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Wang R, Liu X, Han Q, Wang X. Characterisation, evolution and expression analysis of the interferon regulatory factor (IRF) family from olive flounder (Paralichthys olivaceus) in response to Edwardsiella tarda infection and temperature stress. FISH & SHELLFISH IMMUNOLOGY 2023; 142:109115. [PMID: 37758096 DOI: 10.1016/j.fsi.2023.109115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/23/2023] [Accepted: 09/24/2023] [Indexed: 10/02/2023]
Abstract
Interferon regulatory factor (IRF) family involves in the transcriptional regulation of type I Interferons (IFNs) and IFN-stimulated genes (ISGs) and plays a critical role in cytokine signaling and immune response. However, systematic identification of the IRF gene family in teleost has been rarely reported. In this study, twelve IRF members, named PoIRF1, PoIRF2, PoIRF3, PoIRF4a, PoIRF4b, PoIRF5, PoIRF6, PoIRF7, PoIRF8, PoIRF9, PoIRF10 and PoIRF11, were identified from genome-wide data of olive flounder (Paralichthys olivaceus). Phylogenetic analysis indicated that PoIRFs could be classified into four clades, including IRF1 subfamily (PoIRF1, PoIRF11), IRF3 subfamily (PoIRF3, PoIRF7), IRF4 subfamily (PoIRF4a, PoIRF8, PoIRF9, PoIRF10) and IRF5 subfamily (PoIRF5, PoIRF6). They were evolutionarily related to their counterparts in other fish. Gene structure and motif analysis showed that PoIRFs protein sequences were highly conserved. Under normal physiological conditions, all PoIRFs were generally expressed in multiple developmental stages and healthy tissues. After E. tarda attack and temperature stress, twelve PoIRFs showed significant and different changes in mRNA levels. The expression of PoIRF1, PoIRF3, PoIRF4a, PoIRF5, PoIRF7, PoIRF8, PoIRF9, PoIRF10 and PoIRF11 could be markedly induced by E. tarda, indicating that they played a key role in the process of antibacterial immunity. Besides, temperature stress could significantly stimulate the expression of PoIRF3, PoIRF5, PoIRF6 and PoIRF7, indicating that they could transmit signals rapidly when the temperature changes. In conclusion, this study reported the molecular properties and expression analysis of PoIRFs, and explored their role in immune response, which laid a favorable foundation for further studies on the evolution and functional characteristics of the IRF family in teleost fish.
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Affiliation(s)
- Ruoxin Wang
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China.
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, China.
| | - Qingxi Han
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China.
| | - Xubo Wang
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China; National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Key Laboratory of Green Mariculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural, Ningbo University, China.
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Liang Y, Liu R, Zhang J, Chen Y, Shan S, Zhu Y, Yang G, Li H. Negative regulation of interferon regulatory factor 6 (IRF6) in interferon and NF-κB signalling pathways of common carp (Cyprinus carpio L.). BMC Vet Res 2022; 18:433. [PMID: 36503433 PMCID: PMC9743528 DOI: 10.1186/s12917-022-03538-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Interferon (IFN) regulatory factors (IRFs) is a kind of transcription factors, which play an important role in regulating the expression of type I IFN and related genes. In mammals, IRF6 is not relevant with IFN expression, while zebrafish IRF6 was reported to be a positive regulator of IFN expression and could be phosphorylated by both MyD88 and TBK1. However, the role of IRF6 in the immune response and IFN transcription of common carp is unknown. RESULTS In the present study, the cDNA of IRF6 gene (CcIRF6) was cloned from common carp using RACE technique, with a total length of 1905 bp, encoding 471 amino acid residues, which possesses two functional domains of DBD and IAD. Similarity analysis showed that CcIRF6 had more than 50% similarity with IRFs of other vertebrates, and had the highest similarity with grass carp and zebrafish, among which the DBD domain was much more conserved. The phylogenetic analysis showed that CcIRF6 is in the branch of Osteichthyes and has the closest relationship with grass carp. In healthy common carp, the CcIRF6 was expressed in all the examined tissues, with the highest level in the oral epithelium, and the lowest level in the head kidney. After intraperitoneal injection of poly(I:C) or Aeromonas hydrophila, the expression of CcIRF6 increased in spleen, head kidney, foregut and hindgut of common carp. Moreover, poly(I:C), LPS, PGN and flagellin induced the expression of CcIRF6 in peripheral leukocytes and head kidney leukocytes of common carp in vitro. In EPC cells, CcIRF6 inhibited the expression of some IFN-related genes and pro-inflammatory cytokines, and dual luciferase reporter assay showed that CcIRF6 reduced the activity of IFN and NF-κB reporter genes. CONCLUSIONS The present study suggests that CcIRF6 is involved in the antiviral and antibacterial immune response of common carp, and negatively regulate the expression of IFN and NF-κB signalling pathways, which provides a theoretical basis for the study and prevention of fish disease pathogenesis.
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Affiliation(s)
- Yaxin Liang
- grid.410585.d0000 0001 0495 1805Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, No. 88 East Wenhua Road, Jinan, 250014 China
| | - Rongrong Liu
- grid.410585.d0000 0001 0495 1805Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, No. 88 East Wenhua Road, Jinan, 250014 China
| | - Jiahui Zhang
- grid.410585.d0000 0001 0495 1805Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, No. 88 East Wenhua Road, Jinan, 250014 China
| | - Yixin Chen
- grid.410585.d0000 0001 0495 1805Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, No. 88 East Wenhua Road, Jinan, 250014 China
| | - Shijuan Shan
- grid.410585.d0000 0001 0495 1805Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, No. 88 East Wenhua Road, Jinan, 250014 China
| | - Yaoyao Zhu
- grid.449397.40000 0004 1790 3687College of Fisheries and Life Science, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya, 572022 China
| | - Guiwen Yang
- grid.410585.d0000 0001 0495 1805Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, No. 88 East Wenhua Road, Jinan, 250014 China
| | - Hua Li
- grid.410585.d0000 0001 0495 1805Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, No. 88 East Wenhua Road, Jinan, 250014 China
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Truong BT, Artinger KB. The power of zebrafish models for understanding the co-occurrence of craniofacial and limb disorders. Genesis 2021; 59:e23407. [PMID: 33393730 PMCID: PMC8153179 DOI: 10.1002/dvg.23407] [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: 10/23/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 12/30/2022]
Abstract
Craniofacial and limb defects are two of the most common congenital anomalies in the general population. Interestingly, these defects are not mutually exclusive. Many patients with craniofacial phenotypes, such as orofacial clefting and craniosynostosis, also present with limb defects, including polydactyly, syndactyly, brachydactyly, or ectrodactyly. The gene regulatory networks governing craniofacial and limb development initially seem distinct from one another, and yet these birth defects frequently occur together. Both developmental processes are highly conserved among vertebrates, and zebrafish have emerged as an advantageous model due to their high fecundity, relative ease of genetic manipulation, and transparency during development. Here we summarize studies that have used zebrafish models to study human syndromes that present with both craniofacial and limb phenotypes. We discuss the highly conserved processes of craniofacial and limb/fin development and describe recent zebrafish studies that have explored the function of genes associated with human syndromes with phenotypes in both structures. We attempt to identify commonalities between the two to help explain why craniofacial and limb anomalies often occur together.
