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Lorenzo-Martín LF, Bustelo XR. The Rho GTPase exchange factor Vav2 promotes extensive age-dependent rewiring of the hair follicle stem cell transcriptome. Front Cell Dev Biol 2023; 11:1252834. [PMID: 37822868 PMCID: PMC10562702 DOI: 10.3389/fcell.2023.1252834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/11/2023] [Indexed: 10/13/2023] Open
Abstract
Both the number and regenerative activity of hair follicle stem cells (HFSCs) are regulated by Vav2, a GDP/GTP exchange factor involved in the catalytic stimulation of the GTPases Rac1 and RhoA. However, whether Vav2 signaling changes in HFSCs over the mouse lifespan is not yet known. Using a mouse knock-in mouse model, we now show that the expression of a catalytically active version of Vav2 (Vav2Onc) promotes an extensive rewiring of the overall transcriptome of HFSCs, the generation of new transcription factor hubs, and the synchronization of many transcriptional programs associated with specific HFSC states and well-defined signaling pathways. Interestingly, this transcriptome rewiring is not fixed in time, as it involves the induction of 15 gene expression waves with diverse distribution patterns during the life of the animals. These expression waves are consistent with the promotion by Vav2Onc of several functional HFSC states that differ from those normally observed in wild-type HFSCs. These results further underscore the role of Vav2 in the regulation of the functional state of HFSCs. They also indicate that, unlike other Vav2-dependent biological processes, the signaling output of this exchange factor is highly contingent on age-dependent intrinsic and/or extrinsic HFSC factors that shape the final biological readouts triggered in this cell type.
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Affiliation(s)
- L. Francisco Lorenzo-Martín
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca, Salamanca, Spain
- Instituto de Biología Molecular y Celular del Cáncer, CSIC and University of Salamanca, Salamanca, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Salamanca, Spain
| | - Xosé R. Bustelo
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca, Salamanca, Spain
- Instituto de Biología Molecular y Celular del Cáncer, CSIC and University of Salamanca, Salamanca, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Salamanca, Spain
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2
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Brewer MG, Monticelli SR, Moran MC, Miller BL, Beck LA, Ward BM. Conditions That Simulate the Environment of Atopic Dermatitis Enhance Susceptibility of Human Keratinocytes to Vaccinia Virus. Cells 2022; 11:1337. [PMID: 35456017 PMCID: PMC9025056 DOI: 10.3390/cells11081337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/05/2022] [Accepted: 04/12/2022] [Indexed: 02/06/2023] Open
Abstract
Individuals with underlying chronic skin conditions, notably atopic dermatitis (AD), are disproportionately affected by infections from members of the herpesviridae, papovaviridae, and poxviridae families. Many patients with AD experience recurrent, widespread cutaneous viral infections that can lead to viremia, serious organ complications, and even death. Little is known about how the type 2 inflammatory environment observed in the skin of AD patients impacts the susceptibility of epidermal cells (keratinocytes) to viral pathogens. Herein, we studied the susceptibility of keratinocytes to the prototypical poxvirus, vaccinia virus (VV)-the causative agent of eczema vaccinatum-under conditions that simulate the epidermal environment observed in AD. Treatment of keratinocytes with type 2 cytokines (IL-4 and -13) to simulate the inflammatory environment or a tight junction disrupting peptide to mirror the barrier disruption observed in AD patients, resulted in a differentiation-dependent increase in susceptibility to VV. Furthermore, pan JAK inhibition was able to diminish the VV susceptibility occurring in keratinocytes exposed to type 2 cytokines. We propose that in AD, the increased viral susceptibility of keratinocytes leads to enhanced virus production in the skin, which contributes to the rampant dissemination and pathology seen within patients.
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Affiliation(s)
- Matthew G. Brewer
- Department of Dermatology, University of Rochester, Rochester, NY 14642, USA; (B.L.M.); (L.A.B.)
| | - Stephanie R. Monticelli
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA; (S.R.M.); (M.C.M.)
| | - Mary C. Moran
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA; (S.R.M.); (M.C.M.)
| | - Benjamin L. Miller
- Department of Dermatology, University of Rochester, Rochester, NY 14642, USA; (B.L.M.); (L.A.B.)
| | - Lisa A. Beck
- Department of Dermatology, University of Rochester, Rochester, NY 14642, USA; (B.L.M.); (L.A.B.)
| | - Brian M. Ward
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA; (S.R.M.); (M.C.M.)
