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Du Q, Wu Y, Liao Y, Dong R, Shui S, Benjakul S, Zhang B. Investigation of the Alternations in the Muscle Quality of Swimming Crab ( Ovalipes punctatus) during Cold-Chain Transportation Using Physicochemical and TMT-Based Quantitative Proteomic Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11820-11835. [PMID: 38710668 DOI: 10.1021/acs.jafc.4c02224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Physicochemical properties and protein alterations in Ovalipes punctatus during cold-chain transportation were examined via sensory scores, water-holding capacity (WHC), glucose (GLU) content, catalase (CAT) activity, urea nitrogen (UN) content, and tandem mass tag (TMT)-based proteomic analysis. The results revealed that sensory characteristics and texture of crab muscle deteriorated during transportation. Proteomic analysis revealed 442 and 470 different expressed proteins (DEPs) in crabs after 18 h (FC) and 36 h (DC) of transportation compared with live crabs (LC). Proteins related to muscle structure and amino acid metabolism significantly changed, as evidenced by the decreased WHC and sensory scores of crab muscle. Glycolysis, calcium signaling, and peroxisome pathways were upregulated in the FC/LC comparison, aligning with the changes in GLU content and CAT activity, revealing the stress response of energy metabolism and immune response in crabs during 0-18 h of transportation. The downregulated tricarboxylic acid (TCA) cycle and carcinogenesis-reactive oxygen species pathways were correlated with the decreasing trend in CAT activity, suggesting a gradual retardation in both energy and antioxidant metabolism in crabs during 18-36 h of transportation. Furthermore, the regulated purine nucleoside metabolic and nucleoside diphosphate-related processes, with the increasing changes in UN content, revealed the accumulation of metabolites in crabs.
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Affiliation(s)
- Qi Du
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, College of Food Science and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
- College of Food Science and Engineering, Ningbo University, Ningbo 315000, China
| | - Yingru Wu
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, College of Food Science and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
| | - Yueqin Liao
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, College of Food Science and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
| | - Ruyi Dong
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, College of Food Science and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
| | - Shanshan Shui
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, College of Food Science and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
| | - Soottawat Benjakul
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Bin Zhang
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, College of Food Science and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
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2
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Steinbinder J, Sachslehner AP, Holthaus KB, Eckhart L. Comparative genomics of sirenians reveals evolution of filaggrin and caspase-14 upon adaptation of the epidermis to aquatic life. Sci Rep 2024; 14:9278. [PMID: 38653760 PMCID: PMC11039687 DOI: 10.1038/s41598-024-60099-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 04/18/2024] [Indexed: 04/25/2024] Open
Abstract
The mammalian epidermis has evolved to protect the body in a dry environment. Genes of the epidermal differentiation complex (EDC), such as FLG (filaggrin), are implicated in the barrier function of the epidermis. Here, we investigated the molecular evolution of the EDC in sirenians (manatees and dugong), which have adapted to fully aquatic life, in comparison to the EDC of terrestrial mammals and aquatic mammals of the clade Cetacea (whales and dolphins). We show that the main subtypes of EDC genes are conserved or even duplicated, like late cornified envelope (LCE) genes of the dugong, whereas specific EDC genes have undergone inactivating mutations in sirenians. FLG contains premature stop codons in the dugong, and the ortholog of human CASP14 (caspase-14), which proteolytically processes filaggrin, is pseudogenized in the same species. As FLG and CASP14 have also been lost in whales, these mutations represent convergent evolution of skin barrier genes in different lineages of aquatic mammals. In contrast to the dugong, the manatee has retained functional FLG and CASP14 genes. FLG2 (filaggrin 2) is truncated in both species of sirenians investigated. We conclude that the land-to-water transition of sirenians was associated with modifications of the epidermal barrier at the molecular level.
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Affiliation(s)
- Julia Steinbinder
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | | | | | - Leopold Eckhart
- Department of Dermatology, Medical University of Vienna, Vienna, Austria.
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3
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Steinbinder J, Sachslehner AP, Holthaus KB, Eckhart L. Comparative genomics of monotremes provides insights into the early evolution of mammalian epidermal differentiation genes. Sci Rep 2024; 14:1437. [PMID: 38228724 PMCID: PMC10791643 DOI: 10.1038/s41598-024-51926-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/11/2024] [Indexed: 01/18/2024] Open
Abstract
The function of the skin as a barrier against the environment depends on the differentiation of epidermal keratinocytes into highly resilient corneocytes that form the outermost skin layer. Many genes encoding structural components of corneocytes are clustered in the epidermal differentiation complex (EDC), which has been described in placental and marsupial mammals as well as non-mammalian tetrapods. Here, we analyzed the genomes of the platypus (Ornithorhynchus anatinus) and the echidna (Tachyglossus aculeatus) to determine the gene composition of the EDC in the basal clade of mammals, the monotremes. We report that mammal-specific subfamilies of EDC genes encoding small proline-rich proteins (SPRRs) and late cornified envelope proteins as well as single-copy EDC genes such as involucrin are conserved in monotremes, suggesting that they have originated in stem mammals. Monotremes have at least one gene homologous to the group of filaggrin (FLG), FLG2 and hornerin (HRNR) in placental mammals, but no clear one-to-one pairwise ortholog of either FLG, FLG2 or HRNR. Caspase-14, a keratinocyte differentiation-associated protease implicated in the processing of filaggrin, is encoded by at least 3 gene copies in the echidna. Our results reveal evolutionarily conserved and clade-specific features of the genetic regulation of epidermal differentiation in monotremes.
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Affiliation(s)
- Julia Steinbinder
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | | | | | - Leopold Eckhart
- Department of Dermatology, Medical University of Vienna, Vienna, Austria.
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4
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Holthaus KB, Eckhart L. Development-Associated Genes of the Epidermal Differentiation Complex (EDC). J Dev Biol 2024; 12:4. [PMID: 38248869 PMCID: PMC10801484 DOI: 10.3390/jdb12010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/28/2023] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
The epidermal differentiation complex (EDC) is a cluster of genes that encode protein components of the outermost layers of the epidermis in mammals, reptiles and birds. The development of the stratified epidermis from a single-layered ectoderm involves an embryo-specific superficial cell layer, the periderm. An additional layer, the subperiderm, develops in crocodilians and over scutate scales of birds. Here, we review the expression of EDC genes during embryonic development. Several EDC genes are expressed predominantly or exclusively in embryo-specific cell layers, whereas others are confined to the epidermal layers that are maintained in postnatal skin. The S100 fused-type proteins scaffoldin and trichohyalin are expressed in the avian and mammalian periderm, respectively. Scaffoldin forms the so-called periderm granules, which are histological markers of the periderm in birds. Epidermal differentiation cysteine-rich protein (EDCRP) and epidermal differentiation protein containing DPCC motifs (EDDM) are expressed in the avian subperiderm where they are supposed to undergo cross-linking via disulfide bonds. Furthermore, a histidine-rich epidermal differentiation protein and feather-type corneous beta-proteins, also known as beta-keratins, are expressed in the subperiderm. The accumulating evidence for roles of EDC genes in the development of the epidermis has implications on the evolutionary diversification of the skin in amniotes.
