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Schepps S, Xu J, Yang H, Mandel J, Mehta J, Tolotta J, Baker N, Tekmen V, Nikbakht N, Fortina P, Fuentes I, LaFleur B, Cho RJ, South AP. Skin in the game: a review of single-cell and spatial transcriptomics in dermatological research. Clin Chem Lab Med 2024; 0:cclm-2023-1245. [PMID: 38656304 DOI: 10.1515/cclm-2023-1245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/29/2024] [Indexed: 04/26/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) are two emerging research technologies that uniquely characterize gene expression microenvironments on a cellular or subcellular level. The skin, a clinically accessible tissue composed of diverse, essential cell populations, serves as an ideal target for these high-resolution investigative approaches. Using these tools, researchers are assembling a compendium of data and discoveries in healthy skin as well as a range of dermatologic pathophysiologies, including atopic dermatitis, psoriasis, and cutaneous malignancies. The ongoing advancement of single-cell approaches, coupled with anticipated decreases in cost with increased adoption, will reshape dermatologic research, profoundly influencing disease characterization, prognosis, and ultimately clinical practice.
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Affiliation(s)
- Samuel Schepps
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Jonathan Xu
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Henry Yang
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Jenna Mandel
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Jaanvi Mehta
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Julianna Tolotta
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Nicole Baker
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Volkan Tekmen
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Neda Nikbakht
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
- Department of Pharmacology, Physiology and Cancer Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Paolo Fortina
- Department of Pharmacology, Physiology and Cancer Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
- International Federation of Clinical Chemistry Working Group on Single Cell and Spatial Transcriptomics, Milan, Italy
| | - Ignacia Fuentes
- International Federation of Clinical Chemistry Working Group on Single Cell and Spatial Transcriptomics, Milan, Italy
- Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Directora de Investigación Fundación DEBRA Chile, Santiago, Chile
| | - Bonnie LaFleur
- International Federation of Clinical Chemistry Working Group on Single Cell and Spatial Transcriptomics, Milan, Italy
- R. Ken Coit College of Pharmacy, University of Arizona, University of Arizona Cancer Center, Tucson, AZ, USA
| | - Raymond J Cho
- International Federation of Clinical Chemistry Working Group on Single Cell and Spatial Transcriptomics, Milan, Italy
- Department of Dermatology, University of San Francisco, San Francisco, CA, USA
| | - Andrew P South
- Department of Pharmacology, Physiology and Cancer Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
- International Federation of Clinical Chemistry Working Group on Single Cell and Spatial Transcriptomics, Milan, Italy
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Sieminska I, Pieniawska M, Grzywa TM. The Immunology of Psoriasis-Current Concepts in Pathogenesis. Clin Rev Allergy Immunol 2024:10.1007/s12016-024-08991-7. [PMID: 38642273 DOI: 10.1007/s12016-024-08991-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2024] [Indexed: 04/22/2024]
Abstract
Psoriasis is one of the most common inflammatory skin diseases with a chronic, relapsing-remitting course. The last decades of intense research uncovered a pathological network of interactions between immune cells and other types of cells in the pathogenesis of psoriasis. Emerging evidence indicates that dendritic cells, TH17 cells, and keratinocytes constitute a pathogenic triad in psoriasis. Dendritic cells produce TNF-α and IL-23 to promote T cell differentiation toward TH17 cells that produce key psoriatic cytokines IL-17, IFN-γ, and IL-22. Their activity results in skin inflammation and activation and hyperproliferation of keratinocytes. In addition, other cells and signaling pathways are implicated in the pathogenesis of psoriasis, including TH9 cells, TH22 cells, CD8+ cytotoxic cells, neutrophils, γδ T cells, and cytokines and chemokines secreted by them. New insights from high-throughput analysis of lesional skin identified novel signaling pathways and cell populations involved in the pathogenesis. These studies not only expanded our knowledge about the mechanisms of immune response and the pathogenesis of psoriasis but also resulted in a revolution in the clinical management of patients with psoriasis. Thus, understanding the mechanisms of immune response in psoriatic inflammation is crucial for further studies, the development of novel therapeutic strategies, and the clinical management of psoriasis patients. The aim of the review was to comprehensively present the dysregulation of immune response in psoriasis with an emphasis on recent findings. Here, we described the role of immune cells, including T cells, B cells, dendritic cells, neutrophils, monocytes, mast cells, and innate lymphoid cells (ILCs), as well as non-immune cells, including keratinocytes, fibroblasts, endothelial cells, and platelets in the initiation, development, and progression of psoriasis.
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Affiliation(s)
- Izabela Sieminska
- University Centre of Veterinary Medicine, University of Agriculture in Krakow, Krakow, Poland
| | - Monika Pieniawska
- Institute of Human Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Tomasz M Grzywa
- Laboratory of Immunology, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland.
- Department of Methodology, Medical University of Warsaw, Warsaw, Poland.
- The Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, USA.
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3
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Luedke KP, Yoshino J, Yin C, Jiang N, Huang JM, Huynh K, Parrish JZ. Dendrite intercalation between epidermal cells tunes nociceptor sensitivity to mechanical stimuli in Drosophila larvae. PLoS Genet 2024; 20:e1011237. [PMID: 38662763 DOI: 10.1371/journal.pgen.1011237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 05/07/2024] [Accepted: 03/29/2024] [Indexed: 05/07/2024] Open
Abstract
An animal's skin provides a first point of contact with the sensory environment, including noxious cues that elicit protective behavioral responses. Nociceptive somatosensory neurons densely innervate and intimately interact with epidermal cells to receive these cues, however the mechanisms by which epidermal interactions shape processing of noxious inputs is still poorly understood. Here, we identify a role for dendrite intercalation between epidermal cells in tuning sensitivity of Drosophila larvae to noxious mechanical stimuli. In wild-type larvae, dendrites of nociceptive class IV da neurons intercalate between epidermal cells at apodemes, which function as body wall muscle attachment sites, but not at other sites in the epidermis. From a genetic screen we identified miR-14 as a regulator of dendrite positioning in the epidermis: miR-14 is expressed broadly in the epidermis but not in apodemes, and miR-14 inactivation leads to excessive apical dendrite intercalation between epidermal cells. We found that miR-14 regulates expression and distribution of the epidermal Innexins ogre and Inx2 and that these epidermal gap junction proteins restrict epidermal dendrite intercalation. Finally, we found that altering the extent of epidermal dendrite intercalation had corresponding effects on nociception: increasing epidermal intercalation sensitized larvae to noxious mechanical inputs and increased mechanically evoked calcium responses in nociceptive neurons, whereas reducing epidermal dendrite intercalation had the opposite effects. Altogether, these studies identify epidermal dendrite intercalation as a mechanism for mechanical coupling of nociceptive neurons to the epidermis, with nociceptive sensitivity tuned by the extent of intercalation.
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Affiliation(s)
- Kory P Luedke
- Department of Biology, University of Washington, Seattle, Washington State, United States of America
| | - Jiro Yoshino
- Department of Biology, University of Washington, Seattle, Washington State, United States of America
| | - Chang Yin
- Department of Biology, University of Washington, Seattle, Washington State, United States of America
| | - Nan Jiang
- Department of Biology, University of Washington, Seattle, Washington State, United States of America
| | - Jessica M Huang
- Department of Biology, University of Washington, Seattle, Washington State, United States of America
| | - Kevin Huynh
- Department of Biology, University of Washington, Seattle, Washington State, United States of America
| | - Jay Z Parrish
- Department of Biology, University of Washington, Seattle, Washington State, United States of America
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Xiao T, Eze UC, Charruyer-Reinwald A, Weisenberger T, Khalifa A, Abegaze B, Schwab GK, Elsabagh RH, Parenteau TR, Kochanowski K, Piper M, Xia Y, Cheng JB, Cho RJ, Ghadially R. Short cell cycle duration is a phenotype of human epidermal stem cells. Stem Cell Res Ther 2024; 15:76. [PMID: 38475896 DOI: 10.1186/s13287-024-03670-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND A traditional view is that stem cells (SCs) divide slowly. Meanwhile, both embryonic and pluripotent SCs display a shorter cell cycle duration (CCD) in comparison to more committed progenitors (CPs). METHODS We examined the in vitro proliferation and cycling behavior of somatic adult human cells using live cell imaging of passage zero keratinocytes and single-cell RNA sequencing. RESULTS We found two populations of keratinocytes: those with short CCD and protracted near exponential growth, and those with long CCD and terminal differentiation. Applying the ergodic principle, the comparative numbers of cycling cells in S phase in an enriched population of SCs confirmed a shorter CCD than CPs. Further, analysis of single-cell RNA sequencing of cycling adult human keratinocyte SCs and CPs indicated a shortening of both G1 and G2M phases in the SC. CONCLUSIONS Contrary to the pervasive paradigm, SCs progress through cell cycle more quickly than more differentiated dividing CPs. Thus, somatic human adult keratinocyte SCs may divide infrequently, but divide rapidly when they divide. Additionally, it was found that SC-like proliferation persisted in vitro.
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Affiliation(s)
- Tong Xiao
- Department of Dermatology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Department of Dermatology, San Francisco Co-Director Epithelial Section Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, 1700 Owens Street, San Francisco, CA, 94158, USA
- Department of Dermatology, VA Medical Center, San Francisco, CA, USA
| | - Ugomma C Eze
- Department of Dermatology, San Francisco Co-Director Epithelial Section Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, 1700 Owens Street, San Francisco, CA, 94158, USA
| | - Alex Charruyer-Reinwald
- Department of Dermatology, San Francisco Co-Director Epithelial Section Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, 1700 Owens Street, San Francisco, CA, 94158, USA
- Department of Dermatology, VA Medical Center, San Francisco, CA, USA
| | - Tracy Weisenberger
- Department of Dermatology, San Francisco Co-Director Epithelial Section Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, 1700 Owens Street, San Francisco, CA, 94158, USA
- Department of Dermatology, VA Medical Center, San Francisco, CA, USA
| | - Ayman Khalifa
- Department of Dermatology, San Francisco Co-Director Epithelial Section Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, 1700 Owens Street, San Francisco, CA, 94158, USA
- Department of Dermatology, VA Medical Center, San Francisco, CA, USA
- Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Brook Abegaze
- Department of Dermatology, San Francisco Co-Director Epithelial Section Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, 1700 Owens Street, San Francisco, CA, 94158, USA
| | - Gabrielle K Schwab
- Department of Dermatology, San Francisco Co-Director Epithelial Section Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, 1700 Owens Street, San Francisco, CA, 94158, USA
- Department of Dermatology, VA Medical Center, San Francisco, CA, USA
| | - Rasha H Elsabagh
- Immunology Department, Animal Health Research Institute (AHRI), Giza, Egypt
| | | | - Karl Kochanowski
- Department of Pharmaceutical Chemistry, UC San Francisco, San Francisco, CA, USA
| | - Merisa Piper
- Department of Plastic Surgery, UC San Francisco, San Francisco, CA, USA
| | - Yumin Xia
- Department of Dermatology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jeffrey B Cheng
- Department of Dermatology, San Francisco Co-Director Epithelial Section Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, 1700 Owens Street, San Francisco, CA, 94158, USA
- Department of Dermatology, VA Medical Center, San Francisco, CA, USA
| | - Raymond J Cho
- Department of Dermatology, San Francisco Co-Director Epithelial Section Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, 1700 Owens Street, San Francisco, CA, 94158, USA
| | - Ruby Ghadially
- Department of Dermatology, San Francisco Co-Director Epithelial Section Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, 1700 Owens Street, San Francisco, CA, 94158, USA.
- Department of Dermatology, VA Medical Center, San Francisco, CA, USA.
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Zhang J, Xiang F, Ding Y, Hu W, Wang H, Zhang X, Lei Z, Li T, Wang P, Kang X. Identification and validation of RNA-binding protein SLC3A2 regulates melanocyte ferroptosis in vitiligo by integrated analysis of single-cell and bulk RNA-sequencing. BMC Genomics 2024; 25:236. [PMID: 38438962 PMCID: PMC10910712 DOI: 10.1186/s12864-024-10147-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 02/20/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND The pathogenesis of vitiligo remains unclear. The genes encoding vitiligo-related RNA-binding proteins (RBPs) and their underlying pathogenic mechanism have not been determined. RESULTS Single-cell transcriptome sequencing (scRNA-seq) data from the CNCB database was obtained to identify distinct cell types and subpopulations and the relative proportion changes in vitiligo and healthy samples. We identified 14 different cell types and 28 cell subpopulations. The proportion of each cell subpopulation significantly differed between the patients with vitiligo and healthy groups. Using RBP genes for unsupervised clustering, we obtained the specific RBP genes of different cell types in vitiligo and healthy groups. The RBP gene expression was highly heterogeneous; there were significant differences in some cell types, such as keratinocytes, Langerhans, and melanocytes, while there were no significant differences in other cells, such as T cells and fibroblasts, in the two groups. The melanocyte-specific RBP genes were enriched in the apoptosis and immune-related pathways in the patients with vitiligo. Combined with the bulk RNA-seq data of melanocytes, key RBP genes related to melanocytes were identified, including eight upregulated RBP genes (CDKN2A, HLA-A, RPL12, RPL29, RPL31, RPS19, RPS21, and RPS28) and one downregulated RBP gene (SLC3A2). Cell experiments were conducted to explore the role of the key RBP gene SLC3A2 in vitiligo. Cell experiments confirmed that melanocyte proliferation decreased, whereas apoptosis increased, after SLC3A2 knockdown. SLC3A2 knockdown in melanocytes also decreased the SOD activity and melanin content; increased the Fe2+, ROS, and MDA content; significantly increased the expression levels of TYR and COX2; and decreased the expression levels of glutathione and GPX4. CONCLUSION We identified the RBP genes of different cell subsets in patients with vitiligo and confirmed that downregulating SLC3A2 can promote ferroptosis in melanocytes. These findings provide new insights into the pathogenesis of vitiligo.
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Affiliation(s)
- Jingzhan Zhang
- Department of Dermatology and Venereology, People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
- Xinjiang Clinical Research Center for Dermatology and Venereology, Xinjiang, China
- Xinjiang Key Laboratory of Dermatology Research, Xinjiang, China
| | - Fang Xiang
- Department of Dermatology and Venereology, People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
- Xinjiang Clinical Research Center for Dermatology and Venereology, Xinjiang, China
- Xinjiang Key Laboratory of Dermatology Research, Xinjiang, China
| | - Yuan Ding
- Department of Dermatology and Venereology, People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
- Xinjiang Clinical Research Center for Dermatology and Venereology, Xinjiang, China
- Xinjiang Key Laboratory of Dermatology Research, Xinjiang, China
| | - Wen Hu
- Department of Dermatology and Venereology, People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
- Xinjiang Clinical Research Center for Dermatology and Venereology, Xinjiang, China
- Xinjiang Key Laboratory of Dermatology Research, Xinjiang, China
| | - Hongjuan Wang
- Department of Dermatology and Venereology, People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
- Xinjiang Clinical Research Center for Dermatology and Venereology, Xinjiang, China
- Xinjiang Key Laboratory of Dermatology Research, Xinjiang, China
| | - Xiangyue Zhang
- Department of Dermatology and Venereology, People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
- Xinjiang Clinical Research Center for Dermatology and Venereology, Xinjiang, China
- Xinjiang Key Laboratory of Dermatology Research, Xinjiang, China
| | - Zixian Lei
- Department of Dermatology and Venereology, People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
- Xinjiang Clinical Research Center for Dermatology and Venereology, Xinjiang, China
- Xinjiang Key Laboratory of Dermatology Research, Xinjiang, China
| | - Tingting Li
- Department of Dermatology and Venereology, People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
- Xinjiang Clinical Research Center for Dermatology and Venereology, Xinjiang, China
- Xinjiang Key Laboratory of Dermatology Research, Xinjiang, China
| | - Peng Wang
- Department of Dermatology and Venereology, People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
- Xinjiang Clinical Research Center for Dermatology and Venereology, Xinjiang, China
- Xinjiang Key Laboratory of Dermatology Research, Xinjiang, China
| | - Xiaojing Kang
- Department of Dermatology and Venereology, People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China.
