1
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Hornigold K, Baker MJ, Machin PA, Chetwynd SA, Johnsson AK, Pantarelli C, Islam P, Stammers M, Crossland L, Oxley D, Okkenhaug H, Walker S, Walker R, Segonds-Pichon A, Fukui Y, Malliri A, Welch HCE. The Rac-GEF Tiam1 controls integrin-dependent neutrophil responses. Front Immunol 2023; 14:1223653. [PMID: 38077328 PMCID: PMC10703174 DOI: 10.3389/fimmu.2023.1223653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/20/2023] [Indexed: 12/18/2023] Open
Abstract
Rac GTPases are required for neutrophil adhesion and migration, and for the neutrophil effector responses that kill pathogens. These Rac-dependent functions are impaired when neutrophils lack the activators of Rac, Rac-GEFs from the Prex, Vav, and Dock families. In this study, we demonstrate that Tiam1 is also expressed in neutrophils, governing focal complexes, actin cytoskeletal dynamics, polarisation, and migration, in a manner depending on the integrin ligand to which the cells adhere. Tiam1 is dispensable for the generation of reactive oxygen species but mediates degranulation and NETs release in adherent neutrophils, as well as the killing of bacteria. In vivo, Tiam1 is required for neutrophil recruitment during aseptic peritonitis and for the clearance of Streptococcus pneumoniae during pulmonary infection. However, Tiam1 functions differently to other Rac-GEFs. Instead of promoting neutrophil adhesion to ICAM1 and stimulating β2 integrin activity as could be expected, Tiam1 restricts these processes. In accordance with these paradoxical inhibitory roles, Tiam1 limits the fMLP-stimulated activation of Rac1 and Rac2 in adherent neutrophils, rather than activating Rac as expected. Tiam1 promotes the expression of several regulators of small GTPases and cytoskeletal dynamics, including αPix, Psd4, Rasa3, and Tiam2. It also controls the association of Rasa3, and potentially αPix, Git2, Psd4, and 14-3-3ζ/δ, with Rac. We propose these latter roles of Tiam1 underlie its effects on Rac and β2 integrin activity and on cell responses. Hence, Tiam1 is a novel regulator of Rac-dependent neutrophil responses that functions differently to other known neutrophil Rac-GEFs.
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Affiliation(s)
- Kirsti Hornigold
- Signalling Programme, Babraham Institute, Cambridge, United Kingdom
| | - Martin J. Baker
- Signalling Programme, Babraham Institute, Cambridge, United Kingdom
- Cell Signalling Group, Cancer Research UK Manchester Institute, University of Manchester, Macclesfield, United Kingdom
| | - Polly A. Machin
- Signalling Programme, Babraham Institute, Cambridge, United Kingdom
| | | | | | | | - Priota Islam
- Signalling Programme, Babraham Institute, Cambridge, United Kingdom
| | | | | | - David Oxley
- Mass Spectrometry Facility, Babraham Institute, Cambridge, United Kingdom
| | | | - Simon Walker
- Imaging Facility, Babraham Institute, Cambridge, United Kingdom
| | - Rachael Walker
- Flow Cytometry Facility, Babraham Institute, Cambridge, United Kingdom
| | | | - Yoshinori Fukui
- Division of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Angeliki Malliri
- Cell Signalling Group, Cancer Research UK Manchester Institute, University of Manchester, Macclesfield, United Kingdom
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Mielczarek O, Rogers CH, Zhan Y, Matheson LS, Stubbington MJT, Schoenfelder S, Bolland DJ, Javierre BM, Wingett SW, Várnai C, Segonds-Pichon A, Conn SJ, Krueger F, Andrews S, Fraser P, Giorgetti L, Corcoran AE. Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes. Cell Rep 2023; 42:113074. [PMID: 37676766 PMCID: PMC10548092 DOI: 10.1016/j.celrep.2023.113074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/28/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023] Open
Abstract
To produce a diverse antibody repertoire, immunoglobulin heavy-chain (Igh) loci undergo large-scale alterations in structure to facilitate juxtaposition and recombination of spatially separated variable (VH), diversity (DH), and joining (JH) genes. These chromosomal alterations are poorly understood. Uncovering their patterns shows how chromosome dynamics underpins antibody diversity. Using tiled Capture Hi-C, we produce a comprehensive map of chromatin interactions throughout the 2.8-Mb Igh locus in progenitor B cells. We find that the Igh locus folds into semi-rigid subdomains and undergoes flexible looping of the VH genes to its 3' end, reconciling two views of locus organization. Deconvolution of single Igh locus conformations using polymer simulations identifies thousands of different structures. This heterogeneity may underpin the diversity of V(D)J recombination events. All three immunoglobulin loci also participate in a highly specific, developmentally regulated network of interchromosomal interactions with genes encoding B cell-lineage factors. This suggests a model of interchromosomal coordination of B cell development.
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Affiliation(s)
- Olga Mielczarek
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Carolyn H Rogers
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Yinxiu Zhan
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Louise S Matheson
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Michael J T Stubbington
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Stefan Schoenfelder
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Daniel J Bolland
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Biola M Javierre
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Steven W Wingett
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Csilla Várnai
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Anne Segonds-Pichon
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Simon J Conn
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Felix Krueger
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Simon Andrews
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Peter Fraser
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Anne E Corcoran
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
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3
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Chessa TAM, Jung P, Anwar A, Suire S, Anderson KE, Barneda D, Kielkowska A, Sadiq BA, Lai IW, Felisbino S, Turnham DJ, Pearson HB, Phillips WA, Sasaki J, Sasaki T, Oxley D, Spensberger D, Segonds-Pichon A, Wilson M, Walker S, Okkenhaug H, Cosulich S, Hawkins PT, Stephens LR. PLEKHS1 drives PI3Ks and remodels pathway homeostasis in PTEN-null prostate. Mol Cell 2023; 83:2991-3009.e13. [PMID: 37567175 DOI: 10.1016/j.molcel.2023.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 05/05/2023] [Accepted: 07/13/2023] [Indexed: 08/13/2023]
Abstract
The PIP3/PI3K network is a central regulator of metabolism and is frequently activated in cancer, commonly by loss of the PIP3/PI(3,4)P2 phosphatase, PTEN. Despite huge research investment, the drivers of the PI3K network in normal tissues and how they adapt to overactivation are unclear. We find that in healthy mouse prostate PI3K activity is driven by RTK/IRS signaling and constrained by pathway feedback. In the absence of PTEN, the network is dramatically remodeled. A poorly understood YXXM- and PIP3/PI(3,4)P2-binding PH domain-containing adaptor, PLEKHS1, became the dominant activator and was required to sustain PIP3, AKT phosphorylation, and growth in PTEN-null prostate. This was because PLEKHS1 evaded pathway-feedback and experienced enhanced PI3K- and Src-family kinase-dependent phosphorylation of Y258XXM, eliciting PI3K activation. hPLEKHS1 mRNA and activating Y419 phosphorylation of hSrc correlated with PI3K pathway activity in human prostate cancers. We propose that in PTEN-null cells receptor-independent, Src-dependent tyrosine phosphorylation of PLEKHS1 creates positive feedback that escapes homeostasis, drives PIP3 signaling, and supports tumor progression.
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Affiliation(s)
| | - Piotr Jung
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Arqum Anwar
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Sabine Suire
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Karen E Anderson
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - David Barneda
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Anna Kielkowska
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Barzan A Sadiq
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Ieng Wai Lai
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Sergio Felisbino
- Department of Structural and Functional Biology, São Paulo State University, Botucatu, SP CEP: 18618-689, Brazil
| | - Daniel J Turnham
- European Cancer Stem Cell Research Institute, Cardiff University, Cardiff CF24 4HQ, UK
| | - Helen B Pearson
- European Cancer Stem Cell Research Institute, Cardiff University, Cardiff CF24 4HQ, UK
| | - Wayne A Phillips
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Junko Sasaki
- Department of Biochemical Pathophysiology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Takehiko Sasaki
- Department of Biochemical Pathophysiology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - David Oxley
- Mass Spectrometry Facility, Babraham Institute, Cambridge CB22 3AT, UK
| | | | | | - Michael Wilson
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Simon Walker
- Imaging Facility, Babraham Institute, Cambridge CB22 3AT, UK
| | | | | | | | - Len R Stephens
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, UK.
