1
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Chen X, Moran Torres JP, Tedjai SVK, Lugones LG, Wösten HAB. Functional analysis of FlbA-regulated transcription factor genes in Aspergillus niger using a multiplexed CRISPRoff system. Int J Biol Macromol 2024; 277:134326. [PMID: 39089555 DOI: 10.1016/j.ijbiomac.2024.134326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/31/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024]
Abstract
FlbA of Aspergillus niger (indirectly) regulates 36 transcription factor (TF) genes. As a result, it promotes sporulation and represses vegetative growth, protein secretion and lysis. In this study, the functions of part of the FlbA-regulated TF genes were studied by using CRISPRoff. This system was recently introduced as an epigenetic tool for modulating gene expression in A. niger. A plasmid encompassing an optimized CRISPRoff system as well as a library of sgRNA genes that target the promoters of the 36 FlbA-regulated TF genes was introduced in A. niger. Out of 24 transformants that exhibited a sporulation phenotype, 12 and 18 strains also showed a biomass and secretion phenotype, respectively. The transforming sgRNAs, and thus the genes responsible for the phenotypes, were identified from five of the transformants. The results show that the genes dofA, dofB, dofC, dofD, and socA are involved in sporulation and extracellular enzyme activity, while dofA and socA also play roles in biomass formation. Overall, this study shows that the multiplexed CRISPRoff system can be effectively used for functional analysis of genes in a fungus.
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Affiliation(s)
- Xiaoyi Chen
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands.
| | - Juan P Moran Torres
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands.
| | - S Vyanjan K Tedjai
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands.
| | - Luis G Lugones
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands.
| | - Han A B Wösten
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands.
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2
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Zhang Y, Yang Y, Hou Y, Yan W, Zhang X, Huang X, Song Q, He F, Wang J, Sun A, Tian C. ZNF8 promotes progression of gastrointestinal cancers via a p53-dependent mechanism. Cell Signal 2024; 123:111354. [PMID: 39173856 DOI: 10.1016/j.cellsig.2024.111354] [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: 03/20/2024] [Revised: 07/09/2024] [Accepted: 08/18/2024] [Indexed: 08/24/2024]
Abstract
p53 is a critical tumor suppressor, and the disruption of its normal function is often a prerequisite for the development or progression of tumors. Our previous works revealed that multiple members of Krüppel-associated box (KRAB) domain zinc-finger proteins (KZFPs) family regulate p53 transcriptional activity by interacting with it. But the tumor biology functions of these members have not been fully elucidated. Here, the pan-cancer analysis related to gastrointestinal cancers (GICs) revealed that ZNF8, a p53-interacting protein, is an unfavorable prognostic factor for patients with malignancies. ZNF8 interacts with p53 and further depresses its transcriptional activity in colon cancer cells. The knockdown of ZNF8 or the overexpression of ZNF8 inhibits or facilitates the in vitro colony formation, migration, invasion, and angiogenesis of p53+/+ colon cancer HCT116 cells, HepG2 cells and EC109 cells rather than p53-/- colon cancer HCT116 cells and p53-knockout HepG2 cells, respectively. Xenograft experiments conducted in vivo also showed that the knockdown of ZNF8 in p53+/+ but not in p53-/- HCT116 cells curbs the tumor growth and metastasis to lung, leading to an extended life span for tumor-bearing mice. Clinically, two independent immunohistochemistry cohorts of colon cancer and esophageal cancer also indicated that ZNF8 is higher expression in carcinoma tissues than adjacent tissues and this is associated with worse overall survival outcomes in patients without harboring p53 mutation. Together, our results provide insight into the p53-specific tumor oncogenic function of ZNF8. ZNF8 may prove to be a potential target for GICs treatment.
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Affiliation(s)
- Yiming Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Yingchuan Yang
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Yushan Hou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Wei Yan
- The First Medical Center of Chinese PLA General Hospital, Beijing 100036, China
| | - Xiuyuan Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Xiaofen Huang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; College of Life Sciences, Hebei University, Baoding 071002, Hebei, China
| | - Qin Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; College of Life Sciences, Hebei University, Baoding 071002, Hebei, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Jian Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China; College of Life Sciences, Hebei University, Baoding 071002, Hebei, China.
| | - Aihua Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China; College of Life Sciences, Hebei University, Baoding 071002, Hebei, China.
| | - Chunyan Tian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China; College of Life Sciences, Hebei University, Baoding 071002, Hebei, China.
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3
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Domingo J, Minaeva M, Morris JA, Ghatan S, Ziosi M, Sanjana NE, Lappalainen T. Non-linear transcriptional responses to gradual modulation of transcription factor dosage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.582837. [PMID: 38464330 PMCID: PMC10925300 DOI: 10.1101/2024.03.01.582837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Genomic loci associated with common traits and diseases are typically non-coding and likely impact gene expression, sometimes coinciding with rare loss-of-function variants in the target gene. However, our understanding of how gradual changes in gene dosage affect molecular, cellular, and organismal traits is currently limited. To address this gap, we induced gradual changes in gene expression of four genes using CRISPR activation and inactivation. Downstream transcriptional consequences of dosage modulation of three master trans-regulators associated with blood cell traits (GFI1B, NFE2, and MYB) were examined using targeted single-cell multimodal sequencing. We showed that guide tiling around the TSS is the most effective way to modulate cis gene expression across a wide range of fold-changes, with further effects from chromatin accessibility and histone marks that differ between the inhibition and activation systems. Our single-cell data allowed us to precisely detect subtle to large gene expression changes in dozens of trans genes, revealing that many responses to dosage changes of these three TFs are non-linear, including non-monotonic behaviours, even when constraining the fold-changes of the master regulators to a copy number gain or loss. We found that the dosage properties are linked to gene constraint and that some of these non-linear responses are enriched for disease and GWAS genes. Overall, our study provides a straightforward and scalable method to precisely modulate gene expression and gain insights into its downstream consequences at high resolution.
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Affiliation(s)
| | - Mariia Minaeva
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - John A Morris
- New York Genome Center, New York, NY 10013, USA
- Department of Biology, New York University, New York, NY 10003, USA
| | - Sam Ghatan
- New York Genome Center, New York, NY 10013, USA
| | | | - Neville E Sanjana
- New York Genome Center, New York, NY 10013, USA
- Department of Biology, New York University, New York, NY 10003, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY 10013, USA
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
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4
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Melore SM, Hamilton MC, Reddy TE. HyperCas12a enables highly-multiplexed epigenome editing screens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602263. [PMID: 39026853 PMCID: PMC11257430 DOI: 10.1101/2024.07.08.602263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Interactions between multiple genes or cis-regulatory elements (CREs) underlie a wide range of biological processes in both health and disease. High-throughput screens using dCas9 fused to epigenome editing domains have allowed researchers to assess the impact of activation or repression of both coding and non-coding genomic regions on a phenotype of interest, but assessment of genetic interactions between those elements has been limited to pairs. Here, we combine a hyper-efficient version of Lachnospiraceae bacterium dCas12a (dHyperLbCas12a) with RNA Polymerase II expression of long CRISPR RNA (crRNA) arrays to enable efficient highly-multiplexed epigenome editing. We demonstrate that this system is compatible with several activation and repression domains, including the P300 histone acetyltransferase domain and SIN3A interacting domain (SID). We also show that the dCas12a platform can perform simultaneous activation and repression using a single crRNA array via co-expression of multiple dCas12a orthologues. Lastly, demonstrate that the dCas12a system is highly effective for high-throughput screens. We use dHyperLbCas12a-KRAB and a ~19,000-member barcoded library of crRNA arrays containing six crRNAs each to dissect the independent and combinatorial contributions of CREs to the dose-dependent control of gene expression at a glucocorticoid-responsive locus. The tools and methods introduced here create new possibilities for highly multiplexed control of gene expression in a wide variety of biological systems.
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Affiliation(s)
- Schuyler M. Melore
- University Program in Genetics & Genomics, Duke University, Durham, NC, USA
- Department of Biostatistics & Bioinformatics, Duke University School of Medicine, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Center for Combinatorial Gene Regulation, Duke University, Durham, NC, USA
| | - Marisa C. Hamilton
- University Program in Genetics & Genomics, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Center for Combinatorial Gene Regulation, Duke University, Durham, NC, USA
| | - Timothy E. Reddy
- University Program in Genetics & Genomics, Duke University, Durham, NC, USA
- Department of Biostatistics & Bioinformatics, Duke University School of Medicine, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Center for Combinatorial Gene Regulation, Duke University, Durham, NC, USA
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5
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Kang YK, Eom J, Min B, Park JS. SETDB1 deletion causes DNA demethylation and upregulation of multiple zinc-finger genes. Mol Biol Rep 2024; 51:778. [PMID: 38904842 PMCID: PMC11192681 DOI: 10.1007/s11033-024-09703-2] [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: 03/18/2024] [Accepted: 06/04/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND SETDB1 (SET domain bifurcated-1) is a histone H3-lysine 9 (H3K9)-specific methyltransferase that mediates heterochromatin formation and repression of target genes. Despite the assumed functional link between DNA methylation and SETDB1-mediated H3K9 trimethylations, several studies have shown that SETDB1 operates autonomously of DNA methylation in a region- and cell-specific manner. This study analyzes SETDB1-null HAP1 cells through a linked methylome and transcriptome analysis, intending to explore genes controlled by SETDB1-involved DNA methylation. METHODS AND RESULTS We investigated SETDB1-mediated regulation of DNA methylation and gene transcription in human HAP1 cells using reduced-representation bisulfite sequencing (RRBS) and RNA sequencing. While two-thirds of differentially methylated CpGs (DMCs) in genic regions were hypomethylated in SETDB1-null cells, we detected a plethora of C2H2-type zinc-finger protein genes (C2H2-ZFP, 223 of 749) among the DMC-associated genes. Most C2H2-ZFPs with DMCs in their promoters were found hypomethylated in SETDB1-KO cells, while other non-ZFP genes with promoter DMCs were not. These C2H2-ZFPs with DMCs in their promoters were significantly upregulated in SETDB1-KO cells. Similarly, C2H2-ZFP genes were upregulated in SETDB1-null 293T cells, suggesting that SETDB1's function in ZFP gene repression is widespread. There are several C2H2-ZFP gene clusters on chromosome 19, which were selectively hypomethylated in SETDB1-KO cells. CONCLUSIONS SETDB1 collectively and specifically represses a substantial fraction of the C2H2-ZFP gene family. Through the en-bloc silencing of a set of ZFP genes, SETDB1 may help establish a panel of ZFP proteins that are expressed cell-type specifically and thereby can serve as signature proteins for cellular identity.
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Affiliation(s)
- Yong-Kook Kang
- Development and Differentiation Research Center, Aging Convergence Research Center (ACRC), Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea.
- Department of Functional Genomics, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, South Korea.
| | - Jaemin Eom
- Development and Differentiation Research Center, Aging Convergence Research Center (ACRC), Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
- Department of Functional Genomics, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, South Korea
| | - Byungkuk Min
- Development and Differentiation Research Center, Aging Convergence Research Center (ACRC), Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Jung Sun Park
- Development and Differentiation Research Center, Aging Convergence Research Center (ACRC), Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
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6
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Wang M, Yan X, Dong Y, Li X, Gao B. From driver genes to gene families: A computational analysis of oncogenic mutations and ubiquitination anomalies in hepatocellular carcinoma. Comput Biol Chem 2024; 112:108119. [PMID: 38852361 DOI: 10.1016/j.compbiolchem.2024.108119] [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: 03/19/2024] [Revised: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024]
Abstract
Hepatocellular carcinoma (HCC) is a widespread primary liver cancer with a high fatality rate. Despite several genes with oncogenic effects in HCC have been identified, many remain undiscovered. In this study, we conducted a comprehensive computational analysis to explore the involvement of genes within the same families as known driver genes in HCC. Specifically, we expanded the concept beyond single-gene mutations to encompass gene families sharing homologous structures, integrating various omics data to comprehensively understand gene abnormalities in cancer. Our analysis identified 74 domains with an enriched mutation burden, 404 domain mutation hotspots, and 233 dysregulated driver genes. We observed that specific low-frequency somatic mutations may contribute to HCC occurrence, potentially overlooked by single-gene algorithms. Furthermore, we systematically analyzed how abnormalities in the ubiquitinated proteasome system (UPS) impact HCC, finding that abnormal genes in E3, E2, DUB families, and Degron genes often result in HCC by affecting the stability of oncogenic or tumor suppressor proteins. In conclusion, expanding the exploration of driver genes to include gene families with homologous structures emerges as a promising strategy for uncovering additional oncogenic alterations in HCC.