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Moran MC, Pandya RP, Leffler KA, Yoshida T, Beck LA, Brewer MG. Characterization of Human Keratinocyte Cell Lines for Barrier Studies. JID INNOVATIONS 2021; 1:100018. [PMID: 34909717 PMCID: PMC8659750 DOI: 10.1016/j.xjidi.2021.100018] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 02/05/2023] Open
Abstract
Epidermal cell models are critical for studying skin biology. The gold standard used by the scientific community has historically been primary cell cultures from discarded tissue, typically from neonates (foreskin). Although directly applicable to humans, this system suffers from multiple issues, including substantial donor-to-donor variability and a finite number of divisions in culture. As such, we have identified a faithful alternative called N/TERT2G cells. These cells show many of the characteristics of primary cells, including barrier formation, differentiation kinetics and/or protein expression, and pathogenesis. From our observations, N/TERT2G cells can serve as a reproducible and genetically manipulatable platform in studying skin biology.
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Affiliation(s)
- Mary C Moran
- Department of Microbiology & Immunology, University of Rochester Medical Center, Rochester, New York, USA.,Department of Dermatology, University of Rochester Medical Center, Rochester, New York, USA
| | - Radha P Pandya
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York, USA
| | - Kimberly A Leffler
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York, USA
| | - Takeshi Yoshida
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York, USA
| | - Lisa A Beck
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York, USA
| | - Matthew G Brewer
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York, USA
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4
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Mahanty S, Setty SRG. Epidermal Lamellar Body Biogenesis: Insight Into the Roles of Golgi and Lysosomes. Front Cell Dev Biol 2021; 9:701950. [PMID: 34458262 PMCID: PMC8387949 DOI: 10.3389/fcell.2021.701950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/09/2021] [Indexed: 12/25/2022] Open
Abstract
Epidermal lamellar bodies (eLBs) are secretory organelles that carry a wide variety of secretory cargo required for skin homeostasis. eLBs belong to the class of lysosome-related organelles (LROs), which are cell-type-specific organelles that perform diverse functions. The formation of eLBs is thought to be related to that of other LROs, which are formed either through the gradual maturation of Golgi/endosomal precursors or by the conversion of conventional lysosomes. Current evidence suggests that eLB biogenesis presumably initiate from trans-Golgi network and receive cargo from endosomes, and also acquire lysosome characteristics during maturation. These multistep biogenesis processes are frequently disrupted in human skin disorders. However, many gaps remain in our understanding of eLB biogenesis and their relationship to skin diseases. Here, we describe our current understanding on eLB biogenesis with a focus on cargo transport to this LRO and highlight key areas where future research is needed.
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Affiliation(s)
| | - Subba Rao Gangi Setty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
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5
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Zhang H, Weström S, Kappelin P, Virtanen M, Vahlquist A, Törmä H. Exploration of novel candidate genes involved in epidermal keratinocyte differentiation and skin barrier repair in man. Differentiation 2021; 119:19-27. [PMID: 34029921 DOI: 10.1016/j.diff.2021.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/11/2021] [Accepted: 04/27/2021] [Indexed: 12/26/2022]
Abstract
A proper skin barrier function requires constant formation of stratum corneum, i.e. the outermost layer of epidermis composed of terminally differentiated keratinocytes. The complex process of converting proliferative basal keratinocytes into corneocytes relies on programmed changes in the activity of many well-established genes. Much remains however to be investigated about this process, e.g. in conjunction with epidermal barrier defects due to genetic errors as in ichthyosis. To this end, we re-analyzed two sets of microarray-data comparing altered gene expression in differentiated vs. proliferating keratinocytes and in the skin of patients with autosomal recessive congenital ichthyosis (ARCI) vs. healthy controls, respectively. We thus identified 24 genes to be upregulated in both sets of array and not previously associated with keratinocyte differentiation. For 10 of these genes (AKR1B10, BLNK, ENDOU, GCNT4, GLTP, RHCG, SLC15A1, TMEM45B, TMEM86A and VSNL1), qPCR analysis confirmed the array results and subsequent immunostainings of normal epidermis showed superficial expression of several of the proteins. Furthermore, induction of keratinocyte differentiation using phorbol esters (PMA) resulted in increased expression of eight of the genes, whereas siRNA silencing of PPARδ, a transcription factor supporting differentiation, had the opposite effect. In summary, our results identify ten new candidate genes seemingly involved in human epidermal keratinocyte differentiation and possibly important for epidermal repair in a genetic skin disease characterized by barrier failure.