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Affiliation(s)
| | - Leopold Eckhart
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
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5
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Nagasawa K, Kitano T. Pseudogenization of the Hair-Related Genes PADI3 and S100A3 in Cetaceans and Hippopotamus amphibius. J Mol Evol 2023; 91:745-760. [PMID: 37787841 DOI: 10.1007/s00239-023-10133-0] [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: 04/18/2023] [Accepted: 09/05/2023] [Indexed: 10/04/2023]
Abstract
Hair-related genes in mammals play important roles in the development and maintenance of hair and other keratinous structures in mammals. The peptidyl arginine deiminase 3 (PADI3) gene encodes an enzyme that catalyzes the conversion of arginine residues to citrulline. The S100 calcium binding protein A3 (S100A3) gene encodes a protein that is highly expressed in the hair cuticle and contains arginine residues that are converted to citrullines by PADI enzymes. In this study, we investigated the pseudogenization events of PADI3 and S100A3 in cetaceans and Hippopotamus amphibius. We found that PADI3 underwent three independent pseudogenization events during cetacean evolution, in baleen whales, toothed cetaceans other than Physeter catodon, and P. catodon. Notably, the entire PADI3 gene is absent in the baleen whales. Pseudogenization of S100A3 occurred independently in cetaceans and H. amphibius. Interestingly, we found that in cetaceans S100A3 underwent pseudogenization before PADI3, suggesting that differential selection pressures were acting on the two genes. Our findings provide valuable insights into the molecular evolution of these genes in cetaceans and hippopotamuses, highlighting their importance for understanding the evolution of hair-related genes.
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Affiliation(s)
- Kyomi Nagasawa
- Graduate School of Science and Engineering, Ibaraki University, 4-12-1 Nakanarusawa-Cho, Hitachi, Ibaraki, 316-8511, Japan
| | - Takashi Kitano
- Graduate School of Science and Engineering, Ibaraki University, 4-12-1 Nakanarusawa-Cho, Hitachi, Ibaraki, 316-8511, Japan.
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Surbek M, Sukseree S, Sachslehner AP, Copic D, Golabi B, Nagelreiter IM, Tschachler E, Eckhart L. Heme Oxygenase-1 Is Upregulated during Differentiation of Keratinocytes but Its Expression Is Dispensable for Cornification of Murine Epidermis. J Dev Biol 2023; 11:12. [PMID: 36976101 PMCID: PMC10058925 DOI: 10.3390/jdb11010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/15/2023] Open
Abstract
The epidermal barrier of mammals is initially formed during embryonic development and continuously regenerated by the differentiation and cornification of keratinocytes in postnatal life. Cornification is associated with the breakdown of organelles and other cell components by mechanisms which are only incompletely understood. Here, we investigated whether heme oxygenase 1 (HO-1), which converts heme into biliverdin, ferrous iron and carbon monoxide, is required for normal cornification of epidermal keratinocytes. We show that HO-1 is transcriptionally upregulated during the terminal differentiation of human keratinocytes in vitro and in vivo. Immunohistochemistry demonstrated expression of HO-1 in the granular layer of the epidermis where keratinocytes undergo cornification. Next, we deleted the Hmox1 gene, which encodes HO-1, by crossing Hmox1-floxed and K14-Cre mice. The epidermis and isolated keratinocytes of the resulting Hmox1f/f K14-Cre mice lacked HO-1 expression. The genetic inactivation of HO-1 did not impair the expression of keratinocyte differentiation markers, loricrin and filaggrin. Likewise, the transglutaminase activity and formation of the stratum corneum were not altered in Hmox1f/f K14-Cre mice, suggesting that HO-1 is dispensable for epidermal cornification. The genetically modified mice generated in this study may be useful for future investigations of the potential roles of epidermal HO-1 in iron metabolism and responses to oxidative stress.
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Affiliation(s)
- Marta Surbek
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
| | - Supawadee Sukseree
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
| | | | - Dragan Copic
- Clinical Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, 1090 Vienna, Austria
| | - Bahar Golabi
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
| | | | - Erwin Tschachler
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
| | - Leopold Eckhart
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
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Menon GK, Elias PM, Wakefield JS, Crumrine D. Cetacean epidermal specialization: A review. Anat Histol Embryol 2022; 51:563-575. [PMID: 35758554 PMCID: PMC9464690 DOI: 10.1111/ahe.12829] [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: 04/21/2022] [Revised: 06/08/2022] [Accepted: 06/15/2022] [Indexed: 12/01/2022]
Abstract
Cetacean skin continues to be the investigative focus of researchers from several different scientific disciplines. Yet, most research on the basic functions of lipo-keratinocytes, which constitute most of the cetacean epidermis, providing the first layer of protection against various environmental aggressors (including an ever-increasing level of pollutants), is restricted to specialized literature on the permeability barrier only. In this review, we have attempted to bring together much of the recent research on the functional biology of cetacean skin, including special adaptations at the cellular, genetic and molecular level. We have correlated these data with the cetacean permeability barrier's unique structural and metabolic adaptations to fully aquatic life, including the development of secondary barriers to ward off challenges such as biofouling as well as exposure to extreme cold for the epidermis, which is outside of the insulation provided by blubber. An apparent contradiction exists between some of the reported gene loss for lipogenic enzymes in cetacean skin and the high degree of cetacean epidermal lipogenesis, as well as loss of desmocollin 1 and desmoplakin genes [while immunolocalization of these proteins is reported (Journal of Anatomy, 234, 201)] warrants a re-evaluation of the gene loss data.
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Affiliation(s)
- Gopinathan K. Menon
- Department of Birds & Mammals, California Academy of Sciences, San Francisco, California USA
| | - Peter M. Elias
- Department of Birds & Mammals, California Academy of Sciences, San Francisco, California USA
- Department of Dermatology, University of California, San Francisco and Veterans Affairs Health Care System, San Francisco, California USA
| | - Joan S. Wakefield
- Department of Dermatology, University of California, San Francisco and Veterans Affairs Health Care System, San Francisco, California USA
| | - Debra Crumrine
- Department of Dermatology, University of California, San Francisco and Veterans Affairs Health Care System, San Francisco, California USA
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8
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Loricrin at the Boundary between Inside and Outside. Biomolecules 2022; 12:biom12050673. [PMID: 35625601 PMCID: PMC9138667 DOI: 10.3390/biom12050673] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 04/30/2022] [Accepted: 05/04/2022] [Indexed: 02/04/2023] Open
Abstract
Cornification is a specialized mode of the cell-death program exclusively allowed for terrestrial amniotes. Recent investigations suggest that loricrin (LOR) is an important cornification effector. As the connotation of its name (“lorica” meaning an armor in Latin) suggests, the keratin-associated protein LOR promotes the maturation of the epidermal structure through organizing covalent cross-linkages, endowing the epidermis with the protection against oxidative injuries. By reviewing cornification mechanisms, we seek to classify ichthyosiform dermatoses based on their function, rather than clinical manifestations. We also reviewed recent mechanistic insights into the Kelch-like erythroid cell-derived protein with the cap “n” collar homology-associated protein 1/nuclear factor erythroid 2-related factor 2 (NRF2) signaling pathway in skin health and diseases, as LOR and NRF2 coordinate the epidermis-intrinsic xenobiotic metabolism. Finally, we refine the theoretical framework of cross-talking between keratinocytes and epidermal resident leukocytes, dissecting an LOR immunomodulatory function.
