1
|
Sinha BK, Kumar D, Meher P, Kumari S, Prakash K, Gourinath S, Kashav T. Biophysical and functional characterization of N-terminal domain of Human Interferon Regulatory Factor 6. Mol Biol Rep 2024; 51:380. [PMID: 38429584 DOI: 10.1007/s11033-024-09205-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/02/2024] [Indexed: 03/03/2024]
Abstract
BACKGROUND Interferon regulatory factor 6 (IRF6) has a key function in palate fusion during palatogenesis during embryonic development, and mutations in IRF6 cause orofacial clefting disorders. METHODS AND RESULTS The in silico analysis of IRF6 is done to obtain leads for the domain boundaries and subsequently the sub-cloning of the N-terminal domain of IRF6 into the pGEX-2TK expression vector and successfully optimized the overexpression and purification of recombinant glutathione S-transferase-fused NTD-IRF6 protein under native conditions. After cleavage of the GST tag, NTD-IRF6 was subjected to protein folding studies employing Circular Dichroism and Intrinsic fluorescence spectroscopy at variable pH, temperature, and denaturant. CD studies showed predominantly alpha-helical content and the highest stability of NTD-IRF6 at pH 9.0. A comparison of native and renatured protein depicts loss in the secondary structural content. Intrinsic fluorescence and quenching studies have identified that tryptophan residues are majorly present in the buried areas of the protein and a small fraction was on or near the protein surface. Upon the protein unfolding with a higher concentration of denaturant urea, the peak of fluorescence intensity decreased and red shifted, confirming that tryptophan residues are majorly present in a more polar environment. While regulating IFNβ gene expression during viral infection, the N-terminal domain binds to the promoter region of Virus Response Element-Interferon beta (VRE-IFNβ). Along with the protein folding analysis, this study also aimed to identify the DNA-binding activity and determine the binding affinities of NTD-IRF6 with the VRE-IFNβ promoter region. The protein-DNA interaction is specific as demonstrated by gel retardation assay and the kinetics of molecular interactions as quantified by Biolayer Interferometry showed a strong affinity with an affinity constant (KD) value of 7.96 × 10-10 M. CONCLUSION NTD-IRF6 consists of a mix of α-helix and β-sheets that show temperature-dependent cooperative unfolding between 40 °C and 55 °C. Urea-induced unfolding shows moderate tolerance to urea as the mid-transition concentration of urea (Cm) is 3.2 M. The tryptophan residues are majorly buried as depicted by fluorescence quenching studies. NTD-IRF6 has a specific and high affinity toward the promoter region of VRE-IFNβ.
Collapse
Affiliation(s)
- Binita Kumari Sinha
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar, 824236, India
| | - Devbrat Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Priyabrata Meher
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar, 824236, India
| | - Shilpi Kumari
- Department of Biochemical Engineering and Biotechnology, IIT Delhi, New Delhi, India
| | - Krishna Prakash
- Department of Biotechnology, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar, India
| | | | - Tara Kashav
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar, 824236, India.
