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Kim SK, Seo S, Stein-O'Brien G, Jaishankar A, Ogawa K, Micali N, Luria V, Karger A, Wang Y, Kim H, Hyde TM, Kleinman JE, Voss T, Fertig EJ, Shin JH, Bürli R, Cross AJ, Brandon NJ, Weinberger DR, Chenoweth JG, Hoeppner DJ, Sestan N, Colantuoni C, McKay RD. Individual variation in the emergence of anterior-to-posterior neural fates from human pluripotent stem cells. Stem Cell Reports 2024; 19:1336-1350. [PMID: 39151428 DOI: 10.1016/j.stemcr.2024.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 07/16/2024] [Accepted: 07/16/2024] [Indexed: 08/19/2024] Open
Abstract
Variability between human pluripotent stem cell (hPSC) lines remains a challenge and opportunity in biomedicine. In this study, hPSC lines from multiple donors were differentiated toward neuroectoderm and mesendoderm lineages. We revealed dynamic transcriptomic patterns that delineate the emergence of these lineages, which were conserved across lines, along with individual line-specific transcriptional signatures that were invariant throughout differentiation. These transcriptomic signatures predicted an antagonism between SOX21-driven forebrain fates and retinoic acid-induced hindbrain fates. Replicate lines and paired adult tissue demonstrated the stability of these line-specific transcriptomic traits. We show that this transcriptomic variation in lineage bias had both genetic and epigenetic origins, aligned with the anterior-to-posterior structure of early mammalian development, and was present across a large collection of hPSC lines. These findings contribute to developing systematic analyses of PSCs to define the origin and consequences of variation in the early events orchestrating individual human development.
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Affiliation(s)
- Suel-Kee Kim
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Seungmae Seo
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | | | - Amritha Jaishankar
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Kazuya Ogawa
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Nicola Micali
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Victor Luria
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amir Karger
- IT-Research Computing, Harvard Medical School, Boston, MA 02115, USA
| | - Yanhong Wang
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Hyojin Kim
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Departments of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Departments of Psychiatry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Departments of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Ty Voss
- Division of Preclinical Innovation, Nation Center for Advancing Translational Science, NIH, Bethesda, MD 20892, USA
| | - Elana J Fertig
- Departments of Oncology, Biomedical Engineering, and Applied Mathematics and Statistics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Joo-Heon Shin
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Roland Bürli
- Astra-Zeneca Neuroscience iMED., 141 Portland Street, Cambridge, MA 01239, USA
| | - Alan J Cross
- Astra-Zeneca Neuroscience iMED., 141 Portland Street, Cambridge, MA 01239, USA
| | - Nicholas J Brandon
- Astra-Zeneca Neuroscience iMED., 141 Portland Street, Cambridge, MA 01239, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Departments of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Departments of Psychiatry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Departments of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Joshua G Chenoweth
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Daniel J Hoeppner
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Departments of Genetics, Psychiatry, and Comparative Medicine, Kavli Institute for Neuroscience, Program in Cellular Neuroscience, Neurodegeneration and Repair, Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA.
| | - Carlo Colantuoni
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Departments of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Departments of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Ronald D McKay
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Departments of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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Cao Q, Gao Y, Zhou C, Yan Y, Yu J, Wang P, Zhang B, Sun L. Intervention of epithelial mesenchymal transition against colon cancer cell growth and metastasis based on SOX21/POU4F2/Hedgehog signaling axis. Life Sci 2024; 352:122905. [PMID: 38992573 DOI: 10.1016/j.lfs.2024.122905] [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: 05/05/2024] [Revised: 06/28/2024] [Accepted: 07/06/2024] [Indexed: 07/13/2024]
Abstract
AIMS Colon cancer poses a major threat to human health and a heavy burden on the national economy. As a member of the SOX transcription factor family, SRY-box transcription factor 21 (SOX21) is associated with various cancers, but its mechanism of action in colon cancer remains unclear. This study focused on the molecular mechanisms of transcription factor SOX21 in proliferation and metastasis of colon cancer cells. MAIN METHODS We analyzed SOX21 expression level and its impact on survival in colon cancer patients by bioinformatics analysis. We used public databases for gene correlation, GSEA enrichment analysis. Cell function experiments (colony formation assay, wound healing assay, Transwell migration and invasion assay) were utilized to determine the impact of SOX21 silencing and over-expression on cell proliferation and metastasis. The luciferase reporter assay, CUT&RUN-qPCR assay and Methylation Specific PCR were used to explore SOX21-POU class 4 homeobox 2 (POU4F2) molecular interactions. The molecular mechanisms were verified by Quantitative real-time PCR and Western blot analysis. KEY FINDINGS SOX21 is highly expressed and affects the overall survival of colon cancer patients. SOX21 can attenuates POU4F2 methylation state by binding with it. In addition, this interaction facilitate its transcriptional activation of Hedgehog pathway, mediates epithelial-mesenchymal transition (EMT), consequently promoting the proliferation and metastasis of colon cancer cells. SIGNIFICANCE Our study reveals that SOX21 is an oncogenic molecule and suggests its regulatory role in colon carcinogenesis and progression, providing new insights into the treatment of this disease.
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Affiliation(s)
- Qiaochang Cao
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou 310006, China
| | - Yangyang Gao
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou 310006, China
| | - Chenxi Zhou
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou 310006, China
| | - Yici Yan
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou 310006, China
| | - Jieru Yu
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Peipei Wang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.
| | - Bo Zhang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.
| | - Leitao Sun
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou 310006, China; Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou 310053, China; Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
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3
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Damuth DL, Cunningham DD, Silva EM. Sox21 homeologs autoregulate expression levels to control progression through neurogenesis. Genesis 2024; 62:e23612. [PMID: 39054872 DOI: 10.1002/dvg.23612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 05/29/2024] [Accepted: 06/10/2024] [Indexed: 07/27/2024]
Abstract
The SRY HMG box transcription factor Sox21 plays multiple critical roles in neurogenesis, with its function dependent on concentration and developmental stage. In the allotetraploid Xenopus laevis, there are two homeologs of sox21, namely sox21.S and sox21.L. Previous studies focused on Sox21.S, but its amino acid sequence is divergent, lacking conserved poly-A stretches and bearing more similarity with ancestral homologs. In contrast, Sox21.L shares higher sequence similarity with mouse and chick Sox21. To determine if Sox21.S and Sox21.L have distinct functions, we conducted gain and loss-of-function studies in Xenopus embryos. Our studies revealed that Sox21.S and Sox21.L are functionally redundant, but Sox21.L is more effective at driving changes than Sox21.S. These results also support our earlier findings in ectodermal explants, demonstrating that Sox21 function is dose-dependent. While Sox21 is necessary for primary neuron formation, high levels prevent their formation. Strikingly, these proteins autoregulate, with high levels of Sox21.L reducing sox21.S and sox21.L mRNA levels, and decreased Sox21.S promoting increased expression of sox21.L. Our findings shed light on the intricate concentration-dependent roles of Sox21 homeologs in Xenopus neurogenesis.
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Affiliation(s)
- Dillon L Damuth
- Department of Biology, Georgetown University, Washington, DC, USA
| | | | - Elena M Silva
- Department of Biology, Georgetown University, Washington, DC, USA
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Banerjee D, Bagchi S, Liu Z, Chou HC, Xu M, Sun M, Aloisi S, Vaksman Z, Diskin SJ, Zimmerman M, Khan J, Gryder B, Thiele CJ. Lineage specific transcription factor waves reprogram neuroblastoma from self-renewal to differentiation. Nat Commun 2024; 15:3432. [PMID: 38653778 DOI: 10.1038/s41467-024-47166-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 03/22/2024] [Indexed: 04/25/2024] Open
Abstract
Temporal regulation of super-enhancer (SE) driven transcription factors (TFs) underlies normal developmental programs. Neuroblastoma (NB) arises from an inability of sympathoadrenal progenitors to exit a self-renewal program and terminally differentiate. To identify SEs driving TF regulators, we use all-trans retinoic acid (ATRA) to induce NB growth arrest and differentiation. Time-course H3K27ac ChIP-seq and RNA-seq reveal ATRA coordinated SE waves. SEs that decrease with ATRA link to stem cell development (MYCN, GATA3, SOX11). CRISPR-Cas9 and siRNA verify SOX11 dependency, in vitro and in vivo. Silencing the SOX11 SE using dCAS9-KRAB decreases SOX11 mRNA and inhibits cell growth. Other TFs activate in sequential waves at 2, 4 and 8 days of ATRA treatment that regulate neural development (GATA2 and SOX4). Silencing the gained SOX4 SE using dCAS9-KRAB decreases SOX4 expression and attenuates ATRA-induced differentiation genes. Our study identifies oncogenic lineage drivers of NB self-renewal and TFs critical for implementing a differentiation program.
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Affiliation(s)
- Deblina Banerjee
- Cell & Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | - Sukriti Bagchi
- Cell & Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Zhihui Liu
- Cell & Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Hsien-Chao Chou
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Man Xu
- Cell & Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Ming Sun
- Cell & Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Sara Aloisi
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | | | - Sharon J Diskin
- Department of Pediatrics, Division of Oncology, Perelman School of Medicine, Philadelphia, PA, USA
| | - Mark Zimmerman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Berkley Gryder
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA.
| | - Carol J Thiele
- Cell & Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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5
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Hung YH, Capeling M, Villanueva JW, Kanke M, Shanahan MT, Huang S, Cubitt R, Rinaldi VD, Schimenti JC, Spence JR, Sethupathy P. Integrative genome-scale analyses reveal post-transcriptional signatures of early human small intestinal development in a directed differentiation organoid model. BMC Genomics 2023; 24:641. [PMID: 37884859 PMCID: PMC10601309 DOI: 10.1186/s12864-023-09743-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/14/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are important post-transcriptional gene regulators controlling cellular lineage specification and differentiation during embryonic development, including the gastrointestinal system. However, miRNA-mediated regulatory mechanisms involved in early embryonic development of human small intestine (SI) remains underexplored. To explore candidate roles for miRNAs in prenatal SI lineage specification in humans, we used a multi-omic analysis strategy in a directed differentiation model that programs human pluripotent stem cells toward the SI lineage. RESULTS We leveraged small RNA-seq to define the changing miRNA landscape, and integrated chromatin run-on sequencing (ChRO-seq) and RNA-seq to define genes subject to significant post-transcriptional regulation across the different stages of differentiation. Small RNA-seq profiling revealed temporal dynamics of miRNA signatures across different developmental events of the model, including definitive endoderm formation, SI lineage specification and SI regional patterning. Our multi-omic, integrative analyses showed further that the elevation of miR-182 and reduction of miR-375 are key events during SI lineage specification. We demonstrated that loss of miR-182 leads to an increase in the foregut master marker SOX2. We also used single-cell analyses in murine adult intestinal crypts to support a life-long role for miR-375 in the regulation of Zfp36l2. Finally, we uncovered opposing roles of SMAD4 and WNT signaling in regulating miR-375 expression during SI lineage specification. Beyond the mechanisms highlighted in this study, we also present a web-based application for exploration of post-transcriptional regulation and miRNA-mediated control in the context of early human SI development. CONCLUSION The present study uncovers a novel facet of miRNAs in regulating prenatal SI development. We leveraged multi-omic, systems biology approaches to discover candidate miRNA regulators associated with early SI developmental events in a human organoid model. In this study, we highlighted miRNA-mediated post-transcriptional regulation relevant to the event of SI lineage specification. The candidate miRNA regulators that we identified for the other stages of SI development also warrant detailed characterization in the future.
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Affiliation(s)
- Yu-Han Hung
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Meghan Capeling
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan W Villanueva
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Michael T Shanahan
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Sha Huang
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Rebecca Cubitt
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Vera D Rinaldi
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - John C Schimenti
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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Ju LF, Xu HJ, Yang YG, Yang Y. Omics Views of Mechanisms for Cell Fate Determination in Early Mammalian Development. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:950-961. [PMID: 37075831 PMCID: PMC10928378 DOI: 10.1016/j.gpb.2023.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/18/2023] [Accepted: 03/23/2023] [Indexed: 04/21/2023]
Abstract
During mammalian preimplantation development, a totipotent zygote undergoes several cell cleavages and two rounds of cell fate determination, ultimately forming a mature blastocyst. Along with compaction, the establishment of apicobasal cell polarity breaks the symmetry of an embryo and guides subsequent cell fate choice. Although the lineage segregation of the inner cell mass (ICM) and trophectoderm (TE) is the first symbol of cell differentiation, several molecules have been shown to bias the early cell fate through their inter-cellular variations at much earlier stages, including the 2- and 4-cell stages. The underlying mechanisms of early cell fate determination have long been an important research topic. In this review, we summarize the molecular events that occur during early embryogenesis, as well as the current understanding of their regulatory roles in cell fate decisions. Moreover, as powerful tools for early embryogenesis research, single-cell omics techniques have been applied to both mouse and human preimplantation embryos and have contributed to the discovery of cell fate regulators. Here, we summarize their applications in the research of preimplantation embryos, and provide new insights and perspectives on cell fate regulation.
