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Li X, Bie L, Wang Y, Hong Y, Zhou Z, Fan Y, Yan X, Tao Y, Huang C, Zhang Y, Sun X, Li JXH, Zhang J, Chang Z, Xi Q, Meng A, Shen X, Xie W, Liu N. LINE-1 transcription activates long-range gene expression. Nat Genet 2024; 56:1494-1502. [PMID: 38849613 DOI: 10.1038/s41588-024-01789-5] [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: 10/26/2023] [Accepted: 05/06/2024] [Indexed: 06/09/2024]
Abstract
Long interspersed nuclear element-1 (LINE-1 or L1) is a retrotransposon group that constitutes 17% of the human genome and shows variable expression across cell types. However, the control of L1 expression and its function in gene regulation are incompletely understood. Here we show that L1 transcription activates long-range gene expression. Genome-wide CRISPR-Cas9 screening using a reporter driven by the L1 5' UTR in human cells identifies functionally diverse genes affecting L1 expression. Unexpectedly, altering L1 expression by knockout of regulatory genes impacts distant gene expression. L1s can physically contact their distal target genes, with these interactions becoming stronger upon L1 activation and weaker when L1 is silenced. Remarkably, L1s contact and activate genes essential for zygotic genome activation (ZGA), and L1 knockdown impairs ZGA, leading to developmental arrest in mouse embryos. These results characterize the regulation and function of L1 in long-range gene activation and reveal its importance in mammalian ZGA.
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Affiliation(s)
- Xiufeng Li
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Luyao Bie
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yang Wang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yaqiang Hong
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ziqiang Zhou
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yiming Fan
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaohan Yan
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yibing Tao
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Chunyi Huang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yongyan Zhang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xueyan Sun
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - John Xiao He Li
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jing Zhang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zai Chang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Qiaoran Xi
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Anming Meng
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaohua Shen
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Wei Xie
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Nian Liu
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
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2
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Xia L, Lin H, Cao H, Lian J. Tenascin C as a novel zinc finger protein 750 target regulating the immunogenicity via DNA damage in lung squamous cell carcinoma. BMC Cancer 2024; 24:561. [PMID: 38711034 PMCID: PMC11071264 DOI: 10.1186/s12885-024-12285-8] [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: 01/18/2024] [Accepted: 04/18/2024] [Indexed: 05/08/2024] Open
Abstract
Modulation of DNA damage repair in lung squamous cell carcinoma (LUSC) can result in the generation of neoantigens and heightened immunogenicity. Therefore, understanding DNA damage repair mechanisms holds significant clinical relevance for identifying targets for immunotherapy and devising therapeutic strategies. Our research has unveiled that the tumor suppressor zinc finger protein 750 (ZNF750) in LUSC binds to the promoter region of tenascin C (TNC), leading to reduced TNC expression. This modulation may impact the malignant behavior of tumor cells and is associated with patient prognosis. Additionally, single-cell RNA sequencing (scRNA-seq) of LUSC tissues has demonstrated an inverse correlation between ZNF750/TNC expression levels and immunogenicity. Manipulation of the ZNF750-TNC axis in vitro within LUSC cells has shown differential sensitivity to CD8+ cells, underscoring its pivotal role in regulating cellular immunogenicity. Further transcriptome sequencing analysis, DNA damage repair assay, and single-strand break analyses have revealed the involvement of the ZNF750-TNC axis in determining the preference for homologous recombination (HR) repair or non-homologous end joining (NHEJ) repair of DNA damage. with involvement of the Hippo/ERK signaling pathway. In summary, this study sheds light on the ZNF750-TNC axis's role in DNA damage repair regulation in LUSC, laying a groundwork for future translational research in immune cell therapy for LUSC.
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Affiliation(s)
- Lu Xia
- Xiamen Cell Therapy Research Center, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361000, CN, China.
| | - Hexin Lin
- Department of Gastrointestinal Oncology Surgery, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361000, CN, China
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350000, CN, China
| | - Huifen Cao
- Institute of Genomics, School of Medicine, Huaqiao University, Xiamen, 361000, CN, China.
| | - Jiabian Lian
- Department of Clinical Laboratory, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361000, CN, China.
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Droll SH, Zhang BJ, Levine MC, Xue C, Ho PJ, Bao X. CASZ1 Is Essential for Skin Epidermal Terminal Differentiation. J Invest Dermatol 2024:S0022-202X(24)00172-6. [PMID: 38458428 DOI: 10.1016/j.jid.2024.02.014] [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: 10/16/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/10/2024]
Abstract
The barrier function of skin epidermis is crucial for our bodies to interface with the environment. Because epidermis continuously turns over throughout the lifetime, this barrier must be actively maintained by regeneration. Although several transcription factors have been established as essential activators in epidermal differentiation, it is unclear whether additional factors remain to be identified. In this study, we show that CASZ1, a multi zinc-finger transcription factor previously characterized in nonepithelial cell types, shows highest expression in skin epidermis. CASZ1 expression is upregulated during epidermal terminal differentiation. In addition, CASZ1 expression is impaired in several skin disorders with impaired barrier function, such as atopic dermatitis, psoriasis, and squamous cell carcinoma. Using transcriptome profiling coupled with RNA interference, we identified 674 differentially expressed genes with CASZ1 knockdown. Downregulated genes account for 91.2% of these differentially expressed genes and were enriched for barrier function. In organotypic epidermal regeneration, CASZ1 knockdown promoted proliferation and strongly impaired multiple terminal differentiation markers. Mechanistically, we found that CASZ1 upregulation in differentiation requires the action of both the master transcription factor, p63, and the histone acetyltransferase, p300. Taken together, our findings identify CASZ1 as an essential activator of epidermal differentiation, paving the way for future studies understanding of CASZ1 roles in skin disease.
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Affiliation(s)
- Stephenie H Droll
- Department of Molecular Biosciences, Weinberg College of Arts & Sciences, Northwestern University, Evanston, Illinois, USA
| | - Benny J Zhang
- Department of Molecular Biosciences, Weinberg College of Arts & Sciences, Northwestern University, Evanston, Illinois, USA
| | - Maxwell C Levine
- Department of Molecular Biosciences, Weinberg College of Arts & Sciences, Northwestern University, Evanston, Illinois, USA
| | - Celia Xue
- Department of Molecular Biosciences, Weinberg College of Arts & Sciences, Northwestern University, Evanston, Illinois, USA
| | - Patric J Ho
- Department of Molecular Biosciences, Weinberg College of Arts & Sciences, Northwestern University, Evanston, Illinois, USA
| | - Xiaomin Bao
- Department of Molecular Biosciences, Weinberg College of Arts & Sciences, Northwestern University, Evanston, Illinois, USA; Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA.
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Hu XT, Wu XF, Sui LM, Ao LQ, Pu CX, Yuan M, Xing W, Xu X. The GRHL3-regulated long non-coding RNA lnc-DC modulates keratinocytes differentiation by interacting with IGF2BP2 and up-regulating ZNF750. J Dermatol Sci 2024; 113:93-102. [PMID: 38383230 DOI: 10.1016/j.jdermsci.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 01/18/2024] [Accepted: 02/09/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND Aberrant keratinocytes differentiation has been demonstrated to be associated with a number of skin diseases. The roles of lncRNAs in keratinocytes differentiation remain to be largely unknown. OBJECTIVE Here we aim to investigate the role of lnc-DC in regulating epidermal keratinocytes differentiation. METHODS Expression of lnc-DC in the skin was queried in AnnoLnc and verified by FISH. The lncRNA expression profiles during keratinocytes differentiation were reanalyzed and verified by qPCR and FISH. Gene knock-down and over-expression were used to explore the role of lnc-DC in keratinocytes differentiation. The downstream target of lnc-DC was screened by whole transcriptome sequencing. CUT&RUN assay and siRNAs transfection was used to reveal the regulatory effect of GRHL3 on lnc-DC. The mechanism of lnc-DC regulating ZNF750 was revealed by RIP assay and RNA stability assay. RESULTS Lnc-DC was biasedly expressed in skin and up-regulated during epidermal keratinocytes differentiation. Knockdown lnc-DC repressed epidermal keratinocytes differentiation while over-express lnc-DC showed the opposite effect. GRHL3, a well-known transcription factor regulating keratinocytes differentiation, could bind to the promoter of lnc-DC and regulate its expression. By whole transcriptome sequencing, we identified that ZNF750 was a downstream target of lnc-DC during keratinocytes differentiation. Mechanistically, lnc-DC interacted with RNA binding protein IGF2BP2 to stabilize ZNF750 mRNA and up- regulated its downstream targets TINCR and KLF4. CONCLUSION Our study revealed the novel role of GRHL3/lnc-DC/ZNF750 axis in regulating epidermal keratinocytes differentiation, which may provide new therapeutic targets of aberrant keratinocytes differentiation related skin diseases.
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Affiliation(s)
- Xue-Ting Hu
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China; Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Army Medical University, Chongqing, China
| | - Xiao-Feng Wu
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China
| | - Lu-Min Sui
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China
| | - Luo-Quan Ao
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China
| | - Cheng-Xiu Pu
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China
| | - Mu Yuan
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China
| | - Wei Xing
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China.
| | - Xiang Xu
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China; Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Army Medical University, Chongqing, China.
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5
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Schwartz B, Levi H, Menon G, Maria R, Upcher A, Kotlovski Y, Oss-Ronen L, Cohen I. ZNF750 Regulates Skin Barrier Function by Driving Cornified Envelope and Lipid Processing Pathways. J Invest Dermatol 2024; 144:296-306.e3. [PMID: 37660780 DOI: 10.1016/j.jid.2023.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/02/2023] [Accepted: 08/16/2023] [Indexed: 09/05/2023]
Abstract
The epidermis is a constantly renewing stratified epithelial tissue that provides essential protective barrier functions. The major barrier is located at the outermost layers of the epidermis, formed by terminally differentiated keratinocytes reinforced by proteins of their cornified envelope and sequestered intercellular lipids. Disruptions to epidermal differentiation characterize various skin disorders. ZNF750 is an epithelial transcription factor essential for in vitro keratinocyte differentiation, whose truncating mutation in humans causes autosomal dominant psoriasis-like skin disease. In this study, we utilized an epidermal-specific Znf750 conditional knockout mouse model to uncover the role ZNF750 plays in epidermal development. We show that deletion of Znf750 in the developing skin does not block epidermal differentiation completely, suggesting in vivo compensatory feedback mechanisms, although it does result in impaired barrier function and perinatal lethality. Molecular dissection revealed ultrastructural defects in the differentiated layers of the epidermis, accompanied by alterations in the expression of ZNF750-dependent genes encoding key cornified envelope precursor proteins and lipid-processing enzymes, including gene subsets known to be mutated in human skin diseases involving impaired barrier function. Together, our findings provide molecular insights into the pathogenesis of human skin disease by linking ZNF750 to a subset of epidermal differentiation genes involved in barrier formation pathways.
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Affiliation(s)
- Bar Schwartz
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Hilla Levi
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | | | - Raquel Maria
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Alexander Upcher
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Yulia Kotlovski
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Liat Oss-Ronen
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Idan Cohen
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.
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6
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Smirnov A, Lena AM, Tosetti G, Yang X, Cappello A, Helmer Citterich M, Melino G, Candi E. Epigenetic priming of an epithelial enhancer by p63 and CTCF controls expression of a skin-restricted gene XP33. Cell Death Discov 2023; 9:446. [PMID: 38065940 PMCID: PMC10709559 DOI: 10.1038/s41420-023-01716-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/27/2023] [Accepted: 11/07/2023] [Indexed: 07/11/2024] Open
Abstract
The transcription factor p63 is a renowned master regulator of gene expression of stratified epithelia. While multiple proteins have been identified as p63 bona fide targets, little is known about non-coding RNAs (ncRNAs) whose transcription is controlled by p63. Here, we describe a skin-specific non-coding RNA XP33 as a novel target of p63. XP33 levels are increased during keratinocyte differentiation in vitro, while its depletion results in decreased expression of late cornified gene LCE2D. By using publicly available multi-omics data, we show that CTCF and p63 establish an epithelial enhancer to prime XP33 transcription in a tissue-restricted manner. XP33 promoter and enhancer form a chromatin loop exclusively in keratinocytes but not in other cell types. Moreover, the XP33 enhancer is occupied by differentiation-specific factors that control XP33 transcription. Altogether, we identify a tissue-specific non-coding RNA whose expression is epigenetically regulated by p63 and CTCF.
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Affiliation(s)
- Artem Smirnov
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", via Montpellier 1, 00133, Rome, Italy
- Biochemistry Laboratory, Istituto Dermopatico Immacolata (IDI-IRCCS), 00166, Rome, Italy
| | - Anna Maria Lena
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", via Montpellier 1, 00133, Rome, Italy
| | - Giulia Tosetti
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", via Montpellier 1, 00133, Rome, Italy
| | - Xue Yang
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", via Montpellier 1, 00133, Rome, Italy
- The Third Affiliated Hospital of Soochow University, Institutes for Translational Medicine, Soochow University, 215000, Suzhou, China
| | - Angela Cappello
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", via Montpellier 1, 00133, Rome, Italy
- Interdisciplinary Department of Medicine University of Bari "Aldo Moro", 70124, Bari, Italy
| | - Manuela Helmer Citterich
- Biology Department, University of Rome "Tor Vergata", Via della Ricerca Scientifica, snc, 00133, Rome, Italy
| | - Gerry Melino
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", via Montpellier 1, 00133, Rome, Italy
| | - Eleonora Candi
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", via Montpellier 1, 00133, Rome, Italy.
- Biochemistry Laboratory, Istituto Dermopatico Immacolata (IDI-IRCCS), 00166, Rome, Italy.
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7
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Cui Z, Wei H, Goding C, Cui R. Stem cell heterogeneity, plasticity, and regulation. Life Sci 2023; 334:122240. [PMID: 37925141 DOI: 10.1016/j.lfs.2023.122240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/06/2023]
Abstract
As a population of homogeneous cells with both self-renewal and differentiation potential, stem cell pools are highly compartmentalized and contain distinct subsets that exhibit stable but limited heterogeneity during homeostasis. However, their striking plasticity is showcased under natural or artificial stress, such as injury, transplantation, cancer, and aging, leading to changes in their phenotype, constitution, metabolism, and function. The complex and diverse network of cell-extrinsic niches and signaling pathways, together with cell-intrinsic genetic and epigenetic regulators, tightly regulate both the heterogeneity during homeostasis and the plasticity under perturbation. Manipulating these factors offers better control of stem cell behavior and a potential revolution in the current state of regenerative medicine. However, disruptions of normal regulation by genetic mutation or excessive plasticity acquisition may contribute to the formation of tumors. By harnessing innovative techniques that enhance our understanding of stem cell heterogeneity and employing novel approaches to maximize the utilization of stem cell plasticity, stem cell therapy holds immense promise for revolutionizing the future of medicine.
