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María Del Rocío PB, Palomares Bralo M, Vanhooydonck M, Hamerlinck L, D'haene E, Leimbacher S, Jacobs EZ, De Cock L, D'haenens E, Dheedene A, Malfait Z, Vantomme L, Silva A, Rooney K, Santos-Simarro F, Lleuger-Pujol R, García-Miñaúr S, Losantos-García I, Menten B, Gestri G, Ragge N, Sadikovic B, Bogaert E, Syx D, Callewaert B, Vergult S. Loss-of-function of the Zinc Finger Homeobox 4 ( ZFHX4) gene underlies a neurodevelopmental disorder. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.07.24311381. [PMID: 39148819 PMCID: PMC11326360 DOI: 10.1101/2024.08.07.24311381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
8q21.11 microdeletions encompassing the gene encoding transcription factor ZFHX4, have previously been associated by us with a syndromic form of intellectual disability, hypotonia, decreased balance and hearing loss. Here, we report on 57 individuals, 52 probands and 5 affected family members, with protein truncating variants (n=36), (micro)deletions (n=20) or an inversion (n=1) affecting ZFHX4 with variable developmental delay and intellectual disability, distinctive facial characteristics, morphological abnormalities of the central nervous system, behavioral alterations, short stature, hypotonia, and occasionally cleft palate and anterior segment dysgenesis. The phenotypes associated with 8q21.11 microdeletions and ZFHX4 intragenic loss-of-function variants largely overlap, identifying ZFHX4 as the main driver for the microdeletion syndrome, although leukocyte-derived DNA shows a mild common methylation profile for (micro)deletions only. We identify ZFHX4 as a transcription factor that is increasingly expressed during human brain development and neuronal differentiation. Furthermore, ZFHX4 interacting factors identified via IP-MS in neural progenitor cells, suggest an important role for ZFHX4 in cellular and developmental pathways, especially during histone modifications, cytosolic transport and development. Additionally, using CUT&RUN, we observed that ZFHX4 binds with the promoter regions of genes with crucial roles in embryonic, neuron and axon development. Since loss-of-function variants in ZFHX4 are found with consistent dysmorphic facial features, we investigated whether the disruption of zfhx4 causes craniofacial abnormalities in zebrafish. First-generation (F0) zfhx4 crispant zebrafish, (mosaic) mutant for zfhx4 loss-of-function variants, have significantly shorter Meckel's cartilages and smaller ethmoid plates compared to control zebrafish. Furthermore, behavioral assays show a decreased movement frequency in the zfhx4 crispant zebrafish in comparison with control zebrafish larvae. Although further research is needed, our in vivo work suggests a role for zfhx4 in facial skeleton patterning, palatal development and behavior.
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Affiliation(s)
- Pérez Baca María Del Rocío
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - María Palomares Bralo
- CIBERER-ISCIII and INGEMM, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, Madrid, Spain
- ITHACA- European Reference Network, Spain
| | - Michiel Vanhooydonck
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lisa Hamerlinck
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Eva D'haene
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Sebastian Leimbacher
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Eva Z Jacobs
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Laurenz De Cock
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Erika D'haenens
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Annelies Dheedene
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Zoë Malfait
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lies Vantomme
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Ananilia Silva
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Fernando Santos-Simarro
- Unit of Molecular Diagnostics and Clinical Genetics, Hospital Universitari Son Espases, Health Research Institute of the Balearic Islands (IdiSBa), Palma, Spain
