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Lee SH, Platt S, Lim CH, Ito M, Myung P. The development of hair follicles and nail. Dev Biol 2024; 513:3-11. [PMID: 38759942 DOI: 10.1016/j.ydbio.2024.05.010] [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: 11/27/2023] [Revised: 05/06/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
The hair follicle and nail unit develop and regenerate through epithelial-mesenchymal interactions. Here, we review some of the key signals and molecular interactions that regulate mammalian hair follicle and nail formation during embryonic development and how these interactions are reutilized to promote their regeneration during adult homeostasis and in response to skin wounding. Finally, we highlight the role of some of these signals in mediating human hair follicle and nail conditions.
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Affiliation(s)
- Soung-Hoon Lee
- The Ronald O. Perelman Department of Dermatology and Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Sarah Platt
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA
| | - Chae Ho Lim
- The Ronald O. Perelman Department of Dermatology and Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Mayumi Ito
- The Ronald O. Perelman Department of Dermatology and Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Peggy Myung
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA; Department of Pathology, Yale School of Medicine, New Haven, CT, USA.
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2
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Carron M, Sachslehner AP, Cicekdal MB, Bruggeman I, Demuynck S, Golabi B, De Baere E, Declercq W, Tschachler E, Vleminckx K, Eckhart L. Evolutionary origin of Hoxc13-dependent skin appendages in amphibians. Nat Commun 2024; 15:2328. [PMID: 38499530 PMCID: PMC10948813 DOI: 10.1038/s41467-024-46373-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: 07/02/2023] [Accepted: 02/26/2024] [Indexed: 03/20/2024] Open
Abstract
Cornified skin appendages, such as hair and nails, are major evolutionary innovations of terrestrial vertebrates. Human hair and nails consist largely of special intermediate filament proteins, known as hair keratins, which are expressed under the control of the transcription factor Hoxc13. Here, we show that the cornified claws of Xenopus frogs contain homologs of hair keratins and the genes encoding these keratins are flanked by promoters in which binding sites of Hoxc13 are conserved. Furthermore, these keratins and Hoxc13 are co-expressed in the claw-forming epithelium of frog toe tips. Upon deletion of hoxc13, the expression of hair keratin homologs is abolished and the development of cornified claws is abrogated in X. tropicalis. These results indicate that Hoxc13-dependent expression of hair keratin homologs evolved already in stem tetrapods, presumably as a mechanism for protecting toe tips, and that this ancestral genetic program was coopted to the growth of hair in mammals.
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Affiliation(s)
- Marjolein Carron
- Department of Biomedical Molecular Biology, Ghent University, 9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University and Center for Medical Genetics, Ghent University Hospital, 9000, Ghent, Belgium
| | | | - Munevver Burcu Cicekdal
- Department of Biomedical Molecular Biology, Ghent University, 9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University and Center for Medical Genetics, Ghent University Hospital, 9000, Ghent, Belgium
| | - Inge Bruggeman
- Department of Biomedical Molecular Biology, Ghent University, 9000, Ghent, Belgium
- VIB-Ugent Center for Inflammation Research, 9000, Ghent, Belgium
| | - Suzan Demuynck
- Department of Biomedical Molecular Biology, Ghent University, 9000, Ghent, Belgium
| | - Bahar Golabi
- Department of Dermatology, Medical University of Vienna, 1090, Vienna, Austria
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University and Center for Medical Genetics, Ghent University Hospital, 9000, Ghent, Belgium
| | - Wim Declercq
- Department of Biomedical Molecular Biology, Ghent University, 9000, Ghent, Belgium
- VIB-Ugent Center for Inflammation Research, 9000, Ghent, Belgium
| | - Erwin Tschachler
- Department of Dermatology, Medical University of Vienna, 1090, Vienna, Austria
| | - Kris Vleminckx
- Department of Biomedical Molecular Biology, Ghent University, 9000, Ghent, Belgium.
| | - Leopold Eckhart
- Department of Dermatology, Medical University of Vienna, 1090, Vienna, Austria.