- Xinjiang Clinical Research Center for Dermatology and Venereology, Xinjiang, China.
- Xinjiang Key Laboratory of Dermatology Research, Xinjiang, China.
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6
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Jiang Y, Perez-Moreno M. Translational frontiers: insight from lymphatics in skin regeneration. Front Physiol 2024; 15:1347558. [PMID: 38487264 PMCID: PMC10937408 DOI: 10.3389/fphys.2024.1347558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/01/2024] [Indexed: 03/17/2024] Open
Abstract
The remarkable regenerative ability of the skin, governed by complex molecular mechanisms, offers profound insights into the skin repair processes and the pathogenesis of various dermatological conditions. This understanding, derived from studies in human skin and various model systems, has not only deepened our knowledge of skin regeneration but also facilitated the development of skin substitutes in clinical practice. Recent research highlights the crucial role of lymphatic vessels in skin regeneration. Traditionally associated with fluid dynamics and immune modulation, these vessels are now recognized for interacting with skin stem cells and coordinating regeneration. This Mini Review provides an overview of recent advancements in basic and translational research related to skin regeneration, focusing on the dynamic interplay between lymphatic vessels and skin biology. Key highlights include the critical role of stem cell-lymphatic vessel crosstalk in orchestrating skin regeneration, emerging translational approaches, and their implications for skin diseases. Additionally, the review identifies research gaps and proposes potential future directions, underscoring the significance of this rapidly evolving research arena.
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Affiliation(s)
| | - Mirna Perez-Moreno
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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7
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Sosa J, Oyelakin A, Sinha S. The Reign of Follistatin in Tumors and Their Microenvironment: Implications for Drug Resistance. Biology (Basel) 2024; 13:130. [PMID: 38392348 PMCID: PMC10887188 DOI: 10.3390/biology13020130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/10/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024]
Abstract
Follistatin (FST) is a potent neutralizer of the transforming growth factor-β superfamily and is associated with normal cellular programs and various hallmarks of cancer, such as proliferation, migration, angiogenesis, and immune evasion. The aberrant expression of FST by solid tumors is a well-documented observation, yet how FST influences tumor progression and therapy response remains unclear. The recent surge in omics data has revealed new insights into the molecular foundation underpinning tumor heterogeneity and its microenvironment, offering novel precision medicine-based opportunities to combat cancer. In this review, we discuss these recent FST-centric studies, thereby offering an updated perspective on the protean role of FST isoforms in shaping the complex cellular ecosystem of tumors and in mediating drug resistance.
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Affiliation(s)
- Jennifer Sosa
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Akinsola Oyelakin
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle Children's Hospital, Seattle, WA 98101, USA
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle Children's Hospital, Seattle, WA 98101, USA
| | - Satrajit Sinha
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
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8
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Cohen E, Johnson CN, Wasikowski R, Billi AC, Tsoi LC, Kahlenberg JM, Gudjonsson JE, Coulombe PA. Significance of stress keratin expression in normal and diseased epithelia. iScience 2024; 27:108805. [PMID: 38299111 PMCID: PMC10828818 DOI: 10.1016/j.isci.2024.108805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/30/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024] Open
Abstract
A group of keratin intermediate filament genes, the type II KRT6A-C and type I KRT16 and KRT17, are deemed stress responsive as they are induced in keratinocytes of surface epithelia in response to environmental stressors, in skin disorders (e.g., psoriasis) and in carcinomas. Monitoring stress keratins is widely used to identify keratinocytes in an activated state. Here, we analyze single-cell transcriptomic data from healthy and diseased human skin to explore the properties of stress keratins. Relative to keratins occurring in healthy skin, stress-induced keratins are expressed at lower levels and show lesser type I-type II pairwise regulation. Stress keratins do not "replace" the keratins expressed during normal differentiation nor reflect cellular proliferation. Instead, stress keratins are consistently co-regulated with genes with roles in differentiation, inflammation, and/or activation of innate immunity at the single-cell level. These findings provide a roadmap toward explaining the broad diversity and contextual regulation of keratins.
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Affiliation(s)
- Erez Cohen
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Craig N. Johnson
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Rachael Wasikowski
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Allison C. Billi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lam C. Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - J. Michelle Kahlenberg
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
- Division of Rheumatology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Johann E. Gudjonsson
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
- Division of Rheumatology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Pierre A. Coulombe
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
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9
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Thalheim T, Schneider MR. Skin single-cell transcriptomics reveals a core of sebaceous gland-relevant genes shared by mice and humans. BMC Genomics 2024; 25:137. [PMID: 38310227 PMCID: PMC10837983 DOI: 10.1186/s12864-024-10008-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/11/2024] [Indexed: 02/05/2024] Open
Abstract
BACKGROUND Single-cell RNA sequencing (scRNA-seq) has been widely applied to dissect cellular heterogeneity in normal and diseased skin. Sebaceous glands, essential skin components with established functions in maintaining skin integrity and emerging roles in systemic energy metabolism, have been largely neglected in scRNA-seq studies. METHODS Departing from mouse and human skin scRNA-seq datasets, we identified gene sets expressed especially in sebaceous glands with the open-source R-package oposSOM. RESULTS The identified gene sets included sebaceous gland-typical genes as Scd3, Mgst1, Cidea, Awat2 and KRT7. Surprisingly, however, there was not a single overlap among the 100 highest, exclusively in sebaceous glands expressed transcripts in mouse and human samples. Notably, both species share a common core of only 25 transcripts, including mitochondrial and peroxisomal genes involved in fatty acid, amino acid, and glucose processing, thus highlighting the intense metabolic rate of this gland. CONCLUSIONS This study highlights intrinsic differences in sebaceous lipid synthesis between mice and humans, and indicates an important role for peroxisomal processes in this context. Our data also provides attractive starting points for experimentally addressing novel candidates regulating sebaceous gland homeostasis.
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Affiliation(s)
- Torsten Thalheim
- Interdisciplinary Institute for Bioinformatics (IZBI), University of Leipzig, Härtelstr. 16-18, 04107, Leipzig, Germany
- Present Address: Deutsches Biomasseforschungszentrum gGmbH, Torgauer Str. 116, 04347, Leipzig, Germany
| | - Marlon R Schneider
- Institute of Veterinary Physiology, University of Leipzig, An den Tierkliniken 7, Leipzig, 04103, Germany.
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10
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Xiong Y, Li S, Bai Y, Chen T, Sun W, Chen L, Yu J, Sun L, Li C, Wang J, Wu B. Generating detailed intercellular communication patterns in psoriasis at the single-cell level using social networking, pattern recognition, and manifold learning methods to optimize treatment strategies. Aging (Albany NY) 2024; 16:2194-2231. [PMID: 38289616 PMCID: PMC10911347 DOI: 10.18632/aging.205478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/13/2023] [Indexed: 02/22/2024]
Abstract
Psoriasis, a complex and recurrent chronic inflammatory skin disease involving various inflammatory cell types, requires effective cell communication to maintain the homeostatic balance of inflammation. However, patterns of communication at the single-cell level have not been systematically investigated. In this study, we employed social network analysis tools, pattern recognition, and manifold learning to compare molecular communication features between psoriasis cells and normal skin cells. Utilizing a process that facilitates the discovery of cell type-specific regulons, we analyzed internal regulatory networks among different cells in psoriasis. Advanced techniques for the quantitative detection of non-targeted proteins in pathological tissue sections were employed to demonstrate protein expression. Our findings revealed a synergistic interplay among the communication signals of immune cells in psoriasis. B-cells were activated, while Langerhans cells shifted into the primary signaling output mode to fulfill antigen presentation, mediating T-cell immunity. In contrast to normal skin cells, psoriasis cells shut down numerous signaling pathways, influencing the balance of skin cell renewal and differentiation. Additionally, we identified a significant number of active cell type-specific regulons of resident immune cells around the hair follicle. This study unveiled the molecular communication features of the hair follicle cell-psoriasis axis, showcasing its potential for therapeutic targeting at the single-cell level. By elucidating the pattern of immune cell communication in psoriasis and identifying new molecular features of the hair follicle cell-psoriasis axis, our findings present innovative strategies for drug targeting to enhance psoriasis treatment.
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Affiliation(s)
- Ying Xiong
- Department of Dermatology, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen 518028, China
| | - Sidi Li
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Yunmeng Bai
- Department of Nephrology, Shenzhen key Laboratory of Kidney Diseases, Shenzhen People’s Hospital, The First Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Ting Chen
- Department of Dermatology, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen 518028, China
| | - Wenwen Sun
- Department of Dermatology, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen 518028, China
| | - Lijie Chen
- Department of Dermatology, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen 518028, China
| | - Jia Yu
- Department of Dermatology, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen 518028, China
| | - Liwei Sun
- Department of Dermatology, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen 518028, China
| | - Chijun Li
- Department of Dermatology, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen 518028, China
| | - Jiajian Wang
- Department of Pediatrics, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen 518107, Guangdong, China
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen 518107, Guangdong, China
- Clinical Laboratory Department of The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Shenzhen and Longgang District People’s Hospital of Shenzhen, Shenzhen 518172, China
- Center for Energy Metabolism and Reproduction, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Shenzhen Key Laboratory of Metabolic Health, Shenzhen 518055, China
| | - Bo Wu
- Department of Dermatology, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen 518028, China
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11
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Erbacher C, Britz S, Dinkel P, Klein T, Sauer M, Stigloher C, Üçeyler N. Interaction of human keratinocytes and nerve fiber terminals at the neuro-cutaneous unit. eLife 2024; 13:e77761. [PMID: 38225894 PMCID: PMC10791129 DOI: 10.7554/elife.77761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 12/19/2023] [Indexed: 01/17/2024] Open
Abstract
Traditionally, peripheral sensory neurons are assumed as the exclusive transducers of external stimuli. Current research moves epidermal keratinocytes into focus as sensors and transmitters of nociceptive and non-nociceptive sensations, tightly interacting with intraepidermal nerve fibers at the neuro-cutaneous unit. In animal models, epidermal cells establish close contacts and ensheath sensory neurites. However, ultrastructural morphological and mechanistic data examining the human keratinocyte-nerve fiber interface are sparse. We investigated this exact interface in human skin applying super-resolution array tomography, expansion microscopy, and structured illumination microscopy. We show keratinocyte ensheathment of afferents and adjacent connexin 43 contacts in native skin and have applied a pipeline based on expansion microscopy to quantify these parameter in skin sections of healthy participants versus patients with small fiber neuropathy. We further derived a fully human co-culture system, visualizing ensheathment and connexin 43 plaques in vitro. Unraveling human intraepidermal nerve fiber ensheathment and potential interaction sites advances research at the neuro-cutaneous unit. These findings are crucial on the way to decipher the mechanisms of cutaneous nociception.
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Affiliation(s)
| | - Sebastian Britz
- Imaging Core Facility, Biocenter, University of WürzburgWürzburgGermany
| | - Philine Dinkel
- Department of Neurology, University Hospital of WürzburgWürzburgGermany
| | - Thomas Klein
- Department of Neurology, University Hospital of WürzburgWürzburgGermany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, University of WürzburgWürzburgGermany
| | | | - Nurcan Üçeyler
- Department of Neurology, University Hospital of WürzburgWürzburgGermany
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12
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Ganier C, Mazin P, Herrera-Oropeza G, Du-Harpur X, Blakeley M, Gabriel J, Predeus AV, Cakir B, Prete M, Harun N, Darrigrand JF, Haiser A, Wyles S, Shaw T, Teichmann SA, Haniffa M, Watt FM, Lynch MD. Multiscale spatial mapping of cell populations across anatomical sites in healthy human skin and basal cell carcinoma. Proc Natl Acad Sci U S A 2024; 121:e2313326120. [PMID: 38165934 PMCID: PMC10786309 DOI: 10.1073/pnas.2313326120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 11/13/2023] [Indexed: 01/04/2024] Open
Abstract
Our understanding of how human skin cells differ according to anatomical site and tumour formation is limited. To address this, we have created a multiscale spatial atlas of healthy skin and basal cell carcinoma (BCC), incorporating in vivo optical coherence tomography, single-cell RNA sequencing, spatial global transcriptional profiling, and in situ sequencing. Computational spatial deconvolution and projection revealed the localisation of distinct cell populations to specific tissue contexts. Although cell populations were conserved between healthy anatomical sites and in BCC, mesenchymal cell populations including fibroblasts and pericytes retained signatures of developmental origin. Spatial profiling and in silico lineage tracing support a hair follicle origin for BCC and demonstrate that cancer-associated fibroblasts are an expansion of a POSTN+ subpopulation associated with hair follicles in healthy skin. RGS5+ pericytes are also expanded in BCC suggesting a role in vascular remodelling. We propose that the identity of mesenchymal cell populations is regulated by signals emanating from adjacent structures and that these signals are repurposed to promote the expansion of skin cancer stroma. The resource we have created is publicly available in an interactive format for the research community.