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9
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Fuchs P, Drexler C, Ratajczyk S, Eckhart L. Comparative genomics reveals evolutionary loss of epiplakin in cetaceans. Sci Rep 2022; 12:1112. [PMID: 35064199 PMCID: PMC8782857 DOI: 10.1038/s41598-022-05087-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/06/2022] [Indexed: 12/14/2022] Open
Abstract
The adaptation of vertebrates to different environments was associated with changes in the molecular composition and regulation of epithelia. Whales and dolphins, together forming the clade cetaceans, have lost multiple epithelial keratins during or after their evolutionary transition from life on land to life in water. It is unknown whether the changes in keratins were accompanied by gain or loss of cytoskeletal adapter proteins of the plakin family. Here we investigated whether plakin proteins are conserved in cetaceans and other vertebrates. Comparative analysis of genome sequences showed conservation of dystonin, microtubule actin crosslinking factor 1 (MACF1), plectin, desmoplakin, periplakin and envoplakin in cetaceans. By contrast, EPPK1 (epiplakin) was disrupted by inactivating mutations in all cetaceans investigated. Orthologs of EPPK1 are present in bony and cartilaginous fishes and tetrapods, indicating an evolutionary origin of EPPK1 in a common ancestor of jawed vertebrates (Gnathostomes). In many vertebrates, EPPK1 is flanked by an as-yet uncharacterized gene that encodes protein domains homologous to the carboxy-terminal segment of MACF1. We conclude that epiplakin, unlike other plakins, was lost in cetaceans.
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Affiliation(s)
- Peter Fuchs
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria.
| | - Corinne Drexler
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Sonia Ratajczyk
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Leopold Eckhart
- Skin Biology Laboratory, Department of Dermatology, Medical University of Vienna, Vienna, Austria.
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10
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Shamilov R, Robinson VL, Aneskievich BJ. Seeing Keratinocyte Proteins through the Looking Glass of Intrinsic Disorder. Int J Mol Sci 2021; 22:ijms22157912. [PMID: 34360678 PMCID: PMC8348711 DOI: 10.3390/ijms22157912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/28/2021] [Accepted: 07/20/2021] [Indexed: 02/06/2023] Open
Abstract
Epidermal keratinocyte proteins include many with an eccentric amino acid content (compositional bias), atypical ultrastructural fate (built-in protease sensitivity), or assembly visible at the light microscope level (cytoplasmic granules). However, when considered through the looking glass of intrinsic disorder (ID), these apparent oddities seem quite expected. Keratinocyte proteins with highly repetitive motifs are of low complexity but high adaptation, providing polymers (e.g., profilaggrin) for proteolysis into bioactive derivatives, or monomers (e.g., loricrin) repeatedly cross-linked to self and other proteins to shield underlying tissue. Keratohyalin granules developing from liquid–liquid phase separation (LLPS) show that unique biomolecular condensates (BMC) and proteinaceous membraneless organelles (PMLO) occur in these highly customized cells. We conducted bioinformatic and in silico assessments of representative keratinocyte differentiation-dependent proteins. This was conducted in the context of them having demonstrated potential ID with the prospect of that characteristic driving formation of distinctive keratinocyte structures. Intriguingly, while ID is characteristic of many of these proteins, it does not appear to guarantee LLPS, nor is it required for incorporation into certain keratinocyte protein condensates. Further examination of keratinocyte-specific proteins will provide variations in the theme of PMLO, possibly recognizing new BMC for advancements in understanding intrinsically disordered proteins as reflected by keratinocyte biology.
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Affiliation(s)
- Rambon Shamilov
- Graduate Program in Pharmacology & Toxicology, Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06269, USA;
| | - Victoria L. Robinson
- Department of Molecular and Cellular Biology, College of Liberal Arts & Sciences, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269, USA;
| | - Brian J. Aneskievich
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA
- Correspondence: ; Tel.: +1-860-486-3053
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11
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Gene duplications and gene loss in the epidermal differentiation complex during the evolutionary land-to-water transition of cetaceans. Sci Rep 2021; 11:12334. [PMID: 34112911 PMCID: PMC8192740 DOI: 10.1038/s41598-021-91863-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/26/2021] [Indexed: 01/03/2023] Open
Abstract
Major protein components of the mammalian skin barrier are encoded by genes clustered in the Epidermal Differentiation Complex (EDC). The skin of cetaceans, i.e. whales, porpoises and dolphins, differs histologically from that of terrestrial mammals. However, the genetic regulation of their epidermal barrier is only incompletely known. Here, we investigated the EDC of cetaceans by comparative genomics. We found that important epidermal cornification proteins, such as loricrin and involucrin are conserved and subtypes of small proline-rich proteins (SPRRs) are even expanded in numbers in cetaceans. By contrast, keratinocyte proline rich protein (KPRP), skin-specific protein 32 (XP32) and late-cornified envelope (LCE) genes with the notable exception of LCE7A have been lost in cetaceans. Genes encoding proline rich 9 (PRR9) and late cornified envelope like proline rich 1 (LELP1) have degenerated in subgroups of cetaceans. These data suggest that the evolution of an aquatic lifestyle was accompanied by amplification of SPRR genes and loss of specific other epidermal differentiation genes in the phylogenetic lineage leading to cetaceans.