| | - Roser Lleuger-Pujol
- Hereditary Cancer Program, Catalan Institute of Oncology, Doctor Josep Trueta University Hospital; Precision Oncology Group (OncoGIR-Pro), Institut d'Investigació Biomèdica de Girona (IDIGBI), Girona, Spain
| | - Sixto García-Miñaúr
- CIBERER-ISCIII and INGEMM, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, Madrid, Spain
- ITHACA- European Reference Network, Spain
| | | | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Gaia Gestri
- University College London, London, England, Great Britain
| | - Nicola Ragge
- Birmingham Women's and Children's NHS Foundation Trust, Clinical Genetics Unit, Birmingham Womens Hospital, Lavender House, Mindelsohn Way, Edgbaston, Birmingham B15 2TG
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Elke Bogaert
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Delfien Syx
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Bert Callewaert
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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Gomez GA, Udayakumar A, Pourteymoor S, Dennis G, Xing W, Mohan S. Evaluation of Potential Roles of Zinc Finger Homeobox 3 (Zfhx3) Expressed in Chondrocytes and Osteoblasts on Skeletal Growth in Mice. Calcif Tissue Int 2024:10.1007/s00223-024-01265-6. [PMID: 39085428 DOI: 10.1007/s00223-024-01265-6] [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: 05/24/2024] [Accepted: 07/20/2024] [Indexed: 08/02/2024]
Abstract
Bone formation is tightly modulated by genetically encoded molecular proteins that interact to regulate cellular differentiation and secretion of bony matrix. Many transcription factors are known to coordinate these events by controlling gene transcription within networks. However, not all factors involved are known. Here, we identified a novel function for Zinc Finger Homeobox 3 (Zfhx3), a gene encoding a transcription factor, as a regulator of bone metabolism. We knocked out Zfhx3 conditionally in mice in either chondrocytes or osteoblasts and characterized their bones by micro-CT in 12-week-old mice. We observed a negative effect in linear bone growth in both knockout mice but reduced bone mass only in mice with Zfhx3 deleted in osteoblasts. Loss of Zfhx3 expression in osteoblasts affected trabecular bone mass in femurs and vertebrae in both sexes but influenced cortical bone volume fraction only in females. Moreover, transcriptional analysis of femoral bones in osteoblast Zfhx3 conditional knockout mice revealed a reduced expression of osteoblast genes, and histological evaluation of trabecular bones suggests that Zfhx3 causes changes in bone formation and not resorption. The loss of Zfhx3 causes reductions in trabecular bone area and osteoid volume, but no changes in the expression of osteoclast differentiation markers or number of TRAP stained osteoclasts. These studies introduce Zfhx3 as a relevant factor toward understanding gene regulatory networks that control bone formation and development of peak bone mass.
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Affiliation(s)
- Gustavo A Gomez
- Musculoskeletal Disease Center, VA Loma Linda Healthcare System, 11201 Benton Street, Loma Linda, CA, 92357, USA
| | - Anakha Udayakumar
- Musculoskeletal Disease Center, VA Loma Linda Healthcare System, 11201 Benton Street, Loma Linda, CA, 92357, USA
| | - Sheila Pourteymoor
- Musculoskeletal Disease Center, VA Loma Linda Healthcare System, 11201 Benton Street, Loma Linda, CA, 92357, USA
| | - Garrett Dennis
- Musculoskeletal Disease Center, VA Loma Linda Healthcare System, 11201 Benton Street, Loma Linda, CA, 92357, USA
| | - Weirong Xing
- Musculoskeletal Disease Center, VA Loma Linda Healthcare System, 11201 Benton Street, Loma Linda, CA, 92357, USA
| | - Subburaman Mohan
- Musculoskeletal Disease Center, VA Loma Linda Healthcare System, 11201 Benton Street, Loma Linda, CA, 92357, USA.
- Departments of Medicine, Biochemistry and Orthopedic Surgery, Loma Linda University, Loma Linda, CA, 92354, USA.
