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Niharika, Ureka L, Roy A, Patra SK. Dissecting SOX2 expression and function reveals an association with multiple signaling pathways during embryonic development and in cancer progression. Biochim Biophys Acta Rev Cancer 2024; 1879:189136. [PMID: 38880162 DOI: 10.1016/j.bbcan.2024.189136] [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: 05/09/2023] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 06/18/2024]
Abstract
SRY (Sex Determining Region) box 2 (SOX2) is an essential transcription factor that plays crucial roles in activating genes involved in pre- and post-embryonic development, adult tissue homeostasis, and lineage specifications. SOX2 maintains the self-renewal property of stem cells and is involved in the generation of induced pluripotency stem cells. SOX2 protein contains a particular high-mobility group domain that enables SOX2 to achieve the capacity to participate in a broad variety of functions. The information about the involvement of SOX2 with gene regulatory elements, signaling networks, and microRNA is gradually emerging, and the higher expression of SOX2 is functionally relevant to various cancer types. SOX2 facilitates the oncogenic phenotype via cellular proliferation and enhancement of invasive tumor properties. Evidence are accumulating in favor of three dimensional (higher order) folding of chromatin and epigenetic control of the SOX2 gene by chromatin modifications, which implies that the expression level of SOX2 can be modulated by epigenetic regulatory mechanisms, specifically, via DNA methylation and histone H3 modification. In view of this, and to focus further insights into the roles SOX2 plays in physiological functions, involvement of SOX2 during development, precisely, the advances of our knowledge in pre- and post-embryonic development, and interactions of SOX2 in this scenario with various signaling pathways in tumor development and cancer progression, its potential as a therapeutic target against many cancers are summarized and discussed in this article.
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Affiliation(s)
- Niharika
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Lina Ureka
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Ankan Roy
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
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Yuikawa T, Sato T, Ikeda M, Tsuruoka M, Yasuda K, Sato Y, Nasu K, Yamasu K. Elongation of the developing spinal cord is driven by Oct4-type transcription factor-mediated regulation of retinoic acid signaling in zebrafish embryos. Dev Dyn 2024; 253:404-422. [PMID: 37850839 DOI: 10.1002/dvdy.666] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/19/2023] Open
Abstract
BACKGROUND Elongation of the spinal cord is dependent on neural development from neuromesodermal progenitors in the tail bud. We previously showed the involvement of the Oct4-type gene, pou5f3, in this process in zebrafish mainly by dominant-interference gene induction, but, to compensate for the limitation of this transgene approach, mutant analysis was indispensable. pou5f3 involvement in the signaling pathways was another unsolved question. RESULTS We examined the phenotypes of pou5f3 mutants and the effects of Pou5f3 activation by the tamoxifen-ERT2 system in the posterior neural tube, together confirming the involvement of pou5f3. The reporter assays using P19 cells implicated tail bud-related transcription factors in pou5f3 expression. Regulation of tail bud development by retinoic acid (RA) signaling was confirmed by treatment of embryos with RA and the synthesis inhibitor, and in vitro reporter assays further showed that RA signaling regulated pou5f3 expression. Importantly, the expression of the RA degradation enzyme gene, cyp26a1, was down-regulated in embryos with disrupted pou5f3 activity. CONCLUSIONS The involvement of pou5f3 in spinal cord extension was supported by using mutants and the gain-of-function approach. Our findings further suggest that pou5f3 regulates the RA level, contributing to neurogenesis in the posterior neural tube.
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Affiliation(s)
- Tatsuya Yuikawa
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Saitama, Japan
| | - Takehisa Sato
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Saitama, Japan
| | - Masaaki Ikeda
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Saitama, Japan
| | - Momo Tsuruoka
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Saitama, Japan
| | - Kaede Yasuda
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Saitama, Japan
| | - Yuto Sato
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Saitama, Japan
| | - Kouhei Nasu
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Saitama, Japan
| | - Kyo Yamasu
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Saitama, Japan
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Suzuki A, Uranishi K, Nishimoto M, Mizuno Y, Mizuno S, Takahashi S, Eisenman RN, Okuda A. MAX controls meiotic entry in sexually undifferentiated germ cells. Sci Rep 2024; 14:5236. [PMID: 38433229 PMCID: PMC10909893 DOI: 10.1038/s41598-024-55506-7] [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: 11/16/2023] [Accepted: 02/24/2024] [Indexed: 03/05/2024] Open
Abstract
Meiosis is a specialized type of cell division that occurs physiologically only in germ cells. We previously demonstrated that MYC-associated factor X (MAX) blocks the ectopic onset of meiosis in embryonic and germline stem cells in culture systems. Here, we investigated the Max gene's role in mouse primordial germ cells. Although Max is generally ubiquitously expressed, we revealed that sexually undifferentiated male and female germ cells had abundant MAX protein because of their higher Max gene expression than somatic cells. Moreover, our data revealed that this high MAX protein level in female germ cells declined significantly around physiological meiotic onset. Max disruption in sexually undifferentiated germ cells led to ectopic and precocious expression of meiosis-related genes, including Meiosin, the gatekeeper of meiotic onset, in both male and female germ cells. However, Max-null male and female germ cells did not complete the entire meiotic process, but stalled during its early stages and were eventually eliminated by apoptosis. Additionally, our meta-analyses identified a regulatory region that supports the high Max expression in sexually undifferentiated male and female germ cells. These results indicate the strong connection between the Max gene and physiological onset of meiosis in vivo through dynamic alteration of its expression.
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Affiliation(s)
- Ayumu Suzuki
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1241, Japan
| | - Kousuke Uranishi
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1241, Japan
| | - Masazumi Nishimoto
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1241, Japan
| | - Yosuke Mizuno
- Division of Morphological Science, Biomedical Research Center, Saitama Medical University, 38 Morohongo, Moroyama, Iruma-gun, Saitama, 350-0495, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Satoru Takahashi
- Laboratory Animal Resource Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Robert N Eisenman
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Akihiko Okuda
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1241, Japan.
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Kondoh H. Enhancer Arrays Regulating Developmental Genes: Sox2 Enhancers as a Paradigm. Results Probl Cell Differ 2024; 72:145-166. [PMID: 38509257 DOI: 10.1007/978-3-031-39027-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Enhancers are the primary regulatory DNA sequences in eukaryotes and are mostly located in the non-coding sequences of genes, namely, intergenic regions and introns. The essential characteristic of an enhancer is the ability to activate proximal genes, e.g., a reporter gene in a reporter assay, regardless of orientation, relative position, and distance from the gene. These characteristics are ascribed to the interaction (spatial proximity) of the enhancer sequence and the gene promoter via DNA looping, discussed in the latter part of this chapter.Developmentally regulated genes are associated with multiple enhancers carrying distinct cell and developmental stage specificities, which form arrays on the genome. We discuss the array of enhancers regulating the Sox2 gene as a paradigm. Sox2 enhancers are the best studied enhancers of a single gene in developmental regulation. In addition, the Sox2 gene is located in a genomic region with a very sparse gene distribution (no other protein-coding genes in ~1.6 Mb in the mouse genome), termed a "gene desert," which means that most identified enhancers in the region are associated with Sox2 regulation. Furthermore, the importance of the Sox2 gene in stem cell regulation and neural development justifies focusing on Sox2-associated enhancers.
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Affiliation(s)
- Hisato Kondoh
- Osaka University, Suita, Osaka, Japan
- Biohistory Research Hall, Takatsuki, Osaka, Japan
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Abatti LE, Lado-Fernández P, Huynh L, Collado M, Hoffman M, Mitchell J. Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma. Nucleic Acids Res 2023; 51:10109-10131. [PMID: 37738673 PMCID: PMC10602899 DOI: 10.1093/nar/gkad734] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/18/2023] [Accepted: 08/24/2023] [Indexed: 09/24/2023] Open
Abstract
Enhancer reprogramming has been proposed as a key source of transcriptional dysregulation during tumorigenesis, but the molecular mechanisms underlying this process remain unclear. Here, we identify an enhancer cluster required for normal development that is aberrantly activated in breast and lung adenocarcinoma. Deletion of the SRR124-134 cluster disrupts expression of the SOX2 oncogene, dysregulates genome-wide transcription and chromatin accessibility and reduces the ability of cancer cells to form colonies in vitro. Analysis of primary tumors reveals a correlation between chromatin accessibility at this cluster and SOX2 overexpression in breast and lung cancer patients. We demonstrate that FOXA1 is an activator and NFIB is a repressor of SRR124-134 activity and SOX2 transcription in cancer cells, revealing a co-opting of the regulatory mechanisms involved in early development. Notably, we show that the conserved SRR124 and SRR134 regions are essential during mouse development, where homozygous deletion results in the lethal failure of esophageal-tracheal separation. These findings provide insights into how developmental enhancers can be reprogrammed during tumorigenesis and underscore the importance of understanding enhancer dynamics during development and disease.
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Affiliation(s)
- Luis E Abatti
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Patricia Lado-Fernández
- Laboratory of Cell Senescence, Cancer and Aging, Health Research Institute of Santiago de Compostela (IDIS), Xerencia de Xestión Integrada de Santiago (XXIS/SERGAS), Santiago de Compostela, Spain
- Department of Physiology and Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Linh Huynh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Manuel Collado
- Laboratory of Cell Senescence, Cancer and Aging, Health Research Institute of Santiago de Compostela (IDIS), Xerencia de Xestión Integrada de Santiago (XXIS/SERGAS), Santiago de Compostela, Spain
| | - Michael M Hoffman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada
| | - Jennifer A Mitchell
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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Shojaee A, Huang SSC. Robust discovery of gene regulatory networks from single-cell gene expression data by Causal Inference Using Composition of Transactions. Brief Bioinform 2023; 24:bbad370. [PMID: 37897702 PMCID: PMC10612495 DOI: 10.1093/bib/bbad370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/06/2023] [Accepted: 09/29/2023] [Indexed: 10/30/2023] Open
Abstract
Gene regulatory networks (GRNs) drive organism structure and functions, so the discovery and characterization of GRNs is a major goal in biological research. However, accurate identification of causal regulatory connections and inference of GRNs using gene expression datasets, more recently from single-cell RNA-seq (scRNA-seq), has been challenging. Here we employ the innovative method of Causal Inference Using Composition of Transactions (CICT) to uncover GRNs from scRNA-seq data. The basis of CICT is that if all gene expressions were random, a non-random regulatory gene should induce its targets at levels different from the background random process, resulting in distinct patterns in the whole relevance network of gene-gene associations. CICT proposes novel network features derived from a relevance network, which enable any machine learning algorithm to predict causal regulatory edges and infer GRNs. We evaluated CICT using simulated and experimental scRNA-seq data in a well-established benchmarking pipeline and showed that CICT outperformed existing network inference methods representing diverse approaches with many-fold higher accuracy. Furthermore, we demonstrated that GRN inference with CICT was robust to different levels of sparsity in scRNA-seq data, the characteristics of data and ground truth, the choice of association measure and the complexity of the supervised machine learning algorithm. Our results suggest aiming at directly predicting causality to recover regulatory relationships in complex biological networks substantially improves accuracy in GRN inference.
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Affiliation(s)
- Abbas Shojaee
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Shao-shan Carol Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
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Knudsen TE, Hamilton WB, Proks M, Lykkegaard M, Linneberg-Agerholm M, Nielsen AV, Perera M, Malzard LL, Trusina A, Brickman JM. A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation. Cell Syst 2023; 14:788-805.e8. [PMID: 37633265 DOI: 10.1016/j.cels.2023.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 03/22/2023] [Accepted: 07/28/2023] [Indexed: 08/28/2023]
Abstract
Cooperative DNA binding of transcription factors (TFs) integrates the cellular context to support cell specification during development. Naive mouse embryonic stem cells are derived from early development and can sustain their pluripotent identity indefinitely. Here, we ask whether TFs associated with pluripotency evolved to directly support this state or if the state emerges from their combinatorial action. NANOG and ESRRB are key pluripotency factors that co-bind DNA. We find that when both factors are expressed, ESRRB supports pluripotency. However, when NANOG is absent, ESRRB supports a bistable culture of cells with an embryo-like primitive endoderm identity ancillary to pluripotency. The stoichiometry between NANOG and ESRRB allows quantitative titration of this differentiation, and in silico modeling of bipartite ESRRB activity suggests it safeguards plasticity in differentiation. Thus, the concerted activity of cooperative TFs can transform their effect to sustain intermediate cell identities and allow ex vivo expansion of immortal stem cells. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Teresa E Knudsen
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - William B Hamilton
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark.
| | - Martin Proks
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Maria Lykkegaard
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Madeleine Linneberg-Agerholm
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | | | - Marta Perera
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | | | - Ala Trusina
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joshua M Brickman
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark.
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Wood S, Ishida K, Hagerty JR, Karahodza A, Dennis JN, Jolly ER. Characterization of Schistosome Sox Genes and Identification of a Flatworm Class of Sox Regulators. Pathogens 2023; 12:690. [PMID: 37242360 PMCID: PMC10222431 DOI: 10.3390/pathogens12050690] [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: 04/24/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Schistosome helminths infect over 200 million people across 78 countries and are responsible for nearly 300,000 deaths annually. However, our understanding of basic genetic pathways crucial for schistosome development is limited. The sex determining region Y-box 2 (Sox2) protein is a Sox B type transcriptional activator that is expressed prior to blastulation in mammals and is necessary for embryogenesis. Sox expression is associated with pluripotency and stem cells, neuronal differentiation, gut development, and cancer. Schistosomes express a Sox-like gene expressed in the schistosomula after infecting a mammalian host when schistosomes have about 900 cells. Here, we characterized and named this Sox-like gene SmSOXS1. SmSoxS1 protein is a developmentally regulated activator that localizes to the anterior and posterior ends of the schistosomula and binds to Sox-specific DNA elements. In addition to SmSoxS1, we have also identified an additional six Sox genes in schistosomes, two Sox B, one SoxC, and three Sox genes that may establish a flatworm-specific class of Sox genes with planarians. These data identify novel Sox genes in schistosomes to expand the potential functional roles for Sox2 and may provide interesting insights into early multicellular development of flatworms.
