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Niharika, Ureka L, Roy A, Patra SK. Dissecting SOX2 expression and function reveals an association with multiple signaling pathways during embryonic development and in cancer progression. Biochim Biophys Acta Rev Cancer 2024; 1879:189136. [PMID: 38880162 DOI: 10.1016/j.bbcan.2024.189136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 06/18/2024]
Abstract
SRY (Sex Determining Region) box 2 (SOX2) is an essential transcription factor that plays crucial roles in activating genes involved in pre- and post-embryonic development, adult tissue homeostasis, and lineage specifications. SOX2 maintains the self-renewal property of stem cells and is involved in the generation of induced pluripotency stem cells. SOX2 protein contains a particular high-mobility group domain that enables SOX2 to achieve the capacity to participate in a broad variety of functions. The information about the involvement of SOX2 with gene regulatory elements, signaling networks, and microRNA is gradually emerging, and the higher expression of SOX2 is functionally relevant to various cancer types. SOX2 facilitates the oncogenic phenotype via cellular proliferation and enhancement of invasive tumor properties. Evidence are accumulating in favor of three dimensional (higher order) folding of chromatin and epigenetic control of the SOX2 gene by chromatin modifications, which implies that the expression level of SOX2 can be modulated by epigenetic regulatory mechanisms, specifically, via DNA methylation and histone H3 modification. In view of this, and to focus further insights into the roles SOX2 plays in physiological functions, involvement of SOX2 during development, precisely, the advances of our knowledge in pre- and post-embryonic development, and interactions of SOX2 in this scenario with various signaling pathways in tumor development and cancer progression, its potential as a therapeutic target against many cancers are summarized and discussed in this article.
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Affiliation(s)
- Niharika
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Lina Ureka
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Ankan Roy
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
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2
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Zhao R, Moore EL, Gogol MM, Unruh JR, Yu Z, Scott AR, Wang Y, Rajendran NK, Trainor PA. Identification and characterization of intermediate states in mammalian neural crest cell epithelial to mesenchymal transition and delamination. eLife 2024; 13:RP92844. [PMID: 38873887 PMCID: PMC11178358 DOI: 10.7554/elife.92844] [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] [Indexed: 06/15/2024] Open
Abstract
Epithelial to mesenchymal transition (EMT) is a cellular process that converts epithelial cells to mesenchymal cells with migratory potential in developmental and pathological processes. Although originally considered a binary event, EMT in cancer progression involves intermediate states between a fully epithelial and a fully mesenchymal phenotype, which are characterized by distinct combinations of epithelial and mesenchymal markers. This phenomenon has been termed epithelial to mesenchymal plasticity (EMP), however, the intermediate states remain poorly described and it's unclear whether they exist during developmental EMT. Neural crest cells (NCC) are an embryonic progenitor cell population that gives rise to numerous cell types and tissues in vertebrates, and their formation and delamination is a classic example of developmental EMT. However, whether intermediate states also exist during NCC EMT and delamination remains unknown. Through single-cell RNA sequencing of mouse embryos, we identified intermediate NCC states based on their transcriptional signature and then spatially defined their locations in situ in the dorsolateral neuroepithelium. Our results illustrate the importance of cell cycle regulation and functional role for the intermediate stage marker Dlc1 in facilitating mammalian cranial NCC delamination and may provide new insights into mechanisms regulating pathological EMP.
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Affiliation(s)
- Ruonan Zhao
- Stowers Institute for Medical ResearchKansas CityUnited States
- Department of Anatomy and Cell Biology, University of Kansas Medical CenterKansas CityUnited States
| | - Emma L Moore
- Stowers Institute for Medical ResearchKansas CityUnited States
| | | | - Jay R Unruh
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Zulin Yu
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Allison R Scott
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Yan Wang
- Stowers Institute for Medical ResearchKansas CityUnited States
| | | | - Paul A Trainor
- Stowers Institute for Medical ResearchKansas CityUnited States
- Department of Anatomy and Cell Biology, University of Kansas Medical CenterKansas CityUnited States
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3
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Ambekar YS, Caiaffa CD, Wlodarczyk BJ, Singh M, Schill AW, Steele JW, Zhang J, Aglyamov SR, Scarcelli G, Finnell RH, Larin KV. Optical coherence tomography-guided Brillouin microscopy highlights regional tissue stiffness differences during anterior neural tube closure in the Mthfd1l murine mutant. Development 2024; 151:dev202475. [PMID: 38682273 PMCID: PMC11165724 DOI: 10.1242/dev.202475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 04/18/2024] [Indexed: 05/01/2024]
Abstract
Neurulation is a highly synchronized biomechanical process leading to the formation of the brain and spinal cord, and its failure leads to neural tube defects (NTDs). Although we are rapidly learning the genetic mechanisms underlying NTDs, the biomechanical aspects are largely unknown. To understand the correlation between NTDs and tissue stiffness during neural tube closure (NTC), we imaged an NTD murine model using optical coherence tomography (OCT), Brillouin microscopy and confocal fluorescence microscopy. Here, we associate structural information from OCT with local stiffness from the Brillouin signal of embryos undergoing neurulation. The stiffness of neuroepithelial tissues in Mthfd1l null embryos was significantly lower than that of wild-type embryos. Additionally, exogenous formate supplementation improved tissue stiffness and gross embryonic morphology in nullizygous and heterozygous embryos. Our results demonstrate the significance of proper tissue stiffness in normal NTC and pave the way for future studies on the mechanobiology of normal and abnormal embryonic development.
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Affiliation(s)
| | - Carlo Donato Caiaffa
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pediatrics, Dell Pediatric Research Institute, Dell Medical School, University of Texas at Austin, Austin, TX 78723, USA
| | - Bogdan J. Wlodarczyk
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Manmohan Singh
- Department of Biomedical Engineering, University of Houston, Houston, TX 77204, USA
| | - Alexander W. Schill
- Department of Biomedical Engineering, University of Houston, Houston, TX 77204, USA
| | - John W. Steele
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jitao Zhang
- Department of Biomedical Engineering, Wayne State University, Detroit, MI 48201, USA
| | - Salavat R. Aglyamov
- Department of Mechanical Engineering, University of Houston, Houston, TX 77204, USA
| | - Giuliano Scarcelli
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Richard H. Finnell
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kirill V. Larin
- Department of Biomedical Engineering, University of Houston, Houston, TX 77204, USA
- Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
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Yang S, Jiao D, Song T, Rui P, Fan R, Ma Z. Gene expression profiles of skin from cyclin dependent kinases 5-knockdown mice. Anim Biosci 2024; 37:567-575. [PMID: 37946423 PMCID: PMC10915219 DOI: 10.5713/ab.23.0244] [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: 07/04/2023] [Revised: 07/15/2023] [Accepted: 10/02/2023] [Indexed: 11/12/2023] Open
Abstract
OBJECTIVE This study aimed to identify genes regulated by cyclin dependent kinases 5 (CDK5) that participate in hair pigmentation in mice. METHODS The mRNA expression profiles of skin samples from CDK5-knockdown mice were constructed using high-throughput RNA sequencing and compared with those of wild-type mice. RESULTS In total, 8,002 known genes were differentially expressed between CDK5-knockdown and wild-type mice. Of these, 3,658 were upregulated and 4,344 were downregulated in the skin of CDK5-knockdown mice. An additional 318 previously unknown genes were also differentially expressed, with 171 downregulated and 147 upregulated genes in the skin of CDK5-knockdown mice. Of the known genes expressed in mouse skin, 80 were associated with hair color, with 61 showing lower expression and 19 exhibiting higher expression in skin of CDK5-knockdown mice. Importantly, the expression of the tyrosinase-related protein 1 (TYRP1) and the calcium signaling pathway were also found to be regulated by CDK5, suggesting that pigmentation is regulated by CDK5 via the calcium signaling pathway and TYRP1. CONCLUSION The transcriptome profiles obtained from the skin of CDK5-knockdown mice compared to wild-type mice provide a valuable resource to help understand the mechanism by which CDK5 regulates melanogenesis in mice and other animals.
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Affiliation(s)
- Shanshan Yang
- College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066600,
China
- Hebei Key Laboratory of Veterinary Preventive Medicine, College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066600,
China
| | - Dingxing Jiao
- College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066600,
China
- Hebei Key Laboratory of Veterinary Preventive Medicine, College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066600,
China
| | - Tao Song
- College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066600,
China
- Hebei Key Laboratory of Veterinary Preventive Medicine, College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066600,
China
| | - Ping Rui
- College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066600,
China
- Hebei Key Laboratory of Veterinary Preventive Medicine, College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066600,
China
| | - Ruiwen Fan
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi 030801,
China
| | - Zengjun Ma
- College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066600,
China
- Hebei Key Laboratory of Veterinary Preventive Medicine, College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066600,
China
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Molin AN, Contentin R, Angelozzi M, Karvande A, Kc R, Haseeb A, Voskamp C, de Charleroy C, Lefebvre V. Skeletal growth is enhanced by a shared role for SOX8 and SOX9 in promoting reserve chondrocyte commitment to columnar proliferation. Proc Natl Acad Sci U S A 2024; 121:e2316969121. [PMID: 38346197 PMCID: PMC10895259 DOI: 10.1073/pnas.2316969121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/26/2023] [Indexed: 02/15/2024] Open
Abstract
SOX8 was linked in a genome-wide association study to human height heritability, but roles in chondrocytes for this close relative of the master chondrogenic transcription factor SOX9 remain unknown. We undertook here to fill this knowledge gap. High-throughput assays demonstrate expression of human SOX8 and mouse Sox8 in growth plate cartilage. In situ assays show that Sox8 is expressed at a similar level as Sox9 in reserve and early columnar chondrocytes and turned off when Sox9 expression peaks in late columnar and prehypertrophic chondrocytes. Sox8-/- mice and Sox8fl/flPrx1Cre and Sox9fl/+Prx1Cre mice (inactivation in limb skeletal cells) have a normal or near normal skeletal size. In contrast, juvenile and adult Sox8fl/flSox9fl/+Prx1Cre compound mutants exhibit a 15 to 20% shortening of long bones. Their growth plate reserve chondrocytes progress slowly toward the columnar stage, as witnessed by a delay in down-regulating Pthlh expression, in packing in columns and in elevating their proliferation rate. SOX8 or SOX9 overexpression in chondrocytes reveals not only that SOX8 can promote growth plate cell proliferation and differentiation, even upon inactivation of endogenous Sox9, but also that it is more efficient than SOX9, possibly due to greater protein stability. Altogether, these findings uncover a major role for SOX8 and SOX9 in promoting skeletal growth by stimulating commitment of growth plate reserve chondrocytes to actively proliferating columnar cells. Further, by showing that SOX8 is more chondrogenic than SOX9, they suggest that SOX8 could be preferred over SOX9 in therapies to promote cartilage formation or regeneration in developmental and degenerative cartilage diseases.
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Affiliation(s)
- Arnaud N. Molin
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Romain Contentin
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Marco Angelozzi
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Anirudha Karvande
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Ranjan Kc
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Abdul Haseeb
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Chantal Voskamp
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Charles de Charleroy
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Véronique Lefebvre
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
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Zhao R, Moore EL, Gogol MM, Unruh JR, Yu Z, Scott A, Wang Y, Rajendran NK, Trainor PA. Identification and characterization of intermediate states in mammalian neural crest cell epithelial to mesenchymal transition and delamination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.26.564204. [PMID: 37961316 PMCID: PMC10634855 DOI: 10.1101/2023.10.26.564204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Epithelial to mesenchymal transition (EMT) is a cellular process that converts epithelial cells to mesenchymal cells with migratory potential in both developmental and pathological processes. Although originally considered a binary event, EMT in cancer progression involves intermediate states between a fully epithelial and a fully mesenchymal phenotype, which are characterized by distinct combinations of epithelial and mesenchymal markers. This phenomenon has been termed epithelial to mesenchymal plasticity (EMP), however, the intermediate states remain poorly described and it's unclear whether they exist during developmental EMT. Neural crest cells (NCC) are an embryonic progenitor cell population that gives rise to numerous cell types and tissues in vertebrates, and their formation is a classic example of developmental EMT. An important feature of NCC development is their delamination from the neuroepithelium via EMT, following which NCC migrate throughout the embryo and undergo differentiation. NCC delamination shares similar changes in cellular state and structure with cancer cell invasion. However, whether intermediate states also exist during NCC EMT and delamination remains unknown. Through single cell RNA sequencing, we identified intermediate NCC states based on their transcriptional signature and then spatially defined their locations in situ in the dorsolateral neuroepithelium. Our results illustrate the progressive transcriptional and spatial transitions from premigratory to migratory cranial NCC during EMT and delamination. Of note gene expression and trajectory analysis indicate that distinct intermediate populations of NCC delaminate in either S phase or G2/M phase of the cell cycle, and the importance of cell cycle regulation in facilitating mammalian cranial NCC delamination was confirmed through cell cycle inhibition studies. Additionally, transcriptional knockdown revealed a functional role for the intermediate stage marker Dlc1 in regulating NCC delamination and migration. Overall, our work identifying and characterizing the intermediate cellular states, processes, and molecular signals that regulate mammalian NCC EMT and delamination furthers our understanding of developmental EMP and may provide new insights into mechanisms regulating pathological EMP.
