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Sandoval-Velasco M, Dudchenko O, Rodríguez JA, Pérez Estrada C, Dehasque M, Fontsere C, Mak SST, Khan R, Contessoto VG, Oliveira Junior AB, Kalluchi A, Zubillaga Herrera BJ, Jeong J, Roy RP, Christopher I, Weisz D, Omer AD, Batra SS, Shamim MS, Durand NC, O'Connell B, Roca AL, Plikus MV, Kusliy MA, Romanenko SA, Lemskaya NA, Serdyukova NA, Modina SA, Perelman PL, Kizilova EA, Baiborodin SI, Rubtsov NB, Machol G, Rath K, Mahajan R, Kaur P, Gnirke A, Garcia-Treviño I, Coke R, Flanagan JP, Pletch K, Ruiz-Herrera A, Plotnikov V, Pavlov IS, Pavlova NI, Protopopov AV, Di Pierro M, Graphodatsky AS, Lander ES, Rowley MJ, Wolynes PG, Onuchic JN, Dalén L, Marti-Renom MA, Gilbert MTP, Aiden EL. Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample. Cell 2024; 187:3541-3562.e51. [PMID: 38996487 DOI: 10.1016/j.cell.2024.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 03/07/2024] [Accepted: 06/03/2024] [Indexed: 07/14/2024]
Abstract
Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth's death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.
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Affiliation(s)
| | - Olga Dudchenko
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA.
| | - Juan Antonio Rodríguez
- Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark; Centre Nacional d'Anàlisi Genòmica, CNAG, 08028 Barcelona, Spain
| | - Cynthia Pérez Estrada
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Marianne Dehasque
- Centre for Palaeogenetics, SE-106 91 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Claudia Fontsere
- Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark
| | - Sarah S T Mak
- Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark
| | - Ruqayya Khan
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | - Achyuth Kalluchi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Bernardo J Zubillaga Herrera
- Department of Physics, Northeastern University, Boston, MA 02115, USA; Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02215, USA
| | - Jiyun Jeong
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Renata P Roy
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Departments of Biology and Physics, Texas Southern University, Houston, TX 77004, USA
| | - Ishawnia Christopher
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arina D Omer
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sanjit S Batra
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muhammad S Shamim
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neva C Durand
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Brendan O'Connell
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Alfred L Roca
- Department of Animal Sciences and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Maksim V Plikus
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Mariya A Kusliy
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia
| | | | - Natalya A Lemskaya
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia
| | | | - Svetlana A Modina
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia
| | - Polina L Perelman
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia
| | - Elena A Kizilova
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | | | - Nikolai B Rubtsov
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | - Gur Machol
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Krisha Rath
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ragini Mahajan
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77005, USA
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, University of Western Australia, Perth, WA 6009, Australia
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Rob Coke
- San Antonio Zoo, San Antonio, TX 78212, USA
| | | | | | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia and Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | | | | | - Naryya I Pavlova
- Institute of Biological Problems of Cryolitezone SB RAS, Yakutsk 677000, Russia
| | - Albert V Protopopov
- Academy of Sciences of Sakha Republic, Yakutsk 677000, Russia; North-Eastern Federal University, Yakutsk 677027, Russia
| | - Michele Di Pierro
- Department of Physics, Northeastern University, Boston, MA 02115, USA; Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02215, USA
| | | | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - M Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77005, USA; Departments of Physics, Astronomy, & Chemistry, Rice University, Houston, TX 77005, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77005, USA; Departments of Physics, Astronomy, & Chemistry, Rice University, Houston, TX 77005, USA
| | - Love Dalén
- Centre for Palaeogenetics, SE-106 91 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Marc A Marti-Renom
- Centre Nacional d'Anàlisi Genòmica, CNAG, 08028 Barcelona, Spain; Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain; ICREA, 08010 Barcelona, Spain; Universitat Pompeu Fabra, 08002 Barcelona, Spain.
