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Caetano da Silva C, Macias Trevino C, Mitchell J, Murali H, Tsimbal C, Dalessandro E, Carroll SH, Kochhar S, Curtis SW, Cheng CHE, Wang F, Kutschera E, Carstens RP, Xing Y, Wang K, Leslie EJ, Liao EC. Functional analysis of ESRP1/2 gene variants and CTNND1 isoforms in orofacial cleft pathogenesis. Commun Biol 2024; 7:1040. [PMID: 39179789 PMCID: PMC11344038 DOI: 10.1038/s42003-024-06715-3] [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: 02/15/2024] [Accepted: 08/09/2024] [Indexed: 08/26/2024] Open
Abstract
Orofacial cleft (OFC) is a common human congenital anomaly. Epithelial-specific RNA splicing regulators ESRP1 and ESRP2 regulate craniofacial morphogenesis and their disruption result in OFC in zebrafish, mouse and humans. Using esrp1/2 mutant zebrafish and murine Py2T cell line models, we functionally tested the pathogenicity of human ESRP1/2 gene variants. We found that many variants predicted by in silico methods to be pathogenic were functionally benign. Esrp1 also regulates the alternative splicing of Ctnnd1 and these genes are co-expressed in the embryonic and oral epithelium. In fact, over-expression of ctnnd1 is sufficient to rescue morphogenesis of epithelial-derived structures in esrp1/2 zebrafish mutants. Additionally, we identified 13 CTNND1 variants from genome sequencing of OFC cohorts, confirming CTNND1 as a key gene in human OFC. This work highlights the importance of functional assessment of human gene variants and demonstrates the critical requirement of Esrp-Ctnnd1 acting in the embryonic epithelium to regulate palatogenesis.
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Affiliation(s)
- Caroline Caetano da Silva
- Center for Craniofacial Innovation, Division of Plastic and Reconstructive Surgery, Department of Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | | | - Hemma Murali
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Casey Tsimbal
- Center for Craniofacial Innovation, Division of Plastic and Reconstructive Surgery, Department of Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Shriners Hospital for Children, Tampa, FL, USA
| | - Eileen Dalessandro
- Center for Craniofacial Innovation, Division of Plastic and Reconstructive Surgery, Department of Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shannon H Carroll
- Center for Craniofacial Innovation, Division of Plastic and Reconstructive Surgery, Department of Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Shriners Hospital for Children, Tampa, FL, USA
| | - Simren Kochhar
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Sarah W Curtis
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Ching Hsun Eric Cheng
- Center for Craniofacial Innovation, Division of Plastic and Reconstructive Surgery, Department of Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Feng Wang
- Center for Genomic Medicine, Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eric Kutschera
- Center for Genomic Medicine, Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Russ P Carstens
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yi Xing
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Center for Genomic Medicine, Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kai Wang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric C Liao
- Center for Craniofacial Innovation, Division of Plastic and Reconstructive Surgery, Department of Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Harvard Medical School, Boston, MA, USA.
- Shriners Hospital for Children, Tampa, FL, USA.
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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2
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da Silva CC, Trevino CM, Mitchell J, Murali H, Tsimbal C, Dalessandro E, Carroll SH, Kochhar S, Curtis SW, Cheng CHE, Wang F, Kutschera E, Carstens RP, Xing Y, Wang K, Leslie EJ, Liao EC. Functional analysis of ESRP1/2 gene variants and CTNND1 isoforms in orofacial cleft pathogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601574. [PMID: 39005284 PMCID: PMC11245018 DOI: 10.1101/2024.07.02.601574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Orofacial cleft (OFC) is a common human congenital anomaly. Epithelial-specific RNA splicing regulators ESRP1 and ESRP2 regulate craniofacial morphogenesis and their disruption result in OFC in zebrafish, mouse and humans. Using esrp1/2 mutant zebrafish and murine Py2T cell line models, we functionally tested the pathogenicity of human ESRP1/2 gene variants. We found that many variants predicted by in silico methods to be pathogenic were functionally benign. Esrp1 also regulates the alternative splicing of Ctnnd1 and these genes are co-expressed in the embryonic and oral epithelium. In fact, over-expression of ctnnd1 is sufficient to rescue morphogenesis of epithelial-derived structures in esrp1/2 zebrafish mutants. Additionally, we identified 13 CTNND1 variants from genome sequencing of OFC cohorts, confirming CTNND1 as a key gene in human OFC. This work highlights the importance of functional assessment of human gene variants and demonstrates the critical requirement of Esrp-Ctnnd1 acting in the embryonic epithelium to regulate palatogenesis.