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Affiliation(s)
- Ziyang Cui
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing 100034, China.
| | - Hope Wei
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, United States of America
| | - Colin Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX37DQ, UK
| | - Rutao Cui
- Skin Disease Research Institute, The 2nd Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
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8
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Rua AJ, Whitehead RD, Alexandrescu AT. NMR structure verifies the eponymous zinc finger domain of transcription factor ZNF750. J Struct Biol X 2023; 8:100093. [PMID: 37655311 PMCID: PMC10465944 DOI: 10.1016/j.yjsbx.2023.100093] [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: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023] Open
Abstract
ZNF750 is a nuclear transcription factor that activates skin differentiation and has tumor suppressor roles in several cancers. Unusually, ZNF750 has only a single zinc-finger (ZNF) domain, Z*, with an amino acid sequence that differs markedly from the CCHH family consensus. Because of its sequence differences Z* is classified as degenerate, presumed to have lost the ability to bind the zinc ion required for folding. AlphaFold predicts an irregular structure for Z* with low confidence. Low confidence predictions are often inferred to be intrinsically disordered regions of proteins, which would be the case if Z* did not bind Zn2+. We use NMR and CD spectroscopy to show that a 25-51 segment of ZNF750 corresponding to the Z* domain folds into a well-defined antiparallel ββα tertiary structure with a pM dissociation constant for Zn2+ and a thermal stability >80 °C. Of three alternative Zn2+ ligand sets, Z* uses a CCHC rather than the expected CCHH ligating motif. The switch in the last ligand maintains the folding topology and hydrophobic core of the classical ZNF motif. CCHC ZNFs are typically associated with protein-protein interactions, raising the possibility that ZNF750 interacts with DNA through other proteins rather than directly. The structure of Z* provides context for understanding the function of the domain and its cancer-associated mutations. We expect other ZNFs currently classified as degenerate could be CCHC-type structures like Z*.
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Affiliation(s)
- Antonio J. Rua
- Department of Molecular and Cellular Biology, University of Connecticut, United States
| | - Richard D. Whitehead
- Department of Molecular and Cellular Biology, University of Connecticut, United States
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9
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Malin J, Martinez-Ruiz GU, Zhao Y, Shissler SC, Cowan JE, Ding Y, Morales-Sanchez A, Ishikawa M, Lavaert M, Das A, Butcher D, Warner AC, Kallarakal M, Chen J, Kedei N, Kelly M, Brinster LR, Allman D, Bhandoola A. Expression of the transcription factor Klf6 by thymic epithelial cells is required for thymus development. SCIENCE ADVANCES 2023; 9:eadg8126. [PMID: 37967174 PMCID: PMC10651122 DOI: 10.1126/sciadv.adg8126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 10/16/2023] [Indexed: 11/17/2023]
Abstract
Thymic epithelial cells (TEC) control T cell development and play essential roles in establishing self-tolerance. By using Foxn1-Cre-driven ablation of Klf6 gene in TEC, we identified Klf6 as a critical factor in TEC development. Klf6 deficiency resulted in a hypoplastic thymus-evident from fetal stages into adulthood-in which a dramatic increase in the frequency of apoptotic TEC was observed. Among cortical TEC (cTEC), a previously unreported cTEC population expressing the transcription factor Sox10 was relatively expanded. Within medullary TEC (mTEC), mTEC I and Tuft-like mTEC IV were disproportionately decreased. Klf6 deficiency altered chromatin accessibility and affected TEC chromatin configuration. Consistent with these defects, naïve conventional T cells and invariant natural killer T cells were reduced in the spleen. Late stages of T cell receptor-dependent selection of thymocytes were affected, and mice exhibited autoimmunity. Thus, Klf6 has a prosurvival role and affects the development of specific TEC subsets contributing to thymic function.
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Affiliation(s)
- Justin Malin
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gustavo Ulises Martinez-Ruiz
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Research Division, Faculty of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
- Children’s Hospital Federico Gomez, Mexico City, Mexico
| | - Yongge Zhao
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Susannah C. Shissler
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer E. Cowan
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Institute of Immunity and Transplantation, University College London, London, UK
| | - Yi Ding
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Abigail Morales-Sanchez
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Children’s Hospital Federico Gomez, Mexico City, Mexico
| | - Masaki Ishikawa
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Marieke Lavaert
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Arundhoti Das
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Donna Butcher
- Molecular Histopathology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Andrew C. Warner
- Molecular Histopathology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Melissa Kallarakal
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jingqiu Chen
- Office of Science and Technology Resources, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- ACROBiosystems, Newark, DE, USA
| | - Noemi Kedei
- Office of Science and Technology Resources, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael Kelly
- Single Cell Analysis Facility, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lauren R. Brinster
- Division of Veterinary Resources, Office of Research Services, National Institutes of Health, Bethesda, MD, USA
| | - David Allman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Avinash Bhandoola
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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10
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Rua AJ, Whitehead Iii RD, Alexandrescu AT. WITHDRAWN: NMR structure verifies the eponymous zinc finger domain of transcription factor ZNF750. J Struct Biol 2023:108003. [PMID: 37487847 DOI: 10.1016/j.jsb.2023.108003] [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: 06/21/2023] [Revised: 07/16/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023]
Abstract
This article was initially published in the Journal of Structural Biology, instead of the Journal of Structural Biology: X, due to a publisher error. We regret the inconvenience. The link to the article published in Journal of Structural Biology: X is presented below: https://www.sciencedirect.com/science/article/pii/S2590152423000090. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/policies/article-withdrawal.
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Affiliation(s)
- Antonio J Rua
- Department of Molecular and Cellular Biology, University of Connecticut
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11
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Yi Q, Zhao Y, Xia R, Wei Q, Chao F, Zhang R, Bian P, Lv L. TRIM29 hypermethylation drives esophageal cancer progression via suppression of ZNF750. Cell Death Discov 2023; 9:191. [PMID: 37365152 DOI: 10.1038/s41420-023-01491-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 06/06/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023] Open
Abstract
Esophageal cancer (ESCA) is the seventh most frequent and deadly neoplasm. Due to the lack of early diagnosis and high invasion/metastasis, the prognosis of ESCA remains very poor. Herein, we identify skin-related signatures as the most deficient signatures in invasive ESCA, which are regulated by the transcription factor ZNF750. Of note, we find that TRIM29 level strongly correlated with the expression of many genes in the skin-related signatures, including ZNF750. TRIM29 is significantly down-regulated due to hypermethylation of its promoter in both ESCA and precancerous lesions compared to normal tissues. Low TRIM29 expression and high methylation levels of its promoter are associated with malignant progression and poor clinical outcomes in ESCA patients. Functionally, TRIM29 overexpression markedly hinders proliferation, migration, invasion, and epithelial-mesenchymal transition of esophageal cancer cells, whereas opposing results are observed when TRIM29 is silenced in vitro. In addition, TRIM29 inhibits metastasis in vivo. Mechanistically, TRIM29 downregulation suppresses the expression of the tumor suppressor ZNF750 by activating the STAT3 signaling pathway. Overall, our study demonstrates that TRIM29 expression and its promoter methylation status could be potential early diagnostic and prognostic markers. It highlights the role of the TRIM29-ZNF750 signaling axis in modulating tumorigenesis and metastasis of esophageal cancer.
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Affiliation(s)
- Qiyi Yi
- School of Basic Medical Sciences, Anhui Medical University, 230032, Hefei, Anhui, China
| | - Yujia Zhao
- School of Basic Medical Sciences, Anhui Medical University, 230032, Hefei, Anhui, China
- Department of education training, The First People's Hospital of Changzhou, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Ran Xia
- Department of Cancer Epigenetics Program, Anhui Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230031, Hefei, Anhui, China
| | - Qinqin Wei
- School of Basic Medical Sciences, Anhui Medical University, 230032, Hefei, Anhui, China
| | - Fengmei Chao
- Department of Cancer Epigenetics Program, Anhui Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230031, Hefei, Anhui, China
| | - Rui Zhang
- Department of Oncology, The First Affiliated Hospital of Anhui University of Chinese Medicine, 230031, Hefei, Anhui, China
| | - Po Bian
- School of Basic Medical Sciences, Anhui Medical University, 230032, Hefei, Anhui, China.
| | - Lei Lv
- Department of Cancer Epigenetics Program, Anhui Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230031, Hefei, Anhui, China.
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12
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Fierro C, Gatti V, La Banca V, De Domenico S, Scalera S, Corleone G, Fanciulli M, De Nicola F, Mauriello A, Montanaro M, Calin GA, Melino G, Peschiaroli A. The long non-coding RNA NEAT1 is a ΔNp63 target gene modulating epidermal differentiation. Nat Commun 2023; 14:3795. [PMID: 37365156 DOI: 10.1038/s41467-023-39011-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
The transcription factor ΔNp63 regulates epithelial stem cell function and maintains the integrity of stratified epithelial tissues by acting as transcriptional repressor or activator towards a distinct subset of protein-coding genes and microRNAs. However, our knowledge of the functional link between ∆Np63 transcriptional activity and long non-coding RNAs (lncRNAs) expression is quite limited. Here, we show that in proliferating human keratinocytes ∆Np63 represses the expression of the lncRNA NEAT1 by recruiting the histone deacetylase HDAC1 to the proximal promoter of NEAT1 genomic locus. Upon induction of differentiation, ∆Np63 down-regulation is associated by a marked increase of NEAT1 RNA levels, resulting in an increased assembly of paraspeckles foci both in vitro and in human skin tissues. RNA-seq analysis associated with global DNA binding profile (ChIRP-seq) revealed that NEAT1 associates with the promoter of key epithelial transcription factors sustaining their expression during epidermal differentiation. These molecular events might explain the inability of NEAT1-depleted keratinocytes to undergo the proper formation of epidermal layers. Collectively, these data uncover the lncRNA NEAT1 as an additional player of the intricate network orchestrating epidermal morphogenesis.
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Affiliation(s)
- Claudia Fierro
- Department of Experimental Medicine, Tor Vergata Oncoscience Research (TOR), University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
- Translational Pediatrics and Clinical Genetics Research Division, Bambino Gesù Children's Hospital, IRCSS, Piazza Sant'Onofrio, 4, Rome, Italy
| | - Veronica Gatti
- Institute of Translational Pharmacology (IFT), CNR, Via Fosso del Cavaliere 100, 00133, Rome, Italy
| | - Veronica La Banca
- Department of Experimental Medicine, Tor Vergata Oncoscience Research (TOR), University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Sara De Domenico
- Department of Experimental Medicine, Tor Vergata Oncoscience Research (TOR), University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Stefano Scalera
- UOSD SAFU, Department of Research, Advanced Diagnostics, and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giacomo Corleone
- UOSD SAFU, Department of Research, Advanced Diagnostics, and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Maurizio Fanciulli
- UOSD SAFU, Department of Research, Advanced Diagnostics, and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Francesca De Nicola
- UOSD SAFU, Department of Research, Advanced Diagnostics, and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Alessandro Mauriello
- Department of Experimental Medicine, Tor Vergata Oncoscience Research (TOR), University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Manuela Montanaro
- Department of Experimental Medicine, Tor Vergata Oncoscience Research (TOR), University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - George A Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Gerry Melino
- Department of Experimental Medicine, Tor Vergata Oncoscience Research (TOR), University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Angelo Peschiaroli
- Institute of Translational Pharmacology (IFT), CNR, Via Fosso del Cavaliere 100, 00133, Rome, Italy.
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13
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Mudambi S, Fitzgerald M, Pera P, Washington D, Chamberlain S, Fidrus E, Hegedűs C, Remenyik E, Shafirstein G, Bellnier D, Paragh G. KDM1A inhibition increases UVA toxicity and enhances photodynamic therapy efficacy. PHOTODERMATOLOGY, PHOTOIMMUNOLOGY & PHOTOMEDICINE 2023; 39:226-234. [PMID: 35968606 PMCID: PMC10089661 DOI: 10.1111/phpp.12826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 07/25/2022] [Accepted: 08/08/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Lysine-specific histone demethylase 1 (KDM1A/LSD1) regulates multiple cellular functions, including cellular proliferation, differentiation, and DNA repair. KDM1A is overexpressed in squamous cell carcinoma of the skin and inhibition of KDM1A can suppress cutaneous carcinogenesis. Despite the role of KDM1A in skin and DNA repair, the effect of KDM1A inhibition on cellular ultraviolet (UV) response has not been studied. METHODS The ability of KDM1A inhibitor bizine to modify cell death after UVA and UVB exposure was tested in normal human keratinocytes and melanocytes, HaCaT, and FaDu cell lines. KDM1A was also downregulated using shRNA and inhibited by phenelzine in HaCaT and FaDu cells to confirm the role of KDM1A in UVA response. In addition, cellular reactive oxygen species (ROS) changes were assessed by a lipid-soluble fluorescent indicator of lipid oxidation, and ROS-related gene regulation using qPCR. During photodynamic therapy (PDT) studies HaCaT and FaDu cells were treated with aminolaevulinic acid (5-ALA) or HPPH (2-[1-hexyloxyethyl]-2-devinyl pyropheophorbide-a) sodium and irradiated with 0-8 J/cm2 red LED light. RESULTS KDM1A inhibition sensitized cells to UVA radiation-induced cell death but not to UVB. KDM1A inhibition increased ROS generation as detected by increased lipid peroxidation and the upregulation of ROS-responsive genes. The effectiveness of both ALA and HPPH PDT significantly improved in vitro in HaCaT and FaDu cells after KDM1A inhibition. CONCLUSION KDM1A is a regulator of cellular UV response and KDM1A inhibition can improve PDT efficacy.
