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Kooblall KG, Stevenson M, Heilig R, Stewart M, Wright B, Lockstone H, Buck D, Fischer R, Wells S, Lines KE, Teboul L, Hennekam RC, Thakker RV. Identification of cellular retinoic acid binding protein 2 (CRABP2) as downstream target of nuclear factor I/X (NFIX): implications for skeletal dysplasia syndromes. JBMR Plus 2024; 8:ziae060. [PMID: 38827116 PMCID: PMC11144382 DOI: 10.1093/jbmrpl/ziae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/04/2024] [Indexed: 06/04/2024] Open
Abstract
Nuclear factor I/X (NFIX) mutations are associated with 2 skeletal dysplasias, Marshall-Smith (MSS) and Malan (MAL) syndromes. NFIX encodes a transcription factor that regulates expression of genes, including Bobby sox (BBX) and glial fibrillary acidic protein (GFAP) in neural progenitor cells and astrocytes, respectively. To elucidate the role of NFIX mutations in MSS, we studied their effects in fibroblast cell lines obtained from 5 MSS unrelated patients and 3 unaffected individuals. The 5 MSS NFIX frameshift mutations in exons 6-8 comprised 3 deletions (c.819-732_1079-948del, c.819-471_1079-687del, c.819-592_1079-808del), an insertion (c.1037_1038insT), and a duplication (c.1090dupG). Quantitative reverse transcription polymerase chain reaction (qRT-PCR) and western blot analyses using MSS and unrelated control fibroblasts and in vitro expression studies in monkey kidney fibroblast (COS-7) cells showed that frameshift mutations in NFIX exons 6-8 generated mutant transcripts that were not cleared by nonsense-mediated-decay mechanisms and encoded truncated NFIX proteins. Moreover, BBX or GFAP expression was unaffected in the majority of MSS fibroblasts. To identify novel NFIX downstream target genes, RNA sequencing and proteomics analyses were performed on mouse embryonic fibroblast (MEF) cells derived from control Nfix+/+, Nfix+/Del2, Nfix+/Del24, NfixDel24/Del24, Nfix+/Del140, and NfixDel140/Del140 mice, compared with NfixDel2/Del2 mice which had developmental, skeletal, and neural abnormalities. This identified 191 transcripts and 815 proteins misregulated in NfixDel2/Del2 MEFs with ≥2-fold-change (P <0 .05). Validation studies using qRT-PCR and western blot analyses confirmed that 2 genes, cellular retinoic acid binding protein 2 (Crabp2) and vascular cell adhesion molecule 1 (Vcam1), were misregulated at the RNA and protein levels in NfixDel2/Del2 MEFs, and that CRABP2 and VCAM1 expressions were altered in 60%-100% of MSS fibroblast cells. Furthermore, in vitro luciferase reporter assays confirmed that NFIX directly regulates CRABP2 promoter activity. Thus, these altered genes and pathways may represent possible targets for drugs as potential treatments and therapies for MSS.
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Affiliation(s)
- Kreepa G Kooblall
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), University of Oxford, Churchill Hospital, Headington, Oxford OX3 7LJ, United Kingdom
| | - Mark Stevenson
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), University of Oxford, Churchill Hospital, Headington, Oxford OX3 7LJ, United Kingdom
| | - Raphael Heilig
- Target Discovery Unit, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Michelle Stewart
- MRC Harwell, Mary Lyon Centre, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, United Kingdom
| | - Benjamin Wright
- Oxford Genomics Centre, The Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Helen Lockstone
- Oxford Genomics Centre, The Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - David Buck
- Oxford Genomics Centre, The Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Roman Fischer
- Target Discovery Unit, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Sara Wells
- MRC Harwell, Mary Lyon Centre, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, United Kingdom
| | - Kate E Lines
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), University of Oxford, Churchill Hospital, Headington, Oxford OX3 7LJ, United Kingdom
| | - Lydia Teboul
- MRC Harwell, Mary Lyon Centre, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, United Kingdom
| | - Raoul C Hennekam
- Department of Pediatrics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - Rajesh V Thakker
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), University of Oxford, Churchill Hospital, Headington, Oxford OX3 7LJ, United Kingdom
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Martínez D, Nualart D, Loncoman C, Opazo JC, Zabala K, Morera FJ, Mardones GA, Vargas-Chacoff L. Discovery of BbX transcription factor in the patagonian blennie: Exploring expression changes following combined bacterial and thermal stress exposure. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 149:105056. [PMID: 37730191 DOI: 10.1016/j.dci.2023.105056] [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: 03/31/2023] [Revised: 09/10/2023] [Accepted: 09/10/2023] [Indexed: 09/22/2023]
Abstract
High-Mobility Group (HMG) proteins are involved in different processes such as transcription, replication, DNA repair, and immune response. The role of HMG proteins in the immune response of fish has been studied mainly for HMGB1, where its expression can be induced by the stimulation of viral/bacterial PAMPs and can act as a proinflammatory mediator and as a global regulator of transcription in response to temperature. However, for BbX this role remains to be discovered. In this work, we identified the BbX of E. maclovinus and evaluated the temporal expression levels after simultaneous challenge with P. salmonis and thermal stress. Phylogenetic analysis does not significantly deviate from the expected organismal relationships suggesting orthologous relationships and that BbX was present in the common ancestor of the group. BbX mRNA expression levels were very high in the intestinal tissue of E. maclovinus (foregut, midgut, and hindgut). Nevertheless, the protein levels analyzed by WB showed the highest levels of BbX protein in the liver (constitutive expression). On the other hand, the mRNA expression levels of BbX in the liver of E. maclovinus injected with P. salmonis and subjected to thermal stress showed an increase at days 16 and 20 in all treatments applied at 12 °C and 18 °C. Meanwhile, the protein levels quantified by WB showed a statistically significant increase in the HMG-Bbx at all experimental times (4, 8, 12, 16, and 20 dpi). However, at 4 dpi the HMG-Bbx protein levels were much higher than the other days evaluated. The results suggest that BbX protein may be implicated in the response mechanism to temperature and bacterial stimulation in the foregut, midgut, hindgut, and liver, according to our findings at the level of mRNA and protein. Furthermore, our WB analysis suggests an effect of P. salmonis on the expression of this protein that can be observed in condition C+ 12 °C compared to C- 12 °C. Then, there is an effect of temperature that can be evidenced in the condition AM 18 °C and SM 18 °C, compared to AB 18 °C and SB 18 °C at 4, 8, and 12 dpi. We found not differences in the levels of this protein if the thermal stress is achieved through acclimatization or shock. More research is necessary to clarify the importance of this type of HMG in the immune response and thermal tolerance in fish.
