1
|
Dentici ML, Niceta M, Lepri FR, Mancini C, Priolo M, Bonnard AA, Cappelletti C, Leoni C, Ciolfi A, Pizzi S, Cordeddu V, Rossi C, Ferilli M, Mucciolo M, Colona VL, Fauth C, Bellini M, Biasucci G, Sinibaldi L, Briuglia S, Gazzin A, Carli D, Memo L, Trevisson E, Schiavariello C, Luca M, Novelli A, Michot C, Sweertvaegher A, Germanaud D, Scarano E, De Luca A, Zampino G, Zenker M, Mussa A, Dallapiccola B, Cavé H, Digilio MC, Tartaglia M. Loss-of-function variants in ERF are associated with a Noonan syndrome-like phenotype with or without craniosynostosis. Eur J Hum Genet 2024; 32:954-963. [PMID: 38824261 PMCID: PMC11291927 DOI: 10.1038/s41431-024-01642-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/09/2024] [Accepted: 05/20/2024] [Indexed: 06/03/2024] Open
Abstract
Pathogenic, largely truncating variants in the ETS2 repressor factor (ERF) gene, encoding a transcriptional regulator negatively controlling RAS-MAPK signaling, have been associated with syndromic craniosynostosis involving various cranial sutures and Chitayat syndrome, an ultrarare condition with respiratory distress, skeletal anomalies, and facial dysmorphism. Recently, a single patient with craniosynostosis and a phenotype resembling Noonan syndrome (NS), the most common disorder among the RASopathies, was reported to carry a de novo loss-of-function variant in ERF. Here, we clinically profile 26 individuals from 15 unrelated families carrying different germline heterozygous variants in ERF and showing a phenotype reminiscent of NS. The majority of subjects presented with a variable degree of global developmental and/or language delay. Their shared facial features included absolute/relative macrocephaly, high forehead, hypertelorism, palpebral ptosis, wide nasal bridge, and low-set/posteriorly angulated ears. Stature was below the 3rd centile in two-third of the individuals, while no subject showed typical NS cardiac involvement. Notably, craniosynostosis was documented only in three unrelated individuals, while a dolichocephalic aspect of the skull in absence of any other evidence supporting a premature closing of sutures was observed in other 10 subjects. Unilateral Wilms tumor was diagnosed in one individual. Most cases were familial, indicating an overall low impact on fitness. Variants were nonsense and frameshift changes, supporting ERF haploinsufficiency. These findings provide evidence that heterozygous loss-of-function variants in ERF cause a "RASopathy" resembling NS with or without craniosynostosis, and allow a first dissection of the molecular circuits contributing to MAPK signaling pleiotropy.
Collapse
Affiliation(s)
- Maria Lisa Dentici
- Rare Diseases and Medical Genetics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Marcello Niceta
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | | | - Cecilia Mancini
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Manuela Priolo
- Medical and Molecular Genetics, Ospedale Cardarelli, 80131, Naples, Italy
| | - Adeline Alice Bonnard
- Service de de Génétique Moléculaire Hôpital Robert Debré, GHU AP-HP Nord - Université Paris Cité, INSERM UMR_S1131, Institut Universitaire d'Hématologie, Université Paris Cité, Paris-Cité, 75019, Paris, France
| | - Camilla Cappelletti
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
- Department of Biomedicine and Prevention, Università di Roma "Tor Vergata", 00133, Rome, Italy
| | - Chiara Leoni
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
- Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Simone Pizzi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Viviana Cordeddu
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Cesare Rossi
- Medical Genetics, IRCSS Azienda Ospedaliero-Universitaria di Bologna, 40138, Bologna, Italy
| | - Marco Ferilli
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Mafalda Mucciolo
- Translational Cytogenomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Vito Luigi Colona
- Rare Diseases and Medical Genetics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Christine Fauth
- Institute for Human Genetics, Medical University Innsbruck, 6020, Innsbruck, Austria
| | - Melissa Bellini
- Pediatrics and Neonatology, Gugliemo da Saliceto Hospital, 29121, Piacenza, Italy
| | - Giacomo Biasucci
- Pediatrics and Neonatology, Gugliemo da Saliceto Hospital, 29121, Piacenza, Italy
| | - Lorenzo Sinibaldi
- Rare Diseases and Medical Genetics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Silvana Briuglia
- Genetics and Pharmacogenetics, Ospedale Universitario "Gaetano Martino", 98125, Messina, Italy
