1
|
Quenneville J, Feghaly A, Tual M, Thomas K, Major F, Gagnon E. Long-term severe hypoxia adaptation induces non-canonical EMT and a novel Wilms Tumor 1 (WT1) isoform. Cancer Gene Ther 2024:10.1038/s41417-024-00795-3. [PMID: 38977895 DOI: 10.1038/s41417-024-00795-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 05/03/2024] [Accepted: 05/30/2024] [Indexed: 07/10/2024]
Abstract
The majority of cancer deaths are caused by solid tumors, where the four most prevalent cancers (breast, lung, colorectal and prostate) account for more than 60% of all cases (1). Tumor cell heterogeneity driven by variable cancer microenvironments, such as hypoxia, is a key determinant of therapeutic outcome. We developed a novel culture protocol, termed the Long-Term Hypoxia (LTHY) time course, to recapitulate the gradual development of severe hypoxia seen in vivo to mimic conditions observed in primary tumors. Cells subjected to LTHY underwent a non-canonical epithelial to mesenchymal transition (EMT) based on miRNA and mRNA signatures as well as displayed EMT-like morphological changes. Concomitant to this, we report production of a novel truncated isoform of WT1 transcription factor (tWt1), a non-canonical EMT driver, with expression driven by a yet undescribed intronic promoter through hypoxia-responsive elements (HREs). We further demonstrated that tWt1 initiates translation from an intron-derived start codon, retains proper subcellular localization and DNA binding. A similar tWt1 is also expressed in LTHY-cultured human cancer cell lines as well as primary cancers and predicts long-term patient survival. Our study not only demonstrates the importance of culture conditions that better mimic those observed in primary cancers, especially with regards to hypoxia, but also identifies a novel isoform of WT1 which correlates with poor long-term survival in ovarian cancer.
Collapse
Affiliation(s)
- Jordan Quenneville
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada.
- Department of Molecular Biology, Université de Montréal, Montréal, QC, Canada.
| | - Albert Feghaly
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Margaux Tual
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Department of Microbiology, Infectiology, and Immunology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Kiersten Thomas
- Department of Integrative Oncology, BC Cancer Research Center, Vancouver, BC, Canada
| | - François Major
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Department of Computer Science and Operations Research, Faculty of Arts and Sciences, Université de Montréal, Montréal, QC, Canada
| | - Etienne Gagnon
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada.
- Department of Microbiology, Infectiology, and Immunology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.
| |
Collapse
|
2
|
Henon C, Vibert J, Eychenne T, Gruel N, Colmet-Daage L, Ngo C, Garrido M, Dorvault N, Marques Da Costa ME, Marty V, Signolle N, Marchais A, Herbel N, Kawai-Kawachi A, Lenormand M, Astier C, Chabanon R, Verret B, Bahleda R, Le Cesne A, Mechta-Grigoriou F, Faron M, Honoré C, Delattre O, Waterfall JJ, Watson S, Postel-Vinay S. Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in DSRCTs. Cell Rep Med 2024; 5:101582. [PMID: 38781959 PMCID: PMC11228554 DOI: 10.1016/j.xcrm.2024.101582] [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: 10/13/2023] [Revised: 02/28/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
Desmoplastic small round cell tumor (DSRCT) is a rare, aggressive sarcoma driven by the EWSR1::WT1 chimeric transcription factor. Despite this unique oncogenic driver, DSRCT displays a polyphenotypic differentiation of unknown causality. Using single-cell multi-omics on 12 samples from five patients, we find that DSRCT tumor cells cluster into consistent subpopulations with partially overlapping lineage- and metabolism-related transcriptional programs. In vitro modeling shows that high EWSR1::WT1 DNA-binding activity associates with most lineage-related states, in contrast to glycolytic and profibrotic states. Single-cell chromatin accessibility analysis suggests that EWSR1::WT1 binding site variability may drive distinct lineage-related transcriptional programs, supporting some level of cell-intrinsic plasticity. Spatial transcriptomics reveals that glycolytic and profibrotic states specifically localize within hypoxic niches at the periphery of tumor cell islets, suggesting an additional role of tumor cell-extrinsic microenvironmental cues. We finally identify a single-cell transcriptomics-derived epithelial signature associated with improved patient survival, highlighting the clinical relevance of our findings.