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Affiliation(s)
- Shaila Mudambi
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, United States 14263
- Department of Dermatology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, United States 14263
| | - Megan Fitzgerald
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, United States 14263
- Department of Dermatology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, United States 14263
| | - Paula Pera
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, United States 14263
- Department of Dermatology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, United States 14263
| | - Deschana Washington
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, United States 14263
| | - Sarah Chamberlain
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, United States 14263
- Photodynamic Therapy Center, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, United States 14263
| | - Eszter Fidrus
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Nagyerdei korut 98, Debrecen, Hungary, H-4032
| | - Csaba Hegedűs
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Nagyerdei korut 98, Debrecen, Hungary, H-4032
| | - Eva Remenyik
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Nagyerdei korut 98, Debrecen, Hungary, H-4032
| | - Gal Shafirstein
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, United States 14263
- Photodynamic Therapy Center, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, United States 14263
| | - David Bellnier
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, United States 14263
- Photodynamic Therapy Center, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, United States 14263
| | - Gyorgy Paragh
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, United States 14263
- Department of Dermatology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, United States 14263
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14
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Butera A, Agostini M, Cassandri M, De Nicola F, Fanciulli M, D’Ambrosio L, Falasca L, Nardacci R, Wang L, Piacentini M, Knight RA, Jia W, Sun Q, Shi Y, Wang Y, Candi E, Melino G. ZFP750 affects the cutaneous barrier through regulating lipid metabolism. SCIENCE ADVANCES 2023; 9:eadg5423. [PMID: 37115925 PMCID: PMC10146900 DOI: 10.1126/sciadv.adg5423] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
An essential function of the epidermis is to provide a physical barrier that prevents the loss of water. Essential mediators of this barrier function include ceramides, cholesterol, and very long chain fatty acids, and their alteration causes human pathologies, including psoriasis and atopic dermatitis. A frameshift mutation in the human ZNF750 gene, which encodes a zinc finger transcription factor, has been shown to cause a seborrhea-like dermatitis. Here, we show that genetic deletion of the mouse homolog ZFP750 results in loss of epidermal barrier function, which is associated with a substantial reduction of ceramides, nonpolar lipids. The alteration of epidermal lipid homeostasis is directly linked to the transcriptional activity of ZFP750. ZFP750 directly and/or indirectly regulates the expression of crucial enzymes primarily involved in the biosynthesis of ceramides. Overall, our study identifies the transcription factor ZFP750 as a master regulator epidermal homeostasis through lipid biosynthesis and thus contributing to our understanding of the pathogenesis of several human skin diseases.
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Affiliation(s)
- Alessio Butera
- Department of Experimental Medicine, TOR, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Massimiliano Agostini
- Department of Experimental Medicine, TOR, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Matteo Cassandri
- Department of Oncohematology, Bambino Gesù Children’s Hospital, 00146 Rome, Italy
| | - Francesca De Nicola
- Department of Research, Advanced Diagnostics, and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Maurizio Fanciulli
- Department of Research, Advanced Diagnostics, and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Lorenzo D’Ambrosio
- Department of Research, Advanced Diagnostics, and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Laura Falasca
- Laboratory of Electron Microscopy, National Institute for Infectious Diseases “L. Spallanzani,” IRCCS, Rome Italy
| | - Roberta Nardacci
- Laboratory of Electron Microscopy, National Institute for Infectious Diseases “L. Spallanzani,” IRCCS, Rome Italy
- Departmental Faculty of Medicine and Surgery, Saint Camillus International University of Health Sciences (UniCamillus), Rome, Italy
| | - Lu Wang
- University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Mauro Piacentini
- Laboratory of Electron Microscopy, National Institute for Infectious Diseases “L. Spallanzani,” IRCCS, Rome Italy
| | - Richard A. Knight
- Department of Experimental Medicine, TOR, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Wei Jia
- University of Hawaii Cancer Center, Honolulu, HI 96813, USA
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Qiang Sun
- Laboratory of Cell Engineering, Institute of Biotechnology, Research Unit of Cell Death Mechanism, 2021RU008, Chinese Academy of Medical Science, 20 Dongda Street, Beijing, 100071, China
| | - Yufang Shi
- The Third Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Soochow University, Suzhou 215123, China
| | - Ying Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Eleonora Candi
- Department of Experimental Medicine, TOR, University of Rome “Tor Vergata”, 00133 Rome, Italy
- IDI-IRCCS, via Monti di Creta, 106, 00166 Rome, Italy
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome “Tor Vergata”, 00133 Rome, Italy
- Corresponding author.
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15
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Montanaro M, Agostini M, Anemona L, Bonanno E, Servadei F, Finazzi Agrò E, Asimakopoulos AD, Ganini C, Cipriani C, Signoretti M, Bove P, Rugolo F, Imperiali B, Melino G, Mauriello A, Scimeca M. ZNF750: A Novel Prognostic Biomarker in Metastatic Prostate Cancer. Int J Mol Sci 2023; 24:ijms24076519. [PMID: 37047491 PMCID: PMC10095592 DOI: 10.3390/ijms24076519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/24/2023] [Accepted: 03/25/2023] [Indexed: 04/03/2023] Open
Abstract
Prostate cancer is the most frequently diagnosed cancer and the fifth leading cause of cancer death among men in 2020. The clinical decision making for prostate cancer patients is based on the stratification of the patients according to both clinical and pathological parameters such as Gleason score and prostate-specific antigen levels. However, these tools still do not adequately predict patient outcome. The aim of this study was to investigate whether ZNF750 could have a role in better stratifying patients, identifying those with a higher risk of metastasis and with the poorest prognosis. The data reported here revealed that ZNF750 protein levels are reduced in human prostate cancer samples, and this reduction is even higher in metastatic samples. Interestingly, nuclear positivity is significantly reduced in patients with metastatic prostate cancer, regardless of both Gleason score and grade group. More importantly, the bioinformatics analysis indicates that ZNF750 expression is positively correlated with better prognosis. Overall, our findings suggest that nuclear expression of ZNF750 may be a reliable prognostic biomarker for metastatic prostate cancer, which lays the foundation for the development of new biological therapies.
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16
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Lou LQ, Zhou WQ, Song X, Chen Z. Elevation of hsa-miR-7-5p level mediated by CtBP1-p300-AP1 complex targets ATXN1 to trigger NF-κB-dependent inflammation response. J Mol Med (Berl) 2023; 101:223-235. [PMID: 36629882 DOI: 10.1007/s00109-022-02274-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 10/18/2022] [Accepted: 11/15/2022] [Indexed: 01/12/2023]
Abstract
Nuclear factor-κB (NF-κB)-mediated inflammation is a major cause of acute respiratory distress syndrome (ARDS). However, the regulatory mechanisms by which NF-κB transactivates proinflammatory cytokines remain unclear in the pathogenesis of ARDS. Herein, we report that the activating protein 1 (AP1) transcription factor recruits a histone acetyltransferase p300 and a transcriptional regulator C-terminal binding protein 1 (CtBP1) to assemble the CtBP1-p300-AP1 complex, which transactivates the expression of hsa-miR-7-5p in ARDS biopsies. Overexpressed hsa-miR-7-5p binds to the three prime untranslated regions (3'-UTRs) of ataxin 1 (ATXN1), suppressing its expression. Decreased ATXN1 expression relieves its repression of NF-κB, causing the induction of proinflammatory cytokine genes and triggering an inflammatory response. Depletion of CtBP1 or treatments with two CtBP1 inhibitors (NSC95397 and 4-methylthio-2-oxobutanoate (MTOB)) in human macrophages impairs the assembly of the CtBP2-p300-AP1 complex, resulting in decreased hsa-miR-7-5p levels, upregulation of ATXN1, and attenuation of proinflammatory cytokines. A similar regulatory mechanism was observed in lipopolysaccharide-treated mice. Our results reveal that increased hsa-miR-7-5p level mediated by the CtBP1-p300-AP1 complex targets ATXN1 to trigger an NF-κB-dependent inflammatory response. Interfering with this signaling pathway to block the inflammatory response may be a strategy for treating ARDS. KEY MESSAGES : The transcription factor AP1 recruits p300 and CtBP1 to form a transcriptional complex, which transactivates the expression of hsa-miR-7-5p in ARDS biopsies. Overexpressed hsa-miR-7-5p binds to the 3'-UTR of ATXN1, suppressing its expression. The decreased ATXN1 impaired its suppression of NF-κB, causing the induction of proinflammatory cytokine genes and triggering inflammation response. Disruption of the assembly of CtBP2-p300-AP1 complex upregulates ATXN1 and attenuates inflammation.
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Affiliation(s)
- Li-Qiong Lou
- Central Supply Service Department, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, 330006, Jiangxi, China
| | - Wen-Qiang Zhou
- Medical Department of Graduate School, Nanchang University, Nanchang, 330006, Jiangxi, China
- Department of Emergency, Donghu District, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, 92 Aiguo Rd, Nanchang, 330006, Jiangxi, China
| | - Xin Song
- Medical Department of Graduate School, Nanchang University, Nanchang, 330006, Jiangxi, China
- Department of Emergency, Donghu District, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, 92 Aiguo Rd, Nanchang, 330006, Jiangxi, China
| | - Zhi Chen
- Department of Emergency, Donghu District, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, 92 Aiguo Rd, Nanchang, 330006, Jiangxi, China.
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17
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Alotaibi A, Gadekar VP, Gundla PS, Mandarthi S, Ravi S, Mallya D, Tungekar A, Lavanya BV, Bhagavath AK, Cordero MW, Pitkaniemi J, Seetharam RN, Bepari A, Hebbar P. A comprehensive analysis of mRNA expression profiles of Esophageal Squamous Cell Carcinoma reveals downregulation of Desmoglein 1 and crucial genomic targets. Cancer Biomark 2023; 38:465-487. [PMID: 38073377 DOI: 10.3233/cbm-230145] [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] [Indexed: 12/26/2023]
Abstract
AIM Esophageal Squamous Cell Carcinoma (ESCC) is a histological subtype of esophageal cancer that begins in the squamous cells in the esophagus. In only 19% of the ESCC-diagnosed patients, a five-year survival rate has been seen. This necessitates the identification of high-confidence biomarkers for early diagnosis, prognosis, and potential therapeutic targets for the mitigation of ESCC. METHOD We performed a meta-analysis of 10 mRNA datasets and identified consistently perturbed genes across the studies. Then, integrated with ESCC ATLAS to segregate 'core' genes to identify consequences of primary gene perturbation events leading to gene-gene interactions and dysregulated molecular signaling pathways. Further, by integrating with toxicogenomics data, inferences were drawn for gene interaction with environmental exposures, trace elements, chemical carcinogens, and drug chemicals. We also deduce the clinical outcomes of candidate genes based on survival analysis using the ESCC related dataset in The Cancer Genome Atlas. RESULT We identified 237 known and 18 novel perturbed candidate genes. Desmoglein 1 (DSG1) is one such gene that we found significantly downregulated (Fold Change =-1.89, p-value = 8.2e-06) in ESCC across six different datasets. Further, we identified 31 'core' genes (that either harbor genetic variants or are regulated by epigenetic modifications) and found regulating key biological pathways via adjoining genes in gene-gene interaction networks. Functional enrichment analysis showed dysregulated biological processes and pathways including "Extracellular matrix", "Collagen trimmer" and "HPV infection" are significantly overrepresented in our candidate genes. Based on the toxicogenomic inferences from Comparative Toxicogenomics Database we report the key genes that interacted with risk factors such as tobacco smoking, zinc, nitroso benzylmethylamine, and drug chemicals such as cisplatin, Fluorouracil, and Mitomycin in relation to ESCC. We also point to the STC2 gene that shows a high risk for mortality in ESCC patients. CONCLUSION We identified novel perturbed genes in relation to ESCC and explored their interaction network. DSG1 is one such gene, its association with microbiota and a clinical presentation seen commonly with ESCC hints that it is a good candidate for early diagnostic marker. Besides, in this study we highlight candidate genes and their molecular connections to risk factors, biological pathways, drug chemicals, and the survival probability of ESCC patients.
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Affiliation(s)
- Amal Alotaibi
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Veerendra P Gadekar
- Mbiomics LLC, Lewes DE, USA
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | | | | | | | | | | | - Ashok Kumar Bhagavath
- Department of Cellular and Molecular Biology, University of Texas Health Science Center, Tyler, Texas, TX, USA
| | - MaryAnne Wong Cordero
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Janne Pitkaniemi
- Finnish Cancer Registry, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Raviraja N Seetharam
- Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India
| | - Asmatanzeem Bepari
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Prashantha Hebbar
- Mbiomics LLC, Lewes DE, USA
- Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India
- Meta Biosciences Pvt Ltd., Manipal - GOK Bioincubator, Advanced Research Center, Manipal, India
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18
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Ferrarese R, Izzo A, Andrieux G, Lagies S, Bartmuss JP, Masilamani AP, Wasilenko A, Osti D, Faletti S, Schulzki R, Yuan S, Kling E, Ribecco V, Heiland DH, Tholen S, Prinz M, Pelicci G, Kammerer B, Boerries M, Carro MS. ZBTB18 inhibits SREBP-dependent lipid synthesis by halting CTBPs and LSD1 activity in glioblastoma. Life Sci Alliance 2022; 6:6/1/e202201400. [PMID: 36414381 PMCID: PMC9684030 DOI: 10.26508/lsa.202201400] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/23/2022] Open
Abstract
Enhanced fatty acid synthesis is a hallmark of tumors, including glioblastoma. SREBF1/2 regulate the expression of enzymes involved in fatty acid and cholesterol synthesis. Yet, little is known about the precise mechanism regulating SREBP gene expression in glioblastoma. Here, we show that a novel interaction between the co-activator/co-repressor CTBP and the tumor suppressor ZBTB18 regulates the expression of SREBP genes. In line with our findings, metabolic assays and glucose tracing analysis confirm the reduction in several phospholipid species upon ZBTB18 expression. Our study identifies CTBP1/2 and LSD1 as co-activators of SREBP genes and indicates that the functional activity of the CTBP-LSD1 complex is altered by ZBTB18. ZBTB18 binding to the SREBP gene promoters is associated with reduced LSD1 demethylase activity of H3K4me2 and H3K9me2 marks. Concomitantly, the interaction between LSD1, CTBP, and ZNF217 is increased, suggesting that ZBTB18 promotes LSD1 scaffolding function. Our results outline a new epigenetic mechanism enrolled by ZBTB18 and its co-factors to regulate fatty acid synthesis that could be targeted to treat glioblastoma patients.