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Affiliation(s)
- Stephanie Wood
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA; (S.W.); (K.I.); (J.R.H.)
| | - Kenji Ishida
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA; (S.W.); (K.I.); (J.R.H.)
| | - James R. Hagerty
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA; (S.W.); (K.I.); (J.R.H.)
| | - Anida Karahodza
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA; (S.W.); (K.I.); (J.R.H.)
| | - Janay N. Dennis
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA; (S.W.); (K.I.); (J.R.H.)
| | - Emmitt R. Jolly
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA; (S.W.); (K.I.); (J.R.H.)
- Center for Global Health and Disease, Case Western Reserve University, Cleveland, OH 44106, USA
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Zhang H, Zhu Y, Jin C, Shi L, Xie Y, Sun X, Li P, Zhu X, Dai Q, Yang F, Xie X, Qin L. Oct4 reduction contributes to testicular injury of unilateral testicular torsion in mice model and apoptotic death of Sertoli cells through mediating CIP2A expression. Gene 2023; 860:147214. [PMID: 36690227 DOI: 10.1016/j.gene.2023.147214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/16/2022] [Accepted: 01/16/2023] [Indexed: 01/22/2023]
Abstract
This study explored the mechanism of ipsilateral testis injury after ipsilateral testicular torsion detorsion (T/D) and the potential testis-protective part of the octamer-binding transcription factor 4 (Oct4)-cancerous inhibitors of protein phosphatase 2A (CIP2A) axis in a T/D animal model and in ischemia-reperfusion (IR)-treated testicular Sertoli TM4 cells. Quantitative Polymerase chain reaction (PCR) and western blot (WB) confirmed the downregulation of both CIP2A and Oct4 expression in the testicular tissue from T/D mice compared with sham-operated mice. T/D model was then established in mice with upregulated Oct4 expression in the testis. Oct4 elevation restored CIP2A expression in testes after T/D treatment. Furthermore, we observed that an increase in Oct4 ameliorated the testicular damage caused by torsion in the testis. Biochemical analysis indicated that T/D treatment increased serum anti-sperm antibody levels, but reduced testosterone levels. Meanwhile, in testicular tissue, reactive oxygen species (ROS), malondialdehyde (MDA), and activity of testicular myeloperoxidase (MPO) enzymes were promoted, while glutathione peroxidase activity (GPx) was decreased by T/D injury. Notably, testicular Oct4 restoration partially counteracted the effect of T/D treatment on these biochemical indices. Hypoxia/reoxygenation (HR) treatment was applied to TM4 cells to mimic TT injury in vitro. A gain-of-function study showed that Oct4 overexpression partly counteracted the promoting role of HR in cell damage, apoptosis, and oxidative stress in TM4 cells. These observations provide novel insights into the possible biochemical mechanism underlying the mediation of the Oct4-CIP2A axis in T/D injury.
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Affiliation(s)
- Haochuan Zhang
- Department of Pediatric Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Yiting Zhu
- Department of Second Clinical Medical School, Whenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Chengli Jin
- Department of First Clinical Medical School, Whenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Lingxin Shi
- Department of Second Clinical Medical School, Whenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Ying Xie
- Department of Second Clinical Medical School, Whenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Xinyi Sun
- Department of Second Clinical Medical School, Whenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Peizhen Li
- Department of Second Clinical Medical School, Whenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Xinyi Zhu
- Department of Second Clinical Medical School, Whenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Quanquan Dai
- Department of Internal Medicine, Wenzhou Yongjia County Traditional Chinese Medicine Hospital, Wenzhou, Zhejiang, China.
| | - Fan Yang
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China; Bio-XInstitutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China; Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China.
| | - Xiaoxiao Xie
- Department of Pediatric Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Le Qin
- Department of Pediatric Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
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Domingo-Muelas A, Morante-Redolat JM, Moncho-Amor V, Jordán-Pla A, Pérez-Villalba A, Carrillo-Barberà P, Belenguer G, Porlan E, Kirstein M, Bachs O, Ferrón SR, Lovell-Badge R, Fariñas I. The rates of adult neurogenesis and oligodendrogenesis are linked to cell cycle regulation through p27-dependent gene repression of SOX2. Cell Mol Life Sci 2023; 80:36. [PMID: 36627412 PMCID: PMC9832098 DOI: 10.1007/s00018-022-04676-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 12/15/2022] [Indexed: 01/12/2023]
Abstract
Cell differentiation involves profound changes in global gene expression that often has to occur in coordination with cell cycle exit. Because cyclin-dependent kinase inhibitor p27 reportedly regulates proliferation of neural progenitor cells in the subependymal neurogenic niche of the adult mouse brain, but can also have effects on gene expression, we decided to molecularly analyze its role in adult neurogenesis and oligodendrogenesis. At the cell level, we show that p27 restricts residual cyclin-dependent kinase activity after mitogen withdrawal to antagonize cycling, but it is not essential for cell cycle exit. By integrating genome-wide gene expression and chromatin accessibility data, we find that p27 is coincidentally necessary to repress many genes involved in the transit from multipotentiality to differentiation, including those coding for neural progenitor transcription factors SOX2, OLIG2 and ASCL1. Our data reveal both a direct association of p27 with regulatory sequences in the three genes and an additional hierarchical relationship where p27 repression of Sox2 leads to reduced levels of its downstream targets Olig2 and Ascl1. In vivo, p27 is also required for the regulation of the proper level of SOX2 necessary for neuroblasts and oligodendroglial progenitor cells to timely exit cell cycle in a lineage-dependent manner.
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Affiliation(s)
- Ana Domingo-Muelas
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Departamento de Biología Celular Biología Funcional y Antropología Física, Universidad de Valencia, 46100, Burjassot, Spain
- Instituto de Biotecnología y Biomedicina (BioTecMed), Universidad de Valencia, Valencia, Spain
- Department of Cell and Developmental Biology, Smilow Center for Translational Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jose Manuel Morante-Redolat
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Departamento de Biología Celular Biología Funcional y Antropología Física, Universidad de Valencia, 46100, Burjassot, Spain
- Instituto de Biotecnología y Biomedicina (BioTecMed), Universidad de Valencia, Valencia, Spain
| | - Verónica Moncho-Amor
- The Francis Crick Institute, London, NW1 1AT, UK
- IIS Biodonostia, 48013, Bilbao, Spain
| | - Antonio Jordán-Pla
- Instituto de Biotecnología y Biomedicina (BioTecMed), Universidad de Valencia, Valencia, Spain
| | - Ana Pérez-Villalba
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Departamento de Biología Celular Biología Funcional y Antropología Física, Universidad de Valencia, 46100, Burjassot, Spain
- Instituto de Biotecnología y Biomedicina (BioTecMed), Universidad de Valencia, Valencia, Spain
| | - Pau Carrillo-Barberà
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Departamento de Biología Celular Biología Funcional y Antropología Física, Universidad de Valencia, 46100, Burjassot, Spain
- Instituto de Biotecnología y Biomedicina (BioTecMed), Universidad de Valencia, Valencia, Spain
- Institute for Research in Biomedicine, 6500, Bellinzona, Switzerland
| | - Germán Belenguer
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Departamento de Biología Celular Biología Funcional y Antropología Física, Universidad de Valencia, 46100, Burjassot, Spain
- Instituto de Biotecnología y Biomedicina (BioTecMed), Universidad de Valencia, Valencia, Spain
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Eva Porlan
- Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
- Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), Instituto de Salud Carlos III, Madrid, Spain
| | - Martina Kirstein
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Departamento de Biología Celular Biología Funcional y Antropología Física, Universidad de Valencia, 46100, Burjassot, Spain
- Instituto de Biotecnología y Biomedicina (BioTecMed), Universidad de Valencia, Valencia, Spain
| | - Oriol Bachs
- Department of Biomedical Sciences, University of Barcelona-IDIBAPS, CIBERONC, Barcelona, Spain
| | - Sacri R Ferrón
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Departamento de Biología Celular Biología Funcional y Antropología Física, Universidad de Valencia, 46100, Burjassot, Spain
- Instituto de Biotecnología y Biomedicina (BioTecMed), Universidad de Valencia, Valencia, Spain
| | | | - Isabel Fariñas
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.
- Departamento de Biología Celular Biología Funcional y Antropología Física, Universidad de Valencia, 46100, Burjassot, Spain.
- Instituto de Biotecnología y Biomedicina (BioTecMed), Universidad de Valencia, Valencia, Spain.
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11
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Patel I, Parchem RJ. Regulation of Oct4 in stem cells and neural crest cells. Birth Defects Res 2022; 114:983-1002. [PMID: 35365980 PMCID: PMC9525453 DOI: 10.1002/bdr2.2007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/25/2022] [Accepted: 03/14/2022] [Indexed: 12/30/2022]
Abstract
During embryonic development, cells gradually restrict their developmental potential as they exit pluripotency and differentiate into various cell types. The POU transcription factor Oct4 (encoded by Pou5f1) lies at the center of the pluripotency machinery that regulates stemness and differentiation in stem cells, and is required for reprogramming of somatic cells into induced pluripotent stem cells (iPSCs). Several studies have revealed that Oct4 and other stemness genes are also expressed in multipotent cell populations such as neural crest cells (NCCs), and are required to expand the NCC developmental potential. Transcriptional regulation of Oct4 has been studied extensively in stem cells during early embryonic development and reprogramming, but not in NCCs. Here, we review how Oct4 is regulated in pluripotent stem cells, and address some of the gaps in knowledge about regulation of the pluripotency network in NCCs.
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Affiliation(s)
- Ivanshi Patel
- Department of Molecular and Cellular BiologyBaylor College of MedicineHoustonTexasUSA,Stem Cells and Regenerative Medicine Center, Center for Cell and Gene TherapyBaylor College of MedicineHoustonTexasUSA,Dan L Duncan Comprehensive Cancer CenterBaylor College of MedicineHoustonTexasUSA
| | - Ronald J. Parchem
- Department of Molecular and Cellular BiologyBaylor College of MedicineHoustonTexasUSA,Stem Cells and Regenerative Medicine Center, Center for Cell and Gene TherapyBaylor College of MedicineHoustonTexasUSA,Dan L Duncan Comprehensive Cancer CenterBaylor College of MedicineHoustonTexasUSA
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12
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MacCarthy CM, Huertas J, Ortmeier C, Vom Bruch H, Tan DS, Reinke D, Sander A, Bergbrede T, Jauch R, Schöler HR, Cojocaru V. OCT4 interprets and enhances nucleosome flexibility. Nucleic Acids Res 2022; 50:10311-10327. [PMID: 36130732 PMCID: PMC9561370 DOI: 10.1093/nar/gkac755] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 07/28/2022] [Accepted: 08/24/2022] [Indexed: 01/06/2023] Open
Abstract
Pioneer transcription factors are proteins that induce cellular identity transitions by binding to inaccessible regions of DNA in nuclear chromatin. They contribute to chromatin opening and recruit other factors to regulatory DNA elements. The structural features and dynamics modulating their interaction with nucleosomes are still unresolved. From a combination of experiments and molecular simulations, we reveal here how the pioneer factor and master regulator of pluripotency, Oct4, interprets and enhances nucleosome structural flexibility. The magnitude of Oct4’s impact on nucleosome dynamics depends on the binding site position and the mobility of the unstructured tails of nucleosomal histone proteins. Oct4 uses both its DNA binding domains to propagate and stabilize open nucleosome conformations, one for specific sequence recognition and the other for nonspecific interactions with nearby regions of DNA. Our findings provide a structural basis for the versatility of transcription factors in engaging with nucleosomes and have implications for understanding how pioneer factors induce chromatin dynamics.
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Affiliation(s)
- Caitlin M MacCarthy
- Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Jan Huertas
- Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Yusuf Hamied Department of Chemistry, University of Cambridge, UK
| | - Claudia Ortmeier
- Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Hermann Vom Bruch
- Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Daisylyn Senna Tan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Deike Reinke
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Astrid Sander
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Hans R Schöler
- Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Medical Faculty, University of Münster, Germany
| | - Vlad Cojocaru
- Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Computational Structural Biology Group, University of Utrecht, The Netherlands.,STAR-UBB Institute, Babeş-Bolyai University, Cluj-Napoca, Romania
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13
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Glover HJ, Shparberg RA, Morris MB. L-Proline Supplementation Drives Self-Renewing Mouse Embryonic Stem Cells to a Partially Primed Pluripotent State: The Early Primitive Ectoderm-Like Cell. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2490:11-24. [PMID: 35486235 DOI: 10.1007/978-1-0716-2281-0_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mouse embryonic stem cells (mESCs) can be grown under a variety of culture conditions as discrete cell states along the pluripotency continuum, ranging from the least mature "ground state" to being "primed" to differentiate. Cells along this continuum are demarcated by differences in gene expression, X chromosome inactivation, ability to form chimeras and epigenetic marks. We have developed a protocol to differentiate "naïve" mESCs to a "partially primed" state by adding the amino acid L-proline to self-renewal medium. These cells express the primitive ectoderm markers Dnmt3b and Fgf5, and are thus called early primitive ectoderm-like (EPL) cells. In addition to changes in gene expression, these cells undergo a morphological change to flattened, dispersed colonies, have an increased proliferation rate, and a predisposition to neural fate. EPL cells can be used to study the cell states along the pluripotency continuum, peri-implantation embryogenesis, and as a starting point for efficient neuronal differentiation.