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12
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Springer MS, Guerrero-Juarez CF, Huelsmann M, Collin MA, Danil K, McGowen MR, Oh JW, Ramos R, Hiller M, Plikus MV, Gatesy J. Genomic and anatomical comparisons of skin support independent adaptation to life in water by cetaceans and hippos. Curr Biol 2021; 31:2124-2139.e3. [PMID: 33798433 PMCID: PMC8154672 DOI: 10.1016/j.cub.2021.02.057] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/21/2021] [Accepted: 02/25/2021] [Indexed: 12/17/2022]
Abstract
The macroevolutionary transition from terra firma to obligatory inhabitance of the marine hydrosphere has occurred twice in the history of Mammalia: Cetacea and Sirenia. In the case of Cetacea (whales, dolphins, and porpoises), molecular phylogenies provide unambiguous evidence that fully aquatic cetaceans and semiaquatic hippopotamids (hippos) are each other's closest living relatives. Ancestral reconstructions suggest that some adaptations to the aquatic realm evolved in the common ancestor of Cetancodonta (Cetacea + Hippopotamidae). An alternative hypothesis is that these adaptations evolved independently in cetaceans and hippos. Here, we focus on the integumentary system and evaluate these hypotheses by integrating new histological data for cetaceans and hippos, the first genome-scale data for pygmy hippopotamus, and comprehensive genomic screens and molecular evolutionary analyses for protein-coding genes that have been inactivated in hippos and cetaceans. We identified eight skin-related genes that are inactivated in both cetaceans and hippos, including genes that are related to sebaceous glands, hair follicles, and epidermal differentiation. However, none of these genes exhibit inactivating mutations that are shared by cetaceans and hippos. Mean dates for the inactivation of skin genes in these two clades serve as proxies for phenotypic changes and suggest that hair reduction/loss, the loss of sebaceous glands, and changes to the keratinization program occurred ∼16 Ma earlier in cetaceans (∼46.5 Ma) than in hippos (∼30.5 Ma). These results, together with histological differences in the integument and prior analyses of oxygen isotopes from stem hippopotamids ("anthracotheres"), support the hypothesis that aquatic skin adaptations evolved independently in hippos and cetaceans.
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Affiliation(s)
- Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA.
| | - Christian F Guerrero-Juarez
- Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
| | - Matthias Huelsmann
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany; Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Matthew A Collin
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA; Department of Botany & Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Kerri Danil
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA 92037, USA
| | - Michael R McGowen
- Department of Vertebrate Zoology, Smithsonian Museum of Natural History, 10th & Constitution Avenue NW, Washington, DC 20560, USA
| | - Ji Won Oh
- Department of Anatomy, School of Medicine, Kyungpook National University, Daegu, Korea; Biomedical Research Institute, Kyungpook National University Hospital, Daegu, Korea; Hair Transplantation Center, Kyungpook National University Hospital, Daegu, Korea
| | - Raul Ramos
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany; Center for Systems Biology Dresden, 01307 Dresden, Germany; LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany; Senckenberg Research Institute, 60325 Frankfurt, Germany; Faculty of Biosciences, Goethe-University, 60438 Frankfurt, Germany.
| | - Maksim V Plikus
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA.
| | - John Gatesy
- Division of Vertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA.
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13
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Turakhia Y, Chen HI, Marcovitz A, Bejerano G. A fully-automated method discovers loss of mouse-lethal and human-monogenic disease genes in 58 mammals. Nucleic Acids Res 2020; 48:e91. [PMID: 32614390 PMCID: PMC7498332 DOI: 10.1093/nar/gkaa550] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/23/2020] [Accepted: 06/23/2020] [Indexed: 01/20/2023] Open
Abstract
Gene losses provide an insightful route for studying the morphological and physiological adaptations of species, but their discovery is challenging. Existing genome annotation tools focus on annotating intact genes and do not attempt to distinguish nonfunctional genes from genes missing annotation due to sequencing and assembly artifacts. Previous attempts to annotate gene losses have required significant manual curation, which hampers their scalability for the ever-increasing deluge of newly sequenced genomes. Using extreme sequence erosion (amino acid deletions and substitutions) and sister species support as an unambiguous signature of loss, we developed an automated approach for detecting high-confidence gene loss events across a species tree. Our approach relies solely on gene annotation in a single reference genome, raw assemblies for the remaining species to analyze, and the associated phylogenetic tree for all organisms involved. Using human as reference, we discovered over 400 unique human ortholog erosion events across 58 mammals. This includes dozens of clade-specific losses of genes that result in early mouse lethality or are associated with severe human congenital diseases. Our discoveries yield intriguing potential for translational medical genetics and evolutionary biology, and our approach is readily applicable to large-scale genome sequencing efforts across the tree of life.
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Affiliation(s)
- Yatish Turakhia
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Heidi I Chen
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Amir Marcovitz
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Gill Bejerano
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
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14
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Ishitsuka Y, Ogawa T, Roop D. The KEAP1/NRF2 Signaling Pathway in Keratinization. Antioxidants (Basel) 2020; 9:E751. [PMID: 32823937 PMCID: PMC7465315 DOI: 10.3390/antiox9080751] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 12/18/2022] Open
Abstract
Keratinization is a tissue adaptation, but aberrant keratinization is associated with skin disorders such as ichthyoses, atopic dermatitis, psoriasis, and acne. The disease phenotype stems from the interaction between genes and the environment; therefore, an understanding of the adaptation machinery may lead to a new appreciation of pathomechanisms. The KEAP1/NRF2 signaling pathway mediates the environmental responses of squamous epithelial tissue. The unpredicted outcome of the Keap1-null mutation in mice allowed us to revisit the basic principle of the biological process of keratinization: sulfur metabolism establishes unparalleled cytoprotection in the body wall of terrestrial mammals. We summarize the recent understanding of the KEAP1/NRF2 signaling pathway, which is a thiol-based sensor-effector apparatus, with particular focuses on epidermal differentiation in the context of the gene-environment interaction, the structure/function principles involved in KEAP1/NRF2 signaling, lessons from mouse models, and their pathological implications. This synthesis may provide insights into keratinization, which provides physical insulation and constitutes an essential innate integumentary defense system.
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Affiliation(s)
- Yosuke Ishitsuka
- Department of Dermatology, Faculty of Medicine, University of Tsukuba 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan;
| | - Tatsuya Ogawa
- Department of Dermatology, Faculty of Medicine, University of Tsukuba 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan;
| | - Dennis Roop
- Department of Dermatology and Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
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15
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Abstract
The terminal differentiation of the epidermis is a complex physiological process. During the past few decades, medical genetics has shown that defects in the stratum corneum (SC) permeability barrier cause a myriad of pathological conditions, ranging from common dry skin to lethal ichthyoses. Contrarily, molecular phylogenetics has revealed that amniotes have acquired a specialized form of cytoprotection cornification that provides mechanical resilience to the SC. This superior biochemical property, along with desiccation tolerance, is attributable to the proper formation of the macromolecular protein-lipid complex termed cornified cell envelopes (CE). Cornification largely depends on the peculiar biochemical and biophysical properties of loricrin, which is a major CE component. Despite its quantitative significance, loricrin knockout (LKO) mice have revealed it to be dispensable for the SC permeability barrier. Nevertheless, LKO mice have brought us valuable lessons. It is also becoming evident that absent loricrin affects skin homeostasis more profoundly in many more aspects than previously expected. Through an extensive review of aggregate evidence, we discuss herein the functional significance of the thiol-rich protein loricrin from a biochemical, genetic, pathological, metabolic, or immunological aspect with some theoretical and speculative perspectives.