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Affiliation(s)
- Roberto Ferrarese
- Department of Neurosurgery, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Breisgau, Germany
| | - Annalisa Izzo
- Department of Neurosurgery, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Breisgau, Germany
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany,German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simon Lagies
- Center for Biological Systems Analysis, University of Freiburg, Breisgau, Germany,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Johanna Paulina Bartmuss
- Department of Neurosurgery, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Breisgau, Germany
| | - Anie Priscilla Masilamani
- Department of Neurosurgery, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Breisgau, Germany
| | - Alix Wasilenko
- Department of Neurosurgery, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Breisgau, Germany
| | - Daniela Osti
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Stefania Faletti
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Rana Schulzki
- Department of Neurosurgery, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Breisgau, Germany
| | - Shuai Yuan
- Department of Neurosurgery, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Breisgau, Germany
| | - Eva Kling
- Department of Neurosurgery, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Breisgau, Germany
| | - Valentino Ribecco
- Department of Neurosurgery, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Breisgau, Germany
| | - Dieter Henrik Heiland
- Department of Neurosurgery, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Breisgau, Germany,German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Tholen
- Institute of Clinical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marco Prinz
- Institute of Neuropathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany,Signaling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany,Center for NeuroModulation (NeuroModul), University of Freiburg, Freiburg, Germany
| | - Giuliana Pelicci
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, Milan, Italy,Department of Translational Medicine, Piemonte Orientale University “Amedeo Avo-Gadro,” Novara, Italy
| | - Bernd Kammerer
- Center for Biological Systems Analysis, University of Freiburg, Breisgau, Germany,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany,BIOSS Centre of Biological Signaling Studies, University of Freiburg, Freiburg Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany,German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maria Stella Carro
- Department of Neurosurgery, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisgau, Germany
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19
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Kantzer CG, Yang W, Grommisch D, Patil KV, Mak KHM, Shirokova V, Genander M. ID1 and CEBPA coordinate epidermal progenitor cell differentiation. Development 2022; 149:282464. [PMID: 36330928 PMCID: PMC9845743 DOI: 10.1242/dev.201262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
Abstract
The regulatory circuits that coordinate epidermal differentiation during development are still not fully understood. Here, we report that the transcriptional regulator ID1 is enriched in mouse basal epidermal progenitor cells and find ID1 expression to be diminished upon differentiation. In utero silencing of Id1 impairs progenitor cell proliferation, leads to precocious delamination of targeted progenitor cells and enables differentiated keratinocytes to retain progenitor markers and characteristics. Transcriptional profiling suggests that ID1 acts by mediating adhesion to the basement membrane while inhibiting spinous layer differentiation. Co-immunoprecipitation reveals ID1 binding to transcriptional regulators of the class I bHLH family. We localize bHLH Tcf3, Tcf4 and Tcf12 to epidermal progenitor cells during epidermal stratification and establish TCF3 as a downstream effector of ID1-mediated epidermal proliferation. Finally, we identify crosstalk between CEBPA, a known mediator of epidermal differentiation, and Id1, and demonstrate that CEBPA antagonizes BMP-induced activation of Id1. Our work establishes ID1 as a key coordinator of epidermal development, acting to balance progenitor proliferation with differentiation and unveils how functional crosstalk between CEBPA and Id1 orchestrates epidermal lineage progression.
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Affiliation(s)
| | - Wei Yang
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - David Grommisch
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Kim Vikhe Patil
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Kylie Hin-Man Mak
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Vera Shirokova
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Maria Genander
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77, Stockholm, Sweden,Author for correspondence ()
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20
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Talabot-Ayer D, Diaz-Barreiro A, Modarressi A, Palmer G. Epigenetic remodeling of downstream enhancer regions is linked to selective expression of the IL1F10 gene in differentiated human keratinocytes. Gene 2022; 842:146800. [PMID: 35961432 DOI: 10.1016/j.gene.2022.146800] [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: 03/23/2022] [Revised: 07/02/2022] [Accepted: 08/05/2022] [Indexed: 11/04/2022]
Abstract
Interleukin (IL)-38, encoded by the IL1F10 gene, is a member of the IL-1 family of cytokines. IL-38 is constitutively expressed in epithelia in healthy humans, and in particular in epidermal keratinocytes in the skin. IL-38 expression is closely correlated with keratinocyte differentiation. The aim of this study was to further characterize the regulation of IL1F10 expression and the mechanisms involved in its selective induction in differentiated human keratinocytes. We observed coordinated expression of two IL1F10 transcripts, transcribed from two different promoters, upon differentiation of primary human keratinocytes. Using ENCODE datasets and ChIP-qPCR on ex vivo isolated normal human epidermis, we identified regulatory regions located downstream of the IL1F10 gene, which displayed features of differentiated keratinocyte-specific enhancers. Expression of the IL1F10 gene was linked to changes in the epigenetic landscape at these downstream enhancer regions in human epidermis. Overexpression of the transcription factors KLF4 and TAp63β in an immortalized normal human keratinocyte (iNHK) cell line promoted the expression of mRNA encoding the differentiation markers keratin 10 and involucrin, and of IL1F10. ChIP-qPCR experiments indicated that KLF4 and TAp63β overexpression also modified the chromatin state of the proximal downstream enhancer region, suggesting a role for KLF4 and TAp63β in directly or indirectly regulating IL1F10 transcription. In conclusion, expression of the IL1F10 gene in differentiated keratinocytes in normal human epidermis involves coordinated transcription from two promoters and is linked to epigenetic remodeling of enhancer regions located downstream of the gene.
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Affiliation(s)
- Dominique Talabot-Ayer
- Division of Rheumatology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Alejandro Diaz-Barreiro
- Division of Rheumatology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Ali Modarressi
- Division of Plastic, Reconstructive & Aesthetic Surgery, Department of Surgery, Geneva University Hospitals, Geneva, Switzerland
| | - Gaby Palmer
- Division of Rheumatology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
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21
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Gahan JM, Leclère L, Hernandez-Valladares M, Rentzsch F. A developmental role for the chromatin-regulating CoREST complex in the cnidarian Nematostella vectensis. BMC Biol 2022; 20:184. [PMID: 35999597 PMCID: PMC9400249 DOI: 10.1186/s12915-022-01385-1] [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: 01/04/2022] [Accepted: 08/08/2022] [Indexed: 11/10/2022] Open
Abstract
Background Chromatin-modifying proteins are key players in the regulation of development and cell differentiation in animals. Most chromatin modifiers, however, predate the evolution of animal multicellularity, and how they gained new functions and became integrated into the regulatory networks underlying development is unclear. One way this may occur is the evolution of new scaffolding proteins that integrate multiple chromatin regulators into larger complexes that facilitate coordinated deposition or removal of different chromatin modifications. We test this hypothesis by analyzing the evolution of the CoREST-Lsd1-HDAC complex. Results Using phylogenetic analyses, we show that a bona fide CoREST homolog is found only in choanoflagellates and animals. We then use the sea anemone Nematostella vectensis as a model for early branching metazoans and identify a conserved CoREST complex by immunoprecipitation and mass spectrometry of an endogenously tagged Lsd1 allele. In addition to CoREST, Lsd1 and HDAC1/2 this complex contains homologs of HMG20A/B and PHF21A, two subunits that have previously only been identified in mammalian CoREST complexes. NvCoREST expression overlaps fully with that of NvLsd1 throughout development, with higher levels in differentiated neural cells. NvCoREST mutants, generated using CRISPR-Cas9, fail to develop beyond the primary polyp stage, thereby revealing essential roles during development and for the differentiation of cnidocytes that phenocopy NvLsd1 mutants. We also show that this requirement is cell autonomous using a cell-type-specific rescue approach. Conclusions The identification of a Nematostella CoREST-Lsd1-HDAC1/2 complex, its similarity in composition with the vertebrate complex, and the near-identical expression patterns and mutant phenotypes of NvCoREST and NvLsd1 suggest that the complex was present before the last common cnidarian-bilaterian ancestor and thus represents an ancient component of the animal developmental toolkit.
Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01385-1.
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Affiliation(s)
- James M Gahan
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway.
| | - Lucas Leclère
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-Sur-Mer (LBDV), 06230, Villefranche-sur-Mer, France
| | - Maria Hernandez-Valladares
- Department of Physical Chemistry, University of Granada, Campus Fuentenueva s/n, 18071, Granada, Spain.,Proteomics Facility of the University of Bergen (PROBE), University of Bergen, 5020, Bergen, Norway
| | - Fabian Rentzsch
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway. .,Department for Biological Sciences, University of Bergen, Thormøhlensgate 53, 5006, Bergen, Norway.
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22
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Xia L, Lin H, Zhou Y, Lian J. ZNF750 facilitates carcinogenesis via promoting the expression of long non-coding RNA CYTOR and influences pharmacotherapy response in colon adenocarcinoma. J Zhejiang Univ Sci B 2022; 23:587-596. [PMID: 35794688 DOI: 10.1631/jzus.b2100939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The epidermal cell differentiation regulator zinc finger protein 750 (ZNF750) is a transcription factor containing the Cys2His2 (C2H2) domain, the zinc finger structure of which is located at the N-terminal 25-46 amino acids of ZNF750. It can promote the expression of differentiation-related factors while inhibiting the expression of progenitor cell-related genes. ZNF750 is directly regulated by p63 (encoded by the TP63 gene, belonging to the TP53 superfamily). The Krüppel-like factor 4 (KLF4), repressor element-1 (RE-1)-silencing transcription factor (REST) corepressor 1 (RCOR1), lysine demethylase 1A (KDM1A), and C-terminal-binding protein 1/2 (CTBP1/2) chromatin regulators cooperate with ZNF750 to repress epidermal progenitor genes and activate the expression of epidermal terminal differentiation genes (Sen et al., 2012; Boxer et al., 2014). Besides, ZNF750 and the regulatory network composed of bone morphogenetic protein (BMP) signaling pathway, long non-coding RNAs (lncRNAs) (anti-differentiation non-coding RNA (ANCR) and tissue differentiation-inducing non-protein coding RNA (TINCR)), musculoaponeurotic fibrosarcoma oncogene (MAF)/MAF family B (MAFB), grainy head-like 3 (GRHL3), and positive regulatory domain zinc finger protein 1 (PRDM1) jointly promote epidermal cell differentiation (Sen et al., 2012).
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Affiliation(s)
- Lu Xia
- Xiamen Cell Therapy Research Center, the First Affiliated Hospital of Xiamen University, Xiamen 361000, China
| | - Hexin Lin
- Department of Colorectal Surgery, the First Affiliated Hospital of Fujian Medical University, Fuzhou 350004, China
| | - Yanming Zhou
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Xiamen University, Xiamen 361000, China
| | - Jiabian Lian
- Department of Clinical Laboratory, the First Affiliated Hospital of Xiamen University, Xiamen 361000, China.
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23
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Malovitski K, Sarig O, Assaf S, Mohamad J, Malki L, Bergson S, Peled A, Eskin-Schwartz M, Gat A, Pavlovsky M, Sprecher E. Loss-of-function variants in KLF4 underlie autosomal dominant palmoplantar keratoderma. Genet Med 2022; 24:1085-1095. [PMID: 35168889 DOI: 10.1016/j.gim.2022.01.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/09/2022] [Accepted: 01/14/2022] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Palmoplantar keratodermas (PPKs) form a group of disorders characterized by thickening of palm and sole skin. Over the past 2 decades, many types of inherited PPKs have been found to result from abnormal expression, processing, or function of adhesion proteins. METHODS We used exome and direct sequencing to detect causative pathogenic variants. Functional analysis of these variants was conducted using reverse transcription quantitative polymerase chain reaction, immunofluorescence confocal microscopy, immunoblotting, a promoter reporter assay, and chromatin immunoprecipitation. RESULTS We identified 2 heterozygous variants (c.1226A>G and c.633_634dupGT) in KLF4 in 3 individuals from 2 different unrelated families affected by a dominant form of PPK. Immunofluorescence staining for a number of functional markers revealed reduced epidermal DSG1 expression in patients harboring heterozygous KLF4 variants. Accordingly, human keratinocytes either transfected with constructs expressing these variants or downregulated for KLF4 displayed reduced DSG1 expression, which in turn has previously been found to be associated with PPK. A chromatin immunoprecipitation assay confirmed direct binding of KLF4 to the DSG1 promoter region. The ability of mutant KLF4 to transactivate the DSG1 promoter was significantly decreased when compared with wild-type KLF4. CONCLUSION Loss-of-function variants in KLF4 cause a novel form of dominant PPK and show its importance in the regulation of epidermal differentiation.
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Affiliation(s)
- Kiril Malovitski
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ofer Sarig
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Sari Assaf
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Janan Mohamad
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Liron Malki
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Shir Bergson
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Alon Peled
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Marina Eskin-Schwartz
- Faculty of Health Sciences, Ben Gurion University of the Negev, Be'er Sheva, Israel; Genetic Institute, Soroka University Medical Center, Be'er Sheva, Israel
| | - Andrea Gat
- Institute of Pathology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Mor Pavlovsky
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Eli Sprecher
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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24
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Chen X, Zhang Q, Dang X, Fan J, Song T, Li Z, Duan N, Zhang W. The CtIP-CtBP1/2-HDAC1-AP1 transcriptional complex is required for the transrepression of DNA damage modulators in the pathogenesis of osteosarcoma. Transl Oncol 2022; 21:101429. [PMID: 35452995 PMCID: PMC9047009 DOI: 10.1016/j.tranon.2022.101429] [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: 01/18/2022] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
CtIP couples with CtBP1/2 heterodimer, HDAC1, and two subunits of AP1 transcription factor to assemble a complex. The CtIP-CtBP1/2-HDAC1-AP1 complex is required for the inhibition of MLH1, MSH3, BRCA1, and CDKN1A in osteosarcoma cells. Overexpression of MLH1, MSH3, BRCA1, and CDKN1A in osteosarcoma cells inhibits tumor cell growth in vitro and in vivo.
Most tumors, including osteosarcomas, have deficiencies in DNA damage repair. However, the regulatory mechanisms underlying dysregulation of DNA damage repair genes are still being investigated. In this study, we reveal that C-terminal binding protein (CtBP) interacting protein (CtIP) couples with three transcriptional regulators, CtBP1/2 heterodimer, histone deacetylase 1 (HDAC1), and two subunits of the activating protein 1 (AP1) transcription factor to assemble a transcriptional complex. This complex specifically controls the expression of four genes involved in DNA damage and repair processes: MutL homolog 1 (MLH1), MutS Homolog 3 (MSH3), breast cancer type 1 (BRCA1), and cyclin dependent kinase inhibitor 1A (CDKN1A). Chromatin immunoprecipitation (ChIP) assay results revealed that the CtIP-CtBP1/2-HDAC1-AP1 complex regulated these four genes by binding to their promoters through the TGAT/CTCA consensus sequence. The depletion of CtIP, CtBP1/2, and HDAC1 increased the expression levels of MLH1, MSH3, BRCA1, and CDKN1A and inhibited in vitro and in vivo osteosarcoma cell growth. Overexpression of MLH1, MSH3, BRCA1, or CDKN1A in osteosarcoma cells can reduce cell viability, colony formation, cell migration, and tumor growth. Our findings suggest that the CtIP-CtBP1/2-HDAC1-AP1 complex is required for mediation of DNA damage processes for the pathogenesis of osteosarcoma.
