1
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Wnt signaling in stem cells during development and cell lineage specification. Curr Top Dev Biol 2023; 153:121-143. [PMID: 36967192 DOI: 10.1016/bs.ctdb.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
During embryo development, cell proliferation, cell fate specification and tissue patterning are coordinated and tightly regulated by a handful of evolutionarily conserved signaling pathways activated by secreted growth factor families including fibroblast growth factor (FGF), Nodal/bone morphogenetic protein (BMP), Hedgehog and Wnt. The spatial and temporal activation of these signaling pathways elicit context-specific cellular responses that ultimately shape the different tissues of the embryo. Extensive efforts have been dedicated to identifying the molecular mechanisms underlying these signaling pathways during embryo development, adult tissue homeostasis and regeneration. In this review, we first describe the role of the Wnt/β-catenin signaling pathway during early embryo development, axis specification and cell differentiation as a prelude to highlight how this knowledge is being leveraged to manipulate Wnt/β-catenin signaling activity with small molecules and biologics for the directed differentiation of pluripotent stem cells into various cell lineages that are physiologically relevant for stem cell therapy and regenerative medicine.
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2
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Schnirman RE, Kuo SJ, Kelly RC, Yamaguchi TP. The role of Wnt signaling in the development of the epiblast and axial progenitors. Curr Top Dev Biol 2023; 153:145-180. [PMID: 36967193 DOI: 10.1016/bs.ctdb.2023.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Understanding how the body plan is established during embryogenesis remains a fundamental biological question. The Wnt/β-catenin signaling pathway plays a crucial and highly conserved role in body plan formation, functioning to polarize the primary anterior-posterior (AP) or head-to-tail body axis in most metazoans. In this chapter, we focus on the roles that the mammalian Wnt/β-catenin pathway plays to prepare the pluripotent epiblast for gastrulation, and to elicit the emergence of multipotent axial progenitors from the caudal epiblast. Interactions between Wnt and retinoic acid (RA), another powerful family of developmental signaling molecules, in axial progenitors will also be discussed. Gastrulation movements and somitogenesis result in the anterior displacement of the RA source (the rostral somites and lateral plate mesoderm (LPM)), from the posterior Wnt source (the primitive streak (PS)), leading to the establishment of antiparallel gradients of RA and Wnt that control the self-renewal and successive differentiation of neck, trunk and tail progenitors.
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Affiliation(s)
| | - Samuel J Kuo
- NCI-Frederick, NIH, Frederick, MD, United States
| | - Ryan C Kelly
- NCI-Frederick, NIH, Frederick, MD, United States
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3
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Shi L, Li H, Huang X, Shu Z, Li J, Wang L, Yan H, Wang L. Integrated analysis of transcriptome and metabolome revealed biological basis of sows from estrus to lactation. iScience 2022; 26:105825. [PMID: 36636351 PMCID: PMC9830223 DOI: 10.1016/j.isci.2022.105825] [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: 08/06/2022] [Revised: 10/10/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Characterization of molecular mechanisms underlying pregnancy development of sows is important for the genetic improvement of pig breeding traits, and also provides resources for biomedical research on human pregnancy diseases. However, the transcriptome and metabolome across multiple developmental stages of sow pregnancy were still lacking. In this study, we obtained 84 distinct RNA sequencing and 42 metabolome datasets of pig blood across six development stages from estrus to lactation. We confirmed the initial sequence and exonic structural features, stage-specific molecules, expression or accumulation pattern of molecules, the regulatory mechanism of transcriptome and metabolome, and important pregnancy-related metabolites both in pigs and humans. In conclusion, we proposed the key differences among the stages of sows from estrus to lactation in RNAs and metabolites and put forward key markers. These data results were expected to provide essential resources for pig breeding and biomedical research on human pregnancy disease.
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Affiliation(s)
- Lijun Shi
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China,Corresponding author
| | - Huihui Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Xiaoyu Huang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Ze Shu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Jingna Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Ligang Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Hua Yan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Lixian Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China,Corresponding author
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4
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Martin BL. Mesoderm induction and patterning: Insights from neuromesodermal progenitors. Semin Cell Dev Biol 2022; 127:37-45. [PMID: 34840081 PMCID: PMC9130346 DOI: 10.1016/j.semcdb.2021.11.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/02/2021] [Accepted: 11/10/2021] [Indexed: 12/23/2022]
Abstract
The discovery of mesoderm inducing signals helped usher in the era of molecular developmental biology, and today the mechanisms of mesoderm induction and patterning are still intensely studied. Mesoderm induction begins during gastrulation, but recent evidence in vertebrates shows that this process continues after gastrulation in a group of posteriorly localized cells called neuromesodermal progenitors (NMPs). NMPs reside within the post-gastrulation embryonic structure called the tailbud, where they make a lineage decision between ectoderm (spinal cord) and mesoderm. The majority of NMP-derived mesoderm generates somites, but also contributes to lateral mesoderm fates such as endothelium. The discovery of NMPs provides a new paradigm in which to study vertebrate mesoderm induction. This review will discuss mechanisms of mesoderm induction within NMPs, and how they have informed our understanding of mesoderm induction more broadly within vertebrates as well as animal species outside of the vertebrate lineage. Special focus will be given to the signaling networks underlying NMP-derived mesoderm induction and patterning, as well as emerging work on the significance of partial epithelial-mesenchymal states in coordinating cell fate and morphogenesis.
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Affiliation(s)
- Benjamin L Martin
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA.
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5
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Cooper F, Tsakiridis A. Towards clinical applications of in vitro-derived axial progenitors. Dev Biol 2022; 489:110-117. [PMID: 35718236 DOI: 10.1016/j.ydbio.2022.06.006] [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: 01/27/2022] [Revised: 04/28/2022] [Accepted: 06/14/2022] [Indexed: 11/19/2022]
Abstract
The production of the tissues that make up the mammalian embryonic trunk takes place in a head-tail direction, via the differentiation of posteriorly-located axial progenitor populations. These include bipotent neuromesodermal progenitors (NMPs), which generate both spinal cord neurectoderm and presomitic mesoderm, the precursor of the musculoskeleton. Over the past few years, a number of studies have described the derivation of NMP-like cells from mouse and human pluripotent stem cells (PSCs). In turn, these have greatly facilitated the establishment of PSC differentiation protocols aiming to give rise efficiently to posterior mesodermal and neural cell types, which have been particularly challenging to produce using previous approaches. Moreover, the advent of 3-dimensional-based culture systems incorporating distinct axial progenitor-derived cell lineages has opened new avenues toward the functional dissection of early patterning events and cell vs non-cell autonomous effects. Here, we provide a brief overview of the applications of these cell types in disease modelling and cell therapy and speculate on their potential uses in the future.
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Affiliation(s)
- Fay Cooper
- Centre for Stem Cell Biology, School of Bioscience, The University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom; Neuroscience Institute, The University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom
| | - Anestis Tsakiridis
- Centre for Stem Cell Biology, School of Bioscience, The University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom; Neuroscience Institute, The University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom.
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6
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Campbell GP, Farkas DR, Chapman DL. Ectopic expression of T in the paraxial mesoderm disrupts somite maturation in the mouse. Dev Biol 2022; 485:37-49. [PMID: 35276131 DOI: 10.1016/j.ydbio.2022.02.010] [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: 06/10/2021] [Revised: 02/19/2022] [Accepted: 02/23/2022] [Indexed: 11/03/2022]
Abstract
T is the founding member of the T-box family of transcription factors; family members are critical for cell fate decisions and tissue morphogenesis throughout the animal kingdom. T is expressed in the primitive streak and notochord with mouse mutant studies revealing its critical role in mesoderm formation in the primitive streak and notochord integrity. We previously demonstrated that misexpression of Tbx6 in the paraxial and lateral plate mesoderm results in embryos resembling Tbx15 and Tbx18 nulls. This, together with results from in vitro transcriptional assays, suggested that ectopically expressed Tbx6 can compete with endogenously expressed Tbx15 and Tbx18 at the binding sites of target genes. Since T-box proteins share a similar DNA binding domain, we hypothesized that misexpressing T in the paraxial and lateral plate mesoderm would also interfere with the endogenous Tbx15 and Tbx18, causing embryonic phenotypes resembling those seen upon Tbx6 expression in the somites and limbs. Interestingly, ectopic T expression led to distinct embryonic phenotypes, specifically, reduced-sized somites in embryos expressing the highest levels of T, which ultimately affects axis length and neural tube morphogenesis. We further demonstrate that ectopic T leads to ectopic expression of Tbx6 and Mesogenin 1, known targets of T. These results suggests that ectopic T expression contributes to the phenotype by activating its own targets rather than via a straight competition with endogenous T-box factors.
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Affiliation(s)
- Gregory P Campbell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Deborah R Farkas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Deborah L Chapman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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7
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Diaz-Cuadros M, Pourquié O, El-Sherif E. Patterning with clocks and genetic cascades: Segmentation and regionalization of vertebrate versus insect body plans. PLoS Genet 2021; 17:e1009812. [PMID: 34648490 PMCID: PMC8516289 DOI: 10.1371/journal.pgen.1009812] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Oscillatory and sequential processes have been implicated in the spatial patterning of many embryonic tissues. For example, molecular clocks delimit segmental boundaries in vertebrates and insects and mediate lateral root formation in plants, whereas sequential gene activities are involved in the specification of regional identities of insect neuroblasts, vertebrate neural tube, vertebrate limb, and insect and vertebrate body axes. These processes take place in various tissues and organisms, and, hence, raise the question of what common themes and strategies they share. In this article, we review 2 processes that rely on the spatial regulation of periodic and sequential gene activities: segmentation and regionalization of the anterior-posterior (AP) axis of animal body plans. We study these processes in species that belong to 2 different phyla: vertebrates and insects. By contrasting 2 different processes (segmentation and regionalization) in species that belong to 2 distantly related phyla (arthropods and vertebrates), we elucidate the deep logic of patterning by oscillatory and sequential gene activities. Furthermore, in some of these organisms (e.g., the fruit fly Drosophila), a mode of AP patterning has evolved that seems not to overtly rely on oscillations or sequential gene activities, providing an opportunity to study the evolution of pattern formation mechanisms.
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Affiliation(s)
- Margarete Diaz-Cuadros
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, United States of America
| | - Ezzat El-Sherif
- Division of Developmental Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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8
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Abstract
Arthropod segmentation and vertebrate somitogenesis are leading fields in the experimental and theoretical interrogation of developmental patterning. However, despite the sophistication of current research, basic conceptual issues remain unresolved. These include: (i) the mechanistic origins of spatial organization within the segment addition zone (SAZ); (ii) the mechanistic origins of segment polarization; (iii) the mechanistic origins of axial variation; and (iv) the evolutionary origins of simultaneous patterning. Here, I explore these problems using coarse-grained models of cross-regulating dynamical processes. In the morphogenetic framework of a row of cells undergoing axial elongation, I simulate interactions between an 'oscillator', a 'switch' and up to three 'timers', successfully reproducing essential patterning behaviours of segmenting systems. By comparing the output of these largely cell-autonomous models to variants that incorporate positional information, I find that scaling relationships, wave patterns and patterning dynamics all depend on whether the SAZ is regulated by temporal or spatial information. I also identify three mechanisms for polarizing oscillator output, all of which functionally implicate the oscillator frequency profile. Finally, I demonstrate significant dynamical and regulatory continuity between sequential and simultaneous modes of segmentation. I discuss these results in the context of the experimental literature.