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Affiliation(s)
- Hanqian Zhang
- Department of Medical Sciences/Dermatology, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Simone Weström
- Department of Medical Sciences/Dermatology, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Per Kappelin
- Department of Medical Sciences/Dermatology, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Marie Virtanen
- Department of Medical Sciences/Dermatology, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Anders Vahlquist
- Department of Medical Sciences/Dermatology, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Hans Törmä
- Department of Medical Sciences/Dermatology, Uppsala University, SE-751 85, Uppsala, Sweden.
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Catozzi S, Halasz M, Kiel C. Predicted 'wiring landscape' of Ras-effector interactions in 29 human tissues. NPJ Syst Biol Appl 2021; 7:10. [PMID: 33580066 PMCID: PMC7881153 DOI: 10.1038/s41540-021-00170-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/19/2020] [Indexed: 02/07/2023] Open
Abstract
Ras is a plasma membrane (PM)-associated signaling hub protein that interacts with its partners (effectors) in a mutually exclusive fashion. We have shown earlier that competition for binding and hence the occurrence of specific binding events at a hub protein can modulate the activation of downstream pathways. Here, using a mechanistic modeling approach that incorporates high-quality proteomic data of Ras and 56 effectors in 29 (healthy) human tissues, we quantified the amount of individual Ras-effector complexes, and characterized the (stationary) Ras "wiring landscape" specific to each tissue. We identified nine effectors that are in significant amount in complex with Ras in at least one of the 29 tissues. We simulated both mutant- and stimulus-induced network re-configurations, and assessed their divergence from the reference scenario, specifically discussing a case study for two stimuli in three epithelial tissues. These analyses pointed to 32 effectors that are in significant amount in complex with Ras only if they are additionally recruited to the PM, e.g. via membrane-binding domains or domains binding to activated receptors at the PM. Altogether, our data emphasize the importance of tissue context for binding events at the Ras signaling hub.
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Affiliation(s)
- Simona Catozzi
- UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Dublin, 4, Ireland
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Melinda Halasz
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Christina Kiel
- UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Dublin, 4, Ireland.
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin, 4, Ireland.
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Egolf S, Aubert Y, Doepner M, Anderson A, Maldonado-Lopez A, Pacella G, Lee J, Ko EK, Zou J, Lan Y, Simpson CL, Ridky T, Capell BC. LSD1 Inhibition Promotes Epithelial Differentiation through Derepression of Fate-Determining Transcription Factors. Cell Rep 2020; 28:1981-1992.e7. [PMID: 31433976 PMCID: PMC6719800 DOI: 10.1016/j.celrep.2019.07.058] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/03/2019] [Accepted: 07/17/2019] [Indexed: 02/08/2023] Open
Abstract
Self-renewing somatic tissues depend upon the proper balance of chromatin-modifying enzymes to coordinate progenitor cell maintenance and differentiation, disruption of which can promote carcinogenesis. As a result, drugs targeting the epigenome hold significant therapeutic potential. The histone demethylase, LSD1 (KDM1A), is overexpressed in numerous cancers, including epithelial cancers; however, its role in the skin is virtually unknown. Here we show that LSD1 directly represses master epithelial transcription factors that promote differentiation. LSD1 inhibitors block both LSD1 binding to chromatin and its catalytic activity, driving significant increases in H3K4 methylation and gene transcription of these fate-determining transcription factors. This leads to both premature epidermal differentiation and the repression of squamous cell carcinoma. Together these data highlight both LSD1’s role in maintaining the epidermal progenitor state and the potential of LSD1 inhibitors for the treatment of keratinocyte cancers, which collectively outnumber all other cancers combined. Egolf et al. demonstrate that inhibition of the epigenetic regulator and histone demethylase, LSD1, promotes activation of the epidermal differentiation transcriptional program and, in turn, represses the invasion of cutaneous squamous cell carcinoma, one of the most common of all human cancers.