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Affiliation(s)
- Brittany T. Truong
- Human Medical Genetics & Genomics Graduate Program, University of Colorado Denver Anschutz Medical Campus, Aurora, CO
- Department of Craniofacial Biology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO
| | - Kristin Bruk Artinger
- Department of Craniofacial Biology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO
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Alade AA, Buxo‐Martinez CJ, Mossey PA, Gowans LJ, Eshete MA, Adeyemo WL, Naicker T, Awotoye WA, Adeleke C, Busch T, Toraño AM, Bello CA, Soto M, Soto M, Ledesma R, Marquez M, Cordero JF, Lopez‐Del Valle LM, Salcedo MI, Debs N, Li M, Petrin A, Olotu J, Aldous C, Olutayo J, Ogunlewe MO, Abate F, Hailu T, Muhammed I, Gravem P, Deribew M, Gesses M, Hassan M, Pape J, Adeniyan OA, Obiri‐Yeboah S, Arthur FK, Oti AA, Olatosi O, Miller SE, Donkor P, Dunnwald MM, Marazita ML, Adeyemo AA, Murray JC, Butali A. Non-random distribution of deleterious mutations in the DNA and protein-binding domains of IRF6 are associated with Van Der Woude syndrome. Mol Genet Genomic Med 2020; 8:e1355. [PMID: 32558391 PMCID: PMC7434609 DOI: 10.1002/mgg3.1355] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/03/2020] [Accepted: 05/19/2020] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The development of the face occurs during the early days of intrauterine life by the formation of facial processes from the first Pharyngeal arch. Derangement in these well-organized fusion events results in Orofacial clefts (OFC). Van der Woude syndrome (VWS) is one of the most common causes of syndromic cleft lip and/or palate accounting for 2% of all cases. Mutations in the IRF6 gene account for 70% of cases with the majority of these mutations located in the DNA-binding (exon 3, 4) or protein-binding domains (exon 7-9). The current study was designed to update the list of IRF6 variants reported for VWS by compiling all the published mutations from 2013 to date as well as including the previously unreported VWS cases from Africa and Puerto Rico. METHODS We used PubMed with the search terms; "Van der Woude syndrome," "Popliteal pterygium syndrome," "IRF6," and "Orofacial cleft" to identify eligible studies. We compiled the CADD score for all the mutations to determine the percentage of deleterious variants. RESULTS Twenty-one new mutations were identified from nine papers. The majority of these mutations were in exon 4. Mutations in exon 3 and 4 had CADD scores between 20 and 30 and mutations in exon 7-9 had CADD scores between 30 and 40. The presence of higher CADD scores in the protein-binding domain (exon 7-9) further confirms the crucial role played by this domain in the function of IRF6. In the new cases, we identified five IRF6 mutations, three novel missense mutations (p.Phe36Tyr, p.Lys109Thr, and p.Gln438Leu), and two previously reported nonsense mutations (p.Ser424*and p.Arg250*). CONCLUSION Mutations in the protein and DNA-binding domains of IRF6 ranked among the top 0.1% and 1% most deleterious genetic mutations, respectively. Overall, these findings expand the range of VWS mutations and are important for diagnostic and counseling purposes.
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Affiliation(s)
- Azeez A. Alade
- Department of Oral Pathology, Radiology and MedicineCollege of DentistryUniversity of IowaIowa CityIAUSA
- Iowa Institute of Oral Health ResearchUniversity of IowaIowa CityIAUSA
- Department of EpidemiologyCollege of Public HealthUniversity of IowaIowa CityIAUSA
| | - Carmen J. Buxo‐Martinez
- Dental and Craniofacial Genomics CoreUniversity of Puerto Rico School of Dental MedicineSan JuanPuerto Rico
| | - Peter A. Mossey
- Department of OrthodonticsUniversity of DundeeDundeeUnited Kingdom
| | - Lord J.J. Gowans
- Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and TechnologyKumasiGhana
| | | | - Wasiu L. Adeyemo
- Department of Oral and Maxillofacial SurgeryUniversity of LagosLagosNigeria
| | - Thirona Naicker
- School of clinical medicineKwaZulu‐Natal UniversityDurbanSouth Africa
| | - Waheed A. Awotoye
- Department of Oral Pathology, Radiology and MedicineCollege of DentistryUniversity of IowaIowa CityIAUSA
- Iowa Institute of Oral Health ResearchUniversity of IowaIowa CityIAUSA
| | - Chinyere Adeleke
- Department of Oral Pathology, Radiology and MedicineCollege of DentistryUniversity of IowaIowa CityIAUSA
| | - Tamara Busch
- Department of Oral Pathology, Radiology and MedicineCollege of DentistryUniversity of IowaIowa CityIAUSA
- Iowa Institute of Oral Health ResearchUniversity of IowaIowa CityIAUSA
| | - Ada M. Toraño
- Dental and Craniofacial Genomics CoreUniversity of Puerto Rico School of Dental MedicineSan JuanPuerto Rico
| | - Carolina A. Bello
- Dental and Craniofacial Genomics CoreUniversity of Puerto Rico School of Dental MedicineSan JuanPuerto Rico
| | - Mairim Soto
- Dental and Craniofacial Genomics CoreUniversity of Puerto Rico School of Dental MedicineSan JuanPuerto Rico
| | - Marilyn Soto
- Dental and Craniofacial Genomics CoreUniversity of Puerto Rico School of Dental MedicineSan JuanPuerto Rico
| | - Ricardo Ledesma
- Dental and Craniofacial Genomics CoreUniversity of Puerto Rico School of Dental MedicineSan JuanPuerto Rico
| | - Myrellis Marquez
- Dental and Craniofacial Genomics CoreUniversity of Puerto Rico School of Dental MedicineSan JuanPuerto Rico
| | - Jose F. Cordero
- Dental and Craniofacial Genomics CoreUniversity of Puerto Rico School of Dental MedicineSan JuanPuerto Rico
| | - Lydia M. Lopez‐Del Valle
- Dental and Craniofacial Genomics CoreUniversity of Puerto Rico School of Dental MedicineSan JuanPuerto Rico
| | - Maria I. Salcedo
- Dental and Craniofacial Genomics CoreUniversity of Puerto Rico School of Dental MedicineSan JuanPuerto Rico
| | - Natalio Debs
- Dental and Craniofacial Genomics CoreUniversity of Puerto Rico School of Dental MedicineSan JuanPuerto Rico
| | - Mary Li
- Department of Oral Pathology, Radiology and MedicineCollege of DentistryUniversity of IowaIowa CityIAUSA
- Iowa Institute of Oral Health ResearchUniversity of IowaIowa CityIAUSA
| | - Aline Petrin
- Iowa Institute of Oral Health ResearchUniversity of IowaIowa CityIAUSA
| | - Joy Olotu
- Department of AnatomyUniversity of Port HarcourtPort HarcourtNigeria
| | - Colleen Aldous
- School of clinical medicineKwaZulu‐Natal UniversityDurbanSouth Africa
| | - James Olutayo
- Department of Oral and Maxillofacial SurgeryUniversity of LagosLagosNigeria
| | - Modupe O. Ogunlewe
- Department of Oral and Maxillofacial SurgeryUniversity of LagosLagosNigeria
| | - Fekir Abate
- School of Public HealthAddis Ababa UniversityAddis AbabaEthiopia
| | - Taye Hailu
- School of Public HealthAddis Ababa UniversityAddis AbabaEthiopia
| | - Ibrahim Muhammed
- School of Public HealthAddis Ababa UniversityAddis AbabaEthiopia
| | - Paul Gravem
- School of Public HealthAddis Ababa UniversityAddis AbabaEthiopia
| | - Milliard Deribew
- School of Public HealthAddis Ababa UniversityAddis AbabaEthiopia
| | - Mulualem Gesses
- School of Public HealthAddis Ababa UniversityAddis AbabaEthiopia
| | - Mohaned Hassan
- Department of Oral Pathology, Radiology and MedicineCollege of DentistryUniversity of IowaIowa CityIAUSA
- Iowa Institute of Oral Health ResearchUniversity of IowaIowa CityIAUSA
| | - John Pape
- Department of Oral Pathology, Radiology and MedicineCollege of DentistryUniversity of IowaIowa CityIAUSA
| | - Oluwole A. Adeniyan
- NHS Foundation Trust, (Queens Hospital, Burton‐On‐Trent)StaffordshireUnited Kingdom
| | - Solomon Obiri‐Yeboah
- Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and TechnologyKumasiGhana
| | - Fareed K.N. Arthur
- Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and TechnologyKumasiGhana
| | - Alexander A. Oti
- Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and TechnologyKumasiGhana
| | | | - Sara E. Miller
- Iowa Institute of Oral Health ResearchUniversity of IowaIowa CityIAUSA
| | - Peter Donkor
- Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and TechnologyKumasiGhana
| | | | - Mary L. Marazita
- Oral BiologyHuman GeneticsUniversity of PittsburghPittsburghPAUSA
| | | | | | - Azeez Butali
- Department of Oral Pathology, Radiology and MedicineCollege of DentistryUniversity of IowaIowa CityIAUSA
- Iowa Institute of Oral Health ResearchUniversity of IowaIowa CityIAUSA
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Inkpen SM, Solbakken MH, Jentoft S, Eslamloo K, Rise ML. Full characterization and transcript expression profiling of the interferon regulatory factor (IRF) gene family in Atlantic cod (Gadus morhua). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 98:166-180. [PMID: 30928323 DOI: 10.1016/j.dci.2019.03.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/22/2019] [Accepted: 03/22/2019] [Indexed: 06/09/2023]
Abstract
