1
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Hu H, Ho D, Tan DS, MacCarthy C, Yu CH, Weng M, Schöler H, Jauch R. Evaluation of the determinants for improved pluripotency induction and maintenance by engineered SOX17. Nucleic Acids Res 2023; 51:8934-8956. [PMID: 37607832 PMCID: PMC10516664 DOI: 10.1093/nar/gkad597] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 08/24/2023] Open
Abstract
An engineered SOX17 variant with point mutations within its DNA binding domain termed SOX17FNV is a more potent pluripotency inducer than SOX2, yet the underlying mechanism remains unclear. Although wild-type SOX17 was incapable of inducing pluripotency, SOX17FNV outperformed SOX2 in mouse and human pluripotency reprogramming. In embryonic stem cells, SOX17FNV could replace SOX2 to maintain pluripotency despite considerable sequence differences and upregulated genes expressed in cleavage-stage embryos. Mechanistically, SOX17FNV co-bound OCT4 more cooperatively than SOX2 in the context of the canonical SoxOct DNA element. SOX2, SOX17, and SOX17FNV were all able to bind nucleosome core particles in vitro, which is a prerequisite for pioneer transcription factors. Experiments using purified proteins and in cellular contexts showed that SOX17 variants phase-separated more efficiently than SOX2, suggesting an enhanced ability to self-organise. Systematic deletion analyses showed that the N-terminus of SOX17FNV was dispensable for its reprogramming activity. However, the C-terminus encodes essential domains indicating multivalent interactions that drive transactivation and reprogramming. We defined a minimal SOX17FNV (miniSOX) that can support reprogramming with high activity, reducing the payload of reprogramming cassettes. This study uncovers the mechanisms behind SOX17FNV-induced pluripotency and establishes engineered SOX factors as powerful cell engineering tools.
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Affiliation(s)
- Haoqing Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Derek Hoi Hang Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Translational Stem Cell Biology, Hong Kong
| | - Daisylyn Senna Tan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | | | - Cheng-han Yu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Mingxi Weng
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Translational Stem Cell Biology, Hong Kong
| | | | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Translational Stem Cell Biology, Hong Kong
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2
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Fu X, Zhuang Q, Babarinde IA, Shi L, Ma G, Hu H, Li Y, Chen J, Xiao Z, Deng B, Sun L, Jauch R, Hutchins AP. Restricting epigenetic activity promotes the reprogramming of transformed cells to pluripotency in a line-specific manner. Cell Death Discov 2023; 9:245. [PMID: 37452056 PMCID: PMC10349098 DOI: 10.1038/s41420-023-01533-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 06/15/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023] Open
Abstract
Somatic cell reprogramming and oncogenic transformation share surprisingly similar features, yet transformed cells are resistant to reprogramming. Epigenetic barriers must block transformed cells from reprogramming, but the nature of those barriers is unclear. In this study, we generated a systematic panel of transformed mouse embryonic fibroblasts (MEFs) using oncogenic transgenes and discovered transformed cell lines compatible with reprogramming when transfected with Oct4/Sox2/Klf4/Myc. By comparing the reprogramming-capable and incapable transformed lines we identified multiple stages of failure in the reprogramming process. Some transformed lines failed at an early stage, whilst other lines seemed to progress through a conventional reprogramming process. Finally, we show that MEK inhibition overcomes one critical reprogramming barrier by indirectly suppressing a hyperacetylated active epigenetic state. This study reveals that diverse epigenetic barriers underly resistance to reprogramming of transformed cells.