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Affiliation(s)
- Hannah J Glover
- Bosch Institute and Discipline of Physiology, School of Medical Sciences, University of Sydney, Camperdown, NSW, Australia.
| | - Rachel A Shparberg
- Bosch Institute and Discipline of Physiology, School of Medical Sciences, University of Sydney, Camperdown, NSW, Australia
| | - Michael B Morris
- Bosch Institute and Discipline of Physiology, School of Medical Sciences, University of Sydney, Camperdown, NSW, Australia.
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14
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Bakhmet EI, Tomilin AN. Key features of the POU transcription factor Oct4 from an evolutionary perspective. Cell Mol Life Sci 2021; 78:7339-7353. [PMID: 34698883 PMCID: PMC11072838 DOI: 10.1007/s00018-021-03975-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/16/2021] [Accepted: 10/12/2021] [Indexed: 01/06/2023]
Abstract
Oct4, a class V POU-domain protein that is encoded by the Pou5f1 gene, is thought to be a key transcription factor in the early development of mammals. This transcription factor plays indispensable roles in pluripotent stem cells as well as in the acquisition of pluripotency during somatic cell reprogramming. Oct4 has also been shown to play a role as a pioneer transcription factor during zygotic genome activation (ZGA) from zebrafish to human. However, during the past decade, several studies have brought these conclusions into question. It was clearly shown that the first steps in mouse development are not affected by the loss of Oct4. Subsequently, the role of Oct4 as a genome activator was brought into doubt. It was also found that the reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) could proceed without Oct4. In this review, we summarize recent findings, reassess the role of Oct4 in reprogramming and ZGA, and point to structural features that may underlie this role. We speculate that pluripotent stem cells resemble neural stem cells more closely than previously thought. Oct4 orthologs within the POUV class hold key roles in genome activation during early development of species with late ZGA. However, in Placentalia, eutherian-specific proteins such as Dux overtake Oct4 in ZGA and endow them with the formation of an evolutionary new tissue-the placenta.
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Affiliation(s)
- Evgeny I Bakhmet
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia.
| | - Alexey N Tomilin
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
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15
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Voigt E, Wallenburg M, Wollenzien H, Thompson E, Kumar K, Feiner J, McNally M, Friesen H, Mukherjee M, Afeworki Y, Kareta MS. Sox2 Is an Oncogenic Driver of Small-Cell Lung Cancer and Promotes the Classic Neuroendocrine Subtype. Mol Cancer Res 2021; 19:2015-2025. [PMID: 34593608 PMCID: PMC8642303 DOI: 10.1158/1541-7786.mcr-20-1006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 06/02/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022]
Abstract
Although many cancer prognoses have improved in the past 50 years due to advancements in treatments, there has been little improvement in therapies for small-cell lung cancer (SCLC). One promising avenue to improve treatment for SCLC is to understand its underlying genetic alterations that drive its formation, growth, and cellular heterogeneity. RB1 loss is one key driver of SCLC, and RB1 loss has been associated with an increase in pluripotency factors such as SOX2. SOX2 is highly expressed and amplified in SCLC and has been associated with SCLC growth. Using a genetically engineered mouse model, we have shown that Sox2 is required for efficient SCLC formation. Furthermore, genome-scale binding assays have indicated that SOX2 can regulate key SCLC pathways such as NEUROD1 and MYC. These data suggest that SOX2 can be associated with the switch of SCLC from an ASCL1 subtype to a NEUROD1 subtype. Understanding this genetic switch is key to understanding such processes as SCLC progression, cellular heterogeneity, and treatment resistance. IMPLICATIONS: Understanding the molecular mechanisms of SCLC initiation and development are key to opening new potential therapeutic options for this devastating disease.
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Affiliation(s)
- Ellen Voigt
- Cancer Biology and Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota
- Genetics & Genomics Group, Sanford Research, Sioux Falls, South Dakota
| | - Madeline Wallenburg
- Cancer Biology and Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota
- Genetics & Genomics Group, Sanford Research, Sioux Falls, South Dakota
| | - Hannah Wollenzien
- Cancer Biology and Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota
- Genetics & Genomics Group, Sanford Research, Sioux Falls, South Dakota
- Division of Basic Biomedical Sciences, University of South Dakota, Vermillion, South Dakota
| | - Ethan Thompson
- Cancer Biology and Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota
- Genetics & Genomics Group, Sanford Research, Sioux Falls, South Dakota
| | - Kirtana Kumar
- Cancer Biology and Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota
- Genetics & Genomics Group, Sanford Research, Sioux Falls, South Dakota
| | | | - Moira McNally
- Cancer Biology and Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota
- Genetics & Genomics Group, Sanford Research, Sioux Falls, South Dakota
| | - Hunter Friesen
- Cancer Biology and Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota
- Genetics & Genomics Group, Sanford Research, Sioux Falls, South Dakota
| | - Malini Mukherjee
- Functional Genomics & Bioinformatics Core, Sanford Research, Sioux Falls, South Dakota
| | - Yohannes Afeworki
- Functional Genomics & Bioinformatics Core, Sanford Research, Sioux Falls, South Dakota
| | - Michael S Kareta
- Cancer Biology and Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota.
- Genetics & Genomics Group, Sanford Research, Sioux Falls, South Dakota
- Division of Basic Biomedical Sciences, University of South Dakota, Vermillion, South Dakota
- Functional Genomics & Bioinformatics Core, Sanford Research, Sioux Falls, South Dakota
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, South Dakota
- Department of Chemistry Biochemistry, South Dakota State University, Brookings, South Dakota
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16
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Schmidtlein PM, Volz C, Hackel A, Thürling I, Castven D, Braun R, Wellner UF, Konukiewitz B, Riemekasten G, Lehnert H, Marquardt JU, Ungefroren H. Activation of a Ductal-to-Endocrine Transdifferentiation Transcriptional Program in the Pancreatic Cancer Cell Line PANC-1 Is Controlled by RAC1 and RAC1b through Antagonistic Regulation of Stemness Factors. Cancers (Basel) 2021; 13:cancers13215541. [PMID: 34771704 PMCID: PMC8583136 DOI: 10.3390/cancers13215541] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 01/29/2023] Open
Abstract
Simple Summary For patients with metastatic pancreatic ductal adenocarcinoma (PDAC) there is currently no cure; hence, novel effective therapies are desperately needed. Among PDAC patients, the tumor cell phenotypes are heterogeneous as a result of epithelial–mesenchymal transition, a process that endows them with the ability to metastasize, resist therapy, and generate cancer stem cells. The heightened plasticity of quasimesenchymal and potentially metastatic tumor cells may, however, also be exploited for their transdifferentiation into benign, highly differentiated or post-mitotic cells. Since PDAC patients often have a need for replacement of insulin-producing cells, conversion of tumor cells with a ductal/exocrine origin to endocrine β cell-like cells is an attractive therapeutic option. Successful transdifferentiation into insulin-producing cells has been reported for the quasimesenchymal cell line PANC-1; however, the mechanistic basis of this transformation process is unknown. Here, we show that the small GTPases, RAC1 and RAC1b control this process by antagonistic regulation of stemness genes. Abstract Epithelial–mesenchymal transition (EMT) is a driving force for tumor growth, metastatic spread, therapy resistance, and the generation of cancer stem cells (CSCs). However, the regained stem cell character may also be exploited for therapeutic conversion of aggressive tumor cells to benign, highly differentiated cells. The PDAC-derived quasimesenchymal-type cell lines PANC-1 and MIA PaCa-2 have been successfully transdifferentiated to endocrine precursors or insulin-producing cells; however, the underlying mechanism of this increased plasticity remains elusive. Given its crucial role in normal pancreatic endocrine development and tumor progression, both of which involve EMT, we analyzed here the role of the small GTPase RAC1. Ectopic expression in PANC-1 cells of dominant negative or constitutively active mutants of RAC1 activation blocked or enhanced, respectively, the cytokine-induced activation of a ductal-to-endocrine transdifferentiation transcriptional program (deTDtP) as revealed by induction of the NEUROG3, INS, SLC2A2, and MAFA genes. Conversely, ectopic expression of RAC1b, a RAC1 splice isoform and functional antagonist of RAC1-driven EMT, decreased the deTDtP, while genetic knockout of RAC1b dramatically increased it. We further show that inhibition of RAC1 activation attenuated pluripotency marker expression and self-renewal ability, while depletion of RAC1b dramatically enhanced stemness features and clonogenic potential. Finally, rescue experiments involving pharmacological or RNA interference-mediated inhibition of RAC1 or RAC1b, respectively, confirmed that both RAC1 isoforms control the deTDtP in an opposite manner. We conclude that RAC1 and RAC1b antagonistically control growth factor-induced activation of an endocrine transcriptional program and the generation of CSCs in quasimesenchymal PDAC cells. Our results have clinical implications for PDAC patients, who in addition to eradication of tumor cells have a need for replacement of insulin-producing cells.
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Affiliation(s)
- Paula Marie Schmidtlein
- First Department of Medicine, University Hospital Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany; (P.M.S.); (C.V.); (I.T.); (D.C.); (J.-U.M.)
| | - Clara Volz
- First Department of Medicine, University Hospital Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany; (P.M.S.); (C.V.); (I.T.); (D.C.); (J.-U.M.)
| | - Alexander Hackel
- Department of Rheumatology and Clinical Immunology, University Hospital Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany; (A.H.); (G.R.)
| | - Isabel Thürling
- First Department of Medicine, University Hospital Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany; (P.M.S.); (C.V.); (I.T.); (D.C.); (J.-U.M.)
| | - Darko Castven
- First Department of Medicine, University Hospital Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany; (P.M.S.); (C.V.); (I.T.); (D.C.); (J.-U.M.)
| | - Rüdiger Braun
- Clinic for Surgery, University Hospital Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany; (R.B.); (U.F.W.)
| | - Ulrich Friedrich Wellner
- Clinic for Surgery, University Hospital Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany; (R.B.); (U.F.W.)
| | - Björn Konukiewitz
- Institute of Pathology, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany;
| | - Gabriela Riemekasten
- Department of Rheumatology and Clinical Immunology, University Hospital Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany; (A.H.); (G.R.)
| | | | - Jens-Uwe Marquardt
- First Department of Medicine, University Hospital Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany; (P.M.S.); (C.V.); (I.T.); (D.C.); (J.-U.M.)
| | - Hendrik Ungefroren
- First Department of Medicine, University Hospital Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany; (P.M.S.); (C.V.); (I.T.); (D.C.); (J.-U.M.)
- Institute of Pathology, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany;
- Center of Brain, Behavior and Metabolism (CBBM), University of Lübeck, D-23538 Lübeck, Germany
- Correspondence:
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17
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Zeng R, Jin C, Zheng C, Li S, Qian S, Pan J, Wang L, Zhao J, Qin L. OCT4 Represses Inflammation and Cell Injury During Orchitis by Regulating CIP2A Expression. Front Cell Dev Biol 2021; 9:683209. [PMID: 34513828 PMCID: PMC8427512 DOI: 10.3389/fcell.2021.683209] [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: 04/09/2021] [Accepted: 08/06/2021] [Indexed: 11/14/2022] Open
Abstract
Octamer-binding transcription factor 4 (OCT4) and cancerous inhibitor of protein phosphatase 2A (CIP2A) are upregulated in testicular cancer and cell lines. However, its contribution to orchitis (testicular inflammation) is unclear and was thus, investigated herein. Cell-based experiments on a lipopolysaccharide (LPS)-induced orchitis mouse model revealed robust inflammation, apoptotic cell death, and redox disorder in the Leydig (interstitial), Sertoli (supporting), and, germ cells. Meanwhile, real-time quantitative PCR revealed low OCT4 and CIP2A levels in testicular tissue and LPS-stimulated cells. A gain-of-function study showed that OCT4 overexpression not only increased CIP2A expression but also repressed LPS-induced inflammation, apoptosis, and redox disorder in the aforementioned cells. Furthermore, the re-inhibition of CIP2A expression by TD-19 in OCT4-overexpressing cells counteracted the effects of OCT4 overexpression on inflammation, apoptosis, and redox equilibrium. In addition, our results indicated that the Keap1-Nrf2-HO-1 signaling pathway was mediated by OCT4 and CIP2A. These findings provide insights into the potential mechanism underlying OCT4- and CIP2A-mediated testicular inflammation.