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Cummins M, Watson C, Edwards RJ, Mattick JS. The Evolution of Ultraconserved Elements in Vertebrates. Mol Biol Evol 2024; 41:msae146. [PMID: 39058500 PMCID: PMC11276968 DOI: 10.1093/molbev/msae146] [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: 03/26/2024] [Revised: 06/29/2024] [Accepted: 07/08/2024] [Indexed: 07/18/2024] Open
Abstract
Ultraconserved elements were discovered two decades ago, arbitrarily defined as sequences that are identical over a length ≥ 200 bp in the human, mouse, and rat genomes. The definition was subsequently extended to sequences ≥ 100 bp identical in at least three of five mammalian genomes (including dog and cow), and shown to have undergone rapid expansion from ancestors in fish and strong negative selection in birds and mammals. Since then, many more genomes have become available, allowing better definition and more thorough examination of ultraconserved element distribution and evolutionary history. We developed a fast and flexible analytical pipeline for identifying ultraconserved elements in multiple genomes, dedUCE, which allows manipulation of minimum length, sequence identity, and number of species with a detectable ultraconserved element according to specified parameters. We suggest an updated definition of ultraconserved elements as sequences ≥ 100 bp and ≥97% sequence identity in ≥50% of placental mammal orders (12,813 ultraconserved elements). By mapping ultraconserved elements to ∼200 species, we find that placental ultraconserved elements appeared early in vertebrate evolution, well before land colonization, suggesting that the evolutionary pressures driving ultraconserved element selection were present in aquatic environments in the Cambrian-Devonian periods. Most (>90%) ultraconserved elements likely appeared after the divergence of gnathostomes from jawless predecessors, were largely established in sequence identity by early Sarcopterygii evolution-before the divergence of lobe-finned fishes from tetrapods-and became near fixed in the amniotes. Ultraconserved elements are mainly located in the introns of protein-coding and noncoding genes involved in neurological and skeletomuscular development, enriched in regulatory elements, and dynamically expressed throughout embryonic development.
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Affiliation(s)
- Mitchell Cummins
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Cadel Watson
- School of Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
| | - John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
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Losa M, Barozzi I, Osterwalder M, Hermosilla-Aguayo V, Morabito A, Chacón BH, Zarrineh P, Girdziusaite A, Benazet JD, Zhu J, Mackem S, Capellini TD, Dickel D, Bobola N, Zuniga A, Visel A, Zeller R, Selleri L. A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2. Nat Commun 2023; 14:3993. [PMID: 37414772 PMCID: PMC10325989 DOI: 10.1038/s41467-023-39443-z] [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: 03/17/2022] [Accepted: 06/14/2023] [Indexed: 07/08/2023] Open
Abstract
A lingering question in developmental biology has centered on how transcription factors with widespread distribution in vertebrate embryos can perform tissue-specific functions. Here, using the murine hindlimb as a model, we investigate the elusive mechanisms whereby PBX TALE homeoproteins, viewed primarily as HOX cofactors, attain context-specific developmental roles despite ubiquitous presence in the embryo. We first demonstrate that mesenchymal-specific loss of PBX1/2 or the transcriptional regulator HAND2 generates similar limb phenotypes. By combining tissue-specific and temporally controlled mutagenesis with multi-omics approaches, we reconstruct a gene regulatory network (GRN) at organismal-level resolution that is collaboratively directed by PBX1/2 and HAND2 interactions in subsets of posterior hindlimb mesenchymal cells. Genome-wide profiling of PBX1 binding across multiple embryonic tissues further reveals that HAND2 interacts with subsets of PBX-bound regions to regulate limb-specific GRNs. Our research elucidates fundamental principles by which promiscuous transcription factors cooperate with cofactors that display domain-restricted localization to instruct tissue-specific developmental programs.
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Affiliation(s)
- Marta Losa
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Iros Barozzi
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, Bern, Switzerland
| | - Viviana Hermosilla-Aguayo
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Angela Morabito
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Brandon H Chacón
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Peyman Zarrineh
- School of Medical Sciences, University of Manchester, Manchester, UK
| | - Ausra Girdziusaite
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Jean Denis Benazet
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Jianjian Zhu
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Susan Mackem
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Diane Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nicoletta Bobola
- School of Medical Sciences, University of Manchester, Manchester, UK
| | - Aimée Zuniga
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- School of Natural Sciences, University of California, Merced, Merced, CA, 95343, USA
| | - Rolf Zeller
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Licia Selleri
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA.