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Affiliation(s)
- Caroline Caetano da Silva
- Center for Craniofacial Innovation, Division of Plastic and Reconstructive Surgery, Department of Surgery, Children’s Hospital of Philadelphia, PA, USA
| | | | | | - Hemma Murali
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Casey Tsimbal
- Center for Craniofacial Innovation, Division of Plastic and Reconstructive Surgery, Department of Surgery, Children’s Hospital of Philadelphia, PA, USA
- Shriners Hospital for Children, Tampa, FL, USA
| | - Eileen Dalessandro
- Center for Craniofacial Innovation, Division of Plastic and Reconstructive Surgery, Department of Surgery, Children’s Hospital of Philadelphia, PA, USA
| | - Shannon H. Carroll
- Center for Craniofacial Innovation, Division of Plastic and Reconstructive Surgery, Department of Surgery, Children’s Hospital of Philadelphia, PA, USA
- Shriners Hospital for Children, Tampa, FL, USA
| | - Simren Kochhar
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Sarah W. Curtis
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Ching Hsun Eric Cheng
- Center for Craniofacial Innovation, Division of Plastic and Reconstructive Surgery, Department of Surgery, Children’s Hospital of Philadelphia, PA, USA
| | - Feng Wang
- Center for Genomic Medicine, Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, PA, USA
| | - Eric Kutschera
- Center for Genomic Medicine, Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, PA, USA
| | - Russ P. Carstens
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yi Xing
- Center for Genomic Medicine, Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kai Wang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Elizabeth J. Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric C. Liao
- Center for Craniofacial Innovation, Division of Plastic and Reconstructive Surgery, Department of Surgery, Children’s Hospital of Philadelphia, PA, USA
- Harvard Medical School, Boston, MA, USA
- Shriners Hospital for Children, Tampa, FL, USA
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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Lan Y, Jiang R. Mouse models in palate development and orofacial cleft research: Understanding the crucial role and regulation of epithelial integrity in facial and palate morphogenesis. Curr Top Dev Biol 2022; 148:13-50. [PMID: 35461563 PMCID: PMC9060390 DOI: 10.1016/bs.ctdb.2021.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cleft lip and cleft palate are common birth defects resulting from genetic and/or environmental perturbations of facial development in utero. Facial morphogenesis commences during early embryogenesis, with cranial neural crest cells interacting with the surface ectoderm to form initially partly separate facial primordia consisting of the medial and lateral nasal prominences, and paired maxillary and mandibular processes. As these facial primordia grow around the primitive oral cavity and merge toward the ventral midline, the surface ectoderm undergoes a critical differentiation step to form an outer layer of flattened and tightly connected periderm cells with a non-stick apical surface that prevents epithelial adhesion. Formation of the upper lip and palate requires spatiotemporally regulated inter-epithelial adhesions and subsequent dissolution of the intervening epithelial seam between the maxillary and medial/lateral nasal processes and between the palatal shelves. Proper regulation of epithelial integrity plays a paramount role during human facial development, as mutations in genes encoding epithelial adhesion molecules and their regulators have been associated with syndromic and non-syndromic orofacial clefts. In this chapter, we summarize mouse genetic studies that have been instrumental in unraveling the mechanisms regulating epithelial integrity and periderm differentiation during facial and palate development. Since proper epithelial integrity also plays crucial roles in wound healing and cancer, understanding the mechanisms regulating epithelial integrity during facial development have direct implications for improvement in clinical care of craniofacial patients.
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Affiliation(s)
- Yu Lan
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; Division of Plastic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Rulang Jiang
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; Division of Plastic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.
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Bishop MR, Diaz Perez KK, Sun M, Ho S, Chopra P, Mukhopadhyay N, Hetmanski JB, Taub MA, Moreno-Uribe LM, Valencia-Ramirez LC, Restrepo Muñeton CP, Wehby G, Hecht JT, Deleyiannis F, Weinberg SM, Wu-Chou YH, Chen PK, Brand H, Epstein MP, Ruczinski I, Murray JC, Beaty TH, Feingold E, Lipinski RJ, Cutler DJ, Marazita ML, Leslie EJ. Genome-wide Enrichment of De Novo Coding Mutations in Orofacial Cleft Trios. Am J Hum Genet 2020; 107:124-136. [PMID: 32574564 PMCID: PMC7332647 DOI: 10.1016/j.ajhg.2020.05.018] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/26/2020] [Indexed: 01/05/2023] Open
Abstract
Although de novo mutations (DNMs) are known to increase an individual's risk of congenital defects, DNMs have not been fully explored regarding orofacial clefts (OFCs), one of the most common human birth defects. Therefore, whole-genome sequencing of 756 child-parent trios of European, Colombian, and Taiwanese ancestry was performed to determine the contributions of coding DNMs to an individual's OFC risk. Overall, we identified a significant excess of loss-of-function DNMs in genes highly expressed in craniofacial tissues, as well as genes associated with known autosomal dominant OFC syndromes. This analysis also revealed roles for zinc-finger homeobox domain and SOX2-interacting genes in OFC etiology.