Collapse
Affiliation(s)
- Clémence Henon
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France; Drug Development Department, DITEP, Gustave Roussy, Villejuif, France
| | - Julien Vibert
- INSERM U830, Équipe labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France; INSERM U830, Integrative Functional Genomics of Cancer Lab, PSL Research University, Institut Curie Research Center, Paris, France; Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Thomas Eychenne
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Nadège Gruel
- INSERM U830, Équipe labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France; Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Léo Colmet-Daage
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Carine Ngo
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France; Department of Pathology, Gustave Roussy, Villejuif, France
| | - Marlène Garrido
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Nicolas Dorvault
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Maria Eugenia Marques Da Costa
- INSERM U1015, Gustave Roussy, Paris Saclay University, Villejuif, France; Department of Pediatric and Adolescent Oncology, Gustave Roussy, Villejuif, France
| | - Virginie Marty
- Experimental and Translational Pathology Platform (PETRA), AMMICa, INSERM US23/UAR3655, Gustave Roussy, Villejuif, France
| | - Nicolas Signolle
- Experimental and Translational Pathology Platform (PETRA), AMMICa, INSERM US23/UAR3655, Gustave Roussy, Villejuif, France
| | - Antonin Marchais
- INSERM U1015, Gustave Roussy, Paris Saclay University, Villejuif, France; Department of Pediatric and Adolescent Oncology, Gustave Roussy, Villejuif, France
| | - Noé Herbel
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Asuka Kawai-Kawachi
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Madison Lenormand
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Clémence Astier
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Roman Chabanon
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Benjamin Verret
- Department of Medical Oncology, Gustave Roussy, Villejuif, France; Breast Cancer Translational Research Group, INSERM U981, Gustave Roussy, Villejuif, France
| | - Rastislav Bahleda
- Drug Development Department, DITEP, Gustave Roussy, Villejuif, France
| | - Axel Le Cesne
- Department of Medical Oncology, Gustave Roussy, Villejuif, France; International Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Fatima Mechta-Grigoriou
- INSERM U830, Equipe labellisée LNCC, Stress et Cancer, PSL Research University, Institut Curie Research Center, Paris, France
| | | | | | - Olivier Delattre
- INSERM U830, Équipe labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Joshua J Waterfall
- INSERM U830, Integrative Functional Genomics of Cancer Lab, PSL Research University, Institut Curie Research Center, Paris, France; Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Sarah Watson
- INSERM U830, Équipe labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France; Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Sophie Postel-Vinay
- ATIP-Avenir INSERM and ERC StG Group, Equipe labellisée ARC Recherche Fondamentale, INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France; Drug Development Department, DITEP, Gustave Roussy, Villejuif, France; University College of London, Cancer Institute, London, UK.
| |
Collapse
|
3
|
Han N, Liu Z. Targeting alternative splicing in cancer immunotherapy. Front Cell Dev Biol 2023; 11:1232146. [PMID: 37635865 PMCID: PMC10450511 DOI: 10.3389/fcell.2023.1232146] [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: 05/31/2023] [Accepted: 08/01/2023] [Indexed: 08/29/2023] Open
Abstract
Tumor immunotherapy has made great progress in cancer treatment but still faces several challenges, such as a limited number of targetable antigens and varying responses among patients. Alternative splicing (AS) is an essential process for the maturation of nearly all mammalian mRNAs. Recent studies show that AS contributes to expanding cancer-specific antigens and modulating immunogenicity, making it a promising solution to the above challenges. The organoid technology preserves the individual immune microenvironment and reduces the time/economic costs of the experiment model, facilitating the development of splicing-based immunotherapy. Here, we summarize three critical roles of AS in immunotherapy: resources for generating neoantigens, targets for immune-therapeutic modulation, and biomarkers to guide immunotherapy options. Subsequently, we highlight the benefits of adopting organoids to develop AS-based immunotherapies. Finally, we discuss the current challenges in studying AS-based immunotherapy in terms of existing bioinformatics algorithms and biological technologies.