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4
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Machin PA, Johnsson AKE, Massey EJ, Pantarelli C, Chetwynd SA, Chu JY, Okkenhaug H, Segonds-Pichon A, Walker S, Malliri A, Fukui Y, Welch HCE. Dock2 generates characteristic spatiotemporal patterns of Rac activity to regulate neutrophil polarisation, migration and phagocytosis. Front Immunol 2023; 14:1180886. [PMID: 37383235 PMCID: PMC10293741 DOI: 10.3389/fimmu.2023.1180886] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/15/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction Rac-GTPases and their Rac-GEF activators play important roles in neutrophil-mediated host defence. These proteins control the adhesion molecules and cytoskeletal dynamics required for neutrophil recruitment to inflamed and infected organs, and the neutrophil effector responses that kill pathogens. Methods Here, we used live cell TIRF-FRET imaging in neutrophils from Rac-FRET reporter mice with deficiencies in the Rac-GEFs Dock2, Tiam1 or Prex1/Vav1 to evaluate if these proteins activate spatiotemporally distinct pools of Rac, and to correlate patterns of Rac activity with the neutrophil responses they control. Results All the GEFs were required for neutrophil adhesion, and Prex1/Vav1 were important during spreading and for the velocity of migration during chemotaxis. However, Dock2 emerged as the prominent regulator of neutrophil responses, as this GEF was required for neutrophil polarisation and random migration, for migration velocity during chemokinesis, for the likelihood to migrate and for the speed of migration and of turning during chemotaxis, as well as for rapid particle engulfment during phagocytosis. We identified characteristic spatiotemporal patterns of Rac activity generated by Dock2 which correlate with the importance of the Rac-GEF in these neutrophil responses. We also demonstrate a requirement for Dock2 in neutrophil recruitment during aseptic peritonitis. Discussion Collectively, our data provide a first direct comparison of the pools of Rac activity generated by different types of Rac-GEFs, and identify Dock2 as a key regulator of polarisation, migration and phagocytosis in primary neutrophils.
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Affiliation(s)
- Polly A. Machin
- Signalling Programme, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Anna-Karin E. Johnsson
- Signalling Programme, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Ellie J. Massey
- Signalling Programme, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Chiara Pantarelli
- Signalling Programme, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Stephen A. Chetwynd
- Signalling Programme, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Julia Y. Chu
- Signalling Programme, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Hanneke Okkenhaug
- Imaging Facility, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Anne Segonds-Pichon
- Bioinformatics Facility, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Simon Walker
- Imaging Facility, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Angeliki Malliri
- Cell Signalling, Cancer Research UK Manchester Institute, Manchester, United Kingdom
| | - Yoshinori Fukui
- Division of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Heidi C. E. Welch
- Signalling Programme, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
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5
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Morgan ER, Segonds-Pichon A, Ferté H, Duncan P, Cabaret J. Anthelmintic Treatment and the Stability of Parasite Distribution in Ruminants. Animals (Basel) 2023; 13:1882. [PMID: 37889834 PMCID: PMC10251989 DOI: 10.3390/ani13111882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 10/29/2023] Open
Abstract
Parasites are generally overdispersed among their hosts, with far-reaching implications for their population dynamics and control. The factors determining parasite overdispersion have long been debated. In particular, stochastic parasite acquisition and individual host variation in density-dependent regulation through acquired host immunity have been identified as key factors, but their relative roles and possible interactions have seen little empirical exploration in parasite populations. Here, Taylor's power law is applied to test the hypothesis that periodic parasite removal destabilises the host-parasite relationship and increases variance in parasite burden around the mean. The slope of the power relationship was compared by analysis of covariance among 325 nematode populations in wild and domestic ruminants, exploiting that domestic ruminants are often routinely treated against parasite infections. In Haemonchus spp. and Trichostrongylus axei in domestic livestock, the slope increased with the frequency of anthelmintic treatment, supporting this hypothesis. In Nematodirus spp., against which acquired immunity is known to be strong, the slope was significantly greater in post-mortem worm burden data than in faecal egg counts, while this relationship did not hold for the less immunogenic genus Marshallagia. Considered together, these findings suggest that immunity acting through an exposure-dependent reduction in parasite fecundity stabilises variance in faecal egg counts, reducing overdispersion, and that periodic anthelmintic treatment interferes with this process and increases overdispersion. The results have implications for the diagnosis and control of parasitic infections in domestic animals, which are complicated by overdispersion, and for our understanding of parasite distribution in free-living wildlife. Parasite-host systems, in which treatment and immunity effectively mimic metapopulation processes of patch extinction and density dependence, could also yield general insights into the spatio-temporal stability of animal distributions.
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Affiliation(s)
- Eric R. Morgan
- School of Biological Sciences, Queen’s University Belfast, 19, Chlorine Gardens, Belfast BT9 5DL, UK
| | | | - Hubert Ferté
- Faculté de Pharmacie, Université de Reims Champagne-Ardenne, SFR Cap Santé, EA7510 ESCAPE–USC VECPAR, 51 rue Cognacq-Jay, 51096 Reims, France;
| | - Patrick Duncan
- Centre d’Etudes Biologiques de Chize, CNRS UPR 1934, 79360 Beauvoir-sur-Niort, France;
| | - Jacques Cabaret
- ISP, INRAE, Université Tours, UMR1282, 37380 Nouzilly, France;
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6
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Demond H, Hanna CW, Castillo-Fernandez J, Santos F, Papachristou EK, Segonds-Pichon A, Kishore K, Andrews S, D'Santos CS, Kelsey G. Multi-omics analyses demonstrate a critical role for EHMT1 methyltransferase in transcriptional repression during oogenesis. Genome Res 2023; 33:18-31. [PMID: 36690445 PMCID: PMC9977154 DOI: 10.1101/gr.277046.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 12/22/2022] [Indexed: 01/25/2023]
Abstract
EHMT1 (also known as GLP) is a multifunctional protein, best known for its role as an H3K9me1 and H3K9me2 methyltransferase through its reportedly obligatory dimerization with EHMT2 (also known as G9A). Here, we investigated the role of EHMT1 in the oocyte in comparison to EHMT2 using oocyte-specific conditional knockout mouse models (Ehmt2 cKO, Ehmt1 cKO, Ehmt1/2 cDKO), with ablation from the early phase of oocyte growth. Loss of EHMT1 in Ehmt1 cKO and Ehmt1/2 cDKO oocytes recapitulated meiotic defects observed in the Ehmt2 cKO; however, there was a significant impairment in oocyte maturation and developmental competence in Ehmt1 cKO and Ehmt1/2 cDKO oocytes beyond that observed in the Ehmt2 cKO. Consequently, loss of EHMT1 in oogenesis results, upon fertilization, in mid-gestation embryonic lethality. To identify H3K9 methylation and other meaningful biological changes in each mutant to explore the molecular functions of EHMT1 and EHMT2, we performed immunofluorescence imaging, multi-omics sequencing, and mass spectrometry (MS)-based proteome analyses in cKO oocytes. Although H3K9me1 was depleted only upon loss of EHMT1, H3K9me2 was decreased, and H3K9me2-enriched domains were eliminated equally upon loss of EHMT1 or EHMT2. Furthermore, there were more significant changes in the transcriptome, DNA methylome, and proteome in Ehmt1/2 cDKO than Ehmt2 cKO oocytes, with transcriptional derepression leading to increased protein abundance and local changes in genic DNA methylation in Ehmt1/2 cDKO oocytes. Together, our findings suggest that EHMT1 contributes to local transcriptional repression in the oocyte, partially independent of EHMT2, and is critical for oogenesis and oocyte developmental competence.
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Affiliation(s)
- Hannah Demond
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom;,Millennium Institute on Immunology and Immunotherapy, Laboratory of Integrative Biology (LIBi), Centro de Excelencia en Medicina Traslacional (CEMT), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4810296, Temuco, Chile
| | - Courtney W. Hanna
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom;,Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom;,Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | | | - Fátima Santos
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom;,Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Evangelia K. Papachristou
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Anne Segonds-Pichon
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Kamal Kishore
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Simon Andrews
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Clive S. D'Santos
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom;,Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom;,Wellcome-MRC Institute of Metabolic Science–Metabolic Research Laboratories, Cambridge CB2 0QQ, United Kingdom
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7
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Channathodiyil P, May K, Segonds-Pichon A, Smith PD, Cook S, Houseley J. Escape from G1 arrest during acute MEK inhibition drives the acquisition of drug resistance. NAR Cancer 2022; 4:zcac032. [PMID: 36267209 PMCID: PMC9575185 DOI: 10.1093/narcan/zcac032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/08/2022] [Accepted: 10/04/2022] [Indexed: 11/13/2022] Open
Abstract
Mutations and gene amplifications that confer drug resistance emerge frequently during chemotherapy, but their mechanism and timing are poorly understood. Here, we investigate BRAFV600E amplification events that underlie resistance to the MEK inhibitor selumetinib (AZD6244/ARRY-142886) in COLO205 cells, a well-characterized model for reproducible emergence of drug resistance, and show that BRAF amplifications acquired de novo are the primary cause of resistance. Selumetinib causes long-term G1 arrest accompanied by reduced expression of DNA replication and repair genes, but cells stochastically re-enter the cell cycle during treatment despite continued repression of pERK1/2. Most DNA replication and repair genes are re-expressed as cells enter S and G2; however, mRNAs encoding a subset of factors important for error-free replication and chromosome segregation, including TIPIN, PLK2 and PLK3, remain at low abundance. This suggests that DNA replication following escape from G1 arrest in drug is more error prone and provides a potential explanation for the DNA damage observed under long-term RAF-MEK-ERK1/2 pathway inhibition. To test the hypothesis that escape from G1 arrest in drug promotes de novo BRAF amplification, we exploited the combination of palbociclib and selumetinib. Combined treatment with selumetinib and a dose of palbociclib sufficient to reinforce G1 arrest in selumetinib-sensitive cells, but not to impair proliferation of resistant cells, delays the emergence of resistant colonies, meaning that escape from G1 arrest is critical in the formation of resistant clones. Our findings demonstrate that acquisition of MEK inhibitor resistance often occurs through de novo gene amplification and can be suppressed by impeding cell cycle entry in drug.