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Affiliation(s)
- Ruonan Zhao
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Emma L. Moore
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | - Jay R. Unruh
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Zulin Yu
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Allison Scott
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Yan Wang
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | - Paul A. Trainor
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, USA
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7
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Piacentino ML, Fasse AJ, Camacho-Avila A, Grabylnikov I, Bronner ME. SMPD3 expression is spatially regulated in the developing embryo by SOXE factors. Dev Biol 2024; 506:31-41. [PMID: 38052296 PMCID: PMC10872304 DOI: 10.1016/j.ydbio.2023.11.011] [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: 08/10/2023] [Revised: 11/20/2023] [Accepted: 11/29/2023] [Indexed: 12/07/2023]
Abstract
During epithelial-to-mesenchymal transition (EMT), significant rearrangements occur in plasma membrane protein and lipid content that are important for membrane function and acquisition of cell motility. To gain insight into how neural crest cells regulate their lipid content at the transcriptional level during EMT, here we identify critical enhancer sequences that regulate the expression of SMPD3, a gene responsible for sphingomyelin hydrolysis to produce ceramide and necessary for neural crest EMT. We uncovered three enhancer regions within the first intron of the SMPD3 locus that drive reporter expression in distinct spatial and temporal domains, together collectively recapitulating the expression domains of endogenous SMPD3 within the ectodermal lineages. We further dissected one enhancer that is specifically active in the migrating neural crest. By mutating putative transcriptional input sites or knocking down upstream regulators, we find that the SOXE-family transcription factors SOX9 and SOX10 regulate the expression of SMPD3 in migrating neural crest cells. Further, ChIP-seq and nascent transcription analysis reveal that SOX10 directly regulates expression of an SMPD3 enhancer specific to migratory neural crest cells. Together these results shed light on how core components of developmental gene regulatory networks interact with metabolic effector genes to control changes in membrane lipid content.
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Affiliation(s)
- Michael L Piacentino
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA; Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Aria J Fasse
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Alexis Camacho-Avila
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Ilya Grabylnikov
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
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8
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Zhang X, Pant SM, Ritch CC, Tang HY, Shao H, Dweep H, Gong YY, Brooks R, Brafford P, Wolpaw AJ, Lee Y, Weeraratna A, Sehgal A, Herlyn M, Kossenkov A, Speicher D, Sorger PK, Santagata S, Dang CV. Cell state dependent effects of Bmal1 on melanoma immunity and tumorigenicity. Nat Commun 2024; 15:633. [PMID: 38245503 PMCID: PMC10799901 DOI: 10.1038/s41467-024-44778-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/05/2024] [Indexed: 01/22/2024] Open
Abstract
The circadian clock regulator Bmal1 modulates tumorigenesis, but its reported effects are inconsistent. Here, we show that Bmal1 has a context-dependent role in mouse melanoma tumor growth. Loss of Bmal1 in YUMM2.1 or B16-F10 melanoma cells eliminates clock function and diminishes hypoxic gene expression and tumorigenesis, which could be rescued by ectopic expression of HIF1α in YUMM2.1 cells. By contrast, over-expressed wild-type or a transcriptionally inactive mutant Bmal1 non-canonically sequester myosin heavy chain 9 (Myh9) to increase MRTF-SRF activity and AP-1 transcriptional signature, and shift YUMM2.1 cells from a Sox10high to a Sox9high immune resistant, mesenchymal cell state that is found in human melanomas. Our work describes a link between Bmal1, Myh9, mouse melanoma cell plasticity, and tumor immunity. This connection may underlie cancer therapeutic resistance and underpin the link between the circadian clock, MRTF-SRF and the cytoskeleton.
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Affiliation(s)
- Xue Zhang
- The Wistar Institute, Philadelphia, PA, USA.
- Ludwig Institute for Cancer Research, New York, NY, USA.
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Shishir M Pant
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Cecily C Ritch
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Yao-Yu Gong
- The Wistar Institute, Philadelphia, PA, USA
- Ludwig Institute for Cancer Research, New York, NY, USA
| | - Rebekah Brooks
- The Wistar Institute, Philadelphia, PA, USA
- Ludwig Institute for Cancer Research, New York, NY, USA
| | - Patricia Brafford
- The Wistar Institute, Philadelphia, PA, USA
- Ludwig Institute for Cancer Research, New York, NY, USA
| | - Adam J Wolpaw
- The Wistar Institute, Philadelphia, PA, USA
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Childhood Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yool Lee
- Department of Translational Medicine and Physiology, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
| | - Ashani Weeraratna
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Amita Sehgal
- Howard Hughes Medical Institute, Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sandro Santagata
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chi V Dang
- The Wistar Institute, Philadelphia, PA, USA.
- Ludwig Institute for Cancer Research, New York, NY, USA.
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
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9
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Merkuri F, Rothstein M, Simoes-Costa M. Histone lactylation couples cellular metabolism with developmental gene regulatory networks. Nat Commun 2024; 15:90. [PMID: 38167340 PMCID: PMC10762033 DOI: 10.1038/s41467-023-44121-1] [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: 03/31/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Embryonic cells exhibit diverse metabolic states. Recent studies have demonstrated that metabolic reprogramming drives changes in cell identity by affecting gene expression. However, the connection between cellular metabolism and gene expression remains poorly understood. Here we report that glycolysis-regulated histone lactylation couples the metabolic state of embryonic cells with chromatin organization and gene regulatory network (GRN) activation. We found that lactylation marks genomic regions of glycolytic embryonic tissues, like the neural crest (NC) and pre-somitic mesoderm. Histone lactylation occurs in the loci of NC genes as these cells upregulate glycolysis. This process promotes the accessibility of active enhancers and the deployment of the NC GRN. Reducing the deposition of the mark by targeting LDHA/B leads to the downregulation of NC genes and the impairment of cell migration. The deposition of lactyl-CoA on histones at NC enhancers is supported by a mechanism that involves transcription factors SOX9 and YAP/TEAD. These findings define an epigenetic mechanism that integrates cellular metabolism with the GRNs that orchestrate embryonic development.
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Affiliation(s)
- Fjodor Merkuri
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Megan Rothstein
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Marcos Simoes-Costa
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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10
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Jacobs-Li J, Tang W, Li C, Bronner ME. Single-cell profiling coupled with lineage analysis reveals vagal and sacral neural crest contributions to the developing enteric nervous system. eLife 2023; 12:e79156. [PMID: 37877560 PMCID: PMC10627514 DOI: 10.7554/elife.79156] [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: 04/01/2022] [Accepted: 10/23/2023] [Indexed: 10/26/2023] Open
Abstract
During development, much of the enteric nervous system (ENS) arises from the vagal neural crest that emerges from the caudal hindbrain and colonizes the entire gastrointestinal tract. However, a second ENS contribution comes from the sacral neural crest that arises in the caudal neural tube and populates the post-umbilical gut. By coupling single-cell transcriptomics with axial-level-specific lineage tracing in avian embryos, we compared the contributions of embryonic vagal and sacral neural crest cells to the chick ENS and the associated peripheral ganglia (Nerve of Remak and pelvic plexuses). At embryonic day (E) 10, the two neural crest populations form overlapping subsets of neuronal and glia cell types. Surprisingly, the post-umbilical vagal neural crest much more closely resembles the sacral neural crest than the pre-umbilical vagal neural crest. However, some differences in cluster types were noted between vagal and sacral derived cells. Notably, RNA trajectory analysis suggests that the vagal neural crest maintains a neuronal/glial progenitor pool, whereas this cluster is depleted in the E10 sacral neural crest which instead has numerous enteric glia. The present findings reveal sacral neural crest contributions to the hindgut and associated peripheral ganglia and highlight the potential influence of the local environment and/or developmental timing in differentiation of neural crest-derived cells in the developing ENS.
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Affiliation(s)
- Jessica Jacobs-Li
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Weiyi Tang
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Can Li
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
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11
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McLean DT, Meudt JJ, Lopez Rivera LD, Schomberg DT, Pavelec DM, Duellman TT, Buehler DG, Schwartz PB, Graham M, Lee LM, Graff KD, Reichert JL, Bon-Durant SS, Konsitzke CM, Ronnekleiv-Kelly SM, Shanmuganayagam D, Rubinstein CD. Single-cell RNA sequencing of neurofibromas reveals a tumor microenvironment favorable for neural regeneration and immune suppression in a neurofibromatosis type 1 porcine model. Front Oncol 2023; 13:1253659. [PMID: 37817770 PMCID: PMC10561395 DOI: 10.3389/fonc.2023.1253659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/11/2023] [Indexed: 10/12/2023] Open
Abstract
Neurofibromatosis Type 1 (NF1) is one of the most common genetically inherited disorders that affects 1 in 3000 children annually. Clinical manifestations vary widely but nearly always include the development of cutaneous, plexiform and diffuse neurofibromas that are managed over many years. Recent single-cell transcriptomics profiling efforts of neurofibromas have begun to reveal cell signaling processes. However, the cell signaling networks in mature, non-cutaneous neurofibromas remain unexplored. Here, we present insights into the cellular composition and signaling within mature neurofibromas, contrasting with normal adjacent tissue, in a porcine model of NF1 using single-cell RNA sequencing (scRNA-seq) analysis and histopathological characterization. These neurofibromas exhibited classic diffuse-type histologic morphology and expected patterns of S100, SOX10, GFAP, and CD34 immunohistochemistry. The porcine mature neurofibromas closely resemble human neurofibromas histologically and contain all known cellular components of their human counterparts. The scRNA-seq confirmed the presence of all expected cell types within these neurofibromas and identified novel populations of fibroblasts and immune cells, which may contribute to the tumor microenvironment by suppressing inflammation, promoting M2 macrophage polarization, increasing fibrosis, and driving the proliferation of Schwann cells. Notably, we identified tumor-associated IDO1 +/CD274+ (PD-L1) + dendritic cells, which represent the first such observation in any NF1 animal model and suggest the role of the upregulation of immune checkpoints in mature neurofibromas. Finally, we observed that cell types in the tumor microenvironment are poised to promote immune evasion, extracellular matrix reconstruction, and nerve regeneration.
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Affiliation(s)
- Dalton T. McLean
- Biotechnology Center, University of Wisconsin–Madison, Madison, WI, United States
- Molecular & Environmental Toxicology Program, University of Wisconsin–Madison, Madison, WI, United States
| | - Jennifer J. Meudt
- Biomedical & Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, WI, United States
| | - Loren D. Lopez Rivera
- Molecular & Environmental Toxicology Program, University of Wisconsin–Madison, Madison, WI, United States
| | - Dominic T. Schomberg
- Biomedical & Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, WI, United States
| | - Derek M. Pavelec
- Biotechnology Center, University of Wisconsin–Madison, Madison, WI, United States
| | - Tyler T. Duellman
- Biotechnology Center, University of Wisconsin–Madison, Madison, WI, United States
| | - Darya G. Buehler
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Patrick B. Schwartz
- Molecular & Environmental Toxicology Program, University of Wisconsin–Madison, Madison, WI, United States
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Melissa Graham
- Research Animal Resources and Compliance (RARC), Office of the Vice Chancellor for Research and Graduate Education, University of Wisconsin–Madison, Madison, WI, United States
| | - Laura M. Lee
- Research Animal Resources and Compliance (RARC), Office of the Vice Chancellor for Research and Graduate Education, University of Wisconsin–Madison, Madison, WI, United States
| | - Keri D. Graff
- Swine Research and Teaching Center, Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, WI, United States
| | - Jamie L. Reichert
- Swine Research and Teaching Center, Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, WI, United States
| | - Sandra S. Bon-Durant
- Biotechnology Center, University of Wisconsin–Madison, Madison, WI, United States
| | - Charles M. Konsitzke
- Biotechnology Center, University of Wisconsin–Madison, Madison, WI, United States
| | - Sean M. Ronnekleiv-Kelly
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Dhanansayan Shanmuganayagam
- Molecular & Environmental Toxicology Program, University of Wisconsin–Madison, Madison, WI, United States
- Biomedical & Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, WI, United States
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
- Center for Biomedical Swine Research and Innovation, University of Wisconsin–Madison, Madison, WI, United States
| | - C. Dustin Rubinstein
- Biotechnology Center, University of Wisconsin–Madison, Madison, WI, United States
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12
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Changmeng Z, Hongfei W, Cheung MCH, Chan YS, Shea GKH. Revealing the developmental origin and lineage predilection of neural progenitors within human bone marrow via single-cell analysis: implications for regenerative medicine. Genome Med 2023; 15:66. [PMID: 37667405 PMCID: PMC10476295 DOI: 10.1186/s13073-023-01224-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 08/24/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Human bone marrow stromal cells (BMSCs) are an easily accessible and expandable progenitor population with the capacity to generate neural cell types in addition to mesoderm. Lineage tracing studies in transgenic animals have indicated Nestin + BMSCs to be descended from the truncal neural crest. Single-cell analysis provides a means to identify the developmental origin and identity of human BMSC-derived neural progenitors when lineage tracing remains infeasible. This is a prerequisite towards translational application. METHODS We attained transcriptomic profiles of embryonic long bone, adult human bone marrow, cultured BMSCs and BMSC-derived neurospheres. Integrated scRNAseq analysis was supplemented by characterization of cells during culture expansion and following provision of growth factors and signalling agonists to bias lineage. RESULTS Reconstructed pseudotime upon the integrated dataset indicated distinct neural and osteogenic differentiation trajectories. The starting state towards the neural differentiation trajectory consisted of Nestin + /MKI67 + BMSCs, which could also be diverted towards the osteogenic trajectory via a branch point. Nestin + /PDGFRA + BMSCs responded to neurosphere culture conditions to generate a subpopulation of cells with a neuronal phenotype according to marker expression and gene ontogeny analysis that occupied the end state along the neural differentiation trajectory. Reconstructed pseudotime also revealed an upregulation of BMP4 expression during culture of BMSC-neurospheres. This provided the rationale for culture supplementation with the BMP signalling agonist SB4, which directed progenitors to upregulate Pax6 and downregulate Nestin. CONCLUSIONS This study suggested BMSCs originating from truncal neural crest to be the source of cells within long bone marrow possessing neural differentiation potential. Unravelling the transcriptomic dynamics of BMSC-derived neural progenitors promises to enhance differentiation efficiency and safety towards clinical application in cell therapy and disease modelling.