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark; University Museum NTNU, 7012 Trondheim, Norway.
| | - Erez Lieberman Aiden
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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Rong Y, Wang X, Na Q, Ao X, Xia Q, Guo F, Han M, Ma R, Shang F, Liu Y, Lv Q, Wang Z, Su R, Zhang Y, Wang R. Genome-wide association study for cashmere traits in Inner Mongolia cashmere goat population reveals new candidate genes and haplotypes. BMC Genomics 2024; 25:658. [PMID: 38956486 PMCID: PMC11218406 DOI: 10.1186/s12864-024-10543-4] [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: 04/09/2024] [Accepted: 06/20/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND The cashmere goat industry is one of the main pillars of animal husbandry in Inner Mongolia Autonomous Region, and plays an irreplaceable role in local economic development. With the change in feeding methods and environment, the cashmere produced by Inner Mongolia cashmere goats shows a tendency of coarser, and the cashmere yield can not meet the consumption demand of people. However, the genetic basis behind these changes is not fully understood. We measured cashmere traits, including cashmere yield (CY), cashmere diameter (CD), cashmere thickness (CT), and fleece length (FL) traits for four consecutive years, and utilized Genome-wide association study of four cashmere traits in Inner Mongolia cashmere goats was carried out using new genomics tools to infer genomic regions and functional loci associated with cashmere traits and to construct haplotypes that significantly affect cashmere traits. RESULTS We estimated the genetic parameters of cashmere traits in Inner Mongolia cashmere goats. The heritability of cashmere yield, cashmere diameter, and fleece length traits of Inner Mongolia cashmere goats were 0.229, 0.359, and 0.250, which belonged to the medium heritability traits (0.2 ~ 0.4). The cashmere thickness trait has a low heritability of 0.053. We detected 151 genome-wide significantly associated SNPs with four cashmere traits on different chromosomes, which were very close to the chromosomes of 392 genes (located within the gene or within ± 500 kb). Notch3, BMPR1B, and CCNA2 have direct functional associations with fibroblasts and follicle stem cells, which play important roles in hair follicle growth and development. Based on GO functional annotation and KEGG enrichment analysis, potential candidate genes were associated with pathways of hair follicle genesis and development (Notch, P13K-Akt, TGF-beta, Cell cycle, Wnt, MAPK). We calculated the effective allele number of the Inner Mongolia cashmere goat population to be 1.109-1.998, the dominant genotypes of most SNPs were wild-type, the polymorphic information content of 57 SNPs were low polymorphism (0 < PIC < 0.25), and the polymorphic information content of 79 SNPs were moderate polymorphism (0.25 < PIC < 0.50). We analyzed the association of SNPs with phenotypes and found that the homozygous mutant type of SNP1 and SNP3 was associated with the highest cashmere yield, the heterozygous mutant type of SNP30 was associated with the lowest cashmere thickness, the wild type of SNP76, SNP77, SNP78, SNP80, and SNP81 was associated with the highest cashmere thickness, and the wild type type of SNP137 was associated with the highest fleece length. 21 haplotype blocks and 68 haplotype combinations were constructed. Haplotypes A2A2, B2B2, C2C2, and D4D4 were associated with increased cashmere yield, haplotypes E2E2, F1F1, G5G5, and G1G5 were associated with decreased cashmere fineness, haplotypes H2H2 was associated with increased cashmere thickness, haplotypes I1I1, I1I2, J1J4, L5L3, N3N2, N3N3, O2O1, P2P2, and Q3Q3 were associated with increased cashmere length. We verified the polymorphism of 8 SNPs by KASP, and found that chr7_g.102631194A > G, chr10_g.82715068 T > C, chr1_g.124483769C > T, chr24_g.12811352C > T, chr6_g.114111249A > G, and chr6_g.115606026 T > C were significantly genotyped in verified populations (P < 0.05). CONCLUSIONS In conclusion, the genetic effect of single SNP on phenotypes is small, and SNPs are more inclined to be inherited as a whole. By constructing haplotypes from SNPs that are significantly associated with cashmere traits, it will help to reveal the complex and potential causal variations in cashmere traits of Inner Mongolia cashmere goats. This will be a valuable resource for genomics and breeding of the cashmere goat.
