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Tan D.W.M.,Wellcome Trust Medical Research Council Cambridge Stem Cell Institute | Jensen K.B.,Wellcome Trust Medical Research Council Cambridge Stem Cell Institute | Trotter M.W.B.,Celgene | Connelly J.T.,Center for Cutaneous Research | And 5 more authors.
Development (Cambridge) | Year: 2013

SUMMARY Human epidermal stem cells express high levels of β1 integrins, delta-like 1 (DLL1) and the EGFR antagonist LRIG1. However, there is cell-to-cell variation in the relative abundance of DLL1 and LRIG1 mRNA transcripts. Single-cell global gene expression profiling showed that undifferentiated cells fell into two clusters delineated by expression of DLL1 and its binding partner syntenin. The DLL1+ cluster had elevated expression of genes associated with endocytosis, integrin-mediated adhesion and receptor tyrosine kinase signaling. Differentially expressed genes were not independently regulated, as overexpression of DLL1 alone or together with LRIG1 led to the upregulation of other genes in the DLL1+ cluster. Overexpression of DLL1 and LRIG1 resulted in enhanced extracellular matrix adhesion and increased caveolin-dependent EGFR endocytosis. Further characterisation of CD46, one of the genes upregulated in the DLL1+ cluster, revealed it to be a novel cell surface marker of human epidermal stem cells. Cells with high endogenous levels of CD46 expressed high levels of β1 integrin and DLL1 and were highly adhesive and clonogenic. Knockdown of CD46 decreased proliferative potential and β1 integrin-mediated adhesion. Thus, the previously unknown heterogeneity revealed by our studies results in differences in the interaction of undifferentiated basal keratinocytes with their environment. © 2013. Published by The Company of Biologists Ltd.


Cambuli F.,Babraham Institute | Cambuli F.,University of Cambridge | Murray A.,Babraham Institute | Murray A.,University of Cambridge | And 11 more authors.
Nature Communications | Year: 2015

Embryonic (ES) and trophoblast (TS) stem cells reflect the first, irrevocable cell fate decision in development that is reinforced by distinct epigenetic lineage barriers. Nonetheless, ES cells can seemingly acquire TS-like characteristics upon manipulation of lineage-determining transcription factors or activation of the extracellular signal-regulated kinase 1/2 (Erk1/2) pathway. Here we have interrogated the progression of reprogramming in ES cell models with regulatable Oct4 and Cdx2 transgenes or conditional Erk1/2 activation. Although trans-differentiation into TS-like cells is initiated, lineage conversion remains incomplete in all models, underpinned by the failure to demethylate a small group of TS cell genes. Forced expression of these non-reprogrammed genes improves trans-differentiation efficiency, but still fails to confer a stable TS cell phenotype. Thus, even ES cells in ground-state pluripotency cannot fully overcome the boundaries that separate the first cell lineages but retain an epigenetic memory of their ES cell origin. © 2014 Macmillan Publishers Limited. All rights reserved.


Cvejic A.,University of Cambridge | Cvejic A.,Wellcome Trust Sanger Institute | Cvejic A.,Wellcome Trust Medical Research Council Cambridge Stem Cell Institute
Immunology and Cell Biology | Year: 2016

Blood stem cells need to both perpetuate themselves (self-renew) and differentiate into all mature blood cells to maintain blood formation throughout life. However, it is unclear how the underlying gene regulatory network maintains this population of self-renewing and differentiating stem cells and how it accommodates the transition from a stem cell to a mature blood cell. Our current knowledge of transcriptomes of various blood cell types has mainly been advanced by population-level analysis. However, a population of seemingly homogenous blood cells may include many distinct cell types with substantially different transcriptomes and abilities to make diverse fate decisions. Therefore, understanding the cell-intrinsic differences between individual cells is necessary for a deeper understanding of the molecular basis of their behaviour. Here we review recent single-cell studies in the haematopoietic system and their contribution to our understanding of the mechanisms governing cell fate choices and lineage commitment. © 2016 Australasian Society for Immunology Inc. All rights reserved.


PubMed | Wellcome Trust Sanger Institute and Wellcome Trust Medical Research Council Cambridge Stem Cell Institute
Type: Journal Article | Journal: Cell reports | Year: 2016

The transcriptional programs that govern hematopoiesis have been investigated primarily by population-level analysis of hematopoietic stem and progenitor cells, which cannot reveal the continuous nature of the differentiation process. Here we applied single-cell RNA-sequencing to a population of hematopoietic cells in zebrafish as they undergo thrombocyte lineage commitment. By reconstructing their developmental chronology computationally, we were able to place each cell along a continuum from stem cell to mature cell, refining the traditional lineage tree. The progression of cells along this continuum is characterized by a highly coordinated transcriptional program, displaying simultaneous suppression of genes involved in cell proliferation and ribosomal biogenesis as the expression of lineage specific genes increases. Within this program, there is substantial heterogeneity in the expression of the key lineage regulators. Overall, the total number of genes expressed, as well as the total mRNA content of the cell, decreases as the cells undergo lineage commitment.