| |
Collapse
|
2
|
Schierz IAM, Amoroso S, Antona V, Giuffrè M, Piro E, Serra G, Corsello G. Novel de novo missense mutation in the interferon regulatory factor 6 gene in an Italian infant with IRF6-related disorder. Ital J Pediatr 2022; 48:132. [PMID: 35906647 PMCID: PMC9338470 DOI: 10.1186/s13052-022-01330-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/19/2022] [Indexed: 11/18/2022] Open
Abstract
Background Congenital maxillomandibular syngnathia is a rare craniofacial anomaly leading to difficulties in feeding, breathing and ability to thrive. The fusion may consist of soft tissue union (synechiae) to hard tissue union. Isolated cases of maxillomandibular fusion are extremely rare, it is most often syndromic in etiology. Case presentation Clinical management of a female newborn with oromaxillofacial abnormities (synechiae, cleft palate, craniofacial dysmorphisms, dental anomaly) and extraoral malformations (skinfold overlying the nails of both halluces, syndactyly, abnormal external genitalia) is presented. The associated malformations addressed to molecular genetic investigations revealing an interferon regulatory factor 6 (IRF6)-related disorder (van der Woude syndrome/popliteal pterygium syndrome). A novel de novo heterozygous mutation in exon 4 of IRF6 gene on chromosome 1q32.2, precisely c.262A > G (p.Asn88Asp), was found. Similarities are discussed with known asparagine missense mutations in the same codon, which may alter IRF6 gene function by reduced DNA-binding ability. A concomitant maternal Xp11.22 duplication involving two microRNA genes could contribute to possible epigenetic effects. Conclusions Our reported case carrying a novel mutation can contribute to expand understandings of molecular mechanisms underlying synechiae and orofacial clefting and to correct diagnosing of incomplete or overlapping features in IRF6-related disorders. Additional multidisciplinary evaluations to establish the phenotypical extent of the IRF6-related disorder and to address family counseling should not only be focused on the surgical corrections of syngnathia and cleft palate, but also involve comprehensive otolaryngologic, audiologic, logopedic, dental, orthopedic, urological and psychological evaluations.
Collapse
Affiliation(s)
- Ingrid Anne Mandy Schierz
- Neonatal Intensive Care Unit, Department of Health Promotion, Mother-Child Care, Internal Medicine and Medical Specialties "G. D'Alessandro", University Hospital "P. Giaccone", Via Alfonso Giordano n. 3, 90127, Palermo, Italy.
| | - Salvatore Amoroso
- Pediatric Surgery Unit, Children's Hospital, ARNAS Civico - Di Cristina - Benfratelli, Palermo, Italy
| | - Vincenzo Antona
- Neonatal Intensive Care Unit, Department of Health Promotion, Mother-Child Care, Internal Medicine and Medical Specialties "G. D'Alessandro", University Hospital "P. Giaccone", Via Alfonso Giordano n. 3, 90127, Palermo, Italy
| | - Mario Giuffrè
- Neonatal Intensive Care Unit, Department of Health Promotion, Mother-Child Care, Internal Medicine and Medical Specialties "G. D'Alessandro", University Hospital "P. Giaccone", Via Alfonso Giordano n. 3, 90127, Palermo, Italy
| | - Ettore Piro
- Neonatal Intensive Care Unit, Department of Health Promotion, Mother-Child Care, Internal Medicine and Medical Specialties "G. D'Alessandro", University Hospital "P. Giaccone", Via Alfonso Giordano n. 3, 90127, Palermo, Italy
| | - Gregorio Serra
- Neonatal Intensive Care Unit, Department of Health Promotion, Mother-Child Care, Internal Medicine and Medical Specialties "G. D'Alessandro", University Hospital "P. Giaccone", Via Alfonso Giordano n. 3, 90127, Palermo, Italy
| | - Giovanni Corsello
- Neonatal Intensive Care Unit, Department of Health Promotion, Mother-Child Care, Internal Medicine and Medical Specialties "G. D'Alessandro", University Hospital "P. Giaccone", Via Alfonso Giordano n. 3, 90127, Palermo, Italy
| |
Collapse
|
3
|