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Affiliation(s)
- Meng Wang
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China
| | - Xinyue Yan
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China
| | - Yanan Dong
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China
| | - Xiaoqin Li
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China.
| | - Bin Gao
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China
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7
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Reyna J, Fetter K, Ignacio R, Marandi CCA, Rao N, Jiang Z, Figueroa DS, Bhattacharyya S, Ay F. Loop Catalog: a comprehensive HiChIP database of human and mouse samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591349. [PMID: 38746164 PMCID: PMC11092438 DOI: 10.1101/2024.04.26.591349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
HiChIP enables cost-effective and high-resolution profiling of regulatory and structural loops. To leverage the increasing number of publicly available HiChIP datasets from diverse cell lines and primary cells, we developed the Loop Catalog (https://loopcatalog.lji.org), a web-based database featuring HiChIP loop calls for 1319 samples across 133 studies and 44 high-resolution Hi-C loop calls. We demonstrate its utility in interpreting fine-mapped GWAS variants (SNP-to-gene linking), in identifying enriched sequence motifs and motif pairs at loop anchors, and in network-level analysis of loops connecting regulatory elements (community detection). Our comprehensive catalog, spanning over 4M unique 5kb loops, along with the accompanying analysis modalities constitutes an important resource for studies in gene regulation and genome organization.
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Affiliation(s)
- Joaquin Reyna
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
- Bioinformatics and Systems Biology Graduate Program University of California, San Diego, La Jolla, CA 92093 USA
| | - Kyra Fetter
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Romeo Ignacio
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
| | - Cemil Can Ali Marandi
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
- Bioinformatics and Systems Biology Graduate Program University of California, San Diego, La Jolla, CA 92093 USA
| | - Nikhil Rao
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Zichen Jiang
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
- Department of Mathematics, University of California San Diego, La Jolla, CA 92093 USA
| | - Daniela Salgado Figueroa
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
- Bioinformatics and Systems Biology Graduate Program University of California, San Diego, La Jolla, CA 92093 USA
| | - Sourya Bhattacharyya
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
| | - Ferhat Ay
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
- Bioinformatics and Systems Biology Graduate Program University of California, San Diego, La Jolla, CA 92093 USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093 USA
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8
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Mohamad Zamberi NN, Abuhamad AY, Low TY, Mohtar MA, Syafruddin SE. dCas9 Tells Tales: Probing Gene Function and Transcription Regulation in Cancer. CRISPR J 2024; 7:73-87. [PMID: 38635328 DOI: 10.1089/crispr.2023.0078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing is evolving into an essential tool in the field of biological and medical research. Notably, the development of catalytically deactivated Cas9 (dCas9) enzyme has substantially broadened its traditional boundaries in gene editing or perturbation. The conjugation of dCas9 with various molecular effectors allows precise control over transcriptional processes, epigenetic modifications, visualization of chromosomal dynamics, and several other applications. This expanded repertoire of CRISPR-Cas9 applications has emerged as an invaluable molecular tool kit that empowers researchers to comprehensively interrogate and gain insights into health and diseases. This review delves into the advancements in Cas9 protein engineering, specifically on the generation of various dCas9 tools that have significantly enhanced the CRISPR-based technology capability and versatility. We subsequently discuss the multifaceted applications of dCas9, especially in interrogating the regulation and function of genes that involve in supporting cancer pathogenesis. In addition, we also delineate the designing and utilization of dCas9-based tools as well as highlighting its current constraints and transformative potentials in cancer research.
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Affiliation(s)
- Nurul Nadia Mohamad Zamberi
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Cheras, Malaysia, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Asmaa Y Abuhamad
- Bionanotechnology Research Group, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Cheras, Malaysia, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - M Aiman Mohtar
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Cheras, Malaysia, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Saiful Effendi Syafruddin
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Cheras, Malaysia, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
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9
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Yi H, Ye R, Xie E, Lu L, Wang Q, Wang S, Sun Y, Tian T, Qiu Y, Wu Q, Zhang G, Wang H. ZNF283, a Krüppel-associated box zinc finger protein, inhibits RNA synthesis of porcine reproductive and respiratory syndrome virus by interacting with Nsp9 and Nsp10. Vet Res 2024; 55:9. [PMID: 38225617 PMCID: PMC10790482 DOI: 10.1186/s13567-023-01263-w] [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: 08/07/2023] [Accepted: 11/15/2023] [Indexed: 01/17/2024] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is a viral pathogen with substantial economic implications for the global swine industry. The existing vaccination strategies and antiviral drugs offer limited protection. Replication of the viral RNA genome encompasses a complex series of steps, wherein a replication complex is assembled from various components derived from both viral and cellular sources, as well as from the viral genomic RNA template. In this study, we found that ZNF283, a Krüppel-associated box (KRAB) containing zinc finger protein, was upregulated in PRRSV-infected Marc-145 cells and porcine alveolar macrophages and that ZNF283 inhibited PRRSV replication and RNA synthesis. We also found that ZNF283 interacts with the viral proteins Nsp9, an RNA-dependent RNA polymerase, and Nsp10, a helicase. The main regions involved in the interaction between ZNF283 and Nsp9 were determined to be the KRAB domain of ZNF283 and amino acids 178-449 of Nsp9. The KRAB domain of ZNF283 plays a role in facilitating Nsp10 binding. In addition, ZNF283 may have an affinity for the 3' untranslated region of PRRSV. These findings suggest that ZNF283 is an antiviral factor that inhibits PRRSV infection and extend our understanding of the interactions between KRAB-containing zinc finger proteins and viruses.
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Affiliation(s)
- Heyou Yi
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, China
| | - Ruirui Ye
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Ermin Xie
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Lechen Lu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Qiumei Wang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Shaojun Wang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Yankuo Sun
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China
| | - Tao Tian
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Yingwu Qiu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Qianwen Wu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Guihong Zhang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China.
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, China.
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.
| | - Heng Wang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China.
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, China.
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.
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10
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Weng K, Li L, Zhou H. Transcription factor ZNF488 accelerates cervical cancer progression through regulating the MEK/ERK signaling pathway. Histol Histopathol 2023; 38:1381-1390. [PMID: 36537752 DOI: 10.14670/hh-18-568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Cervical cancer (CC) is one of the most common gynecological malignancies worldwide. Zinc Finger Protein 488 (ZNF488) has been identified as an oncogene in nasopharyngeal carcinoma. However, its biological role and potential mechanism in CC remain to be elucidated. In the present study, upregulation of ZNF488 expression in human CC tissues was found in clinical samples and analyzed in The Cancer Genome Atlas (TCGA) dataset, which was associated with clinical staging and lymph node metastasis. Quantitative real time polymerase chain reaction (PCR) and western blot assays indicated that the expression of ZNF488 was up-regulated in CC cells. Cell colony formation and cell cycle analysis assays suggested that ZNF488 promoted CC cell proliferation and cycle progression. Knockdown of ZNF488 inhibited tumor growth of xenograft tumor mice in vivo, in agreement with the levels of ZNF488 and Ki-67. Moreover, transwell and western assays demonstrated that ZNF488 enhanced CC cell migration and invasion. Additionally, knockdown of ZNF488 also inhibited lung metastasis of CC cells in vivo. Further mechanism analysis implied that ZNF488 promoted the MEK/ERK signaling pathway. ERK inhibitor PD98059 significantly weakened the proliferation and epithelial-mesenchymal transformation (EMT) promotion effect of ZNF488. Collectively, ZNF488 exerts its oncogene function partially through modulating MEK/ERK signaling pathway in CC, indicating that ZNF488 may provide a promising therapeutic target for the treatment of CC.
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Affiliation(s)
- Kena Weng
- Department of Obstetrics and Gynecology, Affiliated People's Hospital of Ningbo University, Ningbo, China.
| | - Lu Li
- Department of Obstetrics and Gynecology, Affiliated People's Hospital of Ningbo University, Ningbo, China
| | - Haiping Zhou
- Department of Obstetrics and Gynecology, Affiliated People's Hospital of Ningbo University, Ningbo, China
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11
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Liu Y, Yin W, Zeng X, Fan J, Liu C, Gao M, Huang Z, Sun G, Guo M. TBK1-stabilized ZNF268a recruits SETD4 to methylate TBK1 for efficient interferon signaling. J Biol Chem 2023; 299:105428. [PMID: 37926288 DOI: 10.1016/j.jbc.2023.105428] [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: 05/21/2023] [Revised: 10/02/2023] [Accepted: 10/15/2023] [Indexed: 11/07/2023] Open
Abstract
Sufficient activation of interferon signaling is critical for the host to fight against invading viruses, in which post-translational modifications have been demonstrated to play a pivotal role. Here, we demonstrate that the human KRAB-zinc finger protein ZNF268a is essential for virus-induced interferon signaling. We find that cytoplasmic ZNF268a is constantly degraded by lysosome and thus remains low expressed in resting cell cytoplasm. Upon viral infection, TBK1 interacts with cytosolic ZNF268a to catalyze the phosphorylation of Serine 178 of ZNF268a, which prevents the degradation of ZNF268a, resulting in the stabilization and accumulation of ZNF268a in the cytoplasm. Furthermore, we provide evidence that stabilized ZNF268a recruits the lysine methyltransferase SETD4 to TBK1 to induce the mono-methylation of TBK1 on lysine 607, which is critical for the assembly of the TBK1 signaling complex. Notably, ZNF268 S178 is conserved among higher primates but absent in rodents. Meanwhile, rodent TBK1 607th aa happens to be replaced by arginine, possibly indicating a species-specific role of ZNF268a in regulating TBK1 during evolution. These findings reveal novel functions of ZNF268a and SETD4 in regulating antiviral interferon signaling.
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Affiliation(s)
- Yi Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, P.R. China
| | - Wei Yin
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, P.R. China
| | - Xianhuang Zeng
- Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei, P.R. China
| | - Jinhao Fan
- School of Ecology and Environment, Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau of Ministry of Education, Tibet University, Lhasa, Tibet, P.R. China
| | - Chaozhi Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, P.R. China
| | - Mingyu Gao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, P.R. China
| | - Zan Huang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, P.R. China
| | - Guihong Sun
- Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei, P.R. China; Hubei Provincial Key Laboratory of Allergy and Immunology, Wuhan, Hubei, P.R. China
| | - Mingxiong Guo
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, P.R. China; School of Ecology and Environment, Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau of Ministry of Education, Tibet University, Lhasa, Tibet, P.R. China.
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12
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Oleksiewicz U, Machnik M, Sobocińska J, Molenda S, Olechnowicz A, Florczak A, Mierzejewska J, Adamczak D, Smolibowski M, Kaczmarek M, Mackiewicz A. ZNF643/ZFP69B Exerts Oncogenic Properties and Associates with Cell Adhesion and Immune Processes. Int J Mol Sci 2023; 24:16380. [PMID: 38003570 PMCID: PMC10671213 DOI: 10.3390/ijms242216380] [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: 08/30/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
The global cancer burden remains high; thus, a better understanding of the molecular mechanisms driving carcinogenesis is needed to improve current prevention and treatment options. We previously detected the ZNF643/ZFP69B gene upregulated in multiple tumors, and we speculated it may play a role in tumor biology. To test this hypothesis, we employed TCGA-centered databases to correlate ZNF643 status with various clinicopathological parameters. We also performed RNA-seq analysis and in vitro studies assessing cancer cell phenotypes, and we searched for ZNF643-bound genomic loci. Our data indicated higher levels of ZNF643 in most analyzed tumors compared to normal samples, possibly due to copy number variations. ZNF643 mRNA correlated with diverse molecular and immune subtypes and clinicopathological features (tumor stage, grade, patient survival). RNA-seq analysis revealed that ZNF643 silencing triggers the deregulation of the genes implicated in various cancer-related processes, such as growth, adhesion, and immune system. Moreover, we observed that ZNF643 positively influences cell cycle, migration, and invasion. Finally, our ChIP-seq analysis indicated that the genes associated with ZNF643 binding are linked to adhesion and immune signaling. In conclusion, our data confirm the oncogenic properties of ZNF643 and pinpoint its impact on cell adhesion and immune processes.