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Affiliation(s)
- Danixa Martínez
- Laboratorio Institucional de Investigación, Facultad de Ciencias de La Naturaleza, Universidad San Sebastián, Puerto Montt, Chile.
| | - Daniela Nualart
- Escuela de Graduados, Programa de Doctorado en Ciencias de La Acuicultura, Universidad Austral de Chile, Puerto Montt, Chile; Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile; Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems, BASE, University Austral of Chile, Valdivia, Chile; Centro Fondap de Investigación de Altas Latitudes (IDEAL), Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| | - Carlos Loncoman
- Instituto de Bioquímica y Microbiología, Laboratorio de Bioquímica Farmacológica, Virología y Biotecnología, Universidad Austral de Chile, Valdivia, Chile
| | - Juan C Opazo
- Integrative Biology Group, Valdivia, Chile; Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Valdivia, Chile; Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, Chile
| | - Kattina Zabala
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, Chile
| | - Francisco J Morera
- Integrative Biology Group, Valdivia, Chile; Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas y Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gonzalo A Mardones
- Integrative Biology Group, Valdivia, Chile; Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, Chile
| | - Luis Vargas-Chacoff
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile; Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems, BASE, University Austral of Chile, Valdivia, Chile; Centro Fondap de Investigación de Altas Latitudes (IDEAL), Universidad Austral de Chile, Casilla 567, Valdivia, Chile; Integrative Biology Group, Valdivia, Chile.
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Rodríguez-Vega A, Dutra-Tavares AC, Souza TP, Semeão KA, Filgueiras CC, Ribeiro-Carvalho A, Manhães AC, Abreu-Villaça Y. Nicotine Exposure in a Phencyclidine-Induced Mice Model of Schizophrenia: Sex-Selective Medial Prefrontal Cortex Protein Markers of the Combined Insults in Adolescent Mice. Int J Mol Sci 2023; 24:14634. [PMID: 37834084 PMCID: PMC10572990 DOI: 10.3390/ijms241914634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Tobacco misuse as a comorbidity of schizophrenia is frequently established during adolescence. However, comorbidity markers are still missing. Here, the method of label-free proteomics was used to identify deregulated proteins in the medial prefrontal cortex (prelimbic and infralimbic) of male and female mice modelled to schizophrenia with a history of nicotine exposure during adolescence. Phencyclidine (PCP), used to model schizophrenia (SCHZ), was combined with an established model of nicotine minipump infusions (NIC). The combined insults led to worse outcomes than each insult separately when considering the absolute number of deregulated proteins and that of exclusively deregulated ones. Partially shared Reactome pathways between sexes and between PCP, NIC and PCPNIC groups indicate functional overlaps. Distinctively, proteins differentially expressed exclusively in PCPNIC mice reveal unique effects associated with the comorbidity model. Interactome maps of these proteins identified sex-selective subnetworks, within which some proteins stood out: for females, peptidyl-prolyl cis-trans isomerase (Fkbp1a) and heat shock 70 kDa protein 1B (Hspa1b), both components of the oxidative stress subnetwork, and gamma-enolase (Eno2), a component of the energy metabolism subnetwork; and for males, amphiphysin (Amph), a component of the synaptic transmission subnetwork. These are proposed to be further investigated and validated as markers of the combined insult during adolescence.
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Affiliation(s)
- Andrés Rodríguez-Vega
- Laboratório de Neurofisiologia, Departamento de Ciências Fisiológicas, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro 20550-170, RJ, Brazil; (A.R.-V.); (A.C.D.-T.); (T.P.S.); (K.A.S.); (C.C.F.); (A.C.M.)
| | - Ana Carolina Dutra-Tavares
- Laboratório de Neurofisiologia, Departamento de Ciências Fisiológicas, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro 20550-170, RJ, Brazil; (A.R.-V.); (A.C.D.-T.); (T.P.S.); (K.A.S.); (C.C.F.); (A.C.M.)
| | - Thainá P. Souza
- Laboratório de Neurofisiologia, Departamento de Ciências Fisiológicas, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro 20550-170, RJ, Brazil; (A.R.-V.); (A.C.D.-T.); (T.P.S.); (K.A.S.); (C.C.F.); (A.C.M.)
| | - Keila A. Semeão
- Laboratório de Neurofisiologia, Departamento de Ciências Fisiológicas, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro 20550-170, RJ, Brazil; (A.R.-V.); (A.C.D.-T.); (T.P.S.); (K.A.S.); (C.C.F.); (A.C.M.)