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Affiliation(s)
- Youjun Rong
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Xinle Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Qin Na
- Inner Mongolia Autonomous Region Agricultural and Animal Husbandry Technology Extension Center, Hohhot, 010018, China
| | - Xiaofang Ao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Qincheng Xia
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Furong Guo
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Mingxuan Han
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Rong Ma
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Fangzheng Shang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Yan Liu
- College of Vocational and Technical, Inner Mongolia Agricultural University, Baotou, 014109, China
| | - Qi Lv
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Zhiying Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, 010018, China.
- Key Laboratory of Goat and Sheep Genetics, Breeding and Reproduction in Inner Mongolia Autonomous Region, Hohhot, 010018, China.
- Northern Agriculture and Livestock Husbandry Technology Innovation Center, Hohhot, 010018, China.
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.
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Hill ABT, Murphy YM, Polkoff KM, Edwards L, Walker DM, Moatti A, Greenbaum A, Piedrahita JA. A gene edited pig model for studying LGR5 + stem cells: implications for future applications in tissue regeneration and biomedical research. Front Genome Ed 2024; 6:1401163. [PMID: 38903529 PMCID: PMC11187295 DOI: 10.3389/fgeed.2024.1401163] [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: 03/14/2024] [Accepted: 05/15/2024] [Indexed: 06/22/2024] Open
Abstract
Recent advancements in genome editing techniques, notably CRISPR-Cas9 and TALENs, have marked a transformative era in biomedical research, significantly enhancing our understanding of disease mechanisms and helping develop novel therapies. These technologies have been instrumental in creating precise animal models for use in stem cell research and regenerative medicine. For instance, we have developed a transgenic pig model to enable the investigation of LGR5-expressing cells. The model was designed to induce the expression of H2B-GFP under the regulatory control of the LGR5 promoter via CRISPR/Cas9-mediated gene knock-in. Notably, advancements in stem cell research have identified distinct subpopulations of LGR5-expressing cells within adult human, mouse, and pig tissues. LGR5, a leucine-rich repeat-containing G protein-coupled receptor, enhances WNT signaling and these LGR5+ subpopulations demonstrate varied roles and anatomical distributions, underscoring the necessity for suitable translational models. This transgenic pig model facilitates the tracking of LGR5-expressing cells and has provided valuable insights into the roles of these cells across different tissues and species. For instance, in pulmonary tissue, Lgr5+ cells in mice are predominantly located in alveolar compartments, driving alveolar differentiation of epithelial progenitors via Wnt pathway activation. In contrast, in pigs and humans, these cells are situated in a unique sub-basal position adjacent to the airway epithelium. In fetal stages a pattern of LGR5 expression during lung bud tip formation is evident in humans and pigs but is lacking in mice. Species differences with respect to LGR5 expression have also been observed in the skin, intestines, and cochlea further reinforcing the need for careful selection of appropriate translational animal models. This paper discusses the potential utility of the LGR5+ pig model in exploring the role of LGR5+ cells in tissue development and regeneration with the goal of translating these findings into human and animal clinical applications.