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Affiliation(s)
- Erik Clark
- Department of Systems Biology, Harvard Medical School, 210 Longwood Ave, Boston, MA 02115, USA
- Trinity College Cambridge, University of Cambridge, Trinity Street, Cambridge CB2 1TQ, UK
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Wymeersch FJ, Wilson V, Tsakiridis A. Understanding axial progenitor biology in vivo and in vitro. Development 2021; 148:148/4/dev180612. [PMID: 33593754 DOI: 10.1242/dev.180612] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The generation of the components that make up the embryonic body axis, such as the spinal cord and vertebral column, takes place in an anterior-to-posterior (head-to-tail) direction. This process is driven by the coordinated production of various cell types from a pool of posteriorly-located axial progenitors. Here, we review the key features of this process and the biology of axial progenitors, including neuromesodermal progenitors, the common precursors of the spinal cord and trunk musculature. We discuss recent developments in the in vitro production of axial progenitors and their potential implications in disease modelling and regenerative medicine.
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Affiliation(s)
- Filip J Wymeersch
- Laboratory for Human Organogenesis, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Valerie Wilson
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Anestis Tsakiridis
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Western Bank, Sheffield S10 2TN UK .,Neuroscience Institute, The University of Sheffield, Western Bank, Sheffield, S10 2TN UK
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10
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Anderson MJ, Magidson V, Kageyama R, Lewandoski M. Fgf4 maintains Hes7 levels critical for normal somite segmentation clock function. eLife 2020; 9:55608. [PMID: 33210601 PMCID: PMC7717904 DOI: 10.7554/elife.55608] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 11/18/2020] [Indexed: 12/16/2022] Open
Abstract
During vertebrate development, the presomitic mesoderm (PSM) periodically segments into somites, which will form the segmented vertebral column and associated muscle, connective tissue, and dermis. The periodicity of somitogenesis is regulated by a segmentation clock of oscillating Notch activity. Here, we examined mouse mutants lacking only Fgf4 or Fgf8, which we previously demonstrated act redundantly to prevent PSM differentiation. Fgf8 is not required for somitogenesis, but Fgf4 mutants display a range of vertebral defects. We analyzed Fgf4 mutants by quantifying mRNAs fluorescently labeled by hybridization chain reaction within Imaris-based volumetric tissue subsets. These data indicate that FGF4 maintains Hes7 levels and normal oscillatory patterns. To support our hypothesis that FGF4 regulates somitogenesis through Hes7, we demonstrate genetic synergy between Hes7 and Fgf4, but not with Fgf8. Our data indicate that Fgf4 is potentially important in a spectrum of human Segmentation Defects of the Vertebrae caused by defective Notch oscillations.
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Affiliation(s)
- Matthew J Anderson
- Genetics of Vertebrate Development Section, Cancer and Developmental Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, United States
| | - Valentin Magidson
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Ryoichiro Kageyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Mark Lewandoski
- Genetics of Vertebrate Development Section, Cancer and Developmental Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, United States
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11
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Wang Y, Cai H, Luo X, Ai Y, Jiang M, Wen Y. Insight into unique somitogenesis of yak (Bos grunniens) with one additional thoracic vertebra. BMC Genomics 2020; 21:201. [PMID: 32131721 PMCID: PMC7057515 DOI: 10.1186/s12864-020-6598-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 02/19/2020] [Indexed: 01/23/2023] Open
Abstract
Background The yak is a species of livestock which is crucial for local communities of the Qinghai-Tibet Plateau and adjacent regions and naturally owns one more thoracic vertebra than cattle. Recently, a sub-population of yak termed as the Jinchuan yak has been identified with over half its members own a thoracolumbar vertebral formula of T15L5 instead of the natural T14L5 arrangement. The novel T15L5 positioning is a preferred genetic trait leading to enhanced meat and milk production. Selective breeding of this trait would have great agricultural value and exploration of the molecular mechanisms underlying this trait would both accelerate this process and provide us insight into the development and regulation of somitogenesis. Results Here we investigated the genetic background of the Jinchuan yak through resequencing fifteen individuals, comprising five T15L5 individuals and ten T14L5 individuals with an average sequencing depth of > 10X, whose thoracolumbar vertebral formulae were confirmed by anatomical observation. Principal component analysis, linkage disequilibrium analysis, phylogenetic analysis, and selective sweep analysis were carried out to explore Jinchuan yak’s genetic background. Three hundred and thirty candidate markers were identified as associated with the additional thoracic vertebrae and target sequencing was used to validate seven carefully selected markers in an additional 51 Jinchuan yaks. The accuracies of predicting 15 thoracic vertebrae and 20 thoracolumbar vertebrae with these 7 markers were 100.00 and 33.33% despite they both could only represent 20% of all possible genetic diversity. Two genes, PPP2R2B and TBLR1, were found to harbour the most candidate markers associated with the trait and likely contribute to the unique somitic number and identity according to their reported roles in the mechanism of somitogenesis. Conclusions Our findings provide a clear depiction of the Jinchuan yak’s genetic background and a solid foundation for marker-assistant selection. Further exploitation of this unique population and trait could be promoted with the aid of our genomic resource.
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Affiliation(s)
- Yu Wang
- College of Life Science and Technology, Southwest Minzu University, Chengdu, 610041, Sichuan, China
| | - Haoyang Cai
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, 610064, Sichuan, China
| | - Xiaolin Luo
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Yi Ai
- Key Laboratory of Sichuan Province for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation, Chengdu, 610041, China
| | - Mingfeng Jiang
- College of Life Science and Technology, Southwest Minzu University, Chengdu, 610041, Sichuan, China.
| | - Yongli Wen
- Key Laboratory of Sichuan Province for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation, Chengdu, 610041, China.
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12
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Draut H, Liebenstein T, Begemann G. New Insights into the Control of Cell Fate Choices and Differentiation by Retinoic Acid in Cranial, Axial and Caudal Structures. Biomolecules 2019; 9:E860. [PMID: 31835881 PMCID: PMC6995509 DOI: 10.3390/biom9120860] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/06/2019] [Accepted: 12/09/2019] [Indexed: 12/13/2022] Open
Abstract
Retinoic acid (RA) signaling is an important regulator of chordate development. RA binds to nuclear RA receptors that control the transcriptional activity of target genes. Controlled local degradation of RA by enzymes of the Cyp26a gene family contributes to the establishment of transient RA signaling gradients that control patterning, cell fate decisions and differentiation. Several steps in the lineage leading to the induction and differentiation of neuromesodermal progenitors and bone-producing osteogenic cells are controlled by RA. Changes to RA signaling activity have effects on the formation of the bones of the skull, the vertebrae and the development of teeth and regeneration of fin rays in fish. This review focuses on recent advances in these areas, with predominant emphasis on zebrafish, and highlights previously unknown roles for RA signaling in developmental processes.
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Wu J, Matthias N, Lo J, Ortiz-Vitali JL, Shieh AW, Wang SH, Darabi R. A Myogenic Double-Reporter Human Pluripotent Stem Cell Line Allows Prospective Isolation of Skeletal Muscle Progenitors. Cell Rep 2019; 25:1966-1981.e4. [PMID: 30428361 DOI: 10.1016/j.celrep.2018.10.067] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 10/08/2018] [Accepted: 10/18/2018] [Indexed: 02/06/2023] Open
Abstract
Myogenic differentiation of human pluripotent stem cells (hPSCs) has been done by gene overexpression or directed differentiation. However, viral integration, long-term culture, and the presence of unwanted cells are the main obstacles. By using CRISPR/Cas9n, a double-reporter human embryonic stem cell (hESC) line was generated for PAX7/MYF5, allowing prospective readout. This strategy allowed pathway screen to define efficient myogenic induction in hPSCs. Next, surface marker screen allowed identification of CD10 and CD24 for purification of myogenic progenitors and exclusion of non-myogenic cells. CD10 expression was also identified on human satellite cells and skeletal muscle progenitors. In vitro and in vivo studies using transgene and/or reporter-free hPSCs further validated myogenic potential of the cells by formation of new fibers expressing human dystrophin as well as donor-derived satellite cells in NSG-mdx4Cv mice. This study provides biological insights for myogenic differentiation of hPSCs using a double-reporter cell resource and defines an improved myogenic differentiation and purification strategy.
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Affiliation(s)
- Jianbo Wu
- Center for Stem Cell and Regenerative Medicine (CSCRM), The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Nadine Matthias
- Center for Stem Cell and Regenerative Medicine (CSCRM), The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jonathan Lo
- Center for Stem Cell and Regenerative Medicine (CSCRM), The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jose L Ortiz-Vitali
- Center for Stem Cell and Regenerative Medicine (CSCRM), The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Annie W Shieh
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Sidney H Wang
- Center for Human Genetics, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Radbod Darabi
- Center for Stem Cell and Regenerative Medicine (CSCRM), The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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14
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Sun C, Serra C, Lee G, Wagner KR. Stem cell-based therapies for Duchenne muscular dystrophy. Exp Neurol 2019; 323:113086. [PMID: 31639376 DOI: 10.1016/j.expneurol.2019.113086] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 02/08/2023]
Abstract
Muscular dystrophies are a group of genetic muscle disorders that cause progressive muscle weakness and degeneration. Within this group, Duchenne muscular dystrophy (DMD) is the most common and one of the most severe. DMD is an X chromosome linked disease that occurs to 1 in 3500 to 1 in 5000 boys. The cause of DMD is a mutation in the dystrophin gene, whose encoded protein provides both structural support and cell signaling capabilities. So far, there are very limited therapeutic options available and there is no cure for this disease. In this review, we discuss the existing cell therapy research, especially stem cell-based, which utilize myoblasts, satellite cells, bone marrow cells, mesoangioblasts and CD133+ cells. Finally, we focus on human pluripotent stem cells (hPSCs) which hold great potential in treating DMD. hPSCs can be used for autologous transplantation after being specified to a myogenic lineage. Over the last few years, there has been a rapid development of isolation, as well as differentiation, techniques in order to achieve effective transplantation results of myogenic cells specified from hPSCs. In this review, we summarize the current methods of hPSCs myogenic commitment/differentiation, and describe the current status of hPSC-derived myogenic cell transplantation.