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Affiliation(s)
- Shaun Egolf
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Yann Aubert
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Miriam Doepner
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Amy Anderson
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Alexandra Maldonado-Lopez
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Gina Pacella
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jessica Lee
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Eun Kyung Ko
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jonathan Zou
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Yemin Lan
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Cory L Simpson
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Todd Ridky
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Brian C Capell
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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8
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Lederer S, Heskes T, van Heeringen SJ, Albers CA. Investigating the effect of dependence between conditions with Bayesian Linear Mixed Models for motif activity analysis. PLoS One 2020; 15:e0231824. [PMID: 32357166 PMCID: PMC7194367 DOI: 10.1371/journal.pone.0231824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 04/01/2020] [Indexed: 11/19/2022] Open
Abstract
MOTIVATION Cellular identity and behavior is controlled by complex gene regulatory networks. Transcription factors (TFs) bind to specific DNA sequences to regulate the transcription of their target genes. On the basis of these TF motifs in cis-regulatory elements we can model the influence of TFs on gene expression. In such models of TF motif activity the data is usually modeled assuming a linear relationship between the motif activity and the gene expression level. A commonly used method to model motif influence is based on Ridge Regression. One important assumption of linear regression is the independence between samples. However, if samples are generated from the same cell line, tissue, or other biological source, this assumption may be invalid. This same assumption of independence is also applied to different yet similar experimental conditions, which may also be inappropriate. In theory, the independence assumption between samples could lead to loss in signal detection. Here we investigate whether a Bayesian model that allows for correlations results in more accurate inference of motif activities. RESULTS We extend the Ridge Regression to a Bayesian Linear Mixed Model, which allows us to model dependence between different samples. In a simulation study, we investigate the differences between the two model assumptions. We show that our Bayesian Linear Mixed Model implementation outperforms Ridge Regression in a simulation scenario where the noise, which is the signal that can not be explained by TF motifs, is uncorrelated. However, we demonstrate that there is no such gain in performance if the noise has a similar covariance structure over samples as the signal that can be explained by motifs. We give a mathematical explanation to why this is the case. Using four representative real datasets we show that at most ∼​40% of the signal is explained by motifs using the linear model. With these data there is no advantage to using the Bayesian Linear Mixed Model, due to the similarity of the covariance structure. AVAILABILITY & IMPLEMENTATION The project implementation is available at https://github.com/Sim19/SimGEXPwMotifs.
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Affiliation(s)
- Simone Lederer
- Data Science, Radboud University, Institute for Computing and Information Sciences, Nijmegen, The Netherlands
- Molecular Developmental Biology, Radboud University, Research Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- * E-mail: (LS); (VHS)
| | - Tom Heskes
- Data Science, Radboud University, Institute for Computing and Information Sciences, Nijmegen, The Netherlands
| | - Simon J. van Heeringen
- Molecular Developmental Biology, Radboud University, Research Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- * E-mail: (LS); (VHS)
| | - Cornelis A. Albers
- Molecular Developmental Biology, Radboud University, Research Institute for Molecular Life Sciences, Nijmegen, The Netherlands
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In Silico Analysis of the Age-Dependent Evolution of the Transcriptome of Mouse Skin Stem Cells. Cells 2020; 9:cells9010165. [PMID: 31936599 PMCID: PMC7016981 DOI: 10.3390/cells9010165] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/03/2020] [Accepted: 01/06/2020] [Indexed: 12/12/2022] Open
Abstract
The stem cells located in the hair follicle bulge area are critical for skin regeneration and repair. To date, little is known about the evolution of the transcriptome of these cells across time. Here, we have combined genome-wide expression analyses and a variety of in silico tools to determine the age-dependent evolution of the transcriptome of those cells. Our results reveal that the transcriptome of skin stem cells fluctuates extensively along the lifespan of mice. The use of both unbiased and pathway-centered in silico approaches has also enabled the identification of biological programs specifically regulated at those specific time-points. It has also unveiled hubs of highly transcriptionally interconnected genes and transcriptional factors potentially located at the core of those age-specific changes.