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Affiliation(s)
- Yosuke Ishitsuka
- Department of Dermatology, Faculty of Medicine, University of Tsukuba 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Dennis R. Roop
- Department of Dermatology and Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
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16
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Alves LQ, Alves J, Ribeiro R, Ruivo R, Castro F. The dopamine receptor D 5 gene shows signs of independent erosion in toothed and baleen whales. PeerJ 2019; 7:e7758. [PMID: 31616587 PMCID: PMC6791347 DOI: 10.7717/peerj.7758] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/26/2019] [Indexed: 12/30/2022] Open
Abstract
To compare gene loci considering a phylogenetic framework is a promising approach to uncover the genetic basis of human diseases. Imbalance of dopaminergic systems is suspected to underlie some emerging neurological disorders. The physiological functions of dopamine are transduced via G-protein-coupled receptors, including DRD5 which displays a relatively higher affinity toward dopamine. Importantly, DRD5 knockout mice are hypertense, a condition emerging from an increase in sympathetic tone. We investigated the evolution of DRD5, a high affinity receptor for dopamine, in mammals. Surprisingly, among 124 investigated mammalian genomes, we found that Cetacea lineages (Mysticeti and Odontoceti) have independently lost this gene, as well as the burrowing Chrysochloris asiatica (Cape golden mole). We suggest that DRD5 inactivation parallels hypoxia-induced adaptations, such as peripheral vasoconstriction required for deep-diving in Cetacea, in accordance with the convergent evolution of vasoconstrictor genes in hypoxia-exposed animals. Our findings indicate that Cetacea are natural knockouts for DRD5 and might offer valuable insights into the mechanisms of some forms of vasoconstriction responses and hypertension in humans.
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Affiliation(s)
- Luís Q Alves
- CIIMAR-University of Porto, Matosinhos, Portugal.,FCUP-University of Porto, Porto, Portugal
| | - Juliana Alves
- CIIMAR-University of Porto, Matosinhos, Portugal.,FCUP-University of Porto, Porto, Portugal
| | - Rodrigo Ribeiro
- CIIMAR-University of Porto, Matosinhos, Portugal.,FCUP-University of Porto, Porto, Portugal
| | - Raquel Ruivo
- CIIMAR-University of Porto, Matosinhos, Portugal
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17
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Ehrlich F, Laggner M, Langbein L, Burger P, Pollreisz A, Tschachler E, Eckhart L. Comparative genomics suggests loss of keratin K24 in three evolutionary lineages of mammals. Sci Rep 2019; 9:10924. [PMID: 31358806 PMCID: PMC6662840 DOI: 10.1038/s41598-019-47422-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/16/2019] [Indexed: 12/18/2022] Open
Abstract
Keratins are the main cytoskeletal proteins of epithelial cells and changes in the expression of keratins have contributed to the evolutionary adaptation of epithelia to different environments. Keratin K24 was proposed to be a differentiation marker of epidermal keratinocytes but the significance of K24 expression in the epidermis versus other tissues has remained elusive. Here, we show by RT-PCR, western blot, and immunofluorescence analyses that K24 is highly expressed in the epithelium of the cornea whereas its expression levels are significantly lower in other stratified epithelia including in the epidermis. To investigate the evolutionary history of K24, we screened the genome sequences of vertebrates for orthologs of the human KRT24 gene. The results of this comparative genomics study suggested that KRT24 originated in a common ancestor of amniotes and that it was lost independently in three clades of mammals, i.e. camels, cetaceans, and a subclade of pinnipeds comprising eared seals and the walrus. Together, the results of this study identify K24 as component of the cytoskeleton in the human corneal epithelium and reveal previously unknown differences of keratin gene content among mammalian species.
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Affiliation(s)
- Florian Ehrlich
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Maria Laggner
- Department of Ophthalmology, Medical University of Vienna, Vienna, Austria
- Aposcience AG, Vienna, Austria
| | - Lutz Langbein
- German Cancer Research Center, Department of Genetics of Skin Carcinogenesis, Heidelberg, Germany
| | - Pamela Burger
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Andreas Pollreisz
- Department of Ophthalmology, Medical University of Vienna, Vienna, Austria
| | - Erwin Tschachler
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Leopold Eckhart
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria.
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18
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Lopes-Marques M, Machado AM, Alves LQ, Fonseca MM, Barbosa S, Sinding MHS, Rasmussen MH, Iversen MR, Frost Bertelsen M, Campos PF, da Fonseca R, Ruivo R, Castro LFC. Complete Inactivation of Sebum-Producing Genes Parallels the Loss of Sebaceous Glands in Cetacea. Mol Biol Evol 2019; 36:1270-1280. [PMID: 30895322 PMCID: PMC6526905 DOI: 10.1093/molbev/msz068] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genomes are dynamic biological units, with processes of gene duplication and loss triggering evolutionary novelty. The mammalian skin provides a remarkable case study on the occurrence of adaptive morphological innovations. Skin sebaceous glands (SGs), for instance, emerged in the ancestor of mammals serving pivotal roles, such as lubrication, waterproofing, immunity, and thermoregulation, through the secretion of sebum, a complex mixture of various neutral lipids such as triacylglycerol, free fatty acids, wax esters, cholesterol, and squalene. Remarkably, SGs are absent in a few mammalian lineages, including the iconic Cetacea. We investigated the evolution of the key molecular components responsible for skin sebum production: Dgat2l6, Awat1, Awat2, Elovl3, Mogat3, and Fabp9. We show that all analyzed genes have been rendered nonfunctional in Cetacea species (toothed and baleen whales). Transcriptomic analysis, including a novel skin transcriptome from blue whale, supports gene inactivation. The conserved mutational pattern found in most analyzed genes, indicates that pseudogenization events took place prior to the diversification of modern Cetacea lineages. Genome and skin transcriptome analysis of the common hippopotamus highlighted the convergent loss of a subset of sebum-producing genes, notably Awat1 and Mogat3. Partial loss profiles were also detected in non-Cetacea aquatic mammals, such as the Florida manatee, and in terrestrial mammals displaying specialized skin phenotypes such as the African elephant, white rhinoceros and pig. Our findings reveal a unique landscape of “gene vestiges” in the Cetacea sebum-producing compartment, with limited gene loss observed in other mammalian lineages: suggestive of specific adaptations or specializations of skin lipids.