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Affiliation(s)
- Urszula Oleksiewicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
| | - Marta Machnik
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
| | - Joanna Sobocińska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
| | - Sara Molenda
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
- Doctoral School, Poznan University of Medical Sciences, 70 Bukowska Street, 60-812 Poznan, Poland
| | - Anna Olechnowicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Doctoral School, Poznan University of Medical Sciences, 70 Bukowska Street, 60-812 Poznan, Poland
- Department of Histology and Embryology, Poznan University of Medical Sciences, 6 Święcickiego Street, 60-781 Poznan, Poland
| | - Anna Florczak
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
| | - Julia Mierzejewska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
| | - Dominika Adamczak
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
| | - Mikołaj Smolibowski
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
| | - Mariusz Kaczmarek
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
| | - Andrzej Mackiewicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
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13
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Oleksiewicz U, Machnik M, Sobocińska J, Molenda S, Olechnowicz A, Florczak A, Smolibowski M, Kaczmarek M. ZNF714 Supports Pro-Oncogenic Features in Lung Cancer Cells. Int J Mol Sci 2023; 24:15530. [PMID: 37958512 PMCID: PMC10649060 DOI: 10.3390/ijms242115530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/10/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023] Open
Abstract
Despite the ongoing progress in diagnosis and treatments, cancer remains a threat to more than one-third of the human population. The emerging data indicate that many Krüppel-associated box zinc finger proteins (KRAB-ZNF) belonging to a large gene family may be involved in carcinogenesis. Our previous study identified Zinc Finger Protein 714 (ZNF714), a KRAB-ZNF gene of unknown function, as being commonly overexpressed in many tumors, pointing to its hypothetical oncogenic role. Here, we harnessed The Cancer Genome Atlas (TCGA)-centered databases and performed functional studies with transcriptomic and methylomic profiling to explore ZNF714 function in cancer. Our pan-cancer analyses confirmed frequent ZNF714 overexpression in multiple tumors, possibly due to regional amplification, promoter hypomethylation, and Nuclear Transcription Factor Y Subunit Beta (NFYB) signaling. We also showed that ZNF714 expression correlates with tumor immunosuppressive features. The in vitro studies indicated that ZNF714 expression positively associates with proliferation, migration, and invasion. The transcriptomic analysis of ZNF714 knocked-down cells demonstrated deregulation of cell adhesion, migration, proliferation, apoptosis, and differentiation. Importantly, we provided evidence that ZNF714 negatively regulates the expression of several known TSGs indirectly via promoter methylation. However, as ZNF714 did not show nuclear localization in our research model, the regulatory mechanisms exerted by ZNF714 require further investigation. In conclusion, our results reveal, for the first time, that ZNF714 may support pro-oncogenic features in lung cancer cells.
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Affiliation(s)
- Urszula Oleksiewicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
| | - Marta Machnik
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
| | - Joanna Sobocińska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
| | - Sara Molenda
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Doctoral School, Poznan University of Medical Sciences, 60-812 Poznan, Poland
| | - Anna Olechnowicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Doctoral School, Poznan University of Medical Sciences, 60-812 Poznan, Poland
- Department of Histology and Embryology, Poznan University of Medical Sciences, Swiecickiego 6 Street, 60-781 Poznan, Poland
| | - Anna Florczak
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
| | - Mikołaj Smolibowski
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
| | - Mariusz Kaczmarek
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
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14
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Soon HR, Gaunt JR, Bansal VA, Lenherr C, Sze SK, Ch’ng TH. Seizure enhances SUMOylation and zinc-finger transcriptional repression in neuronal nuclei. iScience 2023; 26:107707. [PMID: 37694138 PMCID: PMC10483055 DOI: 10.1016/j.isci.2023.107707] [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: 04/10/2023] [Revised: 05/29/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023] Open
Abstract
A single episode of pilocarpine-induced status epilepticus can trigger the development of spontaneous recurrent seizures in a rodent model for epilepsy. The initial seizure-induced events in neuronal nuclei that lead to long-term changes in gene expression and cellular responses likely contribute toward epileptogenesis. Using a transgenic mouse model to specifically isolate excitatory neuronal nuclei, we profiled the seizure-induced nuclear proteome via tandem mass tag mass spectrometry and observed robust enrichment of nuclear proteins associated with the SUMOylation pathway. In parallel with nuclear proteome, we characterized nuclear gene expression by RNA sequencing which provided insights into seizure-driven transcriptional regulation and dynamics. Strikingly, we saw widespread downregulation of zinc-finger transcription factors, specifically proteins that harbor Krüppel-associated box (KRAB) domains. Our results provide a detailed snapshot of nuclear events induced by seizure activity and demonstrate a robust method for cell-type-specific nuclear profiling that can be applied to other cell types and models.
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Affiliation(s)
- Hui Rong Soon
- School of Biological Science, Nanyang Technological University, Singapore 636551, Singapore
| | - Jessica Ruth Gaunt
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Vibhavari Aysha Bansal
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Clara Lenherr
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
- Centre for Discovery Brain Science, The University of Edinburgh, Edinburgh, UK
| | - Siu Kwan Sze
- Faculty of Applied Health Sciences, Brock University, St. Catherines, ON, Canada
| | - Toh Hean Ch’ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
- School of Biological Science, Nanyang Technological University, Singapore 636551, Singapore
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15
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Yuan P, Wang S, Du T, Liu L, Chen X, Yan J, Han S, Peng B, He X, Liu W. ZNF219, a novel transcriptional repressor, inhibits transcription of the prototype foamy virus by interacting with the viral LTR promoter. Virus Res 2023; 334:199161. [PMID: 37356580 PMCID: PMC10410575 DOI: 10.1016/j.virusres.2023.199161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/16/2023] [Accepted: 06/22/2023] [Indexed: 06/27/2023]
Abstract
Prototype foamy virus (PFV) is an ancient retrovirus that infects humans with persistent latent infections and non-pathogenic consequences. Lifelong latent PFV infections can be caused by restrictive factors in the host. However, the molecular mechanisms underlying host cell regulation during PFV infection are not fully understood. The aim of the study was to investigate whether a zinc finger protein (ZFP), ZNF219, as a transcription factor, can regulate the transcriptional activity of the viral promoter. Here, using transcriptome sequencing, we found that ZNF219, is downregulated in PFV infected cells and that ZNF219 suppresses viral replication by targeting the viral 5'LTR promoter region to repress its transcription. We also found that PFV infection induced abnormal expression of miRNAs targeting the ZNF219-3'UTR to downregulate ZNF219 expression. These findings indicated that ZNF219 may be a potent antiviral factor for suppressing PFV infection, and may shed light on the mechanism of virus-host interactions.
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Affiliation(s)
- Peipei Yuan
- Department of Immunology, School of Basic Medical Sciences, Hubei University of Medicine, Hubei Province, Shiyan 442000, China; Hubei Province Key Laboratory of Allergy and Immunology, Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan 430071, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Hubei Province, Shiyan 442000, China
| | - Shuang Wang
- Hubei Province Key Laboratory of Allergy and Immunology, Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan 430071, China
| | - Tongtong Du
- Hubei Province Key Laboratory of Allergy and Immunology, Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan 430071, China
| | - Luo Liu
- Beijing Bioprocess Key Laboratory, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xiong Chen
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, China
| | - Jun Yan
- Hubei Province Key Laboratory of Allergy and Immunology, Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan 430071, China; Department of Laboratory Medicine, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430071, China
| | - Song Han
- Hubei Province Key Laboratory of Allergy and Immunology, Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan 430071, China
| | - Biwen Peng
- Hubei Province Key Laboratory of Allergy and Immunology, Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan 430071, China
| | - Xiaohua He
- Hubei Province Key Laboratory of Allergy and Immunology, Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan 430071, China
| | - Wanhong Liu
- Hubei Province Key Laboratory of Allergy and Immunology, Taikang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan 430071, China.
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16
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Dong X, Zhang Y, Sun Y, Nan Q, Li M, Ma L, Zhang L, Luo J, Qi Y, Miao Y. Promoter hypermethylation and comprehensive regulation of ncRNA lead to the down-regulation of ZNF880, providing a new insight for the therapeutics and research of colorectal cancer. BMC Med Genomics 2023; 16:148. [PMID: 37370088 PMCID: PMC10294494 DOI: 10.1186/s12920-023-01571-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
The human genome encodes more than 350 kinds of Krüppel-associated box (KRAB) domain-containing zinc-finger proteins (KZFPs), KRAB-type ZNF transcription factor family (KZNF) plays a vital role in gene regulatory networks. The KZNF family members include a large number of highly homologous genes, gene subtypes and pseudogenes, and their expression has a high degree of tissue specificity and precision. Due to the high complexity of its regulatory network, the KZNF gene family has not been researched in sufficient, and the role of its members in the occurrence of cancer is mostly unexplored. In this study, ZNF880 was significantly associated with overall survival (OS) and disease-free survival (DFS) in colorectal carcinoma (CRC) patients. Low ZNF880 expression resulted in shorter OS and DFS. Combined with Colon adenocarcinoma (COAD) and Rectum adenocarcinoma (READ) data collection in the TCGA database, we found that ZNF880 was significantly down-regulated in CRC. Further analysis of the sequence variation of ZNF880 in CRC showed that ZNF880 accumulated a large number of SNV in the C2H2 domain and KRAB domain, while promoter region of ZNF880 also showed high methylation in COAD and READ. Combined with the Cbioportal and TIMER databases, the expression of mutant ZNF880 was significantly lower in COAD compared to the wild type. Simultaneously, the lncRNA-miRNA-ZNF880 ceRNA regulatory network was constructed through co-expression and miRNAs target gene prediction, demonstrating the precision of the ZNF880 regulatory network. In addition, the decreased expression of ZNF880 caused the significant immune infiltration decreases of CD8 + cells in COAD. In contrast, the immune infiltration of CD4 + cells and macrophages in COAD is positively correlated with ZNF880. Finally, through protein-protein interaction (PPI) network analysis and transcription factor target gene prediction, we screened out the genes most likely to be related to the function of ZNF880. CENPK, IFNGR2, REC8 and ZBTB17 were identified as the most closely functioning genes with ZNF880, which may indicate that ZNF880 has important links with the formation of cell centromere, tumor immunity, cell cycle and other pathways closely related to the occurrence of CRC. These studies show that the down-regulation of ZNF880 gene is closely related to CRC, and the targeted change of the expression of its regulatory molecules (miRNA and lncRNA) may be a new perspective for CRC treatment.
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Affiliation(s)
- Xiangqian Dong
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, NO.295 Xichang Road, Kunming, 650032, P.R. China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, 650032, China
| | - Yinghui Zhang
- Department of Gastroenterology, Affiliated Hospital of Yunnan University, Kunming, 650021, China
| | - Yang Sun
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, NO.295 Xichang Road, Kunming, 650032, P.R. China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, 650032, China
| | - Qiong Nan
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, NO.295 Xichang Road, Kunming, 650032, P.R. China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, 650032, China
| | - Maojuan Li
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, NO.295 Xichang Road, Kunming, 650032, P.R. China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, 650032, China
| | - Lanqing Ma
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, NO.295 Xichang Road, Kunming, 650032, P.R. China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, 650032, China
| | - Lei Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, NO.295 Xichang Road, Kunming, 650032, P.R. China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, 650032, China
| | - Juan Luo
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, NO.295 Xichang Road, Kunming, 650032, P.R. China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, 650032, China
| | - Yating Qi
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, NO.295 Xichang Road, Kunming, 650032, P.R. China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, 650032, China
| | - Yinglei Miao
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, NO.295 Xichang Road, Kunming, 650032, P.R. China.
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, 650032, China.
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17
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Chang YJ, Lin S, Kang ZF, Shen BJ, Tsai WH, Chen WC, Lu HP, Su YL, Chou SJ, Lin SY, Lin SW, Huang YJ, Wang HH, Chang CJ. Acetylation-Mimic Mutation of TRIM28-Lys304 to Gln Attenuates the Interaction with KRAB-Zinc-Finger Proteins and Affects Gene Expression in Leukemic K562 Cells. Int J Mol Sci 2023; 24:9830. [PMID: 37372979 DOI: 10.3390/ijms24129830] [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: 04/14/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
TRIM28/KAP1/TIF1β is a crucial epigenetic modifier. Genetic ablation of trim28 is embryonic lethal, although RNAi-mediated knockdown in somatic cells yields viable cells. Reduction in TRIM28 abundance at the cellular or organismal level results in polyphenism. Posttranslational modifications such as phosphorylation and sumoylation have been shown to regulate TRIM28 activity. Moreover, several lysine residues of TRIM28 are subject to acetylation, but how acetylation of TRIM28 affects its functions remains poorly understood. Here, we report that, compared with wild-type TRIM28, the acetylation-mimic mutant TRIM28-K304Q has an altered interaction with Krüppel-associated box zinc-finger proteins (KRAB-ZNFs). The TRIM28-K304Q knock-in cells were created in K562 erythroleukemia cells by CRISPR-Cas9 (Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein nuclease 9) gene editing method. Transcriptome analysis revealed that TRIM28-K304Q and TRIM28 knockout K562 cells had similar global gene expression profiles, yet the profiles differed considerably from wild-type K562 cells. The expression levels of embryonic-related globin gene and a platelet cell marker integrin-beta 3 were increased in TRIM28-K304Q mutant cells, indicating the induction of differentiation. In addition to the differentiation-related genes, many zinc-finger-proteins genes and imprinting genes were activated in TRIM28-K304Q cells; they were inhibited by wild-type TRIM28 via binding with KRAB-ZNFs. These results suggest that acetylation/deacetylation of K304 in TRIM28 constitutes a switch for regulating its interaction with KRAB-ZNFs and alters the gene regulation as demonstrated by the acetylation mimic TRIM28-K304Q.