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Affiliation(s)
- Xun Chen
- Department of Orthopaedics, Honghui Hospital, Xi'an Jiaotong University, 76 Nanguo Rd, Beilin District, Xi'an, Shaanxi 710054, China; Department of Orthopaedics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710005, China
| | - Qian Zhang
- The Department of Surgery Room, Xi'an Daxing Hospital, Xi'an, Shaanxi 710016, China
| | - Xiaoqian Dang
- Department of Orthopaedics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710005, China
| | - Jinzhu Fan
- Department of Orthopaedics, Honghui Hospital, Xi'an Jiaotong University, 76 Nanguo Rd, Beilin District, Xi'an, Shaanxi 710054, China
| | - Tao Song
- Department of Orthopaedics, Honghui Hospital, Xi'an Jiaotong University, 76 Nanguo Rd, Beilin District, Xi'an, Shaanxi 710054, China
| | - Zhong Li
- Department of Orthopaedics, Honghui Hospital, Xi'an Jiaotong University, 76 Nanguo Rd, Beilin District, Xi'an, Shaanxi 710054, China
| | - Ning Duan
- Department of Orthopaedics, Honghui Hospital, Xi'an Jiaotong University, 76 Nanguo Rd, Beilin District, Xi'an, Shaanxi 710054, China.
| | - Wentao Zhang
- Department of Orthopaedics, Honghui Hospital, Xi'an Jiaotong University, 76 Nanguo Rd, Beilin District, Xi'an, Shaanxi 710054, China.
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25
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Inhibition of CtBP-Regulated Proinflammatory Gene Transcription Attenuates Psoriatic Skin Inflammation. J Invest Dermatol 2022; 142:390-401. [PMID: 34293351 PMCID: PMC8770725 DOI: 10.1016/j.jid.2021.06.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/25/2021] [Accepted: 06/03/2021] [Indexed: 02/03/2023]
Abstract
Psoriasis is a chronic immune-mediated disease characterized by excessive proliferation of epidermal keratinocytes and increased immune cell infiltration to the skin. Although it is well-known that psoriasis pathogenesis is driven by aberrant production of proinflammatory cytokines, the mechanisms underlying the imbalance between proinflammatory and anti-inflammatory cytokine expression are incompletely understood. In this study, we report that the transcriptional coregulators CtBP1 and 2 can transactivate a common set of proinflammatory genes both in the skin of imiquimod-induced mouse psoriasis model and in human keratinocytes and macrophages stimulated by imiquimod. We find that mice overexpressing CtBP1 in epidermal keratinocytes display severe skin inflammation phenotypes with increased expression of T helper type 1 and T helper type 17 cytokines. We also find that the expression of CtBPs and CtBP-target genes is elevated both in human psoriatic lesions and in the mouse imiquimod psoriasis model. Moreover, we were able to show that topical treatment with a peptidic inhibitor of CtBP effectively suppresses the CtBP-regulated proinflammatory gene expression and thus attenuates psoriatic inflammation in the imiquimod mouse model. Together, our findings suggest to our knowledge previously unreported strategies for therapeutic modulation of the immune response in inflammatory skin diseases.
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26
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Alterations of Chromatin Regulators in the Pathogenesis of Urinary Bladder Urothelial Carcinoma. Cancers (Basel) 2021; 13:cancers13236040. [PMID: 34885146 PMCID: PMC8656749 DOI: 10.3390/cancers13236040] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Urinary bladder cancer is one of the ten major cancers worldwide, with higher incidences in males, in smokers, and in highly industrialized countries. New therapies beyond cytotoxic chemotherapy are urgently needed to improve treatment of these tumors. A better understanding of the mechanisms underlying their development may help in this regard. Recently, it was discovered that a group of proteins regulating the state of chromatin and thus gene expression is exceptionally and frequently affected by gene mutations in bladder cancers. Altered function of these mutated chromatin regulators must therefore be fundamental in their development, but how and why is poorly understood. Here we review the current knowledge on changes in chromatin regulators and discuss their possible consequences for bladder cancer development and options for new therapies. Abstract Urothelial carcinoma (UC) is the most frequent histological type of cancer in the urinary bladder. Genomic changes in UC activate MAPK and PI3K/AKT signal transduction pathways, which increase cell proliferation and survival, interfere with cell cycle and checkpoint control, and prevent senescence. A more recently discovered additional category of genetic changes in UC affects chromatin regulators, including histone-modifying enzymes (KMT2C, KMT2D, KDM6A, EZH2), transcription cofactors (CREBBP, EP300), and components of the chromatin remodeling complex SWI/SNF (ARID1A, SMARCA4). It is not yet well understood how these changes contribute to the development and progression of UC. Therefore, we review here the emerging knowledge on genomic and gene expression alterations of chromatin regulators and their consequences for cell differentiation, cellular plasticity, and clonal expansion during UC pathogenesis. Our analysis identifies additional relevant chromatin regulators and suggests a model for urothelial carcinogenesis as a basis for further mechanistic studies and targeted therapy development.
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27
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The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation. Nat Genet 2021; 53:1564-1576. [PMID: 34650237 PMCID: PMC8763320 DOI: 10.1038/s41588-021-00947-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 09/01/2021] [Indexed: 01/24/2023]
Abstract
Transcription factors bind DNA sequence motif vocabularies in cis-regulatory elements (CREs) to modulate chromatin state and gene expression during cell state transitions. A quantitative understanding of how motif lexicons influence dynamic regulatory activity has been elusive due to the combinatorial nature of the cis-regulatory code. To address this, we undertook multiomic data profiling of chromatin and expression dynamics across epidermal differentiation to identify 40,103 dynamic CREs associated with 3,609 dynamically expressed genes, then applied an interpretable deep-learning framework to model the cis-regulatory logic of chromatin accessibility. This analysis framework identified cooperative DNA sequence rules in dynamic CREs regulating synchronous gene modules with diverse roles in skin differentiation. Massively parallel reporter assay analysis validated temporal dynamics and cooperative cis-regulatory logic. Variants linked to human polygenic skin disease were enriched in these time-dependent combinatorial motif rules. This integrative approach shows the combinatorial cis-regulatory lexicon of epidermal differentiation and represents a general framework for deciphering the organizational principles of the cis-regulatory code of dynamic gene regulation.
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28
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Na HY, Park JH, Shin SA, Lee S, Lee H, Chae H, Choung H, Kim N, Chung JH, Kim JE. Targeted Sequencing Revealed Distinct Mutational Profiles of Ocular and Extraocular Sebaceous Carcinomas. Cancers (Basel) 2021; 13:4810. [PMID: 34638295 PMCID: PMC8508046 DOI: 10.3390/cancers13194810] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/10/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
The biological behavior of sebaceous carcinoma (SeC) is relatively indolent; however, local invasion or distant metastasis is sometimes reported. Nevertheless, a lack of understanding of the genetic background of SeC makes it difficult to apply effective systemic therapy. This study was designed to investigate major genetic alterations in SeCs in Korean patients. A total of 29 samples, including 20 ocular SeCs (SeC-Os) and 9 extraocular SeCs (SeC-EOs), were examined. Targeted next-generation sequencing tests including 171 cancer-related genes were performed. TP53 and PIK3CA genes were frequently mutated in both SeC-Os and SeC-EOs with slight predominance in SeC-Os, whereas the NOTCH1 gene was more commonly mutated in SeC-EOs. In clinical correlation, mutations in RUNX1 and ATM were associated with development of distant metastases, and alterations in MSH6 and BRCA1 were associated with inferior progression-free survival (all p < 0.05). In conclusion, our study revealed distinct genetic alterations between SeC-Os and SeC-EOs and some important prognostic molecular markers. Mutations in potentially actionable genes, including EGFR, ERBB2, and mismatch repair genes, were noted, suggesting consideration of a clinical trial in intractable cases.
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Affiliation(s)
- Hee Young Na
- Department of Pathology, Seoul National University College of Medicine, Seoul 03080, Korea; (H.Y.N.); (J.H.P.); (S.A.S.)
- Department of Pathology and Translational Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Jeong Hwan Park
- Department of Pathology, Seoul National University College of Medicine, Seoul 03080, Korea; (H.Y.N.); (J.H.P.); (S.A.S.)
- Department of Pathology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul 07067, Korea
| | - Sun Ah Shin
- Department of Pathology, Seoul National University College of Medicine, Seoul 03080, Korea; (H.Y.N.); (J.H.P.); (S.A.S.)
- Department of Pathology, National Cancer Center, Goyang 10408, Korea
| | - Sejoon Lee
- Precision Medicine Center, Seoul National University Bundang Hospital, Seongnam 13620, Korea;
| | - Heonyi Lee
- Bioinformatics Collaboration Unit, Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul 03722, Korea;
| | - Heejoon Chae
- Division of Computer Science, Sookmyung Women’s University, Seoul 04312, Korea;
| | - HoKyung Choung
- Department of Ophthalmology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul 07067, Korea;
| | - Namju Kim
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seongnam 13620, Korea;
| | - Jin-Haeng Chung
- Department of Pathology, Seoul National University College of Medicine, Seoul 03080, Korea; (H.Y.N.); (J.H.P.); (S.A.S.)
- Department of Pathology and Translational Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Ji Eun Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul 03080, Korea; (H.Y.N.); (J.H.P.); (S.A.S.)
- Department of Pathology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul 07067, Korea
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Rusek M, Krasowska D. Non-Coding RNA in Systemic Sclerosis: A Valuable Tool for Translational and Personalized Medicine. Genes (Basel) 2021; 12:1296. [PMID: 34573278 PMCID: PMC8471866 DOI: 10.3390/genes12091296] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023] Open
Abstract
Epigenetic factors are heritable and ultimately play a role in modulating gene expression and, thus, in regulating cell functions. Non-coding RNAs have growing recognition as novel biomarkers and crucial regulators of pathological conditions in humans. Their characteristic feature is being transcribed in a tissue-specific pattern. Now, there is emerging evidence that lncRNAs have been identified to be involved in the differentiation of human skin, wound healing, fibrosis, inflammation, and immunological response. Systemic sclerosis (SSc) is a heterogeneous autoimmune disease characterized by fibrosis, vascular abnormalities, and immune system activation. The pathogenesis remains elusive, but clinical manifestations reveal autoimmunity with the presence of specific autoantibodies, activation of innate and adaptive immunity, vascular changes, and active deposition of extracellular matrix components leading to fibrosis. The use of multi-omics studies, including NGS, RNA-seq, or GWAS, has proposed that the non-coding genome may be a significant player in its pathogenesis. Moreover, it may unravel new therapeutic targets in the future. The aim of this review is to show the pathogenic role of long non-coding RNAs in systemic sclerosis. Investigation of these transcripts' functions has the potential to elucidate the molecular pathology of SSc and provide new opportunities for drug-targeted therapy for this disorder.
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Affiliation(s)
- Marta Rusek
- Department of Dermatology, Venereology and Pediatric Dermatology, Laboratory for Immunology of Skin Diseases, Medical University of Lublin, 20-080 Lublin, Poland;
- Department of Pathophysiology, Medical University of Lublin, 20-090 Lublin, Poland
| | - Dorota Krasowska
- Department of Dermatology, Venereology and Pediatric Dermatology, Laboratory for Immunology of Skin Diseases, Medical University of Lublin, 20-080 Lublin, Poland;
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30
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The transrepression and transactivation roles of CtBPs in the pathogenesis of different diseases. J Mol Med (Berl) 2021; 99:1335-1347. [PMID: 34196767 DOI: 10.1007/s00109-021-02107-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/31/2021] [Accepted: 06/25/2021] [Indexed: 02/06/2023]
Abstract
Gene transcription is strictly controlled by transcriptional complexes, which are assemblies of transcription factors, transcriptional regulators, and co-regulators. Mammalian genomes encode two C-terminal-binding proteins (CtBPs), CtBP1 and CtBP2, which are both well-known transcriptional corepressors of oncogenic processes. Their overexpression in tumors is associated with malignant behavior, such as uncontrolled cell proliferation, migration, and invasion, as well as with an increase in the epithelial-mesenchymal transition. CtBPs coordinate with other transcriptional regulators, such as histone deacetylases (HDACs) and histone acetyltransferases (p300 and CBP [CREBP-binding protein]) that contain the PXDLS motif, and with transcription factors to assemble transcriptional complexes that dock onto the promoters of genes to initiate gene transcription. Emerging evidence suggests that CtBPs function as both corepressors and coactivators in different biological processes ranging from apoptosis to inflammation and osteogenesis. Therapeutic targeting of CtBPs or the interactions required to form transcriptional complexes has also shown promising effects in preventing disease progression. This review summarizes the most recent progress in the study of CtBP functions and therapeutic inhibitors in different biological processes. This knowledge may enable a better understanding of the complexity of the roles of CtBPs, while providing new insights into therapeutic strategies that target CtBPs.
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31
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Chakravarthi VP, Ratri A, Masumi S, Borosha S, Ghosh S, Christenson LK, Roby KF, Wolfe MW, Rumi MAK. Granulosa cell genes that regulate ovarian follicle development beyond the antral stage: The role of estrogen receptor β. Mol Cell Endocrinol 2021; 528:111212. [PMID: 33676987 PMCID: PMC8916094 DOI: 10.1016/j.mce.2021.111212] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023]
Abstract
Follicle development beyond the preantral stage is dependent on gonadotropins. FSH signaling is crucial for the advancement of preantral follicles to the antral stage, and LH signaling is essential for further maturation of preovulatory follicles. Estrogen is intricately tied to gonadotropin signaling during the advanced stages of folliculogenesis. We observed that Erβnull ovarian follicles fail to develop beyond the antral stage, even after exogenous gonadotropin stimulation. As ERβ is primarily expressed in the granulosa cells (GCs), we explored the gonadotropin-regulated GC genes that induce maturation of antral follicles. Synchronized follicle development was induced by administration of exogenous gonadotropins to wildtype 4-wk-old female rats. The GC transcriptome was analyzed via RNA-sequencing before and after gonadotropin stimulation. An Erβnull mutant model that fails to show follicle maturation was also included in order to identify the ERβ-regulated genes involved at this step. We observed that specific groups of genes were differentially expressed in response to PMSG or hCG administration in wildtype rats. While some of the PMSG or hCG-induced genes showed a similar expression pattern in Erβnull GCs, a subset of PMSG- or hCG-induced genes showed a differential expression pattern in Erβnull GCs. These latter ERβ-regulated genes included previously known FSH or LH target genes including Lhcgr, Cyp11a1, Cyp19a1, Pgr, Runx2, Egfr, Kiss1, and Ptgs2, which are involved in follicle development, oocyte maturation, and ovulation. We also identified novel ERβ-regulated genes including Jaml, Galnt6, Znf750, Dusp9, Wnt16, and Mageb16 that failed to respond to gonadotropin stimulation in Erβnull GCs. Our findings indicate that the gonadotropin-induced spatiotemporal pattern of gene expression is essential for ovarian follicle maturation beyond the antral stage. However, expression of a subset of those gonadotropin-induced genes is dependent on transcriptional regulation by ERβ.