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Affiliation(s)
- Congshan Sun
- Departments of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA; Center for Genetic Muscle Disorders, Hugo W. Moser Research Institute at Kennedy Krieger Institute, Baltimore, MD 21205, USA.
| | - Carlo Serra
- Departments of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA; Center for Genetic Muscle Disorders, Hugo W. Moser Research Institute at Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Gabsang Lee
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kathryn R Wagner
- Departments of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA; Center for Genetic Muscle Disorders, Hugo W. Moser Research Institute at Kennedy Krieger Institute, Baltimore, MD 21205, USA
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15
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Tahara N, Kawakami H, Chen KQ, Anderson A, Yamashita Peterson M, Gong W, Shah P, Hayashi S, Nishinakamura R, Nakagawa Y, Garry DJ, Kawakami Y. Sall4 regulates neuromesodermal progenitors and their descendants during body elongation in mouse embryos. Development 2019; 146:dev.177659. [PMID: 31235634 DOI: 10.1242/dev.177659] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/18/2019] [Indexed: 12/24/2022]
Abstract
Bi-potential neuromesodermal progenitors (NMPs) produce both neural and paraxial mesodermal progenitors in the trunk and tail during vertebrate body elongation. We show that Sall4, a pluripotency-related transcription factor gene, has multiple roles in regulating NMPs and their descendants in post-gastrulation mouse embryos. Sall4 deletion using TCre caused body/tail truncation, reminiscent of early depletion of NMPs, suggesting a role of Sall4 in NMP maintenance. This phenotype became significant at the time of the trunk-to-tail transition, suggesting that Sall4 maintenance of NMPs enables tail formation. Sall4 mutants exhibit expanded neural and reduced mesodermal tissues, indicating a role of Sall4 in NMP differentiation balance. Mechanistically, we show that Sall4 promotion of WNT/β-catenin signaling contributes to NMP maintenance and differentiation balance. RNA-Seq and SALL4 ChIP-Seq analyses support the notion that Sall4 regulates both mesodermal and neural development. Furthermore, in the mesodermal compartment, genes regulating presomitic mesoderm differentiation are downregulated in Sall4 mutants. In the neural compartment, we show that differentiation of NMPs towards post-mitotic neuron is accelerated in Sall4 mutants. Our results collectively provide evidence supporting the role of Sall4 in regulating NMPs and their descendants.
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Affiliation(s)
- Naoyuki Tahara
- Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA.,Stem Cell Institute, University of Minnesota, 2001 6th St. SE, Minneapolis, MN 55455, USA.,Developmental Biology Center, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA
| | - Hiroko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA.,Stem Cell Institute, University of Minnesota, 2001 6th St. SE, Minneapolis, MN 55455, USA.,Developmental Biology Center, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA
| | - Katherine Q Chen
- Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA
| | - Aaron Anderson
- Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA
| | - Malina Yamashita Peterson
- Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA
| | - Wuming Gong
- Lillehei Heart Institute, University of Minnesota, 2231 6th St. SE, Minneapolis, MN 55455, USA
| | - Pruthvi Shah
- Lillehei Heart Institute, University of Minnesota, 2231 6th St. SE, Minneapolis, MN 55455, USA
| | - Shinichi Hayashi
- Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA.,Stem Cell Institute, University of Minnesota, 2001 6th St. SE, Minneapolis, MN 55455, USA.,Developmental Biology Center, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA
| | - Ryuichi Nishinakamura
- Department of Kidney Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan 860-0811
| | - Yasushi Nakagawa
- Stem Cell Institute, University of Minnesota, 2001 6th St. SE, Minneapolis, MN 55455, USA.,Developmental Biology Center, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA.,Department of Neuroscience, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA
| | - Daniel J Garry
- Stem Cell Institute, University of Minnesota, 2001 6th St. SE, Minneapolis, MN 55455, USA.,Developmental Biology Center, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA.,Lillehei Heart Institute, University of Minnesota, 2231 6th St. SE, Minneapolis, MN 55455, USA.,Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, 516 Delaware St. SE, Minneapolis, MN 55455, USA
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA .,Stem Cell Institute, University of Minnesota, 2001 6th St. SE, Minneapolis, MN 55455, USA.,Developmental Biology Center, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA
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16
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Razy-Krajka F, Stolfi A. Regulation and evolution of muscle development in tunicates. EvoDevo 2019; 10:13. [PMID: 31249657 PMCID: PMC6589888 DOI: 10.1186/s13227-019-0125-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/08/2019] [Indexed: 12/16/2022] Open
Abstract
For more than a century, studies on tunicate muscle formation have revealed many principles of cell fate specification, gene regulation, morphogenesis, and evolution. Here, we review the key studies that have probed the development of all the various muscle cell types in a wide variety of tunicate species. We seize this occasion to explore the implications and questions raised by these findings in the broader context of muscle evolution in chordates.
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Affiliation(s)
- Florian Razy-Krajka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, USA
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, USA
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17
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Edri S, Hayward P, Baillie-Johnson P, Steventon BJ, Martinez Arias A. An epiblast stem cell-derived multipotent progenitor population for axial extension. Development 2019; 146:dev.168187. [PMID: 31023877 DOI: 10.1242/dev.168187] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 04/10/2019] [Indexed: 12/21/2022]
Abstract
The caudal lateral epiblast of mammalian embryos harbours bipotent progenitors that contribute to the spinal cord and the paraxial mesoderm in concert with the body axis elongation. These progenitors, called neural mesodermal progenitors (NMPs), are identified as cells that co-express Sox2 and T/brachyury, a criterion used to derive NMP-like cells from embryonic stem cells in vitro However, unlike embryonic NMPs, these progenitors do not self-renew. Here, we find that the protocols that yield NMP-like cells in vitro initially produce a multipotent population that, in addition to NMPs, generates progenitors for the lateral plate and intermediate mesoderm. We show that epiblast stem cells (EpiSCs) are an effective source of these multipotent progenitors, which are further differentiated by a balance between BMP and Nodal signalling. Importantly, we show that NMP-like cells derived from EpiSCs exhibit limited self-renewal in vitro and a gene expression signature like their embryonic counterparts.
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Affiliation(s)
- Shlomit Edri
- Department of Genetics, Downing Site, University of Cambridge, Cambridge CB2 3EH, UK
| | - Penny Hayward
- Department of Genetics, Downing Site, University of Cambridge, Cambridge CB2 3EH, UK
| | - Peter Baillie-Johnson
- Department of Genetics, Downing Site, University of Cambridge, Cambridge CB2 3EH, UK
| | - Benjamin J Steventon
- Department of Genetics, Downing Site, University of Cambridge, Cambridge CB2 3EH, UK
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18
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Hu YB, Yan C, Mu L, Mi YL, Zhao H, Hu H, Li XL, Tao DD, Wu YQ, Gong JP, Qin JC. Exosomal Wnt-induced dedifferentiation of colorectal cancer cells contributes to chemotherapy resistance. Oncogene 2019; 38:1951-1965. [PMID: 30390075 PMCID: PMC6756234 DOI: 10.1038/s41388-018-0557-9] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 09/02/2018] [Accepted: 10/02/2018] [Indexed: 12/11/2022]
Abstract
Cancer stem cells (CSCs) are inherently resistant to chemotherapy, and CSCs in chemotherapy-failed recurrent tumors are enriched; however, the cellular origin of chemotherapy-induced CSC enrichment remains unclear. Communication with stromal fibroblasts may induce cancer cell dedifferentiation into CSCs through secreted factors. We recently demonstrated that fibroblast-derived exosomes promote chemoresistance in colorectal cancer (CRC). Here, we report that fibroblasts confer CRC chemoresistance via exosome-induced reprogramming (dedifferentiation) of bulk CRC cells to phenotypic and functional CSCs. At the molecular level, we provided evidence that the major reprogramming regulators in fibroblast-exosomes are Wnts. Exosomal Wnts were found to increase Wnt activity and drug resistance in differentiated CRC cells, and inhibiting Wnt release diminished this effect in vitro and in vivo. Together, our results indicate that exosomal Wnts derived from fibroblasts could induce the dedifferentiation of cancer cells to promote chemoresistance in CRC, and suggest that interfering with exosomal Wnt signaling may help to improve chemosensitivity and the therapeutic window.
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Affiliation(s)
- Y-B Hu
- Department of Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Molecular Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - C Yan
- Department of Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Molecular Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - L Mu
- Department of Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Molecular Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Y-L Mi
- Department of Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Molecular Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - H Zhao
- Department of Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Molecular Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - H Hu
- Department of Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Molecular Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - X-L Li
- Molecular Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - D-D Tao
- Molecular Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Y-Q Wu
- Department of Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - J-P Gong
- Department of Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
- Molecular Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - J-C Qin
- Department of Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
- Molecular Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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19
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Magli A, Perlingeiro RRC. Myogenic progenitor specification from pluripotent stem cells. Semin Cell Dev Biol 2018; 72:87-98. [PMID: 29107681 DOI: 10.1016/j.semcdb.2017.10.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 12/21/2022]
Abstract
Pluripotent stem cells represent important tools for both basic and translational science as they enable to study mechanisms of development, model diseases in vitro and provide a potential source of tissue-specific progenitors for cell therapy. Concomitantly with the increasing knowledge of the molecular mechanisms behind activation of the skeletal myogenic program during embryonic development, novel findings in the stem cell field provided the opportunity to begin recapitulating in vitro the events occurring during specification of the myogenic lineage. In this review, we will provide a perspective of the molecular mechanisms responsible for skeletal myogenic commitment in the embryo and how this knowledge was instrumental for specifying this lineage from pluripotent stem cells. In addition, we will discuss the current limitations for properly recapitulating skeletal myogenesis in the petri dish, and we will provide insights about future applications of pluripotent stem cell-derived myogenic cells.
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Affiliation(s)
- Alessandro Magli
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Rita R C Perlingeiro
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN, USA.
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20
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Hayashi S, Nakahata Y, Kohno K, Matsui T, Bessho Y. Presomitic mesoderm-specific expression of the transcriptional repressor Hes7 is controlled by E-box, T-box, and Notch signaling pathways. J Biol Chem 2018; 293:12167-12176. [PMID: 29895619 DOI: 10.1074/jbc.ra118.003728] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 06/01/2018] [Indexed: 01/06/2023] Open
Abstract
Somites are a pair of epithelial spheres beside a neural tube and are formed with an accurate periodicity during embryogenesis in vertebrates. It has been known that Hes7 is one of the core clock genes for somitogenesis, and its expression domain is restricted in the presomitic mesoderm (PSM). However, the molecular mechanism of how Hes7 transcription is regulated is not clear. Here, using transgenic mice and luciferase-based reporter assays and in vitro binding assays, we unravel the mechanism by which Hes7 is expressed exclusively in the PSM. We identified a Hes7 essential region residing -1.5 to -1.1 kb from the transcription start site of mouse Hes7, and this region was indispensable for PSM-specific Hes7 expression. We also present detailed analyses of cis-regulatory elements within the Hes7 essential region that directs Hes7 expression in the PSM. Hes7 expression in the PSM was up-regulated through the E-box, T-box, and RBPj-binding element in the Hes7 essential region, presumably through synergistic signaling involving mesogenin1, T-box6 (Tbx6), and Notch. Furthermore, we demonstrate that Tbx18, Ripply2, and Hes7 repress the activation of the Hes7 essential region by the aforementioned transcription factors. Our findings reveal that a unified transcriptional regulatory network involving a Hes7 essential region confers robust PSM-specific Hes7 gene expression.
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Affiliation(s)
- Shinichi Hayashi
- Laboratory of Gene Regulation Research, Graduate School of Biological Sciences, Institute for Research Initiatives, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Yasukazu Nakahata
- Laboratory of Gene Regulation Research, Graduate School of Biological Sciences, Institute for Research Initiatives, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan.
| | - Kenji Kohno
- Laboratory of Molecular and Cell Genetics, Graduate School of Biological Sciences, Institute for Research Initiatives, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Takaaki Matsui
- Laboratory of Gene Regulation Research, Graduate School of Biological Sciences, Institute for Research Initiatives, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Yasumasa Bessho
- Laboratory of Gene Regulation Research, Graduate School of Biological Sciences, Institute for Research Initiatives, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan.