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5
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Pires SF, Barros JSD, Costa SSD, Carmo GBD, Scliar MDO, Lengert AVH, Boldrini É, Silva SRMD, Vidal DO, Maschietto M, Krepischi ACV. Analysis of the Mutational Landscape of Osteosarcomas Identifies Genes Related to Metastasis and Prognosis and Disrupted Biological Pathways of Immune Response and Bone Development. Int J Mol Sci 2023; 24:10463. [PMID: 37445641 DOI: 10.3390/ijms241310463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 07/15/2023] Open
Abstract
Osteosarcoma (OS) is the most prevalent type of bone tumor, but slow progress has been achieved in disentangling the full set of genomic events involved in its initiation and progression. We assessed by NGS the mutational spectrum of 28 primary OSs from Brazilian patients, and identified 445 potentially deleterious SNVs/indels and 1176 copy number alterations (CNAs). TP53 was the most recurrently mutated gene, with an overall rate of ~60%, considering SNVs/indels and CNAs. The most frequent CNAs (~60%) were gains at 1q21.2q21.3, 6p21.1, and 8q13.3q24.22, and losses at 10q26 and 13q14.3q21.1. Seven cases presented CNA patterns reminiscent of complex events (chromothripsis and chromoanasynthesis). Putative RB1 and TP53 germline variants were found in five samples associated with metastasis at diagnosis along with complex genomic patterns of CNAs. PTPRQ, KNL1, ZFHX4, and DMD alterations were prevalent in metastatic or deceased patients, being potentially indicative of poor prognosis. TNFRSF11B, involved in skeletal system development and maintenance, emerged as a candidate for osteosarcomagenesis due to its biological function and a high frequency of copy number gains. A protein-protein network enrichment highlighted biological pathways involved in immunity and bone development. Our findings reinforced the high genomic OS instability and heterogeneity, and led to the identification of novel disrupted genes deserving further evaluation as biomarkers due to their association with poor outcomes.
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Affiliation(s)
- Sara Ferreira Pires
- Human Genome and Stem-Cell Research Center, Institute of Biosciences, Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo 05508-090, Brazil
| | - Juliana Sobral de Barros
- Human Genome and Stem-Cell Research Center, Institute of Biosciences, Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo 05508-090, Brazil
| | - Silvia Souza da Costa
- Human Genome and Stem-Cell Research Center, Institute of Biosciences, Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo 05508-090, Brazil
| | - Gabriel Bandeira do Carmo
- Human Genome and Stem-Cell Research Center, Institute of Biosciences, Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo 05508-090, Brazil
| | - Marília de Oliveira Scliar
- Human Genome and Stem-Cell Research Center, Institute of Biosciences, Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo 05508-090, Brazil
| | | | - Érica Boldrini
- Barretos Children's Cancer Hospital, Barretos 14784-400, Brazil
| | | | - Daniel Onofre Vidal
- Molecular Oncology Research Center (CPOM), Barretos Cancer Hospital, Barretos 14784-384, Brazil
| | - Mariana Maschietto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-884, Brazil
| | - Ana Cristina Victorino Krepischi
- Human Genome and Stem-Cell Research Center, Institute of Biosciences, Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo 05508-090, Brazil
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Yamaga S, Tanigaki K, Nakamura E, Sasaki N, Kato Y, Kuboniwa M, Matsusaki M, Amano A, Takeuchi H. Cigarette smoke extract impairs gingival epithelial barrier function. Sci Rep 2023; 13:9228. [PMID: 37286570 PMCID: PMC10244868 DOI: 10.1038/s41598-023-36366-z] [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: 12/13/2022] [Accepted: 06/02/2023] [Indexed: 06/09/2023] Open
Abstract
