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Aurigemma I, Lanzetta O, Cirino A, Allegretti S, Lania G, Ferrentino R, Poondi Krishnan V, Angelini C, Illingworth E, Baldini A. Endothelial gene regulatory elements associated with cardiopharyngeal lineage differentiation. Commun Biol 2024; 7:351. [PMID: 38514806 PMCID: PMC10957928 DOI: 10.1038/s42003-024-06017-8] [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: 07/21/2023] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
Endothelial cells (EC) differentiate from multiple sources, including the cardiopharyngeal mesoderm, which gives rise also to cardiac and branchiomeric muscles. The enhancers activated during endothelial differentiation within the cardiopharyngeal mesoderm are not completely known. Here, we use a cardiogenic mesoderm differentiation model that activates an endothelial transcription program to identify endothelial regulatory elements activated in early cardiogenic mesoderm. Integrating chromatin remodeling and gene expression data with available single-cell RNA-seq data from mouse embryos, we identify 101 putative regulatory elements of EC genes. We then apply a machine-learning strategy, trained on validated enhancers, to predict enhancers. Using this computational assay, we determine that 50% of these sequences are likely enhancers, some of which are already reported. We also identify a smaller set of regulatory elements of well-known EC genes and validate them using genetic and epigenetic perturbation. Finally, we integrate multiple data sources and computational tools to search for transcriptional factor binding motifs. In conclusion, we show EC regulatory sequences with a high likelihood to be enhancers, and we validate a subset of them using computational and cell culture models. Motif analyses show that the core EC transcription factors GATA/ETS/FOS is a likely driver of EC regulation in cardiopharyngeal mesoderm.
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Affiliation(s)
- Ilaria Aurigemma
- PhD program in Molecular Medicine and Medical Biotechnology, University Federico II, Via Sergio Pansini 5, 80131, Naples, Italy
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Italy
| | - Olga Lanzetta
- Institute of Genetics and Biophysics, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Andrea Cirino
- Institute of Genetics and Biophysics, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Sara Allegretti
- PhD program in Molecular Medicine and Medical Biotechnology, University Federico II, Via Sergio Pansini 5, 80131, Naples, Italy
| | - Gabriella Lania
- Institute of Genetics and Biophysics, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Rosa Ferrentino
- Institute of Genetics and Biophysics, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Varsha Poondi Krishnan
- Institute of Genetics and Biophysics, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Claudia Angelini
- Istituto Applicazioni del Calcolo, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Elizabeth Illingworth
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Italy
| | - Antonio Baldini
- PhD program in Molecular Medicine and Medical Biotechnology, University Federico II, Via Sergio Pansini 5, 80131, Naples, Italy.
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, Via Sergio Pansini 5, 80131, Naples, Italy.
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Cirino A, Aurigemma I, Franzese M, Lania G, Righelli D, Ferrentino R, Illingworth E, Angelini C, Baldini A. Chromatin and Transcriptional Response to Loss of TBX1 in Early Differentiation of Mouse Cells. Front Cell Dev Biol 2020; 8:571501. [PMID: 33015063 PMCID: PMC7505952 DOI: 10.3389/fcell.2020.571501] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 06/11/2020] [Accepted: 08/18/2020] [Indexed: 12/19/2022] Open
Abstract
The T-box transcription factor TBX1 has critical roles in the cardiopharyngeal lineage and the gene is haploinsufficient in DiGeorge syndrome, a typical developmental anomaly of the pharyngeal apparatus. Despite almost two decades of research, if and how TBX1 function triggers chromatin remodeling is not known. Here, we explored genome-wide gene expression and chromatin remodeling in two independent cellular models of Tbx1 loss of function, mouse embryonic carcinoma cells P19Cl6, and mouse embryonic stem cells (mESCs). The results of our study revealed that the loss or knockdown of TBX1 caused extensive transcriptional changes, some of which were cell type-specific, some were in common between the two models. However, unexpectedly we observed only limited chromatin changes in both systems. In P19Cl6 cells, differentially accessible regions (DARs) were not enriched in T-BOX binding motifs; in contrast, in mESCs, 34% (n = 47) of all DARs included a T-BOX binding motif and almost all of them gained accessibility in Tbx1 -/- cells. In conclusion, despite a clear transcriptional response of our cell models to loss of TBX1 in early cell differentiation, chromatin changes were relatively modest.