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Affiliation(s)
- Ruifeng Zeng
- Department of Anesthesiology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Chengli Jin
- Department of First Clinical Medical School, Wenzhou Medical University, Wenzhou, China
| | - Chuchu Zheng
- Department of Second Clinical Medical School, Wenzhou Medical University, Wenzhou, China
| | - Shaoqi Li
- Department of Second Clinical Medical School, Wenzhou Medical University, Wenzhou, China
| | - Siyue Qian
- Department of Second Clinical Medical School, Wenzhou Medical University, Wenzhou, China
| | - Jingsa Pan
- Department of Second Clinical Medical School, Wenzhou Medical University, Wenzhou, China
| | - Lvhe Wang
- Department of Second Clinical Medical School, Wenzhou Medical University, Wenzhou, China
| | - Junfeng Zhao
- Department of Pediatric Surgery, Ningbo Women and Children's Hospital, Wenzhou, China
| | - Le Qin
- Department of Pediatric Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
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18
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Li J, Haque M, Shang C, Hassan B, Liu D, Chen W, Lai R. Identification and Characterization of Cancer Stem-Like Cells in ALK-Positive Anaplastic Large Cell Lymphoma Using the SORE6 Reporter. Curr Issues Mol Biol 2021; 43:543-557. [PMID: 34287231 PMCID: PMC8929104 DOI: 10.3390/cimb43020041] [Citation(s) in RCA: 3] [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: 04/23/2021] [Revised: 06/17/2021] [Accepted: 06/24/2021] [Indexed: 01/04/2023] Open
Abstract
Transcription factors Sox2 and Oct4 are essential in maintaining the pluripotency of embryonic stem cells and conferring stemness in cancer stem-like (CSL) cells. SORE6, an in-vitro reporter system, was designed to quantify the transcription activity of Sox2/Oct4 and identify CSL cells in non-hematologic cancers. Using SORE6, we identified and enriched CSL cells in ALK-positive anaplastic large cell lymphoma (ALK + ALCL). Two ALK + ALCL cell lines, SupM2 and UCONN-L2, contained approximately 20% of SORE6+ cells, which were purified based on their expression of green fluorescent protein. We then performed functional studies using single-cell clones derived from SORE6− and SORE6+ cells. Compared to SORE6− cells, SORE6+ cells were significantly more chemoresistant and clonogenic in colony-formation assays. Sox2/Oct4 are directly involved in conferring these CSL properties, since the shRNA knockdown of Sox2 in SORE6+ significantly lowered their chemoresistance, while enforced expression of Sox2/Oct4 in SORE6− cells produced opposite effects. Using Western blots, we found that the expression and subcellular localization of Sox2/Oct4 were similar between SORE6− and SORE6+ cells. However, in SORE6+ but not SORE6− cells, Sox2 and Oct4 abundantly bound to a probe containing the SORE6 consensus sequence. c-Myc, previously shown to regulate cancer stemness in ALK + ALCL, regulated the SORE6 activity. In conclusion, SORE6 is useful in identifying/enriching CSL cells in ALK + ALCL.
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Affiliation(s)
- Jing Li
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2E1, Canada; (J.L.); (M.H.); (C.S.); (B.H.); (D.L.); (W.C.)
- Electron Microscopy Center, Basic Medical Science College, Harbin Medical University, Harbin 150080, China
| | - Moinul Haque
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2E1, Canada; (J.L.); (M.H.); (C.S.); (B.H.); (D.L.); (W.C.)
- College of Medicine and Health, University College Cork, T12 AK54 Cork, Ireland
| | - Chuquan Shang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2E1, Canada; (J.L.); (M.H.); (C.S.); (B.H.); (D.L.); (W.C.)
| | - Bardes Hassan
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2E1, Canada; (J.L.); (M.H.); (C.S.); (B.H.); (D.L.); (W.C.)
- Department of Pathology, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Dongzhe Liu
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2E1, Canada; (J.L.); (M.H.); (C.S.); (B.H.); (D.L.); (W.C.)
- Laboratory of Biology and Chemistry, Basic Medical Science College, Harbin Medical University, Harbin 150080, China
| | - Will Chen
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2E1, Canada; (J.L.); (M.H.); (C.S.); (B.H.); (D.L.); (W.C.)
| | - Raymond Lai
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2E1, Canada; (J.L.); (M.H.); (C.S.); (B.H.); (D.L.); (W.C.)
- Department of Oncology, University of Alberta, Edmonton, AB T6G 2R7, Canada
- Correspondence:
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19
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Barbagallo C, Di Maria A, Alecci A, Barbagallo D, Alaimo S, Colarossi L, Ferro A, Di Pietro C, Purrello M, Pulvirenti A, Ragusa M. VECTOR: An Integrated Correlation Network Database for the Identification of CeRNA Axes in Uveal Melanoma. Genes (Basel) 2021; 12:genes12071004. [PMID: 34210067 PMCID: PMC8305227 DOI: 10.3390/genes12071004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 12/16/2022] Open
Abstract
Uveal melanoma (UM) is the most common primary intraocular malignant tumor in adults and, although its genetic background has been extensively studied, little is known about the contribution of non-coding RNAs (ncRNAs) to its pathogenesis. Indeed, its competitive endogenous RNA (ceRNA) regulatory network comprising microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and mRNAs has been insufficiently explored. Thanks to UM findings from The Cancer Genome Atlas (TCGA), it is now possible to statistically elaborate these data to identify the expression relationships among RNAs and correlative interaction data. In the present work, we propose the VECTOR (uVeal mElanoma Correlation NeTwORk) database, an interactive tool that identifies and visualizes the relationships among RNA molecules, based on the ceRNA model. The VECTOR database contains: (i) the TCGA-derived expression correlation values of miRNA-mRNA, miRNA-lncRNA and lncRNA-mRNA pairs combined with predicted or validated RNA-RNA interactions; (ii) data of sense-antisense sequence overlapping; (iii) correlation values of Transcription Factor (TF)-miRNA, TF-lncRNA, and TF-mRNA pairs associated with ChiPseq data; (iv) expression data of miRNAs, lncRNAs and mRNAs both in UM and physiological tissues. The VECTOR web interface can be queried, by inputting the gene name, to retrieve all the information about RNA signaling and visualize this as a graph. Finally, VECTOR provides a very detailed picture of ceRNA networks in UM and could be a very useful tool for researchers studying RNA signaling in UM. The web version of Vector is freely available at the URL reported at the end of the Introduction.
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Affiliation(s)
- Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (A.A.); (D.B.); (C.D.P.); (M.P.)
| | - Antonio Di Maria
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dipartimento di Matematica e Informatica, Viale A. Doria 6, 95125 Catania, Italy; (A.D.M.); (S.A.); (A.F.); (M.R.)
| | - Adriana Alecci
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (A.A.); (D.B.); (C.D.P.); (M.P.)
| | - Davide Barbagallo
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (A.A.); (D.B.); (C.D.P.); (M.P.)
| | - Salvatore Alaimo
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dipartimento di Matematica e Informatica, Viale A. Doria 6, 95125 Catania, Italy; (A.D.M.); (S.A.); (A.F.); (M.R.)
| | - Lorenzo Colarossi
- Department of Experimental Oncology, Mediterranean Institute of Oncology (IOM), 95029 Catania, Italy;
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dipartimento di Matematica e Informatica, Viale A. Doria 6, 95125 Catania, Italy; (A.D.M.); (S.A.); (A.F.); (M.R.)
| | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (A.A.); (D.B.); (C.D.P.); (M.P.)
| | - Michele Purrello
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (A.A.); (D.B.); (C.D.P.); (M.P.)
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dipartimento di Matematica e Informatica, Viale A. Doria 6, 95125 Catania, Italy; (A.D.M.); (S.A.); (A.F.); (M.R.)
- Correspondence:
| | - Marco Ragusa
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dipartimento di Matematica e Informatica, Viale A. Doria 6, 95125 Catania, Italy; (A.D.M.); (S.A.); (A.F.); (M.R.)
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Saenz-Antoñanzas A, Moncho-Amor V, Auzmendi-Iriarte J, Elua-Pinin A, Rizzoti K, Lovell-Badge R, Matheu A. CRISPR/Cas9 Deletion of SOX2 Regulatory Region 2 ( SRR2) Decreases SOX2 Malignant Activity in Glioblastoma. Cancers (Basel) 2021; 13:cancers13071574. [PMID: 33805518 PMCID: PMC8037847 DOI: 10.3390/cancers13071574] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/12/2021] [Accepted: 03/17/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Understanding how SOX2, a major driver of cancer stem cells, is regulated in cancer cells is relevant to tackle tumorigenesis. In this study, we deleted the SRR2 regulatory region in glioblastoma cells. Our data confirm that the SRR2 enhancer regulates SOX2 expression in cancer and reveal that SRR2 deletion halts malignant activity of SOX2. Abstract SOX2 is a transcription factor associated with stem cell activity in several tissues. In cancer, SOX2 expression is increased in samples from several malignancies, including glioblastoma, and high SOX2 levels are associated with the population of tumor-initiating cells and with poor patient outcome. Therefore, understanding how SOX2 is regulated in cancer cells is relevant to tackle tumorigenesis. The SOX2 regulatory region 2(SRR2) is located downstream of the SOX2 coding region and mediates SOX2 expression in embryonic and adult stem cells. In this study, we deleted SRR2 using CRISPR/Cas9 in glioblastoma cells. Importantly, SRR2-deleted glioblastoma cells presented reduced SOX2 expression and decreased proliferative activity and self-renewal capacity in vitro. In line with these results, SRR2-deleted glioblastoma cells displayed decreased tumor initiation and growth in vivo. These effects correlated with an elevation of p21CIP1 cell cycle and p27KIP1 quiescence regulators. In conclusion, our data reveal that SRR2 deletion halts malignant activity of SOX2 and confirms that the SRR2 enhancer regulates SOX2 expression in cancer.
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Affiliation(s)
- Ander Saenz-Antoñanzas
- Cellular Oncology Group, Biodonostia Health Research Institute, 20014 San Sebastian, Spain; (A.S.-A.); (J.A.-I.); (A.E.-P.)
| | - Veronica Moncho-Amor
- Stem Cell Biology and Developmental Genetics Lab, The Francis Crick Institute, London NW1 1AT, UK; (V.M.-A.); (K.R.); (R.L.-B.)
| | - Jaione Auzmendi-Iriarte
- Cellular Oncology Group, Biodonostia Health Research Institute, 20014 San Sebastian, Spain; (A.S.-A.); (J.A.-I.); (A.E.-P.)
| | - Alejandro Elua-Pinin
- Cellular Oncology Group, Biodonostia Health Research Institute, 20014 San Sebastian, Spain; (A.S.-A.); (J.A.-I.); (A.E.-P.)
- Donostia Hospital, 20014 San Sebastian, Spain
| | - Karine Rizzoti
- Stem Cell Biology and Developmental Genetics Lab, The Francis Crick Institute, London NW1 1AT, UK; (V.M.-A.); (K.R.); (R.L.-B.)
| | - Robin Lovell-Badge
- Stem Cell Biology and Developmental Genetics Lab, The Francis Crick Institute, London NW1 1AT, UK; (V.M.-A.); (K.R.); (R.L.-B.)
| | - Ander Matheu
- Cellular Oncology Group, Biodonostia Health Research Institute, 20014 San Sebastian, Spain; (A.S.-A.); (J.A.-I.); (A.E.-P.)
- CIBER of Frailty and Healthy Aging (CIBERfes), Carlos III Institute, 28029 Madrid, Spain
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain
- Correspondence:
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21
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Batool S, Kayani MA, Valis M, Kuca K. Neural Differentiation of Mouse Embryonic Stem Cells-An in vitro Approach to Profile DNA Methylation of Reprogramming Factor Sox2-SRR2. Front Genet 2021; 12:641095. [PMID: 33828585 PMCID: PMC8019947 DOI: 10.3389/fgene.2021.641095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/02/2021] [Indexed: 12/30/2022] Open
Abstract
Sox2 is one of the core transcription factors maintaining the embryonic stem cells (ES) pluripotency and, also indispensable for cellular reprogramming. However, limited data is available about the DNA methylation of pluripotency genes during lineage-specific differentiations. This study investigated the DNA methylation of Sox2 regulatory region 2 (SRR2) during directed differentiation of mouse ES into neural lineage. ES cells were first grown to form embryoid bodies in suspension which were then dissociated, and cultured in defined medium to promote neural differentiation. Typical neuronal morphology together with the up-regulation of Pax6, neuroepithelial stem cell intermediate filament and β-tubulin III and, down-regulation of pluripotency genes Oct4, Nanog and Sox2 showed the existence of neural phenotype in cells undergoing differentiation. Three CpGs in the core enhancer region of neural-specific SRR2 were individually investigated by direct DNA sequencing post-bisulfite treatment and, found to be unmethylated in differentiated cells at time-points chosen for analysis. This analysis does not limit the possibility of methylation at other CpG sites than those profiled here and/or transient methylation. Hence, similar analyses exploring the DNA methylation at other regions of the Sox2 gene could unravel the onset and transitions of epigenetic signatures influencing the outcome of differentiation pathways and neural development. The data presented here shows that in vitro neural differentiation of embryonic stem cells can be employed to study and characterize molecular regulatory mechanisms governing neurogenesis by applying diverse pharmacological and toxicological agents.
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Affiliation(s)
- Sajida Batool
- Cancer Genetics and Epigenetics Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Mahmood Akhtar Kayani
- Cancer Genetics and Epigenetics Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Martin Valis
- Department of Neurology of the Medical Faculty of Charles University and University Hospital in Hradec Kralove, Hradec Kralove, Czechia
| | - Kamil Kuca
- Department of Chemistry, University of Hradec Kralove, Hradec Kralove, Czechia
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22
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Stirparo GG, Kurowski A, Yanagida A, Bates LE, Strawbridge SE, Hladkou S, Stuart HT, Boroviak TE, Silva JCR, Nichols J. OCT4 induces embryonic pluripotency via STAT3 signaling and metabolic mechanisms. Proc Natl Acad Sci U S A 2021; 118:e2008890118. [PMID: 33452132 PMCID: PMC7826362 DOI: 10.1073/pnas.2008890118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
OCT4 is a fundamental component of the molecular circuitry governing pluripotency in vivo and in vitro. To determine how OCT4 establishes and protects the pluripotent lineage in the embryo, we used comparative single-cell transcriptomics and quantitative immunofluorescence on control and OCT4 null blastocyst inner cell masses at two developmental stages. Surprisingly, activation of most pluripotency-associated transcription factors in the early mouse embryo occurs independently of OCT4, with the exception of the JAK/STAT signaling machinery. Concurrently, OCT4 null inner cell masses ectopically activate a subset of trophectoderm-associated genes. Inspection of metabolic pathways implicates the regulation of rate-limiting glycolytic enzymes by OCT4, consistent with a role in sustaining glycolysis. Furthermore, up-regulation of the lysosomal pathway was specifically detected in OCT4 null embryos. This finding implicates a requirement for OCT4 in the production of normal trophectoderm. Collectively, our findings uncover regulation of cellular metabolism and biophysical properties as mechanisms by which OCT4 instructs pluripotency.