| | - Andrea Gazzin
- Pediatric Clinical Genetics, Ospedale Pediatrico "Regina Margherita", 10126, Torino, Italy
| | - Diana Carli
- Department of Medical Sciences, Università of Torino, 10126, Torino, Italy
| | - Luigi Memo
- Medical Genetics, Institute for Maternal and Child Health-IRCCS, Burlo Garofolo, 34127, Trieste, Italy
| | - Eva Trevisson
- Department of Women's and Children's Health, Università di Padova, 35128, Padova, Italy
| | - Concetta Schiavariello
- Department of Pediatrics, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138, Bologna, Italy
| | - Maria Luca
- Department of Medical Sciences, Università of Torino, 10126, Torino, Italy
| | - Antonio Novelli
- Translational Cytogenomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Caroline Michot
- Center for Skeletal Dysplasia, Necker-Enfants Malades Hospital, Paris Cité University, INSERM UMR 1163, Imagine Institute, 75015, Paris, France
| | - Anne Sweertvaegher
- Service de Pédiatrie, Centre hospitalier de Saint-Quentin, 02321, Saint-Quentin, France
| | - David Germanaud
- Département de Génétique, CEA Paris-Saclay, NeuroSpin, Gif-sur-Yvette, France
- Service de Génétique Clinique, AP-HP, Hôpital Robert-Debré, 75019, Paris, France
| | - Emanuela Scarano
- Department of Pediatrics, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138, Bologna, Italy
| | - Alessandro De Luca
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013, San Giovanni, Rotondo, Italy
| | - Giuseppe Zampino
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
- Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, 39120, Magdeburg, Germany
| | - Alessandro Mussa
- Department of Medical Sciences, Università of Torino, 10126, Torino, Italy
| | - Bruno Dallapiccola
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Helene Cavé
- Service de de Génétique Moléculaire Hôpital Robert Debré, GHU AP-HP Nord - Université Paris Cité, INSERM UMR_S1131, Institut Universitaire d'Hématologie, Université Paris Cité, Paris-Cité, 75019, Paris, France
| | - Maria Cristina Digilio
- Rare Diseases and Medical Genetics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy.
| |
Collapse
|
2
|
Farhangi S, Gòdia M, Derks MFL, Harlizius B, Dibbits B, González-Prendes R, Crooijmans RPMA, Madsen O, Groenen MAM. Expression genome-wide association study identifies key regulatory variants enriched with metabolic and immune functions in four porcine tissues. BMC Genomics 2024; 25:684. [PMID: 38992576 PMCID: PMC11238464 DOI: 10.1186/s12864-024-10583-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Integration of high throughput DNA genotyping and RNA-sequencing data enables the discovery of genomic regions that regulate gene expression, known as expression quantitative trait loci (eQTL). In pigs, efforts to date have been mainly focused on purebred lines for traits with commercial relevance as such growth and meat quality. However, little is known on genetic variants and mechanisms associated with the robustness of an animal, thus its overall health status. Here, the liver, lung, spleen, and muscle transcriptomes of 100 three-way crossbred female finishers were studied, with the aim of identifying novel eQTL regulatory regions and transcription factors (TFs) associated with regulation of porcine metabolism and health-related traits. RESULTS An expression genome-wide association study with 535,896 genotypes and the expression of 12,680 genes in liver, 13,310 genes in lung, 12,650 genes in spleen, and 12,595 genes in muscle resulted in 4,293, 10,630, 4,533, and 6,871 eQTL regions for each of these tissues, respectively. Although only a small fraction of the eQTLs were annotated as cis-eQTLs, these presented a higher number of polymorphisms per region and significantly stronger associations with their target gene compared to trans-eQTLs. Between 20 and 115 eQTL hotspots were identified across the four tissues. Interestingly, these were all enriched for immune-related biological processes. In spleen, two TFs were identified: ERF and ZNF45, with key roles in regulation of gene expression. CONCLUSIONS This study provides a comprehensive analysis with more than 26,000 eQTL regions identified that are now publicly available. The genomic regions and their variants were mostly associated with tissue-specific regulatory roles. However, some shared regions provide new insights into the complex regulation of genes and their interactions that are involved with important traits related to metabolism and immunity.