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Affiliation(s)
- Amanda B. T. Hill
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
| | - Yanet M. Murphy
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
| | - Kathryn M. Polkoff
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
| | - Laura Edwards
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
| | - Derek M. Walker
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
| | - Adele Moatti
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, and North Carolina State University, Raleigh, NC, United States
| | - Alon Greenbaum
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, and North Carolina State University, Raleigh, NC, United States
| | - Jorge A. Piedrahita
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, and North Carolina State University, Raleigh, NC, United States
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Lousada MB, Edelkamp J, Lachnit T, Fehrholz M, Pastar I, Jimenez F, Erdmann H, Bosch TCG, Paus R. Spatial Distribution and Functional Impact of Human Scalp Hair Follicle Microbiota. J Invest Dermatol 2024; 144:1353-1367.e15. [PMID: 38070726 DOI: 10.1016/j.jid.2023.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/17/2023] [Accepted: 11/01/2023] [Indexed: 02/26/2024]
Abstract
Human hair follicles (HFs) constitute a unique microbiota habitat that differs substantially from the skin surface. Traditional HF sampling methods fail to eliminate skin microbiota contaminants or assess the HF microbiota incompletely, and microbiota functions in human HF physiology remain ill explored. Therefore, we used laser-capture microdissection, metagenomic shotgun sequencing, and FISH to characterize the human scalp HF microbiota in defined anatomical compartments. This revealed significant compartment-, tissue lineage-, and donor age-dependent variations in microbiota composition. Greatest abundance variations between HF compartments were observed for viruses, archaea, Staphylococcus epidermidis, Cutibacterium acnes, and Malassezia restricta, with the latter 2 being the most abundant viable HF colonizers (as tested by propidium monoazide assay) and, surprisingly, most abundant in the HF mesenchyme. Transfection of organ-cultured human scalp HFs with S. epidermidis-specific lytic bacteriophages ex vivo downregulated transcription of genes known to regulate HF growth and development, metabolism, and melanogenesis, suggesting that selected microbial products may modulate HF functions. Indeed, HF treatment with butyrate, a metabolite of S. epidermidis and other HF microbiota, delayed catagen and promoted autophagy, mitochondrial activity, and gp100 and dermcidin expression ex vivo. Thus, human HF microbiota show spatial variations in abundance and modulate the physiology of their host, which invites therapeutic targeting.
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Affiliation(s)
- Marta B Lousada
- Monasterium Laboratory, Münster, Germany; Zoological Institute, Christian Albrechts University in Kiel, Kiel, Germany
| | | | - Tim Lachnit
- Zoological Institute, Christian Albrechts University in Kiel, Kiel, Germany
| | | | - Irena Pastar
- Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Francisco Jimenez
- Mediteknia Skin & Hair Lab, Las Palmas de Gran Canaria, Spain; Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | | | - Thomas C G Bosch
- Zoological Institute, Christian Albrechts University in Kiel, Kiel, Germany
| | - Ralf Paus
- Monasterium Laboratory, Münster, Germany; Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA; CUTANEON, Hamburg, Germany.
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Lee EJ, Kim MW, Gil HN, Chung YJ, Kim EM. In vitro hair growth-promoting effect of Lgr5-binding octapeptide in human primary hair cells. J Cosmet Dermatol 2024; 23:986-998. [PMID: 37905348 DOI: 10.1111/jocd.16036] [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: 05/09/2023] [Revised: 06/21/2023] [Accepted: 10/05/2023] [Indexed: 11/02/2023]
Abstract
BACKGROUND Hair loss occurs due to various biological and environmental causes, which can have psychosocial consequences. The Wnt/β-catenin signaling is well-known for its role in hair growth and regeneration, as it induces the proliferation and differentiation of hair cells. When the leucine-rich G protein-coupled receptor 5 (Lgr5) interacts with the R-spondins, the frizzled receptor (FZD), a Wnt receptor, becomes stabilized, resulting in an increased β-catenin activity. AIM We investigated whether the octapeptide that binds to Lgr5 enhances proliferation and differentiation of human primary hair cells through the activation of Wnt/β-catenin signaling. METHODS The binding affinity of the octapeptide to Lgr5 was evaluated using surface plasmon resonance (SPR). We confirmed changes in proliferation and related factors like β-catenin activation and growth factors (GFs) expression in human hair follicle dermal papilla cells (HHFDPCs). Additionally, we observed the proliferation and the expression of differentiation markers in human hair follicle