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Affiliation(s)
- Giuliano G Stirparo
- Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW Cambridge, United Kingdom;
- Living Systems Institute, University of Exeter, EX4 4QD Exeter, United Kingdom
| | - Agata Kurowski
- Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW Cambridge, United Kingdom
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ayaka Yanagida
- Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW Cambridge, United Kingdom
- Living Systems Institute, University of Exeter, EX4 4QD Exeter, United Kingdom
| | - Lawrence E Bates
- Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, CB2 1GA Cambridge, United Kingdom
| | - Stanley E Strawbridge
- Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW Cambridge, United Kingdom
| | - Siarhei Hladkou
- Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, CB2 1GA Cambridge, United Kingdom
| | - Hannah T Stuart
- Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW Cambridge, United Kingdom
| | - Thorsten E Boroviak
- Department of Physiology, Development and Neuroscience, University of Cambridge, CB2 3EG Cambridge, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, CB2 3EG Cambridge, United Kingdom
| | - Jose C R Silva
- Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, CB2 1GA Cambridge, United Kingdom
| | - Jennifer Nichols
- Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW Cambridge, United Kingdom;
- Department of Physiology, Development and Neuroscience, University of Cambridge, CB2 3EG Cambridge, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, CB2 3EG Cambridge, United Kingdom
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23
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Zhang Y, Hu W, Ma K, Zhang C, Fu X. Reprogramming of Keratinocytes as Donor or Target Cells Holds Great Promise for Cell Therapy and Regenerative Medicine. Stem Cell Rev Rep 2020; 15:680-689. [PMID: 31197578 DOI: 10.1007/s12015-019-09900-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
One of the most crucial branches of regenerative medicine is cell therapy, in which cellular material is injected into the patient to initiate the regenerative process. Cells obtained by reprogramming of the patient's own cells offer ethical and clinical advantages could provide a new source of material for therapeutic applications. Studies to date have shown that only a subset of differentiated cell types can be reprogrammed. Among these, keratinocytes, which are the most abundant proliferating cell type in the epidermis, have gained increasing attention as both donor and target cells for reprogramming and have become a new focus of regenerative medicine. As target cells for the treatment of skin defects, keratinocytes can be differentiated or reprogrammed from embryonic stem cells, induced pluripotent stem cells, fibroblasts, adipose tissue stem cells, and mesenchymal cells. As donor cells, keratinocytes can be reprogrammed or direct reprogrammed into a number of cell types, including induced pluripotent stem cells, neural cells, and Schwann cells. In this review, we discuss recent advances in keratinocyte reprogramming, focusing on the induction methods, potential molecular mechanisms, conversion efficiency, and safety for clinical applications. Graphical Abstract KCs as target cells can be reprogrammed or differentiated from fibroblasts, iPSCs, ATSCs, and mesenchymal cells. And as donor cells, KCs can be reprogrammed or directly reprogrammded into iPSCs, neural cells, Schwann cells, and epidermal stem cells.
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Affiliation(s)
- Yuehou Zhang
- School of Medicine, NanKai University, 94 Wei Jin Road, NanKai District, Tianjin, 300071, People's Republic of China.,Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center of General Hospital of PLA, 51 Fu Cheng Road, HaiDian District, Beijing, 100048, People's Republic of China
| | - Wenzhi Hu
- Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center of General Hospital of PLA, 51 Fu Cheng Road, HaiDian District, Beijing, 100048, People's Republic of China
| | - Kui Ma
- Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center of General Hospital of PLA, 51 Fu Cheng Road, HaiDian District, Beijing, 100048, People's Republic of China
| | - Cuiping Zhang
- Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center of General Hospital of PLA, 51 Fu Cheng Road, HaiDian District, Beijing, 100048, People's Republic of China.
| | - Xiaobing Fu
- Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center of General Hospital of PLA, 51 Fu Cheng Road, HaiDian District, Beijing, 100048, People's Republic of China.
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24
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Functional characterization of SOX2 as an anticancer target. Signal Transduct Target Ther 2020; 5:135. [PMID: 32728033 PMCID: PMC7391717 DOI: 10.1038/s41392-020-00242-3] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/01/2020] [Accepted: 06/22/2020] [Indexed: 02/07/2023] Open
Abstract
SOX2 is a well-characterized pluripotent factor that is essential for stem cell self-renewal, reprogramming, and homeostasis. The cellular levels of SOX2 are precisely regulated by a complicated network at the levels of transcription, post-transcription, and post-translation. In many types of human cancer, SOX2 is dysregulated due to gene amplification and protein overexpression. SOX2 overexpression is associated with poor survival of cancer patients. Mechanistically, SOX2 promotes proliferation, survival, invasion/metastasis, cancer stemness, and drug resistance. SOX2 is, therefore, an attractive anticancer target. However, little progress has been made in the efforts to discover SOX2 inhibitors, largely due to undruggable nature of SOX2 as a transcription factor. In this review, we first briefly introduced SOX2 as a transcription factor, its domain structure, normal physiological functions, and its involvement in human cancers. We next discussed its role in embryonic development and stem cell-renewal. We then mainly focused on three aspects of SOX2: (a) the regulatory mechanisms of SOX2, including how SOX2 level is regulated, and how SOX2 cross-talks with multiple signaling pathways to control growth and survival; (b) the role of SOX2 in tumorigenesis and drug resistance; and (c) current drug discovery efforts on targeting SOX2, and the future perspectives to discover specific SOX2 inhibitors for effective cancer therapy.
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25
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Shanak S, Helms V. DNA methylation and the core pluripotency network. Dev Biol 2020; 464:145-160. [PMID: 32562758 DOI: 10.1016/j.ydbio.2020.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 05/01/2020] [Accepted: 06/04/2020] [Indexed: 01/06/2023]
Abstract
From the onset of fertilization, the genome undergoes cell division and differentiation. All of these developmental transitions and differentiation processes include cell-specific signatures and gradual changes of the epigenome. Understanding what keeps stem cells in the pluripotent state and what leads to differentiation are fascinating and biomedically highly important issues. Numerous studies have identified genes, proteins, microRNAs and small molecules that exert essential effects. Notably, there exists a core pluripotency network that consists of several transcription factors and accessory proteins. Three eminent transcription factors, OCT4, SOX2 and NANOG, serve as hubs in this core pluripotency network. They bind to the enhancer regions of their target genes and modulate, among others, the expression levels of genes that are associated with Gene Ontology terms related to differentiation and self-renewal. Also, much has been learned about the epigenetic rewiring processes during these changes of cell fate. For example, DNA methylation dynamics is pivotal during embryonic development. The main goal of this review is to highlight an intricate interplay of (a) DNA methyltransferases controlling the expression levels of core pluripotency factors by modulation of the DNA methylation levels in their enhancer regions, and of (b) the core pluripotency factors controlling the transcriptional regulation of DNA methyltransferases. We discuss these processes both at the global level and in atomistic detail based on information from structural studies and from computer simulations.
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Affiliation(s)
- Siba Shanak
- Faculty of Science, Arab-American University, Jenin, Palestine; Center for Bioinformatics, Saarland University, Saarbruecken, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbruecken, Germany.
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26
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Assoun EN, Meyer AN, Jiang MY, Baird SM, Haas M, Donoghue DJ. Characterization of iPS87, a prostate cancer stem cell-like cell line. Oncotarget 2020; 11:1075-1084. [PMID: 32256979 PMCID: PMC7105161 DOI: 10.18632/oncotarget.27524] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/03/2020] [Indexed: 12/31/2022] Open
Abstract
Prostate cancer affects hundreds of thousands of men and families throughout the world. Although chemotherapy, radiation, surgery, and androgen deprivation therapy are applied, these therapies do not cure metastatic prostate cancer. Patients treated by androgen deprivation often develop castration resistant prostate cancer which is incurable. Novel approaches of treatment are clearly necessary. We have previously shown that prostate cancer originates as a stem cell disease. A prostate cancer patient sample, #87, obtained from prostatectomy surgery, was collected and frozen as single cell suspension. Cancer stem cell cultures were grown, single cell-cloned, and shown to be tumorigenic in SCID mice. However, outside its natural niche, the cultured prostate cancer stem cells lost their tumor-inducing capability and stem cell marker expression after approximately 8 transfers at a 1:3 split ratio. Tumor-inducing activity could be restored by inducing the cells to pluripotency using the method of Yamanaka. Cultures of human prostate-derived normal epithelial cells acquired from commercial sources were similarly induced to pluripotency and these did not acquire a tumor phenotype in vivo. To characterize the iPS87 cell line, cells were stained with antibodies to various markers of stem cells including: ALDH7A1, LGR5, Oct4, Nanog, Sox2, Androgen Receptor, and Retinoid X Receptor. These markers were found to be expressed by iPS87 cells, and the high tumorigenicity in SCID mice of iPS87 was confirmed by histopathology. This research thus characterizes the iPS87 cell line as a cancer-inducing, stem cell-like cell line, which can be used in the development of novel treatments for prostate cancer.
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Affiliation(s)
- Erika N. Assoun
- Division of Biological Sciences, University of California San Diego, La Jolla, San Diego, CA 92093, USA
| | - April N. Meyer
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, CA 92093, USA
| | - Maggie Y. Jiang
- Division of Biological Sciences, University of California San Diego, La Jolla, San Diego, CA 92093, USA
| | - Stephen M. Baird
- Department of Pathology, University of California San Diego, La Jolla, San Diego, CA 92093, USA
| | - Martin Haas
- Moores UCSD Cancer Center, University of California San Diego, La Jolla, San Diego, CA 92093, USA
| | - Daniel J. Donoghue
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, CA 92093, USA
- Moores UCSD Cancer Center, University of California San Diego, La Jolla, San Diego, CA 92093, USA
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27
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Inomata C, Yuikawa T, Nakayama-Sadakiyo Y, Kobayashi K, Ikeda M, Chiba M, Konishi C, Ishioka A, Tsuda S, Yamasu K. Involvement of an Oct4-related PouV gene, pou5f3/pou2, in neurogenesis in the early neural plate of zebrafish embryos. Dev Biol 2020; 457:30-42. [DOI: 10.1016/j.ydbio.2019.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 01/03/2023]
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Abstract
In eukaryotes, DNA is highly compacted within the nucleus into a structure known as chromatin. Modulation of chromatin structure allows for precise regulation of gene expression, and thereby controls cell fate decisions. Specific chromatin organization is established and preserved by numerous factors to generate desired cellular outcomes. In embryonic stem (ES) cells, chromatin is precisely regulated to preserve their two defining characteristics: self-renewal and pluripotent state. This action is accomplished by a litany of nucleosome remodelers, histone variants, epigenetic marks, and other chromatin regulatory factors. These highly dynamic regulatory factors come together to precisely define a chromatin state that is conducive to ES cell maintenance and development, where dysregulation threatens the survival and fitness of the developing organism.
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Affiliation(s)
- David C Klein
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States.
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Baldauf C, Sondhi M, Shin BC, Ko YE, Ye X, Lee KW, Devaskar SU. Murine maternal dietary restriction affects neural Humanin expression and cellular profile. J Neurosci Res 2019; 98:902-920. [PMID: 31840315 DOI: 10.1002/jnr.24568] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/06/2019] [Accepted: 11/15/2019] [Indexed: 11/10/2022]
Abstract
To understand the cellular basis for the neurodevelopmental effects of intrauterine growth restriction (IUGR), we examined the global and regional expression of various cell types within murine (Mus musculus) fetal brain. Our model employed maternal calorie restriction to 50% daily food intake from gestation day 10-19, producing IUGR offspring. Offspring had smaller head sizes with larger head:body ratios indicating a head sparing IUGR effect. IUGR fetuses at embryonic day 19 (E19) had reduced nestin (progenitors), β-III tubulin (immature neurons), Glial fibrillary acidic protein (astrocytes), and O4 (oligodendrocytes) cell lineages via immunofluorescence quantification and a 30% reduction in cortical thickness. No difference was found in Bcl-2 or Bax (apoptosis) between controls and IUGR, though qualitatively, immunoreactivity of doublecortin (migration) and Ki67 (proliferation) was decreased. In the interest of examining a potential therapeutic peptide, we next investigated a novel pro-survival peptide, mouse Humanin (mHN). Ontogeny examination revealed highest mHN expression at E19, diminishing by postnatal day 15 (P15), and nearly absent in adult (3 months). Subanalysis by sex at E19 yielded higher mHN expression among males during fetal life, without significant difference between sexes postnatally. Furthermore, female IUGR mice at E19 had a greater increase in cortical mHN versus the male fetus over their respective controls. We conclude that maternal dietary restriction-associated IUGR interferes with neural progenitors differentiating into the various cellular components populating the cerebral cortex, and reduces cerebral cortical size. mHN expression is developmental stage and sex specific, with IUGR, particularly in the females, adaptively increasing its expression toward mediating a pro-survival approach against nutritional adversity.