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3
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Ayalew W, Wu X, Tarekegn GM, Sisay Tessema T, Naboulsi R, Van Damme R, Bongcam-Rudloff E, Edea Z, Enquahone S, Yan P. Whole-Genome Resequencing Reveals Selection Signatures of Abigar Cattle for Local Adaptation. Animals (Basel) 2023; 13:3269. [PMID: 37893993 PMCID: PMC10603685 DOI: 10.3390/ani13203269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Over time, indigenous cattle breeds have developed disease resistance, heat tolerance, and adaptability to harsh environments. Deciphering the genetic mechanisms underlying adaptive traits is crucial for their improvement and sustainable utilization. For the first time, we performed whole-genome sequencing to unveil the genomic diversity, population structure, and selection signatures of Abigar cattle living in a tropical environment. The population structure analysis revealed that Abigar cattle exhibit high nucleotide diversity and heterozygosity, with low runs of homozygosity and linkage disequilibrium, suggesting a genetic landscape less constrained by inbreeding and enriched by diversity. Using nucleotide diversity (Pi) and population differentiation (FST) selection scan methods, we identified 83 shared genes that are likely associated with tropical adaption. The functional annotation analysis revealed that some of these genes are potentially linked to heat tolerance (HOXC13, DNAJC18, and RXFP2), immune response (IRAK3, MZB1, and STING1), and oxidative stress response (SLC23A1). Given the wider spreading impacts of climate change on cattle production, understanding the genetic mechanisms of adaptation of local breeds becomes crucial to better respond to climate and environmental changes. In this context, our finding establishes a foundation for further research into the mechanisms underpinning cattle adaptation to tropical environments.
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Affiliation(s)
- Wondossen Ayalew
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (G.M.T.); (T.S.T.)
| | - Xiaoyun Wu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
| | - Getinet Mekuriaw Tarekegn
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (G.M.T.); (T.S.T.)
- Scotland’s Rural College (SRUC), Roslin Institute Building, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Tesfaye Sisay Tessema
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (G.M.T.); (T.S.T.)
| | - Rakan Naboulsi
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institute, Tomtebodavägen 18A, 17177 Stockholm, Sweden
| | - Renaud Van Damme
- Department of Animal Breeding and Genetics, Bioinformatics Section, Swedish University of Agricultural Sciences, P.O. Box 7023, S-750 07 Uppsala, Sweden; (R.V.D.); (E.B.-R.)
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, Bioinformatics Section, Swedish University of Agricultural Sciences, P.O. Box 7023, S-750 07 Uppsala, Sweden; (R.V.D.); (E.B.-R.)
| | - Zewdu Edea
- Ethiopian Bio and Emerging Technology Institute, Addis Ababa P.O. Box 5954, Ethiopia;
| | - Solomon Enquahone
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (G.M.T.); (T.S.T.)
| | - Ping Yan
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
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4
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Li H, Gao P, Chen H, Zhao J, Zhang X, Li G, Wang L, Qin L. HOXC13 promotes cell proliferation, metastasis and glycolysis in breast cancer by regulating DNMT3A. Exp Ther Med 2023; 26:439. [PMID: 37614427 PMCID: PMC10443053 DOI: 10.3892/etm.2023.12138] [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: 01/12/2023] [Accepted: 04/25/2023] [Indexed: 08/25/2023] Open
Abstract
Breast cancer (BC) is a life-threatening malignant tumor that affects females more commonly than males. The mechanisms underlying BC proliferation, metastasis and glycolysis require further investigation. Homeobox C13 (HOXC13) is highly expressed in BC; however, the specific mechanisms in BC are yet to be fully elucidated. Therefore, the aim of the present study was to investigate the role of HOXC13 in BC proliferation, migration, invasion and glycolysis. In the present study, the UALCAN database was used to predict the expression levels of HOXC13 in patients with BC. Western blot analysis and reverse transcription-quantitative PCR were used to determine the expression levels of HOXC13 in BC cell lines. Moreover, HOXC13 knockdown was induced using cell transfection, and the viability, proliferation and apoptosis of cells were detected using Cell Counting Kit-8, 5-ethynyl-2'-deoxyuridine staining and flow cytometry. Migration, invasion and epithelial-mesenchymal transition (EMT) were measured using wound healing assay, Transwell assay and western blotting. In addition, XF96 extracellular flux analyzer and corresponding kits were used to detect glycolysis. The JASPAR database was used to predict promoter binding sites for the transcription factors HOXC13 and DNA methyltransferase 3α (DNMT3A). HOXC13 expression was silenced and DNMT3A was simultaneously overexpressed using cell transfection. The results of the present study revealed that HOXC13 expression was significantly elevated in BC tissues and cells. Following HOXC13 knockdown in BC cells, the viability, proliferation, glycolysis, migration, invasion and EMT were significantly decreased, and apoptosis was significantly increased. In addition, HOXC13 positively regulated the transcription of DNMT3A in BC cells, thus playing a regulatory role in the malignant progression of cells. In conclusion, HOXC13 promoted cell viability, proliferation, migration, invasion, EMT and glycolysis in BC by regulating DNMT3A.