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Affiliation(s)
- Lin-Fang Ju
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Heng-Ji Xu
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Yun-Gui Yang
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Ying Yang
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
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7
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Attig J, Pape J, Doglio L, Kazachenka A, Ottina E, Young GR, Enfield KS, Aramburu IV, Ng KW, Faulkner N, Bolland W, Papayannopoulos V, Swanton C, Kassiotis G. Human endogenous retrovirus onco-exaptation counters cancer cell senescence through calbindin. J Clin Invest 2023; 133:e164397. [PMID: 37192000 PMCID: PMC10348765 DOI: 10.1172/jci164397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 05/11/2023] [Indexed: 05/17/2023] Open
Abstract
Increased levels and diversity of human endogenous retrovirus (HERV) transcription characterize most cancer types and are linked with disease outcomes. However, the underlying processes are incompletely understood. Here, we show that elevated transcription of HERVH proviruses predicted survival of lung squamous cell carcinoma (LUSC) and identified an isoform of CALB1, encoding calbindin, ectopically driven by an upstream HERVH provirus under the control of KLF5, as the mediator of this effect. HERVH-CALB1 expression was initiated in preinvasive lesions and associated with their progression. Calbindin loss in LUSC cell lines impaired in vitro and in vivo growth and triggered senescence, consistent with a protumor effect. However, calbindin also directly controlled the senescence-associated secretory phenotype (SASP), marked by secretion of CXCL8 and other neutrophil chemoattractants. In established carcinomas, CALB1-negative cancer cells became the dominant source of CXCL8, correlating with neutrophil infiltration and worse prognosis. Thus, HERVH-CALB1 expression in LUSC may display antagonistic pleiotropy, whereby the benefits of escaping senescence early during cancer initiation and clonal competition were offset by the prevention of SASP and protumor inflammation at later stages.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - George Kassiotis
- Retroviral Immunology
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
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8
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Funke K, Einsfelder U, Hansen A, Arévalo L, Schneider S, Nettersheim D, Stein V, Schorle H. Genome-scale CRISPR screen reveals neddylation to contribute to cisplatin resistance of testicular germ cell tumours. Br J Cancer 2023; 128:2270-2282. [PMID: 37024667 PMCID: PMC10241889 DOI: 10.1038/s41416-023-02247-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Type II testicular germ cell tumours (TGCT) are the most prevalent tumours in young men. Patients suffering from cisplatin-resistant TGCTs are facing very poor prognosis demanding novel therapeutic options. Neddylation is a known posttranslational modification mediating many important biological processes, including tumorigenesis. Overactivation of the neddylation pathway promotes carcinogenesis and tumour progression in various entities by inducing proteasomal degradation of tumour suppressors (e.g., p21, p27). METHODS We used a genome-scale CRISPR/Cas9 activation screen to identify cisplatin resistance factors. TGCT cell lines were treated with the neddylation inhibitor (MLN4924)/cisplatin/combination and investigated for changes in viability (XTT assay), apoptosis/cell cycle (flow cytometry) as well as in the transcriptome (3'mRNA sequencing). RESULTS NAE1 overexpression was detected in cisplatin-resistant colonies from the CRISPR screen. Inhibition of neddylation using MLN4924 increased cisplatin cytotoxicity in TGCT cell lines and sensitised cisplatin-resistant cells towards cisplatin. Apoptosis, G2/M-phase cell cycle arrest, γH2A.X/P27 accumulation and mesoderm/endoderm differentiation were observed in TGCT cells, while fibroblast cells were unaffected. CONCLUSIONS We identified overactivation of neddylation as a factor for cisplatin resistance in TGCTs and highlighted the additive effect of NAE1 inhibition by MLN4924 in combination with cisplatin as a novel treatment option for TGCTs.
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Affiliation(s)
- Kai Funke
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Ulf Einsfelder
- Institute of Physiology II, University Hospital Bonn, Bonn, Germany
| | - Aylin Hansen
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Lena Arévalo
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Simon Schneider
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Daniel Nettersheim
- Department of Urology, Urological Research Laboratory, Translational UroOncology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Valentin Stein
- Institute of Physiology II, University Hospital Bonn, Bonn, Germany
| | - Hubert Schorle
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, Bonn, Germany.
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9
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Ding M, Huang W, Liu G, Zhai B, Yan H, Zhang Y. Integration of ATAC-Seq and RNA-Seq reveals FOSL2 drives human liver progenitor-like cell aging by regulating inflammatory factors. BMC Genomics 2023; 24:260. [PMID: 37173651 PMCID: PMC10182660 DOI: 10.1186/s12864-023-09349-7] [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: 11/24/2022] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Human primary hepatocytes (PHCs) are considered to be the best cell source for cell-based therapies for the treatment of end-stage liver disease and acute liver failure. To obtain sufficient and high-quality functional human hepatocytes, we have established a strategy to dedifferentiate human PHCs into expandable hepatocyte-derived liver progenitor-like cells (HepLPCs) through in vitro chemical reprogramming. However, the reduced proliferative capacity of HepLPCs after long-term culture still limits their utility. Therefore, in this study, we attempted to explore the potential mechanism related to the proliferative ability of HepLPCs in vitro culture. RESULTS In this study, analysis of assay for transposase accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) were performed for PHCs, proliferative HepLPCs (pro-HepLPCs) and late-passage HepLPCs (lp-HepLPCs). Genome-wide transcriptional and chromatin accessibility changes during the conversion and long-term culture of HepLPCs were studied. We found that lp-HepLPCs exhibited an aged phenotype characterized by the activation of inflammatory factors. Epigenetic changes were found to be consistent with our gene expression findings, with promoter and distal regions of many inflammatory-related genes showing increased accessibility in the lp-HepLPCs. FOSL2, a member of the AP-1 family, was found to be highly enriched in the distal regions with increased accessibility in lp-HepLPCs. Its depletion attenuated the expression of aging- and senescence-associated secretory phenotype (SASP)-related genes and resulted in a partial improvement of the aging phenotype in lp-HepLPCs. CONCLUSIONS FOSL2 may drive the aging of HepLPCs by regulating inflammatory factors and its depletion may attenuate this phenotypic shift. This study provides a novel and promising approach for the long-term in vitro culture of HepLPCs.
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Affiliation(s)
- Min Ding
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Department of Interventional Oncology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China
| | - Weijian Huang
- Department of Anesthesiology and Critical Care Medicine, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China
| | - Guifen Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Bo Zhai
- Department of Interventional Oncology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China.
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Hexin Yan
- Department of Interventional Oncology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China.
- Department of Anesthesiology and Critical Care Medicine, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China.
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China.
| | - Yong Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
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10
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Eenjes E, Benthem F, Boerema-de Munck A, Buscop-van Kempen M, Tibboel D, Rottier RJ. Distinct roles for SOX2 and SOX21 in differentiation, distribution and maturation of pulmonary neuroendocrine cells. Cell Mol Life Sci 2023; 80:79. [PMID: 36867267 PMCID: PMC9984344 DOI: 10.1007/s00018-023-04731-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 01/27/2023] [Accepted: 02/20/2023] [Indexed: 03/04/2023]
Abstract
Pulmonary neuroendocrine (NE) cells represent a small population in the airway epithelium, but despite this, hyperplasia of NE cells is associated with several lung diseases, such as congenital diaphragmatic hernia and bronchopulmonary dysplasia. The molecular mechanisms causing the development of NE cell hyperplasia remains poorly understood. Previously, we showed that the SOX21 modulates the SOX2-initiated differentiation of epithelial cells in the airways. Here, we show that precursor NE cells start to develop in the SOX2 + SOX21 + airway region and that SOX21 suppresses the differentiation of airway progenitors to precursor NE cells. During development, clusters of NE cells start to form and NE cells mature by expressing neuropeptide proteins, such as CGRP. Deficiency in SOX2 resulted in decreased clustering, while deficiency in SOX21 increased both the numbers of NE ASCL1 + precursor cells early in development, and the number of mature cell clusters at E18.5. In addition, at the end of gestation (E18.5), a number of NE cells in Sox2 heterozygous mice, did not yet express CGRP suggesting a delay in maturation. In conclusion, SOX2 and SOX21 function in the initiation, migration and maturation of NE cells.
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Affiliation(s)
- Evelien Eenjes
- Department of Pediatric Surgery, Erasmus Medical Center-Sophia Children's Hospital, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Floor Benthem
- Department of Pediatric Surgery, Erasmus Medical Center-Sophia Children's Hospital, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Anne Boerema-de Munck
- Department of Pediatric Surgery, Erasmus Medical Center-Sophia Children's Hospital, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Marjon Buscop-van Kempen
- Department of Pediatric Surgery, Erasmus Medical Center-Sophia Children's Hospital, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Dick Tibboel
- Department of Pediatric Surgery, Erasmus Medical Center-Sophia Children's Hospital, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Robbert J Rottier
- Department of Pediatric Surgery, Erasmus Medical Center-Sophia Children's Hospital, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands.
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11
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Eenjes E, Tibboel D, Wijnen RMH, Schnater JM, Rottier RJ. SOX2 and SOX21 in Lung Epithelial Differentiation and Repair. Int J Mol Sci 2022; 23:13064. [PMID: 36361852 PMCID: PMC9657681 DOI: 10.3390/ijms232113064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 12/05/2022] Open
Abstract
The lung originates from the ventral foregut and develops into an intricate branched structure of airways, alveoli, vessels and support tissue. As the lung develops, cells become specified and differentiate into the various cell lineages. This process is controlled by specific transcription factors, such as the SRY-related HMG-box genes SOX2 and SOX21, that are activated or repressed through intrinsic and extrinsic signals. Disturbances in any of these processes during the development of the lung may lead to various pediatric lung disorders, such as Congenital Diaphragmatic Hernia (CDH), Congenital Pulmonary Airway Malformation (CPAM) and Broncho-Pulmonary Dysplasia (BPD). Changes in the composition of the airways and the alveoli may result in reduced respiratory function and eventually lead to chronic lung disorders. In this concise review, we describe different intrinsic and extrinsic cellular processes required for proper differentiation of the epithelium during development and regeneration, and the influence of the microenvironment on this process with special focus on SOX2 and SOX21.
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Affiliation(s)
- Evelien Eenjes
- Department of Pediatric Surgery, Erasmus MC-Sophia Children’s Hospital, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Dick Tibboel
- Department of Pediatric Surgery, Erasmus MC-Sophia Children’s Hospital, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Rene M. H. Wijnen
- Department of Pediatric Surgery, Erasmus MC-Sophia Children’s Hospital, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Johannes Marco Schnater
- Department of Pediatric Surgery, Erasmus MC-Sophia Children’s Hospital, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Robbert J. Rottier
- Department of Pediatric Surgery, Erasmus MC-Sophia Children’s Hospital, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
- Department of Cell Biology, Erasmus MC, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
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12
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New insights into the epitranscriptomic control of pluripotent stem cell fate. Exp Mol Med 2022; 54:1643-1651. [PMID: 36266446 PMCID: PMC9636187 DOI: 10.1038/s12276-022-00824-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/26/2022] [Accepted: 06/01/2022] [Indexed: 12/29/2022] Open
Abstract
Each cell in the human body has a distinguishable fate. Pluripotent stem cells are challenged with a myriad of lineage differentiation options. Defects are more likely to be fatal to stem cells than to somatic cells due to the broad impact of the former on early development. Hence, a detailed understanding of the mechanisms that determine the fate of stem cells is needed. The mechanisms by which human pluripotent stem cells, although not fully equipped with complex chromatin structures or epigenetic regulatory mechanisms, accurately control gene expression and are important to the stem cell field. In this review, we examine the events driving pluripotent stem cell fate and the underlying changes in gene expression during early development. In addition, we highlight the role played by the epitranscriptome in the regulation of gene expression that is necessary for each fate-related event.