Collapse
Affiliation(s)
- Nan Han
- Chinese Academy of Sciences Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhaoqi Liu
- Chinese Academy of Sciences Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
4
|
A Novel WT1 Mutation Identified in a 46,XX Testicular/Ovotesticular DSD Patient Results in the Retention of Intron 9. BIOLOGY 2021; 10:biology10121248. [PMID: 34943163 PMCID: PMC8698877 DOI: 10.3390/biology10121248] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/24/2021] [Accepted: 11/27/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary Disorders/differences of sexual development are very diverse. Among them is a condition characterized by the presence of testicular tissue in people with female chromosomes, which is typically manifested by male or ambiguous genitalia. While genetic counseling is beneficial for these people and their families, the genetic causes of these cases are only partially understood. We describe a new mutation in the WT1 gene that results in the presence of testicular tissue in a child with a female karyotype. We propose molecular mechanisms disrupted by this mutation. This finding widened our understanding of processes that govern sexual development and can be used to develop diagnostic tests for disorders/differences of sexual development. Abstract The 46,XX testicular DSD (disorder/difference of sexual development) and 46,XX ovotesticular DSD (46,XX TDSD and 46,XX OTDSD) phenotypes are caused by genetic rearrangements or point mutations resulting in imbalance between components of the two antagonistic, pro-testicular and pro-ovarian pathways; however, the genetic causes of 46,XX TDSD/OTDSD are not fully understood, and molecular diagnosis for many patients with the conditions is unavailable. Only recently few mutations in the WT1 (WT1 transcription factor; 11p13) gene were described in a group of 46,XX TDSD and 46,XX OTDSD individuals. The WT1 protein contains a DNA/RNA binding domain consisting of four zinc fingers (ZnF) and a three-amino acid (KTS) motif that is present or absent, as a result of alternative splicing, between ZnF3 and ZnF4 (±KTS isoforms). Here, we present a patient with 46,XX TDSD/OTDSD in whom whole exome sequencing revealed a heterozygous de novo WT1 c.1437A>G mutation within an alternative donor splice site which is used for −KTS WT1 isoform formation. So far, no mutation in this splice site has been identified in any patient group. We demonstrated that the mutation results in the retention of intron 9 in the mature mRNA of the 46,XX TDSD/OTDSD patient. In cases when the erroneous mRNA is translated, exclusively the expression of a truncated WT1 +KTS protein lacking ZnF4 and no −KTS protein occurs from the mutated allele of the patient. We discuss potential mechanisms and pathways which can be disturbed upon two conditions: Absence of Zn4F and altered +KTS/−KTS ratio.
Collapse
|
5
|
Potluri S, Assi SA, Chin PS, Coleman DJL, Pickin A, Moriya S, Seki N, Heidenreich O, Cockerill PN, Bonifer C. Isoform-specific and signaling-dependent propagation of acute myeloid leukemia by Wilms tumor 1. Cell Rep 2021; 35:109010. [PMID: 33882316 DOI: 10.1016/j.celrep.2021.109010] [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: 08/07/2020] [Revised: 02/04/2021] [Accepted: 03/26/2021] [Indexed: 10/21/2022] Open
Abstract
Acute myeloid leukemia (AML) is caused by recurrent mutations in members of the gene regulatory and signaling machinery that control hematopoietic progenitor cell growth and differentiation. Here, we show that the transcription factor WT1 forms a major node in the rewired mutation-specific gene regulatory networks of multiple AML subtypes. WT1 is frequently either mutated or upregulated in AML, and its expression is predictive for relapse. The WT1 protein exists as multiple isoforms. For two main AML subtypes, we demonstrate that these isoforms exhibit differential patterns of binding and support contrasting biological activities, including enhanced proliferation. We also show that WT1 responds to oncogenic signaling and is part of a signaling-responsive transcription factor hub that controls AML growth. WT1 therefore plays a central and widespread role in AML biology.