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Affiliation(s)
- Yao-Jen Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Steven Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Zhi-Fu Kang
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Bin-Jon Shen
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Wen-Hai Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Wen-Ching Chen
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Hsin-Pin Lu
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Yu-Lun Su
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Shu-Jen Chou
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Shu-Yu Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Sheng-Wei Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Yin-Jung Huang
- Department of Pediatrics, Division of Pediatric Immunology and Nephrology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Hsin-Hui Wang
- Department of Pediatrics, Division of Pediatric Immunology and Nephrology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Department of Pediatrics, Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Institute of Emergency and Critical Care Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Ching-Jin Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
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18
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Miller WB, Baluška F, Reber AS. A revised central dogma for the 21st century:all biology is cognitive information processing. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023:S0079-6107(23)00057-3. [PMID: 37268025 DOI: 10.1016/j.pbiomolbio.2023.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/28/2023] [Accepted: 05/30/2023] [Indexed: 06/04/2023]
Abstract
Crick's Central Dogma has been a foundational aspect of 20th century biology, describing an implicit relationship governing the flow of information in biological systems in biomolecular terms. Accumulating scientific discoveries support the need for a revised Central Dogma to buttress evolutionary biology's still-fledgling migration from a Neodarwinian canon. A reformulated Central Dogma to meet contemporary biology is proposed: all biology is cognitive information processing. Central to this contention is the recognition that life is the self-referential state, instantiated within the cellular form. Self-referential cells act to sustain themselves and to do so, cells must be in consistent harmony with their environment. That consonance is achieved by the continuous assimilation of environmental cues and stresses as information to self-referential observers. All received cellular information must be analyzed to be deployed as cellular problem-solving to maintain homeorhetic equipoise. However, the effective implementation of information is definitively a function of orderly information management. Consequently, effective cellular problem-solving is information processing and management. The epicenter of that cellular information processing is its self-referential internal measurement. All further biological self-organization initiates from this obligate activity. As the internal measurement by cells of information is self-referential by definition, self-reference is biological self-organization, underpinning 21st century Cognition-Based Biology.
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Affiliation(s)
| | | | - Arthur S Reber
- Department of Psychology, University of British Columbia, Vancouver, BC, Canada.
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19
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Bandyopadhayaya S, Yadav P, Sharma A, Dey SK, Nag A, Maheshwari R, Ford BM, Mandal CC. Oncogenic role of an uncharacterized cold-induced zinc finger protein 726 in breast cancer. J Cell Biochem 2023. [PMID: 37192271 DOI: 10.1002/jcb.30417] [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: 12/18/2022] [Revised: 03/29/2023] [Accepted: 04/18/2023] [Indexed: 05/18/2023]
Abstract
The unobtrusive cold environmental temperature can be linked to the development of cancer. This study, for the first time, envisaged cold stress-mediated induction of a zinc finger protein 726 (ZNF726) in breast cancer. However, the role of ZNF726 in tumorigenesis has not been defined. This study investigated the putative role of ZNF726 in breast cancer tumorigenic potency. Gene expression analysis using multifactorial cancer databases predicted overexpression of ZNF726 in various cancers, including breast cancer. Experimental observations found that malignant breast tissues and highly aggressive MDA-MB-231 cells showed an elevated ZNF726 expression as compared to benign and luminal A type (MCF-7), respectively. Furthermore, ZNF726 silencing decreased breast cancer cell proliferation, epithelial-mesenchymal transition, and invasion accompanied by the inhibition of colony-forming ability. Concordantly, ZNF726 overexpression significantly demonstrated opposite outcomes than ZNF726 knockdown. Taken together, our findings propose cold-inducible ZNF726 as a functional oncogene demonstrating its prominent role in facilitating breast tumorigenesis. An inverse correlation between environmental temperature and total serum cholesterol was observed in the previous study. Furthermore, experimental outcomes illustrate that cold stress elevated cholesterol content hinting at the involvement of the cholesterol regulatory pathway in cold-induced ZNF726 gene regulation. This observation was bolstered by a positive correlation between the expression of cholesterol-regulatory genes and ZNF726. Exogenous cholesterol treatment elevated ZNF726 transcript levels while knockdown of ZNF726 decreased the cholesterol content via downregulating various cholesterol regulatory gene expressions (e.g., SREBF1/2, HMGCoR, LDLR). Moreover, an underlying mechanism supporting cold-driven tumorigenesis is proposed through interdependent regulation of cholesterol regulatory pathway and cold-inducible ZNF726 expression.
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Affiliation(s)
- Shreetama Bandyopadhayaya
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Pooja Yadav
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Ankit Sharma
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Sanjay Kumar Dey
- Dr. B. R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi, Delhi, India
| | - Alo Nag
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Rekha Maheshwari
- Department of General Surgery, JLN Medical College, Ajmer, Rajasthan, India
| | - Bridget M Ford
- Department of Biology, University of the Incarnate Word, San Antonio, Texas, USA
| | - Chandi C Mandal
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
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20
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Zhang Z, Zhang Y, Hu X, Chen Y, Zhuang L, Zhang S. ZNF677 inhibits oral squamous cell carcinoma growth and tumor stemness by regulating FOXO3a. Hum Cell 2023:10.1007/s13577-023-00910-w. [PMID: 37129799 DOI: 10.1007/s13577-023-00910-w] [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: 10/27/2022] [Accepted: 04/23/2023] [Indexed: 05/03/2023]
Abstract
Oral squamous cell carcinoma (OSCC) is a common cancer with an increasing incidence worldwide. Zinc-finger proteins 677 (ZNF677) is involved in the progression and methylation of various cancers, but its role and mechanism in OSCC remain indeterminate. The expression of ZNF677 was analyzed by online database and immunohistochemistry, while the methylation level of ZNF677 was determined by the methylation-specific PCR. The role and mechanism of ZNF677 in the tumor cell growth, migration, invasion and stemness were addressed by cell counting kit-8 (CCK-8), 5-ethynyl-2'-deoxyuridine (EdU) incorporation, Transwell, wound-healing, sphere‑formation, and western blot assays. In addition, its function was also investigated in a xenografted mice model. The results showed that ZNF677 was lowly expressed in OSCC with a hypermethylation level, which predicted poor overall survival in patients with HNSC. Upregulation of ZNF677 reduced the cell viability, Edu positive cells, numbers of invasion cells, the migration ability, numbers of spheres formation and the expression of proliferation, migration and stemness related proteins in CAL-27 and SCC25 cells. Mechanically, the relative levels of p-AKT/AKT were decreased and the levels of p-FOXO3a/FOXO3a were increased in both cells overexpressed with ZNF677, which were reversed by the SC79 treatment. Moreover, interference of FOXO3a recovered the suppressive effects of ZNF677 overexpression on cell proliferation, migration, invasion and stemness of OSCC cells. Furthermore, overexpression of ZNF677 reduced the tumor volume and weight, and the relative protein level of p-AKT/AKT with an increased level of p-FOXO3a/FOXO3a, and improved pathological symptoms in vivo. Collectively, ZNF677 suppressed OSCC cells growth, migration, invasion and stemness through inhibiting AKT/FOXO3a pathway.
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Affiliation(s)
- Zebiao Zhang
- Department of Stomatology, Quanzhou First Hospital Affiliated to Fujian Medical University, No. 250, East Street, Quanzhou, 362000, Fujian, China
| | - Ying Zhang
- Department of Stomatology, Quanzhou First Hospital Affiliated to Fujian Medical University, No. 250, East Street, Quanzhou, 362000, Fujian, China.
| | - Xiaoyan Hu
- Department of Prosthodontics, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, 350000, Fujian, China
| | - Yanru Chen
- Department of Stomatology, Quanzhou First Hospital Affiliated to Fujian Medical University, No. 250, East Street, Quanzhou, 362000, Fujian, China
| | - Liangliang Zhuang
- Department of Stomatology, Quanzhou First Hospital Affiliated to Fujian Medical University, No. 250, East Street, Quanzhou, 362000, Fujian, China
| | - Shuqin Zhang
- Department of Stomatology, Jinjiang Stomatological Hospital, Quanzhou, 362200, Fujian, China
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21
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Osipovich AB, Dudek KD, Trinh LT, Kim LH, Shrestha S, Cartailler JP, Magnuson MA. ZFP92, a KRAB domain zinc finger protein enriched in pancreatic islets, binds to B1/Alu SINE transposable elements and regulates retroelements and genes. PLoS Genet 2023; 19:e1010729. [PMID: 37155670 PMCID: PMC10166502 DOI: 10.1371/journal.pgen.1010729] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/02/2023] [Indexed: 05/10/2023] Open
Abstract
Repressive KRAB domain-containing zinc-finger proteins (KRAB-ZFPs) are abundant in mammalian genomes and contribute both to the silencing of transposable elements (TEs) and to the regulation of developmental stage- and cell type-specific gene expression. Here we describe studies of zinc finger protein 92 (Zfp92), an X-linked KRAB-ZFP that is highly expressed in pancreatic islets of adult mice, by analyzing global Zfp92 knockout (KO) mice. Physiological, transcriptomic and genome-wide chromatin binding studies indicate that the principal function of ZFP92 in mice is to bind to and suppress the activity of B1/Alu type of SINE elements and modulate the activity of surrounding genomic entities. Deletion of Zfp92 leads to changes in expression of select LINE and LTR retroelements and genes located in the vicinity of ZFP92-bound chromatin. The absence of Zfp92 leads to altered expression of specific genes in islets, adipose and muscle that result in modest sex-specific alterations in blood glucose homeostasis, body mass and fat accumulation. In islets, Zfp92 influences blood glucose concentration in postnatal mice via transcriptional effects on Mafb, whereas in adipose and muscle, it regulates Acacb, a rate-limiting enzyme in fatty acid metabolism. In the absence of Zfp92, a novel TE-Capn11 fusion transcript is overexpressed in islets and several other tissues due to de-repression of an IAPez TE adjacent to ZFP92-bound SINE elements in intron 3 of the Capn11 gene. Together, these studies show that ZFP92 functions both to repress specific TEs and to regulate the transcription of specific genes in discrete tissues.
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Affiliation(s)
- Anna B. Osipovich
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Karrie D. Dudek
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Linh T. Trinh
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Lily H. Kim
- College of Arts and Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Shristi Shrestha
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jean-Philippe Cartailler
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Mark A. Magnuson
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
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22
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Chen X, Moran Torres JP, Li Y, Lugones LG, Wösten HAB. Inheritable CRISPR based epigenetic modification in a fungus. Microbiol Res 2023; 272:127397. [PMID: 37141850 DOI: 10.1016/j.micres.2023.127397] [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: 03/03/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
The CRISPRoff system was recently introduced as a programmable epigenetic memory writer that can be used to silence genes in human cells. The system makes use of a dead Cas9 protein (dCas9) that is fused with the ZNF10 KRAB, Dnmt3A, and Dnmt3L protein domains. The DNA methylation resulting from the CRISPRoff system can be removed by the CRISPRon system that consists of dCas9 fused to the catalytic domain of Tet1. Here, the CRISPRoff and CRISPRon systems were applied for the first time in a fungus. The CRISPRoff system resulted in an inactivation up to 100 % of the target genes flbA and GFP in Aspergillus niger. Phenotypes correlated with the degree of gene silencing in the transformants and were stable when going through a conidiation cycle, even when the CRISPRoff plasmid was removed from the flbA silenced strain. Introducing the CRISPRon system in a strain in which the CRISPRoff plasmid was removed fully reactivated flbA showing a phenotype similar to that of the wildtype. Together, the CRISPRoff and CRISPRon systems can be used to study gene function in A. niger.
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Affiliation(s)
- Xiaoyi Chen
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Juan P Moran Torres
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Yiling Li
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Luis G Lugones
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Han A B Wösten
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
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23
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Kaplow IM, Lawler AJ, Schäffer DE, Srinivasan C, Sestili HH, Wirthlin ME, Phan BN, Prasad K, Brown AR, Zhang X, Foley K, Genereux DP, Karlsson EK, Lindblad-Toh K, Meyer WK, Pfenning AR, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning. Science 2023; 380:eabm7993. [PMID: 37104615 DOI: 10.1126/science.abm7993] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.