outer root sheath cells (HHFORSCs), human hair follicle germinal matrix cells (HHFGMCs), and human hair follicle stem cells (HHFSCs). We used three-dimensional HHFDPC spheroid culture treated with dihydrotestosterone (DHT) to create in vitro conditions that mimic androgenetic alopecia, and we studied the effects of octapeptide on Wnt expression and HHFSC differentiation. RESULTS The binding of the octapeptide to Lgr5 was confirmed using SPR analysis. In HHFDPCs, treatment with octapeptide resulted in a concentration-dependent increase in proliferation. We also observed increased nuclear translocation of β-catenin and increased expression of its downstream targets. HHFDPCs treated with octapeptide exhibited increased expression of growth factors and phosphorylation of Akt and ERK. In addition, we confirmed that octapeptide increased proliferation and induced differentiation in HHFORSCs, HHFGMCs, and HHFSCs. Under the HHFDPC spheroid culture conditions, we found that octapeptide restored the inhibition of Wnt-5a and Wnt-10b expressions by DHT. In HHFSCs treated with HHFDPC spheroid culture media, we observed that octapeptide recovered the inhibition of differentiation by DHT. CONCLUSION We found that octapeptides activated the Wnt/β-catenin signaling and induced the proliferation and differentiation of human primary hair cells by acting as an exogenous ligand for Lgr5. In addition, octapeptides recovered inhibited hair regeneration characters by DHT in androgenetic alopecia-mimic in vitro model. These findings suggest that octapeptides may be a promising therapeutic option for treating hair loss.
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Affiliation(s)
| | | | - Ha-Na Gil
- Caregen R&D center, Anyang-si, Korea
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Abstract
Diseases affecting the hair follicle are common in domestic animals, but despite the importance of an intact skin barrier and a fully functional hair coat, knowledge about the detailed morphological features and the diversity of these complex mini-organs are often limited, although mandatory to evaluate skin biopsies with a history of alopecia. The factors that regulate the innate hair follicle formation and the postnatal hair cycle are still not completely understood in rodents, only rudimentarily known in humans, and are poorly understood in our companion animals. This review aims to summarize the current knowledge about hair follicle and hair shaft anatomy, the arrangement of hair follicles, hair follicle morphogenesis in the embryo, and the lifelong regeneration during the postnatal hair cycle in domestic animals. The role of follicular stem cells and the need for a multitude of interacting signaling events during hair follicle morphogenesis and regeneration is unquestioned. Because of the lack of state of the art methods that can be applied in rodents but are not feasible in companion animals, most of the information in this review is based on rodent studies. However, the few data from domestic animals that are available will be discussed, and it can be assumed that at least the principal molecular mechanisms are similar in rodents and other species.
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Bailey P, Ridgway RA, Cammareri P, Treanor-Taylor M, Bailey UM, Schoenherr C, Bone M, Schreyer D, Purdie K, Thomson J, Rickaby W, Jackstadt R, Campbell AD, Dimonitsas E, Stratigos AJ, Arron ST, Wang J, Blyth K, Proby CM, Harwood CA, Sansom OJ, Leigh IM, Inman GJ. Driver gene combinations dictate cutaneous squamous cell carcinoma disease continuum progression. Nat Commun 2023; 14:5211. [PMID: 37626054 PMCID: PMC10457401 DOI: 10.1038/s41467-023-40822-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
The molecular basis of disease progression from UV-induced precancerous actinic keratosis (AK) to malignant invasive cutaneous squamous cell carcinoma (cSCC) and potentially lethal metastatic disease remains unclear. DNA sequencing studies have revealed a massive mutational burden but have yet to illuminate mechanisms of disease progression. Here we perform RNAseq transcriptomic profiling of 110 patient samples representing normal sun-exposed skin, AK, primary and metastatic cSCC and reveal a disease continuum from a differentiated to a progenitor-like state. This is accompanied by the orchestrated suppression of master regulators of epidermal differentiation, dynamic modulation of the epidermal differentiation complex, remodelling of the immune landscape and an increase in the preponderance of tumour specific keratinocytes. Comparative systems analysis of human cSCC coupled with the generation of genetically engineered murine models reveal that combinatorial sequential inactivation of the tumour suppressor genes Tgfbr2, Trp53, and Notch1 coupled with activation of Ras signalling progressively drives cSCC progression along a differentiated to progenitor axis. Taken together we provide a comprehensive map of the cSCC disease continuum and reveal potentially actionable events that promote and accompany disease progression.