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Affiliation(s)
- Mónica Lopes-Marques
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | - André M Machado
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | - Luís Q Alves
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal.,Department of Biology, Faculty of Sciences, U. Porto-University of Porto, Porto, Portugal
| | - Miguel M Fonseca
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | - Susana Barbosa
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | | | | | | | | | - Paula F Campos
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal.,Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Rute da Fonseca
- Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark.,Center for Macroecology, Evolution, and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Raquel Ruivo
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | - L Filipe C Castro
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal.,Department of Biology, Faculty of Sciences, U. Porto-University of Porto, Porto, Portugal
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19
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Ehrlich F, Fischer H, Langbein L, Praetzel-Wunder S, Ebner B, Figlak K, Weissenbacher A, Sipos W, Tschachler E, Eckhart L. Differential Evolution of the Epidermal Keratin Cytoskeleton in Terrestrial and Aquatic Mammals. Mol Biol Evol 2019; 36:328-340. [PMID: 30517738 PMCID: PMC6367960 DOI: 10.1093/molbev/msy214] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Keratins are the main intermediate filament proteins of epithelial cells. In keratinocytes of the mammalian epidermis they form a cytoskeleton that resists mechanical stress and thereby are essential for the function of the skin as a barrier against the environment. Here, we performed a comparative genomics study of epidermal keratin genes in terrestrial and fully aquatic mammals to determine adaptations of the epidermal keratin cytoskeleton to different environments. We show that keratins K5 and K14 of the innermost (basal), proliferation-competent layer of the epidermis are conserved in all mammals investigated. In contrast, K1 and K10, which form the main part of the cytoskeleton in the outer (suprabasal) layers of the epidermis of terrestrial mammals, have been lost in whales and dolphins (cetaceans) and in the manatee. Whereas in terrestrial mammalian epidermis K6 and K17 are expressed only upon stress-induced epidermal thickening, high levels of K6 and K17 are consistently present in dolphin skin, indicating constitutive expression and substitution of K1 and K10. K2 and K9, which are expressed in a body site-restricted manner in human and mouse suprabasal epidermis, have been lost not only in cetaceans and manatee but also in some terrestrial mammals. The evolution of alternative splicing of K10 and differentiation-dependent upregulation of K23 have increased the complexity of keratin expression in the epidermis of terrestrial mammals. Taken together, these results reveal evolutionary diversification of the epidermal cytoskeleton in mammals and suggest a complete replacement of the quantitatively predominant epidermal proteins of terrestrial mammals by originally stress-inducible keratins in cetaceans.
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Affiliation(s)
- Florian Ehrlich
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Heinz Fischer
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria.,Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Lutz Langbein
- Department of Genetics of Skin Carcinogenesis, German Cancer Research Center, Heidelberg, Germany
| | - Silke Praetzel-Wunder
- Department of Genetics of Skin Carcinogenesis, German Cancer Research Center, Heidelberg, Germany
| | - Bettina Ebner
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Katarzyna Figlak
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria.,Centre for Cell Biology and Cutaneous Research, Blizard Institute, Queen Mary University of London, London, United Kingdom
| | | | - Wolfgang Sipos
- Clinical Department for Farm Animals and Herd Management, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Erwin Tschachler
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Leopold Eckhart
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
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20
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Lopes-Marques M, Alves LQ, Fonseca MM, Secci-Petretto G, Machado AM, Ruivo R, Castro LFC. Convergent inactivation of the skin-specific C-C motif chemokine ligand 27 in mammalian evolution. Immunogenetics 2019; 71:363-372. [PMID: 31049641 DOI: 10.1007/s00251-019-01114-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/05/2019] [Indexed: 12/31/2022]
Abstract
The appearance of mammalian-specific skin features was a key evolutionary event contributing for the elaboration of physiological processes such as thermoregulation, adequate hydration, locomotion, and inflammation. Skin inflammatory and autoimmune processes engage a population of skin-infiltrating T cells expressing a specific C-C chemokine receptor (CCR10) which interacts with an epidermal CC chemokine, the skin-specific C-C motif chemokine ligand 27 (CCL27). CCL27 is selectively produced in the skin by keratinocytes, particularly upon inflammation, mediating the adhesion and homing of skin-infiltrating T cells. Here, we examined the evolution and coding condition of Ccl27 in 112 placental mammalian species. Our findings reveal that a number of open reading frame inactivation events such as insertions, deletions, and start and stop codon mutations independently occurred in Cetacea, Pholidota, Sirenia, Chiroptera, and Rodentia, totalizing 18 species. The diverse habitat settings and lifestyles of Ccl27-eroded lineages probably implied distinct evolutionary triggers rendering this gene unessential. For example, in Cetacea, the rapid renewal of skin layers minimizes the need for an elaborate inflammatory mechanism, mirrored by the absence of epidermal scabs. Our findings suggest that the convergent and independent loss of Ccl27 in mammalian evolution concurred with unique adaptive roads for skin physiology.
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Affiliation(s)
| | - Luís Q Alves
- CIIMAR-UP, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, Rua do Campo Alegre 1021/1055, 4169-007, Porto, Portugal
| | - Miguel M Fonseca
- CIIMAR-UP, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - Giulia Secci-Petretto
- CIIMAR-UP, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, Rua do Campo Alegre 1021/1055, 4169-007, Porto, Portugal
| | - André M Machado
- CIIMAR-UP, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, Rua do Campo Alegre 1021/1055, 4169-007, Porto, Portugal
| | - Raquel Ruivo
- CIIMAR-UP, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.
| | - L Filipe C Castro
- CIIMAR-UP, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal. .,Department of Biology, Faculty of Sciences, Rua do Campo Alegre 1021/1055, 4169-007, Porto, Portugal.
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21
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Zhou X, Sun D, Guang X, Ma S, Fang X, Mariotti M, Nielsen R, Gladyshev VN, Yang G. Molecular Footprints of Aquatic Adaptation Including Bone Mass Changes in Cetaceans. Genome Biol Evol 2018; 10:967-975. [PMID: 29608729 PMCID: PMC5952927 DOI: 10.1093/gbe/evy062] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2018] [Indexed: 01/04/2023] Open
Abstract
Cetaceans (whales, dolphins, and porpoises) are a group of specialized mammals that evolved from terrestrial ancestors and are fully adapted to aquatic habitats. Taking advantage of the recently sequenced finless porpoise genome, we conducted comparative analyses of the genomes of seven cetaceans and related terrestrial species to provide insight into the molecular bases of adaptation of these aquatic mammals. Changes in gene sequences were identified in main lineages of cetaceans, offering an evolutionary picture of cetacean genomes that reveal new pathways that could be associated with adaptation to aquatic lifestyle. We profiled bone microanatomical structures across 28 mammals, including representatives of cetaceans, pinnipeds, and sirenians. Subsequent phylogenetic comparative analyses revealed genes (including leptin, insulin-like growth factor 1, and collagen type I alpha 2 chain) with the root-to-tip substitution rate significantly correlated with bone compactness, implicating these genes could be involved in bone mass control. Overall, this study described adjustments of the genomes of cetaceans according to lifestyle, phylogeny, and bone mass.