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Affiliation(s)
- Xiuling Fu
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Qiang Zhuang
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Isaac A Babarinde
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Liyang Shi
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Gang Ma
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Haoqing Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yuhao Li
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jiao Chen
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Zhen Xiao
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Boping Deng
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Li Sun
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Translational Stem Cell Biology, Hong Kong SAR, China
| | - Andrew P Hutchins
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
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3
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Underwood A, Rasicci DT, Hinds D, Mitchell JT, Zieba JK, Mills J, Arnold NE, Cook TW, Moustaqil M, Gambin Y, Sierecki E, Fontaine F, Vanderweele S, Das AS, Cvammen W, Sirpilla O, Soehnlen X, Bricker K, Alokaili M, Green M, Heeringa S, Wilstermann AM, Freeland TM, Qutob D, Milsted A, Jauch R, Triche TJ, Krawczyk CM, Bupp CP, Rajasekaran S, Francois M, Prokop JW. Evolutionary Landscape of SOX Genes to Inform Genotype-to-Phenotype Relationships. Genes (Basel) 2023; 14:222. [PMID: 36672963 PMCID: PMC9859272 DOI: 10.3390/genes14010222] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
The SOX transcription factor family is pivotal in controlling aspects of development. To identify genotype-phenotype relationships of SOX proteins, we performed a non-biased study of SOX using 1890 open-reading frame and 6667 amino acid sequences in combination with structural dynamics to interpret 3999 gnomAD, 485 ClinVar, 1174 Geno2MP, and 4313 COSMIC human variants. We identified, within the HMG (High Mobility Group)- box, twenty-seven amino acids with changes in multiple SOX proteins annotated to clinical pathologies. These sites were screened through Geno2MP medical phenotypes, revealing novel SOX15 R104G associated with musculature abnormality and SOX8 R159G with intellectual disability. Within gnomAD, SOX18 E137K (rs201931544), found within the HMG box of ~0.8% of Latinx individuals, is associated with seizures and neurological complications, potentially through blood-brain barrier alterations. A total of 56 highly conserved variants were found at sites outside the HMG-box, including several within the SOX2 HMG-box-flanking region with neurological associations, several in the SOX9 dimerization region associated with Campomelic Dysplasia, SOX14 K88R (rs199932938) flanking the HMG box associated with cardiovascular complications within European populations, and SOX7 A379V (rs143587868) within an SOXF conserved far C-terminal domain heterozygous in 0.716% of African individuals with associated eye phenotypes. This SOX data compilation builds a robust genotype-to-phenotype association for a gene family through more robust ortholog data integration.
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Affiliation(s)
- Adam Underwood
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Daniel T Rasicci
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - David Hinds
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Jackson T Mitchell
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Jacob K Zieba
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Joshua Mills
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Nicholas E Arnold
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Taylor W Cook
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Mehdi Moustaqil
- Single Molecule Science, Lowy Cancer Research Centre, The University of New South Wales, Sydney, NSW 2031, Australia
| | - Yann Gambin
- Single Molecule Science, Lowy Cancer Research Centre, The University of New South Wales, Sydney, NSW 2031, Australia
| | - Emma Sierecki
- Single Molecule Science, Lowy Cancer Research Centre, The University of New South Wales, Sydney, NSW 2031, Australia
| | - Frank Fontaine
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sophie Vanderweele
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Akansha S Das
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - William Cvammen
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Olivia Sirpilla
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Xavier Soehnlen
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Kristen Bricker
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Maram Alokaili
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Morgan Green
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA
| | - Sadie Heeringa
- Department of Biology, Calvin University, Grand Rapids, MI 49546, USA
| | - Amy M Wilstermann
- Department of Biology, Calvin University, Grand Rapids, MI 49546, USA
| | - Thomas M. Freeland
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Dinah Qutob
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Amy Milsted
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 518057, China
| | - Timothy J Triche
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Connie M Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Caleb P Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Division of Medical Genetics, Spectrum Health, Grand Rapids, MI 49503, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Office of Research, Spectrum Health, Grand Rapids, MI 49503, USA
| | - Mathias Francois
- The Centenary Institute, The University of Sydney, Royal Prince Alfred Hospital, Sydney, NSW 2006, Australia
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Office of Research, Spectrum Health, Grand Rapids, MI 49503, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
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4
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Tan DS, Cheung SL, Gao Y, Weinbuch M, Hu H, Shi L, Ti SC, Hutchins AP, Cojocaru V, Jauch R. The homeodomain of Oct4 is a dimeric binder of methylated CpG elements. Nucleic Acids Res 2023; 51:1120-1138. [PMID: 36631980 PMCID: PMC9943670 DOI: 10.1093/nar/gkac1262] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023] Open
Abstract
Oct4 is essential to maintain pluripotency and has a pivotal role in establishing the germline. Its DNA-binding POU domain was recently found to bind motifs with methylated CpG elements normally associated with epigenetic silencing. However, the mode of binding and the consequences of this capability has remained unclear. Here, we show that Oct4 binds to a compact palindromic DNA element with a methylated CpG core (CpGpal) in alternative states of pluripotency and during cellular reprogramming towards induced pluripotent stem cells (iPSCs). During cellular reprogramming, typical Oct4 bound enhancers are uniformly demethylated, with the prominent exception of the CpGpal sites where DNA methylation is often maintained. We demonstrate that Oct4 cooperatively binds the CpGpal element as a homodimer, which contrasts with the ectoderm-expressed POU factor Brn2. Indeed, binding to CpGpal is Oct4-specific as other POU factors expressed in somatic cells avoid this element. Binding assays combined with structural analyses and molecular dynamic simulations show that dimeric Oct4-binding to CpGpal is driven by the POU-homeodomain whilst the POU-specific domain is detached from DNA. Collectively, we report that Oct4 exerts parts of its regulatory function in the context of methylated DNA through a DNA recognition mechanism that solely relies on its homeodomain.