| | - Claudio C. Filgueiras
- Laboratório de Neurofisiologia, Departamento de Ciências Fisiológicas, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro 20550-170, RJ, Brazil; (A.R.-V.); (A.C.D.-T.); (T.P.S.); (K.A.S.); (C.C.F.); (A.C.M.)
| | - Anderson Ribeiro-Carvalho
- Departamento de Ciências, Faculdade de Formação de Professores da Universidade do Estado do Rio de Janeiro, São Gonçalo 24435-005, RJ, Brazil;
| | - Alex C. Manhães
- Laboratório de Neurofisiologia, Departamento de Ciências Fisiológicas, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro 20550-170, RJ, Brazil; (A.R.-V.); (A.C.D.-T.); (T.P.S.); (K.A.S.); (C.C.F.); (A.C.M.)
| | - Yael Abreu-Villaça
- Laboratório de Neurofisiologia, Departamento de Ciências Fisiológicas, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro 20550-170, RJ, Brazil; (A.R.-V.); (A.C.D.-T.); (T.P.S.); (K.A.S.); (C.C.F.); (A.C.M.)
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Kooblall KG, Stevenson M, Stewart M, Harris L, Zalucki O, Dewhurst H, Butterfield N, Leng H, Hough TA, Ma D, Siow B, Potter P, Cox RD, Brown SD, Horwood N, Wright B, Lockstone H, Buck D, Vincent TL, Hannan FM, Bassett JD, Williams GR, Lines KE, Piper M, Wells S, Teboul L, Hennekam RC, Thakker RV. A Mouse Model with a Frameshift Mutation in the Nuclear Factor I/X ( NFIX) Gene Has Phenotypic Features of Marshall-Smith Syndrome. JBMR Plus 2023; 7:e10739. [PMID: 37283649 PMCID: PMC10241085 DOI: 10.1002/jbm4.10739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/05/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023] Open
Abstract
The nuclear factor I/X (NFIX) gene encodes a ubiquitously expressed transcription factor whose mutations lead to two allelic disorders characterized by developmental, skeletal, and neural abnormalities, namely, Malan syndrome (MAL) and Marshall-Smith syndrome (MSS). NFIX mutations associated with MAL mainly cluster in exon 2 and are cleared by nonsense-mediated decay (NMD) leading to NFIX haploinsufficiency, whereas NFIX mutations associated with MSS are clustered in exons 6-10 and escape NMD and result in the production of dominant-negative mutant NFIX proteins. Thus, different NFIX mutations have distinct consequences on NFIX expression. To elucidate the in vivo effects of MSS-associated NFIX exon 7 mutations, we used CRISPR-Cas9 to generate mouse models with exon 7 deletions that comprised: a frameshift deletion of two nucleotides (Nfix Del2); in-frame deletion of 24 nucleotides (Nfix Del24); and deletion of 140 nucleotides (Nfix Del140). Nfix +/Del2, Nfix +/Del24, Nfix +/Del140, Nfix Del24/Del24, and Nfix Del140/Del140 mice were viable, normal, and fertile, with no skeletal abnormalities, but Nfix Del2/Del2 mice had significantly reduced viability (p < 0.002) and died at 2-3 weeks of age. Nfix Del2 was not cleared by NMD, and NfixDel2/Del2 mice, when compared to Nfix +/+ and Nfix +/Del2 mice, had: growth retardation; short stature with kyphosis; reduced skull length; marked porosity of the vertebrae with decreased vertebral and femoral bone mineral content; and reduced caudal vertebrae height and femur length. Plasma biochemistry analysis revealed Nfix Del2/Del2 mice to have increased total alkaline phosphatase activity but decreased C-terminal telopeptide and procollagen-type-1-N-terminal propeptide concentrations compared to Nfix +/+ and Nfix +/Del2 mice. Nfix Del2/Del2 mice were also found to have enlarged cerebral cortices and ventricular areas but smaller dentate gyrus compared to Nfix +/+ mice. Thus, Nfix Del2/Del2 mice provide a model for studying the in vivo effects of NFIX mutants that escape NMD and result in developmental abnormalities of the skeletal and neural tissues that are associated with MSS. © 2023 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Kreepa G. Kooblall
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
| | - Mark Stevenson
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
| | - Michelle Stewart
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | | | - Oressia Zalucki
- The School of Biomedical Sciences and The Queensland Brain InstituteThe University of QueenslandBrisbaneAustralia
| | - Hannah Dewhurst
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College LondonHammersmith HospitalLondonUK
| | - Natalie Butterfield
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College LondonHammersmith HospitalLondonUK
| | - Houfu Leng
- Centre for OA Pathogenesis Versus Arthritis, The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS)Medical Sciences Division University of OxfordOxfordUK
| | - Tertius A. Hough
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Da Ma
- Department of Internal MedicineWake Forest University School of MedicineWinston‐SalemNCUSA
| | | | - Paul Potter
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Roger D. Cox
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Stephen D.M. Brown
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Nicole Horwood
- Centre for OA Pathogenesis Versus Arthritis, The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS)Medical Sciences Division University of OxfordOxfordUK
| | - Benjamin Wright
- Oxford Genomics Centre, The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Helen Lockstone
- Oxford Genomics Centre, The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - David Buck
- Oxford Genomics Centre, The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Tonia L. Vincent
- Centre for OA Pathogenesis Versus Arthritis, The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS)Medical Sciences Division University of OxfordOxfordUK
| | - Fadil M. Hannan
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
- Nuffield Department of Women's and Reproductive HealthUniversity of OxfordOxfordUK
| | - J.H. Duncan Bassett
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College LondonHammersmith HospitalLondonUK
| | - Graham R. Williams
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College LondonHammersmith HospitalLondonUK
| | - Kate E. Lines
