1
|
Itai T, Yan F, Liu A, Dai Y, Iwaya C, Curtis SW, Leslie EJ, Simon LM, Jia P, Chen X, Iwata J, Zhao Z. Investigating gene functions and single-cell expression profiles of de novo variants in orofacial clefts. HGG ADVANCES 2024; 5:100313. [PMID: 38807368 DOI: 10.1016/j.xhgg.2024.100313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 05/23/2024] [Accepted: 05/23/2024] [Indexed: 05/30/2024] Open
Abstract
Orofacial clefts (OFCs) are common congenital birth defects with various etiologies, including genetic variants. Online Mendelian Inheritance in Man (OMIM) annotated several hundred genes involving OFCs. Furthermore, several hundreds of de novo variants (DNVs) have been identified from individuals with OFCs. Some DNVs are related to known OFC genes or pathways, but there are still many DNVs whose relevance to OFC development is unknown. To explore novel gene functions and their cellular expression profiles, we focused on DNVs in genes that were not listed in OMIM. We collected 960 DNVs in 853 genes from published studies and curated these genes, based on the DNVs' deleteriousness, into 230 and 23 genes related to cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO), respectively. For comparison, we curated 178 CL/P and 277 CPO genes from OMIM. In CL/P, the pathways enriched in DNV and OMIM genes were significantly overlapped (p = 0.002). Single-cell RNA sequencing (scRNA-seq) analysis of mouse lip development revealed that both gene sets had abundant expression in the ectoderm (DNV genes: adjusted p = 0.032, OMIM genes: adjusted p < 0.0002), while only DNV genes were enriched in the endothelium (adjusted p = 0.032). Although we did not achieve significant findings using CPO gene sets, which was mainly due to the limited number of DNV genes, scRNA-seq analysis implicated various expression patterns among DNV and OMIM genes. Our results suggest that combinatory pathway and scRNA-seq data analyses are helpful for contextualizing genes in OFC development.
Collapse
Affiliation(s)
- Toshiyuki Itai
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Fangfang Yan
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Andi Liu
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, Houston, TX 77030, USA
| | - Yulin Dai
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Chihiro Iwaya
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA; Center for Craniofacial Research, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Sarah W Curtis
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Lukas M Simon
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peilin Jia
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiangning Chen
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Junichi Iwata
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA; Center for Craniofacial Research, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA; Pediatric Research Center, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, Houston, TX 77030, USA; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| |
Collapse
|
2
|
Chen B, Wang L, Pan X, Jiang S, Hu Y. Adipose-derived stem cells modified by TWIST1 silencing accelerates rat sciatic nerve repair and functional recovery. Hum Cell 2024:10.1007/s13577-024-01087-6. [PMID: 38907140 DOI: 10.1007/s13577-024-01087-6] [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: 01/18/2024] [Accepted: 05/11/2024] [Indexed: 06/23/2024]
Abstract
The regeneration of peripheral nerves after injury is often slow and impaired, which may be associated with weakened and denervated muscles subsequently leading to atrophy. Adipose-derived stem cells (ADSCs) are often regarded as cell-based therapeutic candidate due to their regenerative potential. The study aims to assess the therapeutic efficacy of gene-modified ADSCs on sciatic nerve injury. We lentivirally transduced ADSCs with shRNA-TWIST1 and transplanted modified cells to rats undergoing sciatic nerve transection and repair. Results showed that TWIST1 knockdown accelerated functional recovery of rats with sciatic nerve injury as faster nerve conduction velocity and higher wire hang scores obtained by rats transplanted with TWIST1-silenced ADSCs than scramble ADSCs. Although the rats experienced degenerated axons and decreased myelin sheath thickness after sciatic nerve injury 8 weeks after operation, those transplanted with TWIST1-silenced ADSCs exhibited more signs of regenerated nerve fibers surrounded by newly formed myelin sheaths than those with scramble ADSCs. The rats transplanted with TWIST1-silenced ADSCs presented increased expressions of neurotrophic factors including neurotrophin-3 (NT-3), brain-derived neurotrophic factor (BDNF), nerve growth factor (NGF), and glial cell line-derived neurotrophic factor (GDNF) in the sciatic nerves than those with scramble ADSCs. These results suggest that genetically modifying TWIST1 in ADSCs could facilitate peripheral nerve repair after injury in a more efficient way than that with ADSCs alone.
Collapse
Affiliation(s)
- Bo Chen
- Department of Orthopedics, The First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Leining Wang
- Department of Surgery of Hand and Foot, Beilun People's Hospital, Ningbo, 315800, Zhejiang, China
| | - Xiaogui Pan
- Department of Surgery of Hand and Foot, Beilun People's Hospital, Ningbo, 315800, Zhejiang, China
| | - Shuai Jiang
- Department of Orthopedics, The First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Yihe Hu
- Department of Orthopedics, The First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China.
| |
Collapse
|
3
|
Wang B, Zhang Z, Zhao J, Ma Y, Wang Y, Yin N, Song T. Spatiotemporal Evolution of Developing Palate in Mice. J Dent Res 2024; 103:546-554. [PMID: 38619065 PMCID: PMC11145300 DOI: 10.1177/00220345241232317] [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] [Indexed: 04/16/2024] Open
Abstract
The intricate formation of the palate involves a series of complex events, yet its mechanistic basis remains uncertain. To explore major cell populations in the palate and their roles during development, we constructed a spatiotemporal transcription landscape of palatal cells. Palate samples from C57BL/6 J mice at embryonic days 12.5 (E12.5), 14.5 (E14.5), and 16.5 (E16.5) underwent single-cell RNA sequencing (scRNA-seq) to identify distinct cell subsets. In addition, spatial enhanced resolution omics-sequencing (stereo-seq) was used to characterize the spatial distribution of these subsets. Integrating scRNA-seq and stereo-seq with CellTrek annotated mesenchymal and epithelial cellular components of the palate during development. Furthermore, cellular communication networks between these cell subpopulations were analyzed to discover intercellular signaling during palate development. From the analysis of the middle palate, both mesenchymal and epithelial populations were spatially segregated into 3 domains. The middle palate mesenchymal subpopulations were associated with tooth formation, ossification, and tissue remodeling, with initial state cell populations located proximal to the dental lamina. The nasal epithelium of the palatal shelf exhibited richer humoral immune responses than the oral side. Specific enrichment of Tgfβ3 and Pthlh signals in the midline epithelial seam at E14.5 suggested a role in epithelial-mesenchymal transition. In summary, this study provides high-resolution transcriptomic information, contributing to a deeper mechanistic understanding of palate biology and pathophysiology.