Chong R.S.,Singapore National Eye Center | Chong R.S.,Singapore Eye Research Institute | Chong R.S.,Agency for Science, Technology and Research Singapore | Chong R.S.,University of Cambridge | And 6 more authors.
Investigative Ophthalmology and Visual Science | Year: 2016

PURPOSE. Platelet-derived growth factor (PDGF) promotes neuronal survival in experimental glaucoma and recruits glial cells that regulate synapses. We investigated the effects of intravitreal PDGF on the inflammatory milieu and retinal synapses in the presence of raised IOP. METHODS. Animals with laser-induced IOP elevation received intravitreal injections of either saline or 1.5 μg PDGF. At 7 days, a further intravitreal injection was administered so groups received “PDGF–saline” (n = 15), “PDGF–PDGF” (n = 13), or “saline–saline” (n = 20). Platelet-derived growth factor receptor activation was assessed after 2 weeks using Western blot for PI3 kinase. Immunohistochemistry was performed for markers of synapses in the inner plexiform layer (IPL): PSD-95, GluR1, SY38; RGCs: βIII-tubulin, and glial cells: Iba-1, CD45. Real-time quantitative polymerase chain reaction (qPCR) was performed for Arc, selp, MCP-1, IL-6, IL-10, and CX3CR1 (n = 13). RESULTS. A single injection of PDGF increased IPL synaptic density in high IOP eyes (PSD-95= 8.65 ± 0.43, SY38 = 8.68 ± 0.51, GluR1 = 9.03 ± 0.60 puncta/μm3, P < 0.001) and expression of synaptic modulator Arc (6.92 ± 3.71-fold change/control, P < 0.05) in comparison with vehicle (PSD-95 = 4.59 ± 0.41, SY38 = 4.46 ± 0.38, GluR1 = 5.94 ± 0.50 puncta/μm3, Arc = 1.46 6 0.31-fold/control). This was associated with more resident microglia (8.16 ± 1.34-fold change/control, P < 0.001) and infiltrating monocyte-derived macrophages in the retina as well as increased Selp expression (26.8 ± 14.12-fold change/ control, P < 0.05). Optic nerve head (ONH) showed an increased microglia (saline = 1.44 6 0.13 versus PDGF = 2.23 ± 0.18-fold change/control, P < 0.01) but not infiltrating macrophages. IL-10 expression was significantly increased in PDGF-treated eyes (5.43 ± 0.47fold change/control, P < 0.05) relative to vehicle (2.51 ± 0.67-fold change/control). CONCLUSIONS. Platelet-derived growth factor increased microglial and monocyte-derived macrophage populations in the eye and protected intraretinal synapses from degeneration in our experimental glaucoma model. © 2016, Association for Research in Vision and Ophthalmology Inc.. All rights reserved.


Chen Y.,University of Manchester | Chen Y.,Wellcome Trust Medical Research Council Cambridge Stem Cell Institute | Love N.R.,University of Manchester | Love N.R.,RIKEN | Amaya E.,University of Manchester
Biochemical Society Transactions | Year: 2014

Some organisms have a remarkable ability to heal wounds without scars and to regenerate complex tissues following injury. By gaining a more complete understanding of the biological mechanisms that promote scar-free healing and tissue regeneration, it is hoped that novel treatments that can enhance the healing and regenerative capacity of human patients can be found. In the present article, we briefly examine the genetic, molecular and cellular mechanisms underlying the regeneration of the Xenopus tadpole tail. © 2014 Biochemical Society.


PubMed | The BRIC, Wellcome Trust & Medical Research Council Cambridge Stem Cell Institute and Copenhagen University
Type: Journal Article | Journal: Development (Cambridge, England) | Year: 2014

The epidermis is an integral part of our largest organ, the skin, and protects us against the hostile environment. It is a highly dynamic tissue that, during normal steady-state conditions, undergoes constant turnover. Multiple stem cell populations residing in autonomously maintained compartments facilitate this task. In this Review, we discuss stem cell behaviour during normal tissue homeostasis, regeneration and disease within the pilosebaceous unit, an integral structure of the epidermis that is responsible for hair growth and lubrication of the epithelium. We provide an up-to-date view of the pilosebaceous unit, encompassing the heterogeneity and plasticity of multiple discrete stem cell populations that are strongly influenced by external cues to maintain their identity and function.