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21
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Antagonistic Activities of Sox2 and Brachyury Control the Fate Choice of Neuro-Mesodermal Progenitors. Dev Cell 2017; 42:514-526.e7. [DOI: 10.1016/j.devcel.2017.07.021] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 06/07/2017] [Accepted: 07/24/2017] [Indexed: 12/25/2022]
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22
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Nguyen NM, de Oliveira Andrade F, Jin L, Zhang X, Macon M, Cruz MI, Benitez C, Wehrenberg B, Yin C, Wang X, Xuan J, de Assis S, Hilakivi-Clarke L. Maternal intake of high n-6 polyunsaturated fatty acid diet during pregnancy causes transgenerational increase in mammary cancer risk in mice. Breast Cancer Res 2017; 19:77. [PMID: 28673325 PMCID: PMC5494892 DOI: 10.1186/s13058-017-0866-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 06/07/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Maternal and paternal high-fat (HF) diet intake before and/or during pregnancy increases mammary cancer risk in several preclinical models. We studied if maternal consumption of a HF diet that began at a time when the fetal primordial germ cells travel to the genital ridge and start differentiating into germ cells would result in a transgenerational inheritance of increased mammary cancer risk. METHODS Pregnant C57BL/6NTac mouse dams were fed either a control AIN93G or isocaloric HF diet composed of corn oil high in n-6 polyunsaturated fatty acids between gestational days 10 and 20. Offspring in subsequent F1-F3 generations were fed only the control diet. RESULTS Mammary tumor incidence induced by 7,12-dimethylbenz[a]anthracene was significantly higher in F1 (p < 0.016) and F3 generation offspring of HF diet-fed dams (p < 0.040) than in the control offspring. Further, tumor latency was significantly shorter (p < 0.028) and burden higher (p < 0.027) in F1 generation HF offspring, and similar trends were seen in F3 generation HF offspring. RNA sequencing was done on normal mammary glands to identify signaling differences that may predispose to increased breast cancer risk by maternal HF intake. Analysis revealed 1587 and 4423 differentially expressed genes between HF and control offspring in F1 and F3 generations, respectively, of which 48 genes were similarly altered in both generations. Quantitative real-time polymerase chain reaction analysis validated 13 chosen up- and downregulated genes in F3 HF offspring, but only downregulated genes in F1 HF offspring. Ingenuity Pathway Analysis identified upregulation of Notch signaling as a key alteration in HF offspring. Further, knowledge-fused differential dependency network analysis identified ten node genes that in the HF offspring were uniquely connected to genes linked to increased cancer risk (ANKEF1, IGFBP6, SEMA5B), increased resistance to cancer treatments (SLC26A3), poor prognosis (ID4, JAM3, TBX2), and impaired anticancer immunity (EGR3, ZBP1). CONCLUSIONS We conclude that maternal HF diet intake during pregnancy induces a transgenerational increase in offspring mammary cancer risk in mice. The mechanisms of inheritance in the F3 generation may be different from the F1 generation because significantly more changes were seen in the transcriptome.
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Affiliation(s)
- Nguyen M Nguyen
- Department of Oncology, Georgetown University, Research Building, Room E407, 3970 Reservoir Road, NW, Washington, DC, 20057, USA
| | - Fabia de Oliveira Andrade
- Department of Oncology, Georgetown University, Research Building, Room E407, 3970 Reservoir Road, NW, Washington, DC, 20057, USA
| | - Lu Jin
- Department of Oncology, Georgetown University, Research Building, Room E407, 3970 Reservoir Road, NW, Washington, DC, 20057, USA
| | - Xiyuan Zhang
- Department of Oncology, Georgetown University, Research Building, Room E407, 3970 Reservoir Road, NW, Washington, DC, 20057, USA
| | - Madisa Macon
- Department of Oncology, Georgetown University, Research Building, Room E407, 3970 Reservoir Road, NW, Washington, DC, 20057, USA
| | - M Idalia Cruz
- Department of Oncology, Georgetown University, Research Building, Room E407, 3970 Reservoir Road, NW, Washington, DC, 20057, USA
| | - Carlos Benitez
- Department of Oncology, Georgetown University, Research Building, Room E407, 3970 Reservoir Road, NW, Washington, DC, 20057, USA
| | - Bryan Wehrenberg
- UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chao Yin
- Department of Oncology, Georgetown University, Research Building, Room E407, 3970 Reservoir Road, NW, Washington, DC, 20057, USA
| | - Xiao Wang
- Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA, USA
| | - Jianhua Xuan
- Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA, USA
| | - Sonia de Assis
- Department of Oncology, Georgetown University, Research Building, Room E407, 3970 Reservoir Road, NW, Washington, DC, 20057, USA
| | - Leena Hilakivi-Clarke
- Department of Oncology, Georgetown University, Research Building, Room E407, 3970 Reservoir Road, NW, Washington, DC, 20057, USA.
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23
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Gouti M, Delile J, Stamataki D, Wymeersch FJ, Huang Y, Kleinjung J, Wilson V, Briscoe J. A Gene Regulatory Network Balances Neural and Mesoderm Specification during Vertebrate Trunk Development. Dev Cell 2017; 41:243-261.e7. [PMID: 28457792 PMCID: PMC5425255 DOI: 10.1016/j.devcel.2017.04.002] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 02/20/2017] [Accepted: 04/03/2017] [Indexed: 01/02/2023]
Abstract
Transcriptional networks, regulated by extracellular signals, control cell fate decisions and determine the size and composition of developing tissues. One example is the network controlling bipotent neuromesodermal progenitors (NMPs) that fuel embryo elongation by generating spinal cord and trunk mesoderm tissue. Here, we use single-cell transcriptomics to identify the molecular signature of NMPs and reverse engineer the mechanism that regulates their differentiation. Together with genetic perturbations, this reveals a transcriptional network that integrates opposing retinoic acid (RA) and Wnt signals to determine the rate at which cells enter and exit the NMP state. RA, produced by newly generated mesodermal cells, provides feedback that initiates NMP generation and induces neural differentiation, thereby coordinating the production of neural and mesodermal tissue. Together, the data define a regulatory network architecture that balances the generation of different cell types from bipotential progenitors in order to facilitate orderly axis elongation. Single-cell RNA-seq reveals a signature of neuromesodermal progenitors In vitro NMPs resemble and differentiate similar to their in vivo counterparts Dual role for retinoic acid signaling in NMP induction and neural differentiation A transcriptional network regulates neural versus mesodermal allocation
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Affiliation(s)
- Mina Gouti
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK; Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.
| | - Julien Delile
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | | | - Filip J Wymeersch
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Yali Huang
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Jens Kleinjung
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Valerie Wilson
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - James Briscoe
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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24
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Lala-Tabbert N, AlSudais H, Marchildon F, Fu D, Wiper-Bergeron N. CCAAT/enhancer binding protein β is required for satellite cell self-renewal. Skelet Muscle 2016; 6:40. [PMID: 27923399 PMCID: PMC5142279 DOI: 10.1186/s13395-016-0112-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/08/2016] [Indexed: 12/12/2022] Open
Abstract
Background Postnatal growth and repair of skeletal muscle relies upon a population of quiescent muscle precursor cells, called satellite cells that can be activated to proliferate and differentiate into new myofibers, as well as self-renew to replenish the satellite cell population. The balance between differentiation and self-renewal is critical to maintain muscle tissue homeostasis, and alterations in this equilibrium can lead to chronic muscle degeneration. The transcription factor CCAAT/enhancer binding protein beta (C/EBPβ) is expressed in Pax7+ satellite cells of healthy muscle and is downregulated during myoblast differentiation. Persistent expression of C/EBPβ upregulates Pax7, inhibits MyoD, and blocks myogenic differentiation. Methods Using genetic tools to conditionally abrogate C/EBPβ expression in Pax7+ cells, we examined the role of C/EBPβ in self-renewal of satellite cells during muscle regeneration. Results We find that loss of C/EBPβ leads to precocious differentiation at the expense of self-renewal in primary myoblast and myofiber cultures. After a single muscle injury, C/EBPβ-deficient satellite cells fail to self-renew resulting in a reduction of satellite cells available for future rounds of regeneration. After a second round of injury, muscle regeneration is impaired in C/EBPβ conditional knockout mice compared to wild-type control mice. We find that C/EBPβ can regulate Notch2 expression and that restoration of Notch activity in myoblasts lacking C/EBPβ prevents precocious differentiation. Conclusions These findings demonstrate that C/EBPβ is a novel regulator of satellite cell self-renewal during muscle regeneration acting at least in part through Notch2.
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Affiliation(s)
- Neena Lala-Tabbert
- Graduate Program in Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Hamood AlSudais
- Graduate Program in Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - François Marchildon
- Graduate Program in Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Dechen Fu
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Nadine Wiper-Bergeron
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.
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25
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A comprehensive transcriptomic analysis of differentiating embryonic stem cells in response to the overexpression of Mesogenin 1. Aging (Albany NY) 2016; 8:2324-2336. [PMID: 27713115 PMCID: PMC5115891 DOI: 10.18632/aging.101049] [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: 01/18/2016] [Accepted: 09/22/2016] [Indexed: 11/25/2022]
Abstract
The mutation of somitogenesis protein Mesogenin 1 (Msgn1) has been widely used to study the direct link between somitogenesis and the development of an embryo. Several studies have used gene expression profiling of somitogenesis to identify the key genes in the process, but few have focused on the pathways involved and the coexpression patterns of associated pathways. Here we employed time-course microarray datasets of differentiating embryonic stem cells by overexpressing the transcription factor Msgn1 from the public database library of Gene Expression Omnibus (GEO). Then we applied gene set enrichment analysis (GSEA) to the datasets and performed candidate transcription factors selection. As a result, several significantly regulated pathways and transcription factors (TFs), as well as some of the specific signaling pathways, were identified during somitogenesis under Msgn1 overexpression, most of which had not been reported previously. Finally, significant core genes such as Hes1 and Notch1 as well as some of the TFs such as PPARs and FOXs were identified to construct coexpression networks of related pathways, the expression patterns of which had been validated by our following quantitative real-time PCR (qRT-PCR). The results of our study may help us better understand the molecular mechanisms of somitogenesis in mice at the genome-wide level.
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26
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Zfp703 Is a Wnt/β-Catenin Feedback Suppressor Targeting the β-Catenin/Tcf1 Complex. Mol Cell Biol 2016; 36:1793-802. [PMID: 27090637 DOI: 10.1128/mcb.01010-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 04/05/2016] [Indexed: 01/29/2023] Open
Abstract
The Wnt/β-catenin signaling pathway controls embryonic development and adult stem cell maintenance through the regulation of transcription. Failure to downregulate Wnt signaling can result in embryonic malformations and cancer, highlighting the important role of negative regulators of the pathway. The Wnt pathway activates several negative feedback targets, including axin2 and Dkk1, that function at different levels of the signaling cascade; however, none have been identified that directly target active β-catenin/Tcf1 transcriptional complexes. We show that Zfp703 is a Wnt target gene that inhibits Wnt/β-catenin activity in Wnt reporter assays and in Wnt-dependent mesoderm differentiation in embryonic stem cells. Zfp703 binds directly to Tcf1 to inhibit β-catenin/Tcf1 complex formation and does so independently of the Groucho/Tle transcriptional corepressor. We propose that Zfp703 is a novel feedback suppressor of Wnt/β-catenin signaling that functions by inhibiting the association of β-catenin with Tcf1 on Wnt response elements in target gene enhancers.