Collapse
Affiliation(s)
- B. Wang
- Center for Cleft Lip and Palate Treatment, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Z. Zhang
- Center for Ear Reconstruction, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - J. Zhao
- Center for Cleft Lip and Palate Treatment, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Y. Ma
- Center for Cleft Lip and Palate Treatment, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Y. Wang
- Center for Cleft Lip and Palate Treatment, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - N. Yin
- Center for Cleft Lip and Palate Treatment, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - T. Song
- Center for Cleft Lip and Palate Treatment, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
4
|
Yan F, Suzuki A, Iwaya C, Pei G, Chen X, Yoshioka H, Yu M, Simon LM, Iwata J, Zhao Z. Single-cell multiomics decodes regulatory programs for mouse secondary palate development. Nat Commun 2024; 15:821. [PMID: 38280850 PMCID: PMC10821874 DOI: 10.1038/s41467-024-45199-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 01/17/2024] [Indexed: 01/29/2024] Open
Abstract
Perturbations in gene regulation during palatogenesis can lead to cleft palate, which is among the most common congenital birth defects. Here, we perform single-cell multiome sequencing and profile chromatin accessibility and gene expression simultaneously within the same cells (n = 36,154) isolated from mouse secondary palate across embryonic days (E) 12.5, E13.5, E14.0, and E14.5. We construct five trajectories representing continuous differentiation of cranial neural crest-derived multipotent cells into distinct lineages. By linking open chromatin signals to gene expression changes, we characterize the underlying lineage-determining transcription factors. In silico perturbation analysis identifies transcription factors SHOX2 and MEOX2 as important regulators of the development of the anterior and posterior palate, respectively. In conclusion, our study charts epigenetic and transcriptional dynamics in palatogenesis, serving as a valuable resource for further cleft palate research.
Collapse
Affiliation(s)
- Fangfang Yan
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Akiko Suzuki
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of Missouri - Kansas City, Kansas City, Missouri, 64108, USA
| | - Chihiro Iwaya
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
| | - Guangsheng Pei
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Xian Chen
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Hiroki Yoshioka
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
| | - Meifang Yu
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Lukas M Simon
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Junichi Iwata
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA.
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA.
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| |
Collapse
|
5
|
Wang B, Xu M, Zhao J, Yin N, Wang Y, Song T. Single-cell Transcriptomics Reveals Activation of Macrophages in All-trans Retinoic Acid (atRA)-induced Cleft Palate. J Craniofac Surg 2024; 35:177-184. [PMID: 38049149 DOI: 10.1097/scs.0000000000009782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 08/22/2023] [Indexed: 12/06/2023] Open
Abstract
Cleft palate is among the most common birth defects with an impact on swallowing and speaking and is difficult to diagnose with ultrasound during pregnancy. In this study, we systematically capture the cellular composition of all-trans retinoic acid (atRA)-exposed and normal embryonic gestation 16.5 days mouse palate by the single-cell RNA sequencing technique. The authors identified 14 major cell types with the largest proportion of fibroblasts. The proportion of myeloid cells in atRA-exposed palate was markedly higher than those in the normal palate tissue, especially M1-like macrophages and monocytes. The upregulated genes of the different expression genes between atRA-exposed palate and normal palate tissue were linked to the biological processes of leukocyte chemotaxis and migration. Protein TLR2, CXCR4, THBS1, MRC1, transcription factor encoding genes Cebpb, Fos, Jun, Rela, and signaling pathway IL-17 and phagosome were found to be significantly involved in these processes. Subsequently, cellular communication network analysis suggested that myeloid-centered cell interactions SELL, SELPLG, MIF, CXCL, ANNEXIN, THBS, and NECTIN were significantly more activated in atRA-exposed palate. Overall, we delineate the single-cell landscape of atRA-induced cleft palate, revealing the effects of overexposure to atRA during palate tissue development and providing insights for the diagnosis of cleft palate.