Collapse
MESH Headings
- Base Sequence
- Cell Line, Tumor
- Cell Movement
- Cell Proliferation
- Chromatin/chemistry
- Chromatin/metabolism
- Chromosomes, Human, Pair 21
- Chromosomes, Human, Pair 8
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- Early Growth Response Protein 1/genetics
- Early Growth Response Protein 1/metabolism
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Gene Regulatory Networks
- HEK293 Cells
- Humans
- Leukemia, Myeloid, Acute/classification
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Protein Isoforms/antagonists & inhibitors
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RUNX1 Translocation Partner 1 Protein/genetics
- RUNX1 Translocation Partner 1 Protein/metabolism
- Signal Transduction
- Sp1 Transcription Factor/genetics
- Sp1 Transcription Factor/metabolism
- Translocation, Genetic
- WT1 Proteins/antagonists & inhibitors
- WT1 Proteins/genetics
- WT1 Proteins/metabolism
- fms-Like Tyrosine Kinase 3/genetics
- fms-Like Tyrosine Kinase 3/metabolism
Collapse
Affiliation(s)
- Sandeep Potluri
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK.
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Paulynn S Chin
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Dan J L Coleman
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Anna Pickin
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Shogo Moriya
- Department of Biochemistry and Genetics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Naohiko Seki
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Olaf Heidenreich
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Herschel Building, Level 6, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK; Prinses Máxima Centrum for Pediatric Oncology, Postbus 113, 3720 AC Bilthoven, Heidelberglaan 25, 3584CS Utrecht, the Netherlands
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK.
| |
Collapse
|
6
|
Zhang Y, Yan WT, Yang ZY, Li YL, Tan XN, Jiang J, Zhang Y, Qi XW. The role of WT1 in breast cancer: clinical implications, biological effects and molecular mechanism. Int J Biol Sci 2020; 16:1474-1480. [PMID: 32210734 PMCID: PMC7085227 DOI: 10.7150/ijbs.39958] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 01/22/2020] [Indexed: 02/06/2023] Open
Abstract
Although Wilms' tumor gene 1 (WT1) was first cloned and identified as a tumor suppressor gene in nephroblastoma, subsequent studies have demonstrated that it can also play an oncogenic role in leukemia and various solid tumors. WT1 exerts biological functions with high tissue- and cell-specificity. This article reviews the relationship between WT1 and breast cancer from two aspects: (1) clinical application of WT1, including the relationship between expression of WT1 and prognosis of breast cancer patients, and its effectiveness as a target for comprehensive therapy of breast cancer; (2) the biological effects and molecular mechanisms of WT1 in the development and progression of breast cancer, including proliferation, apoptosis, invasion, and metastasis of breast cancer cells.
Collapse
Affiliation(s)
- Ye Zhang
- Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing 400038, China
| | - Wen-Ting Yan
- Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing 400038, China
| | - Ze-Yu Yang
- Breast and Thyroid Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing 400013, China
| | - Yan-Ling Li
- Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing 400038, China
| | - Xuan-Ni Tan
- Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing 400038, China
| | - Jun Jiang
- Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing 400038, China
| | - Yi Zhang
- Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing 400038, China
| | - Xiao-Wei Qi
- Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing 400038, China
| |
Collapse
|
7
|
Hodges AJ, Hudson NO, Buck-Koehntop BA. Cys 2His 2 Zinc Finger Methyl-CpG Binding Proteins: Getting a Handle on Methylated DNA. J Mol Biol 2019:S0022-2836(19)30567-4. [PMID: 31628952 DOI: 10.1016/j.jmb.2019.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 12/12/2022]
Abstract
DNA methylation is an essential epigenetic modification involved in the maintenance of genomic stability, preservation of cellular identity, and regulation of the transcriptional landscape needed to maintain cellular function. In an increasing number of disease conditions, DNA methylation patterns are inappropriately distributed in a manner that supports the disease phenotype. Methyl-CpG binding proteins (MBPs) are specialized transcription factors that read and translate methylated DNA signals into recruitment of protein assemblies that can alter local chromatin architecture and transcription. MBPs thus play a key intermediary role in gene regulation for both normal and diseased cells. Here, we highlight established and potential structure-function relationships for the best characterized members of the zinc finger (ZF) family of MBPs in propagating DNA methylation signals into downstream cellular responses. Current and future investigations aimed toward expanding our understanding of ZF MBP cellular roles will provide needed mechanistic insight into normal and disease state functions, as well as afford evaluation for the potential of these proteins as epigenetic-based therapeutic targets.