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Affiliation(s)
- Clarisse Ganier
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, LondonSE1 9RT, United Kingdom
| | - Pavel Mazin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CambridgeCB10 1SA, United Kingdom
| | - Gabriel Herrera-Oropeza
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, LondonSE1 1UL, United Kingdom
| | - Xinyi Du-Harpur
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, LondonSE1 9RT, United Kingdom
- The Francis Crick Institute, LondonNW1 1AT, United Kingdom
| | - Matthew Blakeley
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, LondonSE1 9RT, United Kingdom
| | - Jeyrroy Gabriel
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, LondonSE1 9RT, United Kingdom
| | - Alexander V. Predeus
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CambridgeCB10 1SA, United Kingdom
| | - Batuhan Cakir
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CambridgeCB10 1SA, United Kingdom
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CambridgeCB10 1SA, United Kingdom
| | - Nasrat Harun
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, LondonSE1 9RT, United Kingdom
| | - Jean-Francois Darrigrand
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, LondonSE1 9RT, United Kingdom
| | - Alexander Haiser
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, LondonSE1 9RT, United Kingdom
| | - Saranya Wyles
- Department of Dermatology, Mayo Clinic, Rochester, MN55905
| | - Tanya Shaw
- Centre for Inflammation Biology and Cancer Immunology, King’s College London, LondonSE1 1UL, United Kingdom
| | - Sarah A. Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CambridgeCB10 1SA, United Kingdom
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, CambridgeCB3 0HE, United Kingdom
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CambridgeCB10 1SA, United Kingdom
- Biosciences Institute, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
- National Institute for Health Research Newcastle Biomedical Research Centre, Newcastle Hospitals National Health Service Foundation Trust, Newcastle upon TyneNE1 4LP, United Kingdom
| | - Fiona M. Watt
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, LondonSE1 9RT, United Kingdom
- Directors’ Unit, European Molecular Biology Laboratory, Heidelberg69117, Germany
| | - Magnus D. Lynch
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, LondonSE1 9RT, United Kingdom
- St. John’s Institute of Dermatology, King’s College London, Guy’s Hospital, LondonSE1 9RT, United Kingdom
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13
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Zou DD, Sun YZ, Li XJ, Wu WJ, Xu D, He YT, Qi J, Tu Y, Tang Y, Tu YH, Wang XL, Li X, Lu FY, Huang L, Long H, He L, Li X. Single-cell sequencing highlights heterogeneity and malignant progression in actinic keratosis and cutaneous squamous cell carcinoma. eLife 2023; 12:e85270. [PMID: 38099574 PMCID: PMC10783873 DOI: 10.7554/elife.85270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
Cutaneous squamous cell carcinoma (cSCC) is the second most frequent of the keratinocyte-derived malignancies with actinic keratosis (AK) as a precancerous lesion. To comprehensively delineate the underlying mechanisms for the whole progression from normal skin to AK to invasive cSCC, we performed single-cell RNA sequencing (scRNA-seq) to acquire the transcriptomes of 138,982 cells from 13 samples of six patients including AK, squamous cell carcinoma in situ (SCCIS), cSCC, and their matched normal tissues, covering comprehensive clinical courses of cSCC. We identified diverse cell types, including important subtypes with different gene expression profiles and functions in major keratinocytes. In SCCIS, we discovered the malignant subtypes of basal cells with differential proliferative and migration potential. Differentially expressed genes (DEGs) analysis screened out multiple key driver genes including transcription factors along AK to cSCC progression. Immunohistochemistry (IHC)/immunofluorescence (IF) experiments and single-cell ATAC sequencing (scATAC-seq) data verified the expression changes of these genes. The functional experiments confirmed the important roles of these genes in regulating cell proliferation, apoptosis, migration, and invasion in cSCC tumor. Furthermore, we comprehensively described the tumor microenvironment (TME) landscape and potential keratinocyte-TME crosstalk in cSCC providing theoretical basis for immunotherapy. Together, our findings provide a valuable resource for deciphering the progression from AK to cSCC and identifying potential targets for anticancer treatment of cSCC.
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Affiliation(s)
- Dan-Dan Zou
- Department of Dermatology, First Affiliated Hospital of Kunming Medical UniversityYunnanChina
- Department of Dermatology, The Affiliated Hospital of Kunming University of Science and Technology, The First People's Hospital of Yunnan Province, KunmingYunnanChina
| | - Ya-Zhou Sun
- Clinical Big Data Research Center, The Seventh Affiliated Hospital of Sun Yat-sen UniversityShenzhen, GuangdongChina
- School of Medical, Shenzhen Campus of Sun Yat-sen UniversityShenzhen, GuangdongChina
| | - Xin-Jie Li
- School of Medical, Shenzhen Campus of Sun Yat-sen UniversityShenzhen, GuangdongChina
| | - Wen-Juan Wu
- Department of Dermatology, First Affiliated Hospital of Kunming Medical UniversityYunnanChina
| | - Dan Xu
- Department of Dermatology, First Affiliated Hospital of Kunming Medical UniversityYunnanChina
| | - Yu-Tong He
- School of Medical, Shenzhen Campus of Sun Yat-sen UniversityShenzhen, GuangdongChina
| | - Jue Qi
- Department of Dermatology, First Affiliated Hospital of Kunming Medical UniversityYunnanChina
| | - Ying Tu
- Department of Dermatology, First Affiliated Hospital of Kunming Medical UniversityYunnanChina
| | - Yang Tang
- Department of Dermatology, First Affiliated Hospital of Kunming Medical UniversityYunnanChina
| | - Yun-Hua Tu
- Department of Dermatology, First Affiliated Hospital of Kunming Medical UniversityYunnanChina
| | - Xiao-Li Wang
- Department of Dermatology, Changzheng Hospital, Naval Medical UniversityShanghaiChina
| | - Xing Li
- Department of Dermatology, People's Hospital of Chuxiong Yi Autonomous Prefecture, ChuxiongYunnanChina
| | - Feng-Yan Lu
- Department of Dermatology, Qujing Affiliated Hospital of Kunming Medical University, The First People’s Hospital of QujingYunnanChina
| | - Ling Huang
- Department of Dermatology, First Affiliated Hospital of Dali University, DaliYunnanChina
| | - Heng Long
- Wenshan Zhuang and Miao Autonomous Prefecture Dermatology Clinic, Wenshan Zhuang and Miao Autonomous Prefecture Specialist Hospital of Dermatology, WenshanYunnanChina
| | - Li He
- Department of Dermatology, First Affiliated Hospital of Kunming Medical UniversityYunnanChina
| | - Xin Li
- School of Medical, Shenzhen Campus of Sun Yat-sen UniversityShenzhen, GuangdongChina
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen UniversityGuangdongChina
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14
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Jin L, Chen Y, Muzaffar S, Li C, Mier-Aguilar CA, Khan J, Kashyap MP, Liu S, Srivastava R, Deshane JS, Townes TM, Elewski BE, Elmets CA, Crossman DK, Raman C, Athar M. Epigenetic switch reshapes epithelial progenitor cell signatures and drives inflammatory pathogenesis in hidradenitis suppurativa. Proc Natl Acad Sci U S A 2023; 120:e2315096120. [PMID: 38011564 PMCID: PMC10710069 DOI: 10.1073/pnas.2315096120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/25/2023] [Indexed: 11/29/2023] Open
Abstract
Hidradenitis suppurativa (HS) is a complex inflammatory skin disease with undefined mechanistic underpinnings. Here, we investigated HS epithelial cells and demonstrated that HS basal progenitors modulate their lineage restriction and give rise to pathogenic keratinocyte clones, resulting in epidermal hyperproliferation and dysregulated inflammation in HS. When comparing to healthy epithelial stem/progenitor cells, in HS, we identified changes in gene signatures that revolve around the mitotic cell cycle, DNA damage response and repair, as well as cell-cell adhesion and chromatin remodeling. By reconstructing cell differentiation trajectory and CellChat modeling, we identified a keratinocyte population specific to HS. This population is marked by S100A7/8/9 and KRT6 family members, triggering IL1, IL10, and complement inflammatory cascades. These signals, along with HS-specific proinflammatory cytokines and chemokines, contribute to the recruitment of certain immune cells during the disease progression. Furthermore, we revealed a previously uncharacterized role of S100A8 in regulating the local chromatin environment of target loci in HS keratinocytes. Through the integration of genomic and epigenomic datasets, we identified genome-wide chromatin rewiring alongside the switch of transcription factors (TFs), which mediated HS transcriptional profiles. Importantly, we identified numerous clinically relevant inflammatory enhancers and their coordinated TFs in HS basal CD49fhigh cells. The disruption of the S100A enhancer using the CRISPR/Cas9-mediated approach or the pharmacological inhibition of the interferon regulatory transcription factor 3 (IRF3) efficiently reduced the production of HS-associated inflammatory regulators. Our study not only uncovers the plasticity of epidermal progenitor cells in HS but also elucidates the epigenetic mechanisms underlying HS pathogenesis.
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Affiliation(s)
- Lin Jin
- Center for Epigenomics and Translational Research in Inflammatory Skin Diseases, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
- Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
| | - Yunjia Chen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL35294
| | - Suhail Muzaffar
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
- Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
| | - Chao Li
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL35294
| | - Carlos A. Mier-Aguilar
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
| | - Jasim Khan
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
- Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
| | - Mahendra P. Kashyap
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
- Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
| | - Shanrun Liu
- Institutional Research Core Program, Flow Cytometry and Singe Cell Core, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
| | - Ritesh Srivastava
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
- Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
| | - Jessy S. Deshane
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL35294
| | - Tim M. Townes
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL35294
| | - Boni E. Elewski
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
| | - Craig A. Elmets
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
| | - David K. Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL35294
| | - Chander Raman
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
| | - Mohammad Athar
- Center for Epigenomics and Translational Research in Inflammatory Skin Diseases, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
- Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
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15
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Tahara U, Matsui T, Atsugi T, Fukuda K, Terooatea TW, Minoda A, Kubo A, Amagai M. Keratinocytes of the Upper Epidermis and Isthmus of Hair Follicles Express Hemoglobin mRNA and Protein. J Invest Dermatol 2023; 143:2346-2355.e10. [PMID: 37981423 DOI: 10.1016/j.jid.2023.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 11/21/2023]
Abstract
The epidermis, the keratinized stratified squamous epithelium surrounding the body surface, offers a valuable framework to investigate how terrestrial animals overcome environmental stresses. However, the mechanisms underlying epidermal barrier function remain nebulous. In this study, we examined genes highly expressed in the human and mouse upper epidermis, the outer frontier that induces various barrier-related genes. Transcriptome analysis revealed that the messenger RNA level of hemoglobin α (HBA), an oxygen carrier in erythroid cells, was enriched in the upper epidermis compared with that in the whole epidermis. Immunostaining analysis confirmed HBA protein expression in human and mouse keratinocytes (KCs) of the stratum spinosum and stratum granulosum. HBA was also expressed in hair follicle KCs in the isthmus region; its expression levels were more prominent than those in interfollicular KCs. HBA expression was not observed in noncutaneous keratinized stratified squamous epithelia of mice, for example, the vagina, esophagus, and forestomach. HBA expression was upregulated in human epidermal KC cultures after UV irradiation, a major cause of skin-specific oxidative stress. Furthermore, HBA knockdown increased UV-induced production of ROS in primary KCs. Our findings suggest that epidermal HBA expression is induced by oxidative stress and acts as an antioxidant, contributing to skin barrier function.
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Affiliation(s)
- Umi Tahara
- Laboratory for Skin Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Takeshi Matsui
- Laboratory for Skin Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Department of Dermatology, Keio University School of Medicine, Tokyo, Japan; Laboratory for Evolutionary Cell Biology of the Skin, School of Bioscience and Biotechnology, Tokyo University of Technology, Hachioji, Japan
| | - Toru Atsugi
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Keitaro Fukuda
- Laboratory for Skin Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Tommy W Terooatea
- Laboratory for Cellular Epigenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Aki Minoda
- Laboratory for Cellular Epigenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Department of Cell Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Akiharu Kubo
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan; Division of Dermatology, Department of Internal Related, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Masayuki Amagai
- Laboratory for Skin Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Department of Dermatology, Keio University School of Medicine, Tokyo, Japan.
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16
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Negri VA, Louis B, Zijl S, Ganier C, Philippeos C, Ali S, Reynolds G, Haniffa M, Watt FM. Single-cell RNA sequencing of human epidermis identifies Lunatic fringe as a novel regulator of the stem cell compartment. Stem Cell Reports 2023; 18:2047-2055. [PMID: 37832539 PMCID: PMC10679657 DOI: 10.1016/j.stemcr.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 10/15/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) of human skin provides a tool for validating observations from in vitro experimental models. By analyzing a published dataset of healthy adult epidermis, we confirm that the basal epidermal layer is heterogeneous, and three subpopulations of non-dividing cells can be distinguished. We show that Delta-like ligand 1 (DLL1) is expressed in a subset of basal cells previously identified as stem cells in cultured human keratinocytes and map the distribution of other Notch ligands and receptors to specific epidermal cell compartments. Although DLL1 is expressed at low levels, it is expressed in the same cell state as the Notch regulator, Lunatic -fringe (LFNG, O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase). Overexpression of LFNG amplifies the effects of DLL1 in cultured keratinocytes, increasing proliferation and colony-forming ability. We conclude that using scRNA-seq resources from healthy human skin not only validates previous experimental data but allows formulation of testable new hypotheses.
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Affiliation(s)
- Victor Augusti Negri
- King's College London Centre for Stem Cells and Regenerative Medicine, Guy's Hospital, London, UK
| | - Blaise Louis
- King's College London Centre for Stem Cells and Regenerative Medicine, Guy's Hospital, London, UK
| | - Sebastiaan Zijl
- King's College London Centre for Stem Cells and Regenerative Medicine, Guy's Hospital, London, UK
| | - Clarisse Ganier
- King's College London Centre for Stem Cells and Regenerative Medicine, Guy's Hospital, London, UK
| | - Christina Philippeos
- King's College London Centre for Stem Cells and Regenerative Medicine, Guy's Hospital, London, UK
| | - Shahnawaz Ali
- King's College London Centre for Stem Cells and Regenerative Medicine, Guy's Hospital, London, UK
| | - Gary Reynolds
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Fiona M Watt
- King's College London Centre for Stem Cells and Regenerative Medicine, Guy's Hospital, London, UK; Directors' Research Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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17
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Gniadecki R, Osman M, Hennesey D, O'Keefe S, Thomsen SF, Iyer A. Architecture of skin inflammation in psoriasis revealed by spatial transcriptomics. Clin Immunol 2023; 256:109771. [PMID: 37708923 DOI: 10.1016/j.clim.2023.109771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/24/2023] [Accepted: 09/10/2023] [Indexed: 09/16/2023]
Abstract
Psoriasis is a chronic inflammatory skin disease, thought to be predominantly mediated by TH17 cells. Significance of other inflammatory pathways and the innate immune system is not well understood and the spatial heterogeneity of inflammation in the skin has largely been overlooked. Our aim was to create a comprehensive map of skin inflammation in psoriasis, exploring the tissue patterning of inflammation. In situ whole transcriptome sequencing (spatial sequencing) was performed on lesional psoriatic skin in four patients with moderate-to-severe disease to quantify all expressed genes within a tissue section. Transcriptional analysis revealed three major inflammatory niches in psoriasis skin, each with distinct cytokine circuits and chemokines: the hyperplastic epidermis, upper (papillary) dermis, and reticular dermis. Interestingly, key cytokines such as IL-23, IL-17 s, and TNFα were not notably present in the skin's transcriptomic signature. Unexpectedly, IL-32 showed strong expression in the dermis. Our findings underscore the complexity of psoriatic inflammation, highlighting its architectural heterogeneity and the roles of innate cytokines. Both IL-32 and IL-1 family cytokines appear to play critical roles in the dermal and epidermal inflammation, respectively, and may provide pharmacological targets to improve the control of the inflammatory process.