Collapse
Affiliation(s)
- Binqing Wang
- Center for Cleft Lip and Palate Treatment, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | | | | | | | | |
Collapse
|
6
|
Robinson K, Mosley TJ, Rivera-González KS, Jabbarpour CR, Curtis SW, Adeyemo WL, Beaty TH, Butali A, Buxó CJ, Cutler DJ, Epstein MP, Gowans LJ, Hecht JT, Murray JC, Shaw GM, Uribe LM, Weinberg SM, Brand H, Marazita ML, Lipinski RJ, Leslie EJ. Trio-based GWAS identifies novel associations and subtype-specific risk factors for cleft palate. HGG ADVANCES 2023; 4:100234. [PMID: 37719664 PMCID: PMC10502411 DOI: 10.1016/j.xhgg.2023.100234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/18/2023] [Indexed: 09/19/2023] Open
Abstract
Cleft palate (CP) is one of the most common craniofacial birth defects; however, there are relatively few established genetic risk factors associated with its occurrence despite high heritability. Historically, CP has been studied as a single phenotype, although it manifests across a spectrum of defects involving the hard and/or soft palate. We performed a genome-wide association study using transmission disequilibrium tests of 435 case-parent trios to evaluate broad risks for any cleft palate (ACP) (n = 435), and subtype-specific risks for any cleft soft palate (CSP), (n = 259) and any cleft hard palate (CHP) (n = 125). We identified a single genome-wide significant locus at 9q33.3 (lead SNP rs7035976, p = 4.24 × 10-8) associated with CHP. One gene at this locus, angiopoietin-like 2 (ANGPTL2), plays a role in osteoblast differentiation. It is expressed both in craniofacial tissue of human embryos and developing mouse palatal shelves. We found 19 additional loci reaching suggestive significance (p < 5 × 10-6), of which only one overlapped between groups (chromosome 17q24.2, ACP and CSP). Odds ratios for the 20 loci were most similar across all 3 groups for SNPs associated with the ACP group, but more distinct when comparing SNPs associated with either subtype. We also found nominal evidence of replication (p < 0.05) for 22 SNPs previously associated with orofacial clefts. Our study to evaluate CP risks in the context of its subtypes and we provide newly reported associations affecting the broad risk for CP as well as evidence of subtype-specific risks.
Collapse
Affiliation(s)
- Kelsey Robinson
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Trenell J. Mosley
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Kenneth S. Rivera-González
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Christopher R. Jabbarpour
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sarah W. Curtis
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Wasiu Lanre Adeyemo
- Department of Oral and Maxillofacial Surgery, College of Medicine, University of Lagos, Lagos 101017, Nigeria
| | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Azeez Butali
- Department of Oral Biology, Radiology, and Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Carmen J. Buxó
- School of Dental Medicine, University of Puerto Rico, San Juan, PR 00925, USA
| | - David J. Cutler
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | | | - Lord J.J. Gowans
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Jacqueline T. Hecht
- Department of Pediatrics, McGovern Medical School University of Texas Health at Houston, Houston, TX 77030, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | - Gary M. Shaw
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Lina Moreno Uribe
- Department of Orthodontics & The Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA 52242, USA
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, and Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, and Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Robert J. Lipinski
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | |
Collapse
|
7
|
Tseng KC, Crump JG. Craniofacial developmental biology in the single-cell era. Development 2023; 150:dev202077. [PMID: 37812056 PMCID: PMC10617621 DOI: 10.1242/dev.202077] [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] [Indexed: 10/10/2023]
Abstract
The evolution of a unique craniofacial complex in vertebrates made possible new ways of breathing, eating, communicating and sensing the environment. The head and face develop through interactions of all three germ layers, the endoderm, ectoderm and mesoderm, as well as the so-called fourth germ layer, the cranial neural crest. Over a century of experimental embryology and genetics have revealed an incredible diversity of cell types derived from each germ layer, signaling pathways and genes that coordinate craniofacial development, and how changes to these underlie human disease and vertebrate evolution. Yet for many diseases and congenital anomalies, we have an incomplete picture of the causative genomic changes, in particular how alterations to the non-coding genome might affect craniofacial gene expression. Emerging genomics and single-cell technologies provide an opportunity to obtain a more holistic view of the genes and gene regulatory elements orchestrating craniofacial development across vertebrates. These single-cell studies generate novel hypotheses that can be experimentally validated in vivo. In this Review, we highlight recent advances in single-cell studies of diverse craniofacial structures, as well as potential pitfalls and the need for extensive in vivo validation. We discuss how these studies inform the developmental sources and regulation of head structures, bringing new insights into the etiology of structural birth anomalies that affect the vertebrate head.
Collapse
Affiliation(s)
- Kuo-Chang Tseng
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA 90033, USA
| | - J. Gage Crump
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA 90033, USA
| |
Collapse
|
8
|
Sun J, Lin Y, Ha N, Zhang J, Wang W, Wang X, Bian Q. Single-cell RNA-Seq reveals transcriptional regulatory networks directing the development of mouse maxillary prominence. J Genet Genomics 2023; 50:676-687. [PMID: 36841529 DOI: 10.1016/j.jgg.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/15/2023] [Accepted: 02/08/2023] [Indexed: 02/27/2023]
Abstract
During vertebrate embryonic development, neural crest-derived ectomesenchyme within the maxillary prominences undergoes precisely coordinated proliferation and differentiation to give rise to diverse craniofacial structures, such as tooth and palate. However, the transcriptional regulatory networks underpinning such an intricate process have not been fully elucidated. Here, we perform single-cell RNA-Seq to comprehensively characterize the transcriptional dynamics during mouse maxillary development from embryonic day (E) 10.5-E14.5. Our single-cell transcriptome atlas of ∼28,000 cells uncovers mesenchymal cell populations representing distinct differentiating states and reveals their developmental trajectory, suggesting that the segregation of dental from the palatal mesenchyme occurs at E11.5. Moreover, we identify a series of key transcription factors (TFs) associated with mesenchymal fate transitions and deduce the gene regulatory networks directed by these TFs. Collectively, our study provides important resources and insights for achieving a systems-level understanding of craniofacial morphogenesis and abnormality.
Collapse
Affiliation(s)
- Jian Sun
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai 200011, China
| | - Yijun Lin
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Nayoung Ha
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai 200011, China
| | - Jianfei Zhang
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai 200011, China
| | - Weiqi Wang
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai 200011, China
| | - Xudong Wang
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai 200011, China.
| | - Qian Bian
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China; Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| |
Collapse
|
9
|
Liu Q, Gao Y, He J. Stem Cells from the Apical Papilla (SCAPs): Past, Present, Prospects, and Challenges. Biomedicines 2023; 11:2047. [PMID: 37509686 PMCID: PMC10377451 DOI: 10.3390/biomedicines11072047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Dental diseases occurring on young permanent teeth usually lead to the premature arrest of tooth root development. Sustained tooth root elongation is necessary to achieve the goal of long-term preservation of affected teeth. To this end, stem cell-based regenerative endodontic treatment has been regarded as one of the most promising strategies for treating young permanent teeth with pulp and periapical infections. Endogenous stem cells residing in the apical papilla, named stem cells from the apical papilla (SCAPs), have been intensively investigated due to their critical roles in pulp regeneration and root redevelopment. The present review summarizes advances in the field of SCAPs studies and discusses the challenges that need to be further addressed.