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Affiliation(s)
- Zhang Changmeng
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Wang Hongfei
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Martin Chi-Hang Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ying-Shing Chan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Graham Ka-Hon Shea
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.
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13
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Wu IC, Liou JW, Yang CH, Chen JH, Chen KY, Hung CH. Self-assembly of gelatin and collagen in the polyvinyl alcohol substrate and its influence on cell adhesion, proliferation, shape, spreading and differentiation. Front Bioeng Biotechnol 2023; 11:1193849. [PMID: 37520293 PMCID: PMC10375239 DOI: 10.3389/fbioe.2023.1193849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 07/03/2023] [Indexed: 08/01/2023] Open
Abstract
Culture substrates display profound influence on biological and developmental characteristic of cells cultured in vitro. This study investigates the influence of polyvinyl alcohol (PVA) substrates blended with different concentration of collagen or/and gelatin on the cell adhesion, proliferation, shape, spreading, and differentiation of stem cells. The collagen/gelatin blended PVA substrates were prepared by air drying. During drying, blended collagen or/and gelatin can self-assemble into macro-scale nucleated particles or branched fibrils in the PVA substrates that can be observed under the optical microscope. These collagen/gelatin blended substrates revealed different surface topography, z-average, roughness, surface adhesion and Young's modulus as examined by the atomic force microscope (AFM). The results of Fourier transform infrared spectroscopy (FTIR) analysis indicated that the absorption of amide I (1,600-1,700 cm-1) and amide II (1,500-1,600 cm-1) groups increased with increasing collagen and gelatin concentration blended and the potential of fibril formation. These collagen or/and gelatin blended PVA substrates showed enhanced NIH-3T3 fibroblast adhesion as comparing with the pure PVA, control tissue culture polystyrene, conventional collagen-coated and gelatin-coated wells. These highly adhesive PVA substrates also exhibit inhibited cell spreading and proliferation. It is also found that the shape of NIH-3T3 fibroblasts can be switched between oval, spindle and flattened shapes depending on the concentration of collagen or/and gelatin blended. For inductive differentiation of stem cells, it is found that number and ration of neural differentiation of rat cerebral cortical neural stem cells increase with the decreasing collagen concentration in the collagen-blended PVA substrates. Moreover, the PVA substrates blended with collagen or collagen and gelatin can efficiently support and conduct human pluripotent stem cells to differentiate into Oil-Red-O- and UCP-1-positive brown-adipocyte-like cells via ectodermal lineage without the addition of mitogenic factors. These results provide a useful and alternative platform for controlling cell behavior in vitro and may be helpful for future application in the field of regenerative medicine and tissue engineering.
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Affiliation(s)
- I-Chi Wu
- Institute of Medical Sciences, Tzu Chi University, Hualien City, Taiwan
- Plastic Surgery Division, Surgical Department, Hualien Armed Forces General Hospital, Hualien City, Taiwan
| | - Je-Wen Liou
- Institute of Medical Sciences, Tzu Chi University, Hualien City, Taiwan
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien City, Taiwan
| | - Chin-Hao Yang
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien City, Taiwan
| | - Jia-Hui Chen
- Institute of Medical Sciences, Tzu Chi University, Hualien City, Taiwan
- Department of Surgery, Taipei Tzu Chi Hospital, New Taipei City, Taiwan
| | - Kuan-Yu Chen
- Institute of Medical Sciences, Tzu Chi University, Hualien City, Taiwan
- Department of Surgery, New Taipei City Hospital, New Taipei City, Taiwan
| | - Chih-Huang Hung
- Institute of Medical Sciences, Tzu Chi University, Hualien City, Taiwan
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14
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Kidwai FK, Canalis E, Robey PG. Induced pluripotent stem cell technology in bone biology. Bone 2023; 172:116760. [PMID: 37028583 PMCID: PMC10228209 DOI: 10.1016/j.bone.2023.116760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
Technologies on the development and differentiation of human induced pluripotent stem cells (hiPSCs) are rapidly improving, and have been applied to create cell types relevant to the bone field. Differentiation protocols to form bona fide bone-forming cells from iPSCs are available, and can be used to probe details of differentiation and function in depth. When applied to iPSCs bearing disease-causing mutations, the pathogenetic mechanisms of diseases of the skeleton can be elucidated, along with the development of novel therapeutics. These cells can also be used for development of cell therapies for cell and tissue replacement.
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Affiliation(s)
- Fahad K Kidwai
- Skeletal Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, United States of America
| | - Ernesto Canalis
- Center for Skeletal Research, Orthopedic Surgery and Medicine, UConn Musculoskeletal Institute, UConn Health, Farmington, CT 06030-4037, United States of America
| | - Pamela G Robey
- Skeletal Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, United States of America.
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15
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Stüfchen I, Beyer F, Staebler S, Fischer S, Kappelmann M, Beckervordersandforth R, Bosserhoff AK. Sox9 regulates melanocytic fate decision of adult hair follicle stem cells. iScience 2023; 26:106919. [PMID: 37283806 PMCID: PMC10239701 DOI: 10.1016/j.isci.2023.106919] [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: 09/24/2022] [Revised: 03/02/2023] [Accepted: 05/14/2023] [Indexed: 06/08/2023] Open
Abstract
The bulge of hair follicles harbors Nestin+ (neural crest like) stem cells, which exhibit the potential to generate various cell types including melanocytes. In this study, we aimed to determine the role of Sox9, an important regulator during neural crest development, in melanocytic differentiation of those adult Nestin+ cells. Immunohistochemical analysis after conditional Sox9 deletion in Nestin+ cells of adult mice revealed that Sox9 is crucial for melanocytic differentiation of these cells and that Sox9 acts as a fate determinant between melanocytic and glial fate. A deeper understanding of factors that regulate fate decision, proliferation and differentiation of these stem cells provides new aspects to melanoma research as melanoma cells share many similarities with neural crest cells. In summary, we here show the important role of Sox9 in melanocytic versus glial fate decision of Nestin+ stem cells in the skin of adult mice.
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Affiliation(s)
- Isabel Stüfchen
- Institute of Biochemistry, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Felix Beyer
- Institute of Biochemistry, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Sebastian Staebler
- Institute of Biochemistry, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Stefan Fischer
- Faculty of Computer Science, Deggendorf Institute of Technology, Deggendorf, Germany
| | - Melanie Kappelmann
- Institute of Biochemistry, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
- Faculty of Computer Science, Deggendorf Institute of Technology, Deggendorf, Germany
| | | | - Anja K. Bosserhoff
- Institute of Biochemistry, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
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16
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Naqvi S, Kim S, Hoskens H, Matthews HS, Spritz RA, Klein OD, Hallgrímsson B, Swigut T, Claes P, Pritchard JK, Wysocka J. Precise modulation of transcription factor levels identifies features underlying dosage sensitivity. Nat Genet 2023; 55:841-851. [PMID: 37024583 PMCID: PMC10181932 DOI: 10.1038/s41588-023-01366-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 03/07/2023] [Indexed: 04/08/2023]
Abstract
Transcriptional regulation exhibits extensive robustness, but human genetics indicates sensitivity to transcription factor (TF) dosage. Reconciling such observations requires quantitative studies of TF dosage effects at trait-relevant ranges, largely lacking so far. TFs play central roles in both normal-range and disease-associated variation in craniofacial morphology; we therefore developed an approach to precisely modulate TF levels in human facial progenitor cells and applied it to SOX9, a TF associated with craniofacial variation and disease (Pierre Robin sequence (PRS)). Most SOX9-dependent regulatory elements (REs) are buffered against small decreases in SOX9 dosage, but REs directly and primarily regulated by SOX9 show heightened sensitivity to SOX9 dosage; these RE responses partially predict gene expression responses. Sensitive REs and genes preferentially affect functional chondrogenesis and PRS-like craniofacial shape variation. We propose that such REs and genes underlie the sensitivity of specific phenotypes to TF dosage, while buffering of other genes leads to robust, nonlinear dosage-to-phenotype relationships.
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Affiliation(s)
- Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Departments of Genetics and Biology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Seungsoo Kim
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Hanne Hoskens
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Harold S Matthews
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Richard A Spritz
- Human Medical Genetics and Genomics Program and Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ophir D Klein
- Departments of Orofacial Sciences and Pediatrics, Program in Craniofacial Biology, and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Benedikt Hallgrímsson
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | | | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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17
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Iyer S, Dhiman N, Zade SP, Mukherjee S, Singla N, Kumar M. Exposure to Tetrabutylammonium Bromide Impairs Cranial Neural Crest Specification, Neurogenic Program, and Brain Morphogenesis. ACS Chem Neurosci 2023; 14:1785-1798. [PMID: 37125651 DOI: 10.1021/acschemneuro.2c00728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Tetrabutylammonium bromide (TBAB) is a widely used industrial reagent and is commonly found in our aquatic ecosystem as an industrial byproduct. In humans, the ingestion of TBAB causes severe neurological impairments and disorders such as vertigo, hallucinations, and delirium. Yet, the extent of environmental risk and TBAB toxicity to human health is poorly understood. In this study, we aim to determine the developmental toxicity of TBAB using zebrafish embryos as a model and provide novel insights into the mechanism of action of such chemicals on neurodevelopment and the overall embryonic program. Our results show that exposure to TBAB results in impaired development of the brain, inner ear, and pharyngeal skeletal elements in the zebrafish embryo. TBAB treatment resulted in aberrations in the specification of the neural crest precursors, hindbrain segmentation, and otic neurogenesis. TBAB treatment also induced a surge in apoptosis in the head, tail, and trunk regions of the developing embryo. Long-term TBAB exposure resulted in cardiac edema and craniofacial defects. Further, in silico molecular docking analysis indicated that TBAB binds to AMPA receptors and modulates neural developmental genes such as olfactomedin and acetylcholinesterase in the embryonic brain. To summarize, our study highlights the novel effects of TBAB on embryonic brain formation and segmentation, ear morphogenesis, and craniofacial skeletal development.
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Affiliation(s)
- Sharada Iyer
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Uppal Road, Habsiguda, Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Neha Dhiman
- Department of Biochemistry, Panjab University, Chandigarh160014, India
| | - Suraj P Zade
- Global Product Compliance─India, 301, Samved Sankul, Near MLA Hostel, Civil Lines, Nagpur 440001, India
| | - Sulagna Mukherjee
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Uppal Road, Habsiguda, Hyderabad 500007, India
| | - Neha Singla
- Department of Biophysics, Panjab University, Chandigarh160014, India
| | - Megha Kumar
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Uppal Road, Habsiguda, Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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18
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Moazeny M, Dehbashi M, Hojati Z, Esmaeili F. Investigating neural differentiation of mouse P19 embryonic stem cells in a time-dependent manner by bioinformatic, microscopic and transcriptional analyses. Mol Biol Rep 2023; 50:2183-2194. [PMID: 36565416 DOI: 10.1007/s11033-022-08166-7] [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: 08/16/2021] [Accepted: 09/23/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND As an available cell line, mouse pluripotent P19 has been widely employed for neuronal differentiation studies. In this research, by applying the in vitro differentiation of this cell line into neuron-like cells through retinoic acid (RA) treatment, the roles of some genes including DNMT3B, ICAM1, IRX3, JAK2, LHX1, SOX9, TBX3 and THY1 in neural differentiation was investigated. METHODS AND RESULTS Bioinformatics, microscopic, and transcriptional studies were conducted in a time-dependent manner after RA-induced neural differentiation. According to bioinformatics studies, we determined the engagement of the metabolic and developmental super-pathways and pathways in neural cell differentiation, particularly focusing on the considered genes. According to our qRT-PCR analyses, JAK2, SOX9, TBX3, LHX1 and IRX3 genes were found to be significantly overexpressed in a time-dependent manner (p < 0.05). In addition, the significant downregulation of THY1, DNMT3B and ICAM1 genes was observed during the experiment (p < 0.05). The optical microscopic investigation showed that the specialized extensions of the neuron-like cells were revealed on day 8 after RA treatment. CONCLUSION Accordingly, the neural differentiation of P19 cell line and the role of the considered genes during the differentiation were proved. However, our results warrant further in vivo studies.