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13
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Fan W, Huang T, Wu T, Bai H, Kawahara M, Takahashi M. Zona pellucida removal by acid Tyrode's solution affects pre- and post-implantation development and gene expression in mouse embryos. Biol Reprod 2022; 107:1228-1241. [PMID: 35948000 DOI: 10.1093/biolre/ioac155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/07/2022] [Accepted: 07/26/2022] [Indexed: 11/15/2022] Open
Abstract
The zona pellucida (ZP) plays a crucial role in the process of fertilization to early embryonic development, including cellular arrangement and communication between blastomeres. However, little is known regarding the role of the ZP in pre- and post-implantation embryonic development associated with gene expression. We investigated the effect of zona pellucida removal (ZPR) on pre- and post-implantation development of mouse embryos. After ZPR of 2-cell stage embryos was performed by acid Tyrode's solution, which is commonly used for ZP treatment, compaction occurred earlier in ZP-free (ZF) than ZP-intact (ZI) embryos. In addition, the expression of differentiation-related genes in the inner cell mass (ICM) and trophectoderm (TE) was significantly altered in ZF blastocyst compared with ZI embryos. After embryo transfer, the rate of implantation and live fetuses was lower in ZF embryos than in control embryos, whereas the fetal weight at E17.5 was not different. However, placental weight significantly increased in ZF embryos. RNA-seq analysis of the placenta showed that a total of 473 differentially expressed genes (DEGs) significantly influenced the biological process. The present study suggests that ZPR by acid Tyrode's solution at the 2-cell stage not only disturbs the expression pattern of ICM/TE-related genes but affects the post-implantation development of mouse embryos. Overall, this study provides deeper insight into the role of the ZP during early embryonic development and the viability of post-implantation development.
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Affiliation(s)
- Weihong Fan
- Graduate School of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
| | - Tengda Huang
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Tian Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, P.R. China
| | - Hanako Bai
- Graduate School of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan.,Research Faculty of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
| | - Manabu Kawahara
- Graduate School of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan.,Research Faculty of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
| | - Masashi Takahashi
- Research Faculty of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan.,Graduate School of Global Food Resources, Hokkaido University, Hokkaido 060-8589, Japan
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14
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Regan JL, Schumacher D, Staudte S, Steffen A, Lesche R, Toedling J, Jourdan T, Haybaeck J, Golob-Schwarzl N, Mumberg D, Henderson D, Győrffy B, Regenbrecht CR, Keilholz U, Schäfer R, Lange M. Identification of a neural development gene expression signature in colon cancer stem cells reveals a role for EGR2 in tumorigenesis. iScience 2022; 25:104498. [PMID: 35720265 PMCID: PMC9204726 DOI: 10.1016/j.isci.2022.104498] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/28/2022] [Accepted: 05/26/2022] [Indexed: 11/12/2022] Open
Abstract
Recent evidence demonstrates that colon cancer stem cells (CSCs) can generate neurons that synapse with tumor innervating fibers required for tumorigenesis and disease progression. Greater understanding of the mechanisms that regulate CSC driven tumor neurogenesis may therefore lead to more effective treatments. RNA-sequencing analyses of ALDHPositive CSCs from colon cancer patient-derived organoids (PDOs) and xenografts (PDXs) showed CSCs to be enriched for neural development genes. Functional analyses of genes differentially expressed in CSCs from PDO and PDX models demonstrated the neural crest stem cell (NCSC) regulator EGR2 to be required for tumor growth and to control expression of homebox superfamily embryonic master transcriptional regulator HOX genes and the neural stem cell and master cell fate regulator SOX2. These data support CSCs as the source of tumor neurogenesis and suggest that targeting EGR2 may provide a therapeutic differentiation strategy to eliminate CSCs and block nervous system driven disease progression.
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Affiliation(s)
- Joseph L. Regan
- Bayer AG, Research and Development, Pharmaceuticals, 13342 Berlin, Germany
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Dirk Schumacher
- Laboratory of Molecular Tumor Pathology, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
- German Cancer Consortium (DKTK), DKFZ, 69120 Heidelberg, Germany
| | - Stephanie Staudte
- Bayer AG, Research and Development, Pharmaceuticals, 13342 Berlin, Germany
- German Cancer Consortium (DKTK), DKFZ, 69120 Heidelberg, Germany
- Department of Radiation Oncology and Radiotherapy, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Andreas Steffen
- Bayer AG, Research and Development, Pharmaceuticals, 13342 Berlin, Germany
| | - Ralf Lesche
- Bayer AG, Research and Development, Pharmaceuticals, 13342 Berlin, Germany
- Nuvisan ICB GmbH, 13353 Berlin, Germany
| | - Joern Toedling
- Bayer AG, Research and Development, Pharmaceuticals, 13342 Berlin, Germany
- Nuvisan ICB GmbH, 13353 Berlin, Germany
| | - Thibaud Jourdan
- Bayer AG, Research and Development, Pharmaceuticals, 13342 Berlin, Germany
| | - Johannes Haybaeck
- Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, 6020 Innsbruck, Austria
- Diagnostic and Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, 8036 Graz, Austria
| | - Nicole Golob-Schwarzl
- Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, 6020 Innsbruck, Austria
- Department of Dermatology and Venereology, Medical University of Graz, 8036 Graz, Austria
| | - Dominik Mumberg
- Bayer AG, Research and Development, Pharmaceuticals, 13342 Berlin, Germany
| | - David Henderson
- Bayer AG, Research and Development, Pharmaceuticals, 13342 Berlin, Germany
- Bayer AG, Business Development and Licensing and Open Innovation, Pharmaceuticals, 13342 Berlin, Germany
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, 1094 Budapest, Hungary
- TTK Cancer Biomarker Research Group, Institute of Enzymology, 1117 Budapest, Hungary
| | - Christian R.A. Regenbrecht
- Laboratory of Molecular Tumor Pathology, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
- CELLphenomics GmbH, 13125 Berlin, Germany
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Reinhold Schäfer
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
- Laboratory of Molecular Tumor Pathology, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
- German Cancer Consortium (DKTK), DKFZ, 69120 Heidelberg, Germany
| | - Martin Lange
- Bayer AG, Research and Development, Pharmaceuticals, 13342 Berlin, Germany
- Nuvisan ICB GmbH, 13353 Berlin, Germany
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15
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Cui G, Xu Y, Cao S, Shi K. Inducing somatic cells into pluripotent stem cells is an important platform to study the mechanism of early embryonic development. Mol Reprod Dev 2022; 89:70-85. [PMID: 35075695 DOI: 10.1002/mrd.23559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 12/16/2021] [Accepted: 01/10/2022] [Indexed: 01/24/2023]
Abstract
The early embryonic development starts with the totipotent zygote upon fertilization of differentiated sperm and egg, which undergoes a range of reprogramming and transformation to acquire pluripotency. Induced pluripotent stem cells (iPSCs), a nonclonal technique to produce stem cells, are originated from differentiated somatic cells via accomplishment of cell reprogramming, which shares common reprogramming process with early embryonic development. iPSCs are attractive in recent years due to the potentially significant applications in disease modeling, potential value in genetic improvement of husbandry animal, regenerative medicine, and drug screening. This review focuses on introducing the research advance of both somatic cell reprogramming and early embryonic development, indicating that the mechanisms of iPSCs also shares common features with that of early embryonic development in several aspects, such as germ cell factors, DNA methylation, histone modification, and/or X chromosome inactivation. As iPSCs can successfully avoid ethical concerns that are naturally present in the embryos and/or embryonic stem cells, the practicality of somatic cell reprogramming (iPSCs) could provide an insightful platform to elucidate the mechanisms underlying the early embryonic development.
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Affiliation(s)
- Guina Cui
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, China
| | - Yanwen Xu
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, China
| | - Shuyuan Cao
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, China
| | - Kerong Shi
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, China
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16
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Miguel V, Tituaña J, Herrero JI, Herrero L, Serra D, Cuevas P, Barbas C, Puyol DR, Márquez-Expósito L, Ruiz-Ortega M, Castillo C, Sheng X, Susztak K, Ruiz-Canela M, Salas-Salvadó J, González MAM, Ortega S, Ramos R, Lamas S. Renal tubule Cpt1a overexpression protects from kidney fibrosis by restoring mitochondrial homeostasis. J Clin Invest 2021; 131:140695. [PMID: 33465052 DOI: 10.1172/jci140695] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 01/13/2021] [Indexed: 12/14/2022] Open
Abstract
Chronic kidney disease (CKD) remains a major epidemiological, clinical, and biomedical challenge. During CKD, renal tubular epithelial cells (TECs) present a persistent inflammatory and profibrotic response. Fatty acid oxidation (FAO), the main source of energy for TECs, is reduced in kidney fibrosis and contributes to its pathogenesis. To determine whether gain of function in FAO (FAO-GOF) could protect from fibrosis, we generated a conditional transgenic mouse model with overexpression of the fatty acid shuttling enzyme carnitine palmitoyl-transferase 1A (CPT1A) in TECs. Cpt1a-knockin (CPT1A-KI) mice subjected to 3 models of renal fibrosis (unilateral ureteral obstruction, folic acid nephropathy [FAN], and adenine-induced nephrotoxicity) exhibited decreased expression of fibrotic markers, a blunted proinflammatory response, and reduced epithelial cell damage and macrophage influx. Protection from fibrosis was also observed when Cpt1a overexpression was induced after FAN. FAO-GOF restored oxidative metabolism and mitochondrial number and enhanced bioenergetics, increasing palmitate oxidation and ATP levels, changes that were also recapitulated in TECs exposed to profibrotic stimuli. Studies in patients showed decreased CPT1 levels and increased accumulation of short- and middle-chain acylcarnitines, reflecting impaired FAO in human CKD. We propose that strategies based on FAO-GOF may constitute powerful alternatives to combat fibrosis inherent to CKD.
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Affiliation(s)
- Verónica Miguel
- Program of Physiological and Pathological Processes, Centro de Biología Molecular "Severo Ochoa" (CBMSO) (CSIC-UAM), Madrid, Spain
| | - Jessica Tituaña
- Program of Physiological and Pathological Processes, Centro de Biología Molecular "Severo Ochoa" (CBMSO) (CSIC-UAM), Madrid, Spain
| | - J Ignacio Herrero
- Program of Physiological and Pathological Processes, Centro de Biología Molecular "Severo Ochoa" (CBMSO) (CSIC-UAM), Madrid, Spain
| | - Laura Herrero
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Dolors Serra
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Paula Cuevas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty, Universidad San Pablo-CEU, Boadilla del Monte, Madrid, Spain
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty, Universidad San Pablo-CEU, Boadilla del Monte, Madrid, Spain
| | - Diego Rodríguez Puyol
- Department of Medicine and Medical Specialties, Research Foundation of the University Hospital "Príncipe de Asturias," IRYCIS, Alcalá University, Alcalá de Henares, Madrid, Spain
| | - Laura Márquez-Expósito
- Cellular and Molecular Biology in Renal and Vascular Pathology Laboratory. Fundación Instituto de Investigación Sanitaria-Fundación Jiménez Díaz-Universidad Autónoma Madrid, Madrid, Spain
| | - Marta Ruiz-Ortega
- Cellular and Molecular Biology in Renal and Vascular Pathology Laboratory. Fundación Instituto de Investigación Sanitaria-Fundación Jiménez Díaz-Universidad Autónoma Madrid, Madrid, Spain
| | - Carolina Castillo
- University Hospital "Príncipe de Asturias", Alcalá de Henares, Madrid, Spain
| | - Xin Sheng
- Division of Nephrology, Department of Medicine, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katalin Susztak
- Division of Nephrology, Department of Medicine, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Miguel Ruiz-Canela
- University of Navarra, Department of Preventive Medicine and Public Health, IdiSNA (Health Research Institute of Navarra), Pamplona, Spain.,CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Jordi Salas-Salvadó
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain.,Human Nutrition Unit, Faculty of Medicine and Health Sciences, Pere Virgili Health Research Institute, Rovira i Virgili University, Reus, Spain
| | - Miguel A Martínez González
- University of Navarra, Department of Preventive Medicine and Public Health, IdiSNA (Health Research Institute of Navarra), Pamplona, Spain.,CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Sagrario Ortega
- Transgenics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ricardo Ramos
- Genomic Facility, Parque Científico de Madrid, Madrid, Spain
| | - Santiago Lamas
- Program of Physiological and Pathological Processes, Centro de Biología Molecular "Severo Ochoa" (CBMSO) (CSIC-UAM), Madrid, Spain
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17
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Mizrak D, Levitin HM, Delgado AC, Crotet V, Yuan J, Chaker Z, Silva-Vargas V, Sims PA, Doetsch F. Single-Cell Analysis of Regional Differences in Adult V-SVZ Neural Stem Cell Lineages. Cell Rep 2020; 26:394-406.e5. [PMID: 30625322 PMCID: PMC6368857 DOI: 10.1016/j.celrep.2018.12.044] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 11/20/2018] [Accepted: 12/11/2018] [Indexed: 12/23/2022] Open
Abstract
The ventricular-subventricular zone (V-SVZ) harbors adult neural stem cells. V-SVZ neural stem cells exhibit features of astrocytes, have a regional identity, and depending on their location in the lateral or septal wall of the lateral ventricle, generate different types of neuronal and glial progeny. We performed large-scale single-cell RNA sequencing to provide a molecular atlas of cells from the lateral and septal adult V-SVZ of male and female mice. This revealed regional and sex differences among adult V-SVZ cells. We uncovered lineage potency bias at the single-cell level among lateral and septal wall astrocytes toward neurogenesis and oligodendrogenesis, respectively. Finally, we identified transcription factor co-expression modules marking key temporal steps in neurogenic and oligodendrocyte lineage progression. Our data suggest functionally important spatial diversity in neurogenesis and oligodendrogenesis in the adult brain and reveal molecular correlates of adult NSC dormancy and lineage specialization. Mizrak et al. performed large-scale, single-cell RNA sequencing of the adult ventricular-subventricular zone neural stem cell niche. They identify regional differences between the lateral wall and septal wall, as well as sex differences in cell types and signaling pathways.