We previously showed that junctional adhesion molecule 1 (JAM1) and coxsackievirus and adenovirus receptor (CXADR), tight junction-associated proteins, have important roles to maintain epithelial barrier function in gingival tissues. Smoking is considered to be a significant risk factor for periodontal disease. The present study was conducted to examine the effects of cigarette smoke extract (CSE) on JAM1 and CXADR in human gingival epithelial cells. CSE was found to cause translocation of JAM1 from the cellular surface to EGFR-positive endosomes, whereas CXADR did not. Using a three-dimensional multilayered gingival epithelial tissue model, CSE administration was found to increase permeability to lipopolysaccharide and peptidoglycan, whereas overexpression of JAM1 in the tissue model prevented penetration by those substrates. Furthermore, vitamin C increased JAM1 expression, and inhibited penetration of LPS and PGN induced by CSE. These findings strongly suggest that CSE disrupts gingival barrier function via dislocation of JAM1, thus allowing bacterial virulence factors to penetrate into subepithelial tissues. Furthermore, they indicate that vitamin C increases JAM1 expression and prevents disruption of gingival barrier function by CSE.
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Affiliation(s)
- Shunsuke Yamaga
- Department of Preventive Dentistry, Graduate School of Dentistry, Osaka University, Suita-Osaka, 565-0871, Japan
| | - Keita Tanigaki
- Department of Preventive Dentistry, Graduate School of Dentistry, Osaka University, Suita-Osaka, 565-0871, Japan
| | - Eriko Nakamura
- Department of Preventive Dentistry, Graduate School of Dentistry, Osaka University, Suita-Osaka, 565-0871, Japan
| | - Naoko Sasaki
- Joint Research Laboratory (TOPPAN) for Advanced Cell Regulatory Chemistry, Graduate School of Engineering, Osaka University, Suita-Osaka, 565-0871, Japan
| | - Yuta Kato
- Department of Preventive Dentistry, Graduate School of Dentistry, Osaka University, Suita-Osaka, 565-0871, Japan
| | - Masae Kuboniwa
- Department of Preventive Dentistry, Graduate School of Dentistry, Osaka University, Suita-Osaka, 565-0871, Japan
| | - Michiya Matsusaki
- Joint Research Laboratory (TOPPAN) for Advanced Cell Regulatory Chemistry, Graduate School of Engineering, Osaka University, Suita-Osaka, 565-0871, Japan
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita-Osaka, 565-0871, Japan
| | - Atsuo Amano
- Department of Preventive Dentistry, Graduate School of Dentistry, Osaka University, Suita-Osaka, 565-0871, Japan
| | - Hiroki Takeuchi
- Department of Preventive Dentistry, Osaka University Dental Hospital, 1-8 Yamadaoka, Suita-Osaka, 565-0871, Japan.
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7
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Tang W, Li ZW, Miao GQ, Li ZP, Gui T, Wu CJ, Li ZY, Yang J, Zhao XD, Liu N, Zha ZG, Yao LT, Zhang HT. Single-Cell RNA Sequencing Reveals Transcriptional Changes in the Cartilage of Subchondral Insufficiency Fracture of the Knee. J Inflamm Res 2022; 15:6105-6112. [PMID: 36386577 PMCID: PMC9645121 DOI: 10.2147/jir.s385648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Purpose Subchondral insufficiency fracture of the knee (SIFK) is a common cause of knee joint pain that mainly afflicts the elderly. Until now, how a sudden insufficiency fracture of subchondral bone affects the transcriptomic profiles of cartilage in SIFK and OA patients are largely unknown. Methods Single-cell RNA sequencing (scRNA-seq) was used to identify various cell subsets and evaluate transcriptomic differences in cartilage of SIFK and OA patients. In addition, the above findings were confirmed by histological evaluation and immunohistochemical (IHC) staining. Results We found that the transcriptomic profiles of cartilage in the SIFK patient was completely different from those of normal and OA patients. Accordingly, several novel cell clusters with activation of hypoxia and endochondral ossification signaling were identified in the SIFK cartilage. Chondrocyte trajectories analysis and IHC staining revealed that transcription factors including TCF4 were found to be highly up-regulated during the occurrence of SIFK, which might drive the reactive formation of cartilage and fibrous tissue and the activation of endochondral ossification. Conclusion This is the first report to elucidate the transcriptomic alterations and distinct cell type subpopulations in the cartilage of SIFK and OA by the use of scRNA-seq, which provides a new insight in the understanding of the initiation and progression of SIFK.