Collapse
Affiliation(s)
- Qi Liu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu 610041, China
- Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yuan Gao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu 610041, China
- Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Jinzhi He
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu 610041, China
- Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| |
Collapse
|
10
|
Vimalraj S, Sekaran S. RUNX Family as a Promising Biomarker and a Therapeutic Target in Bone Cancers: A Review on Its Molecular Mechanism(s) behind Tumorigenesis. Cancers (Basel) 2023; 15:3247. [PMID: 37370857 DOI: 10.3390/cancers15123247] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
The transcription factor runt-related protein (RUNX) family is the major transcription factor responsible for the formation of osteoblasts from bone marrow mesenchymal stem cells, which are involved in bone formation. Accumulating evidence implicates the RUNX family for its role in tumor biology and cancer progression. The RUNX family has been linked to osteosarcoma via its regulation of many tumorigenicity-related factors. In the regulatory network of cancers, with numerous upstream signaling pathways and its potential target molecules downstream, RUNX is a vital molecule. Hence, a pressing need exists to understand the precise process underpinning the occurrence and prognosis of several malignant tumors. Until recently, RUNX has been regarded as one of the therapeutic targets for bone cancer. Therefore, in this review, we have provided insights into various molecular mechanisms behind the tumorigenic role of RUNX in various important cancers. RUNX is anticipated to grow into a novel therapeutic target with the in-depth study of RUNX family-related regulatory processes, aid in the creation of new medications, and enhance clinical efficacy.
Collapse
Affiliation(s)
- Selvaraj Vimalraj
- Department of Prosthodontics, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai 600077, Tamil Nadu, India
| | - Saravanan Sekaran
- Department of Prosthodontics, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai 600077, Tamil Nadu, India
| |
Collapse
|
11
|
Ozekin YH, O’Rourke R, Bates EA. Single cell sequencing of the mouse anterior palate reveals mesenchymal heterogeneity. Dev Dyn 2023; 252:713-727. [PMID: 36734036 PMCID: PMC10238667 DOI: 10.1002/dvdy.573] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/05/2023] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Cleft palate is one of the most prevalent birth defects. Mice are useful for studying palate development because of their morphological and genetic similarities to humans. In mice, palate development occurs between embryonic days (E)11.5 to 15.5. Single cell transcriptional profiles of palate cell populations have been a valuable resource for the craniofacial research community, but we lack a single cell transcriptional profile for anterior palate at E13.5, at the transition from proliferation to shelf elevation. RESULTS A detailed single cell RNA sequencing analysis reveals heterogeneity in expression profiles of the cell populations of the E13.5 anterior palate. Hybridization chain reaction RNA fluorescent in situ hybridization (HCR RNA FISH) reveals epithelial populations segregate into layers. Mesenchymal populations spatially segregate into four domains. One of these mesenchymal populations expresses ligands and receptors distinct from the rest of the mesenchyme, suggesting that these cells have a unique function. RNA velocity analysis shows two terminal cell states that contribute to either the proximal or distal palatal regions emerge from a single progenitor pool. CONCLUSION This single cell resolution expression data and detailed analysis from E13.5 anterior palate provides a powerful resource for mechanistic insight into secondary palate morphogenesis for the craniofacial research community.
Collapse
Affiliation(s)
- Yunus H. Ozekin
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Rebecca O’Rourke
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Emily Anne Bates
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| |
Collapse
|
12
|
Robinson K, Mosley TJ, Rivera-González KS, Jabbarpour CR, Curtis SW, Adeyemo WL, Beaty TH, Butali A, Buxó CJ, Cutler DJ, Epstein MP, Gowans LJ, Hecht JT, Murray JC, Shaw GM, Uribe LM, Weinberg SM, Brand H, Marazita ML, Lipinski RJ, Leslie EJ. Trio-based GWAS identifies novel associations and subtype-specific risk factors for cleft palate. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.01.23286642. [PMID: 37066311 PMCID: PMC10104215 DOI: 10.1101/2023.03.01.23286642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Orofacial clefts (OFCs) are the most common craniofacial birth defects and are often categorized into two etiologically distinct groups: cleft lip with or without cleft palate (CL/P) and isolated cleft palate (CP). CP is highly heritable, but there are still relatively few established genetic risk factors associated with its occurrence compared to CL/P. Historically, CP has been studied as a single phenotype despite manifesting across a spectrum of defects involving the hard and/or soft palate. We performed GWAS using transmission disequilibrium tests using 435 case-parent trios to evaluate broad risks for any cleft palate (ACP, n=435), as well as subtype-specific risks for any cleft soft palate (CSP, n=259) and any cleft hard palate (CHP, n=125). We identified a single genome-wide significant locus at 9q33.3 (lead SNP rs7035976, p=4.24×10 -8 ) associated with CHP. One gene at this locus, angiopoietin-like 2 ( ANGPTL2 ), plays a role in osteoblast differentiation. It is expressed in craniofacial tissue of human embryos, as well as in the developing mouse palatal shelves. We found 19 additional loci reaching suggestive significance (p<5×10 -6 ), of which only one overlapped between groups (chromosome 17q24.2, ACP and CSP). Odds ratios (ORs) for each of the 20 loci were most similar across all three groups for SNPs associated with the ACP group, but more distinct when comparing SNPs associated with either the CSP or CHP groups. We also found nominal evidence of replication (p<0.05) for 22 SNPs previously associated with cleft palate (including CL/P). Interestingly, most SNPs associated with CL/P cases were found to convey the opposite effect in those replicated in our dataset for CP only. Ours is the first study to evaluate CP risks in the context of its subtypes and we provide newly reported associations affecting the broad risk for CP as well as evidence of subtype-specific risks.