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Affiliation(s)
| | - Kieron May
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 4NT, UK
| | | | - Paul D Smith
- Oncology R&D, AstraZeneca CRUK Cambridge Institute, Cambridge, CB2 0AA, UK
| | - Simon J Cook
- Signalling Programme, Babraham Institute, Cambridge, CB22 4NT, UK
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8
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Hornigold K, Chu JY, Chetwynd SA, Machin PA, Crossland L, Pantarelli C, Anderson KE, Hawkins PT, Segonds-Pichon A, Oxley D, Welch HCE. Age-related decline in the resistance of mice to bacterial infection and in LPS/TLR4 pathway-dependent neutrophil responses. Front Immunol 2022; 13:888415. [PMID: 36090969 PMCID: PMC9450589 DOI: 10.3389/fimmu.2022.888415] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/02/2022] [Indexed: 11/23/2022] Open
Abstract
Host defense against bacterial and fungal infections diminishes with age. In humans, impaired neutrophil responses are thought to contribute to this decline. However, it remains unclear whether neutrophil responses are also impaired in old mice. Here, we investigated neutrophil function in old mice, focusing on responses primed by lipopolysaccharide (LPS), an endotoxin released by gram-negative bacteria like E. coli, which signals through toll-like receptor (TLR) 4. We show that old mice have a reduced capacity to clear pathogenic E. coli during septic peritonitis. Neutrophil recruitment was elevated during LPS-induced but not aseptic peritonitis. Neutrophils from old mice showed reduced killing of E. coli. Their reactive oxygen species (ROS) production was impaired upon priming with LPS but not with GM-CSF/TNFα. Phagocytosis and degranulation were reduced in a partially LPS-dependent manner, whereas impairment of NET release in response to S. aureus was independent of LPS. Unexpectedly, chemotaxis was normal, as were Rac1 and Rac2 GTPase activities. LPS-primed activation of Erk and p38 Mapk was defective. PIP3 production was reduced upon priming with LPS but not with GM-CSF/TNFα, whereas PIP2 levels were constitutively low. The expression of 5% of neutrophil proteins was dysregulated in old age. Granule proteins, particularly cathepsins and serpins, as well as TLR-pathway proteins and membrane receptors were upregulated, whereas chromatin and RNA regulators were downregulated. The upregulation of CD180 and downregulation of MyD88 likely contribute to the impaired LPS signaling. In summary, all major neutrophil responses except chemotaxis decline with age in mice, particularly upon LPS priming. This LPS/TLR4 pathway dependence resolves previous controversy regarding effects of age on murine neutrophils and confirms that mice are an appropriate model for the decline in human neutrophil function.
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Affiliation(s)
- Kirsti Hornigold
- Signalling Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Julia Y. Chu
- Signalling Programme, The Babraham Institute, Cambridge, United Kingdom
| | | | - Polly A. Machin
- Signalling Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Laraine Crossland
- Signalling Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Chiara Pantarelli
- Signalling Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Karen E. Anderson
- Signalling Programme, The Babraham Institute, Cambridge, United Kingdom
| | | | | | - David Oxley
- Proteomics Facility, The Babraham Institute, Cambridge, United Kingdom
| | - Heidi C. E. Welch
- Signalling Programme, The Babraham Institute, Cambridge, United Kingdom
- *Correspondence: Heidi C. E. Welch,
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9
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Suriyalaksh M, Raimondi C, Mains A, Segonds-Pichon A, Mukhtar S, Murdoch S, Aldunate R, Krueger F, Guimerà R, Andrews S, Sales-Pardo M, Casanueva O. Gene regulatory network inference in long-lived C. elegans reveals modular properties that are predictive of novel aging genes. iScience 2022; 25:103663. [PMID: 35036864 PMCID: PMC8753122 DOI: 10.1016/j.isci.2021.103663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 09/09/2021] [Accepted: 12/15/2021] [Indexed: 11/24/2022] Open
Abstract
We design a “wisdom-of-the-crowds” GRN inference pipeline and couple it to complex network analysis to understand the organizational principles governing gene regulation in long-lived glp-1/Notch Caenorhabditis elegans. The GRN has three layers (input, core, and output) and is topologically equivalent to bow-tie/hourglass structures prevalent among metabolic networks. To assess the functional importance of structural layers, we screened 80% of regulators and discovered 50 new aging genes, 86% with human orthologues. Genes essential for longevity—including ones involved in insulin-like signaling (ILS)—are at the core, indicating that GRN's structure is predictive of functionality. We used in vivo reporters and a novel functional network covering 5,497 genetic interactions to make mechanistic predictions. We used genetic epistasis to test some of these predictions, uncovering a novel transcriptional regulator, sup-37, that works alongside DAF-16/FOXO. We present a framework with predictive power that can accelerate discovery in C. elegans and potentially humans. Gene-regulatory inference provides global network of long-lived animals The large-scale topology of the network has an hourglass structure Membership to the core of the hourglass is a good predictor of functionality Discovered 50 novel aging genes, including sup-37, a DAF-16 dependent gene
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Affiliation(s)
| | | | - Abraham Mains
- Babraham Institute, Babraham, Cambridge CB22 3AT, UK
| | | | | | | | - Rebeca Aldunate
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Santo Tomas, Santiago, Chile
| | - Felix Krueger
- Babraham Institute, Babraham, Cambridge CB22 3AT, UK
| | - Roger Guimerà
- ICREA, Barcelona 08010, Catalonia, Spain.,Department of Chemical Engineering, Universitat Rovira i Virgili, Tarragona 43007, Catalonia, Spain
| | - Simon Andrews
- Babraham Institute, Babraham, Cambridge CB22 3AT, UK
| | - Marta Sales-Pardo
- Department of Chemical Engineering, Universitat Rovira i Virgili, Tarragona 43007, Catalonia, Spain
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10
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Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann HJ, Lopez-Clavijo AF, Okkenhaug H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett SW, Kienberger H, Kleigrewe K, de Bono M, Wakelam MJO, Casanueva O. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. PLoS Biol 2021; 19:e3001431. [PMID: 34723964 PMCID: PMC8585009 DOI: 10.1371/journal.pbio.3001431] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 11/11/2021] [Accepted: 09/29/2021] [Indexed: 11/18/2022] Open
Abstract
To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell autonomous. We have discovered that, in Caenorhabditis elegans, neuronal heat shock factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR), causes extensive fat remodeling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine and a global shift in the saturation levels of plasma membrane's phospholipids. The observed remodeling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least 6 TAX-2/TAX-4 cyclic guanosine monophosphate (cGMP) gated channel expressing sensory neurons, and transforming growth factor ß (TGF-β)/bone morphogenetic protein (BMP) are required for signaling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodeling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell nonautonomously coordinate membrane saturation and composition across tissues in a multicellular animal.