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10
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Zhang M, Li Z, Wang G, Jang H, Sacks DB, Zhang J, Gaponenko V, Nussinov R. Calmodulin (CaM) Activates PI3Kα by Targeting the "Soft" CaM-Binding Motifs in Both the nSH2 and cSH2 Domains of p85α. J Phys Chem B 2018; 122:11137-11146. [PMID: 30047727 PMCID: PMC6422767 DOI: 10.1021/acs.jpcb.8b05982] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PI3Kα is a key lipid kinase in the PI3K/Akt pathway. Its frequent oncogenic mutations make it a primary drug target. Calmodulin (CaM) activates PI3Kα independently of extracellular signals, indicating a significant role in oncogenic PI3Kα activation. Here, we reveal the atomic-scale structures of CaM in complexes with the nSH2 and cSH2 domains of the regulatory p85α subunit of PI3Kα, and illustrate how CaM activates PI3Kα by targeting the "soft 1-5-10" CaM-binding motifs in both nSH2 and cSH2 domains. Experiment observed CaM binding cSH2 first, followed by nSH2 binding hours later. CaM typically prefers binding helical peptides. Here we observe that, unlike in cSH2, the CaM-binding motif in nSH2 populates a mixed β-sheet/α-helix/random coil structure. The population shift from a β-sheet toward CaM's favored α-helical conformation explains why the nSH2 domain needs a longer time for CaM binding in the experiments. The "soft" CaM-binding motifs in both nSH2 and cSH2 domains establish strong CaM-PI3Kα interactions, collectively facilitating PI3Kα activation. This work uncovers the structural basis for CaM-driven PI3Kα activation.
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Affiliation(s)
- Mingzhen Zhang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, Maryland 21702, United States
| | - Zhigang Li
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Guanqiao Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, Maryland 21702, United States
| | - David B. Sacks
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, Maryland 21702, United States
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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11
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Anderson ED, Sastalla I, Earland NJ, Mahnaz M, Moore IN, Otaizo-Carrasquero F, Myers TG, Myles CA, Datta SK, Myles IA. Prolonging culture of primary human keratinocytes isolated from suction blisters with the Rho kinase inhibitor Y-27632. PLoS One 2018; 13:e0198862. [PMID: 30208113 PMCID: PMC6135349 DOI: 10.1371/journal.pone.0198862] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/27/2018] [Indexed: 12/20/2022] Open
Abstract
Keratinocytes are the most abundant cell type in the epidermis. They prevent desiccation and provide immunological and barrier defense against potential pathogens such as Staphylococcus aureus and Candida albicans. The study of this first line of immune defense may be hindered by invasive isolation methods and/or improper culture conditions to support stem cell maintenance and other potential mechanisms contributing to long-term subcultivation in vitro. Primary keratinocytes have been successfully isolated from blister roofs induced by negative pressure, which separates the epidermis from the dermis in vivo in human subjects. This method allows collection of pure epidermal cells without dermal contamination in a minimally invasive manner. However, the isolated keratinocytes differentiate and senesce when cultured in vitro beyond five passages. Here, we present evidence that the Rho kinase (ROCK) inhibitor Y-27632 can be used to effectively increase the proliferative capabilities of keratinocytes isolated using the suction blister method, similar to what has been previously reported for primary keratinocytes isolated using alternative methods. We show that the increase in passage number is directly correlated to delayed differentiation, and that cells passaged long term with the inhibitor retain their ability to stratify in organotypic raft cultures and respond to cytokine treatment; additionally, the late passage cells have a heterogeneous mix of differentiated and non-differentiated cells which may be predicted by a ratio of select differentiation markers. The described method presents a minimally invasive procedure for keratinocyte isolation and prolonged culture that allows analysis of keratinocyte function in both healthy volunteers and patients with dermatologic diseases.