Collapse
Affiliation(s)
- Amelia J Hodges
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Nicholas O Hudson
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Bethany A Buck-Koehntop
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112, USA.
| |
Collapse
|
8
|
Wang D, Horton JR, Zheng Y, Blumenthal RM, Zhang X, Cheng X. Role for first zinc finger of WT1 in DNA sequence specificity: Denys-Drash syndrome-associated WT1 mutant in ZF1 enhances affinity for a subset of WT1 binding sites. Nucleic Acids Res 2019; 46:3864-3877. [PMID: 29294058 PMCID: PMC5934627 DOI: 10.1093/nar/gkx1274] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/22/2017] [Indexed: 12/14/2022] Open
Abstract
Wilms tumor protein (WT1) is a Cys2-His2 zinc-finger transcription factor vital for embryonic development of the genitourinary system. The protein contains a C-terminal DNA binding domain with four tandem zinc-fingers (ZF1-4). An alternative splicing of Wt1 can add three additional amino acids-lysine (K), threonine (T) and serine (S)-between ZF3 and ZF4. In the -KTS isoform, ZF2-4 determine the sequence-specificity of DNA binding, whereas the function of ZF1 remains elusive. Three X-ray structures are described here for wild-type -KTS isoform ZF1-4 in complex with its cognate DNA sequence. We observed four unique ZF1 conformations. First, like ZF2-4, ZF1 can be positioned continuously in the DNA major groove forming a 'near-cognate' complex. Second, while ZF2-4 make base-specific interactions with one DNA molecule, ZF1 can interact with a second DNA molecule (or, presumably, two regions of the same DNA molecule). Third, ZF1 can intercalate at the joint of two tail-to-head DNA molecules. If such intercalation occurs on a continuous DNA molecule, it would kink the DNA at the ZF1 binding site. Fourth, two ZF1 units can dimerize. Furthermore, we examined a Denys-Drash syndrome-associated ZF1 mutation (methionine at position 342 is replaced by arginine). This mutation enhances WT1 affinity for a guanine base. X-ray crystallography of the mutant in complex with its preferred sequence revealed the interactions responsible for this affinity change. These results provide insight into the mechanisms of action of WT1, and clarify the fact that ZF1 plays a role in determining sequence specificity of this critical transcription factor.
Collapse
Affiliation(s)
- Dongxue Wang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John R Horton
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yu Zheng
- RGENE, Inc., 953 Indiana Street, San Francisco, CA 94107, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| |
Collapse
|
9
|
Genetic and epigenetic evolution as a contributor to WT1-mutant leukemogenesis. Blood 2018; 132:1265-1278. [PMID: 30064973 DOI: 10.1182/blood-2018-03-837468] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/05/2018] [Indexed: 02/03/2023] Open
Abstract
Genetic studies have identified recurrent somatic mutations in acute myeloid leukemia (AML) patients, including in the Wilms' tumor 1 (WT1) gene. The molecular mechanisms by which WT1 mutations contribute to leukemogenesis have not yet been fully elucidated. We investigated the role of Wt1 gene dosage in steady-state and pathologic hematopoiesis. Wt1 heterozygous loss enhanced stem cell self-renewal in an age-dependent manner, which increased stem cell function over time and resulted in age-dependent leukemic transformation. Wt1-haploinsufficient leukemias were characterized by progressive genetic and epigenetic alterations, including those in known leukemia-associated alleles, demonstrating a requirement for additional events to promote hematopoietic transformation. Consistent with this observation, we found that Wt1 depletion cooperates with Flt3-ITD mutation to induce fully penetrant AML. Our studies provide insight into mechanisms of Wt1-loss leukemogenesis and into the evolutionary events required to induce transformation of Wt1-haploinsufficient stem/progenitor cells.