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Affiliation(s)
- Laetitia Chauve
- Epigenetics Department, Babraham Institute, Cambridge, United Kingdom
| | - Francesca Hodge
- Epigenetics Department, Babraham Institute, Cambridge, United Kingdom
| | - Sharlene Murdoch
- Epigenetics Department, Babraham Institute, Cambridge, United Kingdom
| | | | | | | | | | - Greg West
- Babraham Institute, Cambridge, United Kingdom
| | | | | | - Cheryl Li
- Epigenetics Department, Babraham Institute, Cambridge, United Kingdom
| | | | | | - Karin Kleigrewe
- Bavarian Centre for Biomolecular Mass Spectrometry, Freising, Germany
| | - Mario de Bono
- Institute of Science and Technology, Klosterneuburg, Austria
| | | | - Olivia Casanueva
- Epigenetics Department, Babraham Institute, Cambridge, United Kingdom
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11
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Panta P, Reddy P, Misra SR, Segonds-Pichon A, Patil S. Impact of COVID-19 Lockdown on Oral Oncology-related Outpatient Volume at Indian Dental Institutions. J Contemp Dent Pract 2021; 22:501-505. [PMID: 34318767 DOI: 10.5005/jp-journals-10024-3036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
AIM AND OBJECTIVE This study aimed to evaluate the impact of the lockdown on oral oncology-related out-patient volume at Indian dental institutions. MATERIALS AND METHODS The total number of newly diagnosed cases of oral submucous fibrosis, oral leukoplakia, oral lichen planus, and oral cancers, recorded at two dental institutional settings before lockdown (January-March 2020) and after lockdown (June-August 2020), were included retrospectively and compared. RESULTS The study included a total of 797 cases at both institutions. At Institution-I, a total of 312 cases were recorded before the lockdown, and 63 cases were recorded after the lockdown. At Institution-II, a total of 311 cases were reported before lockdown, and 111 cases were recorded after lockdown. Comparisons between the pre-lockdown and post-lockdown data yielded a significant change in the proportions of oral sub-mucous fibrosis, oral leukoplakia, oral lichen planus, and oral cancers at both institutions (Chi-square test; p < 0.001). Following the lockdown, a substantial reduction was observed in the proportion of oral submucous fibrosis (OSMF) cases at both institutions, and the proportion of oral cancers increased at both institutions. There was a significant difference between the proportions of cases reported before lockdown at both institutions (p < 0.001). However, after-lockdown, no such differences were noted (p = 0.69); the absence of significance could most likely be due to the low sample size or low-power during the post-lockdown period. CONCLUSION The oral potentially malignant disorders (OPMD) and oral cancer (OC) patient volumes reduced substantially following lockdown. During the post-lockdown period, the proportion of oral cancers increased, whereas the proportion of OSMF cases decreased. Results indicate that OPMD and oral cancer patients were impacted differently by the lockdown. CLINICAL SIGNIFICANCE This study provides insight into the impact of lockdown and highlights the importance of reestablishing oral oncology-related patient care. A vital discussion is also provided on useful compensatory strategies that may reduce delays during the ongoing crisis. How to cite this article: Panta P, Reddy P, Misra SR, et al. Impact of COVID-19 Lockdown on Oral Oncology-related Outpatient Volume at Indian Dental Institutions. J Contemp Dent Pract 2021;22(5):501-505.
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Affiliation(s)
- Prashanth Panta
- Department of Oral Medicine and Radiology, MNR Dental College and Hospital, Sangareddy, Telangana, India, Phone: +91 9701806830, e-mail:
| | - Prashanthi Reddy
- Department of Oral Medicine and Radiology, Government College of Dentistry, Indore, Madhya Pradesh, India
| | - Satya Ranjan Misra
- Department of Oral Medicine and Radiology, Institute of Dental Sciences, Bhubaneswar, Odisha, India
| | - Anne Segonds-Pichon
- Department of Bioinformatics, The Babraham Institute, Cambridge, United Kingdom
| | - Shankargouda Patil
- Department of Maxillofacial Surgery and Diagnostic Sciences, Division of Oral Pathology, College of Dentistry, Jazan University, Jazan, Saudi Arabia
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12
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Stammers M, Ivanova IM, Niewczas IS, Segonds-Pichon A, Streeter M, Spiegel DA, Clark J. Age-related changes in the physical properties, cross-linking, and glycation of collagen from mouse tail tendon. J Biol Chem 2020; 295:10562-10571. [PMID: 32381510 PMCID: PMC7397091 DOI: 10.1074/jbc.ra119.011031] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 05/04/2020] [Indexed: 12/18/2022] Open
Abstract
Collagen is a structural protein whose internal cross-linking critically determines the properties and functions of connective tissue. Knowing how the cross-linking of collagen changes with age is key to understanding why the mechanical properties of tissues change over a lifetime. The current scientific consensus is that collagen cross-linking increases with age and that this increase leads to tendon stiffening. Here, we show that this view should be reconsidered. Using MS-based analyses, we demonstrated that during aging of healthy C57BL/6 mice, the overall levels of collagen cross-linking in tail tendon decreased with age. However, the levels of lysine glycation in collagen, which is not considered a cross-link, increased dramatically with age. We found that in 16-week-old diabetic db/db mice, glycation reaches levels similar to those observed in 98-week-old C57BL/6 mice, while the other cross-links typical of tendon collagen either decreased or remained the same as those observed in 20-week-old WT mice. These results, combined with findings from mechanical testing of tendons from these mice, indicate that overall collagen cross-linking in mouse tendon decreases with age. Our findings also reveal that lysine glycation appears to be an important factor that contributes to tendon stiffening with age and in diabetes.
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Affiliation(s)
| | - Irina M Ivanova
- Babraham Institute, Cambridge, United Kingdom
- John Innes Centre, Norwich, United Kingdom
| | | | | | - Matthew Streeter
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | - David A Spiegel
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
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Stammers M, Niewczas IS, Segonds-Pichon A, Clark J. Mechanical stretching changes crosslinking and glycation levels in the collagen of mouse tail tendon. J Biol Chem 2020; 295:10572-10580. [PMID: 32546479 PMCID: PMC7397108 DOI: 10.1074/jbc.ra119.012067] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 06/09/2020] [Indexed: 12/20/2022] Open
Abstract
Collagen I is a major tendon protein whose polypeptide chains are linked by covalent crosslinks. It is unknown how the crosslinking contributes to the mechanical properties of tendon or whether crosslinking changes in response to stretching or relaxation. Since their discovery, imine bonds within collagen have been recognized as being important in both crosslink formation and collagen structure. They are often described as acidic or thermally labile, but no evidence is available from direct measurements of crosslink levels whether these bonds contribute to the mechanical properties of collagen. Here, we used MS to analyze these imine bonds after reduction with sodium borohydride while under tension and found that their levels are altered in stretched tendon. We studied the changes in crosslink bonding in tail tendon from 11-week-old C57Bl/6 mice at 4% physical strain, at 10% strain, and at breaking point. The crosslinks hydroxy-lysino-norleucine (HLNL), dihydroxy-lysino-norleucine (DHLNL), and lysino-norleucine (LNL) in-creased or decreased depending on the specific crosslink and amount of mechanical strain. We also noted a decrease in glycated lysine residues in collagen, indicating that the imine formed between circulating glucose and lysine is also stress labile. We also carried out mechanical testing, including cyclic testing at 4% strain, stress relaxation tests, and stress-strain profiles taken at breaking point, both with and without sodium borohydride reduction. The results from both the MS studies and mechanical testing provide insights into the chemical changes during tendon stretching and directly link these chemical changes to functional collagen properties.