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Affiliation(s)
- Daisylyn Senna Tan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Shun Lai Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ya Gao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Maike Weinbuch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China,Institute for Molecular Medicine, Ulm University, Ulm, Germany
| | - Haoqing Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Liyang Shi
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shih-Chieh Ti
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Andrew P Hutchins
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Vlad Cojocaru
- STAR-UBB Institute, Babeş-Bolyai University, Cluj-Napoca, Romania,Computational Structural Biology Group, Utrecht University, The Netherlands,Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Ralf Jauch
- To whom correspondence should be addressed. Tel: +852 3917 9511; Fax: +852 28559730;
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5
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Ervin EH, French R, Chang CH, Pauklin S. Inside the stemness engine: Mechanistic links between deregulated transcription factors and stemness in cancer. Semin Cancer Biol 2022; 87:48-83. [PMID: 36347438 DOI: 10.1016/j.semcancer.2022.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/22/2022] [Accepted: 11/03/2022] [Indexed: 11/07/2022]
Abstract
Cell identity is largely determined by its transcriptional profile. In tumour, deregulation of transcription factor expression and/or activity enables cancer cell to acquire a stem-like state characterised by capacity to self-renew, differentiate and form tumours in vivo. These stem-like cancer cells are highly metastatic and therapy resistant, thus warranting a more complete understanding of the molecular mechanisms downstream of the transcription factors that mediate the establishment of stemness state. Here, we review recent research findings that provide a mechanistic link between the commonly deregulated transcription factors and stemness in cancer. In particular, we describe the role of master transcription factors (SOX, OCT4, NANOG, KLF, BRACHYURY, SALL, HOX, FOX and RUNX), signalling-regulated transcription factors (SMAD, β-catenin, YAP, TAZ, AP-1, NOTCH, STAT, GLI, ETS and NF-κB) and unclassified transcription factors (c-MYC, HIF, EMT transcription factors and P53) across diverse tumour types, thereby yielding a comprehensive overview identifying shared downstream targets, highlighting unique mechanisms and discussing complexities.
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Affiliation(s)
- Egle-Helene Ervin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
| | - Rhiannon French
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
| | - Chao-Hui Chang
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
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6
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Ullah H, Zhang B, Sharma NK, McCrea PD, Srivastava Y. In-silico probing of AML related RUNX1 cancer-associated missense mutations: Predicted relationships to DNA binding and drug interactions. Front Mol Biosci 2022; 9:981020. [PMID: 36090034 PMCID: PMC9454315 DOI: 10.3389/fmolb.2022.981020] [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: 06/29/2022] [Accepted: 07/19/2022] [Indexed: 11/24/2022] Open
Abstract
The molecular consequences of cancer associated mutations in Acute myeloid leukemia (AML) linked factors are not very well understood. Here, we interrogated the COSMIC database for missense mutations associated with the RUNX1 protein, that is frequently mis-regulated in AML, where we sought to identify recurrently mutated positions at the DNA-interacting interface. Indeed, six of the mutated residues, out of a total 417 residues examined within the DNA binding domain, evidenced reduced DNA association in in silico predictions. Further, given the prominence of RUNX1’s compromised function in AML, we asked the question if the mutations themselves might alter RUNX1’s interaction (off-target) with known FDA-approved drug molecules, including three currently used in treating AML. We identified several AML-associated mutations in RUNX1 that were calculated to enhance RUNX1’s interaction with specific drugs. Specifically, we retrieved data from the COSMIC database for cancer-associated mutations of RUNX1 by using R package “data.table” and “ggplot2” modules. In the presence of DNA and/or drug, we used docking scores and energetics of the complexes as tools to evaluate predicted interaction strengths with RUNX1. For example, we performed predictions of drug binding pockets involving Enasidenib, Giltertinib, and Midostaurin (AML associated), as well as ten different published cancer associated drug compounds. Docking of wild type RUNX1 with these 13 different cancer-associated drugs indicates that wild-type RUNX1 has a lower efficiency of binding while RUNX1 mutants R142K, D171N, R174Q, P176H, and R177Q suggested higher affinity of drug association. Literature evidence support our prediction and suggests the mutation R174Q affects RUNX1 DNA binding and could lead to compromised function. We conclude that specific RUNX1 mutations that lessen DNA binding facilitate the binding of a number of tested drug molecules. Further, we propose that molecular modeling and docking studies for RUNX1 in the presence of DNA and/or drugs enables evaluation of the potential impact of RUNX1 cancer associated mutations in AML.