Collapse
Affiliation(s)
| | - Trenell J Mosley
- Department of Human Genetics, Emory University, Atlanta, GA
- Current address: Chief Officer for Scientific Workforce Diversity Office, National Institutes of Health, Bethesda, MD
| | - Kenneth S Rivera-González
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI
| | - Christopher R Jabbarpour
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI
| | - Sarah W Curtis
- Department of Human Genetics, Emory University, Atlanta, GA
| | - Wasiu Lanre Adeyemo
- Department of Oral and Maxillofacial Surgery, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD
| | - Azeez Butali
- Department of Oral Biology, Radiology, and Medicine, University of Iowa, Iowa City, IA
| | - Carmen J Buxó
- School of Dental Medicine, University of Puerto Rico, San Juan, Puerto Rico
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA
| | | | - Lord Jj Gowans
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Jacqueline T Hecht
- Department of Pediatrics, McGovern Medical School University of Texas Health at Houston, Houston, TX
| | | | - Gary M Shaw
- Department of Pediatrics, Stanford University, Stanford, CA
| | - Lina Moreno Uribe
- Department of Orthodontics & The Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, and Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, and Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Robert J Lipinski
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI
| | | |
Collapse
|
13
|
Yang CW, You Y, Sun JL, Shi B, Jia ZL. Integrated Analysis of the Association Between Variants at PAX7 and NSCL/P in the Han Population. Cleft Palate Craniofac J 2023:10556656231163398. [PMID: 36919448 DOI: 10.1177/10556656231163398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
OBJECTIVE Paired box 7 (PAX7) has been considered as a candidate gene for non-syndromic cleft lip with or without palate (NSCL/P). However, there is no research for the XXX, and previous studies concentrated on limited variants. This study aimed to conduct sufficiently dense and powerful scans of variants at PAX7 and explored the roles of variants at PAX7 in NSCL/P among the XXX. DESIGN Targeted region sequencing was performed to thoroughly screen variations, followed by a two-phase association analysis. 159 NSCL/P cases and 542 controls were analyzed in phase 1. Then in phase 2, the validation study was performed using 1626 cases and 2255 controls. We also explored the roles of variants at PAX7 gene in NSCL/P subtypes. Additionally, indirect associations were found by calculating LD and haplotypes. SETTING The study was conducted in XXX. PATIENTS, PARTICIPANTS 159 NSCL/P cases and 542 controls were analyzed in phase 1. Then in phase 2, the validation study was performed using 1626 cases and 2255 controls. INTERVENTIONS Blood samples were collected. MAIN OUTCOME MEASURES To explore the association analysis between variants at PAX7 and NSCL/P in XXX. RESULTS The results showed that rs2236810, rs114882979 and rs2236804 were significantly associated with NSCL/P, which were predicted to have regulatory functions. Besides, variants at PAX7 function differently in the NSCL/P subtypes. We also discovered a PAX7 missense variant, NM_001135254 p.A369 V (NM_002584.2:c.1106C > T). CONCLUSIONS In summary, we confirmed 3 SNPs at PAX7 were significantly associated with NSCL/P in XXX and identified a missense variant, NM_001135254 p.A369 V (NM_002584.2:c.1106C > T).
Collapse
Affiliation(s)
- Cheng-Wei Yang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, 12530Sichuan University, Chengdu, China
| | - Yue You
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, 12530Sichuan University, Chengdu, China
| | - Jia-Lin Sun
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, 12530Sichuan University, Chengdu, China
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, 12530Sichuan University, Chengdu, China
| | - Zhong-Lin Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, 12530Sichuan University, Chengdu, China
| |
Collapse
|
14
|
Janečková E, Feng J, Guo T, Han X, Ghobadi A, Araujo-Villalba A, Rahman MS, Ziaei H, Ho TV, Pareek S, Alvarez J, Chai Y. Canonical Wnt signaling regulates soft palate development by mediating ciliary homeostasis. Development 2023; 150:dev201189. [PMID: 36825984 PMCID: PMC10108707 DOI: 10.1242/dev.201189] [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: 08/03/2022] [Accepted: 02/10/2023] [Indexed: 02/25/2023]
Abstract
Craniofacial morphogenesis requires complex interactions involving different tissues, signaling pathways, secreted factors and organelles. The details of these interactions remain elusive. In this study, we have analyzed the molecular mechanisms and homeostatic cellular activities governing soft palate development to improve regenerative strategies for individuals with cleft palate. We have identified canonical Wnt signaling as a key signaling pathway primarily active in cranial neural crest (CNC)-derived mesenchymal cells surrounding soft palatal myogenic cells. Using Osr2-Cre;β-cateninfl/fl mice, we show that Wnt signaling is indispensable for mesenchymal cell proliferation and subsequently for myogenesis through mediating ciliogenesis. Specifically, we have identified that Wnt signaling directly regulates expression of the ciliary gene Ttll3. Impaired ciliary disassembly leads to differentiation defects in mesenchymal cells and indirectly disrupts myogenesis through decreased expression of Dlk1, a mesenchymal cell-derived pro-myogenesis factor. Moreover, we show that siRNA-mediated reduction of Ttll3 expression partly rescues mesenchymal cell proliferation and myogenesis in the palatal explant cultures from Osr2-Cre;β-cateninfl/fl embryos. This study highlights the role of Wnt signaling in palatogenesis through the control of ciliary homeostasis, which establishes a new mechanism for Wnt-regulated craniofacial morphogenesis.