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Anderson MJ, Schimmang T, Lewandoski M. An FGF3-BMP Signaling Axis Regulates Caudal Neural Tube Closure, Neural Crest Specification and Anterior-Posterior Axis Extension. PLoS Genet 2016; 12:e1006018. [PMID: 27144312 PMCID: PMC4856314 DOI: 10.1371/journal.pgen.1006018] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 04/08/2016] [Indexed: 01/08/2023] Open
Abstract
During vertebrate axis extension, adjacent tissue layers undergo profound morphological changes: within the neuroepithelium, neural tube closure and neural crest formation are occurring, while within the paraxial mesoderm somites are segmenting from the presomitic mesoderm (PSM). Little is known about the signals between these tissues that regulate their coordinated morphogenesis. Here, we analyze the posterior axis truncation of mouse Fgf3 null homozygotes and demonstrate that the earliest role of PSM-derived FGF3 is to regulate BMP signals in the adjacent neuroepithelium. FGF3 loss causes elevated BMP signals leading to increased neuroepithelium proliferation, delay in neural tube closure and premature neural crest specification. We demonstrate that elevated BMP4 depletes PSM progenitors in vitro, phenocopying the Fgf3 mutant, suggesting that excessive BMP signals cause the Fgf3 axis defect. To test this in vivo we increased BMP signaling in Fgf3 mutants by removing one copy of Noggin, which encodes a BMP antagonist. In such mutants, all parameters of the Fgf3 phenotype were exacerbated: neural tube closure delay, premature neural crest specification, and premature axis termination. Conversely, genetically decreasing BMP signaling in Fgf3 mutants, via loss of BMP receptor activity, alleviates morphological defects. Aberrant apoptosis is observed in the Fgf3 mutant tailbud. However, we demonstrate that cell death does not cause the Fgf3 phenotype: blocking apoptosis via deletion of pro-apoptotic genes surprisingly increases all Fgf3 defects including causing spina bifida. We demonstrate that this counterintuitive consequence of blocking apoptosis is caused by the increased survival of BMP-producing cells in the neuroepithelium. Thus, we show that FGF3 in the caudal vertebrate embryo regulates BMP signaling in the neuroepithelium, which in turn regulates neural tube closure, neural crest specification and axis termination. Uncovering this FGF3-BMP signaling axis is a major advance toward understanding how these tissue layers interact during axis extension with important implications in human disease. During embryological development, the vertebrate embryo undergoes profound growth in a head-to-tail direction. During this process, formation of different structures within adjacent tissue layers must occur in a coordinated fashion. Insights into how these adjacent tissues molecularly communicate with each other is essential to understanding both basic embryology and the underlying causes of human birth defects. Mice lacking Fgf3, which encodes a secreted signaling factor, have long been known to have premature axis termination, but the underlying mechanism has not been studied until now. Through a series of complex genetic experiments, we show that FGF3 is an essential factor for coordination of neural tube development and axis extension. FGF3 is secreted from the mesodermal layer, which is the major driver of extending the axis, and negatively regulates expression of another class of secreted signaling molecules in the neuroepithelium, BMPs. In the absence of FGF3, excessive BMP signals cause a delay in neural tube closure, premature specification of neural crest cells and negatively affect the mesoderm, causing a premature termination of the embryological axis. Our work suggests that FGF3 may be a player in the complex etiology of the human birth defect, spina bifida, the failure of posterior neural tube closure.
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Affiliation(s)
- Matthew J. Anderson
- Genetics of Vertebrate Development Section, Cancer and Developmental Biology Lab, National Cancer Institute, National Institutes of Health, Frederick, Maryland, United States of America
| | - Thomas Schimmang
- Instituto de Biología y Genética Molecular, Universidad de Valladolid y Consejo Superior de Investigaciones Científicas, Valladolid, Spain
| | - Mark Lewandoski
- Genetics of Vertebrate Development Section, Cancer and Developmental Biology Lab, National Cancer Institute, National Institutes of Health, Frederick, Maryland, United States of America
- * E-mail:
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Sudheer S, Liu J, Marks M, Koch F, Anurin A, Scholze M, Senft AD, Wittler L, Macura K, Grote P, Herrmann BG. Different Concentrations of FGF Ligands, FGF2 or FGF8 Determine Distinct States of WNT-Induced Presomitic Mesoderm. Stem Cells 2016; 34:1790-800. [DOI: 10.1002/stem.2371] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 02/07/2016] [Accepted: 03/03/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Smita Sudheer
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU; United Kingdom
| | - Jinhua Liu
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Matthias Marks
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Frederic Koch
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Anna Anurin
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
- Department of Biology; Chemistry and Pharmacy, Free University Berlin; Berlin Germany
| | - Manuela Scholze
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Anna Dorothea Senft
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE; United Kingdom
| | - Lars Wittler
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Karol Macura
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Phillip Grote
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
- Institute of Cardiovascular Regeneration, Center for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main; Germany
| | - Bernhard G. Herrmann
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
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Sp5 and Sp8 recruit β-catenin and Tcf1-Lef1 to select enhancers to activate Wnt target gene transcription. Proc Natl Acad Sci U S A 2016; 113:3545-50. [PMID: 26969725 DOI: 10.1073/pnas.1519994113] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The ancient, highly conserved, Wnt signaling pathway regulates cell fate in all metazoans. We have previously shown that combined null mutations of the specificity protein (Sp) 1/Klf-like zinc-finger transcription factors Sp5 and Sp8 (i.e., Sp5/8) result in an embryonic phenotype identical to that observed when core components of the Wnt/β-catenin pathway are mutated; however, their role in Wnt signal transduction is unknown. Here, we show in mouse embryos and differentiating embryonic stem cells that Sp5/8 are gene-specific transcriptional coactivators in the Wnt/β-catenin pathway. Sp5/8 bind directly to GC boxes in Wnt target gene enhancers and to adjacent, or distally positioned, chromatin-bound T-cell factor (Tcf) 1/lymphoid enhancer factor (Lef) 1 to facilitate recruitment of β-catenin to target gene enhancers. Because Sp5 is itself directly activated by Wnt signals, we propose that Sp5 is a Wnt/β-catenin pathway-specific transcript on factor that functions in a feed-forward loop to robustly activate select Wnt target genes.
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Liu Z, Sneve M, Haroldson TA, Smith JP, Drewes LR. Regulation of Monocarboxylic Acid Transporter 1 Trafficking by the Canonical Wnt/β-Catenin Pathway in Rat Brain Endothelial Cells Requires Cross-talk with Notch Signaling. J Biol Chem 2016; 291:8059-69. [PMID: 26872974 DOI: 10.1074/jbc.m115.710277] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Indexed: 12/20/2022] Open
Abstract
The transport of monocarboxylate fuels such as lactate, pyruvate, and ketone bodies across brain endothelial cells is mediated by monocarboxylic acid transporter 1 (MCT1). Although the canonical Wnt/β-catenin pathway is required for rodent blood-brain barrier development and for the expression of associated nutrient transporters, the role of this pathway in the regulation of brain endothelial MCT1 is unknown. Here we report expression of nine members of the frizzled receptor family by the RBE4 rat brain endothelial cell line. Furthermore, activation of the canonical Wnt/β-catenin pathway in RBE4 cells via nuclear β-catenin signaling with LiCl does not alter brain endothelialMct1mRNA but increases the amount of MCT1 transporter protein. Plasma membrane biotinylation studies and confocal microscopic examination of mCherry-tagged MCT1 indicate that increased transporter results from reduced MCT1 trafficking from the plasma membrane via the endosomal/lysosomal pathway and is facilitated by decreased MCT1 ubiquitination following LiCl treatment. Inhibition of the Notch pathway by the γ-secretase inhibitorN-[N-(3,5-difluorophenacetyl)-l-alanyl]-S-phenylglycinet-butyl ester negated the up-regulation of MCT1 by LiCl, demonstrating a cross-talk between the canonical Wnt/β-catenin and Notch pathways. Our results are important because they show, for the first time, the regulation of MCT1 in cerebrovascular endothelial cells by the multifunctional canonical Wnt/β-catenin and Notch signaling pathways.
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Affiliation(s)
- Zejian Liu
- From the Department of Biomedical Sciences, University of Minnesota Medical School Duluth, Duluth, Minnesota 55812 and
| | - Mary Sneve
- From the Department of Biomedical Sciences, University of Minnesota Medical School Duluth, Duluth, Minnesota 55812 and
| | - Thomas A Haroldson
- From the Department of Biomedical Sciences, University of Minnesota Medical School Duluth, Duluth, Minnesota 55812 and
| | - Jeffrey P Smith
- the Department of Biology, Colorado State University, Pueblo, Colorado 81001
| | - Lester R Drewes
- From the Department of Biomedical Sciences, University of Minnesota Medical School Duluth, Duluth, Minnesota 55812 and
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31
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Martin BL. Factors that coordinate mesoderm specification from neuromesodermal progenitors with segmentation during vertebrate axial extension. Semin Cell Dev Biol 2016; 49:59-67. [DOI: 10.1016/j.semcdb.2015.11.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 11/25/2015] [Accepted: 11/26/2015] [Indexed: 12/15/2022]
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Li ASW, Marikawa Y. An in vitro gastrulation model recapitulates the morphogenetic impact of pharmacological inhibitors of developmental signaling pathways. Mol Reprod Dev 2015; 82:1015-36. [PMID: 26387793 DOI: 10.1002/mrd.22585] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 09/17/2015] [Indexed: 12/21/2022]
Abstract
Certain chemical agents act as teratogens, causing birth defects and fetal deaths when pregnant women are exposed to them. The establishment of in vitro models that recapitulate crucial embryonic events is therefore vital to facilitate screening of potential teratogens. Previously, we created a three-dimensional culture method for mouse P19C5 embryonal carcinoma stem cells that, when cultured as embryoid bodies, display elongation morphogenesis resembling gastrulation, which is the critical event resulting in the germ layers and major body axes. Determination of how well this in vitro morphogenesis represents in vivo gastrulation is essential to assess its applicability as well as to identify limitations of the model for detecting teratogenic agents. Here, we investigated the morphological and molecular characteristics of P19C5 morphogenesis using pharmacological agents that are known to cause abnormal patterning in the embryo in vivo by inhibiting major developmental signaling--e.g., involving Wnt, Nodal, Bone morphogenic protein (Bmp), Fibroblast growth factor (Fgf), Retinoic acid, Notch, and Hedgehog pathways. Inhibitors of Wnt, Nodal, Bmp, Fgf, and Retinoic acid signaling caused distinct changes in P19C5 morphogenesis that were quantifiable using morphometric parameters. These five inhibitors, plus the Notch inhibitor, also altered temporal expression profiles of developmental regulator genes in a manner consistent with the in vivo roles of the corresponding signaling pathways. In contrast, the Hedgehog inhibitor did not have any impact on the process, suggesting an absence of active Hedgehog signaling in these embryoid bodies. These results indicate that the P19C5 in vitro gastrulation model is a promising tool to screen for teratogenic agents that interfere with many of the key developmental signals.