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Affiliation(s)
- Xuming Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, China.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Di Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, China
| | - Xuanmin Guang
- BGI-Shenzhen, Shenzhen, China.,The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Siming Ma
- Genome Institute of Singapore, Singapore
| | | | - Marco Mariotti
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, China
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22
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Cetacea are natural knockouts for IL20. Immunogenetics 2018; 70:681-687. [DOI: 10.1007/s00251-018-1071-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 07/01/2018] [Indexed: 10/28/2022]
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23
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Epidermal cornification is preceded by the expression of a keratinocyte-specific set of pyroptosis-related genes. Sci Rep 2017; 7:17446. [PMID: 29234126 PMCID: PMC5727156 DOI: 10.1038/s41598-017-17782-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/30/2017] [Indexed: 01/01/2023] Open
Abstract
The homeostasis of the epidermis depends on keratinocyte differentiation and cornification, a mode of programmed cell death that does not elicit inflammation. Here, we report that cornification is associated with the expression of specific genes that control multiple steps of pyroptosis, another form of cell death that involves the processing and release of interleukin-1 family (IL1F) cytokines. Expression levels of pro-inflammatory IL1A and IL1B and of the pyroptotic pore-forming gasdermin (GSDM) D were downregulated during terminal differentiation of human keratinocytes in vitro. By contrast, negative regulators of IL-1 processing, including NLR family pyrin domain containing 10 (NLRP10) and pyrin domain-containing 1 (PYDC1), the anti-inflammatory IL1F members IL-37 (IL1F7) and IL-38 (IL1F10), and GSDMA, were strongly induced in differentiated keratinocytes. In human tissues, these keratinocyte differentiation-associated genes are expressed in the skin at higher levels than in any other organ, and mammalian species, that have lost the epidermal cornification program during evolution, i.e. whales and dolphins, lack homologs of these genes. Together, our results suggest that human epidermal cornification is accompanied by a tight control of pyroptosis and warrant further studies of potential defects in the balance between cornification and pyroptosis in skin pathologies.
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24
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Whittaker Hawkins RF, Patenaude A, Dumas A, Jain R, Tesfagiorgis Y, Kerfoot S, Matsui T, Gunzer M, Poubelle PE, Larochelle C, Pelletier M, Vallières L. ICAM1+ neutrophils promote chronic inflammation via ASPRV1 in B cell-dependent autoimmune encephalomyelitis. JCI Insight 2017; 2:96882. [PMID: 29212956 DOI: 10.1172/jci.insight.96882] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 10/23/2017] [Indexed: 12/16/2022] Open
Abstract
Neutrophils contribute to demyelinating autoimmune diseases, yet their phenotype and functions have been elusive to date. Here, we demonstrate that ICAM1 surface expression distinguishes extra- from intravascular neutrophils in the mouse CNS during experimental autoimmune encephalomyelitis (EAE). Transcriptomic analysis of these 2 subpopulations indicated that neutrophils, once extravasated, acquire macrophage-like properties, including the potential for immunostimulation and MHC class II-mediated antigen presentation. In corroboration, super-resolution (3D stimulated emission-depletion [STED]) microscopy revealed neutrophils forming synapses with T and B cells in situ. Further, neutrophils specifically express the aspartic retroviral-like protease ASPRV1, which increases in the CNS during EAE and severe cases of multiple sclerosis. Without ASPRV1, mice immunized with a new B cell-dependent myelin antigen (but not with the traditional myelin oligodendrocyte glycoprotein peptide) develop a chronic phase of EAE that is less severe and even completely fades in many individuals. Therefore, ICAM1+ macrophage-like neutrophils can play both shared and nonredundant roles in autoimmune demyelination, among them perpetuating inflammation via ASPRV1.
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Affiliation(s)
- Ryder F Whittaker Hawkins
- Neuroscience Unit, University Hospital Center of Quebec - Laval University, Quebec City, Quebec, Canada
| | - Alexandre Patenaude
- Neuroscience Unit, University Hospital Center of Quebec - Laval University, Quebec City, Quebec, Canada
| | - Aline Dumas
- Neuroscience Unit, University Hospital Center of Quebec - Laval University, Quebec City, Quebec, Canada
| | - Rajiv Jain
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
| | - Yodit Tesfagiorgis
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
| | - Steven Kerfoot
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
| | - Takeshi Matsui
- Laboratory for Skin Homeostasis, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Matthias Gunzer
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen, Germany
| | - Patrice E Poubelle
- Infectious and Immune Disease Unit, University Hospital Center of Quebec - Laval University, Quebec City, Quebec, Canada
| | - Catherine Larochelle
- Neuroimmunology Research Laboratory, University of Montreal Hospital Research Center, Montreal, Quebec, Canada
| | - Martin Pelletier
- Infectious and Immune Disease Unit, University Hospital Center of Quebec - Laval University, Quebec City, Quebec, Canada
| | - Luc Vallières
- Neuroscience Unit, University Hospital Center of Quebec - Laval University, Quebec City, Quebec, Canada
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25
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Mlitz V, Hussain T, Tschachler E, Eckhart L. Filaggrin has evolved from an "S100 fused-type protein" (SFTP) gene present in a common ancestor of amphibians and mammals. Exp Dermatol 2017; 26:955-957. [PMID: 28191671 DOI: 10.1111/exd.13317] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2017] [Indexed: 12/23/2022]
Abstract
The expression of filaggrin in differentiated keratinocytes and the association of filaggrin mutations with ichthyosis vulgaris and atopic dermatitis suggest that this prototypical member of the S100 fused-type protein (SFTP) family plays a key role in the epidermal barrier to the environment. Here, we report that SFTP genes are present not only in amniotes but also in amphibians. Four SFTPs are expressed in the skin of the frog Xenopus laevis. The results of this study indicate that filaggrin has evolved from an ancestral SFTP that may have contributed to skin modifications during the evolutionary transition to terrestrial life.
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Affiliation(s)
- Veronika Mlitz
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Tajamul Hussain
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Erwin Tschachler
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Leopold Eckhart
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
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26
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Identification and comparative analysis of the epidermal differentiation complex in snakes. Sci Rep 2017; 7:45338. [PMID: 28345630 PMCID: PMC5366951 DOI: 10.1038/srep45338] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/22/2017] [Indexed: 12/13/2022] Open
Abstract
The epidermis of snakes efficiently protects against dehydration and mechanical stress. However, only few proteins of the epidermal barrier to the environment have so far been identified in snakes. Here, we determined the organization of the Epidermal Differentiation Complex (EDC), a cluster of genes encoding protein constituents of cornified epidermal structures, in snakes and compared it to the EDCs of other squamates and non-squamate reptiles. The EDC of snakes displays shared synteny with that of the green anole lizard, including the presence of a cluster of corneous beta-protein (CBP)/beta-keratin genes. We found that a unique CBP comprising 4 putative beta-sheets and multiple cysteine-rich EDC proteins are conserved in all snakes and other squamates investigated. Comparative genomics of squamates suggests that the evolution of snakes was associated with a gene duplication generating two isoforms of the S100 fused-type protein, scaffoldin, the origin of distinct snake-specific EDC genes, and the loss of other genes that were present in the EDC of the last common ancestor of snakes and lizards. Taken together, our results provide new insights into the evolution of the skin in squamates and a basis for the characterization of the molecular composition of the epidermis in snakes.