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Affiliation(s)
- Hongrui Li
- Department of Thyroid and Breast Diseases, Jincheng People's Hospital, Jincheng, Shanxi 048000, P.R. China
- Department of Thyroid and Breast Diseases, Jincheng Hospital Affiliated to Changzhi Medical College, Jincheng, Shanxi 048000, P.R. China
| | - Pengcheng Gao
- Department of Thyroid and Breast Diseases, Jincheng People's Hospital, Jincheng, Shanxi 048000, P.R. China
- Department of Thyroid and Breast Diseases, Jincheng Hospital Affiliated to Changzhi Medical College, Jincheng, Shanxi 048000, P.R. China
| | - Haifeng Chen
- Department of Thyroid and Breast Diseases, Jincheng People's Hospital, Jincheng, Shanxi 048000, P.R. China
- Department of Thyroid and Breast Diseases, Jincheng Hospital Affiliated to Changzhi Medical College, Jincheng, Shanxi 048000, P.R. China
| | - Junjie Zhao
- Department of Thyroid and Breast Diseases, Jincheng People's Hospital, Jincheng, Shanxi 048000, P.R. China
- Department of Thyroid and Breast Diseases, Jincheng Hospital Affiliated to Changzhi Medical College, Jincheng, Shanxi 048000, P.R. China
| | - Xiangzhong Zhang
- Department of Thyroid and Breast Diseases, Jincheng People's Hospital, Jincheng, Shanxi 048000, P.R. China
- Department of Thyroid and Breast Diseases, Jincheng Hospital Affiliated to Changzhi Medical College, Jincheng, Shanxi 048000, P.R. China
| | - Ganggang Li
- Department of Thyroid and Breast Diseases, Jincheng People's Hospital, Jincheng, Shanxi 048000, P.R. China
- Department of Thyroid and Breast Diseases, Jincheng Hospital Affiliated to Changzhi Medical College, Jincheng, Shanxi 048000, P.R. China
| | - Liting Wang
- Department of Thyroid and Breast Diseases, Jincheng People's Hospital, Jincheng, Shanxi 048000, P.R. China
- Department of Thyroid and Breast Diseases, Jincheng Hospital Affiliated to Changzhi Medical College, Jincheng, Shanxi 048000, P.R. China
| | - Long Qin
- Department of Thyroid and Breast Diseases, Jincheng People's Hospital, Jincheng, Shanxi 048000, P.R. China
- Department of Thyroid and Breast Diseases, Jincheng Hospital Affiliated to Changzhi Medical College, Jincheng, Shanxi 048000, P.R. China
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5
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Castilla-Ibeas A, Zdral S, Galán L, Haro E, Allou L, Campa VM, Icardo JM, Mundlos S, Oberg KC, Ros MA. Failure of digit tip regeneration in the absence of Lmx1b suggests Lmx1b functions disparate from dorsoventral polarity. Cell Rep 2023; 42:111975. [PMID: 36641754 DOI: 10.1016/j.celrep.2022.111975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 11/07/2022] [Accepted: 12/22/2022] [Indexed: 01/15/2023] Open
Abstract
Mammalian digit tip regeneration is linked to the presence of nail tissue, but a nail-explicit model is missing. Here, we report that nail-less double-ventral digits of ΔLARM1/2 mutants that lack limb-specific Lmx1b enhancers fail to regenerate. To separate the nail's effect from the lack of dorsoventral (DV) polarity, we also interrogate double-dorsal double-nail digits and show that they regenerate. Thus, DV polarity is not a prerequisite for regeneration, and the nail requirement is supported. Transcriptomic comparison between wild-type and non-regenerative ΔLARM1/2 mutant blastemas reveals differential upregulation of vascularization and connective tissue functional signatures in wild type versus upregulation of inflammation in the mutant. These results, together with the finding of Lmx1b expression in the postnatal dorsal dermis underneath the nail and uniformly in the regenerative blastema, open the possibility of additional Lmx1b roles in digit tip regeneration, in addition to the indirect effect of mediating the formation of the nail.