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14
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Saenz-de-Juano MD, Ivanova E, Romero S, Lolicato F, Sánchez F, Van Ranst H, Krueger F, Segonds-Pichon A, De Vos M, Andrews S, Smitz J, Kelsey G, Anckaert E. DNA methylation and mRNA expression of imprinted genes in blastocysts derived from an improved in vitro maturation method for oocytes from small antral follicles in polycystic ovary syndrome patients. Hum Reprod 2019; 34:1640-1649. [PMID: 31398248 DOI: 10.1093/humrep/dez121] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 06/04/2019] [Accepted: 06/17/2019] [Indexed: 11/08/2023] Open
Abstract
STUDY QUESTION Does imprinted DNA methylation or imprinted gene expression differ between human blastocysts from conventional ovarian stimulation (COS) and an optimized two-step IVM method (CAPA-IVM) in age-matched polycystic ovary syndrome (PCOS) patients? SUMMARY ANSWER No significant differences in imprinted DNA methylation and gene expression were detected between COS and CAPA-IVM blastocysts. WHAT IS KNOWN ALREADY Animal models have revealed alterations in DNA methylation maintenance at imprinted germline differentially methylated regions (gDMRs) after use of ARTs. This effect increases as more ART interventions are applied to oocytes or embryos. IVM is a minimal-stimulation ART with reduced hormone-related side effects and risks for patients. CAPA-IVM is an improved IVM system that includes a pre-maturation step (CAPA), followed by an IVM step, both in the presence of physiological compounds that promote oocyte developmental capacity. STUDY DESIGN, SIZE, DURATION For DNA methylation analysis 20 CAPA-IVM blastocysts were compared to 12 COS blastocysts. For RNA-Seq analysis a separate set of 15 CAPA-IVM blastocysts were compared to 5 COS blastocysts. PARTICIPANTS/MATERIALS, SETTING, METHODS COS embryos originated from 12 patients with PCOS (according to Rotterdam criteria) who underwent conventional ovarian stimulation. For CAPA-IVM 23 women were treated for 3-5 days with highly purified hMG (HP-hMG) and no hCG trigger was given before oocyte retrieval. Oocytes were first cultured in pre-maturation medium (CAPA for 24 h containing C-type natriuretic peptide), followed by an IVM step (30 h) in medium containing FSH and Amphiregulin. After ICSI, Day 5 or 6 embryos in both groups were vitrified and used for post-bisulphite adaptor tagging (PBAT) DNA methylation analysis or RNA-seq gene expression analysis of individual embryos. Data from specific genes and gDMRs were extracted from the PABT and RNA-seq datasets. MAIN RESULTS AND THE ROLE OF CHANCE CAPA-IVM blastocysts showed similar rates of methylation and gene expression at gDMRs compared to COS embryos. In addition, expression of major epigenetic regulators was similar between the groups. LIMITATIONS, REASONS FOR CAUTION The embryos from the COS group were generated in a range of culture media. The CAPA-IVM embryos were all generated using the same sperm donor. The DNA methylation level of gDMRs in purely in vivo-derived human blastocysts is not known. WIDER IMPLICATIONS OF THE FINDINGS A follow-up of children born after CAPA-IVM is important as it is for other new ARTs, which are generally introduced into clinical practice without prior epigenetic safety studies on human blastocysts. CAPA-IVM opens new perspectives for patient-friendly ART in PCOS. STUDY FUNDING/COMPETING INTEREST(S) IVM research at the Vrije Universiteit Brussel has been supported by grants from the Institute for the Promotion of Innovation by Science and Technology in Flanders (Agentschap voor Innovatie door Wetenschap en Technologie-IWT, project 110680), the Fund for Research Flanders (Fonds voor Wetenschappelijk Onderzoek-Vlaanderen-FWO-AL 679 project, project G.0343.13), the Belgian Foundation Against Cancer (HOPE project, Dossier C69Ref Nr 2016-119) and the Vrije Universiteit Brussel (IOF Project 4R-ART Nr 2042). Work in G.K.'s laboratory is supported by the UK Biotechnology and Biological Sciences Research Council and Medical Research Council. The authors have no conflicts of interest.
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Affiliation(s)
- M D Saenz-de-Juano
- Follicle Biology Laboratory (FOBI), UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Switzerland
| | - E Ivanova
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - S Romero
- Follicle Biology Laboratory (FOBI), UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
- Laboratory of Reproductive Biology and Fertility Preservation, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - F Lolicato
- Follicle Biology Laboratory (FOBI), UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
- Fertilab Barcelona, Via Augusta, 237-239, Barcelona 08021, Spain
| | - F Sánchez
- Follicle Biology Laboratory (FOBI), UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
- Laboratory of Reproductive Biology and Fertility Preservation, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - H Van Ranst
- Follicle Biology Laboratory (FOBI), UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - F Krueger
- Bioinformatics Unit, The Babraham Institute, Cambridge, UK
| | | | - M De Vos
- Follicle Biology Laboratory (FOBI), UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
- Centre for Reproductive Medicine, UZ Brussel, Brussels 1090, Belgium
| | - S Andrews
- Bioinformatics Unit, The Babraham Institute, Cambridge, UK
| | - J Smitz
- Follicle Biology Laboratory (FOBI), UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - G Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - E Anckaert
- Follicle Biology Laboratory (FOBI), UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
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15
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Novo CL, Javierre BM, Cairns J, Segonds-Pichon A, Wingett SW, Freire-Pritchett P, Furlan-Magaril M, Schoenfelder S, Fraser P, Rugg-Gunn PJ. Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition. Cell Rep 2019. [PMID: 29514091 PMCID: PMC5863031 DOI: 10.1016/j.celrep.2018.02.040] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Transcriptional enhancers, including super-enhancers (SEs), form physical interactions with promoters to regulate cell-type-specific gene expression. SEs are characterized by high transcription factor occupancy and large domains of active chromatin, and they are commonly assigned to target promoters using computational predictions. How promoter-SE interactions change upon cell state transitions, and whether transcription factors maintain SE interactions, have not been reported. Here, we used promoter-capture Hi-C to identify promoters that interact with SEs in mouse embryonic stem cells (ESCs). We found that SEs form complex, spatial networks in which individual SEs contact multiple promoters, and a rewiring of promoter-SE interactions occurs between pluripotent states. We also show that long-range promoter-SE interactions are more prevalent in ESCs than in epiblast stem cells (EpiSCs) or Nanog-deficient ESCs. We conclude that SEs form cell-type-specific interaction networks that are partly dependent on core transcription factors, thereby providing insights into the gene regulatory organization of pluripotent cells. Promoter-capture Hi-C identifies 3D interactions in mouse pluripotent cells Super-enhancers (SEs) form complex spatial networks contacting multiple promoters Rewiring of promoter-SE interactions between ESC and EpiSC pluripotent states Long-range SE interactions are a hallmark of mouse ESCs
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Affiliation(s)
- Clara Lopes Novo
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Jonathan Cairns
- Nuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Steven W Wingett
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, UK
| | | | | | | | - Peter Fraser
- Nuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK.
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16
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Suire S, Baltanas FC, Segonds-Pichon A, Davidson K, Santos E, Hawkins PT, Stephens LR. Frontline Science: TNF-α and GM-CSF1 priming augments the role of SOS1/2 in driving activation of Ras, PI3K-γ, and neutrophil proinflammatory responses. J Leukoc Biol 2019; 106:815-822. [PMID: 30720883 PMCID: PMC6977543 DOI: 10.1002/jlb.2hi0918-359rr] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/27/2018] [Accepted: 11/28/2018] [Indexed: 12/31/2022] Open
Abstract
Circulating neutrophils are, by necessity, quiescent and relatively unresponsive to acute stimuli. In regions of inflammation, mediators can prime neutrophils to react to acute stimuli with stronger proinflammatory, pathogen-killing responses. In neutrophils G protein-coupled receptor (GPCR)-driven proinflammatory responses, such as reactive oxygen species (ROS) formation and accumulation of the key intracellular messenger phosphatidylinositol (3,4,5)-trisphosphate (PIP3 ), are highly dependent on PI3K-γ, a Ras-GTP, and Gβγ coincidence detector. In unprimed cells, the major GPCR-triggered activator of Ras is the Ras guanine nucleotide exchange factor (GEF), Ras guanine nucleotide releasing protein 4 (RasGRP4). Although priming is known to increase GPCR-PIP3 signaling, the mechanisms underlying this augmentation remain unclear. We used genetically modified mice to address the role of the 2 RasGEFs, RasGRP4 and son of sevenless (SOS)1/2, in neutrophil priming. We found that following GM-CSF/TNFα priming, RasGRP4 had only a minor role in the enhanced responses. In contrast, SOS1/2 acquired a substantial role in ROS formation, PIP3 accumulation, and ERK activation in primed cells. These results suggest that SOS1/2 signaling plays a key role in determining the responsiveness of neutrophils in regions of inflammation.
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Affiliation(s)
- Sabine Suire
- Inositide Laboratory, The Babraham Institute, Cambridge, UK
| | - Fernando C Baltanas
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer, (CSIC- Universitad de Salamanca) and CiberONC, Salamanca, Spain
| | | | - Keith Davidson
- Inositide Laboratory, The Babraham Institute, Cambridge, UK
| | - Eugenio Santos
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer, (CSIC- Universitad de Salamanca) and CiberONC, Salamanca, Spain
| | | | - Len R Stephens
- Inositide Laboratory, The Babraham Institute, Cambridge, UK
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17
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Smyrnias I, Goodwin N, Wachten D, Skogestad J, Aronsen JM, Robinson EL, Demydenko K, Segonds-Pichon A, Oxley D, Sadayappan S, Sipido K, Bootman MD, Roderick HL. Contractile responses to endothelin-1 are regulated by PKC phosphorylation of cardiac myosin binding protein-C in rat ventricular myocytes. J Mol Cell Cardiol 2018; 117:1-18. [DOI: 10.1016/j.yjmcc.2018.02.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 02/02/2018] [Accepted: 02/16/2018] [Indexed: 01/07/2023]
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18
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Milagre I, Stubbs TM, King MR, Spindel J, Santos F, Krueger F, Bachman M, Segonds-Pichon A, Balasubramanian S, Andrews SR, Dean W, Reik W. Gender Differences in Global but Not Targeted Demethylation in iPSC Reprogramming. Cell Rep 2017; 18:1079-1089. [PMID: 28147265 PMCID: PMC5300890 DOI: 10.1016/j.celrep.2017.01.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 12/23/2016] [Accepted: 01/06/2017] [Indexed: 01/08/2023] Open
Abstract
Global DNA demethylation is an integral part of reprogramming processes in vivo and in vitro, but whether it occurs in the derivation of induced pluripotent stem cells (iPSCs) is not known. Here, we show that iPSC reprogramming involves both global and targeted demethylation, which are separable mechanistically and by their biological outcomes. Cells at intermediate-late stages of reprogramming undergo transient genome-wide demethylation, which is more pronounced in female cells. Global demethylation requires activation-induced cytidine deaminase (AID)-mediated downregulation of UHRF1 protein, and abolishing demethylation leaves thousands of hypermethylated regions in the iPSC genome. Independently of AID and global demethylation, regulatory regions, particularly ESC enhancers and super-enhancers, are specifically targeted for hypomethylation in association with transcription of the pluripotency network. Our results show that global and targeted DNA demethylation are conserved and distinct reprogramming processes, presumably because of their respective roles in epigenetic memory erasure and in the establishment of cell identity.