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Affiliation(s)
- Dogukan Mizrak
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Hanna Mendes Levitin
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Ana C Delgado
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Valerie Crotet
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Jinzhou Yuan
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Zayna Chaker
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | - Peter A Sims
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA; Sulzberger Columbia Genome Center, Columbia University Medical Center, New York, NY 10032, USA; Department of Biochemistry & Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA.
| | - Fiona Doetsch
- Biozentrum, University of Basel, 4056 Basel, Switzerland.
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18
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Li C, Barton C, Henke K, Daane J, Treaster S, Caetano-Lopes J, Tanguay RL, Harris MP. celsr1a is essential for tissue homeostasis and onset of aging phenotypes in the zebrafish. eLife 2020; 9:50523. [PMID: 31985398 PMCID: PMC7010407 DOI: 10.7554/elife.50523] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 01/24/2020] [Indexed: 12/11/2022] Open
Abstract
The use of genetics has been invaluable in defining the complex mechanisms of aging and longevity. Zebrafish, while a prominent model for vertebrate development, have not been used systematically to address questions of how and why we age. In a mutagenesis screen focusing on late developmental phenotypes, we identified a new mutant that displays aging phenotypes at young adult stages. We find that the phenotypes are due to loss-of-function in the non-classical cadherin celsr1a. The premature aging is not associated with increased cellular senescence or telomere length but is a result of a failure to maintain progenitor cell populations. We show that celsr1a is essential for maintenance of stem cell progenitors in late stages. Caloric restriction can ameliorate celsr1a aging phenotypes. These data suggest that celsr1a function helps to mediate stem cell maintenance during maturation and homeostasis of tissues and thus regulates the onset or expressivity of aging phenotypes.
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Affiliation(s)
- Chunmei Li
- Department of Genetics, Harvard Medical School, Boston, United States.,Department of Orthopedics, Boston Children's Hospital, Boston, United States
| | - Carrie Barton
- Department of Environmental and Molecular Toxicology, Oregon State University, Sinnhuber Aquatic Research Laboratory, Corvallis, United States
| | - Katrin Henke
- Department of Genetics, Harvard Medical School, Boston, United States.,Department of Orthopedics, Boston Children's Hospital, Boston, United States
| | - Jake Daane
- Department of Genetics, Harvard Medical School, Boston, United States.,Department of Orthopedics, Boston Children's Hospital, Boston, United States
| | - Stephen Treaster
- Department of Genetics, Harvard Medical School, Boston, United States.,Department of Orthopedics, Boston Children's Hospital, Boston, United States
| | - Joana Caetano-Lopes
- Department of Genetics, Harvard Medical School, Boston, United States.,Department of Orthopedics, Boston Children's Hospital, Boston, United States
| | - Robyn L Tanguay
- Department of Environmental and Molecular Toxicology, Oregon State University, Sinnhuber Aquatic Research Laboratory, Corvallis, United States
| | - Matthew P Harris
- Department of Genetics, Harvard Medical School, Boston, United States.,Department of Orthopedics, Boston Children's Hospital, Boston, United States
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19
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Mori K, Tamada K, Kurooka H, Matsui M, Takumi T, Yokota Y. Gene expression profile data of the developing small intestine of Id2-deficient mice. Data Brief 2019; 24:103717. [PMID: 30984807 PMCID: PMC6444121 DOI: 10.1016/j.dib.2019.103717] [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: 11/14/2018] [Revised: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 11/25/2022] Open
Abstract
This article contains data related to the research article entitled “Id2 determines intestinal identity through repression of the foregut transcription factor, Irx5” [1]. Id2 deficient (Id2−/−) mice developed gastric tumors and heterotopic squamous epithelium in the small intestine. These tumors and heterotopic tissues were derived from ectopic gastric cells and squamous cells formed in the small intestine respectively during development. In this study, microarray data of the developing small intestine of Id2−/− mice was analyzed.
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Affiliation(s)
- Kentaro Mori
- Department of Neurology, Kanazawa Medical University, 1-1 Uchinada, Ishikawa 920-0293, Japan.,Division of Molecular Genetics, Department of Biochemistry and Bioinformative Sciences, School of Medicine, Faculty of Medical Sciences, University of Fukui, 23-3 Matsuoka-Shimoaizuki, Eiheiji, Fukui 910-1193, Japan
| | - Kota Tamada
- RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hisanori Kurooka
- Division of Molecular Genetics, Department of Biochemistry and Bioinformative Sciences, School of Medicine, Faculty of Medical Sciences, University of Fukui, 23-3 Matsuoka-Shimoaizuki, Eiheiji, Fukui 910-1193, Japan.,Faculty of Nutritional Science, Department of Nutritional Management, Sagami Women's University, Sagamihara, Kanagawa, 252-0383, Japan
| | - Makoto Matsui
- Department of Neurology, Kanazawa Medical University, 1-1 Uchinada, Ishikawa 920-0293, Japan
| | - Toru Takumi
- RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yoshifumi Yokota
- Division of Molecular Genetics, Department of Biochemistry and Bioinformative Sciences, School of Medicine, Faculty of Medical Sciences, University of Fukui, 23-3 Matsuoka-Shimoaizuki, Eiheiji, Fukui 910-1193, Japan
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20
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Lush ME, Diaz DC, Koenecke N, Baek S, Boldt H, St Peter MK, Gaitan-Escudero T, Romero-Carvajal A, Busch-Nentwich EM, Perera AG, Hall KE, Peak A, Haug JS, Piotrowski T. scRNA-Seq reveals distinct stem cell populations that drive hair cell regeneration after loss of Fgf and Notch signaling. eLife 2019; 8:e44431. [PMID: 30681411 PMCID: PMC6363392 DOI: 10.7554/elife.44431] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 01/24/2019] [Indexed: 12/25/2022] Open
Abstract
Loss of sensory hair cells leads to deafness and balance deficiencies. In contrast to mammalian hair cells, zebrafish ear and lateral line hair cells regenerate from poorly characterized support cells. Equally ill-defined is the gene regulatory network underlying the progression of support cells to differentiated hair cells. scRNA-Seq of lateral line organs uncovered five different support cell types, including quiescent and activated stem cells. Ordering of support cells along a developmental trajectory identified self-renewing cells and genes required for hair cell differentiation. scRNA-Seq analyses of fgf3 mutants, in which hair cell regeneration is increased, demonstrates that Fgf and Notch signaling inhibit proliferation of support cells in parallel by inhibiting Wnt signaling. Our scRNA-Seq analyses set the foundation for mechanistic studies of sensory organ regeneration and is crucial for identifying factors to trigger hair cell production in mammals. The data is searchable and publicly accessible via a web-based interface.
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Affiliation(s)
- Mark E Lush
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Daniel C Diaz
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Nina Koenecke
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Sungmin Baek
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Helena Boldt
- Stowers Institute for Medical ResearchKansas CityUnited States
| | | | | | - Andres Romero-Carvajal
- Stowers Institute for Medical ResearchKansas CityUnited States
- Pontificia Universidad Catolica del EcuadorCiencias BiologicasQuitoEcuador
| | - Elisabeth M Busch-Nentwich
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Department of MedicineUniversity of CambridgeCambridgeUnited Kingdom
| | - Anoja G Perera
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Kathryn E Hall
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Allison Peak
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Jeffrey S Haug
- Stowers Institute for Medical ResearchKansas CityUnited States
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21
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Doupé DP, Marshall OJ, Dayton H, Brand AH, Perrimon N. Drosophila intestinal stem and progenitor cells are major sources and regulators of homeostatic niche signals. Proc Natl Acad Sci U S A 2018; 115:12218-12223. [PMID: 30404917 PMCID: PMC6275525 DOI: 10.1073/pnas.1719169115] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Epithelial homeostasis requires the precise balance of epithelial stem/progenitor proliferation and differentiation. While many signaling pathways that regulate epithelial stem cells have been identified, it is probable that other regulators remain unidentified. Here, we use gene-expression profiling by targeted DamID to identify the stem/progenitor-specific transcription and signaling factors in the Drosophila midgut. Many signaling pathway components, including ligands of most major pathways, exhibit stem/progenitor-specific expression and have regulatory regions bound by both intrinsic and extrinsic transcription factors. In addition to previously identified stem/progenitor-derived ligands, we show that both the insulin-like factor Ilp6 and TNF ligand eiger are specifically expressed in the stem/progenitors and regulate normal tissue homeostasis. We propose that intestinal stem cells not only integrate multiple signals but also contribute to and regulate the homeostatic signaling microenvironmental niche through the expression of autocrine and paracrine factors.
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Affiliation(s)
- David P Doupé
- Department of Genetics, Harvard Medical School, Boston, MA 02115;
- Department of Biosciences, Durham University, DH1 3LE Durham, United Kingdom
| | - Owen J Marshall
- The Gurdon Institute, University of Cambridge, CB2 1QN Cambridge, United Kingdom
- Department of Physiology Development and Neuroscience, University of Cambridge, CB2 1QN Cambridge, United Kingdom
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Hannah Dayton
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Andrea H Brand
- The Gurdon Institute, University of Cambridge, CB2 1QN Cambridge, United Kingdom
- Department of Physiology Development and Neuroscience, University of Cambridge, CB2 1QN Cambridge, United Kingdom
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA 02115;
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115
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22
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Wollenzien H, Voigt E, Kareta MS. Somatic Pluripotent Genes in Tissue Repair, Developmental Disease, and Cancer. SPG BIOMED 2018; 1. [PMID: 31172135 DOI: 10.32392/biomed.18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Embryonic stem cells possess the ability to differentiate into all cell types of the body. This pliable developmental state is achieved by the function of a series of pluripotency factors, classically identified as OCT4, SOX2, and NANOG. These pluripotency factors are responsible for activating the larger pluripotency networks and the self-renewal programs which give ES cells their unique characteristics. However, during differentiation pluripotency networks become downregulated as cells achieve greater lineage specification and exit the cell cycle. Typically the repression of pluripotency is viewed as a positive factor to ensure the fidelity of cellular identity by restricting cellular pliancy. Consistent with this view, the expression of pluripotency factors is greatly restricted in somatic cells. However, there are examples whereby cells either maintain or reactivate pluripotency factors to preserve the increased potential for the healing of wounds or tissue homeostasis. Additionally there are many examples where these pluripotency factors become reactivated in a variety of human pathologies, particularly cancer. In this review, we will summarize the somatic repression of pluripotency factors, their role in tissue homeostasis and wound repair, and the human diseases that are associated with pluripotency factor misregulation with an emphasis on their role in the etiology of multiple cancers.