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Affiliation(s)
- Marzieh Moazeny
- Division of Genetics, Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, 81746-73441, Isfahan, Iran
| | - Moein Dehbashi
- Division of Genetics, Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, 81746-73441, Isfahan, Iran
| | - Zohreh Hojati
- Division of Genetics, Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, 81746-73441, Isfahan, Iran.
| | - Fariba Esmaeili
- Division of Animal Sciences, Department of Plant and Animal Biology, Faculty of Biological Science and Technology, University of Isfahan, 81746-73441, Isfahan, Iran
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19
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Shin H, Min JK, Kim NR, Seo KY, Chin HS, Lee S, Jung JW. Effects of Y-27632, a Rho-associated Kinase Inhibitor, on Human Corneal Endothelial Cells Cultured by Isolating Human Corneal Endothelial Progenitor Cells. KOREAN JOURNAL OF OPHTHALMOLOGY 2023; 37:31-41. [PMID: 36549303 PMCID: PMC9935058 DOI: 10.3341/kjo.2022.0133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/05/2022] [Indexed: 12/24/2022] Open
Abstract
CONCLUSIONS Y-27632 enabled the isolation and expansion of HCEPs. It also enhanced the proliferation, viability, and migration of differentiated HCEPs. METHODS HCEPs were isolated and expanded in a medium with and without 10μM Y-27632, and then differentiated into HCECs in a medium with fetal bovine serum. The characteristics of HCEPs and differentiated HCEPs were confirmed by immunofluorescence staining. The proliferation, viability, morphology, and wound-healing ability of differentiated HCEPs were assessed in the presence of different concentrations of Y-27632. PURPOSE Human corneal endothelial progenitor cells (HCEPs), which has been selectively isolated and differentiated into human corneal endothelial cells (HCECs), are crucial for repairing corneal endothelial damage. In this study, we evaluated the roles of a Rho-assisted kinase (ROCK) inhibitor, Y-27632, on the isolation and expansion of HCEPs, and assessed the in vitro effects of different concentrations of Y-27632 on the differentiated HCEPs. RESULTS Y-27632 enabled the isolation and expansion of HCEPs from the corneal endothelium. The differentiated HCEPs showed an optimal increase in proliferation and survival in the presence of 10μM Y-27632. As the concentration of Y-27632 increased, differentiated HCEPs became elongated, and actin filaments were redistributed to the periphery of cells. Y-27632 also caused a concentration-dependent enhancement in the wound-healing ability of differentiated HCEPs.
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Affiliation(s)
- Haeeun Shin
- Department of Ophthalmology, Inha Vision Science Laboratory, Inha University College of Medicine, Incheon,
Korea
| | - Joon Ki Min
- Department of Ophthalmology, Inha Vision Science Laboratory, Inha University College of Medicine, Incheon,
Korea
| | - Na Rae Kim
- Department of Ophthalmology, Inha Vision Science Laboratory, Inha University College of Medicine, Incheon,
Korea
| | - Kyoung Yul Seo
- Department of Ophthalmology, Severance Hospital, Yonsei University College of Medicine, Seoul,
Korea
| | - Hee Seung Chin
- Department of Ophthalmology, Inha Vision Science Laboratory, Inha University College of Medicine, Incheon,
Korea
| | - Soyoung Lee
- Translational Research Center, Inha University College of Medicine, Incheon,
Korea
| | - Ji Won Jung
- Department of Ophthalmology, Inha Vision Science Laboratory, Inha University College of Medicine, Incheon,
Korea
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20
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Chromatin remodeler CHD7 targets active enhancer region to regulate cell type-specific gene expression in human neural crest cells. Sci Rep 2022; 12:22648. [PMID: 36587182 PMCID: PMC9805427 DOI: 10.1038/s41598-022-27293-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023] Open
Abstract
A mutation in the chromatin remodeler chromodomain helicase DNA-binding 7 (CHD7) gene causes the multiple congenital anomaly CHARGE syndrome. The craniofacial anomalies observed in CHARGE syndrome are caused by dysfunctions of neural crest cells (NCCs), which originate from the neural tube. However, the mechanism by which CHD7 regulates the function of human NCCs (hNCCs) remains unclear. We aimed to characterize the cis-regulatory elements governed by CHD7 in hNCCs by analyzing genome-wide ChIP-Seq data and identifying hNCC-specific CHD7-binding profiles. We compared CHD7-binding regions among cell types, including human induced pluripotent stem cells and human neuroepithelial cells, to determine the comprehensive properties of CHD7-binding in hNCCs. Importantly, analysis of the hNCC-specific CHD7-bound region revealed transcription factor AP-2α as a potential co-factor facilitating the cell type-specific transcriptional program in hNCCs. CHD7 was strongly associated with active enhancer regions, permitting the expression of hNCC-specific genes to sustain the function of hNCCs. Our findings reveal the regulatory mechanisms of CHD7 in hNCCs, thus providing additional information regarding the transcriptional programs in hNCCs.
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21
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Elf3 deficiency during zebrafish development alters extracellular matrix organization and disrupts tissue morphogenesis. PLoS One 2022; 17:e0276255. [DOI: 10.1371/journal.pone.0276255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 10/03/2022] [Indexed: 11/17/2022] Open
Abstract
E26 transformation specific (ETS) family transcription factors are expressed during embryogenesis and are involved in various cellular processes such as proliferation, migration, differentiation, angiogenesis, apoptosis, and survival of cellular lineages to ensure appropriate development. Dysregulated expression of many of the ETS family members is detected in different cancers. The human ELF3, a member of the ETS family of transcription factors, plays a role in the induction and progression of human cancers is well studied. However, little is known about the role of ELF3 in early development. Here, the zebrafish elf3 was cloned, and its expression was analyzed during zebrafish development. Zebrafish elf3 is maternally deposited. At different developmental stages, elf3 expression was detected in different tissue, mainly neural tissues, endoderm-derived tissues, cartilage, heart, pronephric duct, blood vessels, and notochord. The expression levels were high at the tissue boundaries. Elf3 loss-of-function consequences were examined by using translation blocking antisense morpholino oligonucleotides, and effects were validated using CRISPR/Cas9 knockdown. Elf3-knockdown produced short and bent larvae with notochord, craniofacial cartilage, and fin defects. The extracellular matrix (ECM) in the fin and notochord was disorganized. Neural defects were also observed. Optic nerve fasciculation (bundling) and arborization in the optic tectum were defective in Elf3-morphants, and fragmentation of spinal motor neurons were evident. Dysregulation of genes encoding ECM proteins and matrix metalloprotease (MMP) and disorganization of ECM may play a role in the observed defects in Elf3 morphants. We conclude that zebrafish Elf3 is required for epidermal, mesenchymal, and neural tissue development.
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22
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Transcriptome Analyses Provide Insights into the Auditory Function in Trachemys scripta elegans. Animals (Basel) 2022; 12:ani12182410. [PMID: 36139269 PMCID: PMC9495000 DOI: 10.3390/ani12182410] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/05/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
An auditory ability is essential for communication in vertebrates, and considerable attention has been paid to auditory sensitivity in mammals, birds, and frogs. Turtles were thought to be deaf for a long time; however, recent studies have confirmed the presence of an auditory ability in Trachemys scripta elegans as well as sex-related differences in hearing sensitivity. Earlier studies mainly focused on the morphological and physiological functions of the hearing organ in turtles; thus, the gene expression patterns remain unclear. In this study, 36 transcriptomes from six tissues (inner ear, tympanic membrane, brain, eye, lung, and muscle) were sequenced to explore the gene expression patterns of the hearing system in T. scripta elegans. A weighted gene co-expression network analysis revealed that hub genes related to the inner ear and tympanic membrane are involved in development and signal transduction. Moreover, we identified six differently expressed genes (GABRA1, GABRG2, GABBR2, GNAO1, SLC38A1, and SLC12A5) related to the GABAergic synapse pathway as candidate genes to explain the differences in sexually dimorphic hearing sensitivity. Collectively, this study provides a critical foundation for genetic research on auditory functions in turtles.
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Abstract
Neural crest cells (NCCs) are a dynamic, multipotent, vertebrate-specific population of embryonic stem cells. These ectodermally-derived cells contribute to diverse tissue types in developing embryos including craniofacial bone and cartilage, the peripheral and enteric nervous systems and pigment cells, among a host of other cell types. Due to their contribution to a significant number of adult tissue types, the mechanisms that drive their formation, migration and differentiation are highly studied. NCCs have a unique ability to transition from tightly adherent epithelial cells to mesenchymal and migratory cells by altering their polarity, expression of cell-cell adhesion molecules and gaining invasive abilities. In this Review, we discuss classical and emerging factors driving NCC epithelial-to-mesenchymal transition and migration, highlighting the role of signaling and transcription factors, as well as novel modifying factors including chromatin remodelers, small RNAs and post-translational regulators, which control the availability and longevity of major NCC players.
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24
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Sá da Bandeira D, Kilpatrick AM, Marques M, Gomez-Salazar M, Ventura T, Gonzalez ZN, Stefancova D, Rossi F, Vermeren M, Vink CS, Beltran M, Henderson NC, Jung B, van der Linden R, van de Werken HJG, van Ijcken WFJ, Betsholtz C, Forbes SJ, Cuervo H, Crisan M. PDGFRβ + cells play a dual role as hematopoietic precursors and niche cells during mouse ontogeny. Cell Rep 2022; 40:111114. [PMID: 35858557 PMCID: PMC9638014 DOI: 10.1016/j.celrep.2022.111114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/18/2022] [Accepted: 06/28/2022] [Indexed: 11/27/2022] Open
Abstract
Hematopoietic stem cell (HSC) generation in the aorta-gonad-mesonephros region requires HSC specification signals from the surrounding microenvironment. In zebrafish, PDGF-B/PDGFRβ signaling controls hematopoietic stem/progenitor cell (HSPC) generation and is required in the HSC specification niche. Little is known about murine HSPC specification in vivo and whether PDGF-B/PDGFRβ is involved. Here, we show that PDGFRβ is expressed in distinct perivascular stromal cell layers surrounding the mid-gestation dorsal aorta, and its deletion impairs hematopoiesis. We demonstrate that PDGFRβ+ cells play a dual role in murine hematopoiesis. They act in the aortic niche to support HSPCs, and in addition, PDGFRβ+ embryonic precursors give rise to a subset of HSPCs that persist into adulthood. These findings provide crucial information for the controlled production of HSPCs in vitro. PDGFRβ deletion affects hematopoietic development in the AGM in vivo The transcriptome and hematopoietic support of the PDGFRβ-KO niche are altered The osteogenic gene profile and differentiation of KO AGM MSCs are affected PDGFRβ+ early embryonic precursors contribute to EC and HSPC lineages in vivo
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Affiliation(s)
- Diana Sá da Bandeira
- Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, EH16 4TJ Edinburgh, UK; Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, EH16 4UU Edinburgh, UK
| | - Alastair Morris Kilpatrick
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, EH16 4UU Edinburgh, UK
| | - Madalena Marques
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, EH16 4UU Edinburgh, UK
| | - Mario Gomez-Salazar
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, EH16 4UU Edinburgh, UK
| | - Telma Ventura
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, EH16 4UU Edinburgh, UK
| | - Zaniah Nashira Gonzalez
- Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, EH16 4TJ Edinburgh, UK; Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, EH16 4UU Edinburgh, UK
| | - Dorota Stefancova
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, EH16 4UU Edinburgh, UK
| | - Fiona Rossi
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, EH16 4UU Edinburgh, UK
| | - Matthieu Vermeren
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, EH16 4UU Edinburgh, UK
| | - Chris Sebastiaan Vink
- Centre for Inflammation Research, Institute for Regeneration and Repair, The Queen's Medical Research Institute, University of Edinburgh, EH16 4TJ Edinburgh, UK
| | - Mariana Beltran
- Centre for Inflammation Research, Institute for Regeneration and Repair, The Queen's Medical Research Institute, University of Edinburgh, EH16 4TJ Edinburgh, UK
| | - Neil Cowan Henderson
- Centre for Inflammation Research, Institute for Regeneration and Repair, The Queen's Medical Research Institute, University of Edinburgh, EH16 4TJ Edinburgh, UK; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH4 2XU Edinburgh, UK
| | - Bongnam Jung
- Department of Immunology, Genetics, and Pathology, Uppsala University, 751 85 Uppsala, Sweden; Harvard Medical School, Department of Surgery, Boston Children's Hospital, Boston, MA 02115, USA
| | - Reinier van der Linden
- Hubrecht Institute, Department van Oudenaarden Quantitative Biology, 3584 Utrecht, the Netherlands
| | - Harmen Jan George van de Werken
- Erasmus MC Cancer Institute, University Medical Center, Cancer Computational Biology Center, and Departments of Urology and Immunology, 3000 Rotterdam, the Netherlands
| | - Wilfred F J van Ijcken
- Center for Biomics, Department of Cell Biology, Erasmus MC University Medical Centre, 3015 Rotterdam, the Netherlands
| | - Christer Betsholtz
- Department of Immunology, Genetics, and Pathology, Uppsala University, 751 85 Uppsala, Sweden; Department of Medicine Huddinge, Karolinska Institutet, 141 57 Huddinge, Sweden
| | - Stuart John Forbes
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, EH16 4UU Edinburgh, UK
| | - Henar Cuervo
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Mihaela Crisan
- Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, EH16 4TJ Edinburgh, UK; Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, EH16 4UU Edinburgh, UK.