Atlantic cod (Gadus morhua) represents a unique immune system among teleost fish, making it a species of interest for immunological studies, and especially for investigating the evolutionary history of immune gene families. The interferon regulatory factor (IRF) gene family encodes transcription factors which function in the interferon pathway, but also in areas including leukocyte differentiation, cell growth, autoimmunity, and development. We previously characterized several IRF family members in Atlantic cod (Irf4a, Irf4b, Irf7, Irf8, and two Irf10 splice variants) at the cDNA and putative amino acid levels, and in the current study we took advantage of the new and improved Atlantic cod genome assembly in combination with rapid amplification of cDNA ends (RACE) to characterize the remaining family members (i.e. Irf3, Irf5, Irf6, Irf9, and two Irf2 splice variants). Real-time quantitative PCR (QPCR) was used to investigate constitutive expression of all IRF transcripts during embryonic development, suggesting several putative maternal transcripts, and potential stage-specific roles. QPCR studies also showed 11 of 13 transcripts were responsive to stimulation with poly(I:C), while 6 of 13 transcripts were responsive to lipopolysaccharide (LPS) in Atlantic cod head kidney macrophages, indicating roles for cod IRF family members in both antiviral and antibacterial responses. This study is the first to investigate expression of the complete IRF family in Atlantic cod, and suggests potential novel roles for several of these transcription factors within immunity as well as in early development of this species.
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Affiliation(s)
- Sabrina M Inkpen
- Department of Ocean Sciences, Memorial University of Newfoundland, NL, A1C 5S7, Canada.
| | - Monica H Solbakken
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
| | - Khalil Eslamloo
- Department of Ocean Sciences, Memorial University of Newfoundland, NL, A1C 5S7, Canada.
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, NL, A1C 5S7, Canada.
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Zhan FB, Jakovlić I, Wang WM. Identification, characterization and expression in response to Aeromonas hydrophila challenge of five interferon regulatory factors in Megalobrama amblycephala. FISH & SHELLFISH IMMUNOLOGY 2019; 86:204-212. [PMID: 30336285 DOI: 10.1016/j.fsi.2018.10.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/08/2018] [Accepted: 10/14/2018] [Indexed: 06/08/2023]
Abstract
Interferon regulatory factor (Irf) family represents one of the most important transcription factor families, with multiple biological roles. In this study, we characterized five Irf family members (irf4a, irf4b, irf6, irf8 and irf10) in Megalobrama amblycephala at the cDNA and (predicted) amino acid levels, analyzed them phylogenetically, and developed gene-specific primers for qPCR analysis. All five irfs were constitutively expressed in all examined tissues, but their transcription was significantly higher in lymphoid organs and tissues, such as kidney, spleen and intestine. Exceptions were irf8, which was expressed at a high level in heart and brain tissues, and irf6, expressed at low levels in most tissues. After a bacterial immune challenge with Aeromonas hydrophila, the expression of irfs in liver was up-regulated: mairf4a 8.12-fold, mairf4b 29.9-fold, mairf6 1.38-fold and mairf10 1.65-fold (mairf8 was an exception: 0.07-fold). In spleen, kidney, intestine and gills, transcript levels of studied irfs increased only at specific time-points. The results suggested that irfs are involved in the immune response to bacterial infection in M. amblycephala, which will help elucidate the biological functions of irfs in the immune system of teleost fish.
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Affiliation(s)
- Fan-Bin Zhan
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education / Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Wei-Min Wang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education / Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China.
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Duncan KM, Mukherjee K, Cornell RA, Liao EC. Zebrafish models of orofacial clefts. Dev Dyn 2017; 246:897-914. [PMID: 28795449 DOI: 10.1002/dvdy.24566] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/06/2017] [Accepted: 07/31/2017] [Indexed: 12/12/2022] Open
Abstract
Zebrafish is a model organism that affords experimental advantages toward investigating the normal function of genes associated with congenital birth defects. Here we summarize zebrafish studies of genes implicated in orofacial cleft (OFC). The most common use of zebrafish in this context has been to explore the normal function an OFC-associated gene product in craniofacial morphogenesis by inhibiting expression of its zebrafish ortholog. The most frequently deployed method has been to inject embryos with antisense morpholino oligonucleotides targeting the desired transcript. However, improvements in targeted mutagenesis strategies have led to widespread adoption of CRISPR/Cas9 technology. A second application of zebrafish has been for functional assays of gene variants found in OFC patients; such in vivo assays are valuable because the success of in silico methods for testing allele severity has been mixed. Finally, zebrafish have been used to test the tissue specificity of enhancers that harbor single nucleotide polymorphisms associated with risk for OFC. We review examples of each of these approaches in the context of genes that are implicated in syndromic and non-syndromic OFC. Developmental Dynamics 246:897-914, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Kaylia M Duncan
- Department of Anatomy and Cell Biology, Molecular and Cell Biology Graduate Program, University of Iowa, Iowa City, Iowa
| | - Kusumika Mukherjee
- Center for Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Robert A Cornell
- Department of Anatomy and Cell Biology, Molecular and Cell Biology Graduate Program, University of Iowa, Iowa City, Iowa
| | - Eric C Liao
- Center for Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
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8
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Rapid functional analysis of computationally complex rare human IRF6 gene variants using a novel zebrafish model. PLoS Genet 2017; 13:e1007009. [PMID: 28945736 PMCID: PMC5628943 DOI: 10.1371/journal.pgen.1007009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 10/05/2017] [Accepted: 09/07/2017] [Indexed: 11/19/2022] Open
Abstract
Large-scale sequencing efforts have captured a rapidly growing catalogue of genetic variations. However, the accurate establishment of gene variant pathogenicity remains a central challenge in translating personal genomics information to clinical decisions. Interferon Regulatory Factor 6 (IRF6) gene variants are significant genetic contributors to orofacial clefts. Although approximately three hundred IRF6 gene variants have been documented, their effects on protein functions remain difficult to interpret. Here, we demonstrate the protein functions of human IRF6 missense gene variants could be rapidly assessed in detail by their abilities to rescue the irf6-/- phenotype in zebrafish through variant mRNA microinjections at the one-cell stage. The results revealed many missense variants previously predicted by traditional statistical and computational tools to be loss-of-function and pathogenic retained partial or full protein function and rescued the zebrafish irf6-/- periderm rupture phenotype. Through mRNA dosage titration and analysis of the Exome Aggregation Consortium (ExAC) database, IRF6 missense variants were grouped by their abilities to rescue at various dosages into three functional categories: wild type function, reduced function, and complete loss-of-function. This sensitive and specific biological assay was able to address the nuanced functional significances of IRF6 missense gene variants and overcome many limitations faced by current statistical and computational tools in assigning variant protein function and pathogenicity. Furthermore, it unlocked the possibility for characterizing yet undiscovered human IRF6 missense gene variants from orofacial cleft patients, and illustrated a generalizable functional genomics paradigm in personalized medicine. Advances in sequencing technologies have led to rapid increases in personalized genetics information. Millions of differences exist when comparing the genomes of two individuals, accounting for the diversity of humans and occasionally disease pathogenicity. Accurate determination of the functional consequences of these differences is critical for translating personal genetic information into clinical decision. Various methods have been devised to meet this challenge. However, they are imperfect, especially in their abilities to interpret rare variants. Rare variants must be evaluated by multi-pronged approaches to establish disease pathogenicity, one crucial approach being functional testing through experimental models. Here, we utilized a zebrafish model to rapidly evaluate the protein functions of rare gene variants of IRF6, a gene of established importance in orofacial cleft pathogenesis. IRF6 functions are well-conserved across species, and allowed us to test the functions of human IRF6 variants by their abilities to rescue zebrafish embryos depleted of irf6. Many variants previously labeled pathogenic and loss-of-function retained full wild type-level protein activity, suggesting they could potentially represent benign, rather than disease-causing genetic variations. This paradigm is applicable to other genes and will allow researchers to rapidly triage gene variants for further study and clinicians to provide more accurate genetic diagnoses.