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Affiliation(s)
| | - Anamika Ratri
- Department of Molecular and Integrative Physiology, Kansas City, KS, USA
| | - Saeed Masumi
- Department of Pathology and Laboratory Medicine, Kansas City, KS, USA
| | - Shaon Borosha
- Department of Pathology and Laboratory Medicine, Kansas City, KS, USA
| | - Subhra Ghosh
- Department of Pathology and Laboratory Medicine, Kansas City, KS, USA
| | - Lane K Christenson
- Department of Molecular and Integrative Physiology, Kansas City, KS, USA; Institute for Reproduction and Perinatal Research, University of Kansas Medical Center, Kansas City, KS, USA
| | - Katherine F Roby
- Department of Anatomy and Cell Biology, Kansas City, KS, USA; Institute for Reproduction and Perinatal Research, University of Kansas Medical Center, Kansas City, KS, USA
| | - Michael W Wolfe
- Department of Molecular and Integrative Physiology, Kansas City, KS, USA; Institute for Reproduction and Perinatal Research, University of Kansas Medical Center, Kansas City, KS, USA
| | - M A Karim Rumi
- Department of Pathology and Laboratory Medicine, Kansas City, KS, USA; Institute for Reproduction and Perinatal Research, University of Kansas Medical Center, Kansas City, KS, USA.
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32
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Ana Choi SS, Ko JMY, Yu VZ, Ning L, Lung ML. Differentiation-related zinc finger protein 750 suppresses cell growth in esophageal squamous cell carcinoma. Oncol Lett 2021; 22:513. [PMID: 33986873 DOI: 10.3892/ol.2021.12774] [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: 11/08/2020] [Accepted: 03/12/2021] [Indexed: 11/06/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a deadly squamous cell carcinoma (SCC) of the esophagus. Development of SCCs is associated with the deregulation of the squamous cell lineage program and/or keratinocyte terminal differentiation by genomic and genetic aberrations; thus, these processes must be tightly controlled to maintain normal squamous cell development. Zinc finger protein 750 (ZNF750) is a gene involved in keratinocyte terminal differentiation and is frequently mutated and putatively silenced in ESCC, which implicates its function as a potential differentiation-related suppressor of ESCC. The present study aimed to elucidate the relationship between ZNF750 function to induce keratinocyte differentiation and tumor suppression in ESCC. The results demonstrated that chemical manipulation of esophageal keratinocyte differentiation in mouse normal esophageal epithelial organoids (mNEEO) implicated the involvement of the mouse homologue of ZNF750, Zfp750, in keratinocyte differentiation in premalignant cells. Bioinformatics analyses of data from high ZNF750-expressing ESCC tumors obtained from public databases and ZNF750-overexpressing ESCC cells compared with low ZNF750-expressing ESCC tumors and GFP-expressing ESCC cells, respectively, revealed enrichment of keratinocyte differentiation-related gene sets in these samples. Finally, the induction through to terminal differentiation of the keratinocyte by all-trans retinoic acid on parental ESCC cell lines led to the upregulation of the terminal differentiation marker Involucrin and a decrease in cell viability similar to that observed in ZNF750-overexpressing ESCC cells. The results of the present study demonstrated a functional link between the ability of ZNF750 to induce cell differentiation through to terminal differentiation and its function as a growth suppressor in ESCC. This study provides improved understanding of the role of ZNF750, a frequently mutated differentiation-related gene in ESCC, and its effects in ESCC pathogenesis.
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Affiliation(s)
- Sheyne Sta Ana Choi
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, SAR, P.R. China
| | - Josephine Mun-Yee Ko
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, SAR, P.R. China
| | - Valen Zhuoyou Yu
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, SAR, P.R. China
| | - Lvwen Ning
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, SAR, P.R. China
| | - Maria Li Lung
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, SAR, P.R. China
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Cong S, Guo Q, Cheng Y, Gao J, Sun L, Wang J, Wu H, Liang T, Zhang G. Identification and Analyzation of Differentially Expressed Transcription Factors in Endometriosis. Front Mol Biosci 2021; 7:614427. [PMID: 33490107 PMCID: PMC7817971 DOI: 10.3389/fmolb.2020.614427] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/02/2020] [Indexed: 11/13/2022] Open
Abstract
Background: Endometriosis is interpreted as the existence of endometrium outside the uterine cavity, such as ovaries, fallopian tubes and pelvic cavity. Dysmenorrhea, abnormal menstruation, infertility, and chronic pelvic pain are the primary symptoms of endometriosis. Although there are many theories about the origin of endometriosis, the exact factor of the disease has not been confirmed. Therefore, many other mechanisms are still worth exploring. Materials and Methods: The gene lists of the transcription factors (TFs) were selected from the intersections of three databases. The limma R package was used to analyze the differentially expressed genes (DEGs) of GSE6364 and GSE7305 and the DEGs intersected with the TFs to obtain the differentially expressed TFs (DETFs). Subsequently, one-way ANOVA and Student's t-test were used to analyze the expression of DETFs in different phases of the endometrium and the endometrium of the infertile and fertile females with endometriosis, respectively. Enrichment analysis and PPI network were performed to reveal the molecular mechanisms of endometriosis. Finally, the plotROC R package was used to evaluate the sensitivity and specificity of hub TFs for the diagnosis of endometriosis. Results: A total of 54 DETFs were screened out in endometriosis. The expression of up-regulated DETFs was gradually increased from the early secretory to the proliferative phase of the endometrium. Most up-regulated DETFs increased expression in the endometrium of infertile females. The pathways of DETFs were mainly enriched in stem cell differentiation, transcription activity, steroid hormone receptor activity and herpes simplex virus. Two hub TFs (RUNX2 and BATF) and two sub-networks were finally acquired from the PPI network. RUNX2 and BATF also had high diagnostic value in endometriosis. Conclusion: We discovered and analyzed 54 DETFs that were closely related to endometriosis, which would contribute to explore new mechanisms of endometriosis and search for new diagnostic markers and effective therapeutic targets.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Guangmei Zhang
- Department of Gynecology, The First Affiliated Hospital, Harbin Medical University, Harbin, China
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34
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Chen X, Zhang Q, Dang X, Song T, Wang Y, Yu Z, Zhang S, Fan J, Cong F, Zhang W, Duan N. Targeting the CtBP1-FOXM1 transcriptional complex with small molecules to overcome MDR1-mediated chemoresistance in osteosarcoma cancer stem cells. J Cancer 2021; 12:482-497. [PMID: 33391445 PMCID: PMC7739006 DOI: 10.7150/jca.50255] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/24/2020] [Indexed: 12/13/2022] Open
Abstract
Chemoresistance is a major barrier for the chemotherapy of osteosarcoma. The induction of multidrug resistance protein 1 (MDR1), an ATP-dependent transporter, can efflux anti-cancer drugs, thereby decreasing chemosensitivity. However, an actual involvement of MDR1 in the chemoresistance of osteosarcoma cells has not been established. We obtained two cisplatin (CDDP)-resistant osteosarcoma cancer stem cell (CSC) lines using sphere formation medium supplemented with CDDP. These two CDDP-resistant CSC cell lines showed substantial cell proliferation, colony formation, cell invasion, and in vivo tumor growth in the presence of CDDP. Microarray analysis revealed that three genes, MDR1, FOXM1 (forkhead box M1), and CtBP1 (C-Terminal binding protein 1), showed significant overexpression in both cell lines. Mechanistically, CtBP1 assembled with FOXM1 to form a transcriptional complex, which docked onto the MDR1 promoter to activate MDR1 expression. Knockdown or inhibition of the CtBP1-FOXM1 components with specific small molecules, including NSM00158 and NSC95397 for CtBP1 and RCM1 for FOXM1, significantly repressed MDR1 expression. Administration of these three small molecules also significantly inhibited tumor growth in mouse tumor xenograft model. The MDR1-mediated chemoresistance could be reversed by NSM00158 and RCM1. Collectively, our data revealed that the CtBP1-FOXM1 complex activated MDR1 expression and that targeting this complex with their specific inhibitors could reverse MDR1-mediated chemoresistance both in vitro and in vivo. Our results indicate a new therapeutic strategy for overcoming chemoresistance during osteosarcoma treatment.
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Affiliation(s)
- Xun Chen
- Department of Orthopaedics, Honghui Hospital, Xi'an Jiaotong University, Xi'an 710054, Shaanxi, China
| | - Qian Zhang
- The department of surgery room, Xi'an Daxing Hospital, Xi'an 710016, Shaanxi, China.1Department of Orthopedics, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710005, Shaanxi, China
| | - Xiaoqian Dang
- Department of Orthopedics, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710005, Shaanxi, China
| | - Tao Song
- Department of Orthopaedics, Honghui Hospital, Xi'an Jiaotong University, Xi'an 710054, Shaanxi, China
| | - Yufei Wang
- Department of Orthopaedics, Honghui Hospital, Xi'an Jiaotong University, Xi'an 710054, Shaanxi, China
| | - Zirui Yu
- Department of Orthopaedics, Honghui Hospital, Xi'an Jiaotong University, Xi'an 710054, Shaanxi, China
| | - Shihui Zhang
- Department of Orthopaedics, Honghui Hospital, Xi'an Jiaotong University, Xi'an 710054, Shaanxi, China
| | - Jinzhu Fan
- Department of Orthopaedics, Honghui Hospital, Xi'an Jiaotong University, Xi'an 710054, Shaanxi, China
| | - Fei Cong
- Department of Orthopaedics, Honghui Hospital, Xi'an Jiaotong University, Xi'an 710054, Shaanxi, China
| | - Wentao Zhang
- Department of Orthopaedics, Honghui Hospital, Xi'an Jiaotong University, Xi'an 710054, Shaanxi, China
| | - Ning Duan
- Department of Orthopaedics, Honghui Hospital, Xi'an Jiaotong University, Xi'an 710054, Shaanxi, China
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Guan Y, Yang YJ, Nagarajan P, Ge Y. Transcriptional and signalling regulation of skin epithelial stem cells in homeostasis, wounds and cancer. Exp Dermatol 2020; 30:529-545. [PMID: 33249665 DOI: 10.1111/exd.14247] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/10/2020] [Accepted: 11/13/2020] [Indexed: 02/06/2023]
Abstract
The epidermis and skin appendages are maintained by their resident epithelial stem cells, which undergo long-term self-renewal and multilineage differentiation. Upon injury, stem cells are activated to mediate re-epithelialization and restore tissue function. During this process, they often mount lineage plasticity and expand their fates in response to damage signals. Stem cell function is tightly controlled by transcription machineries and signalling transductions, many of which derail in degenerative, inflammatory and malignant dermatologic diseases. Here, by describing both well-characterized and newly emerged pathways, we discuss the transcriptional and signalling mechanisms governing skin epithelial homeostasis, wound repair and squamous cancer. Throughout, we highlight common themes underscoring epithelial stem cell plasticity and tissue-level crosstalk in the context of skin physiology and pathology.
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Affiliation(s)
- Yinglu Guan
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Youn Joo Yang
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Priyadharsini Nagarajan
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yejing Ge
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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36
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Riege K, Kretzmer H, Sahm A, McDade SS, Hoffmann S, Fischer M. Dissecting the DNA binding landscape and gene regulatory network of p63 and p53. eLife 2020; 9:e63266. [PMID: 33263276 PMCID: PMC7735755 DOI: 10.7554/elife.63266] [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: 09/21/2020] [Accepted: 12/01/2020] [Indexed: 12/13/2022] Open
Abstract
The transcription factor p53 is the best-known tumor suppressor, but its sibling p63 is a master regulator of epidermis development and a key oncogenic driver in squamous cell carcinomas (SCC). Despite multiple gene expression studies becoming available, the limited overlap of reported p63-dependent genes has made it difficult to decipher the p63 gene regulatory network. Particularly, analyses of p63 response elements differed substantially among the studies. To address this intricate data situation, we provide an integrated resource that enables assessing the p63-dependent regulation of any human gene of interest. We use a novel iterative de novo motif search approach in conjunction with extensive ChIP-seq data to achieve a precise global distinction between p53-and p63-binding sites, recognition motifs, and potential co-factors. We integrate these data with enhancer:gene associations to predict p63 target genes and identify those that are commonly de-regulated in SCC representing candidates for prognosis and therapeutic interventions.
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Affiliation(s)
- Konstantin Riege
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI)JenaGermany
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Arne Sahm
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI)JenaGermany
| | - Simon S McDade
- Patrick G Johnston Centre for Cancer Research, Queen's University BelfastBelfastUnited Kingdom
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI)JenaGermany
| | - Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI)JenaGermany
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37
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Butera A, Cassandri M, Rugolo F, Agostini M, Melino G. The ZNF750-RAC1 axis as potential prognostic factor for breast cancer. Cell Death Discov 2020; 6:135. [PMID: 33298895 PMCID: PMC7701147 DOI: 10.1038/s41420-020-00371-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/14/2022] Open
Abstract
The human zinc finger (C2H2-type) protein ZNF750 is a transcription factor regulated by p63 that plays a critical role in epithelial tissues homoeostasis, as well as being involved in the pathogenesis of cancer. Indeed, missense mutations, truncation and genomic deletion have been found in oesophageal squamous cell carcinoma. In keeping, we showed that ZNF750 negatively regulates cell migration and invasion in breast cancer cells; in particular, ZNF750 binds and recruits KDM1A and HDAC1 on the LAMB3 and CTNNAL1 promoters. This interaction, in turn, represses the transcription of LAMB3 and CTNNAL1 genes, which are involved in cell migration and invasion. Given that ZNF750 is emerging as a crucial transcription factor that acts as tumour suppressor gene, here, we show that ZNF750 represses the expression of the small GTPase, Ras-related C3 botulinum toxin substrate 1 (RAC1) in breast cancer cell lines, by directly binding its promoter region. In keeping with ZNF750 controlling RAC1 expression, we found an inverse correlation between ZNF750 and RAC1 in human breast cancer datasets. More importantly, we found a significant upregulation of RAC1 in human breast cancer datasets and we identified a direct correlation between RAC1 expression and the survival rate of breast cancer patient. Overall, our findings provide a novel molecular mechanism by which ZNF750 acts as tumour suppressor gene. Hence, we report a potential clinical relevance of ZNF750/RAC1 axis in breast cancer.