Collapse
Affiliation(s)
- Samin Farhangi
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Marta Gòdia
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands.
| | - Martijn F L Derks
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
- Topigs Norsvin Research Center, 's-Hertogenbosch, The Netherlands
| | | | - Bert Dibbits
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Rayner González-Prendes
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
- Ausnutria BV, Zwolle, The Netherlands
| | | | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| |
Collapse
|
3
|
Lackner A, Müller M, Gamperl M, Stoeva D, Langmann O, Papuchova H, Roitinger E, Dürnberger G, Imre R, Mechtler K, Latos PA. The Fgf/Erf/NCoR1/2 repressive axis controls trophoblast cell fate. Nat Commun 2023; 14:2559. [PMID: 37137875 DOI: 10.1038/s41467-023-38101-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/15/2023] [Indexed: 05/05/2023] Open
Abstract
Placental development relies on coordinated cell fate decisions governed by signalling inputs. However, little is known about how signalling cues are transformed into repressive mechanisms triggering lineage-specific transcriptional signatures. Here, we demonstrate that upon inhibition of the Fgf/Erk pathway in mouse trophoblast stem cells (TSCs), the Ets2 repressor factor (Erf) interacts with the Nuclear Receptor Co-Repressor Complex 1 and 2 (NCoR1/2) and recruits it to key trophoblast genes. Genetic ablation of Erf or Tbl1x (a component of the NCoR1/2 complex) abrogates the Erf/NCoR1/2 interaction. This leads to mis-expression of Erf/NCoR1/2 target genes, resulting in a TSC differentiation defect. Mechanistically, Erf regulates expression of these genes by recruiting the NCoR1/2 complex and decommissioning their H3K27ac-dependent enhancers. Our findings uncover how the Fgf/Erf/NCoR1/2 repressive axis governs cell fate and placental development, providing a paradigm for Fgf-mediated transcriptional control.
Collapse
Affiliation(s)
- Andreas Lackner
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090, Vienna, Austria
| | - Michael Müller
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090, Vienna, Austria
| | - Magdalena Gamperl
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090, Vienna, Austria
| | - Delyana Stoeva
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090, Vienna, Austria
| | - Olivia Langmann
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090, Vienna, Austria
| | - Henrieta Papuchova
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090, Vienna, Austria
| | | | | | - Richard Imre
- Institute of Molecular Pathology, A-1030, Vienna, Austria
| | - Karl Mechtler
- Institute of Molecular Pathology, A-1030, Vienna, Austria
| | - Paulina A Latos
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090, Vienna, Austria.