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Carpinelli MR, de Vries ME, Jane SM, Dworkin S. Grainyhead-like Transcription Factors in Craniofacial Development. J Dent Res 2017; 96:1200-1209. [PMID: 28697314 DOI: 10.1177/0022034517719264] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Craniofacial development in vertebrates involves the coordinated growth, migration, and fusion of several facial prominences during embryogenesis, processes governed by strict genetic and molecular controls. A failure in any of the precise spatiotemporal sequences of events leading to prominence fusion often leads to anomalous facial, skull, and jaw formation-conditions termed craniofacial defects (CFDs). Affecting approximately 0.1% to 0.3% of live births, CFDs are a highly heterogeneous class of developmental anomalies, which are often underpinned by genetic mutations. Therefore, identifying novel disease-causing mutations in genes that regulate craniofacial development is a critical prerequisite to develop new preventive or therapeutic measures. The Grainyhead-like ( GRHL) transcription factors are one such gene family, performing evolutionarily conserved roles in craniofacial patterning. The antecedent member of this family, Drosophila grainyhead ( grh), is required for head skeleton development in fruit flies, loss or mutation of Grhl family members in mouse and zebrafish models leads to defects of both maxilla and mandible, and recently, mutations in human GRHL3 have been shown to cause or contribute to both syndromic (Van Der Woude syndrome) and nonsyndromic palatal clefts. In this review, we summarize the current knowledge regarding the craniofacial-specific function of the Grainyhead-like family in multiple model species, identify some of the major target genes regulated by the Grhl transcription factors in craniofacial patterning, and, by examining animal models, draw inferences as to how these data will inform the likely roles of GRHL factors in human CFDs comprising palatal clefting. By understanding the molecular networks regulated by Grhl2 and Grhl3 target genes in other systems, we can propose likely pathways that mediate the effects of these transcription factors in human palatogenesis.
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Affiliation(s)
- M R Carpinelli
- 1 Central Clinical School, Monash University, Prahran, VIC, Australia
| | - M E de Vries
- 2 Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - S M Jane
- 1 Central Clinical School, Monash University, Prahran, VIC, Australia
| | - S Dworkin
- 2 Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
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Exploring the Underlying Genetics of Craniofacial Morphology through Various Sources of Knowledge. BIOMED RESEARCH INTERNATIONAL 2016; 2016:3054578. [PMID: 28053980 PMCID: PMC5178329 DOI: 10.1155/2016/3054578] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 11/15/2016] [Indexed: 12/23/2022]
Abstract
The craniofacial complex is the billboard of sorts containing information about sex, health, ancestry, kinship, genes, and environment. A thorough knowledge of the genes underlying craniofacial morphology is fundamental to understanding craniofacial biology and evolution. These genes can also provide an important foundation for practical efforts like predicting faces from DNA and phenotype-based facial diagnostics. In this work, we focus on the various sources of knowledge regarding the genes that affect patterns of craniofacial development. Although tremendous successes recently have been made using these sources in both methodology and biology, many challenges remain. Primary among these are precise phenotyping techniques and efficient modeling methods.
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TLR3 drives IRF6-dependent IL-23p19 expression and p19/EBI3 heterodimer formation in keratinocytes. Immunol Cell Biol 2015; 93:771-9. [PMID: 26303210 DOI: 10.1038/icb.2015.77] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 07/28/2015] [Accepted: 07/29/2015] [Indexed: 12/20/2022]
Abstract
Interferon regulatory factor (IRF) family members impart cell-type specificity to toll-like receptor (TLR) signalling, and we recently identified a role for IRF6 in TLR2 signalling in epithelial cells. TLR3 has a well-characterized role in wound healing in the skin, and here, we examined TLR3-dependent IRF6 functions in human keratinocytes. Primary keratinocytes responded robustly to the TLR3 agonist poly(IC) with upregulation of mRNAs for interferon-β (IFN-β), the interleukin-12 (IL-12) family member IL-23p19 and the chemokines IL-8 and chemokine (C-C motif) ligand 5 (CCL5). Silencing of IRF6 expression enhanced poly(IC)-inducible IFN-β mRNA levels and inhibited poly(IC)-inducible IL-23p19 mRNA expression in primary keratinocytes. Consistent with these data, co-transfection of IRF6 increased poly(IC)-inducible IL-23p19 promoter activity, but inhibited poly(IC)-inducible IFN-β promoter activity in reporter assays. Surprisingly, poly(IC) did not regulate IL-12p40 expression in keratinocytes, suggesting that TLR3-inducible IL-23p19 may have an IL-23-independent function in these cells. The only other IL-12 family member that was strongly poly(IC) inducible was EBI3, which has not been shown to heterodimerize with IL-23p19. Both co-immunoprecipitation and proximity ligation assays revealed that IL-23p19 and EBI3 interact in cells. Co-expression of IL-23p19 and EBI3, as compared with IL-23p19 alone, resulted in increased levels of secreted IL-23p19, implying a functional role for this heterodimer. In summary, we report that IRF6 regulates a subset of TLR3 responses in human keratinocytes, including the production of a novel IL-12 family heterodimer (p19/EBI3). We propose that the TLR3-IRF6-p19/EBI3 axis may regulate keratinocyte and/or immune cell functions in the context of cell damage and wound healing in the skin.