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Affiliation(s)
- Wang Tang
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, People’s Republic of China
| | - Zhen-Wei Li
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, People’s Republic of China
| | - Gui-Qiang Miao
- Department of Orthopedics, Foshan Fosun Chancheng Hospital, Foshan, 528010, People’s Republic of China
| | - Zhi-Peng Li
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, People’s Republic of China
| | - Tao Gui
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, People’s Republic of China
| | - Chong-Jie Wu
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, People’s Republic of China
| | - Zhen-Yan Li
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, People’s Republic of China
| | - Jie Yang
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, People’s Republic of China
| | - Xiao-Dong Zhao
- Department of Orthopedics, Foshan Fosun Chancheng Hospital, Foshan, 528010, People’s Republic of China
| | - Ning Liu
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, People’s Republic of China
| | - Zhen-Gang Zha
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, People’s Republic of China
| | - Lu-Tian Yao
- Department of Orthopedics, The First Hospital of China Medical University, Shenyang, 110001, People’s Republic of China
- Correspondence: Lu-Tian Yao; Huan-Tian Zhang, Email ;
| | - Huan-Tian Zhang
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, People’s Republic of China
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Lysko DE, Meireles AM, Folland C, McNamara E, Laing NG, Lamont PJ, Ravenscroft G, Talbot WS. Partial loss-of-function variant in neuregulin 1 identified in family with heritable peripheral neuropathy. Hum Mutat 2022; 43:1216-1223. [PMID: 35485770 PMCID: PMC9357049 DOI: 10.1002/humu.24393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/24/2022] [Accepted: 04/27/2022] [Indexed: 11/11/2022]
Abstract
Neuregulin 1 signals are essential for the development and function of Schwann cells, which form the myelin sheath on peripheral axons. Disruption of myelin in the peripheral nervous system can lead to peripheral neuropathy, which is characterized by reduced axonal conduction velocity and sensorimotor deficits. Charcot-Marie-Tooth disease is a group of heritable peripheral neuropathies that may be caused by variants in nearly 100 genes. Despite the evidence that Neuregulin 1 is essential for many aspects of Schwann cell development, previous studies have not reported variants in the neuregulin 1 gene (NRG1) in patients with peripheral neuropathy. We have identified a rare missense variant in NRG1 that is homozygous in a patient with sensory and motor deficits consistent with mixed axonal and de-myelinating peripheral neuropathy. Our in vivo functional studies in zebrafish indicate that the patient variant partially reduces NRG1 function. This study tentatively suggests that variants at the NRG1 locus may cause peripheral neuropathy and that NRG1 should be investigated in families with peripheral neuropathy of unknown cause.