Ghorbani M.,Brunel University | Ghorbani M.,Wellcome Trust Medical Research Council Cambridge Stem Cell Institute | Themis M.,Brunel University | Payne A.,Brunel University
Computers in Biology and Medicine | Year: 2016

This study identifies common methylation patterns across different cancer types in an effort to identify common molecular events in diverse types of cancer cells and provides evidence for the sequence surrounding a CpG to influence its susceptibility to aberrant methylation. CpG sites throughout the genome were divided into four classes: sites that either become hypo or hyper-methylated in a variety cancers using all the freely available microarray data (HypoCancer and HyperCancer classes) and those found in a constant hypo (Never methylated class) or hyper-methylated (Always methylated class) state in both normal and cancer cells. Our data shows that most CpG sites included in the HumanMethylation450K microarray remain unmethylated in normal and cancerous cells; however, certain sites in all the cancers investigated become specifically modified. More detailed analysis of the sites revealed that majority of those in the never methylated class were in CpG islands whereas those in the HyperCancer class were mostly associated with miRNA coding regions. The sites in the Hypermethylated class are associated with genes involved in initiating or maintaining the cancerous state, being enriched for processes involved in apoptosis, and with transcription factors predicted to bind to these genes linked to apoptosis and tumourgenesis (notably including E2F). Further we show that more LINE elements are associated with the HypoCancer class and more Alu repeats are associated with the HyperCancer class. Motifs that classify the classes were identified to distinguish them based on the surrounding DNA sequence alone, and for the identification of DNA sequences that could render sites more prone to aberrant methylation in cancer cells. This provides evidence that the sequence surrounding a CpG site has an influence on whether a site is hypo or hyper methylated. © 2015 Elsevier Ltd.


Tassoni A.,University of Cambridge | Gutteridge A.,Pfizer | Barber A.C.,University of Cambridge | Osborne A.,University of Cambridge | And 4 more authors.
Stem Cells | Year: 2015

A variety of diseases lead to degeneration of retinal ganglion cells (RGCs) and their axons within the optic nerve resulting in loss of visual function. Although current therapies may delay RGC loss, they do not restore visual function or completely halt disease progression. Regenerative medicine has recently focused on stem cell therapy for both neuroprotective and regenerative purposes. However, significant problems remain to be addressed, such as the long-term impact of reactive gliosis occurring in the host retina in response to transplanted stem cells. The aim of this work was to investigate retinal glial responses to intravitreally transplanted bone marrow mesenchymal stem cells (BM-MSCs) to help identify factors able to modulate graft-induced reactive gliosis. We found in vivo that intravitreal BM-MSC transplantation is associated with gliosis-mediated retinal folding, upregulation of intermediate filaments, and recruitment of macrophages. These responses were accompanied by significant JAK/STAT3 and MAPK (ERK1/2 and JNK) cascade activation in retinal Muller glia. Lipocalin-2 (Lcn-2) was identified as a potential new indicator of graft-induced reactive gliosis. Pharmacological inhibition of STAT3 in BM-MSC cocultured retinal explants successfully reduced glial fibrillary acidic protein expression in retinal Muller glia and increased BM-MSC retinal engraftment. Inhibition of stem cell-induced reactive gliosis is critical for successful transplantation-based strategies for neuroprotection, replacement, and regeneration of the optic nerve. © 2015 The Authors. STEM CELLS Published by Wiley Periodicals, Inc.


Sinha S.,University of Cambridge | Sinha S.,Wellcome Trust Medical Research Council Cambridge Stem Cell Institute | Iyer D.,University of Cambridge | Iyer D.,Wellcome Trust Medical Research Council Cambridge Stem Cell Institute | And 2 more authors.
Cellular and Molecular Life Sciences | Year: 2014

Vascular smooth muscle cells (SMCs) arise from multiple origins during development, raising the possibility that differences in embryological origins between SMCs could contribute to site-specific localization of vascular diseases. In this review, we first examine the developmental pathways and embryological origins of vascular SMCs and then discuss in vitro strategies for deriving SMCs from human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). We then review in detail the potential for vascular disease modeling using iPSC-derived SMCs and consider the pathological implications of heterogeneous embryonic origins. Finally, we touch upon the role of human ESC-derived SMCs in therapeutic revascularization and the challenges remaining before regenerative medicine using ESC- or iPSC-derived cells comes of age. © 2014 Springer Basel.

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