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Affiliation(s)
- Irene M Kaplow
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Alyssa J Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Daniel E Schäffer
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Chaitanya Srinivasan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Heather H Sestili
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Morgan E Wirthlin
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - BaDoi N Phan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kavya Prasad
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ashley R Brown
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiaomeng Zhang
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kathleen Foley
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Diane P Genereux
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Elinor K Karlsson
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kerstin Lindblad-Toh
- Broad Institute, Cambridge, MA, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Wynn K Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Andreas R Pfenning
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
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Yang B, Tang H, Wang N, Gu J, Wang Q. Targeted DNA demethylation of the ZNF334 promoter inhibits colorectal cancer growth. Cell Death Dis 2023; 14:210. [PMID: 36966142 PMCID: PMC10039945 DOI: 10.1038/s41419-023-05743-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 03/11/2023] [Accepted: 03/15/2023] [Indexed: 03/27/2023]
Abstract
Colorectal cancer (CRC) is a leading cause of cancer deaths worldwide. Aberrant regulation of DNA methylation in promoters of tumor suppressor genes or proto-oncogenes is one of the fundamental processes driving the initiation and progression of CRC. Zinc-finger proteins (ZNFs) are one of the most abundant groups of proteins and function in many important biological processes related to tumorigenesis. Herein, we detected abnormal hypermethylation of the ZNF334 gene in CRC tissues compared with normal tissues, and this modification downregulated the expression of ZNF334. Furthermore, ten-eleven translocation 1 (TET1) was identified to be involved in regulating the methylation level of ZNF334. Next, a dCas9-multiGCN4/scFv-TET1CD-sgZNF334-targeted demethylation system was constructed to reverse the expression of ZNF334 through sgRNA targeting the ZNF334 promoter. Both in vitro and in vivo experiments demonstrated the targeted demethylation system upregulated ZNF334 expression and inhibited CRC growth. Collectively, targeted DNA demethylation of the ZNF334 promoter sheds light on the precise treatment of CRC.
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Affiliation(s)
- Bin Yang
- School of Pharmacy, Southwest Minzu University, Chengdu, 610225, Sichuan, China
| | - Haiyu Tang
- School of Pharmacy, Southwest Minzu University, Chengdu, 610225, Sichuan, China
| | - Nan Wang
- School of Pharmacy, Southwest Minzu University, Chengdu, 610225, Sichuan, China
| | - Jian Gu
- School of Pharmacy, Southwest Minzu University, Chengdu, 610225, Sichuan, China
| | - Qin Wang
- School of Pharmacy, Southwest Minzu University, Chengdu, 610225, Sichuan, China.
- BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, Sichuan, China.
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RNAseq Analysis of FABP4 Knockout Mouse Hippocampal Transcriptome Suggests a Role for WNT/β-Catenin in Preventing Obesity-Induced Cognitive Impairment. Int J Mol Sci 2023; 24:ijms24043381. [PMID: 36834799 PMCID: PMC9961923 DOI: 10.3390/ijms24043381] [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: 12/22/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Microglial fatty-acid binding protein 4 (FABP4) is a regulator of neuroinflammation. We hypothesized that the link between lipid metabolism and inflammation indicates a role for FABP4 in regulating high fat diet (HFD)-induced cognitive decline. We have previously shown that obese FABP4 knockout mice exhibit decreased neuroinflammation and cognitive decline. FABP4 knockout and wild type mice were fed 60% HFD for 12 weeks starting at 15 weeks old. Hippocampal tissue was dissected and RNA-seq was performed to measure differentially expressed transcripts. Reactome molecular pathway analysis was utilized to examine differentially expressed pathways. Results showed that HFD-fed FABP4 knockout mice have a hippocampal transcriptome consistent with neuroprotection, including associations with decreased proinflammatory signaling, ER stress, apoptosis, and cognitive decline. This is accompanied by an increase in transcripts upregulating neurogenesis, synaptic plasticity, long-term potentiation, and spatial working memory. Pathway analysis revealed that mice lacking FABP4 had changes in metabolic function that support reduction in oxidative stress and inflammation, and improved energy homeostasis and cognitive function. Analysis suggested a role for WNT/β-Catenin signaling in the protection against insulin resistance, alleviating neuroinflammation and cognitive decline. Collectively, our work shows that FABP4 represents a potential target in alleviating HFD-induced neuroinflammation and cognitive decline and suggests a role for WNT/β-Catenin in this protection.
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Carbon Monoxide Stimulates Both Mitophagy And Mitochondrial Biogenesis to Mediate Protection Against Oxidative Stress in Astrocytes. Mol Neurobiol 2023; 60:851-863. [PMID: 36378469 DOI: 10.1007/s12035-022-03108-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022]
Abstract
Astrocytes are key glial cells for the metabolic and functional support of the brain. Mitochondrial quality control (MQC), in particular the balance between mitophagy and mitochondrial biogenesis, is a major event for the maintenance of cellular homeostasis. Carbon monoxide (CO) is an endogenous gasotransmitter that inhibits cell death and inflammation by targeting mitochondria. It is well established that CO promotes cytoprotection by increasing mitochondrial population and metabolism (oxidative phosphorylation). Thus, it is hypothesized that CO-induced cytoprotection may also be mediated by the balance between mitophagy and mitochondrial biogenesis. Herein, the carbon monoxide releasing molecule-A1 (CORM-A1) was used in primary cultures of astrocytes to assess CO role on mitochondrial turnover. PINK1/Parkin-dependent mitophagy was stimulated by CORM-A1 following 1 h of treatment. While at 24 h after treatment, CORM-A1 increased mitochondrial population, which may indicate mitochondrial biogenesis. In fact, mitochondrial biogenesis was confirmed by the enhancement of PGC-1α expression that upregulates several mitochondrial transcription factors. Furthermore, inhibition of mitophagy by knocking down PINK1 expression reverted CO-induced mitochondrial biogenesis, indicating that mitochondrial turnover is dependent on modulation of mitophagy. Finally, CORM-A1 prevented astrocytic cell death induced by oxidative stress in a mitophagy-dependent manner. In fact, whenever PINK1 was knocked down, CORM-A1-induced cytoprotection was lost. In summary, CORM-A1 stimulates mitochondrial turnover, which in turn prevents astrocytic cell death. CO cytoprotection depends on increasing mitochondrial population and on eliminating dysfunctional mitochondria.
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27
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Pang B, van Weerd JH, Hamoen FL, Snyder MP. Identification of non-coding silencer elements and their regulation of gene expression. Nat Rev Mol Cell Biol 2022; 24:383-395. [DOI: 10.1038/s41580-022-00549-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2022] [Indexed: 11/09/2022]
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28
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Wang X, Wei X, Cao Y, Xing P. ZNF33A Promotes Tumor Progression and BET Inhibitor Resistance in Triple-Negative Breast Cancer. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:1458-1469. [PMID: 35843263 DOI: 10.1016/j.ajpath.2022.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 06/04/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Overexpression of ZNF33A (Krüppel-type zinc finger 33A) promotes carcinogenesis in several malignant tumors. However, the biochemical role and clinical importance of ZNF33A in triple-negative breast cancer (TNBC) still need to be explored. In this study, overexpression of ZNF33A in TNBC patient tissues and cell lines led to a worse prognosis. ZNF33A promoted cell growth and facilitated the resistance of cancer cells to inhibitors of bromodomain and extraterminal domain (BET) in TNBC. ZNF33A also promoted the induction of c-Myc, the primary player for the resistance to BET inhibitors in TNBC. In conclusion, ZNF33A may be a tumor growth-promoting factor associated with TNBC prognosis, and ZNF33A repression may sensitize TNBC cells to BET inhibitors.
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Affiliation(s)
- Xu Wang
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xiaolin Wei
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yu Cao
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Peng Xing
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China.
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29
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Zhang M, Current JZ, Chaney HL, Yao J. Identification of the DNA binding element of ZNFO, an oocyte-specific zinc finger transcription factor in cattle. Gene 2022; 834:146655. [PMID: 35680024 DOI: 10.1016/j.gene.2022.146655] [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: 03/18/2022] [Revised: 05/14/2022] [Accepted: 06/02/2022] [Indexed: 11/04/2022]
Abstract
The maternal effect genes are essential components of oocyte competence, which orchestrate the early developmental events before zygotic genome activation (ZGA). The Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KRAB-ZFPs) constitute the largest transcription factor family in mammals. As a novel maternal effect gene, ZNFO was identified previously in our laboratory. The gene codes for a KRAB-ZFP specifically expressed in bovine oocytes and early embryos and gene silencing experiments have demonstrated that ZNFO is required for early embryonic development in cattle. In the present study, we identified a consensus sequence, ATATCCTGTTTAAACCCC, as the DNA binding element of ZNFO (ZNFOBE) using a library of random oligonucleotides by cyclic amplification of sequence target (CAST) analysis. Sequence-specific binding of ZNFO to the DNA binding element was confirmed by an electrophoretic mobility shift assay (EMSA), and the key nucleotides in the ZNFOBE that are required for specific binding by ZNFO were further determined by a competitive EMSA using mutant competitors. Through a luciferase-based reporter assay, it was confirmed that the interaction between ZNFO and ZNFOBE is required for the repressive function of ZNFO. These results provide an essential step towards the identification of ZNFO regulated genes that play important roles during early embryonic development.
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Affiliation(s)
- Mingxiang Zhang
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Jaelyn Z Current
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Heather L Chaney
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Jianbo Yao
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA.
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30
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Rasmussen SV, Jin JX, Bickford LR, Woods AD, Sahm F, Crawford KA, Nagamori K, Goto H, Torres KE, Sidoni A, Rudzinski ER, Thway K, Jones RL, Ciulli A, Wright H, Lathara M, Srinivasa G, Kannan K, Huang PH, Grünewald TGP, Berlow NE, Keller C. Functional genomic analysis of epithelioid sarcoma reveals distinct proximal and distal subtype biology. Clin Transl Med 2022; 12:e961. [PMID: 35839307 PMCID: PMC9286527 DOI: 10.1002/ctm2.961] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/13/2022] [Accepted: 06/17/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Metastatic epithelioid sarcoma (EPS) remains a largely unmet clinical need in children, adolescents and young adults despite the advent of EZH2 inhibitor tazemetostat. METHODS In order to realise consistently effective drug therapies, a functional genomics approach was used to identify key signalling pathway vulnerabilities in a spectrum of EPS patient samples. EPS biopsies/surgical resections and cell lines were studied by next-generation DNA exome and RNA deep sequencing, then EPS cell cultures were tested against a panel of chemical probes to discover signalling pathway targets with the most significant contributions to EPS tumour cell maintenance. RESULTS Other biologically inspired functional interrogations of EPS cultures using gene knockdown or chemical probes demonstrated only limited to modest efficacy in vitro. However, our molecular studies uncovered distinguishing features (including retained dysfunctional SMARCB1 expression and elevated GLI3, FYN and CXCL12 expression) of distal, paediatric/young adult-associated EPS versus proximal, adult-associated EPS. CONCLUSIONS Overall results highlight the complexity of the disease and a limited chemical space for therapeutic advancement. However, subtle differences between the two EPS subtypes highlight the biological disparities between younger and older EPS patients and emphasise the need to approach the two subtypes as molecularly and clinically distinct diseases.