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Affiliation(s)
- Robert Gniadecki
- Division of Dermatology, Department of Medicine, University of Alberta, Canada.
| | - Mohammed Osman
- Division of Rheumatology, Department of Medicine, University of Alberta, Canada
| | - Dylan Hennesey
- Division of Dermatology, Department of Medicine, University of Alberta, Canada
| | - Sandra O'Keefe
- Division of Dermatology, Department of Medicine, University of Alberta, Canada
| | | | - Aishwarya Iyer
- Division of Dermatology, Department of Medicine, University of Alberta, Canada
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18
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Thrane K, Winge MCG, Wang H, Chen L, Guo MG, Andersson A, Abalo XM, Yang X, Kim DS, Longo SK, Soong BY, Meyers JM, Reynolds DL, McGeever A, Demircioglu D, Hasson D, Mirzazadeh R, Rubin AJ, Bae GH, Karkanias J, Rieger K, Lundeberg J, Ji AL. Single-Cell and Spatial Transcriptomic Analysis of Human Skin Delineates Intercellular Communication and Pathogenic Cells. J Invest Dermatol 2023; 143:2177-2192.e13. [PMID: 37142187 PMCID: PMC10592679 DOI: 10.1016/j.jid.2023.02.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 01/26/2023] [Accepted: 02/16/2023] [Indexed: 05/06/2023]
Abstract
Epidermal homeostasis is governed by a balance between keratinocyte proliferation and differentiation with contributions from cell-cell interactions, but conserved or divergent mechanisms governing this equilibrium across species and how an imbalance contributes to skin disease are largely undefined. To address these questions, human skin single-cell RNA sequencing and spatial transcriptomics data were integrated and compared with mouse skin data. Human skin cell-type annotation was improved using matched spatial transcriptomics data, highlighting the importance of spatial context in cell-type identity, and spatial transcriptomics refined cellular communication inference. In cross-species analyses, we identified a human spinous keratinocyte subpopulation that exhibited proliferative capacity and a heavy metal processing signature, which was absent in mouse and may account for species differences in epidermal thickness. This human subpopulation was expanded in psoriasis and zinc-deficiency dermatitis, attesting to disease relevance and suggesting a paradigm of subpopulation dysfunction as a hallmark of the disease. To assess additional potential subpopulation drivers of skin diseases, we performed cell-of-origin enrichment analysis within genodermatoses, nominating pathogenic cell subpopulations and their communication pathways, which highlighted multiple potential therapeutic targets. This integrated dataset is encompassed in a publicly available web resource to aid mechanistic and translational studies of normal and diseased skin.
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Affiliation(s)
- Kim Thrane
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
| | - Mårten C G Winge
- Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Hongyu Wang
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Black Family Stem Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA; School of Computer Science and Engineering, Northwestern Polytechnical University, Xi'an, China
| | - Larry Chen
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Black Family Stem Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Margaret G Guo
- Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA; Biomedical Informatics Program, Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California, USA
| | - Alma Andersson
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
| | - Xesús M Abalo
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
| | - Xue Yang
- Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Daniel S Kim
- Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA; Biomedical Informatics Program, Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California, USA
| | - Sophia K Longo
- Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Brian Y Soong
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Black Family Stem Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jordan M Meyers
- Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - David L Reynolds
- Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Aaron McGeever
- Chan Zuckerberg Biohub San Francisco, San Francisco, California, USA
| | - Deniz Demircioglu
- Bioinformatics for Next Generation Sequencing Core, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Dan Hasson
- Bioinformatics for Next Generation Sequencing Core, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Reza Mirzazadeh
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
| | - Adam J Rubin
- Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Gordon H Bae
- Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Jim Karkanias
- Chan Zuckerberg Biohub San Francisco, San Francisco, California, USA
| | - Kerri Rieger
- Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
| | - Andrew L Ji
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Black Family Stem Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
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19
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Gottschlich A, Thomas M, Grünmeier R, Lesch S, Rohrbacher L, Igl V, Briukhovetska D, Benmebarek MR, Vick B, Dede S, Müller K, Xu T, Dhoqina D, Märkl F, Robinson S, Sendelhofert A, Schulz H, Umut Ö, Kavaka V, Tsiverioti CA, Carlini E, Nandi S, Strzalkowski T, Lorenzini T, Stock S, Müller PJ, Dörr J, Seifert M, Cadilha BL, Brabenec R, Röder N, Rataj F, Nüesch M, Modemann F, Wellbrock J, Fiedler W, Kellner C, Beltrán E, Herold T, Paquet D, Jeremias I, von Baumgarten L, Endres S, Subklewe M, Marr C, Kobold S. Single-cell transcriptomic atlas-guided development of CAR-T cells for the treatment of acute myeloid leukemia. Nat Biotechnol 2023; 41:1618-1632. [PMID: 36914885 PMCID: PMC7615296 DOI: 10.1038/s41587-023-01684-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 01/20/2023] [Indexed: 03/16/2023]
Abstract
Chimeric antigen receptor T cells (CAR-T cells) have emerged as a powerful treatment option for individuals with B cell malignancies but have yet to achieve success in treating acute myeloid leukemia (AML) due to a lack of safe targets. Here we leveraged an atlas of publicly available RNA-sequencing data of over 500,000 single cells from 15 individuals with AML and tissue from 9 healthy individuals for prediction of target antigens that are expressed on malignant cells but lacking on healthy cells, including T cells. Aided by this high-resolution, single-cell expression approach, we computationally identify colony-stimulating factor 1 receptor and cluster of differentiation 86 as targets for CAR-T cell therapy in AML. Functional validation of these established CAR-T cells shows robust in vitro and in vivo efficacy in cell line- and human-derived AML models with minimal off-target toxicity toward relevant healthy human tissues. This provides a strong rationale for further clinical development.
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Affiliation(s)
- Adrian Gottschlich
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Moritz Thomas
- Institute of AI for Health, Helmholtz Munich, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Ruth Grünmeier
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Stefanie Lesch
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Lisa Rohrbacher
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- Laboratory for Translational Cancer Immunology, Gene Center, LMU Munich, Munich, Germany
| | - Veronika Igl
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Daria Briukhovetska
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Mohamed-Reda Benmebarek
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Binje Vick
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Munich, German Research Center for Environmental Health (HMGU), Munich, Germany
- Department of Pediatrics, University Hospital, LMU Munich, Munich, Germany
| | - Sertac Dede
- Department of Neurology, University Hospital, LMU Munich, Munich, Germany
| | - Katharina Müller
- Department of Neurology, University Hospital, LMU Munich, Munich, Germany
| | - Tao Xu
- Department of Neurology, University Hospital, LMU Munich, Munich, Germany
| | - Dario Dhoqina
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Florian Märkl
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Sophie Robinson
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | | | - Heiko Schulz
- Institute of Pathology, LMU Munich, Munich, Germany
| | - Öykü Umut
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Vladyslav Kavaka
- Institute of Clinical Neuroimmunology, University Hospital, LMU Munich, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Christina Angeliki Tsiverioti
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Emanuele Carlini
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Sayantan Nandi
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Thaddäus Strzalkowski
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Theo Lorenzini
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Sophia Stock
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Philipp Jie Müller
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Janina Dörr
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Matthias Seifert
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Bruno L Cadilha
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Ruben Brabenec
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- Institute of AI for Health, Helmholtz Munich, Neuherberg, Germany
| | - Natalie Röder
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Felicitas Rataj
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Manuel Nüesch
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Franziska Modemann
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald University Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf Hamburg, Hamburg, Germany
| | - Jasmin Wellbrock
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald University Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Walter Fiedler
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald University Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Kellner
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, LMU Munich, Munich, Germany
| | - Eduardo Beltrán
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Institute of Clinical Neuroimmunology, University Hospital, LMU Munich, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Dominik Paquet
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Munich, German Research Center for Environmental Health (HMGU), Munich, Germany
- Department of Pediatrics, University Hospital, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Louisa von Baumgarten
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
- Department of Neurosurgery, LMU Munich, Munich, Germany
| | - Stefan Endres
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
- Einheit für Klinische Pharmakologie (EKLiP), Helmholtz Munich, Research Center for Environmental Health (HMGU), Neuherberg, Germany
| | - Marion Subklewe
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- Laboratory for Translational Cancer Immunology, Gene Center, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Carsten Marr
- Institute of AI for Health, Helmholtz Munich, Neuherberg, Germany
| | - Sebastian Kobold
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany.
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.
- Einheit für Klinische Pharmakologie (EKLiP), Helmholtz Munich, Research Center for Environmental Health (HMGU), Neuherberg, Germany.
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20
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Li J, Xia Y, Kong S, Yang K, Chen H, Zhang Y, Liu D, Chen L, Sun X. Single-cell RNA-seq reveals actinic keratosis-specific keratinocyte subgroups and their crosstalk with secretory-papillary fibroblasts. J Eur Acad Dermatol Venereol 2023; 37:2273-2283. [PMID: 37357444 DOI: 10.1111/jdv.19289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/09/2023] [Indexed: 06/27/2023]
Abstract
BACKGROUND AND AIM Actinic keratosis (AK) represents an intraepidermal malignant neoplasm with the proliferation of atypical keratinocytes. AK lesions are regarded as early in situ squamous cell carcinomas (SCCs) having the potential to progress into invasive SCC (iSCC) and metastasize, causing death. This study aimed to investigate the heterogeneity of keratinocytes and how this heterogeneity promoted AK development and progression. METHODS We employed single-cell RNA sequencing (scRNA-seq) to examine the heterogeneity of keratinocytes and dermal fibroblast clusters in AKs and adjacent normal skins. Cell clustering, pseudotime trajectory construction, gene ontology enrichment analysis, transcription factor network analysis, and cell-cell communication were used to investigate the heterogeneity of keratinocytes in AK. The cellular identity and function were verified by immunohistochemical and immunofluorescence staining. RESULTS Using scRNA-seq, we revealed 13 keratinocyte subgroups (clusters 0-12) in AK tissues and characterized 2 AK-specific clusters. Cluster 9 displayed high levels of IL1R2 and WFDC2, and cluster 11 showed high levels of FADS2 and FASN. The percentages of cells in these two clusters significantly increased in AK compared with normal tissues. The existence and spatial localization of AK-specific IL1R2+WFDC2+ cluster were verified by immunohistochemical and immunofluorescence staining. Functional studies indicated that the genes identified in the IL1R2+WFDC2+ cluster were crucial for epithelial cell proliferation, migration, and angiogenesis. Further immunofluorescent staining revealed the interactions between AK-specific keratinocytes and secretory-papillary fibroblasts mainly through ANGPTL4-ITGA5 signalling pathway rarely seen in normal tissues. CONCLUSION The findings of this study might help better understand AK pathogenesis.
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Affiliation(s)
- Jun Li
- Department of Dermatology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Ying Xia
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Shumin Kong
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Kun Yang
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Hui Chen
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Yong Zhang
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Dongxian Liu
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Lan Chen
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Xiaoyan Sun
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
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21
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Fiskin E, Eraslan G, Alora-Palli MB, Leyva-Castillo JM, Kim S, Choe H, Lareau CA, Lau H, Finan EP, Teixeira-Soldano I, LaBere B, Chu A, Woods B, Chou J, Slyper M, Waldman J, Islam S, Schneider L, Phipatanakul W, Platt C, Rozenblatt-Rosen O, Delorey TM, Deguine J, Smith GP, Geha R, Regev A, Xavier R. Multi-modal skin atlas identifies a multicellular immune-stromal community associated with altered cornification and specific T cell expansion in atopic dermatitis. bioRxiv 2023:2023.10.29.563503. [PMID: 37961084 PMCID: PMC10634929 DOI: 10.1101/2023.10.29.563503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
In healthy skin, a cutaneous immune system maintains the balance between tolerance towards innocuous environmental antigens and immune responses against pathological agents. In atopic dermatitis (AD), barrier and immune dysfunction result in chronic tissue inflammation. Our understanding of the skin tissue ecosystem in AD remains incomplete with regard to the hallmarks of pathological barrier formation, and cellular state and clonal composition of disease-promoting cells. Here, we generated a multi-modal cell census of 310,691 cells spanning 86 cell subsets from whole skin tissue of 19 adult individuals, including non-lesional and lesional skin from 11 AD patients, and integrated it with 396,321 cells from four studies into a comprehensive human skin cell atlas in health and disease. Reconstruction of human keratinocyte differentiation from basal to cornified layers revealed a disrupted cornification trajectory in AD. This disrupted epithelial differentiation was associated with signals from a unique immune and stromal multicellular community comprised of MMP12 + dendritic cells (DCs), mature migratory DCs, cycling ILCs, NK cells, inflammatory CCL19 + IL4I1 + fibroblasts, and clonally expanded IL13 + IL22 + IL26 + T cells with overlapping type 2 and type 17 characteristics. Cell subsets within this immune and stromal multicellular community were connected by multiple inter-cellular positive feedback loops predicted to impact community assembly and maintenance. AD GWAS gene expression was enriched both in disrupted cornified keratinocytes and in cell subsets from the lesional immune and stromal multicellular community including IL13 + IL22 + IL26 + T cells and ILCs, suggesting that epithelial or immune dysfunction in the context of the observed cellular communication network can initiate and then converge towards AD. Our work highlights specific, disease-associated cell subsets and interactions as potential targets in progression and resolution of chronic inflammation.
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22
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Fassett MS, Braz JM, Castellanos CA, Salvatierra JJ, Sadeghi M, Yu X, Schroeder AW, Caston J, Munoz-Sandoval P, Roy S, Lazarevsky S, Mar DJ, Zhou CJ, Shin JS, Basbaum AI, Ansel KM. IL-31-dependent neurogenic inflammation restrains cutaneous type 2 immune response in allergic dermatitis. Sci Immunol 2023; 8:eabi6887. [PMID: 37831760 PMCID: PMC10890830 DOI: 10.1126/sciimmunol.abi6887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/18/2023] [Indexed: 10/15/2023]
Abstract
Despite robust literature associating IL-31 with pruritic inflammatory skin diseases, its influence on cutaneous inflammation and the interplay between inflammatory and neurosensory pathways remain unmapped. Here, we examined the consequences of disrupting Il31 and its receptor Il31ra in a mouse model of house dust mite (HDM)-induced allergic dermatitis. Il31-deficient mice displayed a deficit in HDM dermatitis-associated scratching, consistent with its well-established role as a pruritogen. In contrast, Il31 deficiency increased the number and proportion of cutaneous type 2 cytokine-producing CD4+ T cells and serum IgE in response to HDM. Furthermore, Il4ra+ monocytes and macrophages capable of fueling a feedforward type 2 inflammatory loop were selectively enriched in Il31ra-deficient HDM dermatitis skin. Thus, IL-31 is not strictly a proinflammatory cytokine but rather an immunoregulatory factor that limits the magnitude of type 2 inflammatory responses in skin. Our data support a model wherein IL-31 activation of IL31RA+ pruritoceptors triggers release of calcitonin gene-related protein (CGRP), which can mediate neurogenic inflammation, inhibit CD4+ T cell proliferation, and reduce T cell production of the type 2 cytokine IL-13. Together, these results illustrate a previously unrecognized neuroimmune pathway that constrains type 2 tissue inflammation in the setting of chronic cutaneous allergen exposure and may explain paradoxical dermatitis flares in atopic patients treated with anti-IL31RA therapy.