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
| | - Michael Piper
- The School of Biomedical Sciences and The Queensland Brain InstituteThe University of QueenslandBrisbaneAustralia
| | - Sara Wells
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Lydia Teboul
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Raoul C. Hennekam
- Department of Pediatrics, Amsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Rajesh V. Thakker
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
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Aygün N, Liang D, Crouse WL, Keele GR, Love MI, Stein JL. Inferring cell-type-specific causal gene regulatory networks during human neurogenesis. Genome Biol 2023; 24:130. [PMID: 37254169 PMCID: PMC10230710 DOI: 10.1186/s13059-023-02959-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/05/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND Genetic variation influences both chromatin accessibility, assessed in chromatin accessibility quantitative trait loci (caQTL) studies, and gene expression, assessed in expression QTL (eQTL) studies. Genetic variants can impact either nearby genes (cis-eQTLs) or distal genes (trans-eQTLs). Colocalization between caQTL and eQTL, or cis- and trans-eQTLs suggests that they share causal variants. However, pairwise colocalization between these molecular QTLs does not guarantee a causal relationship. Mediation analysis can be applied to assess the evidence supporting causality versus independence between molecular QTLs. Given that the function of QTLs can be cell-type-specific, we performed mediation analyses to find epigenetic and distal regulatory causal pathways for genes within two major cell types of the developing human cortex, progenitors and neurons. RESULTS We find that the expression of 168 and 38 genes is mediated by chromatin accessibility in progenitors and neurons, respectively. We also find that the expression of 11 and 12 downstream genes is mediated by upstream genes in progenitors and neurons. Moreover, we discover that a genetic locus associated with inter-individual differences in brain structure shows evidence for mediation of SLC26A7 through chromatin accessibility, identifying molecular mechanisms of a common variant association to a brain trait. CONCLUSIONS In this study, we identify cell-type-specific causal gene regulatory networks whereby the impacts of variants on gene expression were mediated by chromatin accessibility or distal gene expression. Identification of these causal paths will enable identifying and prioritizing actionable regulatory targets perturbing these key processes during neurodevelopment.
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Affiliation(s)
- Nil Aygün
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Dan Liang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Wesley L Crouse
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Gregory R Keele
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Michael I Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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Cui X, Dong Y, Li M, Wang X, Jiang M, Yang W, Liu G, Sun S, Xu W. A circular RNA from NFIX facilitates oxidative stress-induced H9c2 cells apoptosis. In Vitro Cell Dev Biol Anim 2020; 56:715-722. [PMID: 33067659 DOI: 10.1007/s11626-020-00476-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 06/11/2020] [Indexed: 02/07/2023]
Abstract
Myocardial infarction is the leading cause of death worldwide, and cardiomyocyte apoptosis during myocardial infarction and reperfusion is a significant factor of poor prognosis. As important regulatory molecules, biofunctions of circRNAs in the pathogenesis of myocardial infarction remain elusive. To confirm the expression level and biological function of circNFIX in cardiomyocytes upon oxidative stress. Divergent polymerase chain reaction and Sanger sequencing were performed to verify the circular structure. The stability of circNFIX was confirmed by RNase R treatment and actinomycin D assay. In order to simulate oxidative stress during myocardial infarction, H9c2 cells were subjected to hydrogen peroxide and hypoxia stimulation. In vivo, mouse models of myocardial ischemia were established. The biological function of circNFIX in cardiomyocytes was investigated through loss- and gain-of-function assays, and cardiomyocyte apoptosis level was detected by the terminal deoxyribonucleotidyl transferase-mediated TdT-mediated dUTP nick end labeling assay and Western blot. CircNFIX is abundant, conserved, and stable in H9c2 cells. The expression of circNFIX was significantly downregulated in cardiomyocytes subjected to oxidative stress. Enforced CircNFIX promotes H9c2 cells apoptosis induced by hydrogen peroxide, in sharp contrast to circNFIX knockdown. In this study, we found that circNFIX served as a pro-apoptosis factor in cardiomyocyte apoptosis. CircNFIX possesses potential to be the biomarker and therapeutic target in myocardial infarction.
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Affiliation(s)
- Xianglun Cui
- Department of Inspection, The Medical Faculty, Qingdao University, Qingdao, 266003, China
| | - Yanhan Dong
- Institute for Translational Medicine, Qingdao University, Deng Zhou Road 38, Qingdao, 266021, China
| | - Mingyu Li
- Department of Inspection, The Medical Faculty, Qingdao University, Qingdao, 266003, China
| | - Xuekang Wang
- Department of Inspection, The Medical Faculty, Qingdao University, Qingdao, 266003, China
| | - Meiqing Jiang
- Department of Inspection, The Medical Faculty, Qingdao University, Qingdao, 266003, China
| | - Weiwei Yang
- Department of Inspection, The Medical Faculty, Qingdao University, Qingdao, 266003, China
| | - Gege Liu
- Department of Inspection, The Medical Faculty, Qingdao University, Qingdao, 266003, China
| | - Shuqi Sun
- Department of Inspection, The Medical Faculty, Qingdao University, Qingdao, 266003, China
| | - Wenhua Xu
- Department of Inspection, The Medical Faculty, Qingdao University, Qingdao, 266003, China.