| |
Collapse
|
4
|
Vogiatzi A, Keklikoglou K, Makris K, Argyrou DS, Zacharopoulos A, Sotiropoulou V, Parthenios N, Gkikas A, Kokkori M, Richardson MSW, Fenwick AL, Archontidi S, Arvanitidis C, Robertson J, Parthenios J, Zacharakis G, Twigg SRF, Wilkie AOM, Mavrothalassitis G. Development of Erf-Mediated Craniosynostosis and Pharmacological Amelioration. Int J Mol Sci 2023; 24:7961. [PMID: 37175668 PMCID: PMC10178537 DOI: 10.3390/ijms24097961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/19/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
ETS2 repressor factor (ERF) insufficiency causes craniosynostosis (CRS4) in humans and mice. ERF is an ETS domain transcriptional repressor regulated by Erk1/2 phosphorylation via nucleo-cytoplasmic shuttling. Here, we analyze the onset and development of the craniosynostosis phenotype in an Erf-insufficient mouse model and evaluate the potential of the residual Erf activity augmented by pharmacological compounds to ameliorate the disease. Erf insufficiency appears to cause an initially compromised frontal bone formation and subsequent multisuture synostosis, reflecting distinct roles of Erf on the cells that give rise to skull and facial bones. We treated animals with Mek1/2 and nuclear export inhibitors, U0126 and KPT-330, respectively, to increase Erf activity by two independent pathways. We implemented both a low dosage locally over the calvaria and a systemic drug administration scheme to evaluate the possible indirect effects from other systems and minimize toxicity. The treatment of mice with either the inhibitors or the administration scheme alleviated the synostosis phenotype with minimal adverse effects. Our data suggest that the ERF level is an important regulator of cranial bone development and that pharmacological modulation of its activity may represent a valid intervention approach both in CRS4 and in other syndromic forms of craniosynostosis mediated by the FGFR-RAS-ERK-ERF pathway.
Collapse
Affiliation(s)
- Angeliki Vogiatzi
- Medical School, University of Crete, 71003 Heraklion, Crete, Greece
- IMBB, FORTH, 71003 Heraklion, Crete, Greece
| | - Kleoniki Keklikoglou
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), P.O. Box 2214, 71003 Heraklion, Crete, Greece
- Biology Department, University of Crete, 71003 Heraklion, Crete, Greece
| | | | | | | | | | | | - Angelos Gkikas
- Medical School, University of Crete, 71003 Heraklion, Crete, Greece
| | - Maria Kokkori
- Medical School, University of Crete, 71003 Heraklion, Crete, Greece
| | - Melodie S. W. Richardson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Aimée L. Fenwick
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Sofia Archontidi
- Medical School, University of Crete, 71003 Heraklion, Crete, Greece
| | - Christos Arvanitidis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), P.O. Box 2214, 71003 Heraklion, Crete, Greece
- LifeWatch ERIC, Sector II-II, Plaza de España, 41071 Seville, Spain
| | - Jeremy Robertson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | | | | | - Stephen R. F. Twigg
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Andrew O. M. Wilkie
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - George Mavrothalassitis
- Medical School, University of Crete, 71003 Heraklion, Crete, Greece
- IMBB, FORTH, 71003 Heraklion, Crete, Greece
| |
Collapse
|
5
|
Yurduseven K, Babal YK, Celik E, Kerman BE, Kurnaz IA. Multiple Sclerosis Biomarker Candidates Revealed by Cell-Type-Specific Interactome Analysis. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:305-317. [PMID: 35483054 DOI: 10.1089/omi.2022.0023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Multiple sclerosis (MS) is a demyelinating disorder that affects multiple regions of the central nervous system such as the brain, spinal cord, and optic nerves. Susceptibility to MS, as well as disease progression rates, displays marked patient-to-patient variability. To date, biomarkers that forecast differences in clinical phenotypes and outcomes have been limited. In this context, cell-type-specific interactome analyses offer important prospects and hope for novel diagnostics and therapeutics. We report here an original study using bioinformatic analysis of MS data sets that revealed interaction profiles as well as specific hub proteins in white matter (WM) and gray matter (GM) that appear critical for disease mechanisms. First, cell-type-specific interactome analyses suggested that while interactions within the WM were focused on oligodendrocytes, interactions within the GM were mostly neuron centric. Second, hub proteins such as APP, EGLN3, PTEN, and LRRK2 were identified to be differentially regulated in MS data sets. Lastly, a comparison of the brain and peripheral blood samples identified biomarker candidates such as NRGN, CRTC1, CDC42, and IFITM3 to be differentially expressed in different types of MS. These findings offer a unique cell-type-specific cell-to-cell interaction network in MS and identify potential biomarkers by comparative analysis of the brain and the blood transcriptomics. From a study design and methodology perspective, we suggest that the cell-type-specific interactome analysis is an important systems science frontier that might offer new insights on other neurodegenerative and brain disorders as well.