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Affiliation(s)
- Marlys S Fassett
- Department of Dermatology, University of California, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center (SABRe), San Francisco, CA, USA
| | - Joao M Braz
- Department of Anatomy, University of California, San Francisco, CA, USA
| | - Carlos A Castellanos
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center (SABRe), San Francisco, CA, USA
| | | | - Mahsa Sadeghi
- Department of Anatomy, University of California, San Francisco, CA, USA
| | - Xiaobing Yu
- Department of Anatomy, University of California, San Francisco, CA, USA
- Department of Anesthesiology, University of California, San Francisco, CA, USA
| | | | - Jaela Caston
- Department of Dermatology, University of California, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Priscila Munoz-Sandoval
- Department of Dermatology, University of California, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center (SABRe), San Francisco, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA 94143, USA
| | - Suparna Roy
- Department of Dermatology, University of California, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center (SABRe), San Francisco, CA, USA
| | - Steven Lazarevsky
- Department of Dermatology, University of California, San Francisco, CA, USA
| | - Darryl J Mar
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Connie J Zhou
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Jeoung-Sook Shin
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center (SABRe), San Francisco, CA, USA
| | - Allan I Basbaum
- Department of Anatomy, University of California, San Francisco, CA, USA
| | - K Mark Ansel
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center (SABRe), San Francisco, CA, USA
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23
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Xu Y, Cohen E, Johnson CN, Parent CA, Coulombe PA. Keratin 17- and PKCα-dependent transient amplification of neutrophil influx after repeated stress to the skin. bioRxiv 2023:2023.10.11.561954. [PMID: 37873256 PMCID: PMC10592713 DOI: 10.1101/2023.10.11.561954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Neutrophils contribute to the pathogenesis of chronic inflammatory skin diseases. Little is known about the source and identity of the signals mediating their recruitment in inflamed skin. We used the phorbol ester TPA and UVB, alone or in combination, to induce sterile inflammation in mouse skin and assess whether keratinocyte-derived signals impact neutrophil recruitment. A single TPA treatment results in a neutrophil influx in the dermis that peaks at 12h and resolves within 24h. A second TPA treatment or a UVB challenge, when applied at 24h but not 48h later, accelerates, amplifies, and prolongs neutrophil infiltration. This transient amplification response (TAR) is mediated by local signals in inflamed skin, can be recapitulated in ex vivo culture, and involves the K17-dependent sustainment of protein kinase Cα (PKCα) activity and release of neutrophil chemoattractants by stressed keratinocytes. We show that K17 binds RACK1, a scaffold essential for PKCα activity. Finally, analyses of RNAseq data reveal the presence of a transcriptomic signature consistent with TAR and PKCα activation in chronic inflammatory skin diseases. These findings uncover a novel, transient, and keratin-dependent mechanism that amplifies neutrophil recruitment to the skin under stress, with direct implications for inflammatory skin disorders.
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Gaydosik AM, Stonesifer CJ, Tabib T, Lafyatis R, Geskin LJ, Fuschiotti P. The mycosis fungoides cutaneous microenvironment shapes dysfunctional cell trafficking, antitumor immunity, matrix interactions, and angiogenesis. JCI Insight 2023; 8:e170015. [PMID: 37669110 PMCID: PMC10619438 DOI: 10.1172/jci.insight.170015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/31/2023] [Indexed: 09/07/2023] Open
Abstract
Malignant T lymphocyte proliferation in mycosis fungoides (MF) is largely restricted to the skin, implying that malignant cells are dependent on their specific cutaneous tumor microenvironment (TME), including interactions with non-malignant immune and stromal cells, cytokines, and other immunomodulatory factors. To explore these interactions, we performed a comprehensive transcriptome analysis of the TME in advanced-stage MF skin tumors by single-cell RNA sequencing. Our analysis identified cell-type compositions, cellular functions, and cell-to-cell interactions in the MF TME that were distinct from those from healthy skin and benign dermatoses. While patterns of gene expression were common among patient samples, high transcriptional diversity was also observed in immune and stromal cells, with dynamic interactions and crosstalk between these cells and malignant T lymphocytes. This heterogeneity mapped to processes such as cell trafficking, matrix interactions, angiogenesis, immune functions, and metabolism that affect cancer cell growth, migration, and invasion, as well as antitumor immunity. By comprehensively characterizing the transcriptomes of immune and stromal cells within the cutaneous microenvironment of individual MF tumors, we have identified patterns of dysfunction common to all tumors that represent a resource for identifying candidates with therapeutic potential as well as patient-specific heterogeneity that has important implications for personalized disease management.
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Affiliation(s)
- Alyxzandria M. Gaydosik
- Department of Medicine, Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | | | - Tracy Tabib
- Department of Medicine, Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Robert Lafyatis
- Department of Medicine, Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | | | - Patrizia Fuschiotti
- Department of Medicine, Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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25
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Jackson R, Rajadhyaksha EV, Loeffler RS, Flores CE, Van Doorslaer K. Characterization of 3D organotypic epithelial tissues reveals tonsil-specific differences in tonic interferon signaling. PLoS One 2023; 18:e0292368. [PMID: 37792852 PMCID: PMC10550192 DOI: 10.1371/journal.pone.0292368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023] Open
Abstract
Three-dimensional (3D) culturing techniques can recapitulate the stratified nature of multicellular epithelial tissues. Organotypic 3D epithelial tissue culture methods have several applications, including the study of tissue development and function, drug discovery and toxicity testing, host-pathogen interactions, and the development of tissue-engineered constructs for use in regenerative medicine. We grew 3D organotypic epithelial tissues from foreskin, cervix, and tonsil-derived primary cells and characterized the transcriptome of these in vitro tissue equivalents. Using the same 3D culturing method, all three tissues yielded stratified squamous epithelium, validated histologically using basal and superficial epithelial cell markers. The goal of this study was to use RNA-seq to compare gene expression patterns in these three types of epithelial tissues to gain a better understanding of the molecular mechanisms underlying their function and identify potential therapeutic targets for various diseases. Functional profiling by over-representation and gene set enrichment analysis revealed tissue-specific differences: i.e., cutaneous homeostasis and lipid metabolism in foreskin, extracellular matrix remodeling in cervix, and baseline innate immune differences in tonsil. Specifically, tonsillar epithelia may play an active role in shaping the immune microenvironment of the tonsil balancing inflammation and immune responses in the face of constant exposure to microbial insults. Overall, these data serve as a resource, with gene sets made available for the research community to explore, and as a foundation for understanding the epithelial heterogeneity and how it may impact their in vitro use. An online resource is available to investigate these data (https://viz.datascience.arizona.edu/3DEpiEx/).
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Affiliation(s)
- Robert Jackson
- School of Animal and Comparative Biomedical Sciences, College of Agriculture and Life Sciences, University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
| | - Esha V. Rajadhyaksha
- College of Medicine and College of Science, University of Arizona, Tucson, Arizona, United States of America
| | - Reid S. Loeffler
- Biosystems Engineering, College of Agriculture and Life Sciences, College of Engineering, University of Arizona, Tucson, Arizona, United States of America
| | - Caitlyn E. Flores
- School of Animal and Comparative Biomedical Sciences, College of Agriculture and Life Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, College of Agriculture and Life Sciences, University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
- Department of Immunobiology, Cancer Biology Graduate Interdisciplinary Program, Genetics Graduate Interdisciplinary Program, and University of Arizona Cancer Center, University of Arizona, Tucson, Arizona, United States of America
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26
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Zhang B, Zhu G, Liu J, Zhang C, Yao K, Huang X, Cen X, Zhao Z. Single-cell transcriptional profiling reveals immunomodulatory properties of stromal and epithelial cells in periodontal immune milieu with diabetes in rats. Int Immunopharmacol 2023; 123:110715. [PMID: 37562294 DOI: 10.1016/j.intimp.2023.110715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/01/2023] [Accepted: 07/24/2023] [Indexed: 08/12/2023]
Abstract
Periodontitis is the sixth major complication of diabetes. Gingiva, as an important component of periodontal tissues, serves as the first defense barrier against infectious stimuli. However, relatively little is known about cellular heterogeneity and cell-specific changes in gingiva in response to diabetes-associated periodontitis. To characterize molecular changes linking diabetes with periodontitis, we profiled single-cell transcriptome analyses of a total of 45,259 cells from rat gingiva with periodontitis under normoglycemic and diabetic condition. The single-cell profiling revealed that stromal and epithelial cells of gingiva contained inflammation-related subclusters enriched in functions of immune cell recruitment. Compared to normoglycemic condition, diabetes led to a reduction in epithelial basal cells, fibroblasts and smooth muscle cells in gingiva with periodontitis. Analysis of differentially expressed genes indicated that stromal and epithelial populations were reprogrammed towards pro-inflammatory phenotypes promoting immune cell recruitment in diabetes-related periodontitis. In aspect of immune cells, diabetes prominently enhanced neutrophil and M1 macrophage infiltration in periodontitis lesions. Cell-cell communications revealed enhanced crosstalk between stromal/epithelial cells and immune cells mediating by chemokine/chemokine receptor interplay in diabetes-associated periodontitis. Our findings deconvolved cellular heterogeneity of rat gingiva associated with periodontitis and diabetes, uncovered altered immune milieu caused by the disease, and revealed immunomodulatory functions of stromal and epithelial cells in gingival immune niche. The present study improves the understanding of the link between the diabetes and periodontitis and helps in formulating precise therapeutic strategies for diabetes-enhanced periodontitis.
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Affiliation(s)
- Bo Zhang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Guanyin Zhu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Junqi Liu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Chenghao Zhang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Ke Yao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Xinqi Huang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Xiao Cen
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Zhihe Zhao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China.
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27
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Shin S, Choi EJ, Moon SW, Lee SB, Chung YJ, Lee SH. Leprosy-specific subsets of macrophages and Schwann cells identified by single-cell RNA-sequencing. Pathol Res Pract 2023; 250:154821. [PMID: 37757621 DOI: 10.1016/j.prp.2023.154821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/10/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023]
Abstract
In Mycobacterium leprae (M. leprae)-infection, inflammatory cells' subsets and dynamics as well as the interactions with Schwann cells have remained elusive. We investigated individual cells in M. leprae-inoculated nude mice by single-cell RNA-sequencing (scRNA-seq). For macrophages, we dissected two M1-like subsets and five M2-like subsets, where lipid-associated signatures were pervasive in both M1-like and M2-like subsets. There were four macrophage trajectories showing: (i) pro-inflammatory (M1), (ii) lipid metabolism-related (M2), (iii) anti-inflammatory (M2), and (iv) interferon-stimulated gene-related (M2) fates. They displayed early divergence without ever rejoining along the paths, suggesting simultaneous or continuous stimuli for macrophage activation in leprosy. The scRNA-seq predicted Schwann cell-macrophage interactions (Notch1-Jag1, Plxnb1-Sema4d interactions). An immature Schwann cell subset showing Tfap2a expression was identified, indicating Schwann cell dedifferentiation in leprosy tissues. Expressions of Notch1, Jag1, Plxnb1, Sema4d, and Tfap2a were validated in mouse or human leprosy tissues by immunohistochemistry. We identified both pro-inflammatory and inflammation-resolution signatures, where lipid-associated signatures were pervasive to the macrophages, representing leprosy-specific macrophage states for prolonged and repeated episodes of inflammation and resolution. Our study identified refined molecular states and interactions of macrophages and Schwann cells, suggesting novel insights into the pathogenesis of unhealed inflammation with neuropathy and potential therapeutic targets for leprosy.
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Affiliation(s)
- Sun Shin
- Departments of Microbiology, College of Medicine, The Catholic University of Korea, Republic of Korea; Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Eun Ji Choi
- Departments of Pathology, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Seong Won Moon
- Departments of Pathology, College of Medicine, The Catholic University of Korea, Republic of Korea; Departments of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Seong-Beom Lee
- Institute of Hansen's Disease, College of Medicine, The Catholic University of Korea, Republic of Korea; Departments of Pathology, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Yeun-Jun Chung
- Departments of Microbiology, College of Medicine, The Catholic University of Korea, Republic of Korea; Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Republic of Korea; Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Republic of Korea.
| | - Sug Hyung Lee
- Departments of Pathology, College of Medicine, The Catholic University of Korea, Republic of Korea; Departments of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Republic of Korea; Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Republic of Korea.
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28
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Gao Y, Na M, Yao X, Li C, Li L, Yang G, Li Y, Hu Y. Integrative single-cell transcriptomic investigation unveils long non-coding RNAs associated with localized cellular inflammation in psoriasis. Front Immunol 2023; 14:1265517. [PMID: 37822943 PMCID: PMC10562854 DOI: 10.3389/fimmu.2023.1265517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/11/2023] [Indexed: 10/13/2023] Open
Abstract
Psoriasis is a complex, chronic autoimmune disorder predominantly affecting the skin. Accumulating evidence underscores the critical role of localized cellular inflammation in the development and persistence of psoriatic skin lesions, involving cell types such as keratinocytes, mesenchymal cells, and Schwann cells. However, the underlying mechanisms remain largely unexplored. Long non-coding RNAs (lncRNAs), known to regulate gene expression across various cellular processes, have been particularly implicated in immune regulation. We utilized our neural-network learning pipeline to integrate 106,675 cells from healthy human skin and 79,887 cells from psoriatic human skin. This formed the most extensive cell transcriptomic atlas of human psoriatic skin to date. The robustness of our reclassified cell-types, representing full-layer zonation in human skin, was affirmed through neural-network learning-based cross-validation. We then developed a publicly available website to present this integrated dataset. We carried out analysis for differentially expressed lncRNAs, co-regulated gene patterns, and GO-bioprocess enrichment, enabling us to pinpoint lncRNAs that modulate localized cellular inflammation in psoriasis at the single-cell level. Subsequent experimental validation with skin cell lines and primary cells from psoriatic skin confirmed these lncRNAs' functional role in localized cellular inflammation. Our study provides a comprehensive cell transcriptomic atlas of full-layer human skin in both healthy and psoriatic conditions, unveiling a new regulatory mechanism that governs localized cellular inflammation in psoriasis and highlights the therapeutic potential of lncRNAs in this disease's management.
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Affiliation(s)
- Yuge Gao
- Department of Dermatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Mengxue Na
- Department of Dermatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xinyu Yao
- Department of Dermatology, Peking University First Hospital, Beijing, China
| | - Chao Li
- Department of Dermatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Li Li
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Guangyu Yang
- Department of Dermatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yuzhen Li
- Department of Dermatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yizhou Hu
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
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29
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Veniaminova NA, Jia YY, Hartigan AM, Huyge TJ, Tsai SY, Grachtchouk M, Nakagawa S, Dlugosz AA, Atwood SX, Wong SY. Distinct mechanisms for sebaceous gland self-renewal and regeneration provide durability in response to injury. Cell Rep 2023; 42:113121. [PMID: 37715952 PMCID: PMC10591672 DOI: 10.1016/j.celrep.2023.113121] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/01/2023] [Accepted: 08/25/2023] [Indexed: 09/18/2023] Open
Abstract
Sebaceous glands (SGs) release oils that protect our skin, but how these glands respond to injury has not been previously examined. Here, we report that SGs are largely self-renewed by dedicated stem cell pools during homeostasis. Using targeted single-cell RNA sequencing, we uncovered both direct and indirect paths by which resident SG progenitors ordinarily differentiate into sebocytes, including transit through a Krt5+PPARγ+ transitional basal cell state. Upon skin injury, however, SG progenitors depart their niche, reepithelialize the wound, and are replaced by hair-follicle-derived stem cells. Furthermore, following targeted genetic ablation of >99% of SGs from dorsal skin, these glands unexpectedly regenerate within weeks. This regenerative process is mediated by alternative stem cells originating from the hair follicle bulge, is dependent upon FGFR2 signaling, and can be accelerated by inducing hair growth. Altogether, our studies demonstrate that stem cell plasticity promotes SG durability following injury.