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Affiliation(s)
- Aileen S W Li
- Developmental and Reproductive Biology Graduate Program, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Hawaii
| | - Yusuke Marikawa
- Developmental and Reproductive Biology Graduate Program, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Hawaii
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Müller M, Schröer J, Azoitei N, Eiseler T, Bergmann W, Köhntop R, Lin Q, Costa IG, Zenke M, Genze F, Weidgang C, Seufferlein T, Liebau S, Kleger A. A time frame permissive for Protein Kinase D2 activity to direct angiogenesis in mouse embryonic stem cells. Sci Rep 2015; 5:11742. [PMID: 26148697 PMCID: PMC4493579 DOI: 10.1038/srep11742] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 05/15/2015] [Indexed: 01/18/2023] Open
Abstract
The protein kinase D isoenzymes PKD1/2/3 are prominent downstream targets of PKCs (Protein Kinase Cs) and phospholipase D in various biological systems. Recently, we identified PKD isoforms as novel mediators of tumour cell-endothelial cell communication, tumour cell motility and metastasis. Although PKD isoforms have been implicated in physiological/tumour angiogenesis, a role of PKDs during embryonic development, vasculogenesis and angiogenesis still remains elusive. We investigated the role of PKDs in germ layer segregation and subsequent vasculogenesis and angiogenesis using mouse embryonic stem cells (ESCs). We show that mouse ESCs predominantly express PKD2 followed by PKD3 while PKD1 displays negligible levels. Furthermore, we demonstrate that PKD2 is specifically phosphorylated/activated at the time of germ layer segregation. Time-restricted PKD2-activation limits mesendoderm formation and subsequent cardiovasculogenesis during early differentiation while leading to branching angiogenesis during late differentiation. In line, PKD2 loss-of-function analyses showed induction of mesendodermal differentiation in expense of the neuroectodermal germ layer. Our in vivo findings demonstrate that embryoid bodies transplanted on chicken chorioallantoic membrane induced an angiogenic response indicating that timed overexpression of PKD2 from day 4 onwards leads to augmented angiogenesis in differentiating ESCs. Taken together, our results describe novel and time-dependent facets of PKD2 during early cell fate determination.
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Affiliation(s)
- Martin Müller
- Department of Internal Medicine I, Ulm University, Ulm, Germany
| | - Jana Schröer
- Department of Internal Medicine I, Ulm University, Ulm, Germany
| | - Ninel Azoitei
- Department of Internal Medicine I, Ulm University, Ulm, Germany
| | - Tim Eiseler
- Department of Internal Medicine I, Ulm University, Ulm, Germany
| | - Wendy Bergmann
- Department of Internal Medicine I, Ulm University, Ulm, Germany
| | - Ralf Köhntop
- Department of Internal Medicine I, Ulm University, Ulm, Germany
| | - Qiong Lin
- Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Ivan G Costa
- IZKF Computational Biology Research Group, RWTH Aachen University Medical School, Aachen, Germany
| | - Martin Zenke
- Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | | | - Clair Weidgang
- Department of Internal Medicine I, Ulm University, Ulm, Germany
| | | | - Stefan Liebau
- Institute of Neuroanatomy, Eberhard Karls University Tuebingen, Tuebingen, Germany
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Hsu CH, Lin JS, Po Lai K, Li JW, Chan TF, You MS, Tse WKF, Jiang YJ. A new mib allele with a chromosomal deletion covering foxc1a exhibits anterior somite specification defect. Sci Rep 2015; 5:10673. [PMID: 26039894 PMCID: PMC4454137 DOI: 10.1038/srep10673] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 04/23/2015] [Indexed: 12/20/2022] Open
Abstract
mibnn2002, found from an allele screen, showed early segmentation defect and severe cell death phenotypes, which are different from previously known mib mutants. Despite distinct morphological phenotypes, the typical mib molecular phenotypes: her4 down-regulation, neurogenic phenotype and cold sensitive dlc expression pattern, still remained. The linkage analysis also indicated that mibnn2002 is a new mib allele. Failure of specification in anterior 7-10 somites is likely due to lack of foxc1a expression in mibnn2002 homozygotes. Somites and somite markers gradually appeared after 7-10 somite stage, suggesting that foxc1a is only essential for the formation of anterior 7-10 somites. Apoptosis began around 16-somite stage with p53 up-regulation. To find the possible links of mib, foxc1a and apoptosis, transcriptome analysis was employed. About 140 genes, including wnt3a, foxc1a and mib, were not detected in the homozygotes. Overexpression of foxc1a mRNA in mibnn2002 homozygotes partially rescued the anterior somite specification. In the process of characterizing mibnn2002 mutation, we integrated the scaffolds containing mib locus into chromosome 2 (or linkage group 2, LG2) based on synteny comparison and transcriptome results. Genomic PCR analysis further supported the conclusion and showed that mibnn2002 has a chromosomal deletion with the size of about 9.6 Mbp.
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Affiliation(s)
- Chia-Hao Hsu
- 1] Institute of Molecular and Genomic Medicine, National Health Research Institutes, Taiwan [2] Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Taiwan
| | - Ji-Sheng Lin
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Taiwan
| | - Keng Po Lai
- School of Biological Sciences, The University of Hong Kong, Hong Kong
| | - Jing-Woei Li
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Ting-Fung Chan
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - May-Su You
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Taiwan
| | | | - Yun-Jin Jiang
- 1] Institute of Molecular and Genomic Medicine, National Health Research Institutes, Taiwan [2] Biotechnology Center, National Chung Hsing University, Taiwan [3] Institute of Molecular and Cellular Biology, National Taiwan University, Taiwan
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Gupte A, Baker EK, Wan SS, Stewart E, Loh A, Shelat AA, Gould CM, Chalk AM, Taylor S, Lackovic K, Karlström Å, Mutsaers AJ, Desai J, Madhamshettiwar PB, Zannettino ACW, Burns C, Huang DCS, Dyer MA, Simpson KJ, Walkley CR. Systematic Screening Identifies Dual PI3K and mTOR Inhibition as a Conserved Therapeutic Vulnerability in Osteosarcoma. Clin Cancer Res 2015; 21:3216-29. [PMID: 25862761 PMCID: PMC4506243 DOI: 10.1158/1078-0432.ccr-14-3026] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 03/26/2015] [Indexed: 01/08/2023]
Abstract
PURPOSE Osteosarcoma is the most common cancer of bone occurring mostly in teenagers. Despite rapid advances in our knowledge of the genetics and cell biology of osteosarcoma, significant improvements in patient survival have not been observed. The identification of effective therapeutics has been largely empirically based. The identification of new therapies and therapeutic targets are urgently needed to enable improved outcomes for osteosarcoma patients. EXPERIMENTAL DESIGN We have used genetically engineered murine models of human osteosarcoma in a systematic, genome-wide screen to identify new candidate therapeutic targets. We performed a genome-wide siRNA screen, with or without doxorubicin. In parallel, a screen of therapeutically relevant small molecules was conducted on primary murine- and primary human osteosarcoma-derived cell cultures. All results were validated across independent cell cultures and across human and mouse osteosarcoma. RESULTS The results from the genetic and chemical screens significantly overlapped, with a profound enrichment of pathways regulated by PI3K and mTOR pathways. Drugs that concurrently target both PI3K and mTOR were effective at inducing apoptosis in primary osteosarcoma cell cultures in vitro in both human and mouse osteosarcoma, whereas specific PI3K or mTOR inhibitors were not effective. The results were confirmed with siRNA and small molecule approaches. Rationale combinations of specific PI3K and mTOR inhibitors could recapitulate the effect on osteosarcoma cell cultures. CONCLUSIONS The approaches described here have identified dual inhibition of the PI3K-mTOR pathway as a sensitive, druggable target in osteosarcoma, and provide rationale for translational studies with these agents.
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Affiliation(s)
- Ankita Gupte
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia. Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Emma K Baker
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia. Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Soo-San Wan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Elizabeth Stewart
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Amos Loh
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Anang A Shelat
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Cathryn M Gould
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Alistair M Chalk
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia. Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Scott Taylor
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia. Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Kurt Lackovic
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Åsa Karlström
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Anthony J Mutsaers
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia. Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia. Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Jayesh Desai
- Department of Medical Oncology, Royal Melbourne Hospital, Melbourne, Victoria, Australia. Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Piyush B Madhamshettiwar
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Andrew C W Zannettino
- Myeloma Research Laboratory, School of Medical Sciences, Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia, Australia. Cancer Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Chris Burns
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - David C S Huang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee. Howard Hughes Medical Institute, Chevy Chase, Maryland.
| | - Kaylene J Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia. Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Carl R Walkley
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia. Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia. ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia.
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Modelling coupled oscillations in the Notch, Wnt, and FGF signaling pathways during somitogenesis: a comprehensive mathematical model. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2015; 2015:387409. [PMID: 25866502 PMCID: PMC4381657 DOI: 10.1155/2015/387409] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/22/2015] [Indexed: 12/18/2022]
Abstract
Somite formation in the early stage of vertebrate embryonic development is controlled by a complicated gene network named segmentation clock, which is defined by the periodic expression of genes related to the Notch, Wnt, and the fibroblast growth factor (FGF) pathways. Although in recent years some findings about crosstalk among the Notch, Wnt, and FGF pathways in somitogenesis have been reported, the investigation of their crosstalk mechanisms from a systematic point of view is still lacking. In this study, a more comprehensive mathematical model was proposed to simulate the dynamics of the Notch, Wnt, and FGF pathways in the segmentation clock. Simulations and bifurcation analyses of this model suggested that the concentration gradients of both Wnt, and FGF signals along the presomitic mesoderm (PSM) are corresponding to the whole process from start to stop of the segmentation clock. A number of highly sensitive parameters to the segmentation clock's oscillatory pattern were identified. By further bifurcation analyses for these sensitive parameters, and several complementary mechanisms in respect of the maintenance of the stable oscillation of the segmentation clock were revealed.
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37
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Lin IH, Chen DT, Chang YF, Lee YL, Su CH, Cheng C, Tsai YC, Ng SC, Chen HT, Lee MC, Chen HW, Suen SH, Chen YC, Liu TT, Chang CH, Hsu MT. Hierarchical clustering of breast cancer methylomes revealed differentially methylated and expressed breast cancer genes. PLoS One 2015; 10:e0118453. [PMID: 25706888 PMCID: PMC4338251 DOI: 10.1371/journal.pone.0118453] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 01/20/2015] [Indexed: 01/18/2023] Open
Abstract
Oncogenic transformation of normal cells often involves epigenetic alterations, including histone modification and DNA methylation. We conducted whole-genome bisulfite sequencing to determine the DNA methylomes of normal breast, fibroadenoma, invasive ductal carcinomas and MCF7. The emergence, disappearance, expansion and contraction of kilobase-sized hypomethylated regions (HMRs) and the hypomethylation of the megabase-sized partially methylated domains (PMDs) are the major forms of methylation changes observed in breast tumor samples. Hierarchical clustering of HMR revealed tumor-specific hypermethylated clusters and differential methylated enhancers specific to normal or breast cancer cell lines. Joint analysis of gene expression and DNA methylation data of normal breast and breast cancer cells identified differentially methylated and expressed genes associated with breast and/or ovarian cancers in cancer-specific HMR clusters. Furthermore, aberrant patterns of X-chromosome inactivation (XCI) was found in breast cancer cell lines as well as breast tumor samples in the TCGA BRCA (breast invasive carcinoma) dataset. They were characterized with differentially hypermethylated XIST promoter, reduced expression of XIST, and over-expression of hypomethylated X-linked genes. High expressions of these genes were significantly associated with lower survival rates in breast cancer patients. Comprehensive analysis of the normal and breast tumor methylomes suggests selective targeting of DNA methylation changes during breast cancer progression. The weak causal relationship between DNA methylation and gene expression observed in this study is evident of more complex role of DNA methylation in the regulation of gene expression in human epigenetics that deserves further investigation.