Collapse
Affiliation(s)
- Kübra Yurduseven
- Institute of Biotechnology, Gebze Technical University, Kocaeli, Turkey
- Regenerative and Restorative Medical Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Yigit Koray Babal
- Institute of Biotechnology, Gebze Technical University, Kocaeli, Turkey
| | - Esref Celik
- Regenerative and Restorative Medical Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Bilal Ersen Kerman
- Regenerative and Restorative Medical Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Işıl Aksan Kurnaz
- Institute of Biotechnology, Gebze Technical University, Kocaeli, Turkey
| |
Collapse
|
6
|
Tsiomita S, Liveri EM, Vardaka P, Vogiatzi A, Skiadaresis A, Saridis G, Tsigkas I, Michaelidis TM, Mavrothalassitis G, Thyphronitis G. ETS2 repressor factor (ERF) is involved in T lymphocyte maturation acting as regulator of thymocyte lineage commitment. J Leukoc Biol 2022; 112:641-657. [PMID: 35258130 DOI: 10.1002/jlb.1a0720-439r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 11/30/2021] [Indexed: 11/12/2022] Open
Abstract
Thymocyte differentiation and lineage commitment is regulated by an extensive network of transcription factors and signaling molecules among which Erk plays a central role. However, Erk effectors as well as the molecular mechanisms underlying this network are not well understood. Erf is a ubiquitously expressed transcriptional repressor regulated by Erk-dependent phosphorylation. Here, we investigated the role of Erf in T cell maturation and lineage commitment, using a double-fluorescent Erf-floxed mouse to produce thymus-specific Erf knockouts. We observed significant accumulation of thymocytes in the CD4/CD8 DP stage, followed by a significant reduction in CD4SP cells, a trend for lower CD8SP cell frequency, and an elevated percentage of γδ expressing thymocytes in Erf-deficient mice. Also, an elevated number of CD69+ TCRβ+ cells indicates that thymocytes undergoing positive selection accumulate at this stage. The expression of transcription factors Gata3, ThPOK, and Socs1 that promote CD4+ cell commitment was significantly decreased in Erf-deficient mice. These findings suggest that Erf is involved in T cell maturation, acting as a positive regulator during CD4 and eventually CD8 lineage commitment, while negatively regulates the production of γδ T cells. In addition, Erf-deficient mice displayed decreased percentages of CD4+ and CD8+ splenocytes and elevated levels of IL-4 indicating that Erf may have an additional role in the homeostasis, differentiation, and immunologic response of helper and cytotoxic T cells in the periphery. Overall, our results show, for the first time, Erf's involvement in T cell biology suggesting that Erf acts as a potential regulator during thymocyte maturation and thymocyte lineage commitment, in γδ T cell generation, as well as in Th cell differentiation.