Collapse
Affiliation(s)
- Eva Janečková
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Jifan Feng
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Tingwei Guo
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Xia Han
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Aileen Ghobadi
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Angelita Araujo-Villalba
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Md Shaifur Rahman
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Heliya Ziaei
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Thach-Vu Ho
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Siddhika Pareek
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Jasmine Alvarez
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Yang Chai
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| |
Collapse
|
15
|
Shi Y, Ye Z, Liu Y, Wang H, You M. Detection and diagnosis of cleidocranial dysplasia by panoramic radiography: a retrospective study. BMC Oral Health 2022; 22:558. [PMID: 36456973 PMCID: PMC9714060 DOI: 10.1186/s12903-022-02610-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Cleidocranial dysplasia (CCD) is a rare and underdiagnosed congenital disorder in dentistry. The purpose of this study was to illustrate and quantify the maxillofacial bone abnormalities detected on panoramic radiographs from a relatively large retrospective case series and to provide a series of diagnostic references for dentists to indicate the presence of disease and help in making an early and accurate diagnosis. METHODS The dental panoramic radiographs of thirty CCD patients aged 11 to 45 years (18 males and 12 females) were examined retrospectively. The dentition states, including supernumerary teeth and impacted teeth, were recorded. Twelve quantified measurements were adopted to determine the abnormalities of maxillofacial bones, including the degree of the zygomatic arch downward bend, bicondylar breadth, ramal height, mandibular height, mandibular aspect ratio, mandibular body height, condylar height, coronoid height, distance between the coronoid process and the condyle, bigonial width, gonial angle and best-fit gonial circle diameter. The Wilcoxon rank-sum test was used to compare the findings of the CCD patients with those of their matched controls (n = 300). RESULTS Supernumerary teeth were detected in 27 patients (90.0%), and all 30 patients presented impacted teeth. Compared to the matched controls, the CCD patients had a significantly larger degree of zygomatic arch downward bend (ZAD), a larger diameter of the best-fit gonial circle (BGC), and a shorter distance between the coronoid process and the condyle (DCC) in panoramic radiographs (P < 0.001). According to the reference cutoff values established from the 5th or 95th percentile of the measurements in the control group, ZAD higher than 6.90 mm, DDC less than 22.37 mm and BGC higher than 52.41 mm were significantly associated with the CCD features identified. Other panoramic measurements were not significantly different between the two groups. CONCLUSIONS Panoramic radiographs had great value in the diagnosis of CCD. In this study, we identified some dental and maxillofacial features on panoramic radiographs from a relatively large retrospective case series of CCD. A series of reliable quantitative indicators were provided for dentists that can indicate the presence of disease and improve the diagnostic specificity.
Collapse
Affiliation(s)
- Yuchao Shi
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of Oral Radiology, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, Ren Min South Road, Chengdu, 610041 Sichuan China
| | - Zelin Ye
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of Oral Radiology, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, Ren Min South Road, Chengdu, 610041 Sichuan China
| | - Yuanyuan Liu
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of Oral Radiology, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, Ren Min South Road, Chengdu, 610041 Sichuan China
| | - Hu Wang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of Oral Radiology, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, Ren Min South Road, Chengdu, 610041 Sichuan China
| | - Meng You
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of Oral Radiology, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, Ren Min South Road, Chengdu, 610041 Sichuan China
| |
Collapse
|
16
|
Chen J, Yao Y, Wang Y, Wang X, Peng X, Li T, Liu Y, Du J. Autophagy triggered by the ROS/ERK signaling pathway protects mouse embryonic palatal cells from apoptosis induced by nicotine. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:81909-81922. [PMID: 35739442 DOI: 10.1007/s11356-022-21496-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/12/2022] [Indexed: 06/15/2023]
Abstract
Maternal cigarette smoking during pregnancy is a known high-risk factor for having a child with a cleft lip and/or palate (CLP), a common congenital malformation. Nicotine is the major teratogen component of cigarettes and e-cigarettes, and nicotine plays an important role in the development of CLP. However, the mechanism underlying nicotine's effect on CLP remains unclear. Here, we aimed to determine the role and molecular mechanisms of nicotine-induced autophagy, an important process involved in regulating the cellular stress response in mouse embryonic palatal cells (MEPCs). First, we found that nicotine promoted MEPCs proliferation and inhibited their apoptosis from 0 to 12 h. After 12 h, the proliferation was inhibited, and apoptosis was promoted. The migration of MEPCs was also inhibited by nicotine. Simultaneously, long-term nicotine stimulation inhibited the osteogenic differentiation of MEPCs. We then found that nicotine significantly increased autophagy flux in MEPCs at 12 h by increasing the expression of microtubule-associated protein light chain 3 (LC3) and reducing P62 expression levels. After nicotine exposure, intracellular reactive oxygen species (ROS) and extracellular signal-regulated kinase-1/2 (ERK1/2) expression significantly increased, and the expression of ERK1/2 was reversed by the ROS scavenging agent N-acetylcysteine (NAC). Moreover, the autophagy induced by nicotine was reversed by SCH772984, a specific inhibitor of ERK1/2, and the autophagy inhibitor chloroquine (CQ). These results suggest that in the early stage of nicotine exposure, MEPCs may trigger autophagy through the ROS/ERK1/2 signaling pathway to avoid cell damage caused by nicotine.