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Affiliation(s)
- Alejandro Castilla-Ibeas
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC; CSIC-SODERCAN-UC), Santander, Spain
| | - Sofía Zdral
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC; CSIC-SODERCAN-UC), Santander, Spain
| | - Laura Galán
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC; CSIC-SODERCAN-UC), Santander, Spain
| | - Endika Haro
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC; CSIC-SODERCAN-UC), Santander, Spain
| | - Lila Allou
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Víctor M Campa
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC; CSIC-SODERCAN-UC), Santander, Spain
| | - Jose M Icardo
- Departamento de Anatomía y Biología Celular, Universidad de Cantabria, Santander, Spain
| | - Stefan Mundlos
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Kerby C Oberg
- Department of Pathology and Human Anatomy, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Marian A Ros
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC; CSIC-SODERCAN-UC), Santander, Spain.
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6
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Single-cell chromatin landscapes of mouse skin development. Sci Data 2022; 9:741. [PMID: 36460683 PMCID: PMC9718782 DOI: 10.1038/s41597-022-01839-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 11/09/2022] [Indexed: 12/03/2022] Open
Abstract
The coat of mammals is produced by hair follicles, and hair follicle is an important and complex accessory organ of skin. As a complex physiological regulation process, hair follicle morphogenesis is regulated by a series of signal pathway factors, involves the interaction of multiple cell types and begins in the early embryonic stage. However, its transcriptional regulatory mechanism is unclear. We have therefore utilized single-cell ATAC sequencing to obtain the chromatin accessibility landscapes of 6,928, 6,961 and 7,374 high-quality cells from the dorsal skins of E13.5, E16.5 and P0 mice (Mus musculus), respectively. Based on marker gene activity clustering, we defined 6, 8 and 5 distinct cell types in E13.5, E16.5 and P0 stages, respectively. Furtherly, we integrated the fibroblasts and keratinocytes clusters, performed further analysis and re-clustered. The single cell map of the chromatin open area was drawn from each cell type and the mechanism of cell transcription regulation was explored. Collectively, our data provide a reference for deeply exploring the epigenetic regulation mechanism of mouse hair follicles development.
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7
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Shim J, Park J, Abudureyimu G, Kim MH, Shim JS, Jang KT, Kwon EJ, Jang HS, Yeo E, Lee JH, Lee D. Comparative Spatial Transcriptomic and Single-Cell Analyses of Human Nail Units and Hair Follicles Show Transcriptional Similarities between the Onychodermis and Follicular Dermal Papilla. J Invest Dermatol 2022; 142:3146-3157.e12. [PMID: 35853486 DOI: 10.1016/j.jid.2022.06.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 01/05/2023]
Abstract
The nail unit and hair follicle are both hard keratin-producing organs that share various biological features. In this study, we used digital spatial profiling and single-cell RNA sequencing to define a spatially resolved expression profile of the human nail unit and hair follicle. Our approach showed the presence of a nail-specific mesenchymal population called onychofibroblasts within the onychodermis. Onychodermis and follicular dermal papilla both expressed Wnt and bone morphogenetic protein signaling molecules. In addition, nail matrix epithelium and hair matrix showed very similar expressions profile, including the expression of hard keratins and HOXC13, a transcriptional regulator of the hair shaft. Integration of single-cell RNA sequencing and digital spatial profiling data through computational deconvolution methods estimated epithelial and mesenchymal cell abundance in the nail- and hair-specific regions of interest and revealed close transcriptional similarity between these major skin appendages. To analyze the function of bone morphogenetic proteins in nail differentiation, we treated cultured human nail matrix keratinocytes with BMP5, which are highly expressed by onychofibroblasts. We observed increased expressions of hard keratin and its regulator genes such as HOXC13. Collectively, our data suggest that onychodermis is the counterpart of dermal papilla and that BMP5 in onychofibroblasts plays a key role in the differentiation of nail matrix keratinocytes.