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Affiliation(s)
- Hannah Wollenzien
- Genetics and Genomics Group, Cellular Therapies and Stem Cell Biology Group, and the Cancer Biology and Immunotherapies Group, Sanford Research, 2301 East 60th Street North, Sioux Falls, SD 57104, USA.,Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, 414 E. Clark St. Vermillion, SD 57069, USA
| | - Ellen Voigt
- Genetics and Genomics Group, Cellular Therapies and Stem Cell Biology Group, and the Cancer Biology and Immunotherapies Group, Sanford Research, 2301 East 60th Street North, Sioux Falls, SD 57104, USA
| | - Michael S Kareta
- Genetics and Genomics Group, Cellular Therapies and Stem Cell Biology Group, and the Cancer Biology and Immunotherapies Group, Sanford Research, 2301 East 60th Street North, Sioux Falls, SD 57104, USA.,Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, 414 E. Clark St. Vermillion, SD 57069, USA.,Department of Pediatrics, Sanford School of Medicine, 1400 W. 22nd St., Sioux Falls, SD 57105, USA.,Department of Chemistry and Biochemistry, South Dakota State University, 1175 Medary Ave, Brookings, SD 57006, USA
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23
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Zaletel I, Schwirtlich M, Perović M, Jovanović M, Stevanović M, Kanazir S, Puškaš N. Early Impairments of Hippocampal Neurogenesis in 5xFAD Mouse Model of Alzheimer’s Disease Are Associated with Altered Expression of SOXB Transcription Factors. J Alzheimers Dis 2018; 65:963-976. [DOI: 10.3233/jad-180277] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Ivan Zaletel
- Institute of Histology and Embryology “Aleksandar Đ Kostić”, School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Marija Schwirtlich
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Milka Perović
- Institute for Biological Research “Siniša Stanković”, University of Belgrade, Belgrade, Serbia
| | - Mirna Jovanović
- Institute for Biological Research “Siniša Stanković”, University of Belgrade, Belgrade, Serbia
| | - Milena Stevanović
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
- University of Belgrade, Faculty of Biology, Belgrade, Serbia
- Serbian Academy of Sciences and Arts, Belgrade, Serbia
| | - Selma Kanazir
- Institute for Biological Research “Siniša Stanković”, University of Belgrade, Belgrade, Serbia
| | - Nela Puškaš
- Institute of Histology and Embryology “Aleksandar Đ Kostić”, School of Medicine, University of Belgrade, Belgrade, Serbia
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24
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Makrides N, Panayiotou E, Fanis P, Karaiskos C, Lapathitis G, Malas S. Sequential Role of SOXB2 Factors in GABAergic Neuron Specification of the Dorsal Midbrain. Front Mol Neurosci 2018; 11:152. [PMID: 29867344 PMCID: PMC5952183 DOI: 10.3389/fnmol.2018.00152] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/17/2018] [Indexed: 12/23/2022] Open
Abstract
Studies proposed a model for embryonic neurogenesis where the expression levels of the SOXB2 and SOXB1 factors regulate the differentiation status of the neural stem cells. However, the precise role of the SOXB2 genes remains controversial. Therefore, this study aims to investigate the effects of individual deletions of the SOX21 and SOX14 genes during the development of the dorsal midbrain. We show that SOX21 and SOX14 function distinctly during the commitment of the GABAergic lineage. More explicitly, deletion of SOX21 reduced the expression of the GABAergic precursor marker GATA3 and BHLHB5 while the expression of GAD6, which marks GABAergic terminal differentiation, was not affected. In contrast deletion of SOX14 alone was sufficient to inhibit terminal differentiation of the dorsal midbrain GABAergic neurons. Furthermore, we demonstrate through gain-of-function experiments, that despite the homology of SOX21 and SOX14, they have unique gene targets and cannot compensate for the loss of each other. Taken together, these data do not support a pan-neurogenic function for SOXB2 genes in the dorsal midbrain, but instead they influence, sequentially, the specification of GABAergic neurons.
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Affiliation(s)
- Neoklis Makrides
- Developmental and Functional Genetics Group, The Cyprus Institute of Neurology & Genetics and Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Elena Panayiotou
- Neurologic Clinic A, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Pavlos Fanis
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Christos Karaiskos
- Neuroscience Laboratory, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - George Lapathitis
- Neuroscience Laboratory, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Stavros Malas
- Developmental and Functional Genetics Group, The Cyprus Institute of Neurology & Genetics and Cyprus School of Molecular Medicine, Nicosia, Cyprus
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25
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Id2 Determines Intestinal Identity through Repression of the Foregut Transcription Factor Irx5. Mol Cell Biol 2018; 38:MCB.00250-17. [PMID: 29463648 PMCID: PMC5902590 DOI: 10.1128/mcb.00250-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 02/13/2018] [Indexed: 12/12/2022] Open
Abstract
The cellular components and function of the gastrointestinal epithelium exhibit distinct characteristics depending on the region, e.g., stomach or intestine. How these region-specific epithelial characteristics are generated during development remains poorly understood. Here, we report on the involvement of the helix-loop-helix inhibitor Id2 in establishing the specific characteristics of the intestinal epithelium. Id2−/− mice developed tumors in the small intestine. Histological analysis indicated that the intestinal tumors were derived from gastric metaplasia formed in the small intestine during development. Heterotopic Id2 expression in developing gastric epithelium induced a fate change to intestinal epithelium. Gene expression analysis revealed that foregut-enriched genes encoding Irx3 and Irx5 were highly induced in the midgut of Id2−/− embryos, and transgenic mice expressing Irx5 in the midgut endoderm developed tumors recapitulating the characteristics of Id2−/− mice. Altogether, our results demonstrate that Id2 plays a crucial role in the development of regional specificity in the gastrointestinal epithelium.
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26
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Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors. Nat Commun 2017; 8:1221. [PMID: 29089486 PMCID: PMC5663922 DOI: 10.1038/s41467-017-01355-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 09/12/2017] [Indexed: 11/23/2022] Open
Abstract
Homozygous deletions are rare in cancers and often target tumour suppressor genes. Here, we build a compendium of 2218 primary tumours across 12 human cancer types and systematically screen for homozygous deletions, aiming to identify rare tumour suppressors. Our analysis defines 96 genomic regions recurrently targeted by homozygous deletions. These recurrent homozygous deletions occur either over tumour suppressors or over fragile sites, regions of increased genomic instability. We construct a statistical model that separates fragile sites from regions showing signatures of positive selection for homozygous deletions and identify candidate tumour suppressors within those regions. We find 16 established tumour suppressors and propose 27 candidate tumour suppressors. Several of these genes (including MGMT, RAD17, and USP44) show prior evidence of a tumour suppressive function. Other candidate tumour suppressors, such as MAFTRR, KIAA1551, and IGF2BP2, are novel. Our study demonstrates how rare tumour suppressors can be identified through copy number meta-analysis. Homozygous deletions are rare in cancers and often target tumour suppressor genes. Here, the authors conduct pan-cancer analyses and apply statistical modelling to identify 27 candidate tumour suppressors, including MAFTRR, KIAA1551, and IGF2BP2.
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27
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Julian LM, McDonald AC, Stanford WL. Direct reprogramming with SOX factors: masters of cell fate. Curr Opin Genet Dev 2017; 46:24-36. [PMID: 28662445 DOI: 10.1016/j.gde.2017.06.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 04/25/2017] [Accepted: 06/09/2017] [Indexed: 12/13/2022]
Abstract
Over the last decade significant advances have been made toward reprogramming the fate of somatic cells, typically by overexpression of cell lineage-determinant transcription factors. As key regulators of cell fate, the SOX family of transcription factors has emerged as potent drivers of direct somatic cell reprogramming into multiple lineages, in some cases as the sole overexpressed factor. The vast capacity of SOX factors, especially those of the SOXB1, E and F subclasses, to reprogram cell fate is enlightening our understanding of organismal development, cancer and disease, and offers tremendous potential for regenerative medicine and cell-based therapies. Understanding the molecular mechanisms through which SOX factors reprogram cell fate is essential to optimize the development of novel somatic cell transdifferentiation strategies.
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Affiliation(s)
- Lisa M Julian
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario K1L8L6, Canada
| | - Angela Ch McDonald
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, 686 Bay Street, Toronto, Ontario M5G0A4, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S3G9, Canada
| | - William L Stanford
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario K1L8L6, Canada; Department of Cellular and Molecular Medicine, Faulty of Medicine, University of Ottawa, 451 Smyth Rd, Ottawa, Ontario K1H8M5, Canada; Department of Biochemistry, Microbiology and Immunology, Faulty of Medicine, University of Ottawa, 451 Smyth Rd, Ottawa, Ontario K1H8M5, Canada; Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Rd, Ottawa, Ontario K1H8M5, Canada.
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28
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Keysar SB, Le PN, Miller B, Jackson BC, Eagles JR, Nieto C, Kim J, Tang B, Glogowska MJ, Morton JJ, Padilla-Just N, Gomez K, Warnock E, Reisinger J, Arcaroli JJ, Messersmith WA, Wakefield LM, Gao D, Tan AC, Serracino H, Vasiliou V, Roop DR, Wang XJ, Jimeno A. Regulation of Head and Neck Squamous Cancer Stem Cells by PI3K and SOX2. J Natl Cancer Inst 2016; 109:2905790. [PMID: 27634934 DOI: 10.1093/jnci/djw189] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 07/19/2016] [Indexed: 12/26/2022] Open
Abstract
Background We have an incomplete understanding of the differences between cancer stem cells (CSCs) in human papillomavirus-positive (HPV-positive) and -negative (HPV-negative) head and neck squamous cell cancer (HNSCC). The PI3K pathway has the most frequent activating genetic events in HNSCC (especially HPV-positive driven), but the differential signaling between CSCs and non-CSCs is also unknown. Methods We addressed these unresolved questions using CSCs identified from 10 HNSCC patient-derived xenografts (PDXs). Sored populations were serially passaged in nude mice to evaluate tumorigenicity and tumor recapitulation. The transcription profile of HNSCC CSCs was characterized by mRNA sequencing, and the susceptibility of CSCs to therapy was investigated using an in vivo model. SOX2 transcriptional activity was used to follow the asymmetric division of PDX-derived CSCs. All statistical tests were two-sided. Results CSCs were enriched by high aldehyde dehydrogenase (ALDH) activity and CD44 expression and were similar between HPV-positive and HPV-negative cases (percent tumor formation injecting ≤ 1x10(3) cells: ALDH(+)CD44(high) = 65.8%, ALDH(-)CD44(high) = 33.1%, ALDH(+)CD44(high) = 20.0%; and injecting 1x10(5) cells: ALDH(-)CD44(low) = 4.4%). CSCs were resistant to conventional therapy and had PI3K/mTOR pathway overexpression (GSEA pathway enrichment, P < .001), and PI3K inhibition in vivo decreased their tumorigenicity (40.0%-100.0% across cases). PI3K/mTOR directly regulated SOX2 protein levels, and SOX2 in turn activated ALDH1A1 (P < .001 013C and 067C) expression and ALDH activity (ALDH(+) [%] empty-control vs SOX2, 0.4% ± 0.4% vs 14.5% ± 9.8%, P = .03 for 013C and 1.7% ± 1.3% vs 3.6% ± 3.4%, P = .04 for 067C) in 013C and 067 cells. SOX2 enhanced sphere and tumor growth (spheres/well, 013C P < .001 and 067C P = .04) and therapy resistance. SOX2 expression prompted mesenchymal-to-epithelial transition (MET) by inducing CDH1 (013C P = .002, 067C P = .01), followed by asymmetric division and proliferation, which contributed to tumor formation. Conclusions The molecular link between PI3K activation and CSC properties found in this study provides insights into therapeutic strategies for HNSCC. Constitutive expression of SOX2 in HNSCC cells generates a CSC-like population that enables CSC studies.
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Affiliation(s)
- Stephen B Keysar
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - Phuong N Le
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - Bettina Miller
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - Brian C Jackson
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - Justin R Eagles
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - Cera Nieto
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - Jihye Kim
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - Binwu Tang
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - Magdalena J Glogowska
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - J Jason Morton
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - Nuria Padilla-Just
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - Karina Gomez
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - Emily Warnock
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - Julie Reisinger
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - John J Arcaroli
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - Wells A Messersmith
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - Lalage M Wakefield
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - Dexiang Gao
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - Aik-Choon Tan
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - Hilary Serracino
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - Vasilis Vasiliou
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - Dennis R Roop
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - Xiao-Jing Wang
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
| | - Antonio Jimeno
- Affiliations of authors: Division of Medical Oncology, Department of Medicine (SBK, PNL, BM, BCJ, JRE, CN, JK, MJG, JJM, NPJ, KG, EW, JR, JJA, WAM, ACT, AJ), Department of Biostatistics and Informatics (JK, DG, ACT), Department of Pathology (HS, XJW), Department of Dermatology (DRR), and Gates Center for Regenerative Medicine (DRR, XJW, AJ), University of Colorado Denver School of Medicine, Denver, CO; Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD (BT, LMW); Department of Environmental Health Sciences, Yale School of Public Health, Yale School of Medicine, New Haven, CT (VV)
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Mandalos NP, Remboutsika E. Sox2: To crest or not to crest? Semin Cell Dev Biol 2016; 63:43-49. [PMID: 27592260 DOI: 10.1016/j.semcdb.2016.08.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 08/29/2016] [Accepted: 08/30/2016] [Indexed: 12/12/2022]
Abstract
Precise control of neural progenitor transformation into neural crest stem cells ensures proper craniofacial and head development. In the neural progenitor pool, SoxB factors play an essential role as cell fate determinants of neural development, whereas during neural crest stem cell formation, Sox2 plays a predominant role as a guardian of the developmental clock that ensures precision of cell flow in the developing head.