Collapse
|
10
|
Ullmark T, Montano G, Gullberg U. DNA and RNA binding by the Wilms' tumour gene 1 (WT1) protein +KTS and −KTS isoforms-From initial observations to recent global genomic analyses. Eur J Haematol 2018; 100:229-240. [DOI: 10.1111/ejh.13010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Tove Ullmark
- Department of Haematology and Transfusion Medicine; Lund University; Lund Sweden
| | - Giorgia Montano
- Department of Haematology and Transfusion Medicine; Lund University; Lund Sweden
| | - Urban Gullberg
- Department of Haematology and Transfusion Medicine; Lund University; Lund Sweden
| |
Collapse
|
11
|
Sacco J, Mann S, Toral K. Single nucleotide polymorphisms and microsatellites in the canine glutathione S-transferase pi 1 ( GSTP1) gene promoter. Canine Genet Epidemiol 2017; 4:9. [PMID: 29046813 PMCID: PMC5635497 DOI: 10.1186/s40575-017-0050-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/19/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Genetic polymorphisms within the glutathione S-transferase P1 (GSTP1) gene affect the elimination of toxic xenobiotics by the GSTP1 enzyme. In dogs, exposure to environmental chemicals that may be GSTP1 substrates is associated with cancer. The objectives of this study were to investigate the genetic variability in the GSTP1 promoter in a diverse population of 278 purebred dogs, compare the incidence of any variants found between breeds, and predict their effects on gene expression. To provide information on ancestral alleles, a number of wolves, coyotes, and foxes were also sequenced. RESULTS Fifteen single nucleotide polymorphisms (SNPs) and two microsatellites were discovered. Three of these loci were only polymorphic in dogs while three other SNPs were unique to wolves and coyotes. The major allele at c.-46 is T in dogs but is C in the wild canids. The c.-185 delT variant was unique to dogs. The microsatellite located in the 5' untranslated region (5'UTR) was a highly polymorphic GCC tandem repeat, consisting of simple and compound alleles that varied in size from 10 to 22-repeat units. The most common alleles consisted of 11, 16, and 17-repeats. The 11-repeat allele was found in 10% of dogs but not in the other canids. Unequal recombination and replication slippage between similar and distinct alleles may be the mechanism for the multiple microsatellites observed. Twenty-eight haplotypes were constructed in the dog, and an additional 8 were observed in wolves and coyotes. While the most common haplotype acrossbreeds was the wild-type *1A(17), other prevalent haplotypes included *3A(11) in Greyhounds, *6A(16) in Labrador Retrievers, *9A(16) in Golden Retrievers, and *8A(19) in Standard Poodles. Boxers and Siberian Huskies exhibited minimal haplotypic diversity. Compared to the simple 16*1 allele, the compound 16*2 allele (found in 12% of dogs) may interfere with transcription factor binding and/or the stability of the GSTP1 transcript. CONCLUSIONS Dogs and other canids exhibit extensive variation in the GSTP1 promoter. Genetic polymorphisms within distinct haplotypes prevalent in certain breeds can affect GSTP1 expression and carcinogen detoxification, and thus may be useful as genetic markers for cancer in dogs.
Collapse
Affiliation(s)
- James Sacco
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, Des Moines, IA 50311 USA
| | - Sarah Mann
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, Des Moines, IA 50311 USA
| | - Keller Toral
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, Des Moines, IA 50311 USA
| |
Collapse
|