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Affiliation(s)
- Alessio Butera
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", 00133, Rome, Italy
| | - Matteo Cassandri
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", 00133, Rome, Italy.,Department of Oncohematology, Bambino Gesu' Children's Hospital, 00146, Rome, Italy
| | - Francesco Rugolo
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", 00133, Rome, Italy
| | - Massimiliano Agostini
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", 00133, Rome, Italy.
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", 00133, Rome, Italy.
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Ortiz-Melo MT, Garcia-Murillo MJ, Salazar-Rojas VM, Campos JE, Castro-Muñozledo F. Transcriptional profiles along cell programming into corneal epithelial differentiation. Exp Eye Res 2020; 202:108302. [PMID: 33098888 DOI: 10.1016/j.exer.2020.108302] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/23/2020] [Accepted: 10/12/2020] [Indexed: 12/15/2022]
Abstract
Using the rabbit corneal epithelial cell line RCE1(5T5) as a model, we analyzed three differentiation stages, distinguished on basis to the growth state of cultured cells and after studying the expression of transcription factors such as Oct4, Pax6 and ΔNp63α, selected differentiation markers, and signaling or epigenetic markers such as Notch receptors and Prdm3. Namely, proliferative non-differentiated cells, committed cells, and cells that constitute a stratified epithelium with a limbal epithelial-like structure. RNAseq based transcriptome analysis showed that 4891 genes were differentially expressed among these stages displaying distinctive gene signatures: proliferative cells had 1278 genes as gene signature, and seem to be early epithelial progenitors with an Oct4+, KLF4+, Myc+, ΔNp63α+, ABCG2+, Vimentin+, Zeb1+, VANGL1+, Krt3-, Krt12- phenotype. Committed cells had a gene signature with 417 genes and displayed markers indicative of the beginning of corneal differentiation, and genes characteristic of proliferative cells; we found the possible participation of Six3 and Six4 transcription factors along this stage. The third stage matches with a stratified corneal epithelium (gene signature comprising 979 genes) and is typified by an increase in the expression of WNT10A and NOTCH 2 and 3 signaling and Cux1 transcription factor, besides Pax6, KLF4 or Sox9. The differentiated cells express about 50% of the genes that belong to the Epidermal Differentiation Complex (EDC). Analysis of the differences between corneal epithelium and epidermis could be crucial to understand the regulatory mechanisms that lead to the expression of the differentiated phenotype.
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Affiliation(s)
- María Teresa Ortiz-Melo
- Department of Cell Biology, Centro de Investigación y de Estudios Avanzados del IPN, Apdo. Postal 14-740. México City, 07000, Mexico; Unidad de Biotecnología y Prototipos, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Ap. Postal 314, 54000, Tlalnepantla, Edo. de México, Mexico; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México. Unidad de Posgrado, Edificio A, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, C.P. 04510, Ciudad de México, Mexico
| | - Maria Jimena Garcia-Murillo
- Department of Cell Biology, Centro de Investigación y de Estudios Avanzados del IPN, Apdo. Postal 14-740. México City, 07000, Mexico
| | - Víctor Manuel Salazar-Rojas
- Unidad de Biotecnología y Prototipos, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Ap. Postal 314, 54000, Tlalnepantla, Edo. de México, Mexico
| | - Jorge E Campos
- Unidad de Biotecnología y Prototipos, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Ap. Postal 314, 54000, Tlalnepantla, Edo. de México, Mexico
| | - Federico Castro-Muñozledo
- Department of Cell Biology, Centro de Investigación y de Estudios Avanzados del IPN, Apdo. Postal 14-740. México City, 07000, Mexico.
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39
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Sahlén P, Spalinskas R, Asad S, Mahapatra KD, Höjer P, Anil A, Eisfeldt J, Srivastava A, Nikamo P, Mukherjee A, Kim KH, Bergman O, Ståhle M, Sonkoly E, Pivarcsi A, Wahlgren CF, Nordenskjöld M, Taylan F, Bradley M, Tapia-Páez I. Chromatin interactions in differentiating keratinocytes reveal novel atopic dermatitis- and psoriasis-associated genes. J Allergy Clin Immunol 2020; 147:1742-1752. [PMID: 33069716 DOI: 10.1016/j.jaci.2020.09.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/14/2020] [Accepted: 09/17/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Hundreds of variants associated with atopic dermatitis (AD) and psoriasis, 2 common inflammatory skin disorders, have previously been discovered through genome-wide association studies (GWASs). The majority of these variants are in noncoding regions, and their target genes remain largely unclear. OBJECTIVE We sought to understand the effects of these noncoding variants on the development of AD and psoriasis by linking them to the genes that they regulate. METHODS We constructed genomic 3-dimensional maps of human keratinocytes during differentiation by using targeted chromosome conformation capture (Capture Hi-C) targeting more than 20,000 promoters and 214 GWAS variants and combined these data with transcriptome and epigenomic data sets. We validated our results with reporter assays, clustered regularly interspaced short palindromic repeats activation, and examination of patient gene expression from previous studies. RESULTS We identified 118 target genes of 82 AD and psoriasis GWAS variants. Differential expression of 58 of the 118 target genes (49%) occurred in either AD or psoriatic lesions, many of which were not previously linked to any skin disease. We highlighted the genes AFG1L, CLINT1, ADO, LINC00302, and RP1-140J1.1 and provided further evidence for their potential roles in AD and psoriasis. CONCLUSIONS Our work focused on skin barrier pathology through investigation of the interaction profile of GWAS variants during keratinocyte differentiation. We have provided a catalogue of candidate genes that could modulate the risk of AD and psoriasis. Given that only 35% of the target genes are the gene nearest to the known GWAS variants, we expect that our work will contribute to the discovery of novel pathways involved in AD and psoriasis.
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Affiliation(s)
- Pelin Sahlén
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden.
| | - Rapolas Spalinskas
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Samina Asad
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kunal Das Mahapatra
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Pontus Höjer
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Anandashankar Anil
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ankit Srivastava
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Pernilla Nikamo
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anaya Mukherjee
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kyu-Han Kim
- Basic Research and Innovation Division, Research and Development Unit, AmorePacific Corporation, Yongin-si, Korea
| | - Otto Bergman
- Division of Cardiovascular Medicine, Center for Molecular Medicine, Department of Medicine Solna, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | - Mona Ståhle
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Enikö Sonkoly
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Dermatology Unit, Karolinska University Hospital, Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Andor Pivarcsi
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Carl-Fredrik Wahlgren
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Bradley
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Dermatology Unit, Karolinska University Hospital, Stockholm, Sweden
| | - Isabel Tapia-Páez
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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When the Search for Stemness Genes Meets the Skin Substitute Bioengineering Field: KLF4 Transcription Factor under the Light. Cells 2020; 9:cells9102188. [PMID: 32998444 PMCID: PMC7601001 DOI: 10.3390/cells9102188] [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: 08/27/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 11/16/2022] Open
Abstract
The transcription factor “Kruppel-like factor 4” (KLF4) is a central player in the field of pluripotent stem cell biology. In particular, it was put under the spotlight as one of the four factors of the cocktail originally described for reprogramming into induced pluripotent stem cells (iPSCs). In contrast, its possible functions in native tissue stem cells remain largely unexplored. We recently published that KLF4 is a regulator of “stemness” in human keratinocytes. We show that reducing the level of expression of this transcription factor by RNA interference or pharmacological repression promotes the ex vivo amplification and regenerative capacity of two types of cells of interest for cutaneous cell therapy: native keratinocyte stem and progenitor cells from adult epidermis, which have been used for more than three decades in skin graft bioengineering, and keratinocytes generated by the lineage-oriented differentiation of embryonic stem cells (ESCs), which have potential for the development of skin bio-bandages. At the mechanistic level, KLF4 repression alters the expression of a large set of genes involved in TGF-β1 and WNT signaling pathways. Major regulators of TGF-β bioavailability and different TGF-β receptors were targeted, notably modulating the ALK1/Smad1/5/9 axis. At a functional level, KLF4 repression produced an antagonist effect on TGF-β1-induced keratinocyte differentiation.
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41
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Zhang L, Niu X, Bi Y, Cui H, Li H, Cheng X. Potential Role of Targeting KDR and Proteasome Inhibitors in the Therapy of Esophageal Squamous Cell Carcinoma. Technol Cancer Res Treat 2020; 19:1533033820948060. [PMID: 32924793 PMCID: PMC7493273 DOI: 10.1177/1533033820948060] [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] [Indexed: 02/03/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most aggressive cancer types in China. In recent years, progress has been made in various types of cancer genomics including ESCC. However, the clinical significance of genomic variation of ESCC remains poorly defined. In the present study, genomic sequencing data from 469 ESCC cases were analyzed and potential therapeutic targets in the Druggable Genome Interaction Database (DGIdb) were screened. A series of potential therapeutic target genes and pathways were identified, of which treatment of ESCC with bortezomib (a specific inhibitor targeting proteasome) potently inhibited the proliferation of 5 ESCC cell lines and administration of bortezomib led to significant tumor xenograft regression in SCID mice. It was also identified that kinase insert domain receptor (KDR), which had drug recommendations from all 6 sources integrated by the DGldb and harbored significant amplification in ESCC, might be a downstream target of zinc finger protein 750 (ZNF750). ZNF750 acts as a transcription factor and has been demonstrated to harbor frequently inactivating mutations in ESCC by previous independent studies. In the present study, KDR was upregulated upon ZNF750 knockdown and the rescue of ZNF750 also led to marked restoration of KDR. KDR knockdown in stable ZNF750-knockdown KYSE150 and KYSE140 ESCC cells significantly attenuated the promotion of cell growth, colony formation, invasion and migration induced by ZNF750 knockdown. Further experiments found that apatinib treatment, a potent inhibitor of KDR, resulted in profound inhibition of cell proliferation and invasion. Collectively, the present study provided insight for genomic alterations as potential therapeutic targets in ESCC and supported the possibility of a therapeutic strategy targeting the proteasome in ESCC. The present results also suggested that targeting KDR may be an effective way to treat ESCC, not only in KDR variant cases, but also in individuals with ZNF750 mutations and deletions.
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Affiliation(s)
- Ling Zhang
- Department of Pathology, 74648Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China.,Translational Medicine Research Center, 74648Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
| | - Xia Niu
- Department of Pathology, 74648Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China.,Translational Medicine Research Center, 74648Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
| | - Yanghui Bi
- Translational Medicine Research Center, 74648Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
| | - Heyang Cui
- Translational Medicine Research Center, 74648Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
| | - Hongyi Li
- Translational Medicine Research Center, 74648Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
| | - Xiaolong Cheng
- Translational Medicine Research Center, 74648Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China.,Department of Anatomy, 74648Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
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42
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Egolf S, Aubert Y, Doepner M, Anderson A, Maldonado-Lopez A, Pacella G, Lee J, Ko EK, Zou J, Lan Y, Simpson CL, Ridky T, Capell BC. LSD1 Inhibition Promotes Epithelial Differentiation through Derepression of Fate-Determining Transcription Factors. Cell Rep 2020; 28:1981-1992.e7. [PMID: 31433976 PMCID: PMC6719800 DOI: 10.1016/j.celrep.2019.07.058] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/03/2019] [Accepted: 07/17/2019] [Indexed: 02/08/2023] Open
Abstract
Self-renewing somatic tissues depend upon the proper balance of chromatin-modifying enzymes to coordinate progenitor cell maintenance and differentiation, disruption of which can promote carcinogenesis. As a result, drugs targeting the epigenome hold significant therapeutic potential. The histone demethylase, LSD1 (KDM1A), is overexpressed in numerous cancers, including epithelial cancers; however, its role in the skin is virtually unknown. Here we show that LSD1 directly represses master epithelial transcription factors that promote differentiation. LSD1 inhibitors block both LSD1 binding to chromatin and its catalytic activity, driving significant increases in H3K4 methylation and gene transcription of these fate-determining transcription factors. This leads to both premature epidermal differentiation and the repression of squamous cell carcinoma. Together these data highlight both LSD1’s role in maintaining the epidermal progenitor state and the potential of LSD1 inhibitors for the treatment of keratinocyte cancers, which collectively outnumber all other cancers combined. Egolf et al. demonstrate that inhibition of the epigenetic regulator and histone demethylase, LSD1, promotes activation of the epidermal differentiation transcriptional program and, in turn, represses the invasion of cutaneous squamous cell carcinoma, one of the most common of all human cancers.
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Affiliation(s)
- Shaun Egolf
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Yann Aubert
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Miriam Doepner
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Amy Anderson
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Alexandra Maldonado-Lopez
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Gina Pacella
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jessica Lee
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Eun Kyung Ko
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jonathan Zou
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Yemin Lan
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Cory L Simpson
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Todd Ridky
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Brian C Capell
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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43
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Jones J, Chen Y, Tiwari M, Li J, Ling J, Sen GL. KLF3 Mediates Epidermal Differentiation through the Epigenomic Writer CBP. iScience 2020; 23:101320. [PMID: 32659720 PMCID: PMC7358749 DOI: 10.1016/j.isci.2020.101320] [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: 12/10/2019] [Revised: 06/02/2020] [Accepted: 06/24/2020] [Indexed: 12/24/2022] Open
Abstract
Impairments in the differentiation process can lead to skin diseases that can afflict ∼20% of the population. Thus, it is of utmost importance to understand the factors that promote the differentiation process. Here we identify the transcription factor KLF3 as a regulator of epidermal differentiation. Knockdown of KLF3 results in reduced differentiation gene expression and increased cell cycle gene expression. Over half of KLF3's genomic binding sites occur at active enhancers. KLF3 binds to active enhancers proximal to differentiation genes that are dependent upon KLF3 for expression. KLF3's genomic binding sites also highly overlaps with CBP, a histone acetyltransferase necessary for activating enhancers. Depletion of KLF3 causes reduced CBP localization at enhancers proximal to differentiation gene clusters, which leads to loss of enhancer activation but not priming. Our results suggest that KLF3 is necessary to recruit CBP to activate enhancers and drive epidermal differentiation gene expression.