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Affiliation(s)
| | - Jia Xiang Jin
- Division of Translational Pediatric Sarcoma Research, Hopp Children's Cancer Center (KiTZ), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | | | - Andrew D Woods
- Children's Cancer Therapy Development Institute, Beaverton, Oregon, USA
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | | | - Kiyo Nagamori
- Children's Cancer Therapy Development Institute, Beaverton, Oregon, USA
| | - Hiroaki Goto
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Keila E Torres
- Sarcoma Surgical Oncology, MD Anderson Cancer Center, Houston, Texas, USA
| | - Angelo Sidoni
- Section of Pathology, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Erin R Rudzinski
- Department of Pathology, Seattle Children's Hospital, Seattle, Washington, USA
| | - Khin Thway
- Sarcoma Unit, Royal Marsden Hospital, Belmont, UK.,Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Robin L Jones
- Sarcoma Unit, Royal Marsden Hospital, Belmont, UK.,Division of Clinical Studies, Institute of Cancer Research, London, UK
| | - Alessio Ciulli
- School of Life Sciences, University of Dundee, Dundee, UK
| | | | | | | | | | - Paul H Huang
- Sarcoma Unit, Royal Marsden Hospital, Belmont, UK.,Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Thomas G P Grünewald
- Division of Translational Pediatric Sarcoma Research, Hopp Children's Cancer Center (KiTZ), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Noah E Berlow
- Children's Cancer Therapy Development Institute, Beaverton, Oregon, USA
| | - Charles Keller
- Children's Cancer Therapy Development Institute, Beaverton, Oregon, USA
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31
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Cheng Z, Yu R, Li L, Mu J, Gong Y, Wu F, Liu Y, Zhou X, Zeng X, Wu Y, Sun R, Xiang T. Disruption of ZNF334 promotes triple-negative breast carcinoma malignancy through the SFRP1/ Wnt/β-catenin signaling axis. Cell Mol Life Sci 2022; 79:280. [PMID: 35507080 PMCID: PMC11072843 DOI: 10.1007/s00018-022-04295-1] [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: 01/18/2022] [Revised: 03/20/2022] [Accepted: 04/06/2022] [Indexed: 11/03/2022]
Abstract
Zinc-finger proteins (ZNFs) constitute the largest transcription factor family in the human genome. The family functions in many important biological processes involved in tumorigenesis. In our research, we identified ZNF334 as a novel tumor suppressor of triple-negative breast cancer (TNBC). ZNF334 expression was usually reduced in breast cancerv (BrCa) tissues and TNBC cell lines MDA-MB-231 (MB231) and YCCB1. We observed that promoter hypermethylation of ZNF334 was common in BrCa cell lines and tissues, which was likely responsible for its reduced expression. Ectopic expression of ZNF334 in TNBC cell lines MB231 and YCCB1 could suppress their growth and metastatic capacity both in vitro and in vivo, and as well induce cell cycle arrest at S phase and cell apoptosis. Moreover, re-expression of ZNF334 in TNBC cell lines could rescue Epithelial-Mesenchymal Transition (EMT) process and restrain stemness, due to up-regulation of SFRP1, which is an antagonist of Wnt/β-catenin signaling. In conclusion, we verified that ZNF334 had a suppressive function of TNBC cell lines by targeting the SFRP1/Wnt/β-catenin signaling axis, which might have the potentials to become a new biomarker for diagnosis and treatment of TNBC patients.
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Affiliation(s)
- Zhaobo Cheng
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Renjie Yu
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Li Li
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Junhao Mu
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yijia Gong
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Fan Wu
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yujia Liu
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiangyi Zhou
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaohua Zeng
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Yongzhong Wu
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Ran Sun
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Tingxiu Xiang
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China.
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32
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Bonchuk AN, Boyko KM, Nikolaeva AY, Burtseva AD, Popov VO, Georgiev PG. Structural insights into highly similar spatial organization of zinc-finger associated domains with a very low sequence similarity. Structure 2022; 30:1004-1015.e4. [DOI: 10.1016/j.str.2022.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/28/2022] [Accepted: 04/21/2022] [Indexed: 10/18/2022]
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33
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Heyliger SO, Soliman KFA, Saulsbury MD, Reams RR. Prognostic Relevance of ZNF844 and Chr 19p13.2 KRAB-Zinc Finger Proteins in Clear Cell Renal Carcinoma. Cancer Genomics Proteomics 2022; 19:305-327. [PMID: 35430565 DOI: 10.21873/cgp.20322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/05/2022] [Accepted: 02/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND/AIM Clear-cell renal cell carcinoma (ccRCC) is the most common and aggressive form of all urological cancers, with poor prognosis and high mortality. Despite growing evidence of involvement in carcinogenesis, the role of KRAB-ZFP in ccRCC has not been fully explored. KRAB Zinc finger proteins (KRAB-ZFPs) are the largest family of mammalian transcription regulators. They are differentially expressed in various tissues during cellular development and phenotypic differentiation. MATERIALS AND METHODS In this study, the levels of transcripts of ccRCC from The Cancer Genome Atlas (TCGA) dataset were used to identify prognostic biomarkers in this disease. RESULTS Using bioinformatics techniques, we demonstrate that approximately 60% of KRAB zinc finger proteins located on chromosome 19p13.2 are differentially expressed, with all but two being down-regulated in ccRCC. Moreover, ZNF844, a paralog of ZNF433, was the most down-regulated across all histological grades and pathological stages (p<0.001). In addition, the decrease in ZNF844 expression was associated with poor patient survival (HR=0.41; 95% CI=0.3-0.56; p<0.0001). Gene Set Enrichment Analysis of genes inversely co-expressed with ZNF844 revealed that enriched pathways were consistently related to immune and translation processes (p<0.05, FDR <0.05). Lastly, ZNF844 expression showed moderate, inverse correlation to Helper T-cell (CD4 or Th1) subtype 1 (R=-0.558, p=5.15×10-39) infiltration and with the exhausted T-cell phenotype (R=-0.37; p=4.1×10-21). CONCLUSION Down-regulation of KRAB-ZFPs at 19p13.2 may represent a signature for ccRCC. Moreover, ZNF844 is a prognostic marker for ccRCC and may serve as a putative immune-related tumor suppressor gene.
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Affiliation(s)
- Simone O Heyliger
- Department of Pharmaceutical Sciences, Hampton University, Hampton, VA, U.S.A
| | - Karam F A Soliman
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, U.S.A
| | - Marilyn D Saulsbury
- Department of Pharmaceutical Sciences, Hampton University, Hampton, VA, U.S.A
| | - R Renee Reams
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, U.S.A.
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Olechnowicz A, Oleksiewicz U, Machnik M. KRAB-ZFPs and cancer stem cells identity. Genes Dis 2022. [PMID: 37492743 PMCID: PMC10363567 DOI: 10.1016/j.gendis.2022.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Studies on carcinogenesis continue to provide new information about different disease-related processes. Among others, much research has focused on the involvement of cancer stem cells (CSCs) in tumor initiation and progression. Studying the similarities and differences between CSCs and physiological stem cells (SCs) allows for a better understanding of cancer biology. Recently, it was shown that stem cell identity is partially governed by the Krϋppel-associated box domain zinc finger proteins (KRAB-ZFPs), the biggest family of transcription regulators. Several KRAB-ZFP factors exert a known effect in tumor cells, acting as tumor suppressor genes (TSGs) or oncogenes, yet their role in CSCs is still poorly characterized. Here, we review recent studies regarding the influence of KRAB-ZFPs and their cofactor protein TRIM28 on CSCs phenotype, stemness features, migration and invasion potential, metastasis, and expression of parental markers.
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35
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Sun M, Ju J, Ding Y, Zhao C, Tian C. The signaling pathways regulated by KRAB zinc-finger proteins in cancer. Biochim Biophys Acta Rev Cancer 2022; 1877:188731. [DOI: 10.1016/j.bbcan.2022.188731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 03/23/2022] [Accepted: 04/20/2022] [Indexed: 12/11/2022]
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36
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Zhang X, Zheng Q, Yue X, Yuan Z, Ling J, Yuan Y, Liang Y, Sun A, Liu Y, Li H, Xu K, He F, Wang J, Wu J, Zhao C, Tian C. ZNF498 promotes hepatocellular carcinogenesis by suppressing p53-mediated apoptosis and ferroptosis via the attenuation of p53 Ser46 phosphorylation. J Exp Clin Cancer Res 2022; 41:79. [PMID: 35227287 PMCID: PMC8883630 DOI: 10.1186/s13046-022-02288-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/14/2022] [Indexed: 02/08/2023] Open
Abstract
Background Dysfunctional p53 signaling is one of the major causes of hepatocellular carcinoma (HCC) tumorigenesis and development, but the mechanisms underlying p53 inactivation in HCC have not been fully clarified. The role of Krüppel-associated box (KRAB)-type zinc-finger protein ZNF498 in tumorigenesis and the underlying mechanisms are poorly understood. Methods Clinical HCC samples were used to assess the association of ZNF498 expression with clinicopathological characteristics and patient outcomes. A mouse model in which HCC was induced by diethylnitrosamine (DEN) was used to explore the role of ZNF498 in HCC initiation and progression. ZNF498 overexpression and knockdown HCC cell lines were employed to examine the effects of ZNF498 on cellular proliferation, apoptosis, ferroptosis and tumor growth. Western blotting, immunoprecipitation, qPCR, luciferase assays and flow cytometry were also conducted to determine the underlying mechanisms related to ZNF498 function. Results ZNF498 was found to be highly expressed in HCC, and increased ZNF498 expression was positively correlated with advanced pathological grade and poor survival in HCC patients. Furthermore, ZNF498 promoted DEN-induced hepatocarcinogenesis and progression in mice. Mechanistically, ZNF498 directly interacted with p53 and suppressed p53 transcriptional activation by inhibiting p53 Ser46 phosphorylation. ZNF498 competed with p53INP1 for p53 binding and suppressed PKCδ- and p53INP1-mediated p53 Ser46 phosphorylation. In addition, functional assays revealed that ZNF498 promoted liver cancer cell growth in vivo and in vitro in a p53-dependent manner. Moreover, ZNF498 inhibited p53-mediated apoptosis and ferroptosis by attenuating p53 Ser46 phosphorylation. Conclusions Our results strongly suggest that ZNF498 suppresses apoptosis and ferroptosis by attenuating p53 Ser46 phosphorylation in hepatocellular carcinogenesis, revealing a novel ZNF498-PKCδ-p53INP1-p53 axis in HCC cells that would enrich the non-mutation p53-inactivating mechanisms in HCC. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02288-3.
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Affiliation(s)
- Xiuyuan Zhang
- School of Life science and Technology, Weifang Medical University, Weifang, 261053, Shandong Province, China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Qijian Zheng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Xiuying Yue
- Tianjin Baodi Hospital, Baodi Clinical College of Tianjin Medical University, Tianjin, 301800, China
| | - Zhanna Yuan
- Tianjin Baodi Hospital, Baodi Clinical College of Tianjin Medical University, Tianjin, 301800, China
| | - Jiming Ling
- School of Life science and Technology, Weifang Medical University, Weifang, 261053, Shandong Province, China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Yanzhi Yuan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Yanying Liang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.,School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271016, Shandong, China
| | - Aihua Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Yuchen Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Hui Li
- Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China
| | - Kaikun Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Jian Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Jin Wu
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200092, China. .,Department of Gastroenterology and Nutrition, Shanghai Institute for Pediatric Research, School of Medicine, Shanghai Jiaotong University, Shanghai, 200092, China.
| | - Chunling Zhao
- School of Life science and Technology, Weifang Medical University, Weifang, 261053, Shandong Province, China.
| | - Chunyan Tian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
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Zinc-finger protein 382 antagonises CDC25A and ZEB1 signaling pathway in breast cancer. Genes Dis 2022; 10:568-582. [DOI: 10.1016/j.gendis.2021.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 11/13/2021] [Accepted: 12/22/2021] [Indexed: 11/23/2022] Open
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Lorenz P, Steinbeck F, Krause L, Thiesen HJ. The KRAB Domain of ZNF10 Guides the Identification of Specific Amino Acids That Transform the Ancestral KRAB-A-Related Domain Present in Human PRDM9 into a Canonical Modern KRAB-A Domain. Int J Mol Sci 2022; 23:1072. [PMID: 35162997 PMCID: PMC8835667 DOI: 10.3390/ijms23031072] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/14/2022] Open
Abstract
Krüppel-associated box (KRAB) zinc finger proteins are a large class of tetrapod transcription factors that usually exert transcriptional repression through recruitment of TRIM28/KAP1. The evolutionary root of modern KRAB domains (mKRAB) can be traced back to an ancestral motif (aKRAB) that occurs even in invertebrates. Here, we first stratified three subgroups of aKRAB sequences from the animal kingdom (PRDM9, SSX and coelacanth KZNF families) and defined ancestral subdomains for KRAB-A and KRAB-B. Using human ZNF10 mKRAB-AB as blueprints for function, we then identified the necessary amino acid changes that transform the inactive aKRAB-A of human PRDM9 into an mKRAB domain capable of mediating silencing and complexing TRIM28/KAP1 in human cells when employed as a hybrid with ZNF10-B. Full gain of function required replacement of residues KR by the conserved motif MLE (positionsA32-A34), which inserted an additional residue, and exchange of A9/S for F, A20/M for L, and A27/R for V. AlphaFold2 modelling documented an evolutionary conserved L-shaped body of two α-helices in all KRAB domains. It is transformed into a characteristic spatial arrangement typical for mKRAB-AB upon the amino acid replacements and in conjunction with a third helix supplied by mKRAB-B. Side-chains pointing outward from the core KRAB 3D structure may reveal a protein-protein interaction code enabling graded binding of TRIM28 to different KRAB domains. Our data provide basic insights into structure-function relationships and emulate transitions of KRAB during evolution.