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Inkpen SM, Hori TS, Gamperl AK, Nash GW, Rise ML. Characterization and expression analyses of five interferon regulatory factor transcripts (Irf4a, Irf4b, Irf7, Irf8, Irf10) in Atlantic cod (Gadus morhua). FISH & SHELLFISH IMMUNOLOGY 2015; 44:365-381. [PMID: 25731920 DOI: 10.1016/j.fsi.2015.02.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 01/30/2015] [Accepted: 02/19/2015] [Indexed: 06/04/2023]
Abstract
The interferon regulatory factor (IRF) family of genes encodes a group of transcription factors that have important roles not only in regulating the expression of Type I interferons (IFNs) and other genes in the IFN pathway, but also in growth, development and the regulation of oncogenesis. In this study, several IRF family members (Irf4a, Irf4b, Irf7, Irf8, Irf10) in Atlantic cod (Gadus morhua) were characterized at the cDNA and putative amino acid levels, allowing for phylogenetic analysis of these proteins in teleost fish, as well as the development of gene-specific primers used in RT-PCR and quantitative PCR (QPCR) analyses. Two Atlantic cod Irf10 splice variants were identified and their presence confirmed by sequencing of the Irf10 genomic region. RT-PCR showed that Irf7, Irf8 and both Irf10 transcripts were expressed in all 15 cod tissues tested, while Irf4a and Irf4b were absent in some tissues. QPCR analysis of spleen expression expanded upon this, and upon previous work. All IRF transcripts in the study were responsive to stimulation by the viral mimic poly(I:C), and all except Irf4a were responsive to exposure to formalin-killed Aeromonas salmonicida (ASAL). These IRF genes, thus, are likely important in the cod immune response to both viral and bacterial infections. Increased temperature (10 °C to 16 °C) was also observed to modulate the antibacterial responses of all IRF transcripts, and the antiviral responses of Irf4b and Irf10-v2. This research supports earlier studies which reported that elevated temperature modulates the expression of many immune genes in Atlantic cod.
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Affiliation(s)
- Sabrina M Inkpen
- Department of Ocean Sciences, Memorial University of Newfoundland, NL, A1C 5S7, Canada.
| | - Tiago S Hori
- Department of Ocean Sciences, Memorial University of Newfoundland, NL, A1C 5S7, Canada.
| | - A Kurt Gamperl
- Department of Ocean Sciences, Memorial University of Newfoundland, NL, A1C 5S7, Canada.
| | - Gordon W Nash
- Department of Ocean Sciences, Memorial University of Newfoundland, NL, A1C 5S7, Canada.
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, NL, A1C 5S7, Canada.
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Zhou Q, Li M, Zhu W, Guo J, Wang Y, Li Y, Li S. Association between Interferon Regulatory Factor 6 Gene Polymorphisms and Nonsyndromic Cleft Lip with or without Cleft Palate in a Chinese Population. Cleft Palate Craniofac J 2013; 50:570-6. [DOI: 10.1597/12-234] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Objective To further confirm the association between two IRF6 single nucleotide polymorphisms and nonsyndromic cleft lip with or without cleft palate in a Chinese population. Participants A total of 106 nonsyndromic cleft lip with or without cleft palate case trios and 129 control trios. Intervention Two IRF6 single nucleotide polymorphisms, rs2235371 and rs642961, were genotyped for all case and control families. Case-control analysis and family-based linkage analysis were both performed for the two single nucleotide polymorphisms. Results The genotype and allele frequencies of rs2235371 (odds ratioAG+AA vs. GG, 0.581; 95% confidence interval, 0.345 to 0.976; P = .039) and rs642961 (odds ratioAG+AA vs. GG, 5.389; 95% confidence interval, 2.936 to 9.893; P = 5e-08) were significantly higher in nonsyndromic cleft lip with or without cleft palate patients compared with controls. There was an obvious dosage effect of allele A at rs642961. The transmission of a major allele (G) of rs2235371 and a minor allele (A) of rs642961 was in disequilibrium ( P < .05) in complete case-parent trios. The association between the two single nucleotide polymorphisms and nonsyndromic cleft lip with or without cleft palate was confirmed by the Family-Based Association Test for rs642961 ( P = .008), but there was no significance for rs2235371 ( P = 0.057). Haplotype analysis found that rs2235371 G/rs642961 A haplotype increased the risk of nonsyndromic cleft lip with or without cleft palate ( P = 2.42e-07); whereas, rs2235371 A/rs642961 G haplotype reduced the risk of nonsyndromic cleft lip with or without cleft palate ( P = 4.37e-05). No evidence of linkage disequilibrium was found between the two single nucleotide polymorphisms (D′ = 0.303, r2 = 0.017). Conclusion Our results confirmed the involvement of the IRF6 variants rs642961 and rs2235371 in the etiology of nonsyndromic cleft lip with or without cleft palate in a Chinese population.
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Affiliation(s)
- Qian Zhou
- Department of Nutrition and Food Hygiene, School of Public Health, Laboratory of Molecular Toxicology and Development Molecular Biology, Peking University, Beijing, People's Republic of China
| | - Mengjie Li
- Department of Nutrition and Food Hygiene, School of Public Health, Laboratory of Molecular Toxicology and Development Molecular Biology, Peking University, Beijing, People's Republic of China
| | - Wenli Zhu
- Department of Nutrition and Food Hygiene, School of Public Health, Laboratory of Molecular Toxicology and Development Molecular Biology, Peking University, Beijing, People's Republic of China
| | - Jinzhen Guo
- Department of Nutrition and Food Hygiene, School of Public Health, Laboratory of Molecular Toxicology and Development Molecular Biology, Peking University, Beijing, People's Republic of China
| | - Yun Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Laboratory of Molecular Toxicology and Development Molecular Biology, Peking University, Beijing, People's Republic of China
| | - Yong Li
- Department of Nutrition and Food Hygiene, School of Public Health, Laboratory of Molecular Toxicology and Development Molecular Biology, Peking University, Beijing, People's Republic of China
| | - Shuqin Li
- Sheng-Jing Hospital of China Medical University, Shenyang, People's Republic of China
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Dougherty M, Kamel G, Grimaldi M, Gfrerer L, Shubinets V, Ethier R, Hickey G, Cornell RA, Liao EC. Distinct requirements for wnt9a and irf6 in extension and integration mechanisms during zebrafish palate morphogenesis. Development 2012; 140:76-81. [PMID: 23154410 DOI: 10.1242/dev.080473] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Development of the palate in vertebrates involves cranial neural crest migration, convergence of facial prominences and extension of the cartilaginous framework. Dysregulation of palatogenesis results in orofacial clefts, which represent the most common structural birth defects. Detailed analysis of zebrafish palatogenesis revealed distinct mechanisms of palatal morphogenesis: extension, proliferation and integration. We show that wnt9a is required for palatal extension, wherein the chondrocytes form a proliferative front, undergo morphological change and intercalate to form the ethmoid plate. Meanwhile, irf6 is required specifically for integration of facial prominences along a V-shaped seam. This work presents a mechanistic analysis of palate morphogenesis in a clinically relevant context.