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Ihn HJ, Kim JA, Lim J, Nam SH, Hwang SH, Kim YK, Kim JY, Kim JE, Cho ES, Jiang R, Park EK. Bobby sox homolog regulates tooth root formation through modulation of dentin sialophosphoprotein. J Cell Physiol 2020; 236:480-488. [PMID: 32537777 DOI: 10.1002/jcp.29875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 06/01/2020] [Accepted: 06/01/2020] [Indexed: 11/09/2022]
Abstract
Tooth root development occurs through the interaction of multiple growth factors and transcription factors expressed in Hertwig's epithelial root sheath (HERS) and dental mesenchyme. Previously, we demonstrated that bobby sox homolog (Bbx) regulates odontoblast differentiation of human dental pulp stem cells. Here, we generated Bbx knockout (Bbx-/- ) mice to address the functional role of Bbx in tooth formation. During tooth development, Bbx was expressed in both dental epithelium and mesenchyme. However, molar and incisor morphology in Bbx-/- mice at postnatal Day 0 (P0) exhibited no prominent abnormalities compared with their wild-type (Bbx+/+ ) littermates. Until P28, the crown morphology in Bbx-/- mice was not distinctively different from Bbx+/+ littermates. Meanwhile, the length of the mandibular base in Bbx-/- mice was notably less at P28. Compared with Bbx+/+ mice, the mesial and distal root lengths of the first molar were reduced by 21.33% and 16.28% at P14 and 16.28% and 16.24% at P28, respectively, in Bbx-/- mice. The second molar of Bbx-/- mice also showed 10.16% and 6.4% reductions at P28 in the mesial and distal lengths, compared with Bbx+/+ mice, respectively. The gene expression analysis during early tooth root formation (P13) showed that the expression of dentin sialophosphoprotein (Dspp) was significantly decreased in Bbx-/- mice. Collectively, our data suggest that Bbx participates in tooth root formation and might be associated with the regulation of Dspp expression.
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Affiliation(s)
- Hye Jung Ihn
- Institute for Hard Tissue and Biotooth Regeneration, Kyungpook National University, Daegu, Republic of Korea
| | - Ju Ang Kim
- Department of Oral Pathology and Regenerative Medicine, School of Dentistry, Institute for Hard Tissue and Biotooth Regeneration, Kyungpook National University, Daegu, Republic of Korea
| | - Jiwon Lim
- Department of Oral Pathology and Regenerative Medicine, School of Dentistry, Institute for Hard Tissue and Biotooth Regeneration, Kyungpook National University, Daegu, Republic of Korea
| | - Sang-Hyeon Nam
- Department of Oral Pathology and Regenerative Medicine, School of Dentistry, Institute for Hard Tissue and Biotooth Regeneration, Kyungpook National University, Daegu, Republic of Korea
| | - So Hyeon Hwang
- Department of Oral Pathology and Regenerative Medicine, School of Dentistry, Institute for Hard Tissue and Biotooth Regeneration, Kyungpook National University, Daegu, Republic of Korea
| | - Young Kyung Kim
- Department of Conservative Dentistry, School of Dentistry, Kyungpook National University, Daegu, Republic of Korea
| | - Jae-Young Kim
- Department of Biochemistry, School of Dentistry, Kyungpook National University, Daegu, Republic of Korea
| | - Jung-Eun Kim
- Department of Molecular Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Eui-Sic Cho
- Cluster for Craniofacial Development and Regeneration Research, Institute of Oral Biosciences, School of Dentistry, Chonbuk National University, Jeonju, Republic of Korea
| | - Rulang Jiang
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Eui Kyun Park
- Department of Oral Pathology and Regenerative Medicine, School of Dentistry, Institute for Hard Tissue and Biotooth Regeneration, Kyungpook National University, Daegu, Republic of Korea
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8
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Fraser J, Essebier A, Brown AS, Davila RA, Sengar AS, Tu Y, Ensbey KS, Day BW, Scott MP, Gronostajski RM, Wainwright BJ, Boden M, Harvey TJ, Piper M. Granule neuron precursor cell proliferation is regulated by NFIX and intersectin 1 during postnatal cerebellar development. Brain Struct Funct 2018; 224:811-827. [PMID: 30511336 DOI: 10.1007/s00429-018-1801-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 11/24/2018] [Indexed: 01/06/2023]
Abstract
Cerebellar granule neurons are the most numerous neuronal subtype in the central nervous system. Within the developing cerebellum, these neurons are derived from a population of progenitor cells found within the external granule layer of the cerebellar anlage, namely the cerebellar granule neuron precursors (GNPs). The timely proliferation and differentiation of these precursor cells, which, in rodents occurs predominantly in the postnatal period, is tightly controlled to ensure the normal morphogenesis of the cerebellum. Despite this, our understanding of the factors mediating how GNP differentiation is controlled remains limited. Here, we reveal that the transcription factor nuclear factor I X (NFIX) plays an important role in this process. Mice lacking Nfix exhibit reduced numbers of GNPs during early postnatal development, but elevated numbers of these cells at postnatal day 15. Moreover, Nfix-/- GNPs exhibit increased proliferation when cultured in vitro, suggestive of a role for NFIX in promoting GNP differentiation. At a mechanistic level, profiling analyses using both ChIP-seq and RNA-seq identified the actin-associated factor intersectin 1 as a downstream target of NFIX during cerebellar development. In support of this, mice lacking intersectin 1 also displayed delayed GNP differentiation. Collectively, these findings highlight a key role for NFIX and intersectin 1 in the regulation of cerebellar development.