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Affiliation(s)
- Peter Lorenz
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
| | - Felix Steinbeck
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
| | - Ludwig Krause
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
| | - Hans-Jürgen Thiesen
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
- Gesellschaft für Individualisierte Medizin (IndyMed) mbH, 17, 18055 Rostock, Germany
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The Molecular Landscape of Medulloblastoma in Teenagers and Young Adults. Cancers (Basel) 2022; 14:cancers14010251. [PMID: 35008416 PMCID: PMC8750554 DOI: 10.3390/cancers14010251] [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: 12/20/2021] [Accepted: 12/29/2021] [Indexed: 02/01/2023] Open
Abstract
Medulloblastoma (MB) is a childhood malignant brain tumour but also occurs in teenagers and young adults (TYA). Considering that MB is heterogeneous, this study aimed to define the molecular landscape of MBs in TYAs. We collated more than 2000 MB samples that included 287 TYA patients (13-24 years). We performed computational analyses consisting of genome-wide methylation and transcriptomic profiles and developed a prognostics model for the TYAs with MB. We identified that TYAs predominantly comprised of Group 4 (40%) and Sonic Hedgehog (SHH)-activated (33%) tumours, with Wingless-type (WNT, 17%) and Group 3 (10%) being less common. TYAs with SHH tumours displayed significantly more gene expression alterations, whereas no gene was detected in the Group 4 tumours. Across MB subgroups, we identified unique and shared sets of TYA-specific differentially methylated probes and DNA-binding motifs. Finally, a 22-gene signature stratified TYA patients into high- and low-risk groups, and the prognostic significance of these risk groups persisted in multivariable regression models (P = 0.001). This study is an important step toward delineating the molecular landscape of TYAs with MB. The emergence of novel genes and pathways may provide a basis for improved clinical management of TYA with MB.
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40
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Liu C, Zhang X, Chai H, Xu S, Liu Q, Luo Y, Li S. Identification of Immune Cells and Key Genes associated with Alzheimer's Disease. Int J Med Sci 2022; 19:112-125. [PMID: 34975305 PMCID: PMC8692117 DOI: 10.7150/ijms.66422] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/18/2021] [Indexed: 12/21/2022] Open
Abstract
Alzheimer's disease (AD) is an age-related neurodegenerative disorder characterized by cognitive impairment and memory loss, for which there is no effective cure to date. In the past several years, numerous studies have shown that increased inflammation in AD is a major cause of cognitive impairment. This study aimed to reveal 22 kinds of peripheral immune cell types and key genes associated with AD. The prefrontal cortex transcriptomic data from Gene Expression Omnibus (GEO) database were collected, and CIBERSORT was used to assess the composition of 22 kinds of immune cells in all samples. Weighted gene co-expression network analysis (WGCNA) was used to construct gene co-expression networks and identified candidate module genes associated with AD. The least absolute shrinkage and selection operator (LASSO) and random forest (RF) models were constructed to analyze candidate module genes, which were selected from the result of WGCNA. The results showed that the immune infiltration in the prefrontal cortex of AD patients was different from healthy samples. Of all 22 kinds of immune cells, M1 macrophages were the most relevant cell type to AD. We revealed 10 key genes associated with AD and M1 macrophages by LASSO and RF analysis, including ARMCX5, EDN3, GPR174, MRPL23, RAET1E, ROD1, TRAF1, WNT7B, OR4K2 and ZNF543. We verified these 10 genes by logistic regression and k-fold cross-validation. We also validated the key genes in an independent dataset, and found GPR174, TRAF1, ROD1, RAET1E, OR4K2, MRPL23, ARMCX5 and EDN3 were significantly different between the AD and healthy controls. Moreover, in the 5XFAD transgenic mice, the differential expression trends of Wnt7b, Gpr174, Ptbp3, Mrpl23, Armcx5 and Raet1e are consistent with them in independent dataset. Our results provided potential therapeutic targets for AD patients.
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Affiliation(s)
- Chenming Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xi Zhang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Huazhen Chai
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Sutong Xu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qiulu Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yuping Luo
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Siguang Li
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
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41
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A Multi-Omics Network of a Seven-Gene Prognostic Signature for Non-Small Cell Lung Cancer. Int J Mol Sci 2021; 23:ijms23010219. [PMID: 35008645 PMCID: PMC8745553 DOI: 10.3390/ijms23010219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 12/30/2022] Open
Abstract
There is an unmet clinical need to identify patients with early-stage non-small cell lung cancer (NSCLC) who are likely to develop recurrence and to predict their therapeutic responses. Our previous study developed a qRT-PCR-based seven-gene microfluidic assay to predict the recurrence risk and the clinical benefits of chemotherapy. This study showed it was feasible to apply this seven-gene panel in RNA sequencing profiles of The Cancer Genome Atlas (TCGA) NSCLC patients (n = 923) in randomly partitioned feasibility-training and validation sets (p < 0.05, Kaplan-Meier analysis). Using Boolean implication networks, DNA copy number variation-mediated transcriptional regulatory network of the seven-gene signature was identified in multiple NSCLC cohorts (n = 371). The multi-omics network genes, including PD-L1, were significantly correlated with immune infiltration and drug response to 10 commonly used drugs for treating NSCLC. ZNF71 protein expression was positively correlated with epithelial markers and was negatively correlated with mesenchymal markers in NSCLC cell lines in Western blots. PI3K was identified as a relevant pathway of proliferation networks involving ZNF71 and its isoforms formulated with CRISPR-Cas9 and RNA interference (RNAi) profiles. Based on the gene expression of the multi-omics network, repositioning drugs were identified for NSCLC treatment.
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Hernández-Quiles M, Baak R, Borgman A, den Haan S, Sobrevals Alcaraz P, van Es R, Kiss-Toth E, Vos H, Kalkhoven E. Comprehensive Profiling of Mammalian Tribbles Interactomes Implicates TRIB3 in Gene Repression. Cancers (Basel) 2021; 13:6318. [PMID: 34944947 PMCID: PMC8699236 DOI: 10.3390/cancers13246318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 12/30/2022] Open
Abstract
The three human Tribbles (TRIB) pseudokinases have been implicated in a plethora of signaling and metabolic processes linked to cancer initiation and progression and can potentially be used as biomarkers of disease and prognosis. While their modes of action reported so far center around protein-protein interactions, the comprehensive profiling of TRIB interactomes has not been reported yet. Here, we have developed a robust mass spectrometry (MS)-based proteomics approach to characterize Tribbles' interactomes and report a comprehensive assessment and comparison of the TRIB1, -2 and -3 interactomes, as well as domain-specific interactions for TRIB3. Interestingly, TRIB3, which is predominantly localized in the nucleus, interacts with multiple transcriptional regulators, including proteins involved in gene repression. Indeed, we found that TRIB3 repressed gene transcription when tethered to DNA in breast cancer cells. Taken together, our comprehensive proteomic assessment reveals previously unknown interacting partners and functions of Tribbles proteins that expand our understanding of this family of proteins. In addition, our findings show that MS-based proteomics provides a powerful tool to unravel novel pseudokinase biology.
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Affiliation(s)
- Miguel Hernández-Quiles
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
| | - Rosalie Baak
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
| | - Anouska Borgman
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
| | - Suzanne den Haan
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
| | - Paula Sobrevals Alcaraz
- Oncode Institute and Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (P.S.A.); (R.v.E.); (H.V.)
| | - Robert van Es
- Oncode Institute and Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (P.S.A.); (R.v.E.); (H.V.)
| | - Endre Kiss-Toth
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2TN, UK;
| | - Harmjan Vos
- Oncode Institute and Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (P.S.A.); (R.v.E.); (H.V.)
| | - Eric Kalkhoven
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
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43
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Underestimation of Heritability across the Molecular Layers of the Gene Expression Process. Processes (Basel) 2021. [DOI: 10.3390/pr9122144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
We investigated the extent of the heritability underestimation for molecules from an infinitesimal model in mixed model analysis. To this end, we estimated the heritability of transcription, ribosome occupancy, and translation in lymphoblastoid cell lines from Yoruba individuals. Upon considering all genome-wide nucleotide variants, a considerable underestimation in heritability was observed for mRNA transcription (−0.52), ribosome occupancy (−0.48), and protein abundance (−0.47). We employed a mixed model with an optimal number of nucleotide variants, which maximized heritability, and identified two novel expression quantitative trait loci (eQTLs; p < 1.0 × 10−5): rs11016815 on chromosome 10 that influences the transcription of SCP2, a trans-eGene on chromosome 1—whose expression increases in response to MGMT downregulation-induced apoptosis, the cis-eGene of rs11016815—and rs1041872 on chromosome 11 that influences the ribosome occupancy of CCDC25 on chromosome 8 and whose cis-eGene encodes ZNF215, a transcription factor that potentially regulates the translation speed of CCDC25. Our results suggest that an optimal number of nucleotide variants should be used in a mixed model analysis to accurately estimate heritability and identify eQTLs. Moreover, a heterogeneous covariance structure based on gene identity and the molecular layers of the gene expression process should be constructed to better explain polygenic effects and reduce errors in identifying eQTLs.
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44
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Khang R, Jo A, Kang H, Kim H, Kwag E, Lee JY, Koo O, Park J, Kim HK, Jo DG, Hwang I, Ahn JY, Lee Y, Choi JY, Lee YS, Shin JH. Loss of zinc-finger protein 212 leads to Purkinje cell death and locomotive abnormalities with phospholipase D3 downregulation. Sci Rep 2021; 11:22745. [PMID: 34815492 PMCID: PMC8610974 DOI: 10.1038/s41598-021-02218-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 11/08/2021] [Indexed: 11/17/2022] Open
Abstract
Although Krüppel-associated box domain-containing zinc-finger proteins (K-ZNFs) may be associated with sophisticated gene regulation in higher organisms, the physiological functions of most K-ZNFs remain unknown. The Zfp212 protein was highly conserved in mammals and abundant in the brain; it was mainly expressed in the cerebellum (Cb). Zfp212 (mouse homolog of human ZNF212) knockout (Zfp212-KO) mice showed a reduction in survival rate compared to wild-type mice after 20 months of age. GABAergic Purkinje cell degeneration in the Cb and aberrant locomotion were observed in adult Zfp212-KO mice. To identify genes related to the ataxia-like phenotype of Zfp212-KO mice, 39 ataxia-associated genes in the Cb were monitored. Substantial alterations in the expression of ataxin 10, protein phosphatase 2 regulatory subunit beta, protein kinase C gamma, and phospholipase D3 (Pld3) were observed. Among them, Pld3 alone was tightly regulated by Flag-tagged ZNF212 overexpression or Zfp212 knockdown in the HT22 cell line. The Cyclic Amplification and Selection of Targets assay identified the TATTTC sequence as a recognition motif of ZNF212, and these motifs occurred in both human and mouse PLD3 gene promoters. Adeno-associated virus-mediated introduction of human ZNF212 into the Cb of 3-week-old Zfp212-KO mice prevented Purkinje cell death and motor behavioral deficits. We confirmed the reduction of Zfp212 and Pld3 in the Cb of an alcohol-induced cerebellar degeneration mouse model, suggesting that the ZNF212–PLD3 relationship is important for Purkinje cell survival.
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Affiliation(s)
- Rin Khang
- Department of Pharmacology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| | - Areum Jo
- Department of Pharmacology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| | - Hojin Kang
- Department of Pharmacology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| | - Hanna Kim
- Department of Pharmacology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| | - Eunsang Kwag
- Department of Pharmacology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| | - Ji-Yeong Lee
- Department of Pharmacology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| | - Okjae Koo
- Laboratory Animal Research Center, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,ToolGen, Seoul, 08501, South Korea
| | - Jinsu Park
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Hark Kyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Dong-Gyu Jo
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, South Korea.,Biomedical Institute for Convergence, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Inwoo Hwang
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| | - Jee-Yin Ahn
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, 06351, South Korea
| | - Yunjong Lee
- Department of Pharmacology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, 06351, South Korea
| | - Jeong-Yun Choi
- Department of Pharmacology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, 06351, South Korea
| | - Yun-Song Lee
- Department of Pharmacology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, 06351, South Korea
| | - Joo-Ho Shin
- Department of Pharmacology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea. .,Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea. .,Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, 06351, South Korea.