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Affiliation(s)
- Erik D. Anderson
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Inka Sastalla
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Noah J. Earland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Minai Mahnaz
- Comparative Medicine Branch, National Institute of Allergy and Infectious Disease, National Institutes of Health, Rockville, MD, United States of America
| | - Ian N. Moore
- Comparative Medicine Branch, National Institute of Allergy and Infectious Disease, National Institutes of Health, Rockville, MD, United States of America
| | - Francisco Otaizo-Carrasquero
- Genomic Technologies Section, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Timothy G. Myers
- Genomic Technologies Section, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | | | - Sandip K. Datta
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Ian A. Myles
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
- * E-mail:
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Besray Unal E, Kiel C, Benisty H, Campbell A, Pickering K, Blüthgen N, Sansom OJ, Serrano L. Systems level expression correlation of Ras GTPase regulators. Cell Commun Signal 2018; 16:46. [PMID: 30111366 PMCID: PMC6094892 DOI: 10.1186/s12964-018-0256-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 08/02/2018] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Proteins of the ubiquitously expressed core proteome are quantitatively correlated across multiple eukaryotic species. In addition, it was found that many protein paralogues exhibit expression anticorrelation, suggesting that the total level of protein with a given functionality must be kept constant. METHODS We performed Spearman's rank correlation analyses of gene expression levels for the RAS GTPase subfamily and their regulatory GEF and GAP proteins across tissues and across individuals for each tissue. A large set of published data for normal tissues from a wide range of species, human cancer tissues and human cell lines was analysed. RESULTS We show that although the multidomain regulatory proteins of Ras GTPases exhibit considerable tissue and individual gene expression variability, their total amounts are balanced in normal tissues. In a given tissue, the sum of activating (GEFs) and deactivating (GAPs) domains of Ras GTPases can vary considerably, but each person has balanced GEF and GAP levels. This balance is impaired in cell lines and in cancer tissues for some individuals. CONCLUSIONS Our results are relevant for critical considerations of knock out experiments, where functionally related homologs may compensate for the down regulation of a protein.
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Affiliation(s)
- E. Besray Unal
- Institute of Pathology, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
- Integrative Research Institute Life Sciences, Humboldt Universität Berlin, 10115 Berlin, Germany
| | - Christina Kiel
- Centre for Genomic Regulation (CRG), Systems Biology Programme. The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003 Spain
- Present address: Systems Biology Ireland & Charles Institute of Dermatology & School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Hannah Benisty
- Centre for Genomic Regulation (CRG), Systems Biology Programme. The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003 Spain
| | - Andrew Campbell
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD UK
| | - Karen Pickering
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD UK
| | - Nils Blüthgen
- Institute of Pathology, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
- Integrative Research Institute Life Sciences, Humboldt Universität Berlin, 10115 Berlin, Germany
| | - Owen J. Sansom
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD UK
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), Systems Biology Programme. The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003 Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
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Zapata L, Pich O, Serrano L, Kondrashov FA, Ossowski S, Schaefer MH. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biol 2018; 19:67. [PMID: 29855388 PMCID: PMC5984361 DOI: 10.1186/s13059-018-1434-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 04/20/2018] [Indexed: 01/08/2023] Open
Abstract
Background Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments. Electronic supplementary material The online version of this article (10.1186/s13059-018-1434-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luis Zapata
- Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Oriol Pich
- Evolutionary Genomics Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Luis Serrano
- Design of Biological Systems Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, 08010, Barcelona, Spain
| | - Fyodor A Kondrashov
- IST Austria (Institute of Science and Technology Austria), Am Campus 1, 3400, Klosterneuburg, Austria
| | - Stephan Ossowski
- Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
| | - Martin H Schaefer
- Design of Biological Systems Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.