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Affiliation(s)
- James Fraser
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Alexandra Essebier
- The School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Alexander S Brown
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Raul Ayala Davila
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Ameet S Sengar
- Program in Neurosciences & Mental Health, The Hospital for Sick Children, Toronto, M5G 0A8, Canada
| | - YuShan Tu
- Program in Neurosciences & Mental Health, The Hospital for Sick Children, Toronto, M5G 0A8, Canada
| | - Kathleen S Ensbey
- Cell and Molecular Biology Department, Translational Brain Cancer Research Laboratory, QIMR Berghofer MRI, Brisbane, QLD, 4006, Australia
| | - Bryan W Day
- Cell and Molecular Biology Department, Translational Brain Cancer Research Laboratory, QIMR Berghofer MRI, Brisbane, QLD, 4006, Australia
| | - Matthew P Scott
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Richard M Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Brandon J Wainwright
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Mikael Boden
- The School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Tracey J Harvey
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia.
| | - Michael Piper
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia. .,Queensland Brain Institute, The University of Queensland, Brisbane, 4072, Australia.
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9
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Zalucki O, Harris L, Harvey TJ, Harkins D, Widagdo J, Oishi S, Matuzelski E, Yong XLH, Schmidt H, Anggono V, Burne THJ, Gronostajski RM, Piper M. NFIX-Mediated Inhibition of Neuroblast Branching Regulates Migration Within the Adult Mouse Ventricular–Subventricular Zone. Cereb Cortex 2018; 29:3590-3604. [DOI: 10.1093/cercor/bhy233] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 08/26/2018] [Accepted: 08/29/2018] [Indexed: 12/13/2022] Open
Abstract
Abstract
Understanding the migration of newborn neurons within the brain presents a major challenge in contemporary biology. Neuronal migration is widespread within the developing brain but is also important within the adult brain. For instance, stem cells within the ventricular–subventricular zone (V-SVZ) and the subgranular zone of dentate gyrus of the adult rodent brain produce neuroblasts that migrate to the olfactory bulb and granule cell layer of the dentate gyrus, respectively, where they regulate key brain functions including innate olfactory responses, learning, and memory. Critically, our understanding of the factors mediating neuroblast migration remains limited. The transcription factor nuclear factor I X (NFIX) has previously been implicated in embryonic cortical development. Here, we employed conditional ablation of Nfix from the adult mouse brain and demonstrated that the removal of this gene from either neural stem and progenitor cells, or neuroblasts, within the V-SVZ culminated in neuroblast migration defects. Mechanistically, we identified aberrant neuroblast branching, due in part to increased expression of the guanylyl cyclase natriuretic peptide receptor 2 (Npr2), as a factor contributing to abnormal migration in Nfix-deficient adult mice. Collectively, these data provide new insights into how neuroblast migration is regulated at a transcriptional level within the adult brain.
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Affiliation(s)
- Oressia Zalucki
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Lachlan Harris
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Tracey J Harvey
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Danyon Harkins
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jocelyn Widagdo
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, QLD, Australia
| | - Sabrina Oishi
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Elise Matuzelski
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Xuan Ling Hilary Yong
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, QLD, Australia
| | - Hannes Schmidt
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Victor Anggono
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, QLD, Australia
| | - Thomas H J Burne
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, QLD, Australia
| | - Richard M Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Michael Piper
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
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10
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Piper M, Gronostajski R, Messina G. Nuclear Factor One X in Development and Disease. Trends Cell Biol 2018; 29:20-30. [PMID: 30287093 DOI: 10.1016/j.tcb.2018.09.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/03/2018] [Accepted: 09/06/2018] [Indexed: 02/06/2023]
Abstract
The past decade has seen incredible advances in the field of stem cell biology that have greatly improved our understanding of development and provided important insights into pathological processes. Transcription factors (TFs) play a central role in mediating stem cell proliferation, quiescence, and differentiation. One TF that contributes to these processes is Nuclear Factor One X (NFIX). Recently, NFIX activity has been shown to be essential in multiple organ systems and to have important translational impacts for human health. Here, we describe recent studies showing the contribution of NFIX to muscle development and muscular dystrophies, hematopoiesis, cancer, and neural stem cell biology, highlighting the importance of this knowledge in the development of therapeutic targets.
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Affiliation(s)
- Michael Piper
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Richard Gronostajski
- Department of Biochemistry, Genetics, Genomics & Bioinformatics Graduate Program, New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Graziella Messina
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy.
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11
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Vidovic D, Davila RA, Gronostajski RM, Harvey TJ, Piper M. Transcriptional regulation of ependymal cell maturation within the postnatal brain. Neural Dev 2018; 13:2. [PMID: 29452604 PMCID: PMC5816376 DOI: 10.1186/s13064-018-0099-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 02/12/2018] [Indexed: 12/11/2022] Open
Abstract
Background Radial glial stem cells within the developing nervous system generate a variety of post-mitotic cells, including neurons and glial cells, as well as the specialised multi-ciliated cells that line the walls of the ventricular system, the ependymal cells. Ependymal cells separate the brain parenchyma from the cerebrospinal fluid and mediate osmotic regulation, the flow of cerebrospinal fluid, and the subsequent dispersion of signalling molecules via the co-ordinated beating of their cilia. Deficits to ependymal cell development and function have been implicated in the formation of hydrocephalus, but the transcriptional mechanisms underpinning ependymal development remain poorly characterised. Findings Here, we demonstrate that the transcription factor nuclear factor IX (NFIX) plays a central role in the development of the ependymal cell layer of the lateral ventricles. Expression of ependymal cell-specific markers is delayed in the absence of Nfix. Moreover, Nfix-deficient mice exhibit aberrant ependymal cell morphology at postnatal day 15, culminating in abnormal thickening and intermittent loss of this cell layer. Finally, we reveal Foxj1, a key factor promoting ependymal cell maturation, as a target for NFIX-mediated transcriptional activation. Conclusions Collectively, our data indicate that ependymal cell development is reliant, at least in part, on NFIX expression, further implicating this transcription factor as a mediator of multiple aspects of radial glial biology during corticogenesis. Electronic supplementary material The online version of this article (10.1186/s13064-018-0099-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diana Vidovic
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Raul Ayala Davila
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Richard M Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York, 14260, USA
| | - Tracey J Harvey
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Michael Piper
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia. .,Queensland Brain Institute, The University of Queensland, Brisbane, 4072, Australia.
