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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] [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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Bangert C, Alkon N, Chennareddy S, Arnoldner T, Levine JP, Pilz M, Medjimorec MA, Ruggiero J, Cohenour ER, Jonak C, Damsky W, Griss J, Brunner PM. Dupilumab-associated head and neck dermatitis shows a pronounced type 22 immune signature mediated by oligoclonally expanded T cells. Nat Commun 2024; 15:2839. [PMID: 38565563 PMCID: PMC10987549 DOI: 10.1038/s41467-024-46540-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 03/01/2024] [Indexed: 04/04/2024] Open
Abstract
Dupilumab, an IL4R-blocking antibody, has shown clinical efficacy for atopic dermatitis (AD) treatment. In addition to conjunctivitis/blepharitis, the de novo appearance of head/neck dermatitis is now recognized as a distinct side effect, occurring in up to 10% of patients. Histopathological features distinct from AD suggest a drug effect, but exact underlying mechanisms remain unknown. We profiled punch biopsies from dupilumab-associated head and neck dermatitis (DAHND) by using single-cell RNA sequencing and compared data with untreated AD and healthy control skin. We show that dupilumab treatment was accompanied by normalization of IL-4/IL-13 downstream activity markers such as CCL13, CCL17, CCL18 and CCL26. By contrast, we found strong increases in type 22-associated markers (IL22, AHR) especially in oligoclonally expanded T cells, accompanied by enhanced keratinocyte activation and IL-22 receptor upregulation. Taken together, we demonstrate that dupilumab effectively dampens conventional type 2 inflammation in DAHND lesions, with concomitant hyperactivation of IL22-associated responses.
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Affiliation(s)
- Christine Bangert
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Natalia Alkon
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | | | - Tamara Arnoldner
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Jasmine P Levine
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- New York Medical College, Valhalla, NY, USA
| | - Magdalena Pilz
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Marco A Medjimorec
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - John Ruggiero
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Emry R Cohenour
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Constanze Jonak
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - William Damsky
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA
| | - Johannes Griss
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
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3
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Seiringer P, Hillig C, Schäbitz A, Jargosch M, Pilz AC, Eyerich S, Szegedi A, Sochorová M, Gruber F, Zouboulis CC, Biedermann T, Menden MP, Eyerich K, Törőcsik D. Spatial transcriptomics reveals altered lipid metabolism and inflammation-related gene expression of sebaceous glands in psoriasis and atopic dermatitis. Front Immunol 2024; 15:1334844. [PMID: 38433843 PMCID: PMC10904577 DOI: 10.3389/fimmu.2024.1334844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/22/2024] [Indexed: 03/05/2024] Open
Abstract
Sebaceous glands drive acne, however, their role in other inflammatory skin diseases remains unclear. To shed light on their potential contribution to disease development, we investigated the spatial transcriptome of sebaceous glands in psoriasis and atopic dermatitis patients across lesional and non-lesional human skin samples. Both atopic dermatitis and psoriasis sebaceous glands expressed genes encoding key proteins for lipid metabolism and transport such as ALOX15B, APOC1, FABP7, FADS1/2, FASN, PPARG, and RARRES1. Also, inflammation-related SAA1 was identified as a common spatially variable gene. In atopic dermatitis, genes mainly related to lipid metabolism (e.g. ACAD8, FADS6, or EBP) as well as disease-specific genes, i.e., Th2 inflammation-related lipid-regulating HSD3B1 were differentially expressed. On the contrary, in psoriasis, more inflammation-related spatially variable genes (e.g. SERPINF1, FKBP5, IFIT1/3, DDX58) were identified. Other psoriasis-specific enriched pathways included lipid metabolism (e.g. ACOT4, S1PR3), keratinization (e.g. LCE5A, KRT5/7/16), neutrophil degranulation, and antimicrobial peptides (e.g. LTF, DEFB4A, S100A7-9). In conclusion, our results show that sebaceous glands contribute to skin homeostasis with a cell type-specific lipid metabolism, which is influenced by the inflammatory microenvironment. These findings further support that sebaceous glands are not bystanders in inflammatory skin diseases, but can actively and differentially modulate inflammation in a disease-specific manner.