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Affiliation(s)
- Joonho Shim
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jihye Park
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Gulimila Abudureyimu
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Min-Hee Kim
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jong Sup Shim
- Department of Orthopedic Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kee-Taek Jang
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Eun Ji Kwon
- Department of Dermatology, Columbia University Irving Medical Center, New York, New York, USA
| | - Hyung-Suk Jang
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Eunhye Yeo
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Jong Hee Lee
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Dongyoun Lee
- Department of Dermatology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
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8
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Hintermann A, Guerreiro I, Lopez-Delisle L, Bolt CC, Gitto S, Duboule D, Beccari L. Developmental and evolutionary comparative analysis of a regulatory landscape in mouse and chicken. Development 2022; 149:275867. [PMID: 35770682 PMCID: PMC9307994 DOI: 10.1242/dev.200594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/23/2022] [Indexed: 12/12/2022]
Abstract
Modifications in gene regulation are driving forces in the evolution of organisms. Part of these changes involve cis-regulatory elements (CREs), which contact their target genes through higher-order chromatin structures. However, how such architectures and variations in CREs contribute to transcriptional evolvability remains elusive. We use Hoxd genes as a paradigm for the emergence of regulatory innovations, as many relevant enhancers are located in a regulatory landscape highly conserved in amniotes. Here, we analysed their regulation in murine vibrissae and chicken feather primordia, two skin appendages expressing different Hoxd gene subsets, and compared the regulation of these genes in these appendages with that in the elongation of the posterior trunk. In the two former structures, distinct subsets of Hoxd genes are contacted by different lineage-specific enhancers, probably as a result of using an ancestral chromatin topology as an evolutionary playground, whereas the gene regulation that occurs in the mouse and chicken embryonic trunk partially relies on conserved CREs. A high proportion of these non-coding sequences active in the trunk have functionally diverged between species, suggesting that transcriptional robustness is maintained, despite considerable divergence in enhancer sequences. Summary: Analyses of the relationships between chromatin architecture and regulatory activities at the HoxD locus show that ancestral transcription patterns can be maintained while new regulations evolve.
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Affiliation(s)
- Aurélie Hintermann
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
| | - Isabel Guerreiro
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
| | - Lucille Lopez-Delisle
- Swiss Institute for Experimental Cancer Research (EPFL ISREC), School of Life Sciences, Federal School of Technology (EPFL) 2 , 1015 Lausanne , Switzerland
| | - Christopher Chase Bolt
- Swiss Institute for Experimental Cancer Research (EPFL ISREC), School of Life Sciences, Federal School of Technology (EPFL) 2 , 1015 Lausanne , Switzerland
| | - Sandra Gitto
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
| | - Denis Duboule
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
- Swiss Institute for Experimental Cancer Research (EPFL ISREC), School of Life Sciences, Federal School of Technology (EPFL) 2 , 1015 Lausanne , Switzerland
- Collège de France 3 , 11 Place Marcelin Berthelot, 75005 Paris , France
| | - Leonardo Beccari
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
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9
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Amândio AR, Beccari L, Lopez-Delisle L, Mascrez B, Zakany J, Gitto S, Duboule D. Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster. Genes Dev 2021; 35:1490-1509. [PMID: 34711654 PMCID: PMC8559674 DOI: 10.1101/gad.348934.121] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 09/21/2021] [Indexed: 12/12/2022]
Abstract
Mammalian Hox gene clusters contain a range of CTCF binding sites. In addition to their importance in organizing a TAD border, which isolates the most posterior genes from the rest of the cluster, the positions and orientations of these sites suggest that CTCF may be instrumental in the selection of various subsets of contiguous genes, which are targets of distinct remote enhancers located in the flanking regulatory landscapes. We examined this possibility by producing an allelic series of cumulative in cis mutations in these sites, up to the abrogation of CTCF binding in the five sites located on one side of the TAD border. In the most impactful alleles, the global chromatin architecture of the locus was modified, yet not drastically, illustrating that CTCF sites located on one side of a strong TAD border are sufficient to organize at least part of this insulation. Spatial colinearity in the expression of these genes along the major body axis was nevertheless maintained, despite abnormal expression boundaries. In contrast, strong effects were scored in the selection of target genes responding to particular enhancers, leading to the misregulation of Hoxd genes in specific structures. Altogether, while most enhancer-promoter interactions can occur in the absence of this series of CTCF sites, the binding of CTCF in the Hox cluster is required to properly transform a rather unprecise process into a highly discriminative mechanism of interactions, which is translated into various patterns of transcription accompanied by the distinctive chromatin topology found at this locus. Our allelic series also allowed us to reveal the distinct functional contributions for CTCF sites within this Hox cluster, some acting as insulator elements, others being necessary to anchor or stabilize enhancer-promoter interactions, and some doing both, whereas they all together contribute to the formation of a TAD border. This variety of tasks may explain the amazing evolutionary conservation in the distribution of these sites among paralogous Hox clusters or between various vertebrates.