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12
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Villalba-Benito L, Torroglosa A, Fernández RM, Ruíz-Ferrer M, Moya-Jiménez MJ, Antiñolo G, Borrego S. Overexpression of DNMT3b target genes during Enteric Nervous System development contribute to the onset of Hirschsprung disease. Sci Rep 2017; 7:6221. [PMID: 28740121 PMCID: PMC5524929 DOI: 10.1038/s41598-017-06539-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/09/2017] [Indexed: 12/27/2022] Open
Abstract
Hirschsprung disease (HSCR) is attributed to a failure of neural crest cells (NCCs) to migrate, proliferate, differentiate and/or survive in the bowel wall during embryonic Enteric Nervous System (ENS) development. ENS formation is the result from a specific gene expression pattern regulated by epigenetic events, such DNA methylation by the DNA methyltransferases (DNMTs), among other mechanisms. Specifically, DNMT3b de novo methyltransferase is associated with NCCs development and has been shown to be implicated in ENS formation and in HSCR. Aiming to elucidate the specific mechanism underlying the DNMT3b role in such processes, we have performed a chromatin immunoprecipitation coupled with massively parallel sequencing analysis to identify the DNMT3B target genes in enteric precursor cells (EPCs) from mice. Moreover, the expression patterns of those target genes have been analyzed in human EPCs from HSCR patients in comparison with controls. Additionally, we have carried out a search of rare variants in those genes in a HSCR series. Through this approach we found 9 genes showing a significantly different expression level in both groups. Therefore, those genes may have a role in the proper human ENS formation and a failure in their expression pattern might contribute to this pathology.
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Affiliation(s)
- Leticia Villalba-Benito
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, 41013, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, 41013, Spain
| | - Ana Torroglosa
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, 41013, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, 41013, Spain
| | - Raquel María Fernández
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, 41013, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, 41013, Spain
| | - Macarena Ruíz-Ferrer
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, 41013, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, 41013, Spain
| | - María José Moya-Jiménez
- Department of Pediatric Surgery, University Hospital Virgen del Rocío, Seville, 41013, Spain
| | - Guillermo Antiñolo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, 41013, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, 41013, Spain
| | - Salud Borrego
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, 41013, Spain.
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, 41013, Spain.
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13
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Wang CY, Tang MC, Chang WC, Furushima K, Jang CW, Behringer RR, Chen CM. PiggyBac Transposon-Mediated Mutagenesis in Rats Reveals a Crucial Role of Bbx in Growth and Male Fertility. Biol Reprod 2016; 95:51. [PMID: 27465138 PMCID: PMC5394979 DOI: 10.1095/biolreprod.116.141739] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 07/14/2016] [Indexed: 12/14/2022] Open
Abstract
Bobby sox homolog (Bbx) is an evolutionally conserved gene, but its biological function remains elusive. Here, we characterized defects of Bbx mutant rats that were created by PiggyBac-mediated insertional mutagenesis. Smaller body size and male infertility were the two major phenotypes of homozygous Bbx mutants. Bbx expression profile analysis showed that Bbx was more highly expressed in the testis and pituitary gland than in other organs. Histology and hormonal gene expression analysis of control and Bbx-null pituitary glands showed that loss of Bbx appeared to be dispensable for pituitary histogenesis and the expression of major hormones. BBX was localized in the nuclei of postmeiotic spermatids and Sertoli cells in wild-type testes, but absent in mutant testes. An increased presence of aberrant multinuclear giant cells and apoptotic cells was observed in mutant seminiferous tubules. TUNEL-positive cells costained with CREM (round spermatid marker), but not PLZF (spermatogonia marker), gammaH2Ax (meiotic spermatocyte marker), or GATA4 (Sertoli cell marker). Finally, there were drastically reduced numbers and motility of epididymal sperm from Bbx-null rats. These results suggest that loss of BBX induces apoptosis of postmeiotic spermatids and results in spermiogenesis defects and infertility.