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Affiliation(s)
- Daniel E Lysko
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Ana M Meireles
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Chiara Folland
- Harry Perkins Institute of Medical Research, Nedlands, WA, 6009, Australia
- Centre of Medical Research, University of Western Australia, Nedlands, WA, 6009, Australia
| | - Elyshia McNamara
- Harry Perkins Institute of Medical Research, Nedlands, WA, 6009, Australia
- Centre of Medical Research, University of Western Australia, Nedlands, WA, 6009, Australia
| | - Nigel G Laing
- Harry Perkins Institute of Medical Research, Nedlands, WA, 6009, Australia
- Centre of Medical Research, University of Western Australia, Nedlands, WA, 6009, Australia
| | | | - Gianina Ravenscroft
- Harry Perkins Institute of Medical Research, Nedlands, WA, 6009, Australia
- Centre of Medical Research, University of Western Australia, Nedlands, WA, 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA, 6009, Australia
| | - William S Talbot
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
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9
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Elblinger E, Bokor J, Bokor Á, Altbäcker V, Nagy J, Szabó J, Sárdi B, Bâlteanu A, Rónai Z, Rózsa L, Rátky J, Anton I, Zsolnai A. Parentage testing and looking for single nucleotide markers associated with antler quality in deer ( Cervus elaphus). Arch Anim Breed 2022; 65:267-274. [PMID: 36035877 PMCID: PMC9399935 DOI: 10.5194/aab-65-267-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 07/12/2022] [Indexed: 11/22/2022] Open
Abstract
To provide a cost-efficient parentage testing kit for red deer (Cervus elaphus), a 63 SNP set has been developed from a high-density Illumina
BovineHD BeadChip containing 777 962 SNPs after filtering of genotypes of 50
stags. The successful genotyping rate was 38.6 % on the chip. The ratio
of polymorphic loci among effectively genotyped loci was 6.5 %. The
selected 63 SNPs have been applied to 960 animals to perform parentage
control. Thirty SNPs out of the 63 had worked on the OpenArray platform. Their
combined value of the probability of identity and exclusion probability was
4.9×10-11 and 0.99803, respectively. A search for loci linked with antler quality was also performed on the
genotypes of the above-mentioned stags. Association studies revealed 14 SNPs
associated with antler quality, where low-quality antlers with short and
thin main beam antlers had values from 1 to 2, while high-quality antlers
with long and strong main beams had values between 4 and 5. The chance for a
stag to be correctly identified as having high-value antlers is expected to
be over 88 %.
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Affiliation(s)
- Edith Elblinger
- Kaposvár
Campus, Hungarian University of Agriculture and Life Sciences, Kaposvár, 7400, Hungary
| | - Julianna Bokor
- Game Management
Landscape Center, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Bőszénfa, 7475, Hungary
| | - Árpád Bokor
- Kaposvár
Campus, Hungarian University of Agriculture and Life Sciences, Kaposvár, 7400, Hungary
| | - Vilmos Altbäcker
- Kaposvár
Campus, Hungarian University of Agriculture and Life Sciences, Kaposvár, 7400, Hungary
| | - János Nagy
- Game Management
Landscape Center, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Bőszénfa, 7475, Hungary
| | - József Szabó
- Game Management
Landscape Center, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Bőszénfa, 7475, Hungary
| | - Bertalan Sárdi
- Game Management
Landscape Center, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Bőszénfa, 7475, Hungary
| | - Adrian Valentin Bâlteanu
- Institute of Life Sciences, University of Agricultural Sciences and Veterinary Medicine,
Cluj-Napoca, Romania
| | - Zsolt Rónai
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Eötvös Loránd University, Budapest, 1053, Hungary
| | - László Rózsa
- Kaposvár
Campus, Hungarian University of Agriculture and Life Sciences, Herceghalom, 2053, Hungary
| | - József Rátky
- Department of Obstetrics
and Food Animal Medicine Clinic, University of Veterinary Medicine Budapest, Budapest, 1078, Hungary
| | - István Anton
- Kaposvár
Campus, Hungarian University of Agriculture and Life Sciences, Herceghalom, 2053, Hungary
| | - Attila Zsolnai
- Kaposvár
Campus, Hungarian University of Agriculture and Life Sciences, Herceghalom, 2053, Hungary
- Institute for Farm Animal Gene Conservation, National Centre for
Biodiversity and Gene Conservation, Gödöllő, 2100, Hungary
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10