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Affiliation(s)
- Claire Baldauf
- Department of Pediatrics, Division of Neonatology & Developmental Biology, UCLA Children's Discovery and Innovation Institute, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA, USA
| | - Monica Sondhi
- Department of Pediatrics, Division of Neonatology & Developmental Biology, UCLA Children's Discovery and Innovation Institute, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA, USA
| | - Bo-Chul Shin
- Department of Pediatrics, Division of Neonatology & Developmental Biology, UCLA Children's Discovery and Innovation Institute, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA, USA
| | - Young Eun Ko
- Department of Pediatrics, Division of Neonatology & Developmental Biology, UCLA Children's Discovery and Innovation Institute, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA, USA
| | - Xin Ye
- Department of Pediatrics, Division of Neonatology & Developmental Biology, UCLA Children's Discovery and Innovation Institute, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA, USA
| | - Kuk-Wha Lee
- Department of Pediatrics, Division of Endocrinology, Neonatal Research Center of the UCLA Children's Discovery and Innovation Institute, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA, USA
| | - Sherin U Devaskar
- Department of Pediatrics, Division of Neonatology & Developmental Biology, UCLA Children's Discovery and Innovation Institute, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA, USA
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Metastatic Phosphatase PRL-3 Induces Ovarian Cancer Stem Cell Sub-population through Phosphatase-Independent Deacetylation Modulations. iScience 2019; 23:100766. [PMID: 31887658 PMCID: PMC6941878 DOI: 10.1016/j.isci.2019.100766] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 09/01/2019] [Accepted: 12/09/2019] [Indexed: 12/18/2022] Open
Abstract
Cancer stem cells (CSCs) are responsible for tumor initiation, chemoresistance, metastasis, and relapse, but the underlying molecular origin of CSCs remains elusive. Here we identified that metastatic phosphatase of regenerating liver 3 (PRL-3) transcriptionally upregulates SOX2 in the expansion of CSC sub-population from normal cancer cells. Mechanistically, SOX2 upregulation is attributed to the binding of the acetylated myocyte enhancer factor 2A (MEF2A) to SOX2 promoter in tumor cells. In parallel, PRL-3 competitively binds to Class IIa histone deacetylase 4 (HDAC4) to facilitate HDAC4 translocation, leading to the disassociation of HDAC4 from MEF2A and histones. The released MEF2A and histones thus remain acetylated and render the subsequent accessibility of the acetylated MEF2A to SOX2 promoter region. Clinical relevance among PRL-3, SOX2, and HDAC4 is validated in ovary cancer samples. Therefore, this PRL-3-HDAC4-MEF2A/histones-SOX2 signaling axis would be a potential therapeutic target in inhibiting ovarian cancer metastasis and relapse. PRL-3 promotes the expansion of CSC-like cells via transcriptional SOX2 upregulation Binding of MEF2A to SOX2 promoter bridges the PRL-3-induced SOX2 upregulation PRL-3 competitively binds HDAC4 to cause the disassociation of HDAC4 from MEF2A Acetylated histones render the accessibility of SOX2 promoter region to MEF2A
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31
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Kime C, Kiyonari H, Ohtsuka S, Kohbayashi E, Asahi M, Yamanaka S, Takahashi M, Tomoda K. Induced 2C Expression and Implantation-Competent Blastocyst-like Cysts from Primed Pluripotent Stem Cells. Stem Cell Reports 2019; 13:485-498. [PMID: 31402336 PMCID: PMC6739768 DOI: 10.1016/j.stemcr.2019.07.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 07/09/2019] [Accepted: 07/15/2019] [Indexed: 12/15/2022] Open
Abstract
Soon after fertilization, the few totipotent cells of mammalian embryos diverge to form a structure called the blastocyst (BC). Although numerous cell types, including germ cells and extended-pluripotency stem cells, have been developed from pluripotent stem cells (PSCs) in vitro, generating functional BCs only from PSCs remains elusive. Here, we describe induced self-organizing 3D BC-like cysts (iBLCs) generated from mouse PSC culture. Resembling natural BCs, iBLCs have a blastocoel-like cavity and were formed with outer cells expressing trophectoderm lineage markers and with inner cells expressing pluripotency markers. iBLCs transplanted to pseudopregnant mice uteruses implanted, induced decidualization, and exhibited growth and development before resorption, demonstrating that iBLCs are implantation competent. iBLC precursor intermediates required the transcription factor Prdm14 and concomitantly activated the totipotency-related cleavage-stage MERVL reporter and 2C genes. Thus, our system may contribute to the understanding of molecular mechanisms underpinning totipotency, embryogenesis, and implantation.
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Affiliation(s)
- Cody Kime
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Lab of Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan.
| | - Hiroshi Kiyonari
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Satoshi Ohtsuka
- Department of Life Science, Medical Research Institute, Kanazawa Medical University, Ishikawa 920-0293, Japan
| | - Eiko Kohbayashi
- Second Department of Internal Medicine, Osaka Medical College, Osaka 569-8686, Japan
| | - Michio Asahi
- Department of Pharmacology, Faculty of Medicine, Osaka Medical College, Osaka 569-8686, Japan
| | - Shinya Yamanaka
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Masayo Takahashi
- Lab of Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Kiichiro Tomoda
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Department of Pharmacology, Faculty of Medicine, Osaka Medical College, Osaka 569-8686, Japan.
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32
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Li S, Zheng EB, Zhao L, Liu S. Nonreciprocal and Conditional Cooperativity Directs the Pioneer Activity of Pluripotency Transcription Factors. Cell Rep 2019; 28:2689-2703.e4. [PMID: 31484078 PMCID: PMC6750763 DOI: 10.1016/j.celrep.2019.07.103] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/24/2019] [Accepted: 07/26/2019] [Indexed: 01/02/2023] Open
Abstract
Cooperative binding of transcription factors (TFs) to chromatin orchestrates gene expression programming and cell fate specification. However, the biophysical principles of TF cooperativity remain incompletely understood. Here we use single-molecule fluorescence microscopy to study the partnership between Sox2 and Oct4, two core members of the pluripotency gene regulatory network. We find that the ability of Sox2 to target DNA inside nucleosomes is strongly affected by the translational and rotational positioning of its binding motif. In contrast, Oct4 can access nucleosomal sites with equal capacities. Furthermore, the Sox2-Oct4 pair displays nonreciprocal cooperativity, with Oct4 modulating interaction of Sox2 with the nucleosome but not vice versa. Such cooperativity is conditional upon the composite motif's residing at specific nucleosomal locations. These results reveal that pioneer factors possess distinct chromatin-binding properties and suggest that the same set of TFs can differentially regulate gene activities on the basis of their motif positions in the nucleosomal context.
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Affiliation(s)
- Sai Li
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY 10065, USA
| | - Eric Bo Zheng
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY 10065, USA.
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NF-YA transcriptionally activates the expression of SOX2 in cervical cancer stem cells. PLoS One 2019; 14:e0215494. [PMID: 31365524 PMCID: PMC6668781 DOI: 10.1371/journal.pone.0215494] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 07/08/2019] [Indexed: 01/06/2023] Open
Abstract
Roles for SOX2 have been extensively studied in several types of cancer, including colorectal cancer, glioblastoma and breast cancer, with particular emphasis placed on the roles of SOX2 in cancer stem cell. Our previous study identified SOX2 as a marker in cervical cancer stem cells driven by a full promoter element of SOX2 EGFP reporter. Here, dual-luciferase reporter and mutagenesis analyses were employed, identifying key cis-elements in the SOX2 promoter, including binding sites for SOX2, OCT4 and NF-YA factors in SOX2 promoter. Mutagenesis analysis provided additional evidence to show that one high affinity-binding domain CCAAT box was precisely recognized and bound by the transcription factor NF-YA. Furthermore, overexpression of NF-YA in primitive cervical cancer cells SiHa and C33A significantly activated the transcription and the protein expression of SOX2. Collectively, our data identified NF-YA box CCAAT as a key cis-element in the SOX2 promoter, suggesting that NF-YA is a potent cellular regulator in the maintenance of SOX2-positive cervical cancer stem cell by specific transcriptional activation of SOX2.
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Cuyàs E, Gumuzio J, Lozano-Sánchez J, Carreras D, Verdura S, Llorach-Parés L, Sanchez-Martinez M, Selga E, Pérez GJ, Scornik FS, Brugada R, Bosch-Barrera J, Segura-Carretero A, Martin ÁG, Encinar JA, Menendez JA. Extra Virgin Olive Oil Contains a Phenolic Inhibitor of the Histone Demethylase LSD1/KDM1A. Nutrients 2019; 11:nu11071656. [PMID: 31331073 PMCID: PMC6683035 DOI: 10.3390/nu11071656] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 12/12/2022] Open
Abstract
The lysine-specific histone demethylase 1A (LSD1) also known as lysine (K)-specific demethylase 1A (KDM1A) is a central epigenetic regulator of metabolic reprogramming in obesity-associated diseases, neurological disorders, and cancer. Here, we evaluated the ability of oleacein, a biophenol secoiridoid naturally present in extra virgin olive oil (EVOO), to target LSD1. Molecular docking and dynamic simulation approaches revealed that oleacein could target the binding site of the LSD1 cofactor flavin adenosine dinucleotide with high affinity and at low concentrations. At higher concentrations, oleacein was predicted to target the interaction of LSD1 with histone H3 and the LSD1 co-repressor (RCOR1/CoREST), likely disturbing the anchorage of LSD1 to chromatin. AlphaScreen-based in vitro assays confirmed the ability of oleacein to act as a direct inhibitor of recombinant LSD1, with an IC50 as low as 2.5 μmol/L. Further, oleacein fully suppressed the expression of the transcription factor SOX2 (SEX determining Region Y-box 2) in cancer stem-like and induced pluripotent stem (iPS) cells, which specifically occurs under the control of an LSD1-targeted distal enhancer. Conversely, oleacein failed to modify ectopic SOX2 overexpression driven by a constitutive promoter. Overall, our findings provide the first evidence that EVOO contains a naturally occurring phenolic inhibitor of LSD1, and support the use of oleacein as a template to design new secoiridoid-based LSD1 inhibitors.
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Affiliation(s)
- Elisabet Cuyàs
- ProCURE (Program Against Cancer Therapeutic Resistance), Metabolism & Cancer Group, Catalan Institute of Oncology, 17007 Girona, Spain
- Girona Biomedical Research Institute (IDIBGI), 17190 Girona, Spain
| | | | - Jesús Lozano-Sánchez
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, 18071 Granada, Spain
- Research and Development Functional Food Centre (CIDAF), PTS Granada, 18100 Granada, Spain
| | - David Carreras
- Girona Biomedical Research Institute (IDIBGI), 17190 Girona, Spain
- Cardiovascular Genetics Centre, Department of Medical Sciences, University of Girona, 17071 Girona, Spain
| | - Sara Verdura
- ProCURE (Program Against Cancer Therapeutic Resistance), Metabolism & Cancer Group, Catalan Institute of Oncology, 17007 Girona, Spain
- Girona Biomedical Research Institute (IDIBGI), 17190 Girona, Spain
| | | | | | - Elisabet Selga
- Cardiovascular Genetics Centre, Department of Medical Sciences, University of Girona, 17071 Girona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
- Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), 08500 Vic, Spain
| | - Guillermo J Pérez
- Cardiovascular Genetics Centre, Department of Medical Sciences, University of Girona, 17071 Girona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Fabiana S Scornik
- Cardiovascular Genetics Centre, Department of Medical Sciences, University of Girona, 17071 Girona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Ramon Brugada
- Girona Biomedical Research Institute (IDIBGI), 17190 Girona, Spain
- Cardiovascular Genetics Centre, Department of Medical Sciences, University of Girona, 17071 Girona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
- Dr. Josep Trueta Hospital of Girona, 17007 Girona, Spain
| | - Joaquim Bosch-Barrera
- Girona Biomedical Research Institute (IDIBGI), 17190 Girona, Spain
- Medical Oncology, Catalan Institute of Oncology (ICO), 17007 Girona, Spain
- Department of Medical Sciences, Medical School University of Girona, 17071 Girona, Spain
| | - Antonio Segura-Carretero
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, 18071 Granada, Spain
- Research and Development Functional Food Centre (CIDAF), PTS Granada, 18100 Granada, Spain
| | | | - José Antonio Encinar
- Institute of Research, Development and Innovation in Biotechnology of Elche (IDiBE) and Molecular and Cell Biology Institute (IBMC), Miguel Hernández University (UMH), 03202 Elche, Spain
| | - Javier A Menendez
- ProCURE (Program Against Cancer Therapeutic Resistance), Metabolism & Cancer Group, Catalan Institute of Oncology, 17007 Girona, Spain.
- Girona Biomedical Research Institute (IDIBGI), 17190 Girona, Spain.
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35
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Alexander JM, Guan J, Li B, Maliskova L, Song M, Shen Y, Huang B, Lomvardas S, Weiner OD. Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity. eLife 2019; 8:e41769. [PMID: 31124784 PMCID: PMC6534382 DOI: 10.7554/elife.41769] [Citation(s) in RCA: 191] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 05/08/2019] [Indexed: 12/13/2022] Open
Abstract
Enhancers are important regulatory elements that can control gene activity across vast genetic distances. However, the underlying nature of this regulation remains obscured because it has been difficult to observe in living cells. Here, we visualize the spatial organization and transcriptional output of the key pluripotency regulator Sox2 and its essential enhancer Sox2 Control Region (SCR) in living embryonic stem cells (ESCs). We find that Sox2 and SCR show no evidence of enhanced spatial proximity and that spatial dynamics of this pair is limited over tens of minutes. Sox2 transcription occurs in short, intermittent bursts in ESCs and, intriguingly, we find this activity demonstrates no association with enhancer proximity, suggesting that direct enhancer-promoter contacts do not drive contemporaneous Sox2 transcription. Our study establishes a framework for interrogation of enhancer function in living cells and supports an unexpected mechanism for enhancer control of Sox2 expression that uncouples transcription from enhancer proximity.