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25
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Inubushi T, Nakanishi Y, Abe M, Takahata Y, Nishimura R, Kurosaka H, Irie F, Yamashiro T, Yamaguchi Y. The cell surface hyaluronidase TMEM2 plays an essential role in mouse neural crest cell development and survival. PLoS Genet 2022; 18:e1009765. [PMID: 35839257 PMCID: PMC9328550 DOI: 10.1371/journal.pgen.1009765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 07/27/2022] [Accepted: 06/29/2022] [Indexed: 11/30/2022] Open
Abstract
Hyaluronan (HA) is a major extracellular matrix component whose tissue levels are dynamically regulated during embryonic development. Although the synthesis of HA has been shown to exert a substantial influence on embryonic morphogenesis, the functional importance of the catabolic aspect of HA turnover is poorly understood. Here, we demonstrate that the transmembrane hyaluronidase TMEM2 plays an essential role in neural crest development and the morphogenesis of neural crest derivatives, as evidenced by the presence of severe craniofacial abnormalities in Wnt1-Cre–mediated Tmem2 knockout (Tmem2CKO) mice. Neural crest cells (NCCs) are a migratory population of cells that gives rise to diverse cell lineages, including the craniofacial complex, the peripheral nervous system, and part of the heart. Analysis of Tmem2 expression during NCC formation and migration reveals that Tmem2 is expressed at the site of NCC delamination and in emigrating Sox9-positive NCCs. In Tmem2CKO embryos, the number of NCCs emigrating from the neural tube is greatly reduced. Furthermore, linage tracing reveals that the number of NCCs traversing the ventral migration pathway and the number of post-migratory neural crest derivatives are both significantly reduced in a Tmem2CKO background. In vitro studies using Tmem2-depleted mouse O9-1 neural crest cells demonstrate that Tmem2 expression is essential for the ability of these cells to form focal adhesions on and to migrate into HA-containing substrates. Additionally, we show that Tmem2-deficient NCCs exhibit increased apoptotic cell death in NCC-derived tissues, an observation that is corroborated by in vitro experiments using O9-1 cells. Collectively, our data demonstrate that TMEM2-mediated HA degradation plays an essential role in normal neural crest development. This study reveals the hitherto unrecognized functional importance of HA degradation in embryonic development and highlights the pivotal role of Tmem2 in the developmental process. As a major component of the extracellular matrix, hyaluronan is particularly abundant in the extracellular matrix of embryonic tissues, where its expression is dynamically regulated during tissue morphogenetic processes. Tissue levels of hyaluronan are regulated not only by its synthesis but also by its degradation. Curiously, however, mice lacking known hyaluronidase molecules, including HYAL1 and HYAL2, exhibit minimal embryonic phenotypes. As a result, our understanding of the role of the catabolic aspect of hyaluronan metabolism in embryonic development is quite limited. Here, we show that TMEM2, a recently identified hyaluronidase that degrades hyaluronan on the cell surface, plays a critical role in the development of neural crest cells and their derivatives. Our analyses of Tmem2 conditional knockout mice, Tmem2 knock-in reporter mice, and in vitro cell cultures demonstrate that TMEM2 is essential for generating a tissue environment needed for efficient migration of neural crest cells from the neural tube. Our paper reveals for the first time that the degradation of hyaluronan plays a specific regulatory role in embryonic morphogenesis, and that dysregulation of hyaluronan degradation leads to severe developmental defects.
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Affiliation(s)
- Toshihiro Inubushi
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Osaka, Japan
- * E-mail:
| | - Yuichiro Nakanishi
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Makoto Abe
- Department of Oral Anatomy and Developmental Biology, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Yoshifumi Takahata
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Riko Nishimura
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Hiroshi Kurosaka
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Fumitoshi Irie
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
| | - Takashi Yamashiro
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Yu Yamaguchi
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
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26
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Gonzalez DM, Schrode N, Ebrahim TAM, Broguiere N, Rossi G, Drakhlis L, Zweigerdt R, Lutolf MP, Beaumont KG, Sebra R, Dubois NC. Dissecting mechanisms of chamber-specific cardiac differentiation and its perturbation following retinoic acid exposure. Development 2022; 149:275658. [DOI: 10.1242/dev.200557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/26/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
The specification of distinct cardiac lineages occurs before chamber formation and acquisition of bona fide atrial or ventricular identity. However, the mechanisms underlying these early specification events remain poorly understood. Here, we performed single cell analysis at the murine cardiac crescent, primitive heart tube and heart tube stages to uncover the transcriptional mechanisms underlying formation of atrial and ventricular cells. We find that progression towards differentiated cardiomyocytes occurs primarily based on heart field progenitor identity, and that progenitors contribute to ventricular or atrial identity through distinct differentiation mechanisms. We identify new candidate markers that define such differentiation processes and examine their expression dynamics using computational lineage trajectory methods. We further show that exposure to exogenous retinoic acid causes defects in ventricular chamber size, dysregulation in FGF signaling and a shunt in differentiation towards orthogonal lineages. Retinoic acid also causes defects in cell-cycle exit resulting in formation of hypomorphic ventricles. Collectively, our data identify, at a single cell level, distinct lineage trajectories during cardiac specification and differentiation, and the precise effects of manipulating cardiac progenitor patterning via retinoic acid signaling.
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Affiliation(s)
- David M. Gonzalez
- Icahn School of Medicine at Mount Sinai 1 Department of Cell, Developmental, and Regenerative Biology , , New York, NY 10029 , USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai 2 , New York, NY 10029 , USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai 3 , New York, NY 10029 , USA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai 4 , New York, NY 10029 , USA
| | - Nadine Schrode
- Icahn School of Medicine at Mount Sinai 5 Department of Genetics and Genomic Sciences , , New York, NY 10029 , USA
| | - Tasneem A. M. Ebrahim
- Icahn School of Medicine at Mount Sinai 1 Department of Cell, Developmental, and Regenerative Biology , , New York, NY 10029 , USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai 2 , New York, NY 10029 , USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai 3 , New York, NY 10029 , USA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai 4 , New York, NY 10029 , USA
| | - Nicolas Broguiere
- School of Life Sciences, EPFL 6 Laboratory of Stem Cell Bioengineering , , Lausanne CH-1015 , Switzerland
| | - Giuliana Rossi
- School of Life Sciences, EPFL 6 Laboratory of Stem Cell Bioengineering , , Lausanne CH-1015 , Switzerland
| | - Lika Drakhlis
- Roche Institute for Translational Bioengineering 7 , Roche Pharma Research and Early Development , Basel 4052 , Switzerland
| | - Robert Zweigerdt
- Roche Institute for Translational Bioengineering 7 , Roche Pharma Research and Early Development , Basel 4052 , Switzerland
| | - Matthias P. Lutolf
- School of Life Sciences, EPFL 6 Laboratory of Stem Cell Bioengineering , , Lausanne CH-1015 , Switzerland
- Roche Institute for Translational Bioengineering 7 , Roche Pharma Research and Early Development , Basel 4052 , Switzerland
| | - Kristin G. Beaumont
- Icahn School of Medicine at Mount Sinai 5 Department of Genetics and Genomic Sciences , , New York, NY 10029 , USA
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO) 8 , Department of Cardiothoracic, Transplantation and Vascular Surgery (HTTG) , , Hannover , Germany
- REBIRTH–Research Center for Translational Regenerative Medicine, Hannover Medical School 8 , Department of Cardiothoracic, Transplantation and Vascular Surgery (HTTG) , , Hannover , Germany
| | - Robert Sebra
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai 3 , New York, NY 10029 , USA
- Icahn School of Medicine at Mount Sinai 5 Department of Genetics and Genomic Sciences , , New York, NY 10029 , USA
- Sema4, a Mount Sinai venture 9 , Stamford, CT 06902 , USA
| | - Nicole C. Dubois
- Icahn School of Medicine at Mount Sinai 1 Department of Cell, Developmental, and Regenerative Biology , , New York, NY 10029 , USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai 2 , New York, NY 10029 , USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai 3 , New York, NY 10029 , USA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai 4 , New York, NY 10029 , USA
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27
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Newton AH. Marsupials and Multi-Omics: Establishing New Comparative Models of Neural Crest Patterning and Craniofacial Development. Front Cell Dev Biol 2022; 10:941168. [PMID: 35813210 PMCID: PMC9260703 DOI: 10.3389/fcell.2022.941168] [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: 05/11/2022] [Accepted: 06/06/2022] [Indexed: 11/15/2022] Open
Abstract
Studies across vertebrates have revealed significant insights into the processes that drive craniofacial morphogenesis, yet we still know little about how distinct facial morphologies are patterned during development. Studies largely point to evolution in GRNs of cranial progenitor cell types such as neural crest cells, as the major driver underlying adaptive cranial shapes. However, this hypothesis requires further validation, particularly within suitable models amenable to manipulation. By utilizing comparative models between related species, we can begin to disentangle complex developmental systems and identify the origin of species-specific patterning. Mammals present excellent evolutionary examples to scrutinize how these differences arise, as sister clades of eutherians and marsupials possess suitable divergence times, conserved cranial anatomies, modular evolutionary patterns, and distinct developmental heterochrony in their NCC behaviours and craniofacial patterning. In this review, I lend perspectives into the current state of mammalian craniofacial biology and discuss the importance of establishing a new marsupial model, the fat-tailed dunnart, for comparative research. Through detailed comparisons with the mouse, we can begin to decipher mammalian conserved, and species-specific processes and their contribution to craniofacial patterning and shape disparity. Recent advances in single-cell multi-omics allow high-resolution investigations into the cellular and molecular basis of key developmental processes. As such, I discuss how comparative evolutionary application of these tools can provide detailed insights into complex cellular behaviours and expression dynamics underlying adaptive craniofacial evolution. Though in its infancy, the field of "comparative evo-devo-omics" presents unparalleled opportunities to precisely uncover how phenotypic differences arise during development.
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28
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Pandey K, Zafar H. Inference of cell state transitions and cell fate plasticity from single-cell with MARGARET. Nucleic Acids Res 2022; 50:e86. [PMID: 35639499 PMCID: PMC9410915 DOI: 10.1093/nar/gkac412] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/27/2022] [Accepted: 05/17/2022] [Indexed: 11/27/2022] Open
Abstract
Despite recent advances in inferring cellular dynamics using single-cell RNA-seq data, existing trajectory inference (TI) methods face difficulty in accurately reconstructing the cell-state manifold and cell-fate plasticity for complex topologies. Here, we present MARGARET (https://github.com/Zafar-Lab/Margaret) for inferring single-cell trajectory and fate mapping for diverse dynamic cellular processes. MARGARET reconstructs complex trajectory topologies using a deep unsupervised metric learning and a graph-partitioning approach based on a novel connectivity measure, automatically detects terminal cell states, and generalizes the quantification of fate plasticity for complex topologies. On a diverse benchmark consisting of synthetic and real datasets, MARGARET outperformed state-of-the-art methods in recovering global topology and cell pseudotime ordering. For human hematopoiesis, MARGARET accurately identified all major lineages and associated gene expression trends and helped identify transitional progenitors associated with key branching events. For embryoid body differentiation, MARGARET identified novel transitional populations that were validated by bulk sequencing and functionally characterized different precursor populations in the mesoderm lineage. For colon differentiation, MARGARET characterized the lineage for BEST4/OTOP2 cells and the heterogeneity in goblet cell lineage in the colon under normal and inflamed ulcerative colitis conditions. Finally, we demonstrated that MARGARET can scale to large scRNA-seq datasets consisting of ∼ millions of cells.