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Affiliation(s)
- I-Hsuan Lin
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Dow-Tien Chen
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Feng Chang
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Yu-Ling Lee
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Chia-Hsin Su
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Ching Cheng
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Chien Tsai
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Swee-Chuan Ng
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Hsiao-Tan Chen
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Mei-Chen Lee
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Hong-Wei Chen
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Shih-Hui Suen
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Yu-Cheng Chen
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Tze-Tze Liu
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
| | - Chuan-Hsiung Chang
- Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei, Taiwan
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Ming-Ta Hsu
- VGH-YM Genome Center, National Yang-Ming University, Taipei, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
- * E-mail:
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Chalamalasetty RB, Garriock RJ, Dunty WC, Kennedy MW, Jailwala P, Si H, Yamaguchi TP. Mesogenin 1 is a master regulator of paraxial presomitic mesoderm differentiation. Development 2015; 141:4285-97. [PMID: 25371364 DOI: 10.1242/dev.110908] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Neuromesodermal (NM) stem cells generate neural and paraxial presomitic mesoderm (PSM) cells, which are the respective progenitors of the spinal cord and musculoskeleton of the trunk and tail. The Wnt-regulated basic helix-loop-helix (bHLH) transcription factor mesogenin 1 (Msgn1) has been implicated as a cooperative regulator working in concert with T-box genes to control PSM formation in zebrafish, although the mechanism is unknown. We show here that, in mice, Msgn1 alone controls PSM differentiation by directly activating the transcriptional programs that define PSM identity, epithelial-mesenchymal transition, motility and segmentation. Forced expression of Msgn1 in NM stem cells in vivo reduced the contribution of their progeny to the neural tube, and dramatically expanded the unsegmented mesenchymal PSM while blocking somitogenesis and notochord differentiation. Expression of Msgn1 was sufficient to partially rescue PSM differentiation in Wnt3a(-/-) embryos, demonstrating that Msgn1 functions downstream of Wnt3a as the master regulator of PSM differentiation. Our data provide new insights into how cell fate decisions are imposed by the expression of a single transcriptional regulator.
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Affiliation(s)
- Ravindra B Chalamalasetty
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, NCI-Frederick, NIH, Frederick, MD 21702, USA
| | - Robert J Garriock
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, NCI-Frederick, NIH, Frederick, MD 21702, USA
| | - William C Dunty
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, NCI-Frederick, NIH, Frederick, MD 21702, USA
| | - Mark W Kennedy
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, NCI-Frederick, NIH, Frederick, MD 21702, USA
| | - Parthav Jailwala
- CCRIFX Bioinformatics Core, Leidos Biomedical Research, FNLCR, Frederick, MD 21702, USA
| | - Han Si
- CCRIFX Bioinformatics Core, Leidos Biomedical Research, FNLCR, Frederick, MD 21702, USA
| | - Terry P Yamaguchi
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, NCI-Frederick, NIH, Frederick, MD 21702, USA
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Dubchak I, Balasubramanian S, Wang S, Meyden C, Sulakhe D, Poliakov A, Börnigen D, Xie B, Taylor A, Ma J, Paciorkowski AR, Mirzaa GM, Dave P, Agam G, Xu J, Al-Gazali L, Mason CE, Ross ME, Maltsev N, Gilliam TC. An integrative computational approach for prioritization of genomic variants. PLoS One 2014; 9:e114903. [PMID: 25506935 PMCID: PMC4266634 DOI: 10.1371/journal.pone.0114903] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 11/15/2014] [Indexed: 12/27/2022] Open
Abstract
An essential step in the discovery of molecular mechanisms contributing to disease phenotypes and efficient experimental planning is the development of weighted hypotheses that estimate the functional effects of sequence variants discovered by high-throughput genomics. With the increasing specialization of the bioinformatics resources, creating analytical workflows that seamlessly integrate data and bioinformatics tools developed by multiple groups becomes inevitable. Here we present a case study of a use of the distributed analytical environment integrating four complementary specialized resources, namely the Lynx platform, VISTA RViewer, the Developmental Brain Disorders Database (DBDB), and the RaptorX server, for the identification of high-confidence candidate genes contributing to pathogenesis of spina bifida. The analysis resulted in prediction and validation of deleterious mutations in the SLC19A placental transporter in mothers of the affected children that causes narrowing of the outlet channel and therefore leads to the reduced folate permeation rate. The described approach also enabled correct identification of several genes, previously shown to contribute to pathogenesis of spina bifida, and suggestion of additional genes for experimental validations. The study demonstrates that the seamless integration of bioinformatics resources enables fast and efficient prioritization and characterization of genomic factors and molecular networks contributing to the phenotypes of interest.
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Affiliation(s)
- Inna Dubchak
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
- * E-mail: (ID); (NM)
| | - Sandhya Balasubramanian
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Sheng Wang
- Toyota Technological Institute at Chicago, Chicago, Illinois, United States of America
| | - Cem Meyden
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, United States of America
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, United States of America
- Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, New York, New York, United States of America
| | - Dinanath Sulakhe
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Computation Institute, University of Chicago/Argonne National Laboratory, Chicago, Illinois, United States of America
| | - Alexander Poliakov
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Daniela Börnigen
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Toyota Technological Institute at Chicago, Chicago, Illinois, United States of America
| | - Bingqing Xie
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Computer Science, Illinois Institute of Technology, Chicago, Illinois, United States of America
| | - Andrew Taylor
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Jianzhu Ma
- Toyota Technological Institute at Chicago, Chicago, Illinois, United States of America
| | - Alex R. Paciorkowski
- Departments of Neurology, Pediatrics, and Biomedical Genetics and Center for Neural Development and Disease, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Ghayda M. Mirzaa
- Seattle Children's Research Institute and Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Paul Dave
- Computation Institute, University of Chicago/Argonne National Laboratory, Chicago, Illinois, United States of America
| | - Gady Agam
- Department of Computer Science, Illinois Institute of Technology, Chicago, Illinois, United States of America
| | - Jinbo Xu
- Toyota Technological Institute at Chicago, Chicago, Illinois, United States of America
| | - Lihadh Al-Gazali
- Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, UAE
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, United States of America
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, United States of America
- Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, New York, New York, United States of America
| | - M. Elizabeth Ross
- Laboratory of Neurogenetics and Development, Weill Cornell Medical College, New York, New York, United States of America
| | - Natalia Maltsev
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Computation Institute, University of Chicago/Argonne National Laboratory, Chicago, Illinois, United States of America
- * E-mail: (ID); (NM)
| | - T. Conrad Gilliam
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Computation Institute, University of Chicago/Argonne National Laboratory, Chicago, Illinois, United States of America
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Bajard L, Morelli LG, Ares S, Pécréaux J, Jülicher F, Oates AC. Wnt-regulated dynamics of positional information in zebrafish somitogenesis. Development 2014; 141:1381-91. [PMID: 24595291 PMCID: PMC3943186 DOI: 10.1242/dev.093435] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
How signaling gradients supply positional information in a field of moving cells is an unsolved question in patterning and morphogenesis. Here, we ask how a Wnt signaling gradient regulates the dynamics of a wavefront of cellular change in a flow of cells during somitogenesis. Using time-controlled perturbations of Wnt signaling in the zebrafish embryo, we changed segment length without altering the rate of somite formation or embryonic elongation. This result implies specific Wnt regulation of the wavefront velocity. The observed Wnt signaling gradient dynamics and timing of downstream events support a model for wavefront regulation in which cell flow plays a dominant role in transporting positional information.
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Affiliation(s)
- Lola Bajard
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307 Dresden, Germany
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42
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Gutiérrez-Avilés D, Rubio-Escudero C. Mining 3D patterns from gene expression temporal data: a new tricluster evaluation measure. ScientificWorldJournal 2014; 2014:624371. [PMID: 25143987 PMCID: PMC3988738 DOI: 10.1155/2014/624371] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 02/26/2014] [Indexed: 11/18/2022] Open
Abstract
Microarrays have revolutionized biotechnological research. The analysis of new data generated represents a computational challenge due to the characteristics of these data. Clustering techniques are applied to create groups of genes that exhibit a similar behavior. Biclustering emerges as a valuable tool for microarray data analysis since it relaxes the constraints for grouping, allowing genes to be evaluated only under a subset of the conditions. However, if a third dimension appears in the data, triclustering is the appropriate tool for the analysis. This occurs in longitudinal experiments in which the genes are evaluated under conditions at several time points. All clustering, biclustering, and triclustering techniques guide their search for solutions by a measure that evaluates the quality of clusters. We present an evaluation measure for triclusters called Mean Square Residue 3D. This measure is based on the classic biclustering measure Mean Square Residue. Mean Square Residue 3D has been applied to both synthetic and real data and it has proved to be capable of extracting groups of genes with homogeneous patterns in subsets of conditions and times, and these groups have shown a high correlation level and they are also related to their functional annotations extracted from the Gene Ontology project.
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Affiliation(s)
- David Gutiérrez-Avilés
- Department of Computer Science, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Cristina Rubio-Escudero
- Department of Computer Science, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
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43
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Dunty WC, Kennedy MWL, Chalamalasetty RB, Campbell K, Yamaguchi TP. Transcriptional profiling of Wnt3a mutants identifies Sp transcription factors as essential effectors of the Wnt/β-catenin pathway in neuromesodermal stem cells. PLoS One 2014; 9:e87018. [PMID: 24475213 PMCID: PMC3901714 DOI: 10.1371/journal.pone.0087018] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 12/17/2013] [Indexed: 01/08/2023] Open
Abstract
Neuromesodermal (NM) stem cells reside in the primitive streak (PS) of gastrulating vertebrate embryos and generate precursors of the spinal cord and musculoskeletal system. Although Wnt3a/β-catenin signaling is crucial for NM stem cell maintenance and differentiation, few key transcriptional effectors have been identified. Through a concerted transcriptional profiling and genetic approach we have determined that two Zn2+-finger transcription factors, Sp5 and Sp8, are regulated by Wnt3a in the PS, and are essential for neural and musculoskeletal patterning. These results identify Sp5 and Sp8 as pivotal downstream effectors of Wnt3a, and suggest that they are essential for the self-renewal and differentiation of NM stem cells.