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Affiliation(s)
- Max Dougherty
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
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15
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Liu Y, Xu J, Fu W, Weng Z, Niu X, Liu J, Ding X, Zhang Q. Tissues Expression, Polymorphisms of IFN Regulatory Factor 6 (IRF6) Gene and Their Associated with Immune Traits in Three Pig Populations. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2012; 25:163-9. [PMID: 25049546 PMCID: PMC4093143 DOI: 10.5713/ajas.2011.11168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 08/19/2011] [Indexed: 11/27/2022]
Abstract
Interferon regulatory factor 6 (IRF6) gene is a member of the IRF-family, and plays functionally diverse roles in the regulation of the immune system. In this report, the 13,720 bp porcine IRF6 genomic DNA structure was firstly identified with a putative IRF6 protein of 467 amino acids. Alignment and phylogenetic analysis of the porcine IRF6 amino acid sequences with their homologies to other species showed high identity (over 96%). Tissues expression of IRF6 mRNA was observed by RT-PCR, the results revealed IRF6 expressed widely in eight tissues. One SNP (HQ026023:1383 G>C) in exon7 and two SNPs (HQ026023:130 G>A; 232 C>T) in the 5 ' promoter region of porcine IRF6 gene were demonstrated b y DNA sequencing analysis. A further analysis of SNP genotypes associated with immune traits including IFN-γ and IL10 concentrations in serum was carried out in three pig populations including Large White, Landraces and Songliao Black pig (a Chinese indigenous breed). The results showed that the SNP (HQ026023:1383 G>C) was significantly associated with the level of IFN-γ (d 20) in serum (p = 0.038) and the ratio of IFN-γ to IL10 (d 20) in serum (p = 0.041); The other two SNPs (HQ026023:130 G>A; 232 C>T) were highly significantly associated with IL10 level in serum both at the day 20 (p = 0.005; p = 0.001) and the day 35 (p = 0.004; p = 0.006). Identification of the porcine IRF6 gene will help our further understanding of the molecular basis of the IFN regulation pathway in the porcine immune response. All these results should indicate that the IRF6 gene can be regarded as a molecular marker associated with the IL10 level in serum and used for genetic selection in the pig breeding.
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Hu G, Yin X, Lou H, Xia J, Dong X, Zhang J, Liu Q. Interferon regulatory factor 3 (IRF-3) in Japanese flounder, Paralichthys olivaceus: sequencing, limited tissue distribution, inducible expression and induction of fish type I interferon promoter. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2011; 35:164-173. [PMID: 20837055 DOI: 10.1016/j.dci.2010.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Revised: 09/06/2010] [Accepted: 09/06/2010] [Indexed: 05/29/2023]
Abstract
Two cDNAs with different 3'-untranslated region (UTR) encoding an interferon regulatory factor 3 (IRF-3) were cloned from head kidney of Japanese flounder, Paralichthys olivaceus, by reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) methods. Sequence analysis reveals that they were generated by alternative polyadenylation. The predicted protein consists of 467 amino acid residues which shares the highest identity of 50.7-57.6% to fish IRF-3 and possesses a DNA-binding domain (DBD), an IRF association domain (IAD) and a serine-rich domain (SRD) of vertebrate IRF-3. The presence of these domains along with phylogenetic analysis places it into the IRF-3 group of the IRF-3 subfamily. RT-PCR analysis revealed that flounder IRF-3 was expressed constitutively in limited tissue types including head kidney, spleen, kidney, heart, gill, intestine and liver. A quantitative real time PCR assay was employed to monitor expression of IRF-3, type I interferon (IFN) and Mx in flounder head kidney and gill. All three genes were up-regulated by polyinosinic:polycytidylic acid (polyI:C) and lymphocystis disease virus (LCDV) with an earlier but slight and less persistent increase in transcription levels seen for the IRF-3. Finally, flounder IRF-3 was proved to induce fish type I IFN promoter in FG9307 cells, a flounder gill cell line, by a luciferase assay. These results provide insights into the roles of fish IRF-3 in the antiviral immunity.
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Affiliation(s)
- Guobin Hu
- College of Marine Life Sciences, Ocean University of China, 5# Yushan Road, Qingdao 266003, China.
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XU QQ, CHANG MX, XIAO FS, LI N, NIE P. EXPRESSION CHARACTERIZATION OF INTERFERON REGULATORY FACTOR 5 (IRF-5) IN GRASS CARP CTENOPHARYNGODON IDELLUS. ACTA ACUST UNITED AC 2010. [DOI: 10.3724/sp.j.1035.2010.01206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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The gene and virus-induced expression of IRF-5 in grass carp Ctenopharyngodon idella. Vet Immunol Immunopathol 2009; 134:269-78. [PMID: 19896215 DOI: 10.1016/j.vetimm.2009.10.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 10/04/2009] [Accepted: 10/06/2009] [Indexed: 11/23/2022]
Abstract
The interferon regulatory factor 5 (IRF-5) is known to be involved in the innate immune response and in the regulation of DNA damage-induced apoptosis. In the present study, the cDNA and genomic sequences of IRF-5 were identified in grass carp (Ctenopharyngodon idella). The cDNA of grass carp IRF-5 (gcIRF-5) contains an open reading frame (ORF) of 1560 nucleotides, encoding a putative 519 amino acid protein, which showed 34.5-83.9% identity to IRF-5 homologues from mammals, amphibian, avian and fish, and 96.2% and 95.0% identity to zebrafish IRF-5 in the DNA-binding domain (DBD) and IRF association domain (IAD), respectively. The genomic DNA sequence of gcIRF-5 contains 6075bp consisting of 9 exons and 8 introns. The expression of gcIRF-5 was observed in all organs examined. The analysis of real-time quantitative RT-PCR revealed that grass carp reovirus (GCRV) induced the expression of gcIRF-5 in spleen and head kidney.
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Jugessur A, Farlie PG, Kilpatrick N. The genetics of isolated orofacial clefts: from genotypes to subphenotypes. Oral Dis 2009; 15:437-53. [DOI: 10.1111/j.1601-0825.2009.01577.x] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Jia ZL, Li Y, Li L, Wu J, Zhu LY, Yang C, Chen CH, Shi B. Association Among IRF6 Polymorphism, Environmental Factors, and Nonsyndromic Orofacial Clefts in Western China. DNA Cell Biol 2009; 28:249-57. [PMID: 19388848 DOI: 10.1089/dna.2008.0837] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Zhong-Lin Jia
- State Key Laboratory of Oral Disease and the Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Yang Li
- State Key Laboratory of Oral Disease and the Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Ling Li
- State Key Laboratory of Oral Disease and the Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Jun Wu
- State Key Laboratory of Oral Disease and the Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Lu-Ying Zhu
- State Key Laboratory of Oral Disease and the Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Chao Yang
- State Key Laboratory of Oral Disease and the Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Chun-Hui Chen
- State Key Laboratory of Oral Disease and the Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Bing Shi
- State Key Laboratory of Oral Disease and the Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, People's Republic of China
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Jugessur A, Shi M, Gjessing HK, Lie RT, Wilcox AJ, Weinberg CR, Christensen K, Boyles AL, Daack-Hirsch S, Trung TN, Bille C, Lidral AC, Murray JC. Genetic determinants of facial clefting: analysis of 357 candidate genes using two national cleft studies from Scandinavia. PLoS One 2009; 4:e5385. [PMID: 19401770 PMCID: PMC2671138 DOI: 10.1371/journal.pone.0005385] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Accepted: 03/20/2009] [Indexed: 11/28/2022] Open
Abstract
Background Facial clefts are common birth defects with a strong genetic component. To identify fetal genetic risk factors for clefting, 1536 SNPs in 357 candidate genes were genotyped in two population-based samples from Scandinavia (Norway: 562 case-parent and 592 control-parent triads; Denmark: 235 case-parent triads). Methodology/Principal Findings We used two complementary statistical methods, TRIMM and HAPLIN, to look for associations across these two national samples. TRIMM tests for association in each gene by using multi-SNP genotypes from case-parent triads directly without the need to infer haplotypes. HAPLIN on the other hand estimates the full haplotype distribution over a set of SNPs and estimates relative risks associated with each haplotype. For isolated cleft lip with or without cleft palate (I-CL/P), TRIMM and HAPLIN both identified significant associations with IRF6 and ADH1C in both populations, but only HAPLIN found an association with FGF12. For isolated cleft palate (I-CP), TRIMM found associations with ALX3, MKX, and PDGFC in both populations, but only the association with PDGFC was identified by HAPLIN. In addition, HAPLIN identified an association with ETV5 that was not detected by TRIMM. Conclusion/Significance Strong associations with seven genes were replicated in the Scandinavian samples and our approach effectively replicated the strongest previously known association in clefting—with IRF6. Based on two national cleft cohorts of similar ancestry, two robust statistical methods and a large panel of SNPs in the most promising cleft candidate genes to date, this study identified a previously unknown association with clefting for ADH1C and provides additional candidates and analytic approaches to advance the field.