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Affiliation(s)
- Peter Bailey
- School of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK.
- Department of Surgery, University of Heidelberg, Heidelberg, 69120, Germany.
- Section Surgical Research, University Clinic Heidelberg, Heidelberg, 69120, Germany.
| | | | - Patrizia Cammareri
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Mairi Treanor-Taylor
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
- Edinburgh Medical School, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | | | | | - Max Bone
- School of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
| | - Daniel Schreyer
- School of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Karin Purdie
- Faculty of Medicine and Dentistry, Queen Mary University of London, London, E1 1BB, UK
| | - Jason Thomson
- Faculty of Medicine and Dentistry, Queen Mary University of London, London, E1 1BB, UK
- Department of Dermatology, Royal London Hospital, Barts Health NHS Trust, London, E1 1BB, UK
| | - William Rickaby
- St John's Institute of Dermatology, St Thomas's Hospital, London, SE1 7EP, UK
| | - Rene Jackstadt
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
- German Cancer Research Centre (DKFZ), Heidelberg, 61920, Germany
| | | | - Emmanouil Dimonitsas
- 1st Department of Dermatology and Venereology, Andreas Sygros Hospital, Medical School, National and Kapodistrian University of Athens, Athens, 16121, Greece
| | - Alexander J Stratigos
- 1st Department of Dermatology and Venereology, Andreas Sygros Hospital, Medical School, National and Kapodistrian University of Athens, Athens, 16121, Greece
| | - Sarah T Arron
- Department of Dermatology, University of of California at San Francisco, San Francisco, CA, USA
| | - Jun Wang
- Faculty of Medicine and Dentistry, Queen Mary University of London, London, E1 1BB, UK
| | - Karen Blyth
- School of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
| | - Charlotte M Proby
- Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee, DD1 4HN, UK
| | - Catherine A Harwood
- Faculty of Medicine and Dentistry, Queen Mary University of London, London, E1 1BB, UK
- Department of Dermatology, Royal London Hospital, Barts Health NHS Trust, London, E1 1BB, UK
| | - Owen J Sansom
- School of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
| | - Irene M Leigh
- Faculty of Medicine and Dentistry, Queen Mary University of London, London, E1 1BB, UK.
| | - Gareth J Inman
- School of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK.
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK.
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8
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Pfisterer K, Wielscher M, Samardzic D, Weinzettl P, Symmank D, Shaw LE, Campana R, Huang HJ, Farlik M, Bangert C, Vrtala S, Valenta R, Weninger W. Non-IgE-reactive allergen peptides deteriorate the skin barrier in house dust mite-sensitized atopic dermatitis patients. Front Cell Dev Biol 2023; 11:1240289. [PMID: 37675143 PMCID: PMC10478000 DOI: 10.3389/fcell.2023.1240289] [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: 06/14/2023] [Accepted: 08/04/2023] [Indexed: 09/08/2023] Open
Abstract
Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by type 2 cytokine-driven skin inflammation and epithelial barrier dysfunction. The latter is believed to allow the increased penetration of chemicals, toxins, and allergens into the skin. House dust mite allergens, particularly Der p 2, are important triggers in sensitized individuals with AD; the precise actions of these allergens in epithelial biology remain, however, incompletely understood. In this study, we compared the effects of the protein allergen Der p 2 and a mix of non-IgE-reactive Der p 2 peptides on skin cells using patch tests in AD patients and healthy participants. We then analyzed mRNA expression profiles of keratinocytes by single-cell RNA-sequencing. We report that existing barrier deficiencies in the non-lesional skin of AD patients allow deep penetration of Der p 2 and its peptides, leading to local microinflammation. Der p 2 protein specifically upregulated genes involved in the innate immune system, stress, and danger signals in suprabasal KC. Der p 2 peptides further downregulated skin barrier genes, in particular the expression of genes involved in cell-matrix and cell-cell adhesion. Peptides also induced genes involved in hyperproliferation and caused disturbances in keratinocyte differentiation. Furthermore, inflammasome-relevant genes and IL18 were overexpressed, while KRT1 was downregulated. Our data suggest that Der p 2 peptides contribute to AD initiation and exacerbation by augmenting hallmark features of AD, such as skin inflammation, barrier disruption, and hyperplasia of keratinocytes.