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Affiliation(s)
- Kushagra Pandey
- Department of Computer Science and Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Hamim Zafar
- Department of Computer Science and Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, India.,Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India.,Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur 208016, India
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29
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Sinegubov A, Andreeva D, Burzak N, Vasyutina M, Murashova L, Dyachuk V. Heterogeneity and Potency of Peripheral Glial Cells in Embryonic Development and Adults. Front Mol Neurosci 2022; 15:737949. [PMID: 35401107 PMCID: PMC8990813 DOI: 10.3389/fnmol.2022.737949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
This review describes the heterogeneity of peripheral glial cell populations, from the emergence of Schwann cells (SCs) in early development, to their involvement, and that of their derivatives in adult glial populations. We focus on the origin of the first glial precursors from neural crest cells (NCCs), and their ability to differentiate into several cell types during development. We also discuss the heterogeneity of embryonic glia in light of the latest data from genetic tracing and transcriptome analysis. Special attention has been paid to the biology of glial populations in adult animals, by highlighting common features of different glial cell types and molecular differences that modulate their functions. Finally, we consider the communication of glial cells with axons of neurons in normal and pathological conditions. In conclusion, the present review details how information available on glial cell types and their functions in normal and pathological conditions may be utilized in the development of novel therapeutic strategies for the treatment of patients with neurodiseases.
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30
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Qiu C, Cao J, Martin BK, Li T, Welsh IC, Srivatsan S, Huang X, Calderon D, Noble WS, Disteche CM, Murray SA, Spielmann M, Moens CB, Trapnell C, Shendure J. Systematic reconstruction of cellular trajectories across mouse embryogenesis. Nat Genet 2022; 54:328-341. [PMID: 35288709 PMCID: PMC8920898 DOI: 10.1038/s41588-022-01018-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 01/21/2022] [Indexed: 12/12/2022]
Abstract
Mammalian embryogenesis is characterized by rapid cellular proliferation and diversification. Within a few weeks, a single-cell zygote gives rise to millions of cells expressing a panoply of molecular programs. Although intensively studied, a comprehensive delineation of the major cellular trajectories that comprise mammalian development in vivo remains elusive. Here, we set out to integrate several single-cell RNA-sequencing (scRNA-seq) datasets that collectively span mouse gastrulation and organogenesis, supplemented with new profiling of ~150,000 nuclei from approximately embryonic day 8.5 (E8.5) embryos staged in one-somite increments. Overall, we define cell states at each of 19 successive stages spanning E3.5 to E13.5 and heuristically connect them to their pseudoancestors and pseudodescendants. Although constructed through automated procedures, the resulting directed acyclic graph (TOME (trajectories of mammalian embryogenesis)) is largely consistent with our contemporary understanding of mammalian development. We leverage TOME to systematically nominate transcription factors (TFs) as candidate regulators of each cell type's specification, as well as 'cell-type homologs' across vertebrate evolution.
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Affiliation(s)
- Chengxiang Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Junyue Cao
- The Rockefeller University, New York, NY, USA
| | - Beth K Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Tony Li
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Xingfan Huang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Diego Calderon
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Christine M Disteche
- Department of Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Malte Spielmann
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Cecilia B Moens
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
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31
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Godden AM, Antonaci M, Ward NJ, van der Lee M, Abu-Daya A, Guille M, Wheeler GN. An efficient miRNA knockout approach using CRISPR-Cas9 in Xenopus. Dev Biol 2022; 483:66-75. [PMID: 34968443 PMCID: PMC8865746 DOI: 10.1016/j.ydbio.2021.12.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 12/15/2021] [Accepted: 12/23/2021] [Indexed: 12/14/2022]
Abstract
In recent years CRISPR-Cas9 knockouts (KO) have become increasingly ultilised to study gene function. MicroRNAs (miRNAs) are short non-coding RNAs, 20-22 nucleotides long, which affect gene expression through post-transcriptional repression. We previously identified miRNAs-196a and -219 as implicated in the development of Xenopus neural crest (NC). The NC is a multipotent stem-cell population, specified during early neurulation. Following EMT, NC cells migrate to various points in the developing embryo where they give rise to a number of tissues including parts of the peripheral nervous system, pigment cells and craniofacial skeleton. Dysregulation of NC development results in many diseases grouped under the term neurocristopathies. As miRNAs are so small, it is difficult to design CRISPR sgRNAs that reproducibly lead to a KO. We have therefore designed a novel approach using two guide RNAs to effectively 'drop out' a miRNA. We have knocked out miR-196a and miR-219 and compared the results to morpholino knockdowns (KD) of the same miRNAs. Validation of efficient CRISPR miRNA KO and phenotype analysis included use of whole-mount in situ hybridization of key NC and neural plate border markers such as Pax3, Xhe2, Sox10 and Snail2, q-RT-PCR and Sanger sequencing. To show specificity we have also rescued the knockout phenotype using miRNA mimics. MiRNA-219 and miR-196a KO's both show loss of NC, altered neural plate and hatching gland phenotypes. Tadpoles show gross craniofacial and pigment phenotypes.
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Affiliation(s)
- Alice M Godden
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Marco Antonaci
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Nicole J Ward
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Michael van der Lee
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Anita Abu-Daya
- King Henry Building, King Henry I St, Portsmouth, PO1 2DY, United Kingdom
| | - Matthew Guille
- King Henry Building, King Henry I St, Portsmouth, PO1 2DY, United Kingdom
| | - Grant N Wheeler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom.
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32
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SOX9 contributes to the progression of ductular reaction for the protection from chronic liver injury. Hum Cell 2022; 35:721-734. [DOI: 10.1007/s13577-022-00683-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/30/2022] [Indexed: 11/26/2022]
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Carotenuto R, Tussellino M, Ronca R, Benvenuto G, Fogliano C, Fusco S, Netti PA. Toxic effects of SiO 2NPs in early embryogenesis of Xenopuslaevis. CHEMOSPHERE 2022; 289:133233. [PMID: 34896176 DOI: 10.1016/j.chemosphere.2021.133233] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
The exposure of organisms to the nanoparticulate is potentially hazardous, particularly when it occurs during embryogenesis. The effects of commercial SiO2NPs in early development were studied, using Xenopus laevis as a model to investigate their possible future employment by means of the Frog Embryo Teratogenesis Assay-Xenopus test (FETAX). The SiO2NPs did not change the survival but produced several abnormalities in developing embryos, in particular, the dorsal pigmentation, the cartilages of the head and branchial arches were modified; the encephalon, spinal cord and nerves are anomalous and the intestinal brush border show signs of suffering; these embryos are also bradycardic. In addition, the expression of genes involved in the early pathways of embryo development was modified. Treated embryos showed an increase of reactive oxygen species. This study suggests that SiO2NPs are toxic but non-lethal and showed potential teratogenic effects in Xenopus. The latter may be due to their cellular accumulation and/or to the effect caused by the interaction of SiO2NPs with cytoplasmic and/or nuclear components. ROS production could contribute to the observed effects. In conclusion, the data indicates that the use of SiO2NPs requires close attention and further studies to better clarify their activity in animals, including humans.
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Affiliation(s)
- Rosa Carotenuto
- Department of Biology, University of Naples Federico II, Naples, Italy.
| | | | - Raffaele Ronca
- Institute of Biostructures and Bioimaging (IBB)-CNR, Naples, Italy
| | | | - Chiara Fogliano
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Sabato Fusco
- Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Campobasso, Italy
| | - Paolo Antonio Netti
- Center for Advanced Biomaterials for Health Care (CABHC), Italian Institute of Technology, Naples, Italy; Interdisciplinary Research Centre on Biomaterials (CRIB), University of Naples Federico II, Naples, Italy; Department of Chemical Materials and Industrial Production (DICMAPI), University of Naples Federico II, Naples, Italy
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SOX9 and SATB2 Immunohistochemistry Cannot Reliably Distinguish Between Osteosarcoma and Chondrosarcoma on Biopsy Material. Hum Pathol 2022; 121:56-64. [PMID: 35016891 DOI: 10.1016/j.humpath.2021.12.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/28/2021] [Accepted: 12/30/2021] [Indexed: 11/23/2022]
Abstract
INTRODUCTION Limited tissue in biopsies of malignant bone lesions can preclude definitive subclassification, especially when cellular or matrix elements are sparse, absent, or confounding. It is uncertain whether IHC for SOX9 (marker of chondrogenesis) and SATB2 (marker of osteoblastic differentiation) may be discriminatory tools towards osteosarcoma and chondrosarcoma. METHODS This study interrogated the pre-resection biopsies of a cohort of osteosarcoma and chondrosarcoma with SATB2 and SOX9 in tandem, to assess their value as diagnostic adjuncts as well as their concordance with final resection diagnoses. RESULTS SATB2 was expressed more frequently in osteosarcoma (46/53, 86%) compared to chondrosarcoma (9/18, 50%); SOX9 was expressed in high frequencies in both osteosarcoma (52/53, 98%) and chondrosarcoma (17/18, 94%), and SATB2 and SOX9 were co-expressed in both osteosarcoma (46/53, 89%) and chondrosarcoma (8/18, 44%). CONCLUSIONS There exists significant overlap in expression of SATB2 and SOX9 in osteosarcoma and chondrosarcoma. These markers are not expressed in a distribution that is unique enough for application towards this particular diagnostic differential.
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Monroy BY, Adamson CJ, Camacho-Avila A, Guerzon CN, Echeverria CV, Rogers CD. Expression atlas of avian neural crest proteins: Neurulation to migration. Dev Biol 2022; 483:39-57. [PMID: 34990731 DOI: 10.1016/j.ydbio.2021.12.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/11/2021] [Accepted: 12/30/2021] [Indexed: 11/20/2022]
Abstract
Neural crest (NC) cells are a dynamic population of embryonic stem cells that create various adult tissues in vertebrate species including craniofacial bone and cartilage and the peripheral and enteric nervous systems. NC development is thought to be a conserved and complex process that is controlled by a tightly-regulated gene regulatory network (GRN) of morphogens, transcription factors, and cell adhesion proteins. While multiple studies have characterized the expression of several GRN factors in single species, a comprehensive protein analysis that directly compares expression across development is lacking. To address this lack in information, we used three closely related avian models, Gallus gallus (chicken), Coturnix japonica (Japanese quail), and Pavo cristatus (Indian peafowl), to compare the localization and timing of four GRN transcription factors, PAX7, SNAI2, SOX9, and SOX10, from the onset of neurulation to migration. While the spatial expression of these factors is largely conserved, we find that quail NC cells express SNAI2, SOX9, and SOX10 proteins at the equivalent of earlier developmental stages than chick and peafowl. In addition, quail NC cells migrate farther and more rapidly than the larger organisms. These data suggest that despite a conservation of NC GRN players, differences in the timing of NC development between species remain a significant frontier to be explored with functional studies.
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Affiliation(s)
- Brigette Y Monroy
- Anatomy, Physiology, and Cell Biology Department, University of California Davis, Davis, CA, 95616, USA
| | - Carly J Adamson
- Anatomy, Physiology, and Cell Biology Department, University of California Davis, Davis, CA, 95616, USA
| | - Alexis Camacho-Avila
- Department of Biology, California State University Northridge, Northridge, CA, 91330, USA
| | - Christian N Guerzon
- Anatomy, Physiology, and Cell Biology Department, University of California Davis, Davis, CA, 95616, USA
| | - Camilo V Echeverria
- Anatomy, Physiology, and Cell Biology Department, University of California Davis, Davis, CA, 95616, USA
| | - Crystal D Rogers
- Anatomy, Physiology, and Cell Biology Department, University of California Davis, Davis, CA, 95616, USA.
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Sox9 + cells are required for salivary gland regeneration after radiation damage via the Wnt/β-catenin pathway. J Genet Genomics 2021; 49:230-239. [PMID: 34757039 DOI: 10.1016/j.jgg.2021.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 12/27/2022]
Abstract
Radiotherapy for head and neck cancer can cause serious side effects, including severe damage to the salivary glands, resulting in symptoms such as xerostomia, dental caries, and oral infection. Due to the lack of long-term treatment for the symptoms of xerostomia, current research has focused on finding endogenous stem cells that can differentiate into various cell lineages to replace lost tissue and restore functions. Here, we report that Sox9+ cells can differentiate into various salivary epithelial cell lineages under homeostatic conditions. After ablating Sox9+ cells, the salivary glands of irradiated mice showed more severe phenotypes and the reduced proliferative capacity. Analysis of online single-cell RNA-sequencing data reveals the enrichment of the Wnt/β-catenin pathway in the Sox9+ cell population. Furthermore, treatment with a Wnt/β-catenin inhibitor in irradiated mice inhibits the regenerative capability of Sox9+ cells. Finally, we show that Sox9+ cells are capable of forming organoids in vitro and that transplanting these organoids into salivary glands after radiation partially restored salivary gland functions. These results suggest that regenerative therapy targeting Sox9+ cells is a promising approach to treat radiation-induced salivary gland injury.