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Affiliation(s)
- Astanand Jugessur
- Craniofacial Development, Musculoskeletal Disorders, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Min Shi
- Biostatistics Branch, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, Durham, North Carolina, United States of America
| | - Håkon Kristian Gjessing
- Department of Epidemiology (EPAM), Norwegian Institute of Public Health, Oslo, Norway
- Section for Epidemiology and Medical Statistics, Department of Public Health and Primary Health Care, University of Bergen, Bergen, Norway
| | - Rolv Terje Lie
- Section for Epidemiology and Medical Statistics, Department of Public Health and Primary Health Care, University of Bergen, Bergen, Norway
- Medical Birth Registry of Norway, Norwegian Institute of Public Health, Bergen, Norway
| | - Allen James Wilcox
- Epidemiology Branch, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, Durham, North Carolina, United States of America
| | - Clarice Ring Weinberg
- Biostatistics Branch, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, Durham, North Carolina, United States of America
| | - Kaare Christensen
- Department of Epidemiology, University of Southern Denmark, Odense, Denmark
| | - Abee Lowman Boyles
- Epidemiology Branch, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, Durham, North Carolina, United States of America
| | - Sandra Daack-Hirsch
- College of Nursing, University of Iowa, Iowa City, Iowa, United States of America
| | - Truc Nguyen Trung
- Medical Birth Registry of Norway, Norwegian Institute of Public Health, Bergen, Norway
| | - Camilla Bille
- Department of Epidemiology, University of Southern Denmark, Odense, Denmark
| | - Andrew Carl Lidral
- Departments of Pediatrics, Epidemiology and Biological Sciences, University of Iowa, Iowa City, Iowa, United States of America
| | - Jeffrey Clark Murray
- Department of Epidemiology, University of Southern Denmark, Odense, Denmark
- Departments of Pediatrics, Epidemiology and Biological Sciences, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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Trune DR, Zheng QY. Mouse models for human otitis media. Brain Res 2009; 1277:90-103. [PMID: 19272362 DOI: 10.1016/j.brainres.2009.02.047] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 02/11/2009] [Accepted: 02/23/2009] [Indexed: 12/20/2022]
Abstract
Otitis media (OM) remains the most common childhood disease and its annual costs exceed $5 billion. Its potential for permanent hearing impairment also emphasizes the need to better understand and manage this disease. The pathogenesis of OM is multifactorial and includes infectious pathogens, anatomy, immunologic status, genetic predisposition, and environment. Recent progress in mouse model development is helping to elucidate the respective roles of these factors and to significantly contribute toward efforts of OM prevention and control. Genetic predisposition is recognized as an important factor in OM and increasing numbers of mouse models are helping to uncover the potential genetic bases for human OM. Furthermore, the completion of the mouse genome sequence has offered a powerful set of tools for investigating gene function and is generating a rich resource of mouse mutants for studying the genetic factors underlying OM.
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Affiliation(s)
- Dennis R Trune
- Oregon Hearing Research Center, Mail Code NRC04, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239-3098, USA
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Fleming JAGW, Song G, Choi Y, Spencer TE, Bazer FW. Interferon regulatory factor 6 (IRF6) is expressed in the ovine uterus and functions as a transcriptional activator. Mol Cell Endocrinol 2009; 299:252-60. [PMID: 19022341 PMCID: PMC2655364 DOI: 10.1016/j.mce.2008.10.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Revised: 10/17/2008] [Accepted: 10/21/2008] [Indexed: 11/30/2022]
Abstract
Interferon tau (IFNT), the maternal recognition of pregnancy signal in sheep and other ruminants, is secreted by the conceptus and regulates the expression of a number of genes in a cell-specific manner within the uterus. The response of different endometrial cell types to IFNT appears to be specified by IFN regulatory factors (IRFs). IRF2, a potent repressor of gene transcription, is expressed only by luminal (LE) and superficial glandular epithelia (sGE), whereas IRF1 and IRF9, activators of gene transcription, are expressed only in GE and stromal cells of the uterus during early pregnancy. In the present study, IRF6 was found to be expressed in LE/sGE and middle GE of the ovine uterine endometrium as well as conceptus trophectoderm. IRF family members can regulate transcription via IFN-stimulated response elements (ISREs). Transient transfection analyses found that IRF6 enhanced basal activity of ISRE-containing promoters, but did not enhance IFNT stimulation of ISRE-containing promoters in variety of different cell types. Further, IRF6 did not cooperate with IRF1 or reduce IRF2 repression of ISRE-containing promoter activity. These results establish that IRF6 is a transcriptional activator that is preferentially expressed in the endometrial epithelia and conceptus trophectoderm. IRF6 is hypothesized to play critical roles in endometrial gene expression as well as in conceptus trophectoderm growth and differentiation.
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Affiliation(s)
- Jo-Ann G W Fleming
- Center for Animal Biotechnology and Genomics and Department of Animal Science, Texas A&M University, College Station, TX 77843, USA
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Murdoch AM, Patir A, Seymen F, Vieira AR. Studies of palatine rugae and interferon regulatory factor 6 variations in a group of families with sporadic hypodontia. J Oral Sci 2009; 51:521-6. [DOI: 10.2334/josnusd.51.521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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Sabel JL, d'Alençon C, O'Brien EK, Van Otterloo E, Lutz K, Cuykendall TN, Schutte BC, Houston DW, Cornell RA. Maternal Interferon Regulatory Factor 6 is required for the differentiation of primary superficial epithelia in Danio and Xenopus embryos. Dev Biol 2008; 325:249-62. [PMID: 19013452 DOI: 10.1016/j.ydbio.2008.10.031] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Revised: 10/16/2008] [Accepted: 10/21/2008] [Indexed: 10/21/2022]
Abstract
Early in the development of animal embryos, superficial cells of the blastula form a distinct lineage and adopt an epithelial morphology. In different animals, the fate of these primary superficial epithelial (PSE) cells varies, and it is unclear whether pathways governing segregation of blastomeres into the PSE lineage are conserved. Mutations in the gene encoding Interferon Regulatory Factor 6 (IRF6) are associated with syndromic and non-syndromic forms of cleft lip and palate, consistent with a role for Irf6 in development of oral epithelia, and mouse Irf6 targeted null mutant embryos display abnormal differentiation of oral epithelia and skin. In Danio rerio (zebrafish) and Xenopus laevis (African clawed frog) embryos, zygotic irf6 transcripts are present in many epithelial tissues including the presumptive PSE cells and maternal irf6 transcripts are present throughout all cells at the blastula stage. Injection of antisense oligonucleotides with ability to disrupt translation of irf6 transcripts caused little or no effect on development. By contrast, injection of RNA encoding a putative dominant negative Irf6 caused epiboly arrest, loss of gene expression characteristic of the EVL, and rupture of the embryo at late gastrula stage. The dominant negative Irf6 disrupted EVL gene expression in a cell autonomous fashion. These results suggest that Irf6 translated in the oocyte or unfertilized egg suffices for early development. Supporting the importance of maternal Irf6, we show that depletion of maternal irf6 transcripts in X. laevis embryos leads to gastrulation defects and rupture of the superficial epithelium. These experiments reveal a conserved role for maternally-encoded Irf6 in differentiation of a simple epithelium in X. laevis and D. rerio. This epithelium constitutes a novel model tissue in which to explore the Irf6 regulatory pathway.