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Affiliation(s)
- Nikolaos Panagiotis Mandalos
- National University of Athens Medical School, Department of Pediatrics, 75 Mikras Asias Str., 115 27, Athens, Greece; Stem Cell Biology Laboratory, Biomedical Sciences Research Centre "Alexander Fleming", 34 Fleming Str., 16672 Vari-Attica, Greece; Adjunct Faculty, The Lieber Institute for Brain Development, Basic Sciences Division, Johns Hopkins Medical Campus, 855 North Wolfe Str., Suite 300, 3rd Floor, Baltimore, MD 21205, USA
| | - Eumorphia Remboutsika
- National University of Athens Medical School, Department of Pediatrics, 75 Mikras Asias Str., 115 27, Athens, Greece; Stem Cell Biology Laboratory, Biomedical Sciences Research Centre "Alexander Fleming", 34 Fleming Str., 16672 Vari-Attica, Greece; Adjunct Faculty, The Lieber Institute for Brain Development, Basic Sciences Division, Johns Hopkins Medical Campus, 855 North Wolfe Str., Suite 300, 3rd Floor, Baltimore, MD 21205, USA.
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30
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Fu L, Shi YB. The Sox transcriptional factors: Functions during intestinal development in vertebrates. Semin Cell Dev Biol 2016; 63:58-67. [PMID: 27567710 DOI: 10.1016/j.semcdb.2016.08.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 08/19/2016] [Accepted: 08/24/2016] [Indexed: 12/28/2022]
Abstract
The intestine has long been studied as a model for adult stem cells due to the life-long self-renewal of the intestinal epithelium through the proliferation of the adult intestinal stem cells. Recent evidence suggests that the formation of adult intestinal stem cells in mammals takes place during the thyroid hormone-dependent neonatal period, also known as postembryonic development, which resembles intestinal remodeling during frog metamorphosis. Studies on the metamorphosis in Xenopus laevis have revealed that many members of the Sox family, a large family of DNA binding transcription factors, are upregulated in the intestinal epithelium during the formation and/or proliferation of the intestinal stem cells. Similarly, a number of Sox genes have been implicated in intestinal development and pathogenesis in mammals. Futures studies are needed to determine the expression and potential involvement of this important gene family in the development of the adult intestinal stem cells. These include the analyses of the expression and regulation of these and other Sox genes during postembryonic development in mammals as well as functional investigations in both mammals and amphibians by using the recently developed gene knockout technologies.
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Affiliation(s)
- Liezhen Fu
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), 18 Library Dr., Bethesda, MD, 20892, United States
| | - Yun-Bo Shi
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), 18 Library Dr., Bethesda, MD, 20892, United States.
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31
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Lundberg IV, Edin S, Eklöf V, Öberg Å, Palmqvist R, Wikberg ML. SOX2 expression is associated with a cancer stem cell state and down-regulation of CDX2 in colorectal cancer. BMC Cancer 2016; 16:471. [PMID: 27411517 PMCID: PMC4944515 DOI: 10.1186/s12885-016-2509-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 06/16/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND To improve current treatment strategies for patients with aggressive colorectal cancer (CRC), the molecular understanding of subgroups of CRC with poor prognosis is of vast importance. SOX2 positive tumors have been associated with a poor patient outcome, but the functional role of SOX2 in CRC patient prognosis is still unclear. METHODS An in vitro cell culture model expressing SOX2 was used to investigate the functional role of SOX2 in CRC. In vitro findings were verified using RNA from fresh frozen tumor tissue or immunohistochemistry on formalin fixed paraffin embedded (FFPE) tumor tissue from a cohort of 445 CRC patients. RESULTS Using our in vitro model, we found that SOX2 expressing cells displayed several characteristics of cancer stem cells; such as a decreased proliferative rate, a spheroid growth pattern, and increased expression of stem cell markers CD24 and CD44. Cells expressing SOX2 also showed down-regulated expression of the intestinal epithelial marker CDX2. We next evaluated CDX2 expression in our patient cohort. CDX2 down-regulation was more often found in right sided tumors of high grade and high stage. Furthermore, a decreased expression of CDX2 was closely linked to MSI, CIMP-high as well as BRAF mutated tumors. A decreased expression of CDX2 was also, in a stepwise manner, strongly correlated to a poor patient prognosis. When looking at SOX2 expression in relation to CDX2, we found that SOX2 expressing tumors more often displayed a down-regulated expression of CDX2. In addition, SOX2 expressing tumors with a down-regulated CDX2 expression had a worse patient prognosis compared to those with retained CDX2 expression. CONCLUSIONS Our results indicate that SOX2 expression induces a cellular stem cell state in human CRC with a decreased expression of CDX2. Furthermore, a down-regulated expression of CDX2 results in a poor patient prognosis in CRC and at least part of the prognostic importance of SOX2 is mediated through CDX2 down-regulation.
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Affiliation(s)
- Ida V Lundberg
- Department of Medical Biosciences, Pathology, Umeå University, Building 6M, SE-90185, Umeå, Sweden
| | - Sofia Edin
- Department of Medical Biosciences, Pathology, Umeå University, Building 6M, SE-90185, Umeå, Sweden.
| | - Vincy Eklöf
- Department of Medical Biosciences, Pathology, Umeå University, Building 6M, SE-90185, Umeå, Sweden
| | - Åke Öberg
- Department of Surgical and Perioperative Sciences, Surgery, Umeå University, Umeå, Sweden
| | - Richard Palmqvist
- Department of Medical Biosciences, Pathology, Umeå University, Building 6M, SE-90185, Umeå, Sweden
| | - Maria L Wikberg
- Department of Medical Biosciences, Pathology, Umeå University, Building 6M, SE-90185, Umeå, Sweden
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32
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Leung CY, Zhu M, Zernicka-Goetz M. Polarity in Cell-Fate Acquisition in the Early Mouse Embryo. Curr Top Dev Biol 2016; 120:203-34. [PMID: 27475853 DOI: 10.1016/bs.ctdb.2016.04.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Establishing polarity is a fundamental part of embryogenesis and can be traced back to the earliest developmental stages. It can be achieved in one of two ways: through the preexisting polarization of germ cells before fertilization or via symmetry breaking after fertilization. In mammals, it seems to be the latter, and we will discuss the various cytological and molecular events that lead up to this event, its mechanisms and the consequences. In mammals, the first polarization event occurs in the preimplantation period, when the embryo is but a cluster of cells, free-floating in the oviduct. This provides a unique, autonomous system to study the de novo polarization that is essential to life. In this review, we will cover modern and past studies on the polarization of the early embryo, using the mouse as a model system, as well as hypothesizing the potential implications and functions of the biological events involved.
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Affiliation(s)
- C Y Leung
- University of Cambridge, Cambridge, United Kingdom
| | - M Zhu
- University of Cambridge, Cambridge, United Kingdom
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33
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Goolam M, Scialdone A, Graham SJL, Macaulay IC, Jedrusik A, Hupalowska A, Voet T, Marioni JC, Zernicka-Goetz M. Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos. Cell 2016; 165:61-74. [PMID: 27015307 PMCID: PMC4819611 DOI: 10.1016/j.cell.2016.01.047] [Citation(s) in RCA: 291] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 11/10/2015] [Accepted: 01/22/2016] [Indexed: 01/08/2023]
Abstract
The major and essential objective of pre-implantation development is to establish embryonic and extra-embryonic cell fates. To address when and how this fundamental process is initiated in mammals, we characterize transcriptomes of all individual cells throughout mouse pre-implantation development. This identifies targets of master pluripotency regulators Oct4 and Sox2 as being highly heterogeneously expressed between blastomeres of the 4-cell embryo, with Sox21 showing one of the most heterogeneous expression profiles. Live-cell tracking demonstrates that cells with decreased Sox21 yield more extra-embryonic than pluripotent progeny. Consistently, decreasing Sox21 results in premature upregulation of the differentiation regulator Cdx2, suggesting that Sox21 helps safeguard pluripotency. Furthermore, Sox21 is elevated following increased expression of the histone H3R26-methylase CARM1 and is lowered following CARM1 inhibition, indicating the importance of epigenetic regulation. Therefore, our results indicate that heterogeneous gene expression, as early as the 4-cell stage, initiates cell-fate decisions by modulating the balance of pluripotency and differentiation.
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Affiliation(s)
- Mubeen Goolam
- Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Antonio Scialdone
- European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Sarah J L Graham
- Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Iain C Macaulay
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Agnieszka Jedrusik
- Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Anna Hupalowska
- Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Thierry Voet
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK; Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - John C Marioni
- European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK; Cancer Research UK-Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, UK.
| | - Magdalena Zernicka-Goetz
- Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK.
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The SOX17/miR-371-5p/SOX2 axis inhibits EMT, stem cell properties and metastasis in colorectal cancer. Oncotarget 2016; 6:9099-112. [PMID: 25868860 PMCID: PMC4496205 DOI: 10.18632/oncotarget.3603] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 02/10/2015] [Indexed: 12/31/2022] Open
Abstract
Cancer stem cells (CSCs) and EMT-type cells, which share molecular characteristics with CSCs, have been believed to play critical roles in tumor metastasis. Although much progress has been garnered in elucidating the molecular pathways that trigger EMT, stemness and metastasis, a number of key mechanistic gaps remain elusive. In the study, miR-371-5p was obviously down-regulated in primary CRC tissues compared with matched adjacent normal mucosa and correlated significantly with differentiation, tumor size, lymphatic and liver metastases. MiR-371-5p could attenuate proliferation, invasion in vitro and metastasis in vivo in CRC cells. It also suppressed EMT by regulating Wnt/β-catenin signaling and strongly decreased the CRC stemness phenotypes. Moreover, demethylation of SOX17 induced miR-371-5p expression and consequently suppressed its direct target SOX2 in CRC cells. MiR-371-5p was necessary for SOX17 mediated cancer-related traits and SOX2 was a functional target of miR-371-5p. A positive relationship between SOX17 and miR-371-5p expression and a negative one between miR-371-5p and SOX2 expression were observed in CRC cell lines and tissues. In conclusion, we identified miR-371-5p as an important “oncosuppressor” in CRC progression and elucidated a novel mechanism of the SOX17/miR-371-5p/SOX2 axis in the regulation of EMT, stemness and metastasis, which may be a potential therapeutic target.
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35
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Saint-André V, Federation AJ, Lin CY, Abraham BJ, Reddy J, Lee TI, Bradner JE, Young RA. Models of human core transcriptional regulatory circuitries. Genome Res 2016; 26:385-96. [PMID: 26843070 PMCID: PMC4772020 DOI: 10.1101/gr.197590.115] [Citation(s) in RCA: 190] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 12/21/2015] [Indexed: 01/06/2023]
Abstract
A small set of core transcription factors (TFs) dominates control of the gene expression program in embryonic stem cells and other well-studied cellular models. These core TFs collectively regulate their own gene expression, thus forming an interconnected auto-regulatory loop that can be considered the core transcriptional regulatory circuitry (CRC) for that cell type. There is limited knowledge of core TFs, and thus models of core regulatory circuitry, for most cell types. We recently discovered that genes encoding known core TFs forming CRCs are driven by super-enhancers, which provides an opportunity to systematically predict CRCs in poorly studied cell types through super-enhancer mapping. Here, we use super-enhancer maps to generate CRC models for 75 human cell and tissue types. These core circuitry models should prove valuable for further investigating cell-type–specific transcriptional regulation in healthy and diseased cells.