Collapse
Affiliation(s)
- Jing Chen
- Laboratory of Orofacial Development, Laboratory of Molecular Signaling and Stem Cells Therapy, Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, 100050, China
| | - Yaxia Yao
- Laboratory of Orofacial Development, Laboratory of Molecular Signaling and Stem Cells Therapy, Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, 100050, China
| | - Yijia Wang
- Laboratory of Orofacial Development, Laboratory of Molecular Signaling and Stem Cells Therapy, Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, 100050, China
| | - Xiaotong Wang
- Laboratory of Orofacial Development, Laboratory of Molecular Signaling and Stem Cells Therapy, Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, 100050, China
| | - Xia Peng
- Laboratory of Orofacial Development, Laboratory of Molecular Signaling and Stem Cells Therapy, Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, 100050, China
| | - Tianli Li
- Laboratory of Orofacial Development, Laboratory of Molecular Signaling and Stem Cells Therapy, Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, 100050, China
| | - Ying Liu
- Laboratory of Orofacial Development, Laboratory of Molecular Signaling and Stem Cells Therapy, Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, 100050, China
| | - Juan Du
- Laboratory of Orofacial Development, Laboratory of Molecular Signaling and Stem Cells Therapy, Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, 100050, China.
| |
Collapse
|
17
|
Abstract
Oral and craniofacial tissues are uniquely adapted for continuous and intricate functioning, including breathing, feeding, and communication. To achieve these vital processes, this complex is supported by incredible tissue diversity, variously composed of epithelia, vessels, cartilage, bone, teeth, ligaments, and muscles, as well as mesenchymal, adipose, and peripheral nervous tissue. Recent single cell and spatial multiomics assays-specifically, genomics, epigenomics, transcriptomics, proteomics, and metabolomics-have annotated known and new cell types and cell states in human tissues and animal models, but these concepts remain limitedly explored in the human postnatal oral and craniofacial complex. Here, we highlight the collaborative and coordinated efforts of the newly established Oral and Craniofacial Bionetwork as part of the Human Cell Atlas, which aims to leverage single cell and spatial multiomics approaches to first understand the cellular and molecular makeup of human oral and craniofacial tissues in health and to then address common and rare diseases. These powerful assays have already revealed the cell types that support oral tissues, and they will unravel cell types and molecular networks utilized across development, maintenance, and aging as well as those affected in diseases of the craniofacial complex. This level of integration and cell annotation with partner laboratories across the globe will be critical for understanding how multiple variables, such as age, sex, race, and ancestry, influence these oral and craniofacial niches. Here, we 1) highlight these recent collaborative efforts to employ new single cell and spatial approaches to resolve our collective biology at a higher resolution in health and disease, 2) discuss the vision behind the Oral and Craniofacial Bionetwork, 3) outline the stakeholders who contribute to and will benefit from this network, and 4) outline directions for creating the first Human Oral and Craniofacial Cell Atlas.
Collapse
Affiliation(s)
- A J Caetano
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK
| | - I Sequeira
- Institute of Dentistry, Barts Centre for Squamous Cancer, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - K M Byrd
- Lab of Oral and Craniofacial Innovation, Department of Innovation and Technology Research, ADA Science and Research Institute, Gaithersburg, MD, USA
| |
Collapse
|
18
|
Gupta S, Kawaguchi R, Heinrichs E, Gallardo S, Castellanos S, Mandric I, Novitch BG, Butler SJ. In vitro atlas of dorsal spinal interneurons reveals Wnt signaling as a critical regulator of progenitor expansion. Cell Rep 2022; 40:111119. [PMID: 35858555 PMCID: PMC9414195 DOI: 10.1016/j.celrep.2022.111119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 04/12/2022] [Accepted: 06/28/2022] [Indexed: 11/03/2022] Open
Abstract
Restoring sensation after injury or disease requires a reproducible method for generating large quantities of bona fide somatosensory interneurons. Toward this goal, we assess the mechanisms by which dorsal spinal interneurons (dIs; dI1-dI6) can be derived from mouse embryonic stem cells (mESCs). Using two developmentally relevant growth factors, retinoic acid (RA) and bone morphogenetic protein (BMP) 4, we recapitulate the complete in vivo program of dI differentiation through a neuromesodermal intermediate. Transcriptional profiling reveals that mESC-derived dIs strikingly resemble endogenous dIs, with the correct molecular and functional signatures. We further demonstrate that RA specifies dI4-dI6 fates through a default multipotential state, while the addition of BMP4 induces dI1-dI3 fates and activates Wnt signaling to enhance progenitor proliferation. Constitutively activating Wnt signaling permits the dramatic expansion of neural progenitor cultures. These cultures retain the capacity to differentiate into diverse populations of dIs, thereby providing a method of increasing neuronal yield.
Collapse
Affiliation(s)
- Sandeep Gupta
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Riki Kawaguchi
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Eric Heinrichs
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Genetics and Genomics Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Salena Gallardo
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Stephanie Castellanos
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; CIRM Bridges to Research Program, California State University, Northridge, Los Angeles, CA, USA
| | - Igor Mandric
- Department of Computer Science, Samueli School of Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Bennett G Novitch
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Intellectual & Developmental Disabilities Research Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Samantha J Butler
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Intellectual & Developmental Disabilities Research Center, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
19
|
Functional validation of variants of unknown significance using CRISPR gene editing and transcriptomics: A Kleefstra syndrome case study. Gene X 2022; 821:146287. [PMID: 35176430 DOI: 10.1016/j.gene.2022.146287] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/20/2021] [Accepted: 02/03/2022] [Indexed: 11/21/2022] Open
Abstract
There are an estimated > 400 million people living with a rare disease globally, with genetic variants the cause of approximately 80% of cases. Next Generation Sequencing (NGS) rapidly identifies genetic variants however they are often of unknown significance. Low throughput functional validation in specialist laboratories is the current ad hoc approach for functional validation of genetic variants, which creating major bottlenecks in patient diagnosis. This study investigates the application of CRISPR gene editing followed by genome wide transcriptomic profiling to facilitate patient diagnosis. As proof-of-concept, we introduced a variant in the Euchromatin histone methyl transferase (EHMT1) gene into HEK293T cells. We identified changes in the regulation of the cell cycle, neural gene expression and suppression of gene expression changes on chromosome 19 and chromosome X, that are in keeping with Kleefstra syndrome clinical phenotype and/or provide insight into disease mechanism. This study demonstrates the utility of genome editing followed by functional readouts to rapidly and systematically validating the function of variants of unknown significance in patients suffering from rare diseases.