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45
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Li S, Shi X, Li J, Zhou X. Pathogenicity of the MAGE family. Oncol Lett 2021; 22:844. [PMID: 34733362 PMCID: PMC8561213 DOI: 10.3892/ol.2021.13105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/07/2021] [Indexed: 12/12/2022] Open
Abstract
The melanoma antigen gene (MAGE) protein family is a group of highly conserved proteins that share a common homology domain. Under normal circumstances, numerous MAGE proteins are only expressed in reproduction-related tissues; however, abnormal expression levels are observed in a variety of tumor tissues. The MAGE family consists of type I and II proteins, several of which are cancer-testis antigens that are highly expressed in cancer and serve a critical role in tumorigenesis. Therefore, this review will use the relationship between MAGEs and tumors as a starting point, focusing on the latest developments regarding the function of MAGEs as oncogenes, and preliminarily reveal their possible mechanisms.
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Affiliation(s)
- Sanyan Li
- Department of Pathology, Qianjiang Central Hospital, Qianjiang, Hubei 433100, P.R. China
| | - Xiang Shi
- Department of Pathology, Qianjiang Central Hospital, Qianjiang, Hubei 433100, P.R. China
| | - Jingping Li
- Department of Respiratory Medicine, Qianjiang Central Hospital, Qianjiang, Hubei 433100, P.R. China
| | - Xianrong Zhou
- Department of Pathology, Qianjiang Central Hospital, Qianjiang, Hubei 433100, P.R. China
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46
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Yazar V, Kang SU, Ha S, Dawson VL, Dawson TM. Integrative genome-wide analysis of dopaminergic neuron-specific PARIS expression in Drosophila dissects recognition of multiple PPAR-γ associated gene regulation. Sci Rep 2021; 11:21500. [PMID: 34728675 PMCID: PMC8563805 DOI: 10.1038/s41598-021-00858-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/19/2021] [Indexed: 01/21/2023] Open
Abstract
The transcriptional repressor called parkin interacting substrate (PARIS; ZNF746) was initially identified as a novel co-substrate of parkin and PINK1 that leads to Parkinson’s disease (PD) by disrupting mitochondrial biogenesis through peroxisome proliferator-activated receptor gamma (PPARγ) coactivator -1α (PGC-1α) suppression. Since its initial discovery, growing evidence has linked PARIS to defective mitochondrial biogenesis observed in PD pathogenesis. Yet, dopaminergic (DA) neuron-specific mechanistic underpinnings and genome-wide PARIS binding landscape has not been explored. We employed conditional translating ribosome affinity purification (TRAP) followed by RNA sequencing (TRAP-seq) for transcriptome profiling of DA neurons in transgenic Drosophila lines expressing human PARIS wild type (WT) or mutant (C571A). We also generated genome-wide maps of PARIS occupancy using ChIP-seq in human SH-SY5Y cells. The results demonstrated that PPARγ functions as a master regulator of PARIS-induced molecular changes at the transcriptome level, confirming that PARIS acts primarily on PGC-1α to lead to neurodegeneration in PD. Moreover, we identified that PARIS actively modulates expression of PPARγ target genes by physically binding to the promoter regions. Together, our work revealed how PARIS drives adverse effects on modulation of PPAR-γ associated gene clusters in DA neurons.
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Affiliation(s)
- Volkan Yazar
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 North Broadway, Suite 711, Baltimore, MD, 21205, USA
| | - Sung-Ung Kang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 North Broadway, Suite 711, Baltimore, MD, 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, 70130-2685, USA.,Diana Helis Henry Medical Research Foundation, New Orleans, LA, 70130-2685, USA
| | - Shinwon Ha
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 North Broadway, Suite 711, Baltimore, MD, 21205, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 North Broadway, Suite 711, Baltimore, MD, 21205, USA. .,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, USA. .,Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, USA. .,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, USA. .,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, 70130-2685, USA. .,Diana Helis Henry Medical Research Foundation, New Orleans, LA, 70130-2685, USA.
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 North Broadway, Suite 711, Baltimore, MD, 21205, USA. .,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, USA. .,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, USA. .,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. .,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, 70130-2685, USA. .,Diana Helis Henry Medical Research Foundation, New Orleans, LA, 70130-2685, USA.
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Cesaro E, Lupo A, Rapuano R, Pastore A, Grosso M, Costanzo P. ZNF224 Protein: Multifaceted Functions Based on Its Molecular Partners. Molecules 2021; 26:molecules26206296. [PMID: 34684876 PMCID: PMC8537547 DOI: 10.3390/molecules26206296] [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: 09/27/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 01/05/2023] Open
Abstract
The transcription factor ZNF224 is a Kruppel-like zinc finger protein that consists of 707 amino acids and contains 19 tandemly repeated C2H2 zinc finger domains that mediate DNA binding and protein-protein interactions. ZNF224 was originally identified as a transcriptional repressor of genes involved in energy metabolism, and it was demonstrated that ZNF224-mediated transcriptional repression needs the interaction of its KRAB repressor domain with the co-repressor KAP1 and its zinc finger domains 1-3 with the arginine methyltransferase PRMT5. Furthermore, the protein ZNF255 was identified as an alternative isoform of ZNF224 that possesses different domain compositions mediating distinctive functional interactions. Subsequent studies showed that ZNF224 is a multifunctional protein able to exert different transcriptional activities depending on the cell context and the variety of its molecular partners. Indeed, it has been shown that ZNF224 can act as a repressor, an activator and a cofactor for other DNA-binding transcription factors in different human cancers. Here, we provide a brief overview of the current knowledge on the multifaceted interactions of ZNF224 and the resulting different roles of this protein in various cellular contexts.
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Affiliation(s)
- Elena Cesaro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (A.P.); (M.G.)
- Correspondence: (E.C.); (P.C.)
| | - Angelo Lupo
- Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Italy; (A.L.); (R.R.)
| | - Roberta Rapuano
- Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Italy; (A.L.); (R.R.)
| | - Arianna Pastore
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (A.P.); (M.G.)
| | - Michela Grosso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (A.P.); (M.G.)
| | - Paola Costanzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (A.P.); (M.G.)
- Correspondence: (E.C.); (P.C.)
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48
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Powers NR, Billings T, Paigen K, Petkov PM. Differential effects of two catalytic mutations on full-length PRDM9 and its isolated PR/SET domain reveal a case of pseudomodularity. Genetics 2021; 219:6385243. [PMID: 34747456 DOI: 10.1093/genetics/iyab172] [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: 09/02/2021] [Accepted: 09/30/2021] [Indexed: 11/14/2022] Open
Abstract
PRDM9 is a DNA-binding histone methyltransferase that designates and activates recombination hotspots in mammals by locally trimethylating lysines 4 and 36 of histone H3. In mice, we recently reported two independently produced point mutations at the same residue, Glu360Pro (Prdm9EP) and Glu360Lys (Prdm9EK), which severely reduce its H3K4 and H3K36 methyltransferase activities in vivo. Prdm9EP is slightly less hypomorphic than Prdm9EK, but both mutations reduce both the number and amplitude of PRDM9-dependent H3K4me3 and H3K36me3 peaks in spermatocytes. While both mutations cause infertility with complete meiotic arrest in males, Prdm9EP, but not Prdm9EK, is compatible with some female fertility. When we tested the effects of these mutations in vitro, both Prdm9EP and Prdm9EK abolished H3K4 and H3K36 methyltransferase activity in full-length PRDM9. However, in the isolated PRDM9 PR/SET domain, these mutations selectively compromised H3K36 methyltransferase activity, while leaving H3K4 methyltransferase activity intact. The difference in these effects on the PR/SET domain vs the full-length protein shows that PRDM9 is not an intrinsically modular enzyme; its catalytic domain is influenced by its tertiary structure and possibly by its interactions with DNA and other proteins in vivo. These two informative mutations illuminate the enzymatic chemistry of PRDM9, and potentially of PR/SET domains in general, reveal the minimal threshold of PRDM9-dependent catalytic activity for female fertility, and potentially have some practical utility for genetic mapping and genomics.
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Czerwinska P, Mackiewicz AA. Low Levels of TRIM28-Interacting KRAB-ZNF Genes Associate with Cancer Stemness and Predict Poor Prognosis of Kidney Renal Clear Cell Carcinoma Patients. Cancers (Basel) 2021; 13:cancers13194835. [PMID: 34638319 PMCID: PMC8508054 DOI: 10.3390/cancers13194835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/16/2021] [Accepted: 09/22/2021] [Indexed: 12/23/2022] Open
Abstract
Simple Summary This is the first report investigating the involvement of TRIM28-interacting KRAB-ZNFs in kidney cancer progression. We demonstrate a significant negative association between KRAB-ZNFs and cancer stemness followed by an attenuated immune-suppressive response and reveal the prognostic role for several KRAB-ZNFs. Our findings may help better understand the molecular basis of kidney cancer and ultimately pave the way to more appropriate prognostic tools and novel therapeutic strategies directly eradicating the dedifferentiated compartment of the tumor. Abstract Krüppel-associated box zinc finger (KRAB-ZNF) proteins are known to regulate diverse biological processes, such as embryonic development, tissue-specific gene expression, and cancer progression. However, their involvement in the regulation of cancer stemness-like phenotype acquisition and maintenance is scarcely explored across solid tumor types, and to date, there are no data for kidney renal clear cell cancer (KIRC). We have harnessed The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) database transcriptomic data and used several bioinformatic tools (i.e., GEPIA2, GSCALite, TISIDB, GSEA, CIBERSORT) to verify the relation between the expression and genomic alterations in KRAB-ZNFs and kidney cancer, focusing primarily on tumor dedifferentiation status and antitumor immune response. Our results demonstrate a significant negative correlation between KRAB-ZNFs and kidney cancer dedifferentiation status followed by an attenuated immune-suppressive response. The transcriptomic profiles of high KRAB-ZNF-expressing kidney tumors are significantly enriched with stem cell markers and show a depletion of several inflammatory pathways known for favoring cancer stemness. Moreover, we show for the first time the prognostic role for several KRAB-ZNFs in kidney cancer. Our results provide new insight into the role of selected KRAB-ZNF proteins in kidney cancer development. We believe that our findings may help better understand the molecular basis of KIRC.
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Affiliation(s)
- Patrycja Czerwinska
- Department of Cancer Immunology, Poznan University of Medical Sciences, 15 Garbary St., 61-866 Poznan, Poland; or
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary St., 61-866 Poznan, Poland
- Correspondence: or
| | - Andrzej Adam Mackiewicz
- Department of Cancer Immunology, Poznan University of Medical Sciences, 15 Garbary St., 61-866 Poznan, Poland; or
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary St., 61-866 Poznan, Poland
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50
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The Identification of Zinc-Finger Protein 433 as a Possible Prognostic Biomarker for Clear-Cell Renal Cell Carcinoma. Biomolecules 2021; 11:biom11081193. [PMID: 34439859 PMCID: PMC8392881 DOI: 10.3390/biom11081193] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/31/2021] [Accepted: 08/06/2021] [Indexed: 11/18/2022] Open
Abstract
Clear-cell renal cell carcinoma (ccRCC) is the most common and aggressive form of all urological cancers, with poor prognosis and high mortality. At late stages, ccRCC is known to be mainly resistant to chemotherapy and radiotherapy. Therefore, it is urgent and necessary to identify biomarkers that can facilitate the early detection of ccRCC in patients. In this study, the levels of transcripts of ccRCC from The Cancer Genome Atlas (TCGA) dataset were used to identify prognostic biomarkers in this disease. Analyzing the data obtained indicated that the KRAB-ZNF protein is significantly suppressed in clear-cell carcinomas. Furthermore, ZNF433 is differentially expressed in ccRCC in a stage- and histological-grade-specific manner. In addition, ZNF433 expression was correlated with metastasis, with greater node involvement associated with lower ZNF433 expression (p < 0.01) and with a more unsatisfactory overall survival outcome (HR, 0.45; 95% CI, 0.33–0.6; p = 8.5 × 10−8). Since ccRCC is characterized by mutations in proteins that alter epigenetic modifications and /or chromatin remodeling, we examined the expression of ZNF433 transcripts in ccRCC with wildtype and mutated forms of BAP1, KDMC5, MTOR, PBRM1, SETD2, and VHL. Analysis revealed that ZNF433 expression was significantly reduced in ccRCC with mutations in the BAP1, SETD2, and KDM5C genes (p < 0.05). In addition, the ZNF433 promoter region was highly methylated, and hypermethylation was significantly associated with mRNA suppression (p < 2.2 × 10−16). In silico analysis of potential ZNF target genes found that the largest group of target genes are involved in cellular metabolic processes, which incidentally are particularly impaired in ccRCC. It was concluded from this study that gene expression of ZNF433 is associated with cancer progression and poorer prognosis, and that ZNF433 behaves in a manner that suggests that it is a prognostic marker and a possible tumor-suppressor gene in clear-cell renal cell carcinoma.
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