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Affiliation(s)
- William C. Dunty
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland, United States of America
| | - Mark W. L. Kennedy
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland, United States of America
| | - Ravindra B. Chalamalasetty
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland, United States of America
| | - Kenneth Campbell
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Terry P. Yamaguchi
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland, United States of America
- * E-mail:
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44
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TCreERT2, a transgenic mouse line for temporal control of Cre-mediated recombination in lineages emerging from the primitive streak or tail bud. PLoS One 2013; 8:e62479. [PMID: 23638095 PMCID: PMC3640045 DOI: 10.1371/journal.pone.0062479] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 03/21/2013] [Indexed: 11/19/2022] Open
Abstract
The study of axis extension and somitogenesis has been greatly advanced through the use of genetic tools such as the TCre mouse line. In this line, Cre is controlled by a fragment of the T (Brachyury) promoter that is active in progenitor cells that reside within the primitive streak and tail bud and which give rise to lineages emerging from these tissues as the embryonic axis extends. However, because TCre-mediated recombination occurs early in development, gene inactivation can result in an axis truncation that precludes the study of gene function in later or more posterior tissues. To address this limitation, we have generated an inducible TCre transgenic mouse line, called TCreERT2, that provides temporal control, through tamoxifen administration, in all cells emerging from the primitive streak or tail bud throughout development. TCreERT2 activity is mostly silent in the absence of tamoxifen and, in its presence, results in near complete recombination of emerging mesoderm from E7.5 through E13.5. We demonstrate the utility of the TCreERT2 line for determining rate of posterior axis extension and somite formation, thus providing the first in vivo tool for such measurements. To test the usefulness of TCreERT2 for genetic manipulation, we demonstrate that an early deletion of ß-Catenin via TCreERT2 induction phenocopies the TCre-mediated deletion of ß-Catenin defect, whereas a later induction bypasses this early phenotype and produces a similar defect in more caudal tissues. TCreERT2 provides a useful and novel tool for the control of gene expression of emerging embryonic lineages throughout development.
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45
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Gaete M, Tucker AS. Organized emergence of multiple-generations of teeth in snakes is dysregulated by activation of Wnt/beta-catenin signalling. PLoS One 2013; 8:e74484. [PMID: 24019968 PMCID: PMC3760860 DOI: 10.1371/journal.pone.0074484] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 08/02/2013] [Indexed: 02/01/2023] Open
Abstract
In contrast to mammals, most reptiles constantly regenerate their teeth. In the snake, the epithelial dental lamina ends in a successional lamina, which proliferates and elongates forming multiple tooth generations, all linked by a permanent dental lamina. To investigate the mechanisms used to control the initiation of new tooth germs in an ordered sequential pattern we utilized the polyphodont (multiple-generation) corn snake (Pantherophis guttatus). We observed that the dental lamina expressed the transcription factor Sox2, a multipotent stem cell marker, whereas the successional lamina cells expressed the transcription factor Lef1, a Wnt/β-catenin pathway target gene. Activation of the Wnt/β-catenin pathway in culture increased the number of developing tooth germs, in comparison to control untreated cultures. These additional tooth germs budded off from ectopic positions along the dental lamina, rather than in an ordered sequence from the successional lamina. Wnt/β-catenin activation enhanced cell proliferation, particularly in normally non-odontogenic regions of the dental lamina, which widely expressed Lef1, restricting the Sox2 domain. This suggests an expansion of the successional lamina at the expense of the dental lamina. Activation of the Wnt/β-catenin pathway in cultured snake dental organs, therefore, led to changes in proliferation and to the molecular pattern of the dental lamina, resulting in loss of the organised emergence of tooth germs. These results suggest that epithelial compartments are critical for the arrangement of organs that develop in sequence, and highlight the role of Wnt/β-catenin signalling in such processes.
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Affiliation(s)
- Marcia Gaete
- Department of Craniofacial Development and Stem Cell Biology, King’s College London, London, United Kingdom
- Department of Anatomy, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Abigail S. Tucker
- Department of Craniofacial Development and Stem Cell Biology, King’s College London, London, United Kingdom
- * E-mail:
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46
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Giampietro PF. Genetic aspects of congenital and idiopathic scoliosis. SCIENTIFICA 2012; 2012:152365. [PMID: 24278672 PMCID: PMC3820596 DOI: 10.6064/2012/152365] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 11/11/2012] [Indexed: 06/02/2023]
Abstract
Congenital and idiopathic scoliosis represent disabling conditions of the spine. While congenital scoliosis (CS) is caused by morphogenic abnormalities in vertebral development, the cause(s) for idiopathic scoliosis is (are) likely to be varied, representing alterations in skeletal growth, neuromuscular imbalances, disturbances involving communication between the brain and spine, and others. Both conditions are characterized by phenotypic and genetic heterogeneities, which contribute to the difficulties in understanding their genetic basis that investigators face. Despite the differences between these two conditions there is observational and experimental evidence supporting common genetic mechanisms. This paper focuses on the clinical features of both CS and IS and highlights genetic and environmental factors which contribute to their occurrence. It is anticipated that emerging genetic technologies and improvements in phenotypic stratification of both conditions will facilitate improved understanding of the genetic basis for these conditions and enable targeted prevention and treatment strategies.
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Affiliation(s)
- Philip F. Giampietro
- Waisman Center, University of Wisconsin-Madison, 1500 Highland Avenue, Madison, WI 53705, USA
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47
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Minami I, Yamada K, Otsuji TG, Yamamoto T, Shen Y, Otsuka S, Kadota S, Morone N, Barve M, Asai Y, Tenkova-Heuser T, Heuser JE, Uesugi M, Aiba K, Nakatsuji N. A small molecule that promotes cardiac differentiation of human pluripotent stem cells under defined, cytokine- and xeno-free conditions. Cell Rep 2012; 2:1448-60. [PMID: 23103164 DOI: 10.1016/j.celrep.2012.09.015] [Citation(s) in RCA: 185] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 05/18/2012] [Accepted: 09/12/2012] [Indexed: 12/15/2022] Open
Abstract
Human pluripotent stem cells (hPSCs), including embryonic stem cells and induced pluripotent stem cells, are potentially useful in regenerative therapies for heart disease. For medical applications, clinical-grade cardiac cells must be produced from hPSCs in a defined, cost-effective manner. Cell-based screening led to the discovery of KY02111, a small molecule that promotes differentiation of hPSCs to cardiomyocytes. Although the direct target of KY02111 remains unknown, results of the present study suggest that KY02111 promotes differentiation by inhibiting WNT signaling in hPSCs but in a manner that is distinct from that of previously studied WNT inhibitors. Combined use of KY02111 and WNT signaling modulators produced robust cardiac differentiation of hPSCs in a xeno-free, defined medium, devoid of serum and any kind of recombinant cytokines and hormones, such as BMP4, Activin A, or insulin. The methodology has potential as a means for the practical production of human cardiomyocytes for regeneration therapies.
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Affiliation(s)
- Itsunari Minami
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan
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Yabe T, Takada S. Mesogenin causes embryonic mesoderm progenitors to differentiate during development of zebrafish tail somites. Dev Biol 2012; 370:213-22. [PMID: 22890044 DOI: 10.1016/j.ydbio.2012.07.029] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 07/29/2012] [Accepted: 07/30/2012] [Indexed: 11/16/2022]
Abstract
The molecular mechanism underlying somite development differs along the embryonic antero-posterior axis. In zebrafish, cell lineage tracing and genetic analysis have revealed a difference in somite development between the trunk and tail. For instance, spadetail/tbx16 (spt) mutant embryos lack trunk somites but not tail ones. Trunk and tail somites are developed from mesodermal progenitor cells (MPCs) located in the tailbud. While the undifferentiated state of MPCs is maintained by mutual activation between Wnt and Brachyury/Ntl, the mechanism by which the MPCs differentiate into presomitic mesoderm (PSM) cells remains largely unclear. Especially, the molecules that promote PSM differentiation during tail development should be clarified. Here, we show that zebrafish embryos defective in mesogenin1 (msgn1) and spt failed to differentiate into PSM cells in tail development and show increased expression of wnt8 and ntl. Msgn1 acted in a cell-autonomous manner and as a transcriptional activator in PSM differentiation. The expression of msgn1 initially overlapped with that of ntl in the ventral tailbud, as previously reported; and its mis-expression caused ectopic expression of tbx24, a PSM marker gene, only in the tailbud and posterior notochord, both of which expressed ntl in zebrafish embryos. Furthermore, the PSM-inducing activity of misexpressed msgn1 was enhanced by co-expression with ntl. Thus, Msgn1 exercised its PSM-inducing activity in cells expressing ntl. Based on these results, we speculate that msgn1 expression in association with that of ntl may allow the differentiation of progenitor cells to proceed during development of somites in the tail.
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Affiliation(s)
- Taijiro Yabe
- Okazaki Institute for Integrative Bioscience and National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
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Hematopoietic stem cell development, niches, and signaling pathways. BONE MARROW RESEARCH 2012; 2012:270425. [PMID: 22900188 PMCID: PMC3413998 DOI: 10.1155/2012/270425] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 05/30/2012] [Accepted: 06/13/2012] [Indexed: 12/22/2022]
Abstract
Hematopoietic stem cells (HSCs) play a key role in hematopoietic system that functions mainly in homeostasis and immune response. HSCs transplantation has been applied for the treatment of several diseases. However, HSCs persist in the small quantity within the body, mostly in the quiescent state. Understanding the basic knowledge of HSCs is useful for stem cell biology research and therapeutic medicine development. Thus, this paper emphasizes on HSC origin, source, development, the niche, and signaling pathways which support HSC maintenance and balance between self-renewal and proliferation which will be useful for the advancement of HSC expansion and transplantation in the future.
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50
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Nowotschin S, Ferrer-Vaquer A, Concepcion D, Papaioannou VE, Hadjantonakis AK. Interaction of Wnt3a, Msgn1 and Tbx6 in neural versus paraxial mesoderm lineage commitment and paraxial mesoderm differentiation in the mouse embryo. Dev Biol 2012; 367:1-14. [PMID: 22546692 DOI: 10.1016/j.ydbio.2012.04.012] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Revised: 03/27/2012] [Accepted: 04/03/2012] [Indexed: 01/28/2023]
Abstract
Paraxial mesoderm is the tissue which gives rise to the skeletal muscles and vertebral column of the body. A gene regulatory network operating in the formation of paraxial mesoderm has been described. This network hinges on three key factors, Wnt3a, Msgn1 and Tbx6, each of which is critical for paraxial mesoderm formation, since absence of any one of these factors results in complete absence of posterior somites. In this study we determined and compared the spatial and temporal patterns of expression of Wnt3a, Msgn1 and Tbx6 at a time when paraxial mesoderm is being formed. Then, we performed a comparative characterization of mutants in Wnt3a, Msgn1 and Tbx6. To determine the epistatic relationship between these three genes, and begin to decipher the complex interplay between them, we analyzed double mutant embryos and compared their phenotypes to the single mutants. Through the analysis of molecular markers in mutants, our data support the bipotential nature of the progenitor cells for paraxial mesoderm and establish regulatory relationships between genes involved in the choice between neural and mesoderm fates.
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Affiliation(s)
- Sonja Nowotschin
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Ave, New York, NY 10065, USA
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