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Affiliation(s)
- Hanif Ullah
- Guangxi Key Laboratory for Genomics and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomics and Personalized Medicine, Guangxi Medical University, Nanning, China
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Baoyun Zhang
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Narendra Kumar Sharma
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Banasthali, Tonk, Rajasthan, India
| | - Pierre D. McCrea
- University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Yogesh Srivastava
- University of Chinese Academy of Sciences, Beijing, China
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Genome Regulation Laboratory; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- *Correspondence: Yogesh Srivastava,
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7
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Wang XH, Zhang SF, Wu HY, Gao J, Wang XH, Gao TH. SOX17 inhibits proliferation and invasion of neuroblastoma through CXCL12/CXCR4 signaling axis. Cell Signal 2021; 87:110093. [PMID: 34302955 DOI: 10.1016/j.cellsig.2021.110093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 07/14/2021] [Accepted: 07/19/2021] [Indexed: 11/30/2022]
Abstract
SOX17 has been shown to be involved in the transcriptional regulation of CXCR4, and CXCL12 functions by binding to its receptor CXCR4. Here, we explored the expression of SOX17 in neuroblastoma (NB), its mutual regulation with CXCL12, and its effects on cancer cell proliferation, migration and invasion. Five human NB cell lines and 15 pairs of NB and adjacent tissue specimens were used, to conduct RT-qPCR, immunohistochemistry, western blot, ELISA, CCK-8, colony formation, Edu, transwell, chromatin immunoprecipitation (ChIP), and dual-luciferase assays, to study the role of SOX17 in NB. SOX17 levels were reduced in both NB tissues and cell lines. SOX17 inhibited NB tumor growth, migration and invasion in vivo and suppressed NB cell proliferation, migration, and invasion in vitro. SOX17 knockdown or overexpression revealed a negative correlation between SOX17 and CXCL12/CXCR4 pathway activation. ChIP and dual-luciferase assays in NB cells demonstrated that SOX17 significantly inhibited CXCL12 gene and protein levels by binding to CXCL12 promoter regions. In vivo and in vitro experiments using the CXCR4 antagonist, AMD3100, demonstrated that cell proliferation, migration and invasion were significantly abrogated by AMD3100 in NB cells with SOX17 knocked down. Further, AMD3100 impaired growth of NB tumors with SOX17 knocked down in mice. Importantly, SOX17 bound to the CXCL12 promoter, which then activated downstream targets to regulate cell viability, proliferation, and migration. In conclusion, our data demonstrate that SOX17 expression is repressed in NB tissues and cells, and that SOX17 suppresses NB tumor formation and proliferation through inhibition of CXCL12/CXCR4 signaling.
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Affiliation(s)
- Xiao-Hui Wang
- Department of Pediatric Surgery, People's Hospital of Zhengzhou University (Henan Provincial People's Hospital), Zhengzhou 450003, Henan Province, PR China
| | - Shu-Feng Zhang
- Department of Pediatric Surgery, People's Hospital of Zhengzhou University (Henan Provincial People's Hospital), Zhengzhou 450003, Henan Province, PR China.