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Affiliation(s)
- Violaine Saint-André
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| | - Alexander J Federation
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Charles Y Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| | - Jessica Reddy
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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A Resource for the Transcriptional Signature of Bona Fide Trophoblast Stem Cells and Analysis of Their Embryonic Persistence. Stem Cells Int 2016; 2015:218518. [PMID: 26783396 PMCID: PMC4691490 DOI: 10.1155/2015/218518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/22/2015] [Indexed: 11/18/2022] Open
Abstract
Trophoblast stem cells (TSCs) represent the multipotent progenitors that give rise to the different cells of the embryonic portion of the placenta. Here, we analysed the expression of key TSC transcription factors Cdx2, Eomes, and Elf5 in the early developing placenta of mouse embryos and in cultured TSCs and reveal surprising heterogeneity in protein levels. We analysed persistence of TSCs in the early placenta and find that TSCs remain in the chorionic hinge until E9.5 and are lost shortly afterwards. To define the transcriptional signature of bona fide TSCs, we used inducible gain- and loss-of-function alleles of Eomes or Cdx2, and EomesGFP, to manipulate and monitor the core maintenance factors of TSCs, followed by genome-wide expression profiling. Combinatorial analysis of resulting expression profiles allowed for defining novel TSC marker genes that might functionally contribute to the maintenance of the TSC state. Analyses by qRT-PCR and in situ hybridisation validated novel TSC- and chorion-specific marker genes, such as Bok/Mtd, Cldn26, Duox2, Duoxa2, Nr0b1, and Sox21. Thus, these expression data provide a valuable resource for the transcriptional signature of bona fide and early differentiating TSCs and may contribute to an increased understanding of the transcriptional circuitries that maintain and/or establish stemness of TSCs.
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Moretto Zita M, Soncin F, Natale D, Pizzo D, Parast M. Gene Expression Profiling Reveals a Novel Regulatory Role for Sox21 Protein in Mouse Trophoblast Stem Cell Differentiation. J Biol Chem 2015; 290:30152-62. [PMID: 26491013 DOI: 10.1074/jbc.m115.659094] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Indexed: 11/06/2022] Open
Abstract
Appropriate self-renewal and differentiation of trophoblast stem cells (TSCs) are key factors for proper placental development and function and, in turn, for appropriate in utero fetal growth. To identify novel TSC-specific genes, we performed genome-wide expression profiling of TSCs, embryonic stem cells, epiblast stem cells, and mouse embryo fibroblasts, derived from mice of the same genetic background. Our analysis revealed a high expression of Sox21 in TSCs compared with other cell types. Sox21 levels were high in undifferentiated TSCs and were dramatically reduced upon differentiation. In addition, modulation of Sox21 expression in TSCs affected lineage-specific differentiation, based on both marker analysis and functional assessment. Our results implicate Sox21 specifically in the promotion of spongiotrophoblast and giant cell differentiation and establish a new mechanism through which trophoblast sublineages are specified.
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Affiliation(s)
| | | | - David Natale
- Reproductive Medicine, University of California San Diego, La Jolla, California 92093
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Poser SW, Chenoweth JG, Colantuoni C, Masjkur J, Chrousos G, Bornstein SR, McKay RD, Androutsellis-Theotokis A. Concise Review: Reprogramming, Behind the Scenes: Noncanonical Neural Stem Cell Signaling Pathways Reveal New, Unseen Regulators of Tissue Plasticity With Therapeutic Implications. Stem Cells Transl Med 2015; 4:1251-7. [PMID: 26371344 DOI: 10.5966/sctm.2015-0105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 07/08/2015] [Indexed: 01/06/2023] Open
Abstract
UNLABELLED Interest is great in the new molecular concepts that explain, at the level of signal transduction, the process of reprogramming. Usually, transcription factors with developmental importance are used, but these approaches give limited information on the signaling networks involved, which could reveal new therapeutic opportunities. Recent findings involving reprogramming by genetic means and soluble factors with well-studied downstream signaling mechanisms, including signal transducer and activator of transcription 3 (STAT3) and hairy and enhancer of split 3 (Hes3), shed new light into the molecular mechanisms that might be involved. We examine the appropriateness of common culture systems and their ability to reveal unusual (noncanonical) signal transduction pathways that actually operate in vivo. We then discuss such novel pathways and their importance in various plastic cell types, culminating in their emerging roles in reprogramming mechanisms. We also discuss a number of reprogramming paradigms (mouse induced pluripotent stem cells, direct conversion to neural stem cells, and in vivo conversion of acinar cells to β-like cells). Specifically for acinar-to-β-cell reprogramming paradigms, we discuss the common view of the underlying mechanism (involving the Janus kinase-STAT pathway that leads to STAT3-tyrosine phosphorylation) and present alternative interpretations that implicate STAT3-serine phosphorylation alone or serine and tyrosine phosphorylation occurring in sequential order. The implications for drug design and therapy are important given that different phosphorylation sites on STAT3 intercept different signaling pathways. We introduce a new molecular perspective in the field of reprogramming with broad implications in basic, biotechnological, and translational research. SIGNIFICANCE Reprogramming is a powerful approach to change cell identity, with implications in both basic and applied biology. Most efforts involve the forced expression of key transcription factors, but recently, success has been reported with manipulating signal transduction pathways that might intercept them. It is important to start connecting the function of the classic reprogramming genes to signaling pathways that also mediate reprogramming, unifying the sciences of signal transduction, stem cell biology, and epigenetics. Neural stem cell studies have revealed the operation of noncanonical signaling pathways that are now appreciated to also operate during reprogramming, offering new mechanistic explanations.
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Affiliation(s)
- Steven W Poser
- Department of Internal Medicine III, Technische Universität Dresden, Dresden, Germany
| | - Josh G Chenoweth
- Lieber Institute for Brain Development, Baltimore, Maryland, USA
| | - Carlo Colantuoni
- Lieber Institute for Brain Development, Baltimore, Maryland, USA
| | - Jimmy Masjkur
- Department of Internal Medicine III, Technische Universität Dresden, Dresden, Germany
| | - George Chrousos
- First Department of Pediatrics, University of Athens Medical School, Athens, Greece Aghia Sophia Children's Hospital, Athens, Greece
| | - Stefan R Bornstein
- Department of Internal Medicine III, Technische Universität Dresden, Dresden, Germany
| | - Ronald D McKay
- Lieber Institute for Brain Development, Baltimore, Maryland, USA
| | - Andreas Androutsellis-Theotokis
- Department of Internal Medicine III, Technische Universität Dresden, Dresden, Germany Center for Regenerative Therapies Dresden, Dresden, Germany
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Aine M, Eriksson P, Liedberg F, Sjödahl G, Höglund M. Biological determinants of bladder cancer gene expression subtypes. Sci Rep 2015; 5:10957. [PMID: 26051783 PMCID: PMC4650643 DOI: 10.1038/srep10957] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/07/2015] [Indexed: 11/09/2022] Open
Abstract
Molecular stratification of tumors by gene expression profiling has been applied to a large number of human malignancies and holds great promise for personalized treatment. Comprehensive classification schemes for urothelial carcinoma have been proposed by three separate groups but have not previously been evaluated simultaneously in independent data. Here we map the interrelations between the proposed molecular subtypes onto the intrinsic structure of a rich independent dataset and show that subtype stratification within each scheme can be explained in terms of a set of common underlying biological processes. We highlight novel biological and genomic drivers of urothelial carcinoma molecular subtypes and show that tumors carrying genomic aberrations characteristic of distinct molecular pathways converge on a common top level phenotype corresponding to the two major molecular subtypes of non-muscle invasive disease.
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Affiliation(s)
- Mattias Aine
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Pontus Eriksson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Fredrik Liedberg
- Division of Urological Research, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Gottfrid Sjödahl
- Division of Urological Research, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Mattias Höglund
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
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Fares-Taie L, Gerber S, Tawara A, Ramirez-Miranda A, Douet JY, Verdin H, Guilloux A, Zenteno J, Kondo H, Moisset H, Passet B, Yamamoto K, Iwai M, Tanaka T, Nakamura Y, Kimura W, Bole-Feysot C, Vilotte M, Odent S, Vilotte JL, Munnich A, Regnier A, Chassaing N, De Baere E, Raymond-Letron I, Kaplan J, Calvas P, Roche O, Rozet JM. Submicroscopic deletions at 13q32.1 cause congenital microcoria. Am J Hum Genet 2015; 96:631-9. [PMID: 25772937 DOI: 10.1016/j.ajhg.2015.01.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 01/20/2015] [Indexed: 11/25/2022] Open
Abstract
Congenital microcoria (MCOR) is a rare autosomal-dominant disorder characterized by inability of the iris to dilate owing to absence of dilator pupillae muscle. So far, a dozen MCOR-affected families have been reported worldwide. By using whole-genome oligonucleotide array CGH, we have identified deletions at 13q32.1 segregating with MCOR in six families originating from France, Japan, and Mexico. Breakpoint sequence analyses showed nonrecurrent deletions in 5/6 families. The deletions varied from 35 kbp to 80 kbp in size, but invariably encompassed or interrupted only two genes: TGDS encoding the TDP-glucose 4,6-dehydratase and GPR180 encoding the G protein-coupled receptor 180, also known as intimal thickness-related receptor (ITR). Unlike TGDS which has no known function in muscle cells, GPR180 is involved in the regulation of smooth muscle cell growth. The identification of a null GPR180 mutation segregating over two generations with iridocorneal angle dysgenesis, which can be regarded as a MCOR endophenotype, is consistent with the view that deletions of this gene, with or without the loss of elements regulating the expression of neighboring genes, are the cause of MCOR.
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41
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Whittington N, Cunningham D, Le TK, De Maria D, Silva EM. Sox21 regulates the progression of neuronal differentiation in a dose-dependent manner. Dev Biol 2015; 397:237-47. [PMID: 25448693 PMCID: PMC4325979 DOI: 10.1016/j.ydbio.2014.11.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/12/2014] [Indexed: 12/27/2022]
Abstract
Members of the SoxB transcription factor family play critical roles in the regulation of neurogenesis. The SoxB1 proteins are required for the induction and maintenance of a proliferating neural progenitor population in numerous vertebrates, however the role of the SoxB2 protein, Sox21, is less clear due to conflicting results. To clarify the role of Sox21 in neurogenesis, we examined its function in the Xenopus neural plate. Here we report that misexpression of Sox21 expands the neural progenitor domain, and represses neuron formation by binding to Neurogenin (Ngn2) and blocking its function. Conversely, we found that Sox21 is also required for neuron formation, as cells lacking Sox21 undergo cell death and thus are unable to differentiate. Together our data indicate that Sox21 plays more than one role in neurogenesis, where a threshold level is required for cell viability and normal differentiation of neurons, but a higher concentration of Sox21 inhibits neuron formation and instead promotes progenitor maintenance.
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Affiliation(s)
- Niteace Whittington
- Department of Biology, Georgetown University, 37th and O Streets NW, Regents Hall 408, Washington, DC 20057, USA.
| | - Doreen Cunningham
- Department of Biology, Georgetown University, 37th and O Streets NW, Regents Hall 408, Washington, DC 20057, USA.
| | - Thien-Kim Le
- Department of Biology, Georgetown University, 37th and O Streets NW, Regents Hall 408, Washington, DC 20057, USA.
| | - David De Maria
- Department of Biology, Georgetown University, 37th and O Streets NW, Regents Hall 408, Washington, DC 20057, USA.
| | - Elena M Silva
- Department of Biology, Georgetown University, 37th and O Streets NW, Regents Hall 408, Washington, DC 20057, USA.
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Can the ‘neuron theory’ be complemented by a universal mechanism for generic neuronal differentiation. Cell Tissue Res 2014; 359:343-84. [DOI: 10.1007/s00441-014-2049-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 10/23/2014] [Indexed: 12/19/2022]
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43
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Camilo V, Garrido M, Valente P, Ricardo S, Amaral AL, Barros R, Chaves P, Carneiro F, David L, Almeida R. Differentiation reprogramming in gastric intestinal metaplasia and dysplasia: role of SOX2 and CDX2. Histopathology 2014; 66:343-50. [PMID: 25196071 DOI: 10.1111/his.12544] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 08/31/2014] [Indexed: 12/12/2022]
Abstract
AIMS Intestinal metaplasia (IM), which results from de-novo expression of CDX2, and dysplasia are precursor lesions of gastric cancer that are associated with an increased risk for cancer development. There is much evidence suggesting a role for the transcription factor SOX2 in gastric differentiation. The aim of this study was to attempt to establish the relationship of SOX2 with CDX2 and with the differentiation reprogramming that characterizes gastric carcinogenesis, to assess their involvement in IM and dysplasia. METHODS AND RESULTS Characterization of gastric (SOX2, MUC5AC, and MUC6) and intestinal (CDX2 and MUC2) markers in normal gastric mucosa, in 55 foci of IM and in 26 foci of dysplasia, was performed by immunohistochemistry. SOX2 was expressed in the normal gastric mucosa, in the presumptive stem cell compartment, and was maintained in 7% of the complete (MUC5AC-negative) and 85% of the incomplete (MUC5AC-positive) IM subtypes. Twelve per cent of the dysplastic lesions expressed SOX2, and the association with MUC5AC was lost. CDX2 was present in all IMs and dysplastic lesions. CONCLUSIONS SOX2 is associated with gastric differentiation in incomplete IM and is lost in the progression to dysplasia, whereas CDX2 is acquired de novo in IM and maintained in dysplasia. This suggests that the balance between gastric and intestinal differentiation programmes impacts on the gastric carcinogenesis cascade progression.