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37
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Epithelial Mesenchymal Transition and its transcription factors. Biosci Rep 2021; 42:230017. [PMID: 34708244 PMCID: PMC8703024 DOI: 10.1042/bsr20211754] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
Epithelial–mesenchymal transition or EMT is an extremely dynamic process involved in conversion of epithelial cells into mesenchymal cells, stimulated by an ensemble of signaling pathways, leading to change in cellular morphology, suppression of epithelial characters and acquisition of properties such as enhanced cell motility and invasiveness, reduced cell death by apoptosis, resistance to chemotherapeutic drugs etc. Significantly, EMT has been found to play a crucial role during embryonic development, tissue fibrosis and would healing, as well as during cancer metastasis. Over the years, work from various laboratories have identified a rather large number of transcription factors (TFs) including the master regulators of EMT, with the ability to regulate the EMT process directly. In this review, we put together these EMT TFs and discussed their role in the process. We have also tried to focus on their mechanism of action, their interdependency, and the large regulatory network they form. Subsequently, it has become clear that the composition and structure of the transcriptional regulatory network behind EMT probably varies based upon various physiological and pathological contexts, or even in a cell/tissue type-dependent manner.
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38
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Jarazo J, Barmpa K, Modamio J, Saraiva C, Sabaté-Soler S, Rosety I, Griesbeck A, Skwirblies F, Zaffaroni G, Smits LM, Su J, Arias-Fuenzalida J, Walter J, Gomez-Giro G, Monzel AS, Qing X, Vitali A, Cruciani G, Boussaad I, Brunelli F, Jäger C, Rakovic A, Li W, Yuan L, Berger E, Arena G, Bolognin S, Schmidt R, Schröder C, Antony PMA, Klein C, Krüger R, Seibler P, Schwamborn JC. Parkinson's Disease Phenotypes in Patient Neuronal Cultures and Brain Organoids Improved by 2-Hydroxypropyl-β-Cyclodextrin Treatment. Mov Disord 2021; 37:80-94. [PMID: 34637165 PMCID: PMC9291890 DOI: 10.1002/mds.28810] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 12/13/2022] Open
Abstract
Background The etiology of Parkinson's disease (PD) is only partially understood despite the fact that environmental causes, risk factors, and specific gene mutations are contributors to the disease. Biallelic mutations in the phosphatase and tensin homolog (PTEN)‐induced putative kinase 1 (PINK1) gene involved in mitochondrial homeostasis, vesicle trafficking, and autophagy are sufficient to cause PD. Objectives We sought to evaluate the difference between controls' and PINK1 patients' derived neurons in their transition from neuroepithelial stem cells to neurons, allowing us to identify potential pathways to target with repurposed compounds. Methods Using two‐dimensional and three‐dimensional models of patients' derived neurons we recapitulated PD‐related phenotypes. We introduced the usage of midbrain organoids for testing compounds. Using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR‐associated protein 9 (Cas9), we corrected the point mutations of three patients' derived cells. We evaluated the effect of the selected compound in a mouse model. Results PD patient‐derived cells presented differences in their energetic profile, imbalanced proliferation, apoptosis, mitophagy, and a reduced differentiation efficiency to tyrosine hydroxylase positive (TH+) neurons compared to controls' cells. Correction of a patient's point mutation ameliorated the metabolic properties and neuronal firing rates as well as reversing the differentiation phenotype, and reducing the increased astrocytic levels. Treatment with 2‐hydroxypropyl‐β‐cyclodextrin increased the autophagy and mitophagy capacity of neurons concomitant with an improved dopaminergic differentiation of patient‐specific neurons in midbrain organoids and ameliorated neurotoxicity in a mouse model. Conclusion We show that treatment with a repurposed compound is sufficient for restoring the impaired dopaminergic differentiation of PD patient‐derived cells. © 2021 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society
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Affiliation(s)
- Javier Jarazo
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine University of Luxembourg, Esch-sur-Alzette, Luxembourg.,OrganoTherapeutics société à responsabilité limitée simplifiée (SARL-S), Esch-sur-Alzette, Luxembourg
| | - Kyriaki Barmpa
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jennifer Modamio
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Cláudia Saraiva
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Sònia Sabaté-Soler
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Isabel Rosety
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | | | - Gaia Zaffaroni
- Institute for Globally Distributed Open Research and Education, Gothenburg, Sweden
| | - Lisa M Smits
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jihui Su
- Institute of Health Sciences, China Medical University, Shenyang, China
| | - Jonathan Arias-Fuenzalida
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jonas Walter
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Gemma Gomez-Giro
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Anna S Monzel
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Xiaobing Qing
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Armelle Vitali
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Gerald Cruciani
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine University of Luxembourg, Esch-sur-Alzette, Luxembourg.,Disease Modeling and Screening Platform, Luxembourg Institute of Systems Biomedicine, University of Luxembourg and Luxembourg Institute of Health, Belvaux, Luxembourg
| | - Ibrahim Boussaad
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine University of Luxembourg, Esch-sur-Alzette, Luxembourg.,Disease Modeling and Screening Platform, Luxembourg Institute of Systems Biomedicine, University of Luxembourg and Luxembourg Institute of Health, Belvaux, Luxembourg
| | | | - Christian Jäger
- Metabolomics Platform, Enzymology and Metabolism, Luxembourg Centre for Systems Biomedicine University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Wen Li
- Institute of Health Sciences, China Medical University, Shenyang, China
| | - Lin Yuan
- Institute of Health Sciences, China Medical University, Shenyang, China
| | - Emanuel Berger
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Giuseppe Arena
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Silvia Bolognin
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | | | - Paul M A Antony
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Rejko Krüger
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine University of Luxembourg, Esch-sur-Alzette, Luxembourg.,Centre Hospitalier de Luxembourg, Parkinson Research Clinic, Luxembourg, Luxembourg.,Transversal Translational Medicine, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Philip Seibler
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Jens C Schwamborn
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine University of Luxembourg, Esch-sur-Alzette, Luxembourg
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PITX1 inhibits the growth and proliferation of melanoma cells through regulation of SOX family genes. Sci Rep 2021; 11:18405. [PMID: 34526609 PMCID: PMC8443576 DOI: 10.1038/s41598-021-97791-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/30/2021] [Indexed: 01/04/2023] Open
Abstract
Melanoma is one of the most aggressive types of cancer wherein resistance to treatment prevails. Therefore, it is important to discover novel molecular targets of melanoma progression as potential treatments. Here we show that paired-like homeodomain transcription factor 1 (PITX1) plays a crucial role in the inhibition of melanoma progression through regulation of SRY-box transcription factors (SOX) gene family mRNA transcription. Overexpression of PITX1 in melanoma cell lines resulted in a reduction in cell proliferation and an increase in apoptosis. Additionally, analysis of protein levels revealed an antagonistic cross-regulation between SOX9 and SOX10. Interestingly, PITX1 binds to the SOX9 promoter region as a positive regulatory transcription factor; PITX1 mRNA expression levels were positively correlated with SOX9 expression, and negatively correlated with SOX10 expression in melanoma tissues. Furthermore, transcription of the long noncoding RNA (lncRNA), survival-associated mitochondrial melanoma-specific oncogenic noncoding RNA (SAMMSON), was decreased in PITX1-overexpressing cells. Taken together, the findings in this study indicate that PITX1 may act as a negative regulatory factor in the development and progression of melanoma via direct targeting of the SOX signaling.
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40
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Martik ML, Bronner ME. Riding the crest to get a head: neural crest evolution in vertebrates. Nat Rev Neurosci 2021; 22:616-626. [PMID: 34471282 PMCID: PMC10168595 DOI: 10.1038/s41583-021-00503-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2021] [Indexed: 12/11/2022]
Abstract
In their seminal 1983 paper, Gans and Northcutt proposed that evolution of the vertebrate 'new head' was made possible by the advent of the neural crest and cranial placodes. The neural crest is a stem cell population that arises adjacent to the forming CNS and contributes to important cell types, including components of the peripheral nervous system and craniofacial skeleton and elements of the cardiovascular system. In the past few years, the new head hypothesis has been challenged by the discovery in invertebrate chordates of cells with some, but not all, characteristics of vertebrate neural crest cells. Here, we discuss recent findings regarding how neural crest cells may have evolved during the course of deuterostome evolution. The results suggest that there was progressive addition of cell types to the repertoire of neural crest derivatives throughout vertebrate evolution. Novel genomic tools have enabled higher resolution insight into neural crest evolution, from both a cellular and a gene regulatory perspective. Together, these data provide clues regarding the ancestral neural crest state and how the neural crest continues to evolve to contribute to the success of vertebrates as efficient predators.
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Affiliation(s)
- Megan L Martik
- Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Marianne E Bronner
- Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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41
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Hatou S, Sayano T, Higa K, Inagaki E, Okano Y, Sato Y, Okano H, Tsubota K, Shimmura S. Transplantation of iPSC-derived corneal endothelial substitutes in a monkey corneal edema model. Stem Cell Res 2021; 55:102497. [PMID: 34411973 DOI: 10.1016/j.scr.2021.102497] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 07/02/2021] [Accepted: 08/05/2021] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE In order to provide regenerative therapy for millions of patients suffering from corneal blindness globally, we derived corneal endothelial cell substitute (CECSi) cells from induced pluripotent stem cells (iPSCs) to treat corneal edema due to endothelial dysfunction (bullous keratopathy). METHODS AND RESULTS We developed an efficient xeno-free protocol to produce CECSi cells from both research grade (Ff-MH09s01 and Ff-I01s04) and clinical grade (QHJI01s04) iPSCs. CECSi cells formed a hexagonal confluent monolayer with Na, K-ATPase alpha 1 subunit expression (ATP1A1), tight junctions, N-cadherin adherence junction formation, and nuclear PITX2 expression, which are all characteristics of corneal endothelial cells. CECSi cells can be cryopreserved, and thawed CECSi cell suspensions also expressed N-cadherin and ATP1A1. Residual undifferentiated iPSCs in QHJI01s04-derived CECSi cells was below 0.01%. Frozen stocks of Ff-I01s04- and QHJI01s04-derived CECSi cells were transported, thawed and transplanted into a monkey corneal edema model. CECSi-transplanted eyes significantly reduced corneal edema compared to control group. CONCLUSION Our results show a promising approach to provide bullous keratopathy patients with an iPS-cell-based cell therapy to recover useful vision.
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Affiliation(s)
- Shin Hatou
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan; Cellusion Inc, Tokyo, Japan
| | - Tomoko Sayano
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan; Cellusion Inc, Tokyo, Japan
| | - Kazunari Higa
- Department of Ophthalmology, Tokyo Dental College Ichikawa General Hospital, Ichikawa, Japan
| | - Emi Inagaki
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Yuji Okano
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Yasunori Sato
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Kazuo Tsubota
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Shigeto Shimmura
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan.
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42
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Li J, Chen X, Zhu L, Lao Z, Zhou T, Zang L, Ge W, Jiang M, Xu J, Cao Y, Du S, Yu Y, Fan G, Wang H. SOX9 is a critical regulator of TSPAN8-mediated metastasis in pancreatic cancer. Oncogene 2021; 40:4884-4893. [PMID: 34163029 PMCID: PMC8321899 DOI: 10.1038/s41388-021-01864-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 04/30/2021] [Accepted: 05/25/2021] [Indexed: 12/16/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the deadliest cancer mainly owing to its proclivity to early metastasis and the lack of effective targeted therapeutic drugs. Hence, understanding the molecular mechanisms underlying early invasion and metastasis by PDAC is imperative for improving patient outcomes. The present study identified that upregulation of TSPAN8 expression in PDAC facilitates metastasis in vivo and in vitro. We found SOX9 as a key transcriptional regulator of TSPAN8 expression in response to EGF stimulation. SOX9 modulation was sufficient to positively regulate endogenous expression of TSPAN8, with concomitant in vitro phenotypic changes such as loss of cell-matrix adherence and increased invasion. Moreover, increased SOX9 and TSPAN8 levels were shown to correlate in human pancreatic cancer specimens and downregulated in vitro by EGFR tyrosine kinase inhibitors. High expression of SOX9 and TSPAN8 has been associated with tumor stage, poor prognosis and poor patient survival in PDAC. In conclusion, this study highlights the importance of the EGF-SOX9-TSPAN8 signaling cascade in the control of PDAC invasion and implies that TSPAN8 may be a promising novel therapeutic target for the treatment of PDAC.