| | - Hai-Ying Wu
- Obstetrical Department, People's Hospital of Zhengzhou University (Henan Provincial People's Hospital), Zhengzhou 450003, Henan Province, PR China
| | - Jian Gao
- Department of Pediatric Surgery, People's Hospital of Zhengzhou University (Henan Provincial People's Hospital), Zhengzhou 450003, Henan Province, PR China
| | - Xu-Hui Wang
- Department of Pediatric Surgery, People's Hospital of Zhengzhou University (Henan Provincial People's Hospital), Zhengzhou 450003, Henan Province, PR China
| | - Tian-Hui Gao
- Medical Oncology, People's Hospital of Zhengzhou University (Henan Provincial People's Hospital), Zhengzhou 450003, Henan Province, PR China
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8
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Tan DS, Chen Y, Gao Y, Bednarz A, Wei Y, Malik V, Ho DHH, Weng M, Ho SY, Srivastava Y, Velychko S, Yang X, Fan L, Kim J, Graumann J, Stormo GD, Braun T, Yan J, Schöler HR, Jauch R. Directed Evolution of an Enhanced POU Reprogramming Factor for Cell Fate Engineering. Mol Biol Evol 2021; 38:2854-2868. [PMID: 33720298 PMCID: PMC8233511 DOI: 10.1093/molbev/msab075] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transcription factor-driven cell fate engineering in pluripotency induction, transdifferentiation, and forward reprogramming requires efficiency, speed, and maturity for widespread adoption and clinical translation. Here, we used Oct4, Sox2, Klf4, and c-Myc driven pluripotency reprogramming to evaluate methods for enhancing and tailoring cell fate transitions, through directed evolution with iterative screening of pooled mutant libraries and phenotypic selection. We identified an artificially evolved and enhanced POU factor (ePOU) that substantially outperforms wild-type Oct4 in terms of reprogramming speed and efficiency. In contrast to Oct4, not only can ePOU induce pluripotency with Sox2 alone, but it can also do so in the absence of Sox2 in a three-factor ePOU/Klf4/c-Myc cocktail. Biochemical assays combined with genome-wide analyses showed that ePOU possesses a new preference to dimerize on palindromic DNA elements. Yet, the moderate capacity of Oct4 to function as a pioneer factor, its preference to bind octamer DNA and its capability to dimerize with Sox2 and Sox17 proteins remain unchanged in ePOU. Compared with Oct4, ePOU is thermodynamically stabilized and persists longer in reprogramming cells. In consequence, ePOU: 1) differentially activates several genes hitherto not implicated in reprogramming, 2) reveals an unappreciated role of thyrotropin-releasing hormone signaling, and 3) binds a distinct class of retrotransposons. Collectively, these features enable ePOU to accelerate the establishment of the pluripotency network. This demonstrates that the phenotypic selection of novel factor variants from mammalian cells with desired properties is key to advancing cell fate conversions with artificially evolved biomolecules.
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Affiliation(s)
- Daisylyn Senna Tan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yanpu Chen
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Ya Gao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Anastasia Bednarz
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.,Department of Biology, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Yuanjie Wei
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Vikas Malik
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
| | - Derek Hoi-Hang Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Mingxi Weng
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Sik Yin Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yogesh Srivastava
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sergiy Velychko
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Xiaoxiao Yang
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ligang Fan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China.,School of Medicine, Northwest University, Xi'an, China
| | - Johnny Kim
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Johannes Graumann
- Max Planck Institute for Heart and Lung Research, Mass Spectrometry Service Group, Bad Nauheim, Germany
| | - Gary D Stormo
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - Thomas Braun
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Jian Yan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China.,School of Medicine, Northwest University, Xi'an, China
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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9
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Mullin NP, Varghese J, Colby D, Richardson JM, Findlay GM, Chambers I. Phosphorylation of NANOG by casein kinase I regulates embryonic stem cell self-renewal. FEBS Lett 2021; 595:14-25. [PMID: 33107035 PMCID: PMC7839479 DOI: 10.1002/1873-3468.13969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022]
Abstract
The self-renewal efficiency of mouse embryonic stem cells (ESCs) is determined by the concentration of the transcription factor NANOG. While NANOG binds thousands of sites in chromatin, the regulatory systems that control DNA binding are poorly characterised. Here, we show that NANOG is phosphorylated by casein kinase I, and identify target residues. Phosphomimetic substitutions at phosphorylation sites within the homeodomain (S130 and S131) have site-specific functional effects. Phosphomimetic substitution of S130 abolishes DNA binding by NANOG and eliminates LIF-independent self-renewal. In contrast, phosphomimetic substitution of S131 enhances LIF-independent self-renewal, without influencing DNA binding. Modelling the DNA-homeodomain complex explains the disparate effects of these phosphomimetic substitutions. These results indicate how phosphorylation may influence NANOG homeodomain interactions that underpin ESC self-renewal.