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Affiliation(s)
- Andrea Cirino
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | - Ilaria Aurigemma
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
- Department of Chemistry and Biology, University of Salerno, Fisciano, Italy
| | - Monica Franzese
- Institute Applicazioni del Calcolo, National Research Council, Naples, Italy
| | - Gabriella Lania
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | - Dario Righelli
- Department of Chemistry and Biology, University of Salerno, Fisciano, Italy
| | - Rosa Ferrentino
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | | | - Claudia Angelini
- Institute Applicazioni del Calcolo, National Research Council, Naples, Italy
| | - Antonio Baldini
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
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Pane LS, Fulcoli FG, Cirino A, Altomonte A, Ferrentino R, Bilio M, Baldini A. Tbx1 represses Mef2c gene expression and is correlated with histone 3 deacetylation of the anterior heart field enhancer. Dis Model Mech 2018; 11:11/9/dmm029967. [PMID: 30166330 PMCID: PMC6176997 DOI: 10.1242/dmm.029967] [Citation(s) in RCA: 9] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/09/2018] [Indexed: 12/19/2022] Open
Abstract
The TBX1 gene is haploinsufficient in 22q11.2 deletion syndrome (22q11.2DS), and genetic evidence from human patients and mouse models points to a major role of this gene in the pathogenesis of this syndrome. Tbx1 can activate and repress transcription, and previous work has shown that one of its functions is to negatively modulate cardiomyocyte differentiation. Tbx1 occupies the anterior heart field (AHF) enhancer of the Mef2c gene, which encodes a key cardiac differentiation transcription factor. Here, we show that increased dosage of Tbx1 correlates with downregulation of Mef2c expression and reduced acetylation of its AHF enhancer in cultured mouse myoblasts. Consistently, 22q11.2DS-derived and in vitro-differentiated human induced pluripotent stem cells (hiPSCs) expressed higher levels of MEF2C and showed increased AHF acetylation, compared with hiPSCs from a healthy donor. Most importantly, we show that in mouse embryos, loss of Tbx1 enhances the expression of the Mef2c-AHF-Cre transgene in a specific region of the splanchnic mesoderm, and in a dosage-dependent manner, providing an in vivo correlate of our cell culture data. These results indicate that Tbx1 regulates the Mef2c AHF enhancer by inducing histone deacetylation.
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Affiliation(s)
- Luna Simona Pane
- CNR Institute of Genetics and Biophysics Adriano Buzzati Traverso, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Filomena Gabriella Fulcoli
- CNR Institute of Genetics and Biophysics Adriano Buzzati Traverso, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Andrea Cirino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Napoli, Italy
| | - Alessandra Altomonte
- CNR Institute of Genetics and Biophysics Adriano Buzzati Traverso, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Rosa Ferrentino
- CNR Institute of Genetics and Biophysics Adriano Buzzati Traverso, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Marchesa Bilio
- CNR Institute of Genetics and Biophysics Adriano Buzzati Traverso, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Antonio Baldini
- CNR Institute of Genetics and Biophysics Adriano Buzzati Traverso, Via Pietro Castellino 111, 80131 Napoli, Italy .,Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Napoli, Italy
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Cuddy S, Kaynor E, Nutakki K, Cirino A, Ho CY, Lakdawala NK. 1469Left atrial remodelling in hypertrophic cardiomyopathy, contributing factors and associated outcomes. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy565.1469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- S Cuddy
- Brigham and Women's Hospital, Non-invasive Cardiovascular Imaging, Boston, United States of America
| | - E Kaynor
- Brigham and Women's Hospital, Cardiology, Boston, United States of America
| | - K Nutakki
- Brigham and Women's Hospital, Cardiology, Boston, United States of America
| | - A Cirino
- Brigham and Women's Hospital, Cardiology, Boston, United States of America
| | - C Y Ho
- Brigham and Women's Hospital, Cardiology, Boston, United States of America
| | - N K Lakdawala
- Brigham and Women's Hospital, Cardiology, Boston, United States of America
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Capasso M, McDaniel LD, Cimmino F, Cirino A, Formicola D, Russell MR, Raman P, Cole KA, Diskin SJ. The functional variant rs34330 of CDKN1B is associated with risk of neuroblastoma. J Cell Mol Med 2017; 21:3224-3230. [PMID: 28667701 PMCID: PMC5706517 DOI: 10.1111/jcmm.13226] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [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: 07/30/2016] [Accepted: 04/07/2017] [Indexed: 11/30/2022] Open
Abstract
The genetic aetiology of sporadic neuroblastoma is still largely unknown. We have identified diverse neuroblastoma susceptibility loci by genomewide association studies (GWASs); however, additional SNPs that likely contribute to neuroblastoma susceptibility prompted this investigation for identification of additional variants that are likely hidden among signals discarded by the multiple testing corrections used in the analysis of genomewide data. There is evidence suggesting the CDKN1B, coding for the cycle inhibitor p27Kip1, is involved in neuroblastoma. We thus assess whether genetic variants of CDKN1B are associated with neuroblastoma. We imputed all possible genotypes across CDKN1B locus on a discovery case series of 2101 neuroblastoma patients and 4202 genetically matched controls of European ancestry. The most significantly associated rs34330 was analysed in an independent Italian cohort of 311 cases and 709 controls. In vitro functional analysis was carried out in HEK293T and in neuroblastoma cell line SHEP‐2, both transfected with pGL3‐CDKN1B‐CC or pGL3‐CDKN1B‐TT constructs. We identified an association of the rs34330 T allele (‐79C/T) with the neuroblastoma risk (Pcombined = 0.002; OR = 1.17). The risk allele (T) of this single nucleotide polymorphism led to a lower transcription rate in cells transfected with a luciferase reporter driven by the polymorphic p27Kip1 promoter (P < 0.05). Three independent sets of neuroblastoma tumours carrying ‐79TT genotype showed a tendency towards lower CDKN1B mRNA levels. Our study shows that a functional variant, associated with a reduced CDKN1B gene transcription, influences neuroblastoma susceptibility.