Collapse
Affiliation(s)
- Spyridoula Tsiomita
- Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece
| | - Effrosyni Maria Liveri
- Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece
| | - Panagiota Vardaka
- Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece
| | - Angeliki Vogiatzi
- Department of Medicine, Medical School, University of Crete, Heraklion, Greece
| | - Argyris Skiadaresis
- Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece
| | - George Saridis
- Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece
| | - Ioannis Tsigkas
- Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece.,Department of Biomedical Research, Institute of Molecular Biology & Biotechnology, Foundation for Research and Technology-Hellas, Ioannina, Greece
| | - Theologos M Michaelidis
- Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece.,Department of Biomedical Research, Institute of Molecular Biology & Biotechnology, Foundation for Research and Technology-Hellas, Ioannina, Greece
| | - George Mavrothalassitis
- Department of Medicine, Medical School, University of Crete, Heraklion, Greece.,IMBB, FORTH, Heraklion, Crete, Greece
| | - George Thyphronitis
- Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece
| |
Collapse
|
7
|
Vogiatzi A, Baltsavia I, Dialynas E, Theodorou V, Zhou Y, Deligianni E, Iliopoulos I, Wilkie AOM, Twigg SRF, Mavrothalassitis G. Erf Affects Commitment and Differentiation of Osteoprogenitor Cells in Cranial Sutures via the Retinoic Acid Pathway. Mol Cell Biol 2021; 41:e0014921. [PMID: 33972395 PMCID: PMC8300784 DOI: 10.1128/mcb.00149-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/22/2021] [Accepted: 04/29/2021] [Indexed: 12/13/2022] Open
Abstract
ETS2 repressor factor (ERF) haploinsufficiency causes late-onset craniosynostosis (CRS) (OMIM entry 600775; CRS4) in humans, while in mice Erf insufficiency also leads to a similar multisuture synostosis phenotype preceded by mildly reduced calvarium ossification. However, neither the cell types affected nor the effects per se have been identified so far. Here, we establish an ex vivo system for the expansion of suture-derived mesenchymal stem and progenitor cells (sdMSCs) and analyze the role of Erf levels in their differentiation. Cellular data suggest that Erf insufficiency specifically decreases osteogenic differentiation of sdMSCs, resulting in the initially delayed mineralization of the calvarium. Transcriptome analysis indicates that Erf is required for efficient osteogenic lineage commitment of sdMSCs. Elevated retinoic acid catabolism due to increased levels of the cytochrome P450 superfamily member Cyp26b1 as a result of decreased Erf levels appears to be the underlying mechanism leading to defective differentiation. Exogenous addition of retinoic acid can rescue the osteogenic differentiation defect, suggesting that Erf affects cranial bone mineralization during skull development through retinoic acid gradient regulation.
Collapse
Affiliation(s)
| | | | | | | | - Yan Zhou
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | | | | | - Andrew O. M. Wilkie
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Stephen R. F. Twigg
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - George Mavrothalassitis
- Medical School, University of Crete, Heraklion, Crete, Greece
- IMBB, FORTH, Heraklion, Crete, Greece
| |
Collapse
|
8
|
Bao X, Zhang X, Wang L, Wang Z, Huang J, Zhang Q, Ye Y, Liu Y, Chen D, Zuo Y, Liu Q, Xu P, Huang B, Fang J, Lao J, Feng X, Li Y, Kurita R, Nakamura Y, Yu W, Ju C, Huang C, Mohandas N, Li D, Zhao C, Xu X. Epigenetic inactivation of ERF reactivates γ-globin expression in β-thalassemia. Am J Hum Genet 2021; 108:709-721. [PMID: 33735615 DOI: 10.1016/j.ajhg.2021.03.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/01/2021] [Indexed: 12/16/2022] Open
Abstract
The fetal-to-adult hemoglobin switch is regulated in a developmental stage-specific manner and reactivation of fetal hemoglobin (HbF) has therapeutic implications for treatment of β-thalassemia and sickle cell anemia, two major global health problems. Although significant progress has been made in our understanding of the molecular mechanism of the fetal-to-adult hemoglobin switch, the mechanism of epigenetic regulation of HbF silencing remains to be fully defined. Here, we performed whole-genome bisulfite sequencing and RNA sequencing analysis of the bone marrow-derived GYPA+ erythroid cells from β-thalassemia-affected individuals with widely varying levels of HbF groups (HbF ≥ 95th percentile or HbF ≤ 5th percentile) to screen epigenetic modulators of HbF and phenotypic diversity of β-thalassemia. We identified an ETS2 repressor factor encoded by ERF, whose promoter hypermethylation and mRNA downregulation are associated with high HbF levels in β-thalassemia. We further observed that hypermethylation of the ERF promoter mediated by enrichment of DNMT3A leads to demethylation of γ-globin genes and attenuation of binding of ERF on the HBG promoter and eventually re-activation of HbF in β-thalassemia. We demonstrated that ERF depletion markedly increased HbF production in human CD34+ erythroid progenitor cells, HUDEP-2 cell lines, and transplanted NCG-Kit-V831M mice. ERF represses γ-globin expression by directly binding to two consensus motifs regulating γ-globin gene expression. Importantly, ERF depletion did not affect maturation of erythroid cells. Identification of alterations in DNA methylation of ERF as a modulator of HbF synthesis opens up therapeutic targets for β-hemoglobinopathies.