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Affiliation(s)
- Nicholas P. Mullin
- Centre for Regenerative MedicineInstitute for Stem Cell ResearchSchool of Biological SciencesUniversity of EdinburghUK
| | - Joby Varghese
- Protein Phosphorylation and Ubiquitylation UnitJames Black CentreSchool of Life SciencesDundeeUK
| | - Douglas Colby
- Centre for Regenerative MedicineInstitute for Stem Cell ResearchSchool of Biological SciencesUniversity of EdinburghUK
| | - Julia M. Richardson
- Institute of Quantitative Biology, Biochemistry and BiotechnologyEdinburghUK
| | - Greg M. Findlay
- Protein Phosphorylation and Ubiquitylation UnitJames Black CentreSchool of Life SciencesDundeeUK
| | - Ian Chambers
- Centre for Regenerative MedicineInstitute for Stem Cell ResearchSchool of Biological SciencesUniversity of EdinburghUK
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10
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Olbromski M, Podhorska-Okołów M, Dzięgiel P. Role of SOX Protein Groups F and H in Lung Cancer Progression. Cancers (Basel) 2020; 12:cancers12113235. [PMID: 33152990 PMCID: PMC7692225 DOI: 10.3390/cancers12113235] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/24/2020] [Accepted: 10/27/2020] [Indexed: 12/15/2022] Open
Abstract
Simple Summary The expression of SOX proteins has been demonstrated in many tissues at various stages of embryogenesis, where they play the role of transcription factors. The SOX18 protein (along with SOX7 and SOX17) belongs to the SOXF group and is mainly involved in the development of the cardiovascular system, where its expression was found in the endothelium. SOX18 expression was also demonstrated in neoplastic lines of gastric, pancreatic and colon adenocarcinomas. The prognostic role of SOX30 expression has only been studied in lung adenocarcinomas, where a low expression of this factor in the stromal tumor was associated with a worse prognosis for patients. Because of the complexity of non-small-cell lung cancer (NSCLC) development, the role of the SOX proteins in this malignancy is still not fully understood. Many recently published papers show that SOX family protein members play a crucial role in the progression of NSCLC. Abstract The SOX family proteins are proved to play a crucial role in the development of the lymphatic ducts and the cardiovascular system. Moreover, an increased expression level of the SOX18 protein has been found in many malignances, such as melanoma, stomach, pancreatic breast and lung cancers. Another SOX family protein, the SOX30 transcription factor, is responsible for the development of male germ cells. Additionally, recent studies have shown its proapoptotic character in non-small cell lung cancer cells. Our preliminary studies showed a disparity in the amount of mRNA of the SOX18 gene relative to the amount of protein. This is why our attention has been focused on microRNA (miRNA) molecules, which could regulate the SOX18 gene transcript level. Recent data point to the fact that, in practically all types of cancer, hundreds of genes exhibit an abnormal methylation, covering around 5–10% of the thousands of CpG islands present in the promoter sequences, which in normal cells should not be methylated from the moment the embryo finishes its development. It has been demonstrated that in non-small-cell lung cancer (NSCLC) cases there is a large heterogeneity of the methylation process. The role of the SOX18 and SOX30 expression in non-small-cell lung cancers (NSCLCs) is not yet fully understood. However, if we take into account previous reports, these proteins may be important factors in the development and progression of these malignancies.
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Affiliation(s)
- Mateusz Olbromski
- Department of Histology and Embryology, Department of Human Morphology and Embryology, Medical University, 50-368 Wroclaw, Poland;
- Correspondence: ; Tel.: +48-717-841-354; Fax: +48-717-840-082
| | - Marzenna Podhorska-Okołów
- Department of Ultrastructural Research, Department of Human Morphology and Embryology, Medical University, 50-368 Wroclaw, Poland;
| | - Piotr Dzięgiel
- Department of Histology and Embryology, Department of Human Morphology and Embryology, Medical University, 50-368 Wroclaw, Poland;
- Department of Physiotherapy, University School of Physical Education, 51-612 Wroclaw, Poland
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