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Affiliation(s)
- Natalia A Veniaminova
- Department of Dermatology, Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yunlong Y Jia
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Adrien M Hartigan
- Department of Dermatology, Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas J Huyge
- Department of Dermatology, Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shih-Ying Tsai
- Department of Dermatology, Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marina Grachtchouk
- Department of Dermatology, Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seitaro Nakagawa
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Dermatology, Department of Cutaneous Immunology and Microbiology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Andrzej A Dlugosz
- Department of Dermatology, Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Scott X Atwood
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA.
| | - Sunny Y Wong
- Department of Dermatology, Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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30
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Luedke KP, Yoshino J, Yin C, Jiang N, Huang JM, Huynh K, Parrish JZ. Dendrite intercalation between epidermal cells tunes nociceptor sensitivity to mechanical stimuli in Drosophila larvae. bioRxiv 2023:2023.09.14.557275. [PMID: 37745567 PMCID: PMC10515945 DOI: 10.1101/2023.09.14.557275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
An animal's skin provides a first point of contact with the sensory environment, including noxious cues that elicit protective behavioral responses. Nociceptive somatosensory neurons densely innervate and intimately interact with epidermal cells to receive these cues, however the mechanisms by which epidermal interactions shape processing of noxious inputs is still poorly understood. Here, we identify a role for dendrite intercalation between epidermal cells in tuning sensitivity of Drosophila larvae to noxious mechanical stimuli. In wild-type larvae, dendrites of nociceptive class IV da neurons intercalate between epidermal cells at apodemes, which function as body wall muscle attachment sites, but not at other sites in the epidermis. From a genetic screen we identified miR-14 as a regulator of dendrite positioning in the epidermis: miR-14 is expressed broadly in the epidermis but not in apodemes, and miR-14 inactivation leads to excessive apical dendrite intercalation between epidermal cells. We found that miR-14 regulates expression and distribution of the epidermal Innexins ogre and Inx2 and that these epidermal gap junction proteins restrict epidermal dendrite intercalation. Finally, we found that altering the extent of epidermal dendrite intercalation had corresponding effects on nociception: increasing epidermal intercalation sensitized larvae to noxious mechanical inputs and increased mechanically evoked calcium responses in nociceptive neurons, whereas reducing epidermal dendrite intercalation had the opposite effects. Altogether, these studies identify epidermal dendrite intercalation as a mechanism for mechanical coupling of nociceptive neurons to the epidermis, with nociceptive sensitivity tuned by the extent of intercalation.
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Affiliation(s)
- Kory P. Luedke
- Department of Biology, University of Washington, Campus Box 351800, Seattle, WA 98195, USA
| | - Jiro Yoshino
- Department of Biology, University of Washington, Campus Box 351800, Seattle, WA 98195, USA
| | - Chang Yin
- Department of Biology, University of Washington, Campus Box 351800, Seattle, WA 98195, USA
| | - Nan Jiang
- Department of Biology, University of Washington, Campus Box 351800, Seattle, WA 98195, USA
| | - Jessica M. Huang
- Department of Biology, University of Washington, Campus Box 351800, Seattle, WA 98195, USA
| | - Kevin Huynh
- Department of Biology, University of Washington, Campus Box 351800, Seattle, WA 98195, USA
| | - Jay Z. Parrish
- Department of Biology, University of Washington, Campus Box 351800, Seattle, WA 98195, USA
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31
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Pacifico P, Coy-Dibley JS, Miller RJ, Menichella DM. Peripheral mechanisms of peripheral neuropathic pain. Front Mol Neurosci 2023; 16:1252442. [PMID: 37781093 PMCID: PMC10537945 DOI: 10.3389/fnmol.2023.1252442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/14/2023] [Indexed: 10/03/2023] Open
Abstract
Peripheral neuropathic pain (PNP), neuropathic pain that arises from a damage or disease affecting the peripheral nervous system, is associated with an extremely large disease burden, and there is an increasing and urgent need for new therapies for treating this disorder. In this review we have highlighted therapeutic targets that may be translated into disease modifying therapies for PNP associated with peripheral neuropathy. We have also discussed how genetic studies and novel technologies, such as optogenetics, chemogenetics and single-cell RNA-sequencing, have been increasingly successful in revealing novel mechanisms underlying PNP. Additionally, consideration of the role of non-neuronal cells and communication between the skin and sensory afferents is presented to highlight the potential use of drug treatment that could be applied topically, bypassing drug side effects. We conclude by discussing the current difficulties to the development of effective new therapies and, most importantly, how we might improve the translation of targets for peripheral neuropathic pain identified from studies in animal models to the clinic.
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Affiliation(s)
- Paola Pacifico
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - James S. Coy-Dibley
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Richard J. Miller
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Daniela M. Menichella
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
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32
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Tan F, Xuan Y, Long L, Yu Y, Zhang C, Liang P, Wang Y, Chen M, Wen J, Chen G. Single-cell analysis of human prepuce reveals dynamic changes in gene regulation and cellular communications. BMC Genomics 2023; 24:514. [PMID: 37658288 PMCID: PMC10474653 DOI: 10.1186/s12864-023-09615-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/22/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND The cellular and molecular dynamics of human prepuce are crucial for understanding its biological and physiological functions, as well as the prevention of related genital diseases. However, the cellular compositions and heterogeneity of human prepuce at single-cell resolution are still largely unknown. Here we systematically dissected the prepuce of children and adults based on the single-cell RNA-seq data of 90,770 qualified cells. RESULTS We identified 15 prepuce cell subtypes, including fibroblast, smooth muscle cells, T/natural killer cells, macrophages, vascular endothelial cells, and dendritic cells. The proportions of these cell types varied among different individuals as well as between children and adults. Moreover, we detected cell-type-specific gene regulatory networks (GRNs), which could contribute to the unique functions of related cell types. The GRNs were also highly dynamic between the prepuce cells of children and adults. Our cell-cell communication network analysis among different cell types revealed a set of child-specific (e.g., CD96, EPO, IFN-1, and WNT signaling pathways) and adult-specific (e.g., BMP10, NEGR, ncWNT, and NPR1 signaling pathways) signaling pathways. The variations of GRNs and cellular communications could be closely associated with prepuce development in children and prepuce maintenance in adults. CONCLUSIONS Collectively, we systematically analyzed the cellular variations and molecular changes of the human prepuce at single-cell resolution. Our results gained insights into the heterogeneity of prepuce cells and shed light on the underlying molecular mechanisms of prepuce development and maintenance.
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Affiliation(s)
- Fei Tan
- School of Medicine, Shanghai Skin Disease Hospital, Tongji University, Shanghai, 200443, China.
- Shanghai Skin Disease Clinical College, The Fifth Clinical Medical College, Anhui Medical University, Shanghai Skin Disease Hospital, Shanghai, 200443, China.
| | - Yuan Xuan
- Shanghai Skin Disease Clinical College, The Fifth Clinical Medical College, Anhui Medical University, Shanghai Skin Disease Hospital, Shanghai, 200443, China
| | - Lan Long
- Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen, 518172, China
| | - Yang Yu
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Chunhua Zhang
- Department of Dermatology, Shanghai Baoshan Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, 201999, China
| | - Pengchen Liang
- School of Microelectronics, Shanghai University, Shanghai, 201800, China
| | - Yaoqun Wang
- Shanghai Skin Disease Clinical College, The Fifth Clinical Medical College, Anhui Medical University, Shanghai Skin Disease Hospital, Shanghai, 200443, China
| | - Meiyu Chen
- Shanghai Skin Disease Clinical College, The Fifth Clinical Medical College, Anhui Medical University, Shanghai Skin Disease Hospital, Shanghai, 200443, China
| | - Jiling Wen
- Department of Urology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China.
| | - Geng Chen
- School of Medicine, Shanghai Skin Disease Hospital, Tongji University, Shanghai, 200443, China.
- Center for Bioinformatics and Computational Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
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33
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Almet AA, Yuan H, Annusver K, Ramos R, Liu Y, Wiedemann J, Sorkin DH, Landén NX, Sonkoly E, Haniffa M, Nie Q, Lichtenberger BM, Luecken MD, Andersen B, Tsoi LC, Watt FM, Gudjonsson JE, Plikus MV, Kasper M. A Roadmap for a Consensus Human Skin Cell Atlas and Single-Cell Data Standardization. J Invest Dermatol 2023; 143:1667-1677. [PMID: 37612031 PMCID: PMC10610458 DOI: 10.1016/j.jid.2023.03.1679] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 08/25/2023]
Abstract
Single-cell technologies have become essential to driving discovery in both basic and translational investigative dermatology. Despite the multitude of available datasets, a central reference atlas of normal human skin, which can serve as a reference resource for skin cell types, cell states, and their molecular signatures, is still lacking. For any such atlas to receive broad acceptance, participation by many investigators during atlas construction is an essential prerequisite. As part of the Human Cell Atlas project, we have assembled a Skin Biological Network to build a consensus Human Skin Cell Atlas and outline a roadmap toward that goal. We define the drivers of skin diversity to be considered when selecting sequencing datasets for the atlas and list practical hurdles during skin sampling that can result in data gaps and impede comprehensive representation and technical considerations for tissue processing and computational analysis, the accounting for which should minimize biases in cell type enrichments and exclusions and decrease batch effects. By outlining our goals for Atlas 1.0, we discuss how it will uncover new aspects of skin biology.
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Affiliation(s)
- Axel A Almet
- Department of Mathematics, University of California, Irvine, Irvine, California, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California, USA
| | - Hao Yuan
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Karl Annusver
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Raul Ramos
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California, USA; Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, California, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, USA
| | - Yingzi Liu
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, California, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, USA
| | - Julie Wiedemann
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, California, USA; Mathematical, Computational & Systems Biology, Department of Medicine, University of California, Irvine, Irvine, California, USA
| | - Dara H Sorkin
- Institute for Clinical & Translational Science, University of California, Irvine, Irvine, California, USA; Department of Medicine, School of Medicine, University of California, Irvine, Irvine, California, USA
| | - Ning Xu Landén
- Dermatology and Venereology Division, Department of Medicine, Solna, Karolinska Institute, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden; Ming Wai Lau Centre for Reparative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Enikö Sonkoly
- Dermatology and Venereology Division, Department of Medicine, Solna, Karolinska Institute, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden; Dermatology and Venereology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom; Biosciences Institute, Newcastle University, Newcastle Upon Tyne, United Kingdom; Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, United Kingdom
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, Irvine, California, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California, USA; Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, California, USA
| | - Beate M Lichtenberger
- Skin & Endothelium Research Division (SERD), Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Malte D Luecken
- Institute of Computational Biology, Helmholtz Munich, Neuherberg, Germany; Institute of Lung Health and Immunity, Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Bogi Andersen
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, USA; Department of Medicine, School of Medicine, University of California, Irvine, Irvine, California, USA; Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California, USA
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA; Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA; Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Fiona M Watt
- Centre for Gene Therapy & Regenerative Medicine, Faculty of Life Sciences & Medicine, School of Basic & Medical Biosciences, King's College London, London, United Kingdom; Directors' Research Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Maksim V Plikus
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California, USA; Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, California, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, USA.
| | - Maria Kasper
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden.
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Wang Q, Fu R, Li G, Xiong S, Zhu Y, Zhang H. Hedgehog receptors exert immune-surveillance roles in the epidermis across species. Cell Rep 2023; 42:112929. [PMID: 37527037 DOI: 10.1016/j.celrep.2023.112929] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 04/29/2023] [Accepted: 07/19/2023] [Indexed: 08/03/2023] Open
Abstract
Hedgehog signaling plays pivotal roles in the development and homeostasis of epithelial barrier tissues. However, whether and how Hedgehog signaling directly regulates innate immunity in epithelial cells remains unknown. By utilizing C. elegans epidermis as the model, we found that several Hedgehog receptors are involved in cell-autonomous regulation of the innate immune response in the epidermis. Particularly, loss of the Patched family receptor induces aberrant up-regulation of epidermal antimicrobial peptides in a STAT-dependent manner. External or internal insult to the epidermis triggers rapid rearrangement of Patched distribution along the plasma membrane, indicating that the Hedgehog (Hh) receptor is likely involved in recognition and defense against epidermal damage. Loss of PTCH1 function in primary human keratinocytes and intact mouse skin also results in STAT-dependent immune activation. These findings reveal an evolutionally conserved immune-surveillance function of Hedgehog receptors and an insult-sensing and response strategy of epithelial tissues.
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Affiliation(s)
- Qin Wang
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Rong Fu
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Gang Li
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Shaojie Xiong
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Yi Zhu
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Huimin Zhang
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Soochow University, Suzhou 215123, China.
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Pénzes Z, Alimohammadi S, Horváth D, Oláh A, Tóth BI, Bácsi A, Szöllősi AG. The dual role of cannabidiol on monocyte-derived dendritic cell differentiation and maturation. Front Immunol 2023; 14:1240800. [PMID: 37680639 PMCID: PMC10482398 DOI: 10.3389/fimmu.2023.1240800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/03/2023] [Indexed: 09/09/2023] Open
Abstract
Introduction Extracts and compounds isolated from hemp (Cannabis sativa) are increasingly gaining popularity in the treatment of a number of diseases, with topical formulations for dermatological conditions leading the way. Phytocannabinoids such as ( )-cannabidiol, ( )-cannabinol and ( )-Δ9-tetrahydrocannabivarin (CBD, CBN, and THCV, respectively), are present in variable amounts in the plant, and have been shown to have mostly anti-inflammatory effects both in vitro and in vivo, albeit dominantly in murine models. The role of phytocannabinoids in regulating responses of dendritic cells (DCs) remains unclear. Methods Our research aimed to investigate the effects of CBD, CBN, and THCV on human DCs differentiated from monocytes (moDCs). moDCs were treated with up to 10 μM of each phytocannabinoid, and their effects on viability, differentiation, and maturation were assessed both alone, and in conjunction with TLR agonists. The effects of CBD on cytokine production, T cell activation and polarization as well as the transcriptome of moDCs was also determined. Results Phytocannabinoids did not influence the viability of moDCs up to 10 μM, and only CBD had effects on maturational markers of moDCs, and neither compound influenced LPS-induced activation at 10 μM. Since only CBD had measurable effects on moDCs, in our subsequent experiments we tested the effect only of that pCB. On moDCs differentiated in the presence of CBD subsequent activation by LPS induced a markedly different, much more tolerogenic response. CBD-treated moDCs also produced significantly more interleukin (IL)-6, TNFα and, importantly, IL-10 in response to LPS, which shows a shift toward anti-inflammatory signaling, as well as a more robust secretory response in general. To rule out the possibility that these effects of CBD are specific to TLR4 signaling, we determined the effect of CBD on TLR7/8-induced maturation as well, and saw similar, although less marked responses. CBD-treated moDCs were also less efficient at activating naïve T cells after LPS stimulation, further supporting the tolerogenic effect of this phytocannabinoid on moDCs. Reactome pathway analysis showed an inflammatory response to LPS in moDCs, and to a lesser extent to CBD as well. In contrast CBD-treated moDCs responded to LPS with a shift towards a more tolerogenic phenotype, as IL-10 signaling was the most prominently induced pathway in this group. Discussion Our results show that CBD achieves an anti-inflammatory effect on adaptive immune responses only in the presence of an activating stimuli on moDCs by reprogramming cells during long-term treatment, and not through acute, short-term effects.