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Affiliation(s)
- Ana Rita Amândio
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Leonardo Beccari
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Bénédicte Mascrez
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Jozsef Zakany
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Sandra Gitto
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Denis Duboule
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
- Collège de France, 75231 Paris, France
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10
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Transcriptional Differences in Lipid-Metabolizing Enzymes in Murine Sebocytes Derived from Sebaceous Glands of the Skin and Preputial Glands. Int J Mol Sci 2021; 22:ijms222111631. [PMID: 34769061 PMCID: PMC8584257 DOI: 10.3390/ijms222111631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 12/18/2022] Open
Abstract
Sebaceous glands are adnexal structures, which critically contribute to skin homeostasis and the establishment of a functional epidermal barrier. Sebocytes, the main cell population found within the sebaceous glands, are highly specialized lipid-producing cells. Sebaceous gland-resembling tissue structures are also found in male rodents in the form of preputial glands. Similar to sebaceous glands, they are composed of lipid-specialized sebocytes. Due to a lack of adequate organ culture models for skin sebaceous glands and the fact that preputial glands are much larger and easier to handle, previous studies used preputial glands as a model for skin sebaceous glands. Here, we compared both types of sebocytes, using a single-cell RNA sequencing approach, to unravel potential similarities and differences between the two sebocyte populations. In spite of common gene expression patterns due to general lipid-producing properties, we found significant differences in the expression levels of genes encoding enzymes involved in the biogenesis of specialized lipid classes. Specifically, genes critically involved in the mevalonate pathway, including squalene synthase, as well as the sphingolipid salvage pathway, such as ceramide synthase, (acid) sphingomyelinase or acid and alkaline ceramidases, were significantly less expressed by preputial gland sebocytes. Together, our data revealed tissue-specific sebocyte populations, indicating major developmental, functional as well as biosynthetic differences between both glands. The use of preputial glands as a surrogate model to study skin sebaceous glands is therefore limited, and major differences between both glands need to be carefully considered before planning an experiment.
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Perez CJ, Mecklenburg L, Fernandez A, Cantero M, de Souza TA, Lin K, Dent SYR, Montoliu L, Awgulewitsch A, Benavides F. Naked (N) mutant mice carry a nonsense mutation in the homeobox of Hoxc13. Exp Dermatol 2021; 31:330-340. [PMID: 34657330 DOI: 10.1111/exd.14469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 08/23/2021] [Accepted: 10/12/2021] [Indexed: 11/28/2022]
Abstract
Loss of function mutations in HOXC13 have been associated with Ectodermal Dysplasia-9, Hair/Nail Type (ECTD9) in consanguineous families, characterized by sparse to complete absence of hair and nail dystrophy. Here we characterize the spontaneous mouse mutation Naked (N) as a terminal truncation in the Hoxc13 (homeobox C13) gene. Similar to previous reports for homozygous Hoxc13 knock-out (KO) mice, homozygous N/N mice exhibit generalized alopecia with abnormal nails and a short lifespan. However, in contrast to Hoxc13 heterozygous KO mice, N/+ mice show generalized or partial alopecia, associated with loss of hair fibres, along with normal lifespan and fertility. Our data point to a lack of nonsense-mediated Hoxc13 transcript decay and the presence of the truncated mutant protein in N/N and N/+ hair follicles, thus suggesting a dominant-negative mutation. To our knowledge, this is the first report of a semi-dominant and potentially dominant-negative mutation affecting Hoxc13/HOXC13. Furthermore, recreating the N mutant allele in mice using CRISPR/Cas9-mediated genome editing resulted in the same spectrum of deficiencies as those associated with the spontaneous Naked mutation, thus confirming that N is indeed a Hoxc13 mutant allele. Considering the low viability of the Hoxc13 KO mice, the Naked mutation provides an attractive new model for studying ECTD9 disease mechanisms.