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Cau L, Pendaries V, Lhuillier E, Thompson PR, Serre G, Takahara H, Méchin MC, Simon M. Lowering relative humidity level increases epidermal protein deimination and drives human filaggrin breakdown. J Dermatol Sci 2017; 86:106-113. [PMID: 28242341 DOI: 10.1016/j.jdermsci.2017.02.280] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/25/2017] [Accepted: 02/15/2017] [Indexed: 01/11/2023]
Abstract
BACKGROUND Deimination (also known as citrullination), the conversion of arginine in a protein to citrulline, is catalyzed by a family of enzymes called peptidylarginine deiminases (PADs). Three PADs are expressed in the epidermis, one of their targets being filaggrin. Filaggrin plays a central role in atopic dermatitis and is a key protein for the epidermal barrier. It aggregates keratins and is cross-linked to cornified envelopes. Following its deimination, it is totally degraded to release free amino acids, contributing to the natural moisturizing factor (NMF). The mechanisms controlling this multistep catabolism in human are unknown. OBJECTIVE To test whether external humidity plays a role, and investigate the molecular mechanisms involved. METHODS Specimens of reconstructed human epidermis (RHEs) produced in humid or dry conditions (>95% or 30-50% relative humidity) were compared. RESULTS RHEs produced in the dry condition presented structural changes, including a thicker stratum corneum and a larger amount of keratohyalin granules. The transepidermal water loss and the stratum corneum pH were decreased whereas the quantity of NMF was greater. This highly suggested that filaggrin proteolysis was up-regulated. The expression/activity of the proteases involved in filaggrin breakdown did not increase while PAD1 expression and the deimination rate of proteins, including filaggrin, were drastically enhanced. Partial inhibition of PADs with Cl-amidine reversed the effect of dryness on filaggrin breakdown. CONCLUSION These results demonstrate the importance of external humidity in the control of human filaggrin metabolism, and suggest that deimination plays a major role in this regulation.
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Affiliation(s)
- Laura Cau
- UDEAR, Institut National de la Santé Et de la Recherche Médicale, Université de Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique, Toulouse, France
| | - Valérie Pendaries
- UDEAR, Institut National de la Santé Et de la Recherche Médicale, Université de Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique, Toulouse, France
| | - Emeline Lhuillier
- UDEAR, Institut National de la Santé Et de la Recherche Médicale, Université de Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique, Toulouse, France; Plateau de Génomique GeT-Purpan, Genotoul, Toulouse, France
| | - Paul R Thompson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Guy Serre
- UDEAR, Institut National de la Santé Et de la Recherche Médicale, Université de Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique, Toulouse, France
| | - Hidenari Takahara
- Department of Applied Biological Resource Sciences, School of Agriculture, University of Ibaraki, Ibaraki, Japan
| | - Marie-Claire Méchin
- UDEAR, Institut National de la Santé Et de la Recherche Médicale, Université de Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique, Toulouse, France
| | - Michel Simon
- UDEAR, Institut National de la Santé Et de la Recherche Médicale, Université de Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique, Toulouse, France.
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Abbas Zadeh S, Mlitz V, Lachner J, Golabi B, Mildner M, Pammer J, Tschachler E, Eckhart L. Phylogenetic profiling and gene expression studies implicate a primary role of PSORS1C2 in terminal differentiation of keratinocytes. Exp Dermatol 2017; 26:352-358. [DOI: 10.1111/exd.13272] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Salman Abbas Zadeh
- Research Division of Biology and Pathobiology of the Skin; Department of Dermatology; Medical University of Vienna; Vienna Austria
| | - Veronika Mlitz
- Research Division of Biology and Pathobiology of the Skin; Department of Dermatology; Medical University of Vienna; Vienna Austria
| | - Julia Lachner
- Research Division of Biology and Pathobiology of the Skin; Department of Dermatology; Medical University of Vienna; Vienna Austria
| | - Bahar Golabi
- Research Division of Biology and Pathobiology of the Skin; Department of Dermatology; Medical University of Vienna; Vienna Austria
| | - Michael Mildner
- Research Division of Biology and Pathobiology of the Skin; Department of Dermatology; Medical University of Vienna; Vienna Austria
| | - Johannes Pammer
- Department of Pathology; Medical University of Vienna; Vienna Austria
| | - Erwin Tschachler
- Research Division of Biology and Pathobiology of the Skin; Department of Dermatology; Medical University of Vienna; Vienna Austria
| | - Leopold Eckhart
- Research Division of Biology and Pathobiology of the Skin; Department of Dermatology; Medical University of Vienna; Vienna Austria
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29
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Miles M, Kitevska-Ilioski T, Hawkins C. Old and Novel Functions of Caspase-2. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2017; 332:155-212. [DOI: 10.1016/bs.ircmb.2016.12.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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30
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Oh JW, Chung O, Cho YS, MacGregor GR, Plikus MV. Gene loss in keratinization programs accompanies adaptation of cetacean skin to aquatic lifestyle. Exp Dermatol 2016; 24:572-3. [PMID: 25959646 DOI: 10.1111/exd.12756] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2015] [Indexed: 12/31/2022]
Affiliation(s)
- Ji Won Oh
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA.,Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA.,Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA
| | - Oksung Chung
- Personal Genomics Institute, Genome Research Foundation, Suwon, Korea
| | - Yun Sung Cho
- Biomedical Engineering Department, The Genomics Institute, UNIST, Ulsan, Korea
| | - Grant R MacGregor
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Maksim V Plikus
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA.,Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA.,Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA
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Adaptive Evolution of Skin in Terrestrial Vertebrates and Possible Involvement of Endogenous Retroviruses. Uirusu 2016; 66:31-38. [PMID: 28484176 DOI: 10.2222/jsv.66.31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The first terrestrial vertebrates emerged from water and adapted to living on land approximately 360 million years ago (late Devonian). In particular, amphibians are thought to have surface epithelia that changed from multilayered epithelia into keratinized stratified squamous epithelia by acquiring stratum corneum (SC), which is composed of several dead cell layers that serve as an air liquid interface barrier. Then, reptiles appeared and became a major terrestrial vertebrate group approximately 340 million years ago by forming hard SC. About 220 million years ago, mammals radiated by acquiring soft and moisturized SC, and endogenous retroviruses were thought to be actively integrated into mammalian genomes. Skin ASpartic Protease (SASPase)/ASPRV1 is the mammalian-specific endogenous retroviral-derived protease. SASPase-deficient mice had dry skin and aberrant accumulation of profilaggrin, which is another mammalian-specific gene that regulates SC barrier function and is a major predisposing factor for atopic dermatitis. These findings indicate that the retroviral element SASPase was integrated into the first mammalian species and was involved in the adaptive evolution of mammals, as it facilitates moisturization of skin SC. It is possible that other uncharacterized endogenous retroviruses were also involved in epidermal barrier function.
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