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Affiliation(s)
- Zsófia Pénzes
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Molecular Medicine, University of Debrecen, Debrecen, Hungary
| | - Shahrzad Alimohammadi
- Doctoral School of Molecular Medicine, University of Debrecen, Debrecen, Hungary
- Department of Dermatology, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Dorottya Horváth
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Molecular Medicine, University of Debrecen, Debrecen, Hungary
| | - Attila Oláh
- Doctoral School of Molecular Medicine, University of Debrecen, Debrecen, Hungary
- Department of Physiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Balázs István Tóth
- Doctoral School of Molecular Medicine, University of Debrecen, Debrecen, Hungary
- Department of Physiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Attila Bácsi
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- ELKH-DE Allergology Research Group, Debrecen, Hungary
| | - Attila Gábor Szöllősi
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Molecular Medicine, University of Debrecen, Debrecen, Hungary
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Cherkashina OL, Morgun EI, Rippa AL, Kosykh AV, Alekhnovich AV, Stoliarzh AB, Terskikh VV, Vorotelyak EA, Kalabusheva EP. Blank Spots in the Map of Human Skin: The Challenge for Xenotransplantation. Int J Mol Sci 2023; 24:12769. [PMID: 37628950 PMCID: PMC10454653 DOI: 10.3390/ijms241612769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/02/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Most of the knowledge about human skin homeostasis, development, wound healing, and diseases has been accumulated from human skin biopsy analysis by transferring from animal models and using different culture systems. Human-to-mouse xenografting is one of the fundamental approaches that allows the skin to be studied in vivo and evaluate the ongoing physiological processes in real time. Humanized animals permit the actual techniques for tracing cell fate, clonal analysis, genetic modifications, and drug discovery that could never be employed in humans. This review recapitulates the novel facts about mouse skin self-renewing, regeneration, and pathology, raises issues regarding the gaps in our understanding of the same options in human skin, and postulates the challenges for human skin xenografting.
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Affiliation(s)
- Olga L. Cherkashina
- Laboratory of Cell Biology, Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Elena I. Morgun
- Laboratory of Cell Biology, Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Alexandra L. Rippa
- Laboratory of Cell Biology, Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Anastasiya V. Kosykh
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Alexander V. Alekhnovich
- Federal Government-Financed Institution “National Medical Research Center of High Medical Technologies n.a. A.A. Vishnevsky”, 143421 Krasnogorsk, Russia
| | - Aleksey B. Stoliarzh
- Federal Government-Financed Institution “National Medical Research Center of High Medical Technologies n.a. A.A. Vishnevsky”, 143421 Krasnogorsk, Russia
| | - Vasiliy V. Terskikh
- Laboratory of Cell Biology, Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Ekaterina A. Vorotelyak
- Laboratory of Cell Biology, Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Ekaterina P. Kalabusheva
- Laboratory of Cell Biology, Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
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Zhu R, Pan X, Wang S, Qiu Z, Gu C, Yao X, Li W. Updated skin transcriptomic atlas depicted by reciprocal contribution of single-nucleus RNA sequencing and single-cell RNA sequencing. J Dermatol Sci 2023; 111:22-31. [PMID: 37407342 DOI: 10.1016/j.jdermsci.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 06/13/2023] [Accepted: 06/17/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND Single-cell RNA sequencing (scRNA-seq) has advanced our understanding of skin biology, but its utility is restricted by the requirement of fresh samples, inadequate dissociation-induced cell loss or death, and activation during tissue digestion. Single-nucleus RNA sequencing (snRNA-seq) can use frozen, hard-to-dissociate materials, which might be a promising method to circumvent the limitations of scRNA-seq for the skin tissue. OBJECTIVE To profile skin cells using snRNA-seq in parallel with scRNA-seq. METHODS We performed snRNA-seq in parallel with scRNA-seq for the bisected skin sample of one person and integrated previously published scRNA-seq data for analysis. We comparatively analyzed the differences in cell proportions and gene expression between the two methods. The differentiation trajectories of keratinocytes and fibroblasts were analyzed by Slingshot analysis. RESULTS snRNA-seq was less susceptible to contamination from mitochondrial and ribosomal RNA, and exhibited a greater capacity to detect transcription factors. snRNA-seq identified more spatially and functionally relevant keratinocyte clusters that constitute cell trajectories with expected differentiation dynamics. Novel markers, e.g., LYPD3, EMP2, and CSTB, were revealed for different differentiation stages of keratinocytes, and NFIB and GRHL1 were identified as transcription factors involving in the proliferation and functional differentiation of keratinocytes. Fibroblasts were found in a state of activation in scRNA-seq. And scRNA-seq detected a greater number of immune cells. CONCLUSIONS We generated an updated atlas of the skin transcriptome based on the reciprocal contribution of scRNA-seq and snRNA-seq.
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Affiliation(s)
- Ronghui Zhu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China
| | - Xiaoyu Pan
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China
| | - Shangshang Wang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China
| | - Zhuoqiong Qiu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China
| | - Chaoying Gu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China
| | - Xu Yao
- Department of Allergy and Rheumatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Wei Li
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China.
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Alkon N, Assen FP, Arnoldner T, Bauer WM, Medjimorec MA, Shaw LE, Rindler K, Holzer G, Weber P, Weninger W, Freystätter C, Chennareddy S, Kinaciyan T, Farlik M, Jonak C, Griss J, Bangert C, Brunner PM. Single-cell RNA sequencing defines disease-specific differences between chronic nodular prurigo and atopic dermatitis. J Allergy Clin Immunol 2023; 152:420-435. [PMID: 37210042 DOI: 10.1016/j.jaci.2023.04.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/12/2023] [Accepted: 04/19/2023] [Indexed: 05/22/2023]
Abstract
BACKGROUND Chronic nodular prurigo (CNPG) is an inflammatory skin disease that is maintained by a chronic itch-scratch cycle likely rooted in neuroimmunological dysregulation. This condition may be associated with atopy in some patients, and there are now promising therapeutic results from blocking type 2 cytokines such as IL-4, IL-13, and IL-31. OBJECTIVES This study aimed to improve the understanding of pathomechanisms underlying CNPG as well as molecular relationships between CNPG and atopic dermatitis (AD). METHODS We profiled skin lesions from patients with CNPG in comparison with AD and healthy control individuals using single-cell RNA sequencing combined with T-cell receptor sequencing. RESULTS We found type 2 immune skewing in both CNPG and AD, as evidenced by CD4+ helper T cells expressing IL13. However, only AD harbored an additional, oligoclonally expanded CD8A+IL9R+IL13+ cytotoxic T-cell population, and immune activation pathways were highly upregulated in AD, but less so in CNPG. Conversely, CNPG showed signatures of extracellular matrix organization, collagen synthesis, and fibrosis, including a unique population of CXCL14-IL24+ secretory papillary fibroblasts. Besides known itch mediators such as IL31 and oncostatin M, we also detected increased levels of neuromedin B in fibroblasts of CNPG lesions compared with AD and HC, with neuromedin B receptors detectable on some nerve endings. CONCLUSIONS These data show that CNPG does not harbor the strong disease-specific immune activation pathways that are typically found in AD but is rather characterized by upregulated stromal remodeling mechanisms that might have a direct impact on itch fibers.
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Affiliation(s)
- Natalia Alkon
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Frank P Assen
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Tamara Arnoldner
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Wolfgang M Bauer
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Marco A Medjimorec
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Lisa E Shaw
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Katharina Rindler
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Gregor Holzer
- Department of Dermatology, Klinik Donaustadt, Vienna, Austria
| | - Philipp Weber
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Weninger
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Christian Freystätter
- Department of Plastic, Reconstructive and Aesthetic Surgery, Medical University of Vienna, Vienna, Austria
| | - Sumanth Chennareddy
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Tamar Kinaciyan
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Matthias Farlik
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Constanze Jonak
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Johannes Griss
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Christine Bangert
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Patrick M Brunner
- Department of Dermatology, Medical University of Vienna, Vienna, Austria; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY.
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40
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Mortlock RD, Ma EC, Cohen JM, Damsky W. Assessment of Treatment-Relevant Immune Biomarkers in Psoriasis and Atopic Dermatitis: Toward Personalized Medicine in Dermatology. J Invest Dermatol 2023; 143:1412-1422. [PMID: 37341663 PMCID: PMC10830170 DOI: 10.1016/j.jid.2023.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/10/2023] [Accepted: 04/13/2023] [Indexed: 06/22/2023]
Abstract
Immunologically targeted therapies have revolutionized the treatment of inflammatory dermatoses, including atopic dermatitis and psoriasis. Although immunologic biomarkers hold great promise for personalized classification of skin disease and tailored therapy selection, there are no approved or widely used approaches for this in dermatology. This review summarizes the translational immunologic approaches to measuring treatment-relevant biomarkers in inflammatory skin conditions. Tape strip profiling, microneedle-based biomarker patches, molecular profiling from epidermal curettage, RNA in situ hybridization tissue staining, and single-cell RNA sequencing have been described. We discuss the advantages and limitations of each and open questions for the future of personalized medicine in inflammatory skin disease.
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Affiliation(s)
- Ryland D Mortlock
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut, USA; Medical Scientist Training Program, Yale School of Medicine, New Haven, Connecticut, USA
| | - Emilie C Ma
- Yale College, Yale University, New Haven, Connecticut, USA
| | - Jeffrey M Cohen
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut, USA
| | - William Damsky
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut, USA; Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA.
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Lang M, Krump C, Meshcheryakova A, Tam-Amersdorfer C, Schwarzenberger E, Passegger C, Connolly S, Mechtcheriakova D, Strobl H. Microenvironmental and cell intrinsic factors governing human cDC2 differentiation and monocyte reprogramming. Front Immunol 2023; 14:1216352. [PMID: 37539048 PMCID: PMC10395083 DOI: 10.3389/fimmu.2023.1216352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/14/2023] [Indexed: 08/05/2023] Open
Abstract
cDC2s occur abundantly in peripheral tissues and arise from circulating blood cDC2s. However, the factors governing cDC2 differentiation in tissues, especially under inflammatory conditions, remained poorly defined. We here found that psoriatic cDC2s express the efferocytosis receptor Axl and exhibit a bone morphogenetic protein (BMP) and p38MAPK signaling signature. BMP7, strongly expressed within the lesional psoriatic epidermis, cooperates with canonical TGF-β1 signaling for inducing Axl+cDC2s from blood cDC2s in vitro. Moreover, downstream induced p38MAPK promotes Axl+cDC2s at the expense of Axl+CD207+ Langerhans cell differentiation from blood cDC2s. BMP7 supplementation allowed to model cDC2 generation and their further differentiation into LCs from CD34+ hematopoietic progenitor cells in defined serum-free medium. Additionally, p38MAPK promoted the generation of another cDC2 subset lacking Axl but expressing the non-classical NFkB transcription factor RelB in vitro. Such RelB+cDC2s occurred predominantly at dermal sites in the inflamed skin. Finally, we found that cDC2s can be induced to acquire high levels of the monocyte lineage identity factor kruppel-like-factor-4 (KLF4) along with monocyte-derived DC and macrophage phenotypic characteristics in vitro. In conclusion, inflammatory and psoriatic epidermal signals instruct blood cDC2s to acquire phenotypic characteristics of several tissue-resident cell subsets.
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Affiliation(s)
- Magdalena Lang
- Division of Immunology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Corinna Krump
- Division of Immunology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Anastasia Meshcheryakova
- Insitute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Carmen Tam-Amersdorfer
- Division of Immunology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Elke Schwarzenberger
- Division of Immunology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Christina Passegger
- Division of Immunology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Sally Connolly
- Division of Immunology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Diana Mechtcheriakova
- Insitute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Herbert Strobl
- Division of Immunology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
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42
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Huang M, Hua N, Zhuang S, Fang Q, Shang J, Wang Z, Tao X, Niu J, Li X, Yu P, Yang W. Cux1+ proliferative basal cells promote epidermal hyperplasia in chronic dry skin disease identified by single-cell RNA transcriptomics. J Pharm Anal 2023; 13:745-759. [PMID: 37577389 PMCID: PMC10422139 DOI: 10.1016/j.jpha.2023.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 08/15/2023] Open
Abstract
Pathological dry skin is a disturbing and intractable healthcare burden, characterized by epithelial hyperplasia and severe itch. Atopic dermatitis (AD) and psoriasis models with complications of dry skin have been studied using single-cell RNA sequencing (scRNA-seq). However, scRNA-seq analysis of the dry skin mouse model (acetone/ether/water (AEW)-treated model) is still lacking. Here, we used scRNA-seq and in situ hybridization to identify a novel proliferative basal cell (PBC) state that exclusively expresses transcription factor CUT-like homeobox 1 (Cux1). Further in vitro study demonstrated that Cux1 is vital for keratinocyte proliferation by regulating a series of cyclin-dependent kinases (CDKs) and cyclins. Clinically, Cux1+ PBCs were increased in patients with psoriasis, suggesting that Cux1+ PBCs play an important part in epidermal hyperplasia. This study presents a systematic knowledge of the transcriptomic changes in a chronic dry skin mouse model, as well as a potential therapeutic target against dry skin-related dermatoses.
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Affiliation(s)
- Minhua Huang
- Department of Biophysics, and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, China
| | - Ning Hua
- Department of Biophysics, and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, China
| | - Siyi Zhuang
- Department of Biophysics, and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, China
| | - Qiuyuan Fang
- Department of Biophysics, and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, China
| | - Jiangming Shang
- Department of Biophysics, and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, China
| | - Zhen Wang
- Laboratory Medicine Center, Allergy Center, Department of Transfusion Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310000, China
| | - Xiaohua Tao
- Department of Dermatology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310000, China
| | - Jianguo Niu
- Key Laboratory of Craniocerebral Diseases of Ningxia Hui Autonomous Region, Ningxia Medical University, Yinchuan, 750000, China
| | - Xiangyao Li
- Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, China
| | - Peilin Yu
- Department of Toxicology, and Department of Medical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, China
| | - Wei Yang
- Department of Biophysics, and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, China
- Laboratory Medicine Center, Allergy Center, Department of Transfusion Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310000, China
- MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou, 310000, China
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43
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Ma F, Plazyo O, Billi AC, Tsoi LC, Xing X, Wasikowski R, Gharaee-Kermani M, Hile G, Jiang Y, Harms PW, Xing E, Kirma J, Xi J, Hsu JE, Sarkar MK, Chung Y, Di Domizio J, Gilliet M, Ward NL, Maverakis E, Klechevsky E, Voorhees JJ, Elder JT, Lee JH, Kahlenberg JM, Pellegrini M, Modlin RL, Gudjonsson JE. Single cell and spatial sequencing define processes by which keratinocytes and fibroblasts amplify inflammatory responses in psoriasis. Nat Commun 2023; 14:3455. [PMID: 37308489 PMCID: PMC10261041 DOI: 10.1038/s41467-023-39020-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/26/2023] [Indexed: 06/14/2023] Open
Abstract
The immunopathogenesis of psoriasis, a common chronic inflammatory disease of the skin, is incompletely understood. Here we demonstrate, using a combination of single cell and spatial RNA sequencing, IL-36 dependent amplification of IL-17A and TNF inflammatory responses in the absence of neutrophil proteases, which primarily occur within the supraspinous layer of the psoriatic epidermis. We further show that a subset of SFRP2+ fibroblasts in psoriasis contribute to amplification of the immune network through transition to a pro-inflammatory state. The SFRP2+ fibroblast communication network involves production of CCL13, CCL19 and CXCL12, connected by ligand-receptor interactions to other spatially proximate cell types: CCR2+ myeloid cells, CCR7+ LAMP3+ dendritic cells, and CXCR4 expressed on both CD8+ Tc17 cells and keratinocytes, respectively. The SFRP2+ fibroblasts also express cathepsin S, further amplifying inflammatory responses by activating IL-36G in keratinocytes. These data provide an in-depth view of psoriasis pathogenesis, which expands our understanding of the critical cellular participants to include inflammatory fibroblasts and their cellular interactions.