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Affiliation(s)
- Inês Milagre
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK.
| | - Thomas M Stubbs
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Michelle R King
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Julia Spindel
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Fátima Santos
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Felix Krueger
- Bioinformatics Group, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Martin Bachman
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | | | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Simon R Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Wendy Dean
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
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19
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Schoenfelder S, Sugar R, Dimond A, Javierre BM, Armstrong H, Mifsud B, Dimitrova E, Matheson L, Tavares-Cadete F, Furlan-Magaril M, Segonds-Pichon A, Jurkowski W, Wingett SW, Tabbada K, Andrews S, Herman B, LeProust E, Osborne CS, Koseki H, Fraser P, Luscombe NM, Elderkin S. Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome. Nat Genet 2015; 47:1179-1186. [PMID: 26323060 PMCID: PMC4847639 DOI: 10.1038/ng.3393] [Citation(s) in RCA: 255] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 08/05/2015] [Indexed: 02/08/2023]
Abstract
The Polycomb repressive complexes PRC1 and PRC2 maintain embryonic stem cell (ESC) pluripotency by silencing lineage-specifying developmental regulator genes. Emerging evidence suggests that Polycomb complexes act through controlling spatial genome organization. We show that PRC1 functions as a master regulator of mouse ESC genome architecture by organizing genes in three-dimensional interaction networks. The strongest spatial network is composed of the four Hox gene clusters and early developmental transcription factor genes, the majority of which contact poised enhancers. Removal of Polycomb repression leads to disruption of promoter-promoter contacts in the Hox gene network. In contrast, promoter-enhancer contacts are maintained in the absence of Polycomb repression, with accompanying widespread acquisition of active chromatin signatures at network enhancers and pronounced transcriptional upregulation of network genes. Thus, PRC1 physically constrains developmental transcription factor genes and their enhancers in a silenced but poised spatial network. We propose that the selective release of genes from this spatial network underlies cell fate specification during early embryonic development.
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Affiliation(s)
| | - Robert Sugar
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Andrew Dimond
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
| | | | - Harry Armstrong
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
| | - Borbala Mifsud
- Cancer Research UK London Research Institute, London, UK
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Emilia Dimitrova
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
- Department of Biochemistry, Oxford University, Oxford, UK
| | - Louise Matheson
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
| | - Filipe Tavares-Cadete
- Cancer Research UK London Research Institute, London, UK
- present address: Okinawa Institute for Science and Technology Graduate University, Okinawa, Japan
| | | | | | - Wiktor Jurkowski
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
| | - Steven W Wingett
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
- Bioinformatics, The Babraham Institute, Cambridge, UK
| | - Kristina Tabbada
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
| | - Simon Andrews
- Bioinformatics, The Babraham Institute, Cambridge, UK
| | - Bram Herman
- Agilent Technologies Inc., Santa Clara, California, USA
| | | | | | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
| | - Nicholas M Luscombe
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Cancer Research UK London Research Institute, London, UK
- Department of Genetics, Evolution & Environment, University College London, London, UK
- Okinawa Institute for Science and Technology Graduate University, Okinawa, Japan
| | - Sarah Elderkin
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
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20
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Cini A, Patalano S, Segonds-Pichon A, Busby GBJ, Cervo R, Sumner S. Social parasitism and the molecular basis of phenotypic evolution. Front Genet 2015; 6:32. [PMID: 25741361 PMCID: PMC4332356 DOI: 10.3389/fgene.2015.00032] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 01/23/2015] [Indexed: 11/21/2022] Open
Abstract
Contrasting phenotypes arise from similar genomes through a combination of losses, gains, co-option and modifications of inherited genomic material. Understanding the molecular basis of this phenotypic diversity is a fundamental challenge in modern evolutionary biology. Comparisons of the genes and their expression patterns underlying traits in closely related species offer an unrivaled opportunity to evaluate the extent to which genomic material is reorganized to produce novel traits. Advances in molecular methods now allow us to dissect the molecular machinery underlying phenotypic diversity in almost any organism, from single-celled entities to the most complex vertebrates. Here we discuss how comparisons of social parasites and their free-living hosts may provide unique insights into the molecular basis of phenotypic evolution. Social parasites evolve from a eusocial ancestor and are specialized to exploit the socially acquired resources of their closely-related eusocial host. Molecular comparisons of such species pairs can reveal how genomic material is re-organized in the loss of ancestral traits (i.e., of free-living traits in the parasites) and the gain of new ones (i.e., specialist traits required for a parasitic lifestyle). We define hypotheses on the molecular basis of phenotypes in the evolution of social parasitism and discuss their wider application in our understanding of the molecular basis of phenotypic diversity within the theoretical framework of phenotypic plasticity and shifting reaction norms. Currently there are no data available to test these hypotheses, and so we also provide some proof of concept data using the paper wasp social parasite/host system (Polistes sulcifer-Polistes dominula). This conceptual framework and first empirical data provide a spring-board for directing future genomic analyses on exploiting social parasites as a route to understanding the evolution of phenotypic specialization.
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Affiliation(s)
- Alessandro Cini
- Dipartimento di Biologia, Università di FirenzeFirenze, Italy
| | - Solenn Patalano
- Institute of Zoology, Zoological Society of LondonLondon, UK
- The Babraham Institute, Babraham Research Campus – CambridgeCambridge, UK
| | | | - George B. J. Busby
- Institute of Zoology, Zoological Society of LondonLondon, UK
- Wellcome Trust Centre for Human GeneticsOxford, UK
| | - Rita Cervo
- Dipartimento di Biologia, Università di FirenzeFirenze, Italy
| | - Seirian Sumner
- Institute of Zoology, Zoological Society of LondonLondon, UK
- School of Biological Sciences, University of BristolBristol, UK
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21
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Nicol AU, Segonds-Pichon A, Magnusson MS. Complex spike patterns in olfactory bulb neuronal networks. J Neurosci Methods 2014; 239:11-7. [PMID: 25256643 DOI: 10.1016/j.jneumeth.2014.09.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 09/13/2014] [Accepted: 09/15/2014] [Indexed: 11/24/2022]
Abstract
BACKGROUND T-pattern analysis is a procedure developed for detecting non-randomly recurring hierarchical and multiordinal real-time sequential patterns (T-patterns). NEW METHOD We have inquired whether such patterns of action potentials (spikes) can be extracted from extracellular activity sampled simultaneously from many neurons across the mitral cell layer of the olfactory bulb (OB). Spikes were sampled from urethane-anaesthetized rats over a 6h recording session, or a period lasting as long as permitted by the physiological condition of the animal. Breathing was recorded to mark peak inhalation and exhalation. RESULTS Complex T-patterns of up to ∼20 elements were identified with functional connections often spanning the full extent of the array. A considerable proportion of these sequences incorporated breathing. COMPARISON WITH EXISTING METHODS In contrast to sequence detection by synfire, the incidence of sequences detected in our real data is very much greater than in the same data when randomized either by shuffling, or an alternative procedure preserving the interval structure of each spike train, and so more conservative. Further, when recordings were terminated before completion of the full recording session, the relative pattern detection in real and randomized data was a strong indicator of physiological condition-in recordings leading up to the preparation becoming physiologically unstable, the number of patterns detected in real data approached that in the randomized data. CONCLUSIONS We conclude that such sequences are an important physiological property of the neural system studied, and suggest that they may form a basis for encoding sensory information.