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Affiliation(s)
- Jeffrey M Alexander
- Cardiovascular Research InstituteUniversity of California, San FranciscoSan FranciscoUnited States
| | - Juan Guan
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoUnited States
| | - Bingkun Li
- Institute for Human GeneticsUniversity of California, San FranciscoSan FranciscoUnited States
| | - Lenka Maliskova
- Institute for Human GeneticsUniversity of California, San FranciscoSan FranciscoUnited States
| | - Michael Song
- Institute for Human GeneticsUniversity of California, San FranciscoSan FranciscoUnited States
- Pharmaceutical Sciences and Pharmacogenomics Graduate ProgramUniversity of California, San FranciscoSan FranciscoUnited States
| | - Yin Shen
- Institute for Human GeneticsUniversity of California, San FranciscoSan FranciscoUnited States
- Pharmaceutical Sciences and Pharmacogenomics Graduate ProgramUniversity of California, San FranciscoSan FranciscoUnited States
- Department of NeurologyUniversity of California, San FranciscoSan FranciscoUnited States
| | - Bo Huang
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and BiophysicsUniversity of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Stavros Lomvardas
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew York CityUnited States
- Mortimer B Zuckerman Mind Brain and Behavior InstituteColumbia UniversityNew York CityUnited States
| | - Orion D Weiner
- Cardiovascular Research InstituteUniversity of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and BiophysicsUniversity of California, San FranciscoSan FranciscoUnited States
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36
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Sybirna A, Wong FCK, Surani MA. Genetic basis for primordial germ cells specification in mouse and human: Conserved and divergent roles of PRDM and SOX transcription factors. Curr Top Dev Biol 2019; 135:35-89. [PMID: 31155363 DOI: 10.1016/bs.ctdb.2019.04.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Primordial germ cells (PGCs) are embryonic precursors of sperm and egg that pass on genetic and epigenetic information from one generation to the next. In mammals, they are induced from a subset of cells in peri-implantation epiblast by BMP signaling from the surrounding tissues. PGCs then initiate a unique developmental program that involves comprehensive epigenetic resetting and repression of somatic genes. This is orchestrated by a set of signaling molecules and transcription factors that promote germ cell identity. Here we review significant findings on mammalian PGC biology, in particular, the genetic basis for PGC specification in mice and human, which has revealed an evolutionary divergence between the two species. We discuss the importance and potential basis for these differences and focus on several examples to illustrate the conserved and divergent roles of critical transcription factors in mouse and human germline.
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Affiliation(s)
- Anastasiya Sybirna
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom; Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, United Kingdom; Wellcome Trust/Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.
| | - Frederick C K Wong
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom; Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, United Kingdom
| | - M Azim Surani
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom; Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, United Kingdom; Wellcome Trust/Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.
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37
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PHF20L1 antagonizes SOX2 proteolysis triggered by the MLL1/WDR5 complexes. J Transl Med 2018; 98:1627-1641. [PMID: 30089852 DOI: 10.1038/s41374-018-0106-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 05/25/2018] [Accepted: 06/13/2018] [Indexed: 01/02/2023] Open
Abstract
Transcriptional factor SOX2 regulates stem cell pluripotency, cell differentiation and tumorigenesis. As a key factor, the expression of SOX2 is tightly regulated at transcriptional and post-translational levels. However, the underlying mechanism of SOX2 protein stability remains to be elucidated. Here we show that the histone-lysine N-methyltransferase MLL1/WDR5 complexes physically interact with SOX2 and evoke SOX2 proteolysis, possibly through methylation on a potential site lysine 42 (K42). Small interfering RNA (siRNA)-mediated gene silencing of the components of the MLL1/WDR5 complexes WDR5, MLL1, RBBP5, and ASH2L lead to the accumulation of SOX2, while forced expression of WDR5 promotes SOX2 ubiquitination and proteolysis. Conversely, PHD finger protein 20-like protein 1 (PHF20L1) associates with SOX2, antagonizes SOX2 ubiquitination and the sequential degradation induced by the MLL1/WDR5 complexes. RNA interferences of PHF20L1 promote the degradation of SOX2, while forced expression of PHF20L1 stabilizes SOX2. Co-silencing of MLL1/WDR5 components and PHF20L1 preclude degradation of SOX2 induced by knockdown of PHF20L1. Moreover, co-expression of PHF20L1 and WDR5 prevent ubiquitination of SOX2 triggered by WDR5 over-expression. However, SOX2 mutant K42R is non-sensitive to the MLL1/WDR5 complexes or PHF20L1. In addition, PHF20L1 may regulate the stability of SOX2 through its malignant brain tumor (MBT) domain, since the degradation of SOX2 is accelerated by UNC1215 and UNC669, inhibitors that bind to the MBT domain. Furthermore, abundant expression of SOX2 is highly correlated to immature ovarian teratoma. Loss of PHF20L1 weakened the tumor initiation ability of PA-1 cells while ablation of MLL1 promoted the growth of tumors. Thus, our studies reveal an antagonistic mechanism by which the protein stability of SOX2 is regulated by the MLL1/WDR5 complexes and PHF20L1, possibly through methylation of SOX2 protein, and provide a novel perspective on SOX2-positive cancer treatment.
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38
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Knauss JL, Miao N, Kim SN, Nie Y, Shi Y, Wu T, Pinto HB, Donohoe ME, Sun T. Long noncoding RNA Sox2ot and transcription factor YY1 co-regulate the differentiation of cortical neural progenitors by repressing Sox2. Cell Death Dis 2018; 9:799. [PMID: 30038234 PMCID: PMC6056501 DOI: 10.1038/s41419-018-0840-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 06/04/2018] [Accepted: 06/18/2018] [Indexed: 01/08/2023]
Abstract
Long noncoding RNAs (lncRNAs) are emerging as key regulators of crucial cellular processes. However, the molecular mechanisms of many lncRNA functions remain uncharacterized. Sox2ot is an evolutionarily conserved lncRNA that transcriptionally overlaps the pluripotency gene Sox2, which maintains the stemness of embryonic stem cells and tissue-specific stem cells. Here, we show that Sox2ot is expressed in the developing mouse cerebral cortex, where it represses neural progenitor (NP) proliferation and promotes neuronal differentiation. Sox2ot negatively regulates self-renewal of neural stem cells, and is predominately expressed in the nucleus and inhibits Sox2 levels. Sox2ot forms a physical interaction with a multifunctional transcriptional regulator YY1, which binds several CpG islands in the Sox2 locus in a Sox2ot-dependent manner. Similar to Sox2ot, YY1 represses NP expansion in vivo. These results demonstrate a regulatory role of Sox2ot in promoting cortical neurogenesis, possibly by repressing Sox2 expression in NPs, through interacting with YY1.
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Affiliation(s)
- Jennifer L Knauss
- Department of Cell and Developmental Biology, Cornell University Weill Medical College, 1300 York Avenue, Box 60, New York, NY, 10065, USA
| | - Nan Miao
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, China, 361021
| | - Seung-Nam Kim
- Department of Cell and Developmental Biology, Cornell University Weill Medical College, 1300 York Avenue, Box 60, New York, NY, 10065, USA
- College of Korean Medicine, Dongguk University, Ilsandonggu, Goyangsi, 10326, Gyeonggido, Korea
| | - Yanzhen Nie
- School of Life Sciences and Technology, Shanghai Jiao Tong University, Shanghai, China, 200240
| | - Yuelin Shi
- School of Life Sciences and Technology, Shanghai Jiao Tong University, Shanghai, China, 200240
| | - Tao Wu
- Burke Medical Research Institute, 785 Mamaroneck Avenue, White Plains, NY, 10605, USA
- Department of Neuroscience, Department of Cell and Developmental Biology, Cornell University Weill Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Hugo Borges Pinto
- Burke Medical Research Institute, 785 Mamaroneck Avenue, White Plains, NY, 10605, USA
- Department of Neuroscience, Department of Cell and Developmental Biology, Cornell University Weill Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Mary E Donohoe
- Burke Medical Research Institute, 785 Mamaroneck Avenue, White Plains, NY, 10605, USA
- Department of Neuroscience, Department of Cell and Developmental Biology, Cornell University Weill Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Tao Sun
- Department of Cell and Developmental Biology, Cornell University Weill Medical College, 1300 York Avenue, Box 60, New York, NY, 10065, USA.
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, China, 361021.
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39
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Gas41 links histone acetylation to H2A.Z deposition and maintenance of embryonic stem cell identity. Cell Discov 2018; 4:28. [PMID: 29900004 PMCID: PMC5995911 DOI: 10.1038/s41421-018-0027-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 01/07/2023] Open
Abstract
The histone variant H2A.Z is essential for maintaining embryonic stem cell (ESC) identity in part by keeping developmental genes in a poised bivalent state. However, how H2A.Z is deposited into the bivalent domains remains unknown. In mammals, two chromatin remodeling complexes, Tip60/p400 and SRCAP, exchange the canonical histone H2A for H2A.Z in the chromatin. Here we show that Glioma Amplified Sequence 41 (Gas41), a shared subunit of the two H2A.Z-depositing complexes, functions as a reader of histone lysine acetylation and recruits Tip60/p400 and SRCAP to deposit H2A.Z into specific chromatin regions including bivalent domains. The YEATS domain of Gas41 bound to acetylated histone H3K27 and H3K14 both in vitro and in cells. The crystal structure of the Gas41 YEATS domain in complex with the H3K27ac peptide revealed that, similar to the AF9 and ENL YEATS domains, Gas41 YEATS forms a serine-lined aromatic cage for acetyllysine recognition. Consistently, mutations in the aromatic residues of the Gas41 YEATS domain abrogated the interaction. In mouse ESCs, knockdown of Gas41 led to flattened morphology of ESC colonies, as the result of derepression of differentiation genes. Importantly, the abnormal morphology was rescued by expressing wild-type Gas41, but not the YEATS domain mutated counterpart that does not recognize histone acetylation. Mechanically, we found that Gas41 depletion led to reduction of H2A.Z levels and a concomitant reduction of H3K27me3 levels on bivalent domains. Together, our study reveals an essential role of the Gas41 YEATS domain in linking histone acetylation to H2A.Z deposition and maintenance of ESC identity.
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40
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Malik V, Zimmer D, Jauch R. Diversity among POU transcription factors in chromatin recognition and cell fate reprogramming. Cell Mol Life Sci 2018; 75:1587-1612. [PMID: 29335749 PMCID: PMC11105716 DOI: 10.1007/s00018-018-2748-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 12/23/2017] [Accepted: 01/08/2018] [Indexed: 12/28/2022]
Abstract
The POU (Pit-Oct-Unc) protein family is an evolutionary ancient group of transcription factors (TFs) that bind specific DNA sequences to direct gene expression programs. The fundamental importance of POU TFs to orchestrate embryonic development and to direct cellular fate decisions is well established, but the molecular basis for this activity is insufficiently understood. POU TFs possess a bipartite 'two-in-one' DNA binding domain consisting of two independently folding structural units connected by a poorly conserved and flexible linker. Therefore, they represent a paradigmatic example to study the molecular basis for the functional versatility of TFs. Their modular architecture endows POU TFs with the capacity to accommodate alternative composite DNA sequences by adopting different quaternary structures. Moreover, associations with partner proteins crucially influence the selection of their DNA binding sites. The plentitude of DNA binding modes confers the ability to POU TFs to regulate distinct genes in the context of different cellular environments. Likewise, different binding modes of POU proteins to DNA could trigger alternative regulatory responses in the context of different genomic locations of the same cell. Prominent POU TFs such as Oct4, Brn2, Oct6 and Brn4 are not only essential regulators of development but have also been successfully employed to reprogram somatic cells to pluripotency and neural lineages. Here we review biochemical, structural, genomic and cellular reprogramming studies to examine how the ability of POU TFs to select regulatory DNA, alone or with partner factors, is tied to their capacity to epigenetically remodel chromatin and drive specific regulatory programs that give cells their identities.
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Affiliation(s)
- Vikas Malik
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 511436, China
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Dennis Zimmer
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 511436, China
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Ralf Jauch
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 511436, China.
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
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41
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Adult Neural Stem Cells: Basic Research and Production Strategies for Neurorestorative Therapy. Stem Cells Int 2018; 2018:4835491. [PMID: 29760724 PMCID: PMC5901847 DOI: 10.1155/2018/4835491] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/01/2018] [Indexed: 12/24/2022] Open
Abstract
Over many decades, constructing genetically and phenotypically stable lines of neural stem cells (NSC) for clinical purposes with the aim of restoring irreversibly lost functions of nervous tissue has been one of the major goals for multiple research groups. The unique ability of stem cells to maintain their own pluripotent state even in the adult body has made them into the choice object of study. With the development of the technology for induced pluripotent stem cells (iPSCs) and direct transdifferentiation of somatic cells into the desired cell type, the initial research approaches based on the use of allogeneic NSCs from embryonic or fetal nervous tissue are gradually becoming a thing of the past. This review deals with basic molecular mechanisms for maintaining the pluripotent state of embryonic/induced stem and reprogrammed somatic cells, as well as with currently existing reprogramming strategies. The focus is on performing direct reprogramming while bypassing the stage of iPSCs which is known for genetic instability and an increased risk of tumorigenesis. A detailed description of various protocols for obtaining reprogrammed neural cells used in the therapy of the nervous system pathology is also provided.