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Affiliation(s)
- Carlos J Perez
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas, USA
| | | | - Almudena Fernandez
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain.,CIBERER-ISCIII, Madrid, Spain
| | - Marta Cantero
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain.,CIBERER-ISCIII, Madrid, Spain
| | | | - Kevin Lin
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas, USA
| | - Sharon Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas, USA.,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas, USA
| | - Lluis Montoliu
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain.,CIBERER-ISCIII, Madrid, Spain
| | - Alexander Awgulewitsch
- Department of Medicine and Department of Regenerative Medicine & Cell Biology, Medical University of South Carolina (MUSC), Charleston, South Carolina, USA
| | - Fernando Benavides
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas, USA.,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas, USA
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Bolt CC, Lopez-Delisle L, Mascrez B, Duboule D. Mesomelic dysplasias associated with the HOXD locus are caused by regulatory reallocations. Nat Commun 2021; 12:5013. [PMID: 34408147 PMCID: PMC8373931 DOI: 10.1038/s41467-021-25330-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/05/2021] [Indexed: 02/07/2023] Open
Abstract
Human families with chromosomal rearrangements at 2q31, where the human HOXD locus maps, display mesomelic dysplasia, a severe shortening and bending of the limb. In mice, the dominant Ulnaless inversion of the HoxD cluster produces a similar phenotype suggesting the same origin for these malformations in humans and mice. Here we engineer 1 Mb inversion including the HoxD gene cluster, which positioned Hoxd13 close to proximal limb enhancers. Using this model, we show that these enhancers contact and activate Hoxd13 in proximal cells, inducing the formation of mesomelic dysplasia. We show that a secondary Hoxd13 null mutation in-cis with the inversion completely rescues the alterations, demonstrating that ectopic HOXD13 is directly responsible for this bone anomaly. Single-cell expression analysis and evaluation of HOXD13 binding sites suggests that the phenotype arises primarily by acting through genes normally controlled by HOXD13 in distal limb cells. Altogether, these results provide a conceptual and mechanistic framework to understand and unify the molecular origins of human mesomelic dysplasia associated with 2q31.
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MESH Headings
- Abnormalities, Multiple/embryology
- Abnormalities, Multiple/genetics
- Abnormalities, Multiple/metabolism
- Animals
- Bone Diseases, Developmental/embryology
- Bone Diseases, Developmental/genetics
- Bone Diseases, Developmental/metabolism
- Disease Models, Animal
- Female
- Gene Deletion
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Limb Deformities, Congenital/embryology
- Limb Deformities, Congenital/genetics
- Limb Deformities, Congenital/metabolism
- Loss of Function Mutation
- Male
- Mice, Inbred C57BL
- Multigene Family
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Mice
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Affiliation(s)
- Christopher Chase Bolt
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Bénédicte Mascrez
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Denis Duboule
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.
- Collège de France, Paris, France.
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13
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Fernandez-Guerrero M, Zdral S, Castilla-Ibeas A, Lopez-Delisle L, Duboule D, Ros MA. Time-sequenced transcriptomes of developing distal mouse limb buds: A comparative tissue layer analysis. Dev Dyn 2021; 251:1550-1575. [PMID: 34254395 DOI: 10.1002/dvdy.394] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The development of the amniote limb has been an important model system to study patterning mechanisms and morphogenesis. For proper growth and patterning, it requires the interaction between the distal sub-apical mesenchyme and the apical ectodermal ridge (AER) that involve the separate implementation of coordinated and tissue-specific genetic programs. RESULTS Here, we produce and analyze the transcriptomes of both distal limb mesenchymal progenitors and the overlying ectodermal cells, following time-coursed dissections that cover from limb bud initiation to fully patterned limbs. The comparison of transcriptomes within each layer as well as between layers over time, allowed the identification of specific transcriptional signatures for each of the developmental stages. Special attention was given to the identification of genes whose transcription dynamics suggest a previously unnoticed role in the context of limb development and also to signaling pathways enriched between layers. CONCLUSION We interpret the transcriptomic data in light of the known development pattern and we conclude that a major transcriptional transition occurs in distal limb buds between E9.5 and E10.5, coincident with the switch from an early phase continuation of the signature of trunk progenitors, related to the initial proximo distal specification, to a late intrinsic phase of development.