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Affiliation(s)
- Karin Pfisterer
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Matthias Wielscher
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - David Samardzic
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Pauline Weinzettl
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Dorte Symmank
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Lisa E. Shaw
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Raffaela Campana
- Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Vienna, Austria
| | - Huey-Jy Huang
- Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Vienna, Austria
- Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Matthias Farlik
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Christine Bangert
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Susanne Vrtala
- Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Vienna, Austria
| | - Rudolf Valenta
- Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Weninger
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
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9
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Xiong J, Chen G, Liu Z, Wu X, Xu S, Xiong J, Ji S, Wu M. Construction of regulatory network for alopecia areata progression and identification of immune monitoring genes based on multiple machine-learning algorithms. PRECISION CLINICAL MEDICINE 2023; 6:pbad009. [PMID: 37333624 PMCID: PMC10268596 DOI: 10.1093/pcmedi/pbad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 05/17/2023] [Indexed: 06/20/2023] Open
Abstract
Objectives Alopecia areata (AA) is an autoimmune-related non-cicatricial alopecia, with complete alopecia (AT) or generalized alopecia (AU) as severe forms of AA. However, there are limitations in early identification of AA, and intervention of AA patients who may progress to severe AA will help to improve the incidence rate and prognosis of severe AA. Methods We obtained two AA-related datasets from the gene expression omnibus database, identified the differentially expressed genes (DEGs), and identified the module genes most related to severe AA through weighted gene co-expression network analysis. Functional enrichment analysis, construction of a protein-protein interaction network and competing endogenous RNA network, and immune cell infiltration analysis were performed to clarify the underlying biological mechanisms of severe AA. Subsequently, pivotal immune monitoring genes (IMGs) were screened through multiple machine-learning algorithms, and the diagnostic effectiveness of the pivotal IMGs was validated by receiver operating characteristic. Results A total of 150 severe AA-related DEGs were identified; the upregulated DEGs were mainly enriched in immune response, while the downregulated DEGs were mainly enriched in pathways related to hair cycle and skin development. Four IMGs (LGR5, SHISA2, HOXC13, and S100A3) with good diagnostic efficiency were obtained. As an important gene of hair follicle stem cells stemness, we verified in vivo that LGR5 downregulation may be an important link leading to severe AA. Conclusion Our findings provide a comprehensive understanding of the pathogenesis and underlying biological processes in patients with AA, and identification of four potential IMGs, which is helpful for the early diagnosis of severe AA.