Girousi E, Muerner L, Parisi L, Rihs S, von Gunten S, Katsaros C, Degen M. Lack of IRF6 Disrupts Human Epithelial Homeostasis by Altering Colony Morphology, Migration Pattern, and Differentiation Potential of Keratinocytes. Front Cell Dev Biol 2021; 9:718066. [PMID: 34660580 PMCID: PMC8514984 DOI: 10.3389/fcell.2021.718066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/16/2021] [Indexed: 12/03/2022] Open
Abstract
Variants within the gene encoding for the transcription factor Interferon Regulatory Factor 6 (IRF6) are associated with syndromic and non-syndromic Cleft Lip/Palate (CLP) cases. IRF6 plays a vital role in the regulation of the proliferation/differentiation balance in keratinocytes and is involved in wound healing and migration. Since a fraction of CLP patients undergoing corrective cleft surgery experience wound healing complications, IRF6 represents an interesting candidate gene linking the two processes. However, Irf6 function has been mainly studied in mice and knowledge on IRF6 in human cells remains sparse. Here, we aimed to elucidate the role of IRF6 in human postnatal skin- and oral mucosa-derived keratinocytes. To do so, we applied CRISPR/Cas9 to ablate IRF6 in two TERT-immortalized keratinocyte cultures, which we used as model cell lines. We show that IRF6 controls the appearance of single cells and colonies, with the latter being less cohesive in its absence. Consequently, IRF6 knockout keratinocytes often moved as single cells instead of a collective epithelial sheet migration but maintained their epithelial character. Lack of IRF6 triggered severe keratinocyte differentiation defects, which were already apparent in the stratum spinosum and extended to the stratum corneum in 3D organotypic skin cultures, while it did not alter their growth rate. Finally, proteomics revealed that most of the differentially expressed proteins in the absence of IRF6 could be associated with differentiation, cell-cell adhesion as well as immune response. Our data expand the knowledge on IRF6 in human postnatal keratinocytes, which will help to better understand IRF6-related pathologies.
Collapse
Affiliation(s)
- Eleftheria Girousi
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| | - Lukas Muerner
- Institute of Pharmacology, University of Bern, Bern, Switzerland
| | - Ludovica Parisi
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| | - Silvia Rihs
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| | | | - Christos Katsaros
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| | - Martin Degen
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| |
Collapse
|
4
|
Vieira AR, Koruyucu M, Bekele EK, Seymen F, Modesto A. IRF6 Genetic Variation and Maternal Smoking During Pregnancy in Cleft Lip/Palate. FRONTIERS IN DENTAL MEDICINE 2021. [DOI: 10.3389/fdmed.2021.632055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The goal of the present work was to revisit published data to test if genetic variation in interferon regulatory factor 6 (IRF6) is associated with children born with cleft lip with or without cleft palate (CL/P) for cases with positive history of maternal smoking. From the 573 individuals originally studied, this reanalysis focused on 57 who had a positive history of maternal smoking during pregnancy (39 born with CL/P and 18 born without CL/P). Seven IRF6 markers (rs4844880, rs2235371, rs2013162, ra861019, rs2073487, rs642961, and rs658860) were tested for over-transmission of alleles and an alpha of 0.05 was considered statistically significant. All individuals born with CL/P were homozygous for the wild type allele of rs2235371 in comparison to just two individuals born without clefts (p = 0.0000001). For rs861019, individuals born with CL/P were more likely to have the variant allele (p = 0.006). A similar trend was seen for rs642961 (p = 0.09). The results suggest that statistical evidence of over-representation of IRF6 alleles in individuals born with CL/P may be unveiled only when maternal smoking during pregnancy is used as the inclusion criterion in the analysis.