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Affiliation(s)
- Vânia Camilo
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
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Sakurai T, Kashida H, Watanabe T, Hagiwara S, Mizushima T, Iijima H, Nishida N, Higashitsuji H, Fujita J, Kudo M. Stress Response Protein Cirp Links Inflammation and Tumorigenesis in Colitis-Associated Cancer. Cancer Res 2014; 74:6119-28. [DOI: 10.1158/0008-5472.can-14-0471] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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45
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Cobler L, Pera M, Garrido M, Iglesias M, de Bolós C. CDX2 can be regulated through the signalling pathways activated by IL-6 in gastric cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:785-92. [PMID: 24953186 DOI: 10.1016/j.bbagrm.2014.06.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/29/2014] [Accepted: 06/12/2014] [Indexed: 12/30/2022]
Abstract
The inflammatory infiltrate of the gastric mucosa associated with Helicobacter pylori infection increases the presence of the pro-inflammatory cytokine IL-6 that activates both the SHP-2/ERK/MAPK and the JAK/STAT signalling pathways. Furthermore, the ectopic expression of CDX2 is detected in pre-neoplasic lesions associated with decreased levels of SOX2, and we found that in gastric adenocarcinomas their expression is inversely correlated. To determine the role of IL-6 in the regulation of CDX2, MKN45 that constitutively expresses p-STAT3, and NUGC-4 gastric cancer cell lines were treated with IL-6, which induced the CDX2 up-regulation and SOX2 down-regulation. ChIP assays determined that in IL-6-treated cells, c-JUN and p-STAT3 bound to CDX2 promoter in MKN45 cells whereas in NUGC-4 cells, p-STAT3 binds to and c-JUN releases from the CDX2 promoter. Specific inhibition of STAT3 and ERK1/2 phosphorylation through AG490 and U0126, respectively, and STAT3 down-regulation using shRNA verified that the SHP-2/ERK/MAPK pathway regulates the expression of CDX2 in basal conditions, and the CDX2 up-regulation by IL-6 is through the JAK/STAT pathway in NUGC-4 cells whereas in MKN45 cells both pathways contribute to the CDX2 up-regulation. In conclusion, the signalling pathways activated by IL-6 have a crucial role in the regulation of CDX2 that is a key factor in the process of gastric carcinogenesis, suggesting that the inflammatory infiltrate in the gastric mucosa is relevant in this process and a potential target for new therapeutic approaches.
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Affiliation(s)
- Lara Cobler
- Gastroesophageal Cancer Research Group, Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Dr. Aiguader, 88, 08003 Barcelona, Spain
| | - Manuel Pera
- Gastroesophageal Cancer Research Group, Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Dr. Aiguader, 88, 08003 Barcelona, Spain
| | - Marta Garrido
- Gastroesophageal Cancer Research Group, Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Dr. Aiguader, 88, 08003 Barcelona, Spain
| | - Mar Iglesias
- Gastroesophageal Cancer Research Group, Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Dr. Aiguader, 88, 08003 Barcelona, Spain
| | - Carme de Bolós
- Gastroesophageal Cancer Research Group, Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Dr. Aiguader, 88, 08003 Barcelona, Spain.
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46
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Chenoweth JG, McKay RD. Speeding to pluripotency. Cell 2014; 156:631-2. [PMID: 24529370 DOI: 10.1016/j.cell.2014.01.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Finding a cell that reprograms in a nonstochastic manner without genetic manipulation has proven elusive. In this issue, Guo et al. report the identification of a cell defined by an ultrafast cycle whose progeny reprogram in a synchronous and rapid manner.
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Affiliation(s)
- Josh G Chenoweth
- Lieber Institute for Brain Development, 855 N. Wolfe Street, Baltimore, MD 21205 USA
| | - Ronald D McKay
- Lieber Institute for Brain Development, 855 N. Wolfe Street, Baltimore, MD 21205 USA.
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47
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Berezovsky AD, Poisson LM, Cherba D, Webb CP, Transou AD, Lemke NW, Hong X, Hasselbach LA, Irtenkauf SM, Mikkelsen T, deCarvalho AC. Sox2 promotes malignancy in glioblastoma by regulating plasticity and astrocytic differentiation. Neoplasia 2014; 16:193-206, 206.e19-25. [PMID: 24726753 DOI: 10.1016/j.neo.2014.03.006] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 02/20/2014] [Accepted: 02/24/2014] [Indexed: 01/10/2023] Open
Abstract
The high-mobility group-box transcription factor sex-determining region Y-box 2 (Sox2) is essential for the maintenance of stem cells from early development to adult tissues. Sox2 can reprogram differentiated cells into pluripotent cells in concert with other factors and is overexpressed in various cancers. In glioblastoma (GBM), Sox2 is a marker of cancer stemlike cells (CSCs) in neurosphere cultures and is associated with the proneural molecular subtype. Here, we report that Sox2 expression pattern in GBM tumors and patient-derived mouse xenografts is not restricted to a small percentage of cells and is coexpressed with various lineage markers, suggesting that its expression extends beyond CSCs to encompass more differentiated neoplastic cells across molecular subtypes. Employing a CSC derived from a patient with GBM and isogenic differentiated cell model, we show that Sox2 knockdown in the differentiated state abolished dedifferentiation and acquisition of CSC phenotype. Furthermore, Sox2 deficiency specifically impaired the astrocytic component of a biphasic gliosarcoma xenograft model while allowing the formation of tumors with sarcomatous phenotype. The expression of genes associated with stem cells and malignancy were commonly downregulated in both CSCs and serum-differentiated cells on Sox2 knockdown. Genes previously shown to be associated with pluripontency and CSCs were only affected in the CSC state, whereas embryonic stem cell self-renewal genes and cytokine signaling were downregulated, and the Wnt pathway activated in differentiated Sox2-deficient cells. Our results indicate that Sox2 regulates the expression of key genes and pathways involved in GBM malignancy, in both cancer stemlike and differentiated cells, and maintains plasticity for bidirectional conversion between the two states, with significant clinical implications.
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Affiliation(s)
| | - Laila M Poisson
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI
| | - David Cherba
- Program of Translational Medicine, Van Andel Research Institute, Grand Rapids, MI
| | - Craig P Webb
- Program of Translational Medicine, Van Andel Research Institute, Grand Rapids, MI
| | | | - Nancy W Lemke
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI
| | - Xin Hong
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI
| | | | | | - Tom Mikkelsen
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI; Department of Neurology, Henry Ford Hospital, Detroit, MI
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Popovic J, Stanisavljevic D, Schwirtlich M, Klajn A, Marjanovic J, Stevanovic M. Expression analysis of SOX14 during retinoic acid induced neural differentiation of embryonal carcinoma cells and assessment of the effect of its ectopic expression on SOXB members in HeLa cells. PLoS One 2014; 9:e91852. [PMID: 24637840 PMCID: PMC3956720 DOI: 10.1371/journal.pone.0091852] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 02/17/2014] [Indexed: 12/01/2022] Open
Abstract
SOX14 is a member of the SOXB2 subgroup of transcription factors implicated in neural development. Although the first SOX14 gene in vertebrates was cloned and characterized more than a decade ago and its expression profile during development was revealed in various animal model systems, the role of this gene during neural development is largely unknown. In the present study we analyzed the expression of SOX14 in human NT2/D1 and mouse P19 pluripotent embryonal carcinoma cells. We demonstrated that it is expressed in both cell lines and upregulated during retinoic acid induced neural differentiation. We showed that SOX14 was expressed in both neuronal and non-neuronal differentiated derivatives, as revealed by immunocytochemistry. Since it was previously proposed that increased SOXB2 proteins level interfere with the activity of SOXB1 counteracting partners, we compared expression patterns of SOXB members during retinoic acid induction of embryonal carcinoma cells. We revealed that upregulation of SOX14 expression is accompanied by alterations in the expression patterns of SOXB1 members. In order to analyze the potential cross-talk between them, we generated SOX14 expression construct. The ectopic expression of SOX14 was demonstrated at the mRNA level in NT2/D1, P19 and HeLa cells, while an increased level of SOX14 protein was detected in HeLa cells only. By transient transfection experiments in HeLa cells we showed for the first time that ectopic expression of SOX14 repressed SOX1 expression, whereas no significant effect on SOX2, SOX3 and SOX21 was observed. Data presented here provide an insight into SOX14 expression during in vitro neural differentiation of embryonal carcinoma cells and demonstrate the effect of its ectopic expression on protein levels of SOXB members in HeLa cells. Obtained results contribute to better understanding the role of one of the most conserved SOX proteins.
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Affiliation(s)
- Jelena Popovic
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
- * E-mail:
| | - Danijela Stanisavljevic
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Marija Schwirtlich
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Andrijana Klajn
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Jelena Marjanovic
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Milena Stevanovic
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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Bhat-Nakshatri P, Goswami CP, Badve S, Sledge GW, Nakshatri H. Identification of FDA-approved drugs targeting breast cancer stem cells along with biomarkers of sensitivity. Sci Rep 2014; 3:2530. [PMID: 23982413 PMCID: PMC3965360 DOI: 10.1038/srep02530] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 08/12/2013] [Indexed: 12/16/2022] Open
Abstract
Recently developed genomics-based tools are allowing repositioning of Food and Drug Administration (FDA)-approved drugs as cancer treatments, which were employed to identify drugs that target cancer stem cells (CSCs) of breast cancer. Gene expression datasets of CSCs from six studies were subjected to connectivity map to identify drugs that may ameliorate gene expression patterns unique to CSCs. All-trans retinoic acid (ATRA) was negatively connected with gene expression in CSCs. ATRA reduced mammosphere-forming ability of a subset of breast cancer cells, which correlated with induction of apoptosis, reduced expression of SOX2 but elevated expression of its antagonist CDX2. SOX2/CDX2 ratio had prognostic relevance in CSC-enriched breast cancers. K-ras mutant breast cancer cell line enriched for CSCs was resistant to ATRA, which was reversed by MAP kinase inhibitors. Thus, ATRA alone or in combination can be tested for efficacy using SOX2, CDX2, and K-ras mutation/MAPK activation status as biomarkers of response.
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50
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Guarino AT, McKinnon RD. Reprogramming cells for brain repair. Brain Sci 2013; 3:1215-28. [PMID: 24961526 PMCID: PMC4061879 DOI: 10.3390/brainsci3031215] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 07/27/2013] [Accepted: 07/30/2013] [Indexed: 12/16/2022] Open
Abstract
At present there are no clinical therapies that can repair traumatic brain injury, spinal cord injury or degenerative brain disease. While redundancy and rewiring of surviving circuits can recover some lost function, the brain and spinal column lack sufficient endogenous stem cells to replace lost neurons or their supporting glia. In contrast, pre-clinical studies have demonstrated that exogenous transplants can have remarkable efficacy for brain repair in animal models. Mesenchymal stromal cells (MSCs) can provide paracrine factors that repair damage caused by ischemic injury, and oligodendrocyte progenitor cell (OPC) grafts give dramatic functional recovery from spinal cord injury. These studies have progressed to clinical trials, including human embryonic stem cell (hESC)-derived OPCs for spinal cord repair. However, ESC-derived allografts are less than optimal, and we need to identify a more appropriate donor graft population. The cell reprogramming field has developed the ability to trans-differentiate somatic cells into distinct cell types, a technology that has the potential to generate autologous neurons and glia which address the histocompatibility concerns of allografts and the tumorigenicity concerns of ESC-derived grafts. Further clarifying how cell reprogramming works may lead to more efficient direct reprogram approaches, and possibly in vivo reprogramming, in order to promote brain and spinal cord repair.
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Affiliation(s)
- Alyx T Guarino
- Neurosurgery, Rutgers-Robert Wood Johnson Medical School, 125 Patterson St. CAB 7084, New Brunswick, NJ 08903, USA.
| | - Randall D McKinnon
- Neurosurgery, Rutgers-Robert Wood Johnson Medical School, 125 Patterson St. CAB 7084, New Brunswick, NJ 08903, USA.
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