Collapse
|
9
|
Altered microRNA expression links IL6 and TNF-induced inflammaging with myeloid malignancy in humans and mice. Blood 2021; 135:2235-2251. [PMID: 32384151 DOI: 10.1182/blood.2019003105] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/20/2020] [Indexed: 12/14/2022] Open
Abstract
Aging is associated with significant changes in the hematopoietic system, including increased inflammation, impaired hematopoietic stem cell (HSC) function, and increased incidence of myeloid malignancy. Inflammation of aging ("inflammaging") has been proposed as a driver of age-related changes in HSC function and myeloid malignancy, but mechanisms linking these phenomena remain poorly defined. We identified loss of miR-146a as driving aging-associated inflammation in AML patients. miR-146a expression declined in old wild-type mice, and loss of miR-146a promoted premature HSC aging and inflammation in young miR-146a-null mice, preceding development of aging-associated myeloid malignancy. Using single-cell assays of HSC quiescence, stemness, differentiation potential, and epigenetic state to probe HSC function and population structure, we found that loss of miR-146a depleted a subpopulation of primitive, quiescent HSCs. DNA methylation and transcriptome profiling implicated NF-κB, IL6, and TNF as potential drivers of HSC dysfunction, activating an inflammatory signaling relay promoting IL6 and TNF secretion from mature miR-146a-/- myeloid and lymphoid cells. Reducing inflammation by targeting Il6 or Tnf was sufficient to restore single-cell measures of miR-146a-/- HSC function and subpopulation structure and reduced the incidence of hematological malignancy in miR-146a-/- mice. miR-146a-/- HSCs exhibited enhanced sensitivity to IL6 stimulation, indicating that loss of miR-146a affects HSC function via both cell-extrinsic inflammatory signals and increased cell-intrinsic sensitivity to inflammation. Thus, loss of miR-146a regulates cell-extrinsic and -intrinsic mechanisms linking HSC inflammaging to the development of myeloid malignancy.
Collapse
|
10
|
Hou C, McCown C, Ivanov DN, Tsodikov OV. Structural Insight into the DNA Binding Function of Transcription Factor ERF. Biochemistry 2020; 59:10.1021/acs.biochem.0c00774. [PMID: 33175491 PMCID: PMC8110599 DOI: 10.1021/acs.biochem.0c00774] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
ETS family transcription factors control development of different cell types in humans, whereas deregulation of these proteins leads to severe developmental syndromes and cancers. One of a few members of the ETS family that are known to act solely as repressors, ERF, is required for normal osteogenesis and hematopoiesis. Another important function of ERF is acting as a tumor suppressor by antagonizing oncogenic fusions involving other ETS family factors. The structure of ERF and the DNA binding properties specific to this protein have not been elucidated. In this study, we determined two crystal structures of the complexes of the DNA binding domain of ERF with DNA. In one, ERF is in a distinct dimeric form, with Cys72 in a reduced state. In the other, two dimers of ERF are assembled into a tetramer that is additionally locked by two Cys72-Cys72 disulfide bonds across the dimers. In the tetramer, the ERF molecules are bound to a pseudocontinuous DNA on the same DNA face at two GGAA binding sites on opposite strands. Sedimentation velocity analysis showed that this tetrameric assembly forms on continuous DNA containing such tandem sites spaced by 7 bp. Our bioinformatic analysis of three previously reported sets of ERF binding loci across entire genomes showed that these loci were enriched in such 7 bp spaced tandem sites. Taken together, these results strongly suggest that the observed tetrameric assembly is a functional state of ERF in the human cell.
Collapse
Affiliation(s)
- Caixia Hou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA
| | - Claudia McCown
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Dmitri N. Ivanov
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Oleg V. Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA
| |
Collapse
|