cultured primary human keratinocytes and noted a robust induction of HOP upon calcium-induced cell differentiation. Immunohistochemistry of human skin localized HOP to the granular layer in the epidermis. Overexpression of HOP using a lentiviral vector up-regulated FLG and LOR expression during keratinocyte differentiation. Conversely, decreasing HOP expression using small interfering RNA markedly reduced the calcium-induced expression of late markers of differentiation in vitro, with the most prominent effect on profilaggrin (FLG) mRNA. Moreover, mRNA levels of profilaggrin and loricrin were downregulated in the epidermis of HOP knockout mice. Analysis of skin disorders revealed altered HOP expression in lichen planus, psoriasis and squamous cell carcinoma (SCC). Our data indicate that HOP is a novel modulator of late terminal differentiation in keratinocytes.
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Affiliation(s)
- Magdalena Obarzanek-Fojt
- Department of Dermatology, University Hospital of Lausanne (CHUV), CH-1011 Lausanne, Switzerland
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