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Singh RK, Dagnino L. CDH1 regulates E2F1 degradation in response to differentiation signals in keratinocytes. Oncotarget 2018; 8:4977-4993. [PMID: 27903963 PMCID: PMC5354885 DOI: 10.18632/oncotarget.13636] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/08/2016] [Indexed: 11/25/2022] Open
Abstract
The E2F1 transcription factor plays key roles in skin homeostasis. In the epidermis, E2F1 expression is essential for normal proliferation of undifferentiated keratinocytes, regeneration after injury and DNA repair following UV radiation-induced photodamage. Abnormal E2F1 expression promotes nonmelanoma skin carcinoma. In addition, E2F1 must be downregulated for proper keratinocyte differentiation, but the relevant mechanisms involved remain poorly understood. We show that differentiation signals induce a series of post-translational modifications in E2F1 that are jointly required for its downregulation. Analysis of the structural determinants that govern these processes revealed a central role for S403 and T433. In particular, substitution of these two amino acid residues with non-phosphorylatable alanine (E2F1 ST/A) interferes with E2F1 nuclear export, K11- and K48-linked polyubiquitylation and degradation in differentiated keratinocytes. In contrast, replacement of S403 and T433 with phosphomimetic aspartic acid to generate a pseudophosphorylated E2F1 mutant protein (E2F1 ST/D) generates a protein that is regulated in a manner indistinguishable from that of wild type E2F1. Cdh1 is an activating cofactor that interacts with the anaphase-promoting complex/cyclosome (APC/C) ubiquitin E3 ligase, promoting proteasomal degradation of various substrates. We found that Cdh1 associates with E2F1 in keratinocytes. Inhibition or RNAi-mediated silencing of Cdh1 prevents E2F1 degradation in response to differentiation signals. Our results reveal novel regulatory mechanisms that jointly modulate post-translational modifications and downregulation of E2F1, which are necessary for proper epidermal keratinocyte differentiation.
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Affiliation(s)
- Randeep K Singh
- Department of Physiology and Pharmacology, Children's Health Research Institute and Lawson Health Research Institute, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Lina Dagnino
- Department of Physiology and Pharmacology, Children's Health Research Institute and Lawson Health Research Institute, The University of Western Ontario, London, Ontario N6A 5C1, Canada
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15
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Zhang M, Jang H, Gaponenko V, Nussinov R. Phosphorylated Calmodulin Promotes PI3K Activation by Binding to the SH 2 Domains. Biophys J 2017; 113:1956-1967. [PMID: 29117520 PMCID: PMC5685777 DOI: 10.1016/j.bpj.2017.09.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/11/2017] [Accepted: 09/12/2017] [Indexed: 02/07/2023] Open
Abstract
How calmodulin (CaM) acts in KRAS-driven cancers is a vastly important question. CaM binds to and stimulates PI3Kα/Akt signaling, promoting cell growth and proliferation. Phosphorylation of CaM at Tyr99 (pY99) enhances PI3Kα activation. PI3Kα is a lipid kinase. It phosphorylates PIP2 to produce PIP3, to which Akt binds. PI3Kα has two subunits: the regulatory p85 and the catalytic p110. Here, exploiting explicit-solvent MD simulations we unveil key interactions between phosphorylated CaM (pCaM) and the two SH2 domains in the p85 subunit, confirm experimental observations, and uncover PI3Kα's mechanism of activation. pCaMs form strong and stable interactions with both nSH2 and cSH2 domains, with pY99 being the dominant contributor. Despite the high structural similarity between the two SH2 domains, we observe that nSH2 prefers an extended CaM conformation, whereas cSH2 prefers a collapsed conformation. Notably, collapsed CaM is observed after binding of an extended CaM to K-Ras4B. Thus, the more populated extended pCaM conformation targets nSH2 to release its autoinhibition of p110 catalytic sites. This executes the key activation step of PI3Kα. Independently, K-Ras4B allosterically activates p110. These events are at the cell membrane, which contributes to tighten the PI3Kα Ras binding domain/K-Ras4B interaction, to accomplish K-Ras4B allosteric activation, with a minor contribution from cSH2.