Collapse
|
20
|
Rios‐Arce ND, Murugesh DK, Hum NR, Sebastian A, Jbeily EH, Christiansen BA, Loots GG. Pre‐existing Type 1 Diabetes Mellitus Blunts the Development of
Post‐Traumatic
Osteoarthritis. JBMR Plus 2022; 6:e10625. [PMID: 35509635 PMCID: PMC9059474 DOI: 10.1002/jbm4.10625] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/26/2022] [Accepted: 03/09/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
- Naiomy D. Rios‐Arce
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratories Livermore CA USA
| | - Deepa K. Murugesh
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratories Livermore CA USA
| | - Nicholas R. Hum
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratories Livermore CA USA
| | - Aimy Sebastian
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratories Livermore CA USA
| | - Elias H. Jbeily
- Department of Orthopedic Surgery UC Davis Medical Center Sacramento CA USA
| | | | - Gabriela G. Loots
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratories Livermore CA USA
- Molecular and Cell Biology School of Natural Sciences, UC Merced Merced CA USA
| |
Collapse
|
21
|
Guo T, Han X, He J, Feng J, Jing J, Janečková E, Lei J, Ho TV, Xu J, Chai Y. KDM6B interacts with TFDP1 to activate P53 signalling in regulating mouse palatogenesis. eLife 2022; 11:74595. [PMID: 35212626 PMCID: PMC9007587 DOI: 10.7554/elife.74595] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
Epigenetic regulation plays extensive roles in diseases and development. Disruption of epigenetic regulation not only increases the risk of cancer, but can also cause various developmental defects. However, the question of how epigenetic changes lead to tissue-specific responses during neural crest fate determination and differentiation remains understudied. Using palatogenesis as a model, we reveal the functional significance of Kdm6b, an H3K27me3 demethylase, in regulating mouse embryonic development. Our study shows that Kdm6b plays an essential role in cranial neural crest development, and loss of Kdm6b disturbs P53 pathway-mediated activity, leading to complete cleft palate along with cell proliferation and differentiation defects in mice. Furthermore, activity of H3K27me3 on the promoter of Trp53 is antagonistically controlled by Kdm6b, and Ezh2 in cranial neural crest cells. More importantly, without Kdm6b, the transcription factor TFDP1, which normally binds to the promoter of Trp53, cannot activate Trp53 expression in palatal mesenchymal cells. Furthermore, the function of Kdm6b in activating Trp53 in these cells cannot be compensated for by the closely related histone demethylase Kdm6a. Collectively, our results highlight the important role of the epigenetic regulator KDM6B and how it specifically interacts with TFDP1 to achieve its functional specificity in regulating Trp53 expression, and further provide mechanistic insights into the epigenetic regulatory network during organogenesis.
Collapse
Affiliation(s)
- Tingwei Guo
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Xia Han
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Jinzhi He
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Jifan Feng
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Junjun Jing
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Eva Janečková
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Jie Lei
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Thach-Vu Ho
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Jian Xu
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Yang Chai
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| |
Collapse
|
22
|
Feng J, Han X, Yuan Y, Cho CK, Janečková E, Guo T, Pareek S, Rahman MS, Zheng B, Bi J, Jing J, Zhang M, Xu J, Ho TV, Chai Y. TGF-β signaling and Creb5 cooperatively regulate Fgf18 to control pharyngeal muscle development. eLife 2022; 11:80405. [PMID: 36542062 PMCID: PMC9771365 DOI: 10.7554/elife.80405] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
The communication between myogenic cells and their surrounding connective tissues is indispensable for muscle morphogenesis. During late embryonic development in mice, myogenic progenitors migrate to discrete sites to form individual muscles. The detailed mechanism of this process remains unclear. Using mouse levator veli palatini (LVP) development as a model, we systematically investigated how a distinct connective tissue subpopulation, perimysial fibroblasts, communicates with myogenic cells to regulate mouse pharyngeal myogenesis. Using single-cell RNAseq data analysis, we identified that TGF-β signaling is a key regulator for the perimysial fibroblasts. Loss of TGF-β signaling in the neural crest-derived palatal mesenchyme leads to defects in perimysial fibroblasts and muscle malformation in the soft palate in Osr2Cre;Tgfbr1fl/fl mice. In particular, Creb5, a transcription factor expressed in the perimysial fibroblasts, cooperates with TGF-β signaling to activate expression of Fgf18. Moreover, Fgf18 supports pharyngeal muscle development in vivo and exogenous Fgf18 can partially rescue myogenic cell numbers in Osr2Cre;Tgfbr1fl/fl samples, illustrating that TGF-β-regulated Fgf18 signaling is required for LVP development. Collectively, our findings reveal the mechanism by which TGF-β signaling achieves its functional specificity in defining the perimysial-to-myogenic signals for pharyngeal myogenesis.
Collapse
Affiliation(s)
- Jifan Feng
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Xia Han
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Yuan Yuan
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Courtney Kyeong Cho
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Eva Janečková
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Tingwei Guo
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Siddhika Pareek
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Md Shaifur Rahman
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Banghong Zheng
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Jing Bi
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Junjun Jing
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Mingyi Zhang
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Jian Xu
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Thach-Vu Ho
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Yang Chai
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| |
Collapse
|