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Affiliation(s)
- Jaime L Sabel
- Interdisciplinary Graduate Program in Genetics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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Stein C, Caccamo M, Laird G, Leptin M. Conservation and divergence of gene families encoding components of innate immune response systems in zebrafish. Genome Biol 2008; 8:R251. [PMID: 18039395 PMCID: PMC2258186 DOI: 10.1186/gb-2007-8-11-r251] [Citation(s) in RCA: 309] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Revised: 10/30/2007] [Accepted: 11/27/2007] [Indexed: 12/12/2022] Open
Abstract
Analysis of several fish genomes reveals components of the innate immune system and identifies orthologous relationships between gene families of fish and mammals. Background The zebrafish has become a widely used model to study disease resistance and immunity. Although the genes encoding many components of immune signaling pathways have been found in teleost fish, it is not clear whether all components are present or whether the complexity of the signaling mechanisms employed by mammals is similar in fish. Results We searched the genomes of the zebrafish Danio rerio and two pufferfish for genes encoding components of the Toll-like receptor and interferon signaling pathways, the NLR (NACHT-domain and leucine rich repeat containing) protein family, and related proteins. We find that most of the components known in mammals are also present in fish, with clearly recognizable orthologous relationships. The class II cytokines and their receptors have diverged extensively, obscuring orthologies, but the number of receptors is similar in all species analyzed. In the family of the NLR proteins, the canonical members are conserved. We also found a conserved NACHT-domain protein with WD40 repeats that had previously not been described in mammals. Additionally, we have identified in each of the three fish a large species-specific subgroup of NLR proteins that contain a novel amino-terminal domain that is not found in mammalian genomes. Conclusion The main innate immune signaling pathways are conserved in mammals and teleost fish. Whereas the components that act downstream of the receptors are highly conserved, with orthologous sets of genes in mammals and teleosts, components that are known or assumed to interact with pathogens are more divergent and have undergone lineage-specific expansions.
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Affiliation(s)
- Cornelia Stein
- Institute for Genetics, University of Cologne, Zuelpicher Str, 47, 50674 Cologne, Germany.
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Jugessur A, Rahimov F, Lie RT, Wilcox AJ, Gjessing HK, Nilsen RM, Nguyen TT, Murray JC. Genetic variants in IRF6 and the risk of facial clefts: single-marker and haplotype-based analyses in a population-based case-control study of facial clefts in Norway. Genet Epidemiol 2008; 32:413-24. [PMID: 18278815 DOI: 10.1002/gepi.20314] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Mutations in the gene encoding interferon regulatory factor 6 (IRF6) underlie a common form of syndromic clefting known as Van der Woude syndrome. Lip pits and missing teeth are the only additional features distinguishing the syndrome from isolated clefts. Van der Woude syndrome, therefore, provides an excellent model for studying the isolated forms of clefting. From a population-based case-control study of facial clefts in Norway (1996-2001), we selected 377 cleft lip with or without cleft palate (CL/P), 196 cleft palate only (CPO), and 763 control infant-parent triads for analysis. We genotyped six single nucleotide polymorphisms within the IRF6 locus and estimated the relative risks (RR) conferred on the child by alleles and haplotypes of the child and of the mother. On the whole, there were strong statistical associations with CL/P but not CPO in our data. In single-marker analyses, mothers with a double-dose of the 'a'-allele at rs4844880 had an increased risk of having a child with CL/P (RR=1.85, 95% confidence interval: 1.04-3.25; P=0.036). An RR of 0.38 (95% confidence interval: 0.16-0.92; P=0.031) was obtained when the child carried a single-dose of the 'a'-allele at rs2235371 (the p.V274I polymorphism). The P-value for the overall test was <0.001. In haplotype analyses, several of the fetal and maternal haplotype relative risks were statistically significant individually but were not strong enough to show up on the overall test (P=0.113). Taken together, these findings further support a role for IRF6 variants in clefting of the lip and provide specific risk estimates in a Norwegian population.
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Affiliation(s)
- Astanand Jugessur
- Section for Epidemiology and Medical Statistics, Department of Public Health and Primary Health Care, University of Bergen, Bergen, Norway.
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Park JW, McIntosh I, Hetmanski JB, Jabs EW, Vander Kolk CA, Wu-Chou YH, Chen PK, Chong SS, Yeow V, Jee SH, Park BY, Fallin MD, Ingersoll R, Scott AF, Beaty TH. Association between IRF6 and nonsyndromic cleft lip with or without cleft palate in four populations. Genet Med 2007; 9:219-27. [PMID: 17438386 PMCID: PMC2846512 DOI: 10.1097/gim.0b013e3180423cca] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
PURPOSE The interferon regulatory factor 6 (IRF6), the gene that causes van der Woude syndrome has been shown to be associated with nonsyndromic cleft lip with or without palate in several populations. This study aimed to confirm the contribution of IRF6 to cleft lip with or without palate risk in additional Asian populations. METHODS A set of 13 single nucleotide polymorphisms was tested for association with cleft lip with or without palate in 77 European American, 146 Taiwanese, 34 Singaporean, and 40 Korean case-parent trios using both the transmission disequilibrium test and conditional logistic regression models. RESULTS Evidence of linkage and association was observed among all four populations; and two specific haplotypes [GC composed of rs2235373-rs2235371 (p.V274I) and AAG of rs599021-rs2235373-rs595918] showed the most significant over- and undertransmission among Taiwanese cases (P=9x10(-6) and P=5x10(-6), respectively). The AGC/CGC diplotype composed of rs599021-rs2235373-rs2013162 showed almost a 7-fold increase in risk among the Taiwanese sample (P<10(-3)). These results confirmed the contribution of this gene to susceptibility of oral clefts across different populations; however, the specific single nucleotide polymorphisms showing statistical significance differed among ethnic groups. CONCLUSION The high-risk genotypes and diplotypes identified here may provide a better understanding of the etiological role of this gene in oral clefts and potential options for genetic counseling.
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Affiliation(s)
- Ji Wan Park
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA, and Department of Medical Research and Craniofacial Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
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Boyadjiev SA, Fromme JC, Ben J, Chong SS, Nauta C, Hur DJ, Zhang G, Hamamoto S, Schekman R, Ravazzola M, Orci L, Eyaid W. Cranio-lenticulo-sutural dysplasia is caused by a SEC23A mutation leading to abnormal endoplasmic-reticulum-to-Golgi trafficking. Nat Genet 2006; 38:1192-7. [PMID: 16980979 DOI: 10.1038/ng1876] [Citation(s) in RCA: 230] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2006] [Accepted: 08/04/2006] [Indexed: 11/08/2022]
Abstract
Cranio-lenticulo-sutural dysplasia (CLSD) is an autosomal recessive syndrome characterized by late-closing fontanels, sutural cataracts, facial dysmorphisms and skeletal defects mapped to chromosome 14q13-q21 (ref. 1). Here we show, using a positional cloning approach, that an F382L amino acid substitution in SEC23A segregates with this syndrome. SEC23A is an essential component of the COPII-coated vesicles that transport secretory proteins from the endoplasmic reticulum to the Golgi complex. Electron microscopy and immunofluorescence show that there is gross dilatation of the endoplasmic reticulum in fibroblasts from individuals affected with CLSD. These cells also exhibit cytoplasmic mislocalization of SEC31. Cell-free vesicle budding assays show that the F382L substitution results in loss of SEC23A function. A phenotype reminiscent of CLSD is observed in zebrafish embryos injected with sec23a-blocking morpholinos. Our observations suggest that disrupted endoplasmic reticulum export of the secretory proteins required for normal morphogenesis accounts for CLSD.
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Affiliation(s)
- Simeon A Boyadjiev
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
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