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Affiliation(s)
- Madison R. Bishop
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kimberly K. Diaz Perez
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Miranda Sun
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Samantha Ho
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nandita Mukhopadhyay
- Department of Oral Biology, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA 15219, USA
| | - Jacqueline B. Hetmanski
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Margaret A. Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Lina M. Moreno-Uribe
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA 52242, USA
| | | | | | - George Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA 52242, USA
| | - Jacqueline T. Hecht
- Department of Pediatrics, McGovern Medical School and School of Dentistry, UT Health at Houston, Houston, TX 77030, USA
| | | | - Seth M. Weinberg
- Department of Oral Biology, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA 15219, USA,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA
| | - Yah Huei Wu-Chou
- Department of Medical Research, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Philip K. Chen
- Craniofacial Centre, Taipei Medical University Hospital and Taipei Medical University, Taipei, Taiwan
| | - Harrison Brand
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Michael P. Epstein
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA
| | - Robert J. Lipinski
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - David J. Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mary L. Marazita
- Department of Oral Biology, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA 15219, USA,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA
| | - Elizabeth J. Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA,Corresponding author
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Liu H, Duncan K, Helverson A, Kumari P, Mumm C, Xiao Y, Carlson JC, Darbellay F, Visel A, Leslie E, Breheny P, Erives AJ, Cornell RA. Analysis of zebrafish periderm enhancers facilitates identification of a regulatory variant near human KRT8/18. eLife 2020; 9:e51325. [PMID: 32031521 PMCID: PMC7039683 DOI: 10.7554/elife.51325] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 02/06/2020] [Indexed: 12/18/2022] Open
Abstract
Genome-wide association studies for non-syndromic orofacial clefting (OFC) have identified single nucleotide polymorphisms (SNPs) at loci where the presumed risk-relevant gene is expressed in oral periderm. The functional subsets of such SNPs are difficult to predict because the sequence underpinnings of periderm enhancers are unknown. We applied ATAC-seq to models of human palate periderm, including zebrafish periderm, mouse embryonic palate epithelia, and a human oral epithelium cell line, and to complementary mesenchymal cell types. We identified sets of enhancers specific to the epithelial cells and trained gapped-kmer support-vector-machine classifiers on these sets. We used the classifiers to predict the effects of 14 OFC-associated SNPs at 12q13 near KRT18. All the classifiers picked the same SNP as having the strongest effect, but the significance was highest with the classifier trained on zebrafish periderm. Reporter and deletion analyses support this SNP as lying within a periderm enhancer regulating KRT18/KRT8 expression.
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Affiliation(s)
- Huan Liu
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan UniversityWuhanChina
- Department of Anatomy and Cell Biology, University of IowaIowa CityUnited States
- Department of Periodontology, School of Stomatology, Wuhan UniversityWuhanChina
| | - Kaylia Duncan
- Interdisciplinary Program in Molecular Medicine, University of IowaIowa CityUnited States
| | - Annika Helverson
- Department of Anatomy and Cell Biology, University of IowaIowa CityUnited States
| | - Priyanka Kumari
- Department of Anatomy and Cell Biology, University of IowaIowa CityUnited States
| | - Camille Mumm
- Department of Anatomy and Cell Biology, University of IowaIowa CityUnited States
| | - Yao Xiao
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan UniversityWuhanChina
| | | | - Fabrice Darbellay
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley LaboratoriesBerkeleyUnited States
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley LaboratoriesBerkeleyUnited States
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley LaboratoriesBerkeleyUnited States
- University of California, MercedMercedUnited States
| | - Elizabeth Leslie
- Department of Human Genetics, Emory University School of MedicineAtlantaGeorgia
| | - Patrick Breheny
- Department of Biostatistics, University of IowaIowa CityUnited States
| | - Albert J Erives
- Department of Biology, University of IowaIowa CityUnited States
| | - Robert A Cornell
- Department of Anatomy and Cell Biology, University of IowaIowa CityUnited States
- Interdisciplinary Program in Molecular Medicine, University of IowaIowa CityUnited States
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Scapoli L, Carinci F, Palmieri A, Cura F, Baj A, Beltramini G, Docimo R, Martinelli M. Copy number variation analysis of twin pairs discordant for cleft lip with or without cleft palate. Int J Immunopathol Pharmacol 2019; 33:2058738419855873. [PMID: 31663445 PMCID: PMC6822181 DOI: 10.1177/2058738419855873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Non-syndromic cleft lip with or without cleft palate (nsCL/P) is a frequent orofacial malformation. The comparison of concordance rate observed in monozygotic and dizygotic twins supports high level of heritability and a strong genetic component. However, phenotype concordance for orofacial cleft in monozygotic twins is about 50%. The aim of the present investigation was to detect postzygotic events that may account for discordance in monozygotic twins. High-density SNP microarrays hybridization was used to genotype two pairs of monozygotic twins discordant for nsCL/P. Discordant SNP genotypes and copy number variants were analyzed to identify genetic differences responsible of phenotype discrepancy. A number of differences were observed, none involving known nsCL/P candidate genes or genomic regions. Considering the limitation of the study, related to the small sample size and to the large-scale investigation method, the results suggest that the detection of discordant events in other monozygotic twin pairs would be remarkable and warrant further investigations.
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Affiliation(s)
- Luca Scapoli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Francesco Carinci
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Annalisa Palmieri
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Francesca Cura
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Alessandro Baj
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy.,Maxillofacial and Dental Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Giada Beltramini
- Maxillofacial and Dental Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Raffaella Docimo
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata," Rome, Italy
| | - Marcella Martinelli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
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