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Affiliation(s)
- Feiyang Ma
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Olesya Plazyo
- Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Allison C Billi
- Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xianying Xing
- Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Rachael Wasikowski
- Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Grace Hile
- Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yanyun Jiang
- Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Paul W Harms
- Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Enze Xing
- Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Joseph Kirma
- Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jingyue Xi
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Jer-En Hsu
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Mrinal K Sarkar
- Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yutein Chung
- Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jeremy Di Domizio
- Department of Dermatology, University Hospital of Lausanne, 1011, Lausanne, Switzerland
| | - Michel Gilliet
- Department of Dermatology, University Hospital of Lausanne, 1011, Lausanne, Switzerland
| | - Nicole L Ward
- Department of Dermatology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Emanual Maverakis
- Department of Dermatology, University of California Davis, Sacramento, CA, USA
| | - Eynav Klechevsky
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - John J Voorhees
- Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA
- Ann Arbor Veterans Affairs Medical Center, Ann Arbor, MI, 48105, USA
| | - Jun Hee Lee
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - J Michelle Kahlenberg
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Robert L Modlin
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
| | - Johann E Gudjonsson
- Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA.
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44
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Wang H, Torous W, Gong B, Purdom E. Visualizing scRNA-Seq Data at Population Scale with GloScope. bioRxiv 2023:2023.05.29.542786. [PMID: 37398321 PMCID: PMC10312527 DOI: 10.1101/2023.05.29.542786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Increasingly scRNA-Seq studies explore the heterogeneity of cell populations across different samples and its effect on an organism's phenotype. However, relatively few bioinformatic methods have been developed which adequately address the variation between samples for such population-level analyses. We propose a framework for representing the entire single-cell profile of a sample, which we call its GloScope representation. We implement GloScope on scRNA-Seq datasets from study designs ranging from 12 to over 300 samples. These examples demonstrate how GloScope allows researchers to perform essential bioinformatic tasks at the sample-level, in particular visualization and quality control assessment.
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Affiliation(s)
- Hao Wang
- Graduate Group in Biostatistics, University of California, Berkeley, USA
| | - William Torous
- Department of Statistics, University of California, Berkeley, USA
| | - Boying Gong
- Graduate Group in Biostatistics, University of California, Berkeley, USA
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, USA
- Center for Computational Biology, University of California, Berkeley, USA
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45
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Stabell AR, Lee GE, Jia Y, Wong KN, Wang S, Ling J, Nguyen SD, Sen GL, Nie Q, Atwood SX. Single-cell transcriptomics of human-skin-equivalent organoids. Cell Rep 2023; 42:112511. [PMID: 37195865 DOI: 10.1016/j.celrep.2023.112511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 03/07/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Several methods for generating human-skin-equivalent (HSE) organoid cultures are in use to study skin biology; however, few studies thoroughly characterize these systems. To fill this gap, we use single-cell transcriptomics to compare in vitro HSEs, xenograft HSEs, and in vivo epidermis. By combining differential gene expression, pseudotime analyses, and spatial localization, we reconstruct HSE keratinocyte differentiation trajectories that recapitulate known in vivo epidermal differentiation pathways and show that HSEs contain major in vivo cellular states. However, HSEs also develop unique keratinocyte states, an expanded basal stem cell program, and disrupted terminal differentiation. Cell-cell communication modeling shows aberrant epithelial-to-mesenchymal transition (EMT)-associated signaling pathways that alter upon epidermal growth factor (EGF) supplementation. Last, xenograft HSEs at early time points post transplantation significantly rescue many in vitro deficits while undergoing a hypoxic response that drives an alternative differentiation lineage. This study highlights the strengths and limitations of organoid cultures and identifies areas for potential innovation.
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Affiliation(s)
- Adam R Stabell
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA
| | - Grace E Lee
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Yunlong Jia
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Kirsten N Wong
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA
| | - Shuxiong Wang
- Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA
| | - Ji Ling
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sandrine D Nguyen
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - George L Sen
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Qing Nie
- Department of Developmental and Cell Biology, 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 Mathematics, University of California, Irvine, Irvine, CA 92697, USA; Center for Complex Biological Systems, Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, USA
| | - Scott X Atwood
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA; Center for Complex Biological Systems, Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, USA; Department of Dermatology, University of California, Irvine, Irvine, CA 92697, USA.
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46
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Polito MP, Marini G, Palamenghi M, Enzo E. Decoding the Human Epidermal Complexity at Single-Cell Resolution. Int J Mol Sci 2023; 24:ijms24108544. [PMID: 37239891 DOI: 10.3390/ijms24108544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 04/27/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
The epidermis is one of the largest tissues in the human body, serving as a protective barrier. The basal layer of the epidermis, which consists of epithelial stem cells and transient amplifying progenitors, represents its proliferative compartment. As keratinocytes migrate from the basal layer to the skin surface, they exit the cell cycle and initiate terminal differentiation, ultimately generating the suprabasal epidermal layers. A deeper understanding of the molecular mechanisms and pathways driving keratinocytes' organization and regeneration is essential for successful therapeutic approaches. Single-cell techniques are valuable tools for studying molecular heterogeneity. The high-resolution characterization obtained with these technologies has identified disease-specific drivers and new therapeutic targets, further promoting the advancement of personalized therapies. This review summarizes the latest findings on the transcriptomic and epigenetic profiling of human epidermal cells, analyzed from human biopsy or after in vitro cultivation, focusing on physiological, wound healing, and inflammatory skin conditions.
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Affiliation(s)
- Maria Pia Polito
- Centre for Regenerative Medicine ''Stefano Ferrari'', University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Grazia Marini
- Centre for Regenerative Medicine ''Stefano Ferrari'', University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Michele Palamenghi
- Centre for Regenerative Medicine ''Stefano Ferrari'', University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Elena Enzo
- Centre for Regenerative Medicine ''Stefano Ferrari'', University of Modena and Reggio Emilia, 41125 Modena, Italy
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47
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Veniaminova NA, Jia Y, Hartigan AM, Huyge TJ, Tsai SY, Grachtchouk M, Nakagawa S, Dlugosz AA, Atwood SX, Wong SY. Distinct mechanisms for sebaceous gland self-renewal and regeneration provide durability in response to injury. bioRxiv 2023:2023.05.05.539454. [PMID: 37205445 PMCID: PMC10187279 DOI: 10.1101/2023.05.05.539454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Sebaceous glands (SGs) release oils that protect our skin, but how these glands respond to injury has not been previously examined. Here, we report that SGs are largely self-renewed by dedicated stem cell pools during homeostasis. Using targeted single cell RNA-sequencing, we uncovered both direct and indirect paths by which these resident SG progenitors ordinarily differentiate into sebocytes, including transit through a PPARγ+Krt5+ transitional cell state. Upon skin injury, however, SG progenitors depart their niche, reepithelialize the wound, and are replaced by hair follicle-derived stem cells. Furthermore, following targeted genetic ablation of >99% of SGs from dorsal skin, these glands unexpectedly regenerate within weeks. This regenerative process is mediated by alternative stem cells originating from the hair follicle bulge, is dependent upon FGFR signaling, and can be accelerated by inducing hair growth. Altogether, our studies demonstrate that stem cell plasticity promotes SG durability following injury.
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Affiliation(s)
- Natalia A. Veniaminova
- Department of Dermatology, Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yunlong Jia
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Adrien M. Hartigan
- Department of Dermatology, Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas J. Huyge
- Department of Dermatology, Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shih-Ying Tsai
- Department of Dermatology, Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marina Grachtchouk
- Department of Dermatology, Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seitaro Nakagawa
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrzej A. Dlugosz
- Department of Dermatology, Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Scott X. Atwood
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Sunny Y. Wong
- Department of Dermatology, Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Lead Contact:
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48
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Zhu R, Liu X, Li X, Yao X, Li W. Response to identifying the epidermal dendritic cell landscape. Immunity 2023; 56:461-462. [PMID: 36921568 DOI: 10.1016/j.immuni.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Affiliation(s)
- Ronghui Zhu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Xiaochun Liu
- Department of Allergy and Rheumatology, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, P.R. China
| | - Xiao Li
- Gene Editing Laboratory, Texas Heart Institute, Houston, TX 77030, USA
| | - Xu Yao
- Department of Allergy and Rheumatology, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, P.R. China.
| | - Wei Li
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China.
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49
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Samuel RM, Navickas A, Maynard A, Gaylord EA, Garcia K, Bhat S, Majd H, Richter MN, Elder N, Le D, Nguyen P, Shibata B, Llabata ML, Selleri L, Laird DJ, Darmanis S, Goodarzi H, Fattahi F. Generation of Schwann cell derived melanocytes from hPSCs identifies pro-metastatic factors in melanoma. bioRxiv 2023:2023.03.06.531220. [PMID: 36945537 PMCID: PMC10028814 DOI: 10.1101/2023.03.06.531220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
The neural crest (NC) is highly multipotent and generates diverse lineages in the developing embryo. However, spatiotemporally distinct NC populations display differences in fate potential, such as increased gliogenic and parasympathetic potential from later migrating, nerve-associated Schwann cell precursors (SCPs). Interestingly, while melanogenic potential is shared by both early migrating NC and SCPs, differences in melanocyte identity resulting from differentiation through these temporally distinct progenitors have not been determined. Here, we leverage a human pluripotent stem cell (hPSC) model of NC temporal patterning to comprehensively characterize human NC heterogeneity, fate bias, and lineage development. We captured the transition of NC differentiation between temporally and transcriptionally distinct melanogenic progenitors and identified modules of candidate transcription factor and signaling activity associated with this transition. For the first time, we established a protocol for the directed differentiation of melanocytes from hPSCs through a SCP intermediate, termed trajectory 2 (T2) melanocytes. Leveraging an existing protocol for differentiating early NC-derived melanocytes, termed trajectory 1 (T1), we performed the first comprehensive comparison of transcriptional and functional differences between these distinct melanocyte populations, revealing differences in pigmentation and unique expression of transcription factors, ligands, receptors and surface markers. We found a significant link between the T2 melanocyte transcriptional signature and decreased survival in melanoma patients in the cancer genome atlas (TCGA). We performed an in vivo CRISPRi screen of T1 and T2 melanocyte signature genes in a human melanoma cell line and discovered several T2-specific markers that promote lung metastasis in mice. We further demonstrated that one of these factors, SNRPB, regulates the splicing of transcripts involved in metastasis relevant functions such as migration, cell adhesion and proliferation. Overall, this study identifies distinct developmental trajectories as a source of diversity in melanocytes and implicates the unique molecular signature of SCP-derived melanocytes in metastatic melanoma.
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Affiliation(s)
- Ryan M. Samuel
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Albertas Navickas
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Current address: Institut Curie, CNRS UMR3348, INSERM U1278, Orsay, France
| | - Ashley Maynard
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Current address: Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Eliza A. Gaylord
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Kristle Garcia
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Samyukta Bhat
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Homa Majd
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Mikayla N. Richter
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Nicholas Elder
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Daniel Le
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Current address: Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech Inc, South San Francisco, CA
| | - Phi Nguyen
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Bradley Shibata
- Biological Electron Microscopy Facility, University of California, Davis, CA 95616, USA
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California, Davis, CA 95616, USA
| | - Marta Losa Llabata
- Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94110, USA
- Current address: Caribou Biosciences, Berkley, CA 94710
| | - Licia Selleri
- Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94110, USA
- Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Diana J. Laird
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Spyros Darmanis
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Current address: Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech Inc, South San Francisco, CA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Faranak Fattahi
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA
- Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94110, USA
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50
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Yan Y, Tian J, Wang Y, Li Y, Zhang C, Zhang S, Lin P, Peng R, Zhao C, Zhuang L, Lai B, Zhou L, Zhang G, Li H. Transcriptomic Heterogeneity of Skin Across Different Anatomic Sites. J Invest Dermatol 2023; 143:398-407.e5. [PMID: 36122800 DOI: 10.1016/j.jid.2022.08.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 08/05/2022] [Accepted: 08/26/2022] [Indexed: 02/05/2023]
Abstract
Multiomic studies, including RNA sequencing, single-cell RNA sequencing, and epigenomics, can provide insight into the connection between anatomically heterogeneous gene expression profile of the skin and dermatoses-predisposed sites, in which RNA sequencing is essential. Therefore, in this study, 159 skin samples collected mainly from discarded normal skin tissue during surgical treatment for benign skin tumors were used for RNA sequencing. On the basis of cluster analysis, the skin was divided into four regions, with each region showing specific physiological characteristics through differentially expressed gene analysis. The results showed that the head and neck region, perineum, and palmoplantar area were closely associated with lipid metabolism, hormone metabolism, blood circulation, and related neural regulation, respectively. Transcription factor enrichment indicated that different regions were associated with the development of adjacent tissues. Specifically, the head and neck region, trunk and extremities, perineum, and palmoplantar area were associated with the central nervous, axial, urogenital, and vascular systems, respectively. The results were imported into an open website (https://dermvis.github.io/) for retrieval. Our transcriptomic data elucidated that human skin exhibits transcriptomic heterogeneity reflecting physiological and developmental variation at different anatomic sites and provided guidance for further studies on skin development and dermatoses predisposed sites.
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Affiliation(s)
- Yicen Yan
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China; Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China; NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Jie Tian
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Yang Wang
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China; Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China; NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Yurong Li
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China; Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China; NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Chong Zhang
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China; Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China; NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Shenxi Zhang
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China; Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China; NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Pingping Lin
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China; Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China; NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Rui Peng
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China; Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China; NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Chunxia Zhao
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China; Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China; NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Le Zhuang
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; Department of Dermatology, Qilu Hospital of Shandong University, Jinan, China
| | - Binbin Lai
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; Institute of Medical Technology, Peking University Health Science Center, Beijing, China; Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Liang Zhou
- National Institute of Health Data Science, Peking University, Beijing, China
| | - Guohong Zhang
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; Pathology Department, Shantou University Medical College, Guangdong, China
| | - Hang Li
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China; Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China; NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China.
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