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Affiliation(s)
- Alister U Nicol
- Department of Physiology, Development and Neuroscience, University of Cambridge, 307 Huntingdon Road, Cambridge CB3 0JX, UK.
| | | | - Magnus S Magnusson
- Human Behaviour Laboratory, University of Iceland, IS-101 Reykjavik, Iceland
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22
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Nicol AU, Sanchez-Andrade G, Collado P, Segonds-Pichon A, Kendrick KM. Olfactory bulb encoding during learning under anesthesia. Front Behav Neurosci 2014; 8:193. [PMID: 24926241 PMCID: PMC4046573 DOI: 10.3389/fnbeh.2014.00193] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Accepted: 05/09/2014] [Indexed: 11/25/2022] Open
Abstract
Neural plasticity changes within the olfactory bulb are important for olfactory learning, although how neural encoding changes support new associations with specific odors and whether they can be investigated under anesthesia, remain unclear. Using the social transmission of food preference olfactory learning paradigm in mice in conjunction with in vivo microdialysis sampling we have shown firstly that a learned preference for a scented food odor smelled on the breath of a demonstrator animal occurs under isofluorane anesthesia. Furthermore, subsequent exposure to this cued odor under anesthesia promotes the same pattern of increased release of glutamate and gamma-aminobutyric acid (GABA) in the olfactory bulb as previously found in conscious animals following olfactory learning, and evoked GABA release was positively correlated with the amount of scented food eaten. In a second experiment, multiarray (24 electrodes) electrophysiological recordings were made from olfactory bulb mitral cells under isofluorane anesthesia before, during and after a novel scented food odor was paired with carbon disulfide. Results showed significant increases in overall firing frequency to the cued-odor during and after learning and decreases in response to an uncued odor. Analysis of patterns of changes in individual neurons revealed that a substantial proportion (>50%) of them significantly changed their response profiles during and after learning with most of those previously inhibited becoming excited. A large number of cells exhibiting no response to the odors prior to learning were either excited or inhibited afterwards. With the uncued odor many previously responsive cells became unresponsive or inhibited. Learning associated changes only occurred in the posterior part of the olfactory bulb. Thus olfactory learning under anesthesia promotes extensive, but spatially distinct, changes in mitral cell networks to both cued and uncued odors as well as in evoked glutamate and GABA release.
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Affiliation(s)
- Alister U Nicol
- Sub-department of Animal Behaviour, University of Cambridge Cambridge, UK
| | | | - Paloma Collado
- Department of Psychobiology, Universidad Nacional Educación a Distancia (UNED) Madrid, Spain
| | | | - Keith M Kendrick
- Key Laboratory for Neuroinformation, University of Electronic Science and Technology of China Chengdu, China
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23
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Johnsson AKE, Dai Y, Nobis M, Baker MJ, McGhee EJ, Walker S, Schwarz JP, Kadir S, Morton JP, Myant KB, Huels DJ, Segonds-Pichon A, Sansom OJ, Anderson KI, Timpson P, Welch HCE. The Rac-FRET mouse reveals tight spatiotemporal control of Rac activity in primary cells and tissues. Cell Rep 2014; 6:1153-1164. [PMID: 24630994 PMCID: PMC3988842 DOI: 10.1016/j.celrep.2014.02.024] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 02/05/2014] [Accepted: 02/15/2014] [Indexed: 01/19/2023] Open
Abstract
The small G protein family Rac has numerous regulators that integrate extracellular signals into tight spatiotemporal maps of its activity to promote specific cell morphologies and responses. Here, we have generated a mouse strain, Rac-FRET, which ubiquitously expresses the Raichu-Rac biosensor. It enables FRET imaging and quantification of Rac activity in live tissues and primary cells without affecting cell properties and responses. We assessed Rac activity in chemotaxing Rac-FRET neutrophils and found enrichment in leading-edge protrusions and unexpected longitudinal shifts and oscillations during protruding and stalling phases of migration. We monitored Rac activity in normal or disease states of intestinal, liver, mammary, pancreatic, and skin tissue, in response to stimulation or inhibition and upon genetic manipulation of upstream regulators, revealing unexpected insights into Rac signaling during disease development. The Rac-FRET strain is a resource that promises to fundamentally advance our understanding of Rac-dependent responses in primary cells and native environments.
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Affiliation(s)
- Anna-Karin E Johnsson
- Signalling Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Yanfeng Dai
- Signalling Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Max Nobis
- Beatson Institute for Cancer Research, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Martin J Baker
- Signalling Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Ewan J McGhee
- Beatson Institute for Cancer Research, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Simon Walker
- Signalling Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Juliane P Schwarz
- Beatson Institute for Cancer Research, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Shereen Kadir
- Beatson Institute for Cancer Research, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Jennifer P Morton
- Beatson Institute for Cancer Research, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Kevin B Myant
- Beatson Institute for Cancer Research, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - David J Huels
- Beatson Institute for Cancer Research, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Anne Segonds-Pichon
- Signalling Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Owen J Sansom
- Beatson Institute for Cancer Research, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Kurt I Anderson
- Beatson Institute for Cancer Research, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Paul Timpson
- Beatson Institute for Cancer Research, Switchback Road, Bearsden, Glasgow G61 1BD, UK; Garvan Institute of Medical Research and Kinghorn Cancer Centre, Cancer Research Program, St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, NSW, 2010 Sydney, Australia.
| | - Heidi C E Welch
- Signalling Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
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24
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Conte N, Varela I, Grove C, Manes N, Yusa K, Moreno T, Segonds-Pichon A, Bench A, Gudgin E, Herman B, Bolli N, Ellis P, Haddad D, Costeas P, Rad R, Scott M, Huntly B, Bradley A, Vassiliou GS. Detailed molecular characterisation of acute myeloid leukaemia with a normal karyotype using targeted DNA capture. Leukemia 2013; 27:1820-5. [PMID: 23702683 PMCID: PMC3768109 DOI: 10.1038/leu.2013.117] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Revised: 03/17/2013] [Accepted: 04/10/2013] [Indexed: 12/13/2022]
Abstract
Advances in sequencing technologies are giving unprecedented insights into the spectrum of somatic mutations underlying acute myeloid leukaemia with a normal karyotype (AML-NK). It is clear that the prognosis of individual patients is strongly influenced by the combination of mutations in their leukaemia and that many leukaemias are composed of multiple subclones, with differential susceptibilities to treatment. Here, we describe a method, employing targeted capture coupled with next-generation sequencing and tailored bioinformatic analysis, for the simultaneous study of 24 genes recurrently mutated in AML-NK. Mutational analysis was performed using open source software and an in-house script (Mutation Identification and Analysis Software), which identified dominant clone mutations with 100% specificity. In each of seven cases of AML-NK studied, we identified and verified mutations in 2-4 genes in the main leukaemic clone. Additionally, high sequencing depth enabled us to identify putative subclonal mutations and detect leukaemia-specific mutations in DNA from remission marrow. Finally, we used normalised read depths to detect copy number changes and identified and subsequently verified a tandem duplication of exons 2-9 of MLL and at least one deletion involving PTEN. This methodology reliably detects sequence and copy number mutations, and can thus greatly facilitate the classification, clinical research, diagnosis and management of AML-NK.
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Affiliation(s)
- N Conte
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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25
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Abstract
Scientists aspire to measure cause and effect. Unfortunately confounding variables, ones that are associated with both the probable cause and the outcome, can lead to an association that is true but potentially misleading. For example, altered body weight is often observed in a gene knockout; however, many other variables, such as lean mass, will also change as the body weight changes. This leaves the researcher asking whether the change in that variable is expected for that change in weight. Ratio correction, which is often referred to as normalization, is a method used commonly to remove the effect of a confounding variable. Although ratio correction is used widely in biological research, it is not the method recommended in the statistical literature to address confounding factors; instead regression methods such as the analysis of covariance (ANCOVA) are proposed. This method examines the difference in means after adjusting for the confounding relationship. Using real data, this manuscript demonstrates how the ratio correction approach is flawed and can result in erroneous calls of significance leading to inappropriate biological conclusions. This arises as some of the underlying assumptions are not met. The manuscript goes on to demonstrate that researchers should use ANCOVA, and discusses how graphical tools can be used readily to judge the robustness of this method. This study is therefore a clear example of why assumption testing is an important component of a study and thus why it is included in the Animal Research: Reporting of In Vivo Experiment (ARRIVE) guidelines.
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Affiliation(s)
- Natasha A Karp
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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26
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Ivanova E, Chen JH, Segonds-Pichon A, Ozanne SE, Kelsey G. DNA methylation at differentially methylated regions of imprinted genes is resistant to developmental programming by maternal nutrition. Epigenetics 2012; 7:1200-10. [PMID: 22968513 PMCID: PMC3469461 DOI: 10.4161/epi.22141] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The nutritional environment in which the mammalian fetus or infant develop is recognized as influencing the risk of chronic diseases, such as type 2 diabetes and hypertension, in a phenomenon that has become known as developmental programming. The late onset of such diseases in response to earlier transient experiences has led to the suggestion that developmental programming may have an epigenetic component, because epigenetic marks such as DNA methylation or histone tail modifications could provide a persistent memory of earlier nutritional states. One class of genes that has been considered a potential target or mediator of programming events is imprinted genes, because these genes critically depend upon epigenetic modifications for correct expression and because many imprinted genes have roles in controlling fetal growth as well as neonatal and adult metabolism. In this study, we have used an established model of developmental programming-isocaloric protein restriction to female mice during gestation or lactation-to examine whether there are effects on expression and DNA methylation of imprinted genes in the offspring. We find that although expression of some imprinted genes in liver of offspring is robustly and sustainably changed, methylation of the differentially methylated regions (DMRs) that control their monoallelic expression remains largely unaltered. We conclude that deregulation of imprinting through a general effect on DMR methylation is unlikely to be a common factor in developmental programming.