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Affiliation(s)
- Jackson Jones
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - Yifang Chen
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - Manisha Tiwari
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - Jingting Li
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - Ji Ling
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - George L Sen
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA.
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44
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Szigety KM, Liu F, Yuan CY, Moran DJ, Horrell J, Gochnauer HR, Cohen RN, Katz JP, Kaestner KH, Seykora JT, Tobias JW, Lazar MA, Xu M, Millar SE. HDAC3 ensures stepwise epidermal stratification via NCoR/SMRT-reliant mechanisms independent of its histone deacetylase activity. Genes Dev 2020; 34:973-988. [PMID: 32467224 PMCID: PMC7328513 DOI: 10.1101/gad.333674.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 04/23/2020] [Indexed: 12/12/2022]
Abstract
Here, Szigety et al. investigated the function of histone deacetylases in epidermal development, and they found that HDAC3 operates in conjunction with KLF4 to repress inappropriate expression of Tgm1, Krt16, and Aqp3, and suppresses expression of inflammatory cytokines through a Rela-dependent mechanism. Their data identify HDAC3 as a hub coordinating multiple aspects of epidermal barrier acquisition. Chromatin modifiers play critical roles in epidermal development, but the functions of histone deacetylases in this context are poorly understood. The class I HDAC, HDAC3, is of particular interest because it plays divergent roles in different tissues by partnering with tissue-specific transcription factors. We found that HDAC3 is expressed broadly in embryonic epidermis and is required for its orderly stepwise stratification. HDAC3 protein stability in vivo relies on NCoR and SMRT, which function redundantly in epidermal development. However, point mutations in the NCoR and SMRT deacetylase-activating domains, which are required for HDAC3's enzymatic function, permit normal stratification, indicating that HDAC3's roles in this context are largely independent of its histone deacetylase activity. HDAC3-bound sites are significantly enriched for predicted binding motifs for critical epidermal transcription factors including AP1, GRHL, and KLF family members. Our results suggest that among these, HDAC3 operates in conjunction with KLF4 to repress inappropriate expression of Tgm1, Krt16, and Aqp3. In parallel, HDAC3 suppresses expression of inflammatory cytokines through a Rela-dependent mechanism. These data identify HDAC3 as a hub coordinating multiple aspects of epidermal barrier acquisition.
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Affiliation(s)
- Katherine M Szigety
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Fang Liu
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Chase Y Yuan
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Deborah J Moran
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jeremy Horrell
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Heather R Gochnauer
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ronald N Cohen
- Section of Endocrinology, Diabetes, and Metabolism, University of Chicago, Chicago, Illinois 60637, USA
| | - Jonathan P Katz
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Klaus H Kaestner
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - John T Seykora
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - John W Tobias
- Penn Genomic Analysis Core, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, Division of Endocrinology, Diabetes, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Mingang Xu
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Sarah E Millar
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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45
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Li R, Li P, Xing W, Qiu H. Heterogeneous genomic aberrations in esophageal squamous cell carcinoma: a review. Am J Transl Res 2020; 12:1553-1568. [PMID: 32509161 PMCID: PMC7269976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 04/25/2020] [Indexed: 06/11/2023]
Abstract
Esophageal cancer (EC) causes hundreds of thousands of deaths a year worldwide, especially the major subtype esophageal squamous cell carcinoma (ESCC). With the advent of next-generation sequencing and the availability of commercial microarrays, abnormities in genetic levels have been revealed in various independent researches. High frequencies of structure variations (SVs), single nucleotide variations (SNVs) and copy-number alterations (CNAs) in ESCCs are uncovered, and ESCC shows high levels of inter- and intratumor heterogeneity, implying diverse evolutionary trajectories. This review tries to explain the pathogenesis of ESCC on the scope of most often mutated genes based on prior studies, hopes to offer some hints for diagnosis and therapy in clinic.
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Affiliation(s)
- Renling Li
- Quality and Standards Academy, Shenzhen Technology UniversityShenzhen 518060, China
| | - Peng Li
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer HospitalZhengzhou 450008, China
| | - Wenqun Xing
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer HospitalZhengzhou 450008, China
| | - Huiling Qiu
- Quality and Standards Academy, Shenzhen Technology UniversityShenzhen 518060, China
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46
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Cassandri M, Butera A, Amelio I, Lena AM, Montanaro M, Mauriello A, Anemona L, Candi E, Knight RA, Agostini M, Melino G. ZNF750 represses breast cancer invasion via epigenetic control of prometastatic genes. Oncogene 2020; 39:4331-4343. [PMID: 32313225 DOI: 10.1038/s41388-020-1277-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 03/05/2020] [Accepted: 03/16/2020] [Indexed: 12/19/2022]
Abstract
Breast cancer is the second leading cause of cancer-related deaths among women, largely due to the progression of a significant fraction of primary tumours to the metastatic stage. Here, we show that zinc-finger protein 750 (ZNF750) opposes the migration and invasion of breast cancer cells by repressing a prometastatic transcriptional programme, which includes genes involved in focal adhesion and extracellular matrix interactions, such as LAMB3 and CTNNAL1. Mechanistically, ZNF750 recruits the epigenetic modifiers KDM1A and HDAC1 to the promoter regions of LAMB3 and CTNNAL1, influencing histone marks and transactivating these genomic sites. Gene expression analysis in cancer patient datasets indicated that ZNF750 and its targets were negative prognostic factors in breast cancer. Together, our findings shed light on the molecular mechanism by which ZNF750 regulates cell migration and invasion, suggesting a role in breast cancer metastasis.
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Affiliation(s)
- Matteo Cassandri
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", 00133, Rome, Italy
- Department of Oncohematology, Bambino Gesu' Children's Hospital, 00146, Rome, Italy
| | - Alessio Butera
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", 00133, Rome, Italy
| | - Ivano Amelio
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", 00133, Rome, Italy
- Department of Pathology, MRC Toxicology Unit, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Anna Maria Lena
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", 00133, Rome, Italy
| | - Manuela Montanaro
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", 00133, Rome, Italy
| | - Alessandro Mauriello
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", 00133, Rome, Italy
| | - Lucia Anemona
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", 00133, Rome, Italy
| | - Eleonora Candi
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", 00133, Rome, Italy
- IDI-IRCCS, via Monti di Creta, 106, 00166, Rome, Italy
| | - Richard A Knight
- Department of Pathology, MRC Toxicology Unit, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Massimiliano Agostini
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", 00133, Rome, Italy.
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", 00133, Rome, Italy.
- Department of Pathology, MRC Toxicology Unit, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.
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47
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Decreased ZNF750 promotes angiogenesis in a paracrine manner via activating DANCR/miR-4707-3p/FOXC2 axis in esophageal squamous cell carcinoma. Cell Death Dis 2020; 11:296. [PMID: 32341351 PMCID: PMC7186230 DOI: 10.1038/s41419-020-2492-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 01/19/2020] [Accepted: 01/20/2020] [Indexed: 11/24/2022]
Abstract
ZNF750 is one novel significantly mutated gene identified in esophageal squamous cell carcinoma (ESCC) using next-generation sequencing. However, its clinically relevant and potential mechanisms have remained elusive. Using genomic sequencing of 612 ESCC patients, we analyzed the associations of ZNF750 mutations with clinicopathologic features and its prognostic value. We further investigated the function and underlying mechanism of ZNF750 in angiogenesis. The results showed ZNF750 mutations/deletions are significantly associated with malignant progression and poor prognosis of ESCC patients. Decreased ZNF750 in ESCC cells induces enhanced angiogenesis of human umbilical vein endothelial cells (HUVECs) and human arterial endothelial cells (HAECs), and the effect may be indirectly mediated by FOXC2. RNA-seq and ChIP shows lncRNA DANCR is a direct downstream target of ZNF750. Furtherly, knockdown ZNF750 evokes DANCR expression, which prevents miR-4707-3p to interact with FOXC2 as a microRNA sponge in a ceRNA manner, leading to enhanced FOXC2 signaling and angiogenesis. In contrast, ZNF750 expression reverses the effect. Our study reveals a novel mechanism of ZNF750, highlights a significance of ZNF750 as a metastatic and prognostic biomarker, and offers potential therapeutic targets for ESCC patients harboring ZNF750 mutations.
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Jones J, Chen Y, Tiwari M, Li J, Ling J, Sen GL. BRD4 Is Necessary for Differentiation Downstream of Epidermal Lineage-Determining Transcription Factors. J Invest Dermatol 2020; 140:2077-2081.e5. [PMID: 32142793 DOI: 10.1016/j.jid.2020.01.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/17/2020] [Accepted: 01/27/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Jackson Jones
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, California, USA
| | - Yifang Chen
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, California, USA
| | - Manisha Tiwari
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, California, USA
| | - Jingting Li
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, California, USA
| | - Ji Ling
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, California, USA
| | - George L Sen
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, California, USA.
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Kim KH, Shim JS, Kim HJ, Son ED. Penta-O-galloyl-β-D-glucose from Paeonia lactiflora Pall. root extract enhances the expression of skin barrier genes via EGR3. JOURNAL OF ETHNOPHARMACOLOGY 2020; 248:112337. [PMID: 31655148 DOI: 10.1016/j.jep.2019.112337] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 09/10/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023]
Abstract
ETHNOPHARMACOLIGICAL RELEVANCE Paeonia lactiflora Pall. has long been used to treat inflammatory skin diseases, such as psoriasis. AIM OF THE STUDY The skin acts as a barrier and provides protection against various stresses by expressing skin barrier genes during keratinocyte differentiation. However, the effect of Paeonia lactiflora Pall. root extract on the expression of skin barrier genes has not been investigated. Here, we aimed to show that treatment of keratinocytes with Paeonia lactiflora Pall. root can upregulate genes related to keratinocyte differentiation. MATERIALS AND METHODS To determine the effect Paeonia lactiflora Pall. root extract, RNA-Seq, gene ontology, and gene set enrichment analysis were performed. Reverse transcriptase quantitative polymerase chain reaction analysis was performed to confirm the increased expression of skin barrier genes. RESULTS Treatment with Paeonia lactiflora Pall. root enhanced the expression of skin barrier genes, including the filaggrin, loricrin, and involucrin. Moreover, we found that penta-O-galloyl-β-D-glucose (PGG), one of the ingredients in Paeonia lactiflora Pall. root, enhanced the expression of skin barrier genes, by upregulating the expression of the transcription factor EGR3. CONCLUSIONS PGG and Paeonia lactiflora Pall. root extract have therapeutic potential for the treatment of diseases related to skin barrier disruption and can be used in cosmetics to enhance skin barrier function.
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Affiliation(s)
- Kyu-Han Kim
- Basic Research & Innovation Division, R&D Unit, AmorePacific Corporation, Yongin-si, Gyeonggi-do, 446-729, South Korea.
| | - Jin Sup Shim
- Basic Research & Innovation Division, R&D Unit, AmorePacific Corporation, Yongin-si, Gyeonggi-do, 446-729, South Korea
| | - Hyoung-June Kim
- Basic Research & Innovation Division, R&D Unit, AmorePacific Corporation, Yongin-si, Gyeonggi-do, 446-729, South Korea
| | - Eui Dong Son
- Basic Research & Innovation Division, R&D Unit, AmorePacific Corporation, Yongin-si, Gyeonggi-do, 446-729, South Korea
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Liu H, Duncan K, Helverson A, Kumari P, Mumm C, Xiao Y, Carlson JC, Darbellay F, Visel A, Leslie E, Breheny P, Erives AJ, Cornell RA. Analysis of zebrafish periderm enhancers facilitates identification of a regulatory variant near human KRT8/18. eLife 2020; 9:e51325. [PMID: 32031521 PMCID: PMC7039683 DOI: 10.7554/elife.51325] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 02/06/2020] [Indexed: 12/18/2022] Open
Abstract
Genome-wide association studies for non-syndromic orofacial clefting (OFC) have identified single nucleotide polymorphisms (SNPs) at loci where the presumed risk-relevant gene is expressed in oral periderm. The functional subsets of such SNPs are difficult to predict because the sequence underpinnings of periderm enhancers are unknown. We applied ATAC-seq to models of human palate periderm, including zebrafish periderm, mouse embryonic palate epithelia, and a human oral epithelium cell line, and to complementary mesenchymal cell types. We identified sets of enhancers specific to the epithelial cells and trained gapped-kmer support-vector-machine classifiers on these sets. We used the classifiers to predict the effects of 14 OFC-associated SNPs at 12q13 near KRT18. All the classifiers picked the same SNP as having the strongest effect, but the significance was highest with the classifier trained on zebrafish periderm. Reporter and deletion analyses support this SNP as lying within a periderm enhancer regulating KRT18/KRT8 expression.
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Affiliation(s)
- Huan Liu
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan UniversityWuhanChina
- Department of Anatomy and Cell Biology, University of IowaIowa CityUnited States
- Department of Periodontology, School of Stomatology, Wuhan UniversityWuhanChina
| | - Kaylia Duncan
- Interdisciplinary Program in Molecular Medicine, University of IowaIowa CityUnited States
| | - Annika Helverson
- Department of Anatomy and Cell Biology, University of IowaIowa CityUnited States
| | - Priyanka Kumari
- Department of Anatomy and Cell Biology, University of IowaIowa CityUnited States
| | - Camille Mumm
- Department of Anatomy and Cell Biology, University of IowaIowa CityUnited States
| | - Yao Xiao
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan UniversityWuhanChina
| | | | - Fabrice Darbellay
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley LaboratoriesBerkeleyUnited States
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley LaboratoriesBerkeleyUnited States
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley LaboratoriesBerkeleyUnited States
- University of California, MercedMercedUnited States
| | - Elizabeth Leslie
- Department of Human Genetics, Emory University School of MedicineAtlantaGeorgia
| | - Patrick Breheny
- Department of Biostatistics, University of IowaIowa CityUnited States
| | - Albert J Erives
- Department of Biology, University of IowaIowa CityUnited States
| | - Robert A Cornell
- Department of Anatomy and Cell Biology, University of IowaIowa CityUnited States
- Interdisciplinary Program in Molecular Medicine, University of IowaIowa CityUnited States
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