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Affiliation(s)
- Mario Capasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,Istituto di Ricerca Diagnostica e Nucleare, IRCCS SDN, Naples, Italy
| | - Lee D McDaniel
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Flora Cimmino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Andrea Cirino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Daniela Formicola
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Mike R Russell
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Pichai Raman
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kristina A Cole
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sharon J Diskin
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
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Bartolotta TV, Ienzi R, Cirino A, Genova C, Ienzi F, Pitarresi D, Safina E, Midiri M. Characterisation of indeterminate focal breast lesions on grey-scale ultrasound: role of ultrasound elastography. Radiol Med 2011; 116:1027-38. [DOI: 10.1007/s11547-011-0648-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 08/30/2010] [Indexed: 12/21/2022]
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Ghannoum M, Long L, Kim H, Rotondo V, Cirino A, Sheehan D. O199 Efficacy of linezolid in the treatment of biofilm-associated infection using a rabbit model of methicillin-resistant Staphylococcus aureus catheter biofilm. Int J Antimicrob Agents 2007. [DOI: 10.1016/s0924-8579(07)70132-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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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Ienzi R, Cirino A, Galia M, Caruso G, Lo Casto A. [Intracystic papillary carcinoma of the breast: mammographic, pneumocystographic, sonographic, power-Doppler and MR appearance: a case report]. Radiol Med 2001; 102:403-5. [PMID: 11779992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Affiliation(s)
- R Ienzi
- Dipartimento d Biotecnologie Mediche e Medicina Legale, Sezione di Scienze Biomediche, Università degli Studi di Palermo, Italy
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Cottini E, Raspagliesi M, Giacone G, Cosentino M, Rando G, Vintaloro G, Cirino A, Spagnoli R. [Longitudinal echocardiographic study of HIV positive patients]. Minerva Cardioangiol 1997; 45:573-9. [PMID: 9549291] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND From May 1992 to June 1996 the authors have studied a group of 39 subjects with positive anti-HIV, with echo 2D color Doppler examination, to evaluate with semi-annual controls, the wide variety of cardiac complications in the various phases of clinical evolution of the illness. METHODS At the moment of recruiting, all the subjects with HIV infection were asymptomatic A1 (HIV + As). The patients whose average age was 29 +/- 5, were composed of 60% drug addicts, 17% homosexuals, 8% haemophiliacs and for the 15% heterosexual. RESULTS The most frequent cardiac complications are represented by hypokinesia of the left ventricle (h-aLV) and by pericardial effusion (PE); more rarely of endocardial vegetations (EV), dilatation of the left ventricle (dLV) and tricuspid insufficiency (TI). The entity of damage and the number of cases observed, are correlated with the grade of clinical severity of the illness. CONCLUSIONS In accordance with the literature data, cardiac pathologies, particularly in the first phases of the illness, are asymptomatic or paucisymptomatic, making the clinical-instrumental observation of the patient useful also in cardiology.
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Affiliation(s)
- E Cottini
- Istituto di Clinica Medica II L. Condorellio, Università degli Studi, Catania
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Fiore CE, Dieli M, Caschetto S, Cirino A, Cottini E. Relative deficiency in circulating levels of insulin-like growth factor I (IGF-I) during long-term treatment with a GnRH agonist. Horm Metab Res 1997; 29:472-4. [PMID: 9370120 DOI: 10.1055/s-2007-979081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- C E Fiore
- Second Department of Internal Medicine, University of Catania, Italy
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Cottini E, Giacone G, Cosentino M, Cirino A, Rando G, Vintaloro G. Evaluation of left ventricular diastolic function by pulmonary venous and mitral flow velocity patterns in endurance veteran athletes. Arch Gerontol Geriatr 1996; 22 Suppl 1:179-86. [DOI: 10.1016/0167-4943(96)86932-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Lagalla R, Triolo L, Brancato C, Canzone G, Cirino A. [Ultrasonic diagnosis of fetal malformations]. Radiol Med 1990; 80:915-25. [PMID: 2281178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- R Lagalla
- Istituto di Radiologia, Università di Palermo
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Carolina A, Caruso G, Cirino A, Di Maria A, Iovane A, Toscano P, Leo P. [Echographic study of cryptorchidism]. G Chir 1990; 11:491-3. [PMID: 1981140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The authors, after a nosologic review of cryptorchidism, illustrate their positive diagnostic experience with ultrasound. Limits as well as clinical advantages, in relation to the diagnosis and follow-up, are also described.
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Affiliation(s)
- A Carolina
- Radiologia Generale C.L.O., Università degli Studi di Palermo
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