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Affiliation(s)
- Junjian Li
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoliang Chen
- The Center for Chronic Disease Control and Prevention, Shenzhen Guangming District Centers for Disease Control and Prevention, Shenzhen, China
| | - Liqun Zhu
- Department of Oncology, Liyang People's Hospital, Liyang, China
| | - Zhenghong Lao
- Department of Oncology, Deqing People's Hospital, Huzhou, China
| | - Tianhao Zhou
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lijuan Zang
- Pathology Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiyu Ge
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mengyi Jiang
- Department of Medical Oncology, Shanghai Jiaotong University Affiliated Sixth People's Hospital East Campus, Shanghai, China
| | - Jingxuan Xu
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuan Cao
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shaoqian Du
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yue Yu
- Shanghai Experimental School, Shanghai, China
| | - Guangjian Fan
- Translational Medicine Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Hongxia Wang
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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43
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Adane B, Alexe G, Seong BKA, Lu D, Hwang EE, Hnisz D, Lareau CA, Ross L, Lin S, Dela Cruz FS, Richardson M, Weintraub AS, Wang S, Iniguez AB, Dharia NV, Conway AS, Robichaud AL, Tanenbaum B, Krill-Burger JM, Vazquez F, Schenone M, Berman JN, Kung AL, Carr SA, Aryee MJ, Young RA, Crompton BD, Stegmaier K. STAG2 loss rewires oncogenic and developmental programs to promote metastasis in Ewing sarcoma. Cancer Cell 2021; 39:827-844.e10. [PMID: 34129824 PMCID: PMC8378827 DOI: 10.1016/j.ccell.2021.05.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 01/28/2021] [Accepted: 05/13/2021] [Indexed: 02/08/2023]
Abstract
The core cohesin subunit STAG2 is recurrently mutated in Ewing sarcoma but its biological role is less clear. Here, we demonstrate that cohesin complexes containing STAG2 occupy enhancer and polycomb repressive complex (PRC2)-marked regulatory regions. Genetic suppression of STAG2 leads to a compensatory increase in cohesin-STAG1 complexes, but not in enhancer-rich regions, and results in reprogramming of cis-chromatin interactions. Strikingly, in STAG2 knockout cells the oncogenic genetic program driven by the fusion transcription factor EWS/FLI1 was highly perturbed, in part due to altered enhancer-promoter contacts. Moreover, loss of STAG2 also disrupted PRC2-mediated regulation of gene expression. Combined, these transcriptional changes converged to modulate EWS/FLI1, migratory, and neurodevelopmental programs. Finally, consistent with clinical observations, functional studies revealed that loss of STAG2 enhances the metastatic potential of Ewing sarcoma xenografts. Our findings demonstrate that STAG2 mutations can alter chromatin architecture and transcriptional programs to promote an aggressive cancer phenotype.
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Affiliation(s)
- Biniam Adane
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabriela Alexe
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Bioinformatics Graduate Program, Boston University, Boston, MA, USA
| | - Bo Kyung A Seong
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Diana Lu
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Elizabeth E Hwang
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Denes Hnisz
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Caleb A Lareau
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Linda Ross
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Shan Lin
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Filemon S Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Abraham S Weintraub
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sarah Wang
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | | | - Neekesh V Dharia
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amy Saur Conway
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Amanda L Robichaud
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | | | | | | | | | - Jason N Berman
- Department of Pediatrics and Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada; Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Andrew L Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Martin J Aryee
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Pathology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brian D Crompton
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Kimberly Stegmaier
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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44
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Dilshat R, Vu HN, Steingrímsson E. Epigenetic regulation during melanocyte development and homeostasis. Exp Dermatol 2021; 30:1033-1050. [PMID: 34003523 DOI: 10.1111/exd.14391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 04/09/2021] [Accepted: 05/09/2021] [Indexed: 12/26/2022]
Abstract
Melanocytes originate in the neural crest as precursor cells which then migrate and proliferate to reach their destination where they differentiate into pigment-producing cells. Melanocytes not only determine the colour of hair, skin and eyes but also protect against the harmful effects of UV irradiation. The establishment of the melanocyte lineage is regulated by a defined set of transcription factors and signalling pathways that direct the specific gene expression programmes underpinning melanoblast specification, survival, migration, proliferation and differentiation. In addition, epigenetic modifiers and replacement histones play key roles in regulating gene expression and its timing during the different steps of this process. Here, we discuss the evidence for the role of epigenetic regulators in melanocyte development and function and how they interact with transcription factors and signalling pathways to establish and maintain this important cell lineage.
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Affiliation(s)
- Ramile Dilshat
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavik, Iceland
| | - Hong Nhung Vu
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavik, Iceland
| | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavik, Iceland
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45
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Sox9a, not sox9b is required for normal cartilage development in zebrafish. AQUACULTURE AND FISHERIES 2021. [DOI: 10.1016/j.aaf.2019.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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46
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Parmar B, Verma U, Khaire K, Danes D, Balakrishnan S. Inhibition of Cyclooxygenase-2 Alters Craniofacial Patterning during Early Embryonic Development of Chick. J Dev Biol 2021; 9:16. [PMID: 33922791 PMCID: PMC8167724 DOI: 10.3390/jdb9020016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/17/2021] [Accepted: 04/20/2021] [Indexed: 12/22/2022] Open
Abstract
A recent study from our lab revealed that the inhibition of cyclooxygenase-2 (COX-2) exclusively reduces the level of PGE2 (Prostaglandin E2) among prostanoids and hampers the normal development of several structures, strikingly the cranial vault, in chick embryos. In order to unearth the mechanism behind the deviant development of cranial features, the expression pattern of various factors that are known to influence cranial neural crest cell (CNCC) migration was checked in chick embryos after inhibiting COX-2 activity using etoricoxib. The compromised level of cell adhesion molecules and their upstream regulators, namely CDH1 (E-cadherin), CDH2 (N-cadherin), MSX1 (Msh homeobox 1), and TGF-β (Transforming growth factor beta), observed in the etoricoxib-treated embryos indicate that COX-2, through its downstream effector PGE2, regulates the expression of these factors perhaps to aid the migration of CNCCs. The histological features and levels of FoxD3 (Forkhead box D3), as well as PCNA (Proliferating cell nuclear antigen), further consolidate the role of COX-2 in the migration and survival of CNCCs in developing embryos. The results of the current study indicate that COX-2 plays a pivotal role in orchestrating craniofacial structures perhaps by modulating CNCC proliferation and migration during the embryonic development of chicks.
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Affiliation(s)
| | | | | | | | - Suresh Balakrishnan
- Department of Zoology, Faculty of Science, The Maharaja Sayajirao University of Baroda, Gujarat 390002, India; (B.P.); (U.V.); (K.K.); (D.D.)
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47
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The role of SOX family transcription factors in gastric cancer. Int J Biol Macromol 2021; 180:608-624. [PMID: 33662423 DOI: 10.1016/j.ijbiomac.2021.02.202] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/26/2021] [Indexed: 02/08/2023]
Abstract
Gastric cancer (GC) is a leading cause of death worldwide. GC is the third-most common cause of cancer-related death after lung and colorectal cancer. It is also the fifth-most commonly diagnosed cancer. Accumulating evidence has revealed the role of signaling networks in GC progression. Identification of these molecular pathways can provide new insight into therapeutic approaches for GC. Several molecular factors involved in GC can play both onco-suppressor and oncogene roles. Sex-determining region Y (Sry)-box-containing (SOX) family members are transcription factors with a well-known role in cancer. SOX proteins can bind to DNA to regulate cellular pathways via a highly conserved domain known as high mobility group (HMG). In the present review, the roles of SOX proteins in the progression and/or inhibition of GC are discussed. The dual role of SOX proteins as tumor-promoting and tumor-suppressing factors is highlighted. SOX members can affect upstream mediators (microRNAs, long non-coding RNAs and NF-κB) and down-stream mediators (FAK, HIF-1α, CDX2 and PTEN) in GC. The possible role of anti-tumor compounds to target SOX pathway members in GC therapy is described. Moreover, SOX proteins may be used as diagnostic or prognostic biomarkers in GC.
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48
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Soto J, Ding X, Wang A, Li S. Neural crest-like stem cells for tissue regeneration. Stem Cells Transl Med 2021; 10:681-693. [PMID: 33533168 PMCID: PMC8046096 DOI: 10.1002/sctm.20-0361] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 12/13/2022] Open
Abstract
Neural crest stem cells (NCSCs) are a transient population of cells that arise during early vertebrate development and harbor stem cell properties, such as self‐renewal and multipotency. These cells form at the interface of non‐neuronal ectoderm and neural tube and undergo extensive migration whereupon they contribute to a diverse array of cell and tissue derivatives, ranging from craniofacial tissues to cells of the peripheral nervous system. Neural crest‐like stem cells (NCLSCs) can be derived from pluripotent stem cells, placental tissues, adult tissues, and somatic cell reprogramming. NCLSCs have a differentiation capability similar to NCSCs, and possess great potential for regenerative medicine applications. In this review, we present recent developments on the various approaches to derive NCLSCs and the therapeutic application of these cells for tissue regeneration.
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Affiliation(s)
- Jennifer Soto
- Department of Bioengineering, University of California Los Angeles, Los Angeles, California, USA
| | - Xili Ding
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, People's Republic of China
| | - Aijun Wang
- Department of Surgery, School of Medicine, University of California Davis, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children, Sacramento, California, USA.,Department of Biomedical Engineering, University of California Davis, Davis, California, USA
| | - Song Li
- Department of Bioengineering, University of California Los Angeles, Los Angeles, California, USA.,Department of Medicine, University of California Los Angeles, Los Angeles, California, USA
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49
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Balakrishnan A, Belfiore L, Chu TH, Fleming T, Midha R, Biernaskie J, Schuurmans C. Insights Into the Role and Potential of Schwann Cells for Peripheral Nerve Repair From Studies of Development and Injury. Front Mol Neurosci 2021; 13:608442. [PMID: 33568974 PMCID: PMC7868393 DOI: 10.3389/fnmol.2020.608442] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 12/31/2020] [Indexed: 12/13/2022] Open
Abstract
Peripheral nerve injuries arising from trauma or disease can lead to sensory and motor deficits and neuropathic pain. Despite the purported ability of the peripheral nerve to self-repair, lifelong disability is common. New molecular and cellular insights have begun to reveal why the peripheral nerve has limited repair capacity. The peripheral nerve is primarily comprised of axons and Schwann cells, the supporting glial cells that produce myelin to facilitate the rapid conduction of electrical impulses. Schwann cells are required for successful nerve regeneration; they partially “de-differentiate” in response to injury, re-initiating the expression of developmental genes that support nerve repair. However, Schwann cell dysfunction, which occurs in chronic nerve injury, disease, and aging, limits their capacity to support endogenous repair, worsening patient outcomes. Cell replacement-based therapeutic approaches using exogenous Schwann cells could be curative, but not all Schwann cells have a “repair” phenotype, defined as the ability to promote axonal growth, maintain a proliferative phenotype, and remyelinate axons. Two cell replacement strategies are being championed for peripheral nerve repair: prospective isolation of “repair” Schwann cells for autologous cell transplants, which is hampered by supply challenges, and directed differentiation of pluripotent stem cells or lineage conversion of accessible somatic cells to induced Schwann cells, with the potential of “unlimited” supply. All approaches require a solid understanding of the molecular mechanisms guiding Schwann cell development and the repair phenotype, which we review herein. Together these studies provide essential context for current efforts to design glial cell-based therapies for peripheral nerve regeneration.
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Affiliation(s)
- Anjali Balakrishnan
- Biological Sciences Platform, Sunnybrook Research Institute (SRI), Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Lauren Belfiore
- Biological Sciences Platform, Sunnybrook Research Institute (SRI), Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Tak-Ho Chu
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Taylor Fleming
- Biological Sciences Platform, Sunnybrook Research Institute (SRI), Toronto, ON, Canada
| | - Rajiv Midha
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jeff Biernaskie
- Department of Comparative Biology and Experimental Medicine, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Carol Schuurmans
- Biological Sciences Platform, Sunnybrook Research Institute (SRI), Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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50
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Tanaka J, Takamatsu K, Yukimori A, Kujiraoka S, Ishida S, Takakura I, Yasuhara R, Mishima K. Sox9 function in salivary gland development. J Oral Biosci 2021; 63:8-13. [PMID: 33497841 DOI: 10.1016/j.job.2021.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/08/2021] [Accepted: 01/13/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Organogenesis is regulated by morphogen signaling and transcription networks. These networks differ between organs, and identifying the organ-specific network is important to clarify the molecular mechanisms of development and regeneration of organs. Several studies have been conducted to identify salivary gland-specific networks using a mouse submandibular gland model. The submandibular glands (SMGs) of mice manifest as a thickening of the oral epithelium at embryonic day 11.5 and invaginate into the underlying mesenchyme. The network between Fgf10 and Sox9 is involved in SMG development in mice. HIGHLIGHT Sox9, a member of the Sox family, is expressed in the SMG in mice from the embryonic stage to the adult stage, although the distribution changes during development. A null mutation of mouse Sox9 is lethal during the neonatal period due to respiratory failure, whereas deletion of Sox9 in the oral epithelium using the Cre/lox P system, can lead to smaller initial buds of SMGs in conditional knockout (cKO) mice than in normal mice. In addition, we showed that adenoviral transduction of Sox9 and Foxc1 genes into mouse embryonic stem cell-derived oral ectoderm could induce salivary gland rudiment in an organoid culture system. ChIP-sequencing revealed that Sox9 possibly regulates several tube- and branching-formation-related genes. CONCLUSION Sox9 may serve as an essential transcription factor for salivary gland development. The Sox9-mediated pathway can be a promising candidate for regenerating damaged salivary glands.
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Affiliation(s)
- Junichi Tanaka
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Koki Takamatsu
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Akane Yukimori
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Satoko Kujiraoka
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Shoko Ishida
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Ikuko Takakura
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Rika Yasuhara
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Kenji Mishima
- Division of Pathology, Department of Oral Diagnostic Sciences, Showa University School of Dentistry, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan.
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