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42
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Wuebben EL, Rizzino A. The dark side of SOX2: cancer - a comprehensive overview. Oncotarget 2018; 8:44917-44943. [PMID: 28388544 PMCID: PMC5546531 DOI: 10.18632/oncotarget.16570] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/16/2017] [Indexed: 12/14/2022] Open
Abstract
The pluripotency-associated transcription factor SOX2 is essential during mammalian embryogenesis and later in life, but SOX2 expression can also be highly detrimental. Over the past 10 years, SOX2 has been shown to be expressed in at least 25 different cancers. This review provides a comprehensive overview of the roles of SOX2 in cancer and focuses on two broad topics. The first delves into the expression and function of SOX2 in cancer focusing on the connection between SOX2 levels and tumor grade as well as patient survival. As part of this discussion, we address the developing connection between SOX2 expression and tumor drug resistance. We also call attention to an under-appreciated property of SOX2, its levels in actively proliferating tumor cells appear to be optimized to maximize tumor growth - too little or too much SOX2 dramatically alters tumor growth. The second topic of this review focuses on the exquisite array of molecular mechanisms that control the expression and transcriptional activity of SOX2. In addition to its complex regulation at the transcriptional level, SOX2 expression and activity are controlled carefully by microRNAs, long non-coding RNAs, and post-translational modifications. In the Conclusion and Future Perspectives section, we point out that there are still important unanswered questions. Addressing these questions is expected to lead to new insights into the functions of SOX2 in cancer, which will help design novels strategies for more effectively treating some of the most deadly cancers.
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Affiliation(s)
- Erin L Wuebben
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Angie Rizzino
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA.,Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
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43
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Akberdin IR, Omelyanchuk NA, Fadeev SI, Leskova NE, Oschepkova EA, Kazantsev FV, Matushkin YG, Afonnikov DA, Kolchanov NA. Pluripotency gene network dynamics: System views from parametric analysis. PLoS One 2018; 13:e0194464. [PMID: 29596533 PMCID: PMC5875786 DOI: 10.1371/journal.pone.0194464] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/02/2018] [Indexed: 01/06/2023] Open
Abstract
Multiple experimental data demonstrated that the core gene network orchestrating self-renewal and differentiation of mouse embryonic stem cells involves activity of Oct4, Sox2 and Nanog genes by means of a number of positive feedback loops among them. However, recent studies indicated that the architecture of the core gene network should also incorporate negative Nanog autoregulation and might not include positive feedbacks from Nanog to Oct4 and Sox2. Thorough parametric analysis of the mathematical model based on this revisited core regulatory circuit identified that there are substantial changes in model dynamics occurred depending on the strength of Oct4 and Sox2 activation and molecular complexity of Nanog autorepression. The analysis showed the existence of four dynamical domains with different numbers of stable and unstable steady states. We hypothesize that these domains can constitute the checkpoints in a developmental progression from naïve to primed pluripotency and vice versa. During this transition, parametric conditions exist, which generate an oscillatory behavior of the system explaining heterogeneity in expression of pluripotent and differentiation factors in serum ESC cultures. Eventually, simulations showed that addition of positive feedbacks from Nanog to Oct4 and Sox2 leads mainly to increase of the parametric space for the naïve ESC state, in which pluripotency factors are strongly expressed while differentiation ones are repressed.
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Affiliation(s)
- Ilya R. Akberdin
- Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
- San Diego State University, San Diego, CA, United States of America
| | - Nadezda A. Omelyanchuk
- Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Stanislav I. Fadeev
- Novosibirsk State University, Novosibirsk, Russia
- Sobolev Institute of Mathematics SB RAS, Novosibirsk, Russia
| | - Natalya E. Leskova
- Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Evgeniya A. Oschepkova
- Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Fedor V. Kazantsev
- Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Yury G. Matushkin
- Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Dmitry A. Afonnikov
- Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Nikolay A. Kolchanov
- Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
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44
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Abstract
Tissue-specific transcription factors primarily act to define the phenotype of the cell. The power of a single transcription factor to alter cell fate is often minimal, as seen in gain-of-function analyses, but when multiple transcription factors cooperate synergistically it potentiates their ability to induce changes in cell fate. By contrast, transcription factor function is often dispensable in the maintenance of cell phenotype, as is evident in loss-of-function assays. Why does this phenomenon, commonly known as redundancy, occur? Here, I discuss the role that transcription factor networks play in collaboratively regulating stem cell fate and differentiation by providing multiple explanations for their functional redundancy.
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Affiliation(s)
- Hitoshi Niwa
- Department of Pluripotent Stem Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
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45
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High Myc expression and transcription activity underlies intra-tumoral heterogeneity in triple-negative breast cancer. Oncotarget 2018; 8:28101-28115. [PMID: 28427212 PMCID: PMC5438634 DOI: 10.18632/oncotarget.15891] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 02/21/2017] [Indexed: 01/11/2023] Open
Abstract
We have previously identified a novel intra-tumoral dichotomy in triple-negative breast cancer (TNBC) based on the differential responsiveness to a reporter containing the Sox2 regulatory region-2 (SRR2), with reporter responsive (RR) cells being more stem-like than reporter unresponsive (RU) cells. Using bioinformatics, we profiled the protein-DNA binding motifs of SRR2 and identified Myc as one of the potential transcription factors driving SRR2 activity. In support of its role, Myc was found to be highly expressed in RR cells as compared to RU cells. Enforced expression of MYC in RU cells resulted in a significant increase in SRR2 activity, Myc-DNA binding, proportion of cellsexpressing CD44+/CD24-, chemoresistance and mammosphere formation. Knockdown of Myc using siRNA in RR cells led to the opposite effects. We also found evidence that the relatively high ERK activation in RR cells contributes to their high expression of Myc and stem-like features. Using confocal microscopy and patient samples, we found a co-localization between Myc and CD44 in the same cell population. Lastly, a high proportion of Myc-positive cells in tumors significantly correlated with a short patient survival. In conclusion, inhibition of the MAPK/ERK/Myc axis may be an effective approach in eliminating stem-like cells in TNBC.
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46
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Kobayashi K, Khan A, Ikeda M, Nakamoto A, Maekawa M, Yamasu K. In vitro analysis of the transcriptional regulatory mechanism of zebrafish pou5f3. Exp Cell Res 2018; 364:28-41. [PMID: 29366809 DOI: 10.1016/j.yexcr.2018.01.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 12/11/2017] [Accepted: 01/17/2018] [Indexed: 12/18/2022]
Abstract
Zebrafish pou5f3 (previously named pou2), a close homologue of mouse Oct4, encodes a PouV-family transcription factor. pou5f3 has been implicated in diverse aspects of developmental regulation during embryogenesis. In the present study, we addressed the molecular function of Pou5f3 as a transcriptional regulator and the mechanism by which pou5f3 expression is transcriptionally regulated. We examined the influence of effector genes on the expression of the luciferase gene under the control of the upstream 2.1-kb regulatory DNA of pou5f3 (Luc-2.2) in HEK293T and P19 cells. We first confirmed that Pou5f3 functions as a transcriptional activator both in cultured cells and embryos, which confirmed autoregulation of pou5f3 in embryos. It was further shown that Luc-2.2 was activated synergistically by pou5f3 and sox3, which is similar to the co-operative activity of Oct4 and Sox2 in mice, although synergy between pou5f3 and sox2 was less obvious in this zebrafish system. The effects of pou5f3 deletion constructs on the regulation of Luc-2.2 expression revealed different roles for the three subregions of the N-terminal region in Pou5f3 in terms of its regulatory functions and co-operativity with Sox3. Electrophoretic mobility shift assays confirmed that Pou5f3 and Sox3 proteins specifically bind to adjacent sites in the 2.1-kb DNA and that there is an interaction between the two proteins. The synergy with sox3 was unique to pou5f3-the other POU factor genes examined did not show such synergy in Luc-2.2 regulation. Finally, functional interaction was observed between pou5f3 and sox3 in embryos in terms of the regulation of dorsoventral patterning and convergent extension movement. These findings together demonstrate co-operative functions of pou5f3 and sox3, which are frequently coexpressed in early embryos, in the regulation of early development.
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Affiliation(s)
- Kana Kobayashi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Alam Khan
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Masaaki Ikeda
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Andrew Nakamoto
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Masato Maekawa
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Kyo Yamasu
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan; Saitama University Brain Science Institute, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan.
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47
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Corsinotti A, Wong FC, Tatar T, Szczerbinska I, Halbritter F, Colby D, Gogolok S, Pantier R, Liggat K, Mirfazeli ES, Hall-Ponsele E, Mullin NP, Wilson V, Chambers I. Distinct SoxB1 networks are required for naïve and primed pluripotency. eLife 2017; 6:27746. [PMID: 29256862 PMCID: PMC5758114 DOI: 10.7554/elife.27746] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 12/18/2017] [Indexed: 12/20/2022] Open
Abstract
Deletion of Sox2 from mouse embryonic stem cells (ESCs) causes trophectodermal differentiation. While this can be prevented by enforced expression of the related SOXB1 proteins, SOX1 or SOX3, the roles of SOXB1 proteins in epiblast stem cell (EpiSC) pluripotency are unknown. Here, we show that Sox2 can be deleted from EpiSCs with impunity. This is due to a shift in the balance of SoxB1 expression in EpiSCs, which have decreased Sox2 and increased Sox3 compared to ESCs. Consistent with functional redundancy, Sox3 can also be deleted from EpiSCs without eliminating self-renewal. However, deletion of both Sox2 and Sox3 prevents self-renewal. The overall SOXB1 levels in ESCs affect differentiation choices: neural differentiation of Sox2 heterozygous ESCs is compromised, while increased SOXB1 levels divert the ESC to EpiSC transition towards neural differentiation. Therefore, optimal SOXB1 levels are critical for each pluripotent state and for cell fate decisions during exit from naïve pluripotency.
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Affiliation(s)
- Andrea Corsinotti
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland.,Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Frederick Ck Wong
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Tülin Tatar
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Iwona Szczerbinska
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Florian Halbritter
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Douglas Colby
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Sabine Gogolok
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Raphaël Pantier
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Kirsten Liggat
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Elham S Mirfazeli
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Elisa Hall-Ponsele
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Nicholas P Mullin
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Valerie Wilson
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Ian Chambers
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
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48
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Tatè R, Zona E, De Cicco R, Trotta V, Urciuoli M, Morelli A, Baiano S, Carnuccio R, Fuggetta MP, Morelli F. Simvastatin inhibits the expression of stemness-related genes and the metastatic invasion of human cancer cells via destruction of the cytoskeleton. Int J Oncol 2017; 51:1851-1859. [DOI: 10.3892/ijo.2017.4158] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/15/2017] [Indexed: 11/06/2022] Open
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49
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Topalovic V, Krstic A, Schwirtlich M, Dolfini D, Mantovani R, Stevanovic M, Mojsin M. Epigenetic regulation of human SOX3 gene expression during early phases of neural differentiation of NT2/D1 cells. PLoS One 2017; 12:e0184099. [PMID: 28886103 PMCID: PMC5590877 DOI: 10.1371/journal.pone.0184099] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 08/17/2017] [Indexed: 01/09/2023] Open
Abstract
Sox3/SOX3 is one of the earliest neural markers in vertebrates. Together with the Sox1/SOX1 and Sox2/SOX2 genes it is implicated in the regulation of stem cell identity. In the present study, we performed the first analysis of epigenetic mechanisms (DNA methylation and histone marks) involved in the regulation of the human SOX3 gene expression during RA-induced neural differentiation of NT2/D1 cells. We show that the promoter of the human SOX3 gene is extremely hypomethylated both in undifferentiated NT2/D1 cells and during the early phases of RA-induced neural differentiation. By employing chromatin immunoprecipitation, we analyze several histone modifications across different regions of the SOX3 gene and their dynamics following initiation of differentiation. In the same timeframe we investigate profiles of selected histone marks on the promoters of human SOX1 and SOX2 genes. We demonstrate differences in histone signatures of SOX1, SOX2 and SOX3 genes. Considering the importance of SOXB1 genes in the process of neural differentiation, the present study contributes to a better understanding of epigenetic mechanisms implicated in the regulation of pluripotency maintenance and commitment towards the neural lineage.
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Affiliation(s)
- Vladanka Topalovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | | | - Marija Schwirtlich
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Diletta Dolfini
- Department of Biosciences, University of Milan, Milan, Italy
| | | | - Milena Stevanovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
- Serbian Academy of Sciences and Arts, Belgrade, Serbia
| | - Marija Mojsin
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
- * E-mail:
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50
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Cyclin-Dependent Kinase-Dependent Phosphorylation of Sox2 at Serine 39 Regulates Neurogenesis. Mol Cell Biol 2017; 37:MCB.00201-17. [PMID: 28584195 DOI: 10.1128/mcb.00201-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 05/25/2017] [Indexed: 01/05/2023] Open
Abstract
Sox2 is known to be important for neuron formation, but the precise mechanism through which it activates a neurogenic program and how this differs from its well-established function in self-renewal of stem cells remain elusive. In this study, we identified a highly conserved cyclin-dependent kinase (Cdk) phosphorylation site on serine 39 (S39) in Sox2. In neural stem cells (NSCs), phosphorylation of S39 enhances the ability of Sox2 to negatively regulate neuronal differentiation, while loss of phosphorylation is necessary for chromatin retention of a truncated form of Sox2 generated during neurogenesis. We further demonstrated that nonphosphorylated cleaved Sox2 specifically induces the expression of proneural genes and promotes neurogenic commitment in vivo Our present study sheds light on how the level of Cdk kinase activity directly regulates Sox2 to tip the balance between self-renewal and differentiation in NSCs.
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