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Affiliation(s)
- Mingzhen Zhang
- Cancer and Inflammation Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
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Rinaldi L, Datta D, Serrat J, Morey L, Solanas G, Avgustinova A, Blanco E, Pons JI, Matallanas D, Von Kriegsheim A, Di Croce L, Benitah SA. Dnmt3a and Dnmt3b Associate with Enhancers to Regulate Human Epidermal Stem Cell Homeostasis. Cell Stem Cell 2016; 19:491-501. [PMID: 27476967 DOI: 10.1016/j.stem.2016.06.020] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 04/25/2016] [Accepted: 06/29/2016] [Indexed: 12/22/2022]
Abstract
The genome-wide localization and function of endogenous Dnmt3a and Dnmt3b in adult stem cells are unknown. Here, we show that in human epidermal stem cells, the two proteins bind in a histone H3K36me3-dependent manner to the most active enhancers and are required to produce their associated enhancer RNAs. Both proteins prefer super-enhancers associated to genes that either define the ectodermal lineage or establish the stem cell and differentiated states. However, Dnmt3a and Dnmt3b differ in their mechanisms of enhancer regulation: Dnmt3a associates with p63 to maintain high levels of DNA hydroxymethylation at the center of enhancers in a Tet2-dependent manner, whereas Dnmt3b promotes DNA methylation along the body of the enhancer. Depletion of either protein inactivates their target enhancers and profoundly affects epidermal stem cell function. Altogether, we reveal novel functions for Dnmt3a and Dnmt3b at enhancers that could contribute to their roles in disease and tumorigenesis.
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Affiliation(s)
- Lorenzo Rinaldi
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, 08003 Barcelona, Spain.
| | - Debayan Datta
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Judit Serrat
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Lluis Morey
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Guiomar Solanas
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Alexandra Avgustinova
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, 08003 Barcelona, Spain
| | - José Ignacio Pons
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - David Matallanas
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| | - Alex Von Kriegsheim
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| | - Luciano Di Croce
- ICREA, Passeig de Lluís Companys 23, 08010 Barcelona, Spain; Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, 08003 Barcelona, Spain.
| | - Salvador Aznar Benitah
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; ICREA, Passeig de Lluís Companys 23, 08010 Barcelona, Spain.
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Joost S, Zeisel A, Jacob T, Sun X, La Manno G, Lönnerberg P, Linnarsson S, Kasper M. Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity. Cell Syst 2016; 3:221-237.e9. [PMID: 27641957 PMCID: PMC5052454 DOI: 10.1016/j.cels.2016.08.010] [Citation(s) in RCA: 256] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 05/11/2016] [Accepted: 08/11/2016] [Indexed: 12/02/2022]
Abstract
The murine epidermis with its hair follicles represents an invaluable model system for tissue regeneration and stem cell research. Here we used single-cell RNA-sequencing to reveal how cellular heterogeneity of murine telogen epidermis is tuned at the transcriptional level. Unbiased clustering of 1,422 single-cell transcriptomes revealed 25 distinct populations of interfollicular and follicular epidermal cells. Our data allowed the reconstruction of gene expression programs during epidermal differentiation and along the proximal-distal axis of the hair follicle at unprecedented resolution. Moreover, transcriptional heterogeneity of the epidermis can essentially be explained along these two axes, and we show that heterogeneity in stem cell compartments generally reflects this model: stem cell populations are segregated by spatial signatures but share a common basal-epidermal gene module. This study provides an unbiased and systematic view of transcriptional organization of adult epidermis and highlights how cellular heterogeneity can be orchestrated in vivo to assure tissue homeostasis. Single-cell RNA-seq analysis identifies 25 populations of epidermal cells Differentiation and spatial gene expression signatures can be defined Interplay of differentiation and spatial signatures explains most heterogeneity Stem cell populations are divided by spatial signatures and only share basal identity
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Affiliation(s)
- Simon Joost
- Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Novum, 141 83 Huddinge, Sweden
| | - Amit Zeisel
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, 171 77 Stockholm, Sweden
| | - Tina Jacob
- Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Novum, 141 83 Huddinge, Sweden
| | - Xiaoyan Sun
- Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Novum, 141 83 Huddinge, Sweden
| | - Gioele La Manno
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, 171 77 Stockholm, Sweden
| | - Peter Lönnerberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, 171 77 Stockholm, Sweden
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, 171 77 Stockholm, Sweden.
| | - Maria Kasper
- Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Novum, 141 83 Huddinge, Sweden.
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