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Yanagi N, Kato S, Fukazawa T, Kubo T. Cellular responses in the FGF10-mediated improvement of hindlimb regenerative capacity in Xenopus laevis revealed by single-cell transcriptomics. Dev Growth Differ 2022; 64:266-278. [PMID: 35642106 DOI: 10.1111/dgd.12795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/16/2022] [Accepted: 05/24/2022] [Indexed: 12/28/2022]
Abstract
Xenopus laevis tadpoles possess regenerative capacity in their hindlimb buds at early developmental stages (stages ~52-54); they can regenerate complete hindlimbs with digits after limb bud amputation. However, they gradually lose their regenerative capacity as metamorphosis proceeds. Tadpoles in late developmental stages regenerate fewer digits (stage ~56), or only form cartilaginous spike without digits or joints (stage ~58 or later) after amputation. Previous studies have shown that administration of fibroblast growth factor 10 (FGF10) in late-stage (stage 56) tadpole hindlimb buds after amputation can improve their regenerative capacity, which means that the cells responding to FGF10 signaling play an important role in limb bud regeneration. In this study, we performed single-cell RNA sequencing (scRNA-seq) of hindlimb buds that were amputated and administered FGF10 by implanting FGF10-soaked beads at a late stage (stage 56), and explored cell clusters exhibiting a differential gene expression pattern compared with that in controls treated with phosphate-buffered saline. The scRNA-seq data showed expansion of fgf8-expressing cells in the cluster of the apical epidermal cap of FGF10-treated hindlimb buds, which was reported previously, indicating that the administration of FGF10 was successful. On analysis, in addition to the epidermal cluster, a subset of myeloid cells and a newly identified cluster of steap4-expressing cells showed remarkable differences in their gene expression profiles between the FGF10- or phosphate-buffered saline-treatment conditions, suggesting a possible role of these clusters in improving the regenerative capacity of hindlimbs via FGF10 administration.
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Affiliation(s)
- Nodoka Yanagi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Sumika Kato
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Taro Fukazawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Takeo Kubo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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11
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Hojo H, Ohba S. Sp7 Action in the Skeleton: Its Mode of Action, Functions, and Relevance to Skeletal Diseases. Int J Mol Sci 2022; 23:5647. [PMID: 35628456 PMCID: PMC9143072 DOI: 10.3390/ijms23105647] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/14/2022] [Accepted: 05/16/2022] [Indexed: 02/01/2023] Open
Abstract
Osteoblast differentiation is a tightly regulated process in which key transcription factors (TFs) and their target genes constitute gene regulatory networks (GRNs) under the control of osteogenic signaling pathways. Among these TFs, Sp7 works as an osteoblast determinant critical for osteoblast differentiation. Following the identification of Sp7 and a large number of its functional studies, recent genome-scale analyses have made a major contribution to the identification of a "non-canonical" mode of Sp7 action as well as "canonical" ones. The analyses have not only confirmed known Sp7 targets but have also uncovered its additional targets and upstream factors. In addition, biochemical analyses have demonstrated that Sp7 actions are regulated by chemical modifications and protein-protein interaction with other transcriptional regulators. Sp7 is also involved in chondrocyte differentiation and osteocyte biology as well as postnatal bone metabolism. The critical role of SP7 in the skeleton is supported by its relevance to human skeletal diseases. This review aims to overview the Sp7 actions in skeletal development and maintenance, particularly focusing on recent advances in our understanding of how Sp7 functions in the skeleton under physiological and pathological conditions.
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Affiliation(s)
- Hironori Hojo
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan;
| | - Shinsuke Ohba
- Department of Cell Biology, Institute of Biomedical Sciences, Nagasaki University, Nagasaki 852-8588, Japan
- Department of Oral Anatomy and Developmental Biology, Osaka University Graduate School of Dentistry, Osaka 565-0871, Japan
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