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Affiliation(s)
| | | | | | - Xuemei Wu
- Department of Plastic Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Sha Xu
- Institute of Translational Medicine, Naval Military Medical University, Shanghai 200433, China
| | - Jun Xiong
- Department of Histology and Embryology, Naval Military Medical University, Shanghai 200433, China
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10
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Schaaf CR, Polkoff KM, Carter A, Stewart AS, Sheahan B, Freund J, Ginzel J, Snyder JC, Roper J, Piedrahita JA, Gonzalez LM. A LGR5 reporter pig model closely resembles human intestine for improved study of stem cells in disease. FASEB J 2023; 37:e22975. [PMID: 37159340 PMCID: PMC10446885 DOI: 10.1096/fj.202300223r] [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: 02/07/2023] [Revised: 04/12/2023] [Accepted: 05/01/2023] [Indexed: 05/11/2023]
Abstract
Intestinal epithelial stem cells (ISCs) are responsible for intestinal epithelial barrier renewal; thereby, ISCs play a critical role in intestinal pathophysiology research. While transgenic ISC reporter mice are available, advanced translational studies lack a large animal model. This study validates ISC isolation in a new porcine Leucine Rich Repeat Containing G Protein-Coupled Receptor 5 (LGR5) reporter line and demonstrates the use of these pigs as a novel colorectal cancer (CRC) model. We applied histology, immunofluorescence, fluorescence-activated cell sorting, flow cytometry, gene expression quantification, and 3D organoid cultures to whole tissue and single cells from the duodenum, jejunum, ileum, and colon of LGR5-H2B-GFP and wild-type pigs. Ileum and colon LGR5-H2B-GFP, healthy human, and murine biopsies were compared by mRNA fluorescent in situ hybridization (FISH). To model CRC, adenomatous polyposis coli (APC) mutation was induced by CRISPR/Cas9 editing in porcine LGR5-H2B-GFP colonoids. Crypt-base, green fluorescent protein (GFP) expressing cells co-localized with ISC biomarkers. LGR5-H2B-GFPhi cells had significantly higher LGR5 expression (p < .01) and enteroid forming efficiency (p < .0001) compared with LGR5-H2B-GFPmed/lo/neg cells. Using FISH, similar LGR5, OLFM4, HOPX, LYZ, and SOX9 expression was identified between human and LGR5-H2B-GFP pig crypt-base cells. LGR5-H2B-GFP/APCnull colonoids had cystic growth in WNT/R-spondin-depleted media and significantly upregulated WNT/β-catenin target gene expression (p < .05). LGR5+ ISCs are reproducibly isolated in LGR5-H2B-GFP pigs and used to model CRC in an organoid platform. The known anatomical and physiologic similarities between pig and human, and those shown by crypt-base FISH, underscore the significance of this novel LGR5-H2B-GFP pig to translational ISC research.
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Affiliation(s)
- Cecilia R. Schaaf
- Department of Clinical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Kathryn M. Polkoff
- Department of Molecular Biomedical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Amber Carter
- Department of Molecular Biomedical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Amy S. Stewart
- Department of Clinical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Breanna Sheahan
- Department of Molecular Biomedical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - John Freund
- Department of Clinical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Joshua Ginzel
- Department of SurgeryDuke UniversityDurhamNorth CarolinaUSA
| | - Joshua C. Snyder
- Department of SurgeryDuke UniversityDurhamNorth CarolinaUSA
- Department of Cell BiologyDuke UniversityDurhamNorth CarolinaUSA
| | - Jatin Roper
- Department of Medicine, Division of GastroenterologyDuke UniversityDurhamNorth CarolinaUSA
- Department of Pharmacology and Cancer BiologyDuke UniversityDurhamNorth CarolinaUSA
| | - Jorge A. Piedrahita
- Department of Molecular Biomedical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Liara M. Gonzalez
- Department of Clinical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
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11
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Ontogeny of cellular organization and LGR5 expression in porcine cochlea revealed using tissue clearing and 3D imaging. iScience 2022; 25:104695. [PMID: 35865132 PMCID: PMC9294204 DOI: 10.1016/j.isci.2022.104695] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/20/2022] [Accepted: 06/27/2022] [Indexed: 11/23/2022] Open
Abstract
Over 11% of the world's population experience hearing loss. Although there are promising studies to restore hearing in rodent models, the size, ontogeny, genetics, and frequency range of hearing of most rodents' cochlea do not match that of humans. The porcine cochlea can bridge this gap as it shares many anatomical, physiological, and genetic similarities with its human counterpart. Here, we provide a detailed methodology to process and image the porcine cochlea in 3D using tissue clearing and light-sheet microscopy. The resulting 3D images can be employed to compare cochleae across different ages and conditions, investigate the ontogeny of cochlear cytoarchitecture, and produce quantitative expression maps of LGR5, a marker of cochlear progenitors in mice. These data reveal that hair cell organization, inner ear morphology, cellular cartography in the organ of Corti, and spatiotemporal expression of LGR5 are dynamic over developmental stages in a pattern not previously documented.
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