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Affiliation(s)
- Elena Ivanova
- Epigenetics Programme; The Babraham Institute; Cambridge, UK
| | - Jian-Hua Chen
- Metabolic Research Laboratories; Institute of Metabolic Science; University of Cambridge; Cambridge UK
| | | | - Susan E. Ozanne
- Metabolic Research Laboratories; Institute of Metabolic Science; University of Cambridge; Cambridge UK
- MRC Centre for Obesity and Related Metabolic Diseases; Cambridge, UK
| | - Gavin Kelsey
- Epigenetics Programme; The Babraham Institute; Cambridge, UK
- Centre for Trophoblast Research; University of Cambridge; Cambridge, UK
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27
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Smallwood SA, Tomizawa SI, Krueger F, Ruf N, Carli N, Segonds-Pichon A, Sato S, Hata K, Andrews SR, Kelsey G. Dynamic CpG island methylation landscape in oocytes and preimplantation embryos. Nat Genet 2011; 43:811-4. [PMID: 21706000 PMCID: PMC3146050 DOI: 10.1038/ng.864] [Citation(s) in RCA: 475] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Accepted: 05/25/2011] [Indexed: 12/12/2022]
Abstract
Elucidating how and to what extent CpG islands (CGIs) are methylated in germ cells is essential to understand genomic imprinting and epigenetic reprogramming. Here we present, to our knowledge, the first integrated epigenomic analysis of mammalian oocytes, identifying over a thousand CGIs methylated in mature oocytes. We show that these CGIs depend on DNMT3A and DNMT3L but are not distinct at the sequence level, including in CpG periodicity. They are preferentially located within active transcription units and are relatively depleted in H3K4me3, supporting a general transcription-dependent mechanism of methylation. Very few methylated CGIs are fully protected from post-fertilization reprogramming but, notably, the majority show incomplete demethylation in embryonic day (E) 3.5 blastocysts. Our study shows that CGI methylation in gametes is not entirely related to genomic imprinting but is a strong factor in determining methylation status in preimplantation embryos, suggesting a need to reassess mechanisms of post-fertilization demethylation.
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28
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Kulkarni S, Sitaru C, Jakus Z, Anderson KE, Damoulakis G, Davidson K, Hirose M, Juss J, Oxley D, Chessa TAM, Ramadani F, Guillou H, Segonds-Pichon A, Fritsch A, Jarvis GE, Okkenhaug K, Ludwig R, Zillikens D, Mocsai A, Vanhaesebroeck B, Stephens LR, Hawkins PT. PI3Kβ plays a critical role in neutrophil activation by immune complexes. Sci Signal 2011; 4:ra23. [PMID: 21487106 DOI: 10.1126/scisignal.2001617] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Neutrophils are activated by immunoglobulin G (IgG)-containing immune complexes through receptors that recognize the Fc portion of IgG (FcγRs). Here, we used genetic and pharmacological approaches to define a selective role for the β isoform of phosphoinositide 3-kinase (PI3Kβ) in FcγR-dependent activation of mouse neutrophils by immune complexes of IgG and antigen immobilized on a plate surface. At low concentrations of immune complexes, loss of PI3Kβ alone substantially inhibited the production of reactive oxygen species (ROS) by neutrophils, whereas at higher doses, similar suppression of ROS production was achieved only by targeting both PI3Kβ and PI3Kδ, suggesting that this pathway displays stimulus strength-dependent redundancy. Activation of PI3Kβ by immune complexes involved cooperation between FcγRs and BLT1, the receptor for the endogenous proinflammatory lipid leukotriene B₄. Coincident activation by a tyrosine kinase-coupled receptor (FcγR) and a heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptor (BLT1) may provide a rationale for the preferential activation of the β isoform of PI3K. PI3Kβ-deficient mice were highly protected in an FcγR-dependent model of autoantibody-induced skin blistering and were partially protected in an FcγR-dependent model of inflammatory arthritis, whereas combined deficiency of PI3Kβ and PI3Kδ resulted in near-complete protection in the latter case. These results define PI3Kβ as a potential therapeutic target in inflammatory disease.
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Affiliation(s)
- Suhasini Kulkarni
- Inositide Laboratory, The Babraham Institute, Cambridge CB22 3AT, UK
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29
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Walters E, Segonds-Pichon A, Nicol AU. The correlation determinant in tests for synchronization in neuronal spike data. J Neurosci Methods 2008; 172:60-6. [PMID: 18499264 DOI: 10.1016/j.jneumeth.2008.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Revised: 03/27/2008] [Accepted: 04/03/2008] [Indexed: 10/22/2022]
Abstract
We present a statistical approach to the identification of correlated activity in multineuron spike data, based on the value of the correlation determinant. This approach is not compromised by the lack of independence often encountered in this kind of data. We illustrate our method by applying it both to simulated data and to data recorded from neurons in a forebrain region (intermediate medial mesopallium, IMM) of the behaving domestic chick and simultaneously from the corresponding contralateral region. There is no direct anatomical connection between the two sites, and the validity of this technique is strongly supported by the observation that when the test indicates significantly correlated activity for neurons within either hemisphere, this correlation is greatly reduced, and ultimately obliterated, by serial incorporation of activity from neurons in the opposite hemisphere. Since the value of individual correlation coefficients allied to the Bonferroni correction is often used as a diagnostic tool, we also present comparisons of that approach with our correlation determinant approach.
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Affiliation(s)
- Eurof Walters
- Department of Bioinformatics, The Babraham Institute, Babraham Research Campus, Cambridge CB22 4AT, United Kingdom
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30
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Chen C, Gilbert CL, Yang G, Guo Y, Segonds-Pichon A, Ma J, Evans G, Brenig B, Sargent C, Affara N, Huang L. Maternal infanticide in sows: Incidence and behavioural comparisons between savaging and non-savaging sows at parturition. Appl Anim Behav Sci 2008. [DOI: 10.1016/j.applanim.2007.02.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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31
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Murrin C, Segonds-Pichon A, Fallon UB, Hannon F, Bury G, Loftus BG, Murphy AW, Morrison JJ, Daly S, Kelleher CC. Self-reported pre-pregnancy maternal body mass index and infant birth-weight. Ir Med J 2007; 100:20-23. [PMID: 17955696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
This analysis examines the association between maternal characteristics, particularly body mass index (BMI) and infant birth weight in 1048 live infants. Mean reported pre pregnancy BMI of mothers was 23.74 kg/m2 (SD 4.21). The educational level of the mother's parents was independently associated with maternal BMI, those with higher educated parents having a lower reported BMI (F = 2.787, p = 0.029). Mean infant birth weight was 3493 g (SD 18.1) and there was a strong graduated relationship to estimated gestational age. In a sub-group of participating maternal grandmothers (n = 171), reported BMI was 26.7Kg/m2. The BMI of expectant mothers was significantly associated with their own mother's BMI. (r = 0.179, p = 0.005) in this sub-group. These preliminary findings, which will be investigated further with recorded height and weight information, suggest that familial factors are influential, perhaps through genetic predisposition or shared socio-cultural factors such as diet.
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Affiliation(s)
- C Murrin
- UCD School of Public Health and Population Science.
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32
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Segonds-Pichon A, Hannon F, Daly S, Morrison JJ, Bury G, Murphy AW, Kelleher CC. Socio-demographic, lifestyle and cross-generation predictors of self-rated health in mothers during pregnancy. Ir Med J 2007; 100:7-12. [PMID: 17955693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The Lifeways Cross-generation study was established to assess the influence of socio-economic and familial characteristics on the health status and early development of children. Between October 2001 and June 2002, 1124 women were recruited to the Lifeways study at booking or first visit to maternity hospital. Lifeways mothers were 29.4 (SD 5.9) years old at recruitment, two-thirds from greater Dublin area, 17.9% held a General Medical Services (GMS) card, 64.3% were married and 40.8% were third level educated. At uni-variate level, GMS eligibility, own and parents' education and marital status all predicted mother's self rated health during pregnancy, whilst in the final multivariate logistic regression model, GMS status, household-adjusted income, marital status and grand-maternal education were each independently predictors. The Lifeways cohort confirms the importance of social position in predicting health in pregnant Irish women.
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