Collapse
|
5
|
Degen M, Girousi E, Feldmann J, Parisi L, La Scala GC, Schnyder I, Schaller A, Katsaros C. A Novel Van der Woude Syndrome-Causing IRF6 Variant Is Subject to Incomplete Non-sense-Mediated mRNA Decay Affecting the Phenotype of Keratinocytes. Front Cell Dev Biol 2020; 8:583115. [PMID: 33117810 PMCID: PMC7552806 DOI: 10.3389/fcell.2020.583115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/03/2020] [Indexed: 01/02/2023] Open
Abstract
Van der Woude syndrome (VWS) is a genetic syndrome that leads to typical phenotypic traits, including lower lip pits and cleft lip/palate (CLP). The majority of VWS-affected patients harbor a pathogenic variant in the gene encoding for the transcription factor interferon regulatory factor 6 (IRF6), a crucial regulator of orofacial development, epidermal differentiation and tissue repair. However, most of the underlying mechanisms leading from pathogenic IRF6 gene variants to phenotypes observed in VWS remain poorly understood and elusive. The availability of one VWS individual within our cohort of CLP patients allowed us to identify a novel VWS-causing IRF6 variant and to functionally characterize it. Using VWS patient-derived keratinocytes, we reveal that most of the mutated IRF6_VWS transcripts are subject to a non-sense-mediated mRNA decay mechanism, resulting in IRF6 haploinsufficiency. While moderate levels of IRF6_VWS remain detectable in the VWS keratinocytes, our data illustrate that the IRF6_VWS protein, which lacks part of its protein-binding domain and its whole C-terminus, is noticeably less stable than its wild-type counterpart. Still, it maintains transcription factor function. As we report and characterize a so far undescribed VWS-causing IRF6 variant, our results shed light on the physiological as well as pathological role of IRF6 in keratinocytes. This acquired knowledge is essential for a better understanding of the molecular mechanisms leading to VWS and CLP.
Collapse
Affiliation(s)
- Martin Degen
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| | - Eleftheria Girousi
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| | - Julia Feldmann
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| | - Ludovica Parisi
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| | - Giorgio C La Scala
- Division of Pediatric Surgery, Department of Pediatrics, University Hospital of Geneva, Geneva, Switzerland
| | - Isabelle Schnyder
- University Clinic for Pediatric Surgery, Bern University Hospital, Bern, Switzerland
| | - André Schaller
- Division of Human Genetics, Bern University Hospital, Bern, Switzerland
| | - Christos Katsaros
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| |
Collapse
|
6
|
Rangel-Huerta E, Guzman A, Maldonado E. The dynamics of epidermal stratification during post-larval development in zebrafish. Dev Dyn 2020; 250:175-190. [PMID: 32877571 DOI: 10.1002/dvdy.249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 08/08/2020] [Accepted: 08/22/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The epidermis, as a defensive barrier, is a consistent trait throughout animal evolution. During post-larval development, the zebrafish epidermis thickens by stratification or addition of new cell layers. Epidermal basal stem cells, expressing the transcription factor p63, are known to be involved in this process. Zebrafish post-larval epidermal stratification is a tractable system to study how stem cells participate in organ growth. METHODS We used immunohistochemistry, in combination with EdU cell proliferation detection, to study zebrafish epidermal stratification. For this procedure, we selected a window of post-larval stages (5-8 mm of standard length or SL, which normalizes age by size). Simultaneously, we used markers for asymmetric cell division and the Notch signaling pathway. RESULTS We found that epidermal stratification is the consequence of several events, including changes in cell shape, active cell proliferation and asymmetrical cell divisions. We identified a subset of highly proliferative epidermal cells with reduced levels of p63, which differed from the basal stem cells with high levels of p63. Additionally, we described different mechanisms that participate in the stratification process, including the phosphorylation of p63, asymmetric cell division regulated by the Par3 and LGN proteins, and expression of Notch genes.
Collapse
Affiliation(s)
- Emma Rangel-Huerta
- EvoDevo Research Group, Unidad de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México (UNAM), Puerto Morelos, Quintana Roo, Mexico.,Posgrado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, UNAM, Puerto Morelos, Quintana Roo, Mexico
| | - Aida Guzman
- EvoDevo Research Group, Unidad de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México (UNAM), Puerto Morelos, Quintana Roo, Mexico.,Estudio Técnico Especializado en Histopatología, Escuela Nacional Preparatoria, ENP, Universidad Nacional Autónoma de México, UNAM, Ciudad de México, Mexico
| | - Ernesto Maldonado
- EvoDevo Research Group, Unidad de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México (UNAM), Puerto Morelos, Quintana Roo, Mexico
| |
Collapse
|