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Affiliation(s)
- Chieh-Ying Wang
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Ming-Chu Tang
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan Laboratory Animal Center, National Yang-Ming University, Taipei, Taiwan
| | - Wen-Chi Chang
- Laboratory Animal Center, National Yang-Ming University, Taipei, Taiwan
| | - Kenryo Furushima
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Chuan-Wei Jang
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Richard R Behringer
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Chun-Ming Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan Laboratory Animal Center, National Yang-Ming University, Taipei, Taiwan
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14
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Vidovic D, Harris L, Harvey TJ, Evelyn Heng YH, Smith AG, Osinski J, Hughes J, Thomas P, Gronostajski RM, Bailey TL, Piper M. Expansion of the lateral ventricles and ependymal deficits underlie the hydrocephalus evident in mice lacking the transcription factor NFIX. Brain Res 2015; 1616:71-87. [DOI: 10.1016/j.brainres.2015.04.057] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 04/20/2015] [Accepted: 04/29/2015] [Indexed: 11/29/2022]
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15
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Villaruz LC, Huang G, Romkes M, Kirkwood JM, Buch SC, Nukui T, Flaherty KT, Lee SJ, Wilson MA, Nathanson KL, Benos PV, Tawbi HA. MicroRNA expression profiling predicts clinical outcome of carboplatin/paclitaxel-based therapy in metastatic melanoma treated on the ECOG-ACRIN trial E2603. Clin Epigenetics 2015; 7:58. [PMID: 26052356 PMCID: PMC4457092 DOI: 10.1186/s13148-015-0092-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/27/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Carboplatin/paclitaxel (CP), with or without sorafenib, result in objective response rates of 18-20 % in unselected chemotherapy-naïve patients. Molecular predictors of survival and response to CP-based chemotherapy in metastatic melanoma (MM) are critical to improving the therapeutic index. Intergroup trial E2603 randomized MM patients to CP with or without sorafenib. Expression data were collected from pre-treatment formalin-fixed paraffin-embedded (FFPE) tumor tissues from 115 of 823 patients enrolled on E2603. The selected patients were balanced across treatment arms, BRAF status, and clinical outcome. We generated data using Nanostring array (microRNA (miRNA) expression) and DNA-mediated annealing, selection, extension and ligation (DASL)/Illumina microarrays (HT12 v4) (mRNA expression) with protocols optimized for FFPE samples. Integrative computational analysis was performed using a novel Tree-guided Recursive Cluster Selection (T-ReCS) [1] algorithm to select the most informative features/genes, followed by TargetScan miRNA target prediction (Human v6.2) and mirConnX [2] for network inference. RESULTS T-ReCS identified PLXNB1 as negatively associated with progression-free survival (PFS) and miR-659-3p as the primary miRNA associated positively with PFS. miR-659-3p was differentially expressed based on PFS but not based on treatment arm, BRAF or NRAS status. Dichotomized by median PFS (less vs greater than 4 months), miR-659-3p expression was significantly different. High miR-659-3p expression distinguished patients with responsive disease (complete or partial response) from patients with stable disease. miR-659-3p predicted gene targets include NFIX, which is a transcription factor known to interact with c-Jun and AP-1 in the context of developmental processes and disease. CONCLUSIONS This novel integrative analysis implicates miR-659-3p as a candidate predictive biomarker for MM patients treated with platinum-based chemotherapy and may serve to improve patient selection.
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Affiliation(s)
- Liza C Villaruz
- University of Pittsburgh Cancer Institute, Pittsburgh, PA USA
| | - Grace Huang
- University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Marjorie Romkes
- University of Pittsburgh Cancer Institute, Pittsburgh, PA USA
| | - John M Kirkwood
- University of Pittsburgh Cancer Institute, Pittsburgh, PA USA
| | - Shama C Buch
- University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Tomoko Nukui
- University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Keith T Flaherty
- University of Pennsylvania, Philadelphia, PA USA.,Massachusetts General Hospital, Boston, MA USA
| | | | - Melissa A Wilson
- University of Pennsylvania, Philadelphia, PA USA.,New York University, New York, NY USA
| | | | | | - Hussein A Tawbi
- University of Pittsburgh Cancer Institute, Pittsburgh, PA USA
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16
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Chen T, Zhou L, Yuan Y, Fang Y, Guo Y, Huang H, Zhou Q, Lv X. Characterization of Bbx, a member of a novel subfamily of the HMG-box superfamily together with Cic. Dev Genes Evol 2014; 224:261-8. [DOI: 10.1007/s00427-014-0476-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 07/17/2014] [Indexed: 01/06/2023]
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17
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Choi YA, Seol MY, Shin HI, Park EK. Bobby Sox homology regulates odontoblast differentiation of human dental pulp stem cells/progenitors. Cell Commun Signal 2014; 12:35. [PMID: 24885382 PMCID: PMC4062286 DOI: 10.1186/1478-811x-12-35] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 05/23/2014] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Transcription factors have been implicated in regulating the differentiation of odontoblasts from dental pulp stem cells/progenitors (DPSCs/progenitors), but their regulatory network is not completely understood. RESULT New transcription factors that control the odontoblast differentiation of human DPSCs/progenitors were analyzed using a microarray. The result revealed bobby sox homolog (BBX) to be expressed most strongly during odontoblast differentiation. Validation using RT-PCR also revealed the strong expression of BBX during the odontoblast differentiation of DPSCs/progenitors. BBX expression was also detected in adult molar odontoblasts and other tissues, including the heart, kidney, testis, and bone marrow. To understand the role of BBX in odontoblast differentiation, BBX variant 1 and 2 cDNA were cloned and overexpressed in DPSCs/progenitors. The results showed that the overexpression of BBX cDNA in DPSCs/progenitors induced substantial mineralization and expression of the odontoblast marker genes, such as ALP, OPN, BSP, DMP1, and DSPP. The knockdown of BBX using shRNA, however, did not affect mineralization, but the expression of ALP and DSPP was decreased substantially. Meanwhile overexpression or knockdown of BBX did not modulate proliferation of DPSCs/progenitors. CONCLUSION Our results suggest that BBX plays an important role during the odontoblast differentiation of human DPSCs/progenitors.
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Affiliation(s)
| | | | | | - Eui Kyun Park
- Department of Oral Pathology and Regenerative Medicine, School of Dentistry, Kyungpook National University, 2177 Dalgubeol-daero, Jung-gu, Daegu 700-412, Korea.
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