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Affiliation(s)
- Marc Fernandez-Guerrero
- Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC (CSIC-University of Cantabria-SODERCAN), Santander, Spain
| | - Sofia Zdral
- Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC (CSIC-University of Cantabria-SODERCAN), Santander, Spain
| | - Alejandro Castilla-Ibeas
- Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC (CSIC-University of Cantabria-SODERCAN), Santander, Spain
| | | | - Denis Duboule
- School of Life Sciences, Federal Institute of Technology, Lausanne, Switzerland.,Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Collège de France, Paris, France
| | - Marian A Ros
- Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC (CSIC-University of Cantabria-SODERCAN), Santander, Spain.,Facultad de Medicina, Departamento de Anatomía y Biología Celular, Universidad de Cantabria, Santander, Spain
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Meyer A, Schloissnig S, Franchini P, Du K, Woltering JM, Irisarri I, Wong WY, Nowoshilow S, Kneitz S, Kawaguchi A, Fabrizius A, Xiong P, Dechaud C, Spaink HP, Volff JN, Simakov O, Burmester T, Tanaka EM, Schartl M. Giant lungfish genome elucidates the conquest of land by vertebrates. Nature 2021; 590:284-289. [PMID: 33461212 PMCID: PMC7875771 DOI: 10.1038/s41586-021-03198-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/06/2021] [Indexed: 01/29/2023]
Abstract
Lungfishes belong to lobe-fined fish (Sarcopterygii) that, in the Devonian period, 'conquered' the land and ultimately gave rise to all land vertebrates, including humans1-3. Here we determine the chromosome-quality genome of the Australian lungfish (Neoceratodus forsteri), which is known to have the largest genome of any animal. The vast size of this genome, which is about 14× larger than that of humans, is attributable mostly to huge intergenic regions and introns with high repeat content (around 90%), the components of which resemble those of tetrapods (comprising mainly long interspersed nuclear elements) more than they do those of ray-finned fish. The lungfish genome continues to expand independently (its transposable elements are still active), through mechanisms different to those of the enormous genomes of salamanders. The 17 fully assembled lungfish macrochromosomes maintain synteny to other vertebrate chromosomes, and all microchromosomes maintain conserved ancient homology with the ancestral vertebrate karyotype. Our phylogenomic analyses confirm previous reports that lungfish occupy a key evolutionary position as the closest living relatives to tetrapods4,5, underscoring the importance of lungfish for understanding innovations associated with terrestrialization. Lungfish preadaptations to living on land include the gain of limb-like expression in developmental genes such as hoxc13 and sall1 in their lobed fins. Increased rates of evolution and the duplication of genes associated with obligate air-breathing, such as lung surfactants and the expansion of odorant receptor gene families (which encode proteins involved in detecting airborne odours), contribute to the tetrapod-like biology of lungfishes. These findings advance our understanding of this major transition during vertebrate evolution.
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Affiliation(s)
- Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany.
| | | | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Kang Du
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
| | | | - Iker Irisarri
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Wai Yee Wong
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | | | - Susanne Kneitz
- Biochemistry and Cell Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Akane Kawaguchi
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | | | - Peiwen Xiong
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Corentin Dechaud
- Institut de Génomique Fonctionnelle, École Normale Superieure, Université Claude Bernard, Lyon, France
| | - Herman P Spaink
- Faculty of Science, Universiteit Leiden, Leiden, The Netherlands
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle, École Normale Superieure, Université Claude Bernard, Lyon, France
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria.
| | | | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna, Austria.
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany.
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.
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