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Affiliation(s)
- Peter Seiringer
- Department of Dermatology and Allergy, Technical University of Munich, Munich, Germany
- Division of Dermatology and Venereology, Department of Medicine Solna, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Christina Hillig
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Munich, Germany
| | - Alexander Schäbitz
- Department of Dermatology and Allergy, Technical University of Munich, Munich, Germany
- Division of Dermatology and Venereology, Department of Medicine Solna, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Manja Jargosch
- Department of Dermatology and Allergy, Technical University of Munich, Munich, Germany
- Zentrum für Allergie und Umwelt (ZAUM) - Center of Allergy and Environment, Technical University of Munich and Helmholtz Zentrum München, Munich, Germany
| | - Anna Caroline Pilz
- Department of Dermatology and Allergy, Technical University of Munich, Munich, Germany
- Department of Dermatology and Venereology, Medical Center, University of Freiburg, Freiburg, Germany
| | - Stefanie Eyerich
- Zentrum für Allergie und Umwelt (ZAUM) - Center of Allergy and Environment, Technical University of Munich and Helmholtz Zentrum München, Munich, Germany
| | - Andrea Szegedi
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Hungarian Research Network (HUN-REN DE), Allergology Research Group, Debrecen, Hungary
| | - Michaela Sochorová
- Division for Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
- Christian Doppler Laboratory for Skin Multimodal Analytical Imaging of Aging and Senescence (SKINMAGINE), Medical University of Vienna, Vienna, Austria
| | - Florian Gruber
- Division for Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
- Christian Doppler Laboratory for Skin Multimodal Analytical Imaging of Aging and Senescence (SKINMAGINE), Medical University of Vienna, Vienna, Austria
| | - Christos C Zouboulis
- Departments of Dermatology, Venereology, Allergology and Immunology, Staedtisches Klinikum Dessau, Brandenburg Medical School Theodor Fontane and Faculty of Health Sciences Brandenburg, Dessau, Germany
| | - Tilo Biedermann
- Department of Dermatology and Allergy, Technical University of Munich, Munich, Germany
| | - Michael P Menden
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Munich, Germany
- Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, Australia
| | - Kilian Eyerich
- Division of Dermatology and Venereology, Department of Medicine Solna, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Dermatology and Venereology, Medical Center, University of Freiburg, Freiburg, Germany
| | - Daniel Törőcsik
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Hungarian Research Network (HUN-REN DE), Allergology Research Group, Debrecen, Hungary
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Wu D, Hailer AA, Wang S, Yuan M, Chan J, El Kurdi A, Han D, Ali H, D'Angio B, Mayer A, Rahim M, Kondo A, Klufas D, Kim E, Shain AH, Choi J, Bhutani T, Simpson G, Grekin RC, Ricardo-Gonzalez R, Purdom E, North JP, Cheng JB, Cho RJ. A single-cell atlas of IL-23 inhibition in cutaneous psoriasis distinguishes clinical response. Sci Immunol 2024; 9:eadi2848. [PMID: 38277466 DOI: 10.1126/sciimmunol.adi2848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 11/22/2023] [Indexed: 01/28/2024]
Abstract
Psoriasis vulgaris and other chronic inflammatory diseases improve markedly with therapeutic blockade of interleukin-23 (IL-23) signaling, but the genetic mechanisms underlying clinical responses remain poorly understood. Using single-cell transcriptomics, we profiled immune cells isolated from lesional psoriatic skin before and during IL-23 blockade. In clinically responsive patients, a psoriatic transcriptional signature in skin-resident memory T cells was strongly attenuated. In contrast, poorly responsive patients were distinguished by persistent activation of IL-17-producing T (T17) cells, a mechanism distinct from alternative cytokine signaling or resistance isolated to epidermal keratinocytes. Even in IL-23 blockade-responsive patients, we detected a recurring set of recalcitrant, disease-specific transcriptional abnormalities. This irreversible immunological state may necessitate ongoing IL-23 inhibition. Spatial transcriptomic analyses also suggested that successful IL-23 blockade requires dampening of >90% of IL-17-induced response in lymphocyte-adjacent keratinocytes, an unexpectedly high threshold. Collectively, our data establish a patient-level paradigm for dissecting responses to immunomodulatory treatments.
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Affiliation(s)
- David Wu
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Ashley A Hailer
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA
- Dermatology Service, San Francisco Veterans Administration Health Care System, San Francisco, CA 94121, USA
| | - Sijia Wang
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA
- Dermatology Service, San Francisco Veterans Administration Health Care System, San Francisco, CA 94121, USA
- Department of Dermatology, Second Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xi'an 710004, China
| | - Michelle Yuan
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Jamie Chan
- Dermatopathology Service, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Abdullah El Kurdi
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - David Han
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Hira Ali
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Blaize D'Angio
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Aaron Mayer
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Maha Rahim
- Enable Medicine, Menlo Park, CA 94025, USA
| | | | - Daniel Klufas
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Esther Kim
- Department of Plastic Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - A Hunter Shain
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Jaehyuk Choi
- Departments of Dermatology and Biochemistry and Molecular Genetics, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Tina Bhutani
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Gregory Simpson
- Department of Dermatology, University of California, Fresno, CA 93701,USA
| | - Roy C Grekin
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Roberto Ricardo-Gonzalez
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jeffrey P North
- Dermatopathology Service, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Jeffrey B Cheng
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA
- Dermatology Service, San Francisco Veterans Administration Health Care System, San Francisco, CA 94121, USA
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA
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5
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Mancini M, Sergio S, Cappello A, Farkas T, Bernassola F, Scarponi C, Albanesi C, Melino G, Candi E. Involvement of transcribed lncRNA uc.291 in hyperproliferative skin disorders. Biol Direct 2023; 18:82. [PMID: 38041107 PMCID: PMC10693168 DOI: 10.1186/s13062-023-00435-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 11/04/2023] [Indexed: 12/03/2023] Open
Abstract
The uc.291 transcript controls keratinocytes differentiation by physical interaction with ACTL6A and subsequent induction of transcription of the genes belonging to the epidermal differentiation complex (EDC). Uc.291 is also implicated in the dedifferentiation phenotype seen in poorly differentiated cutaneous squamous cell carcinomas. Here, we would like to investigate the contribution of uc.291 to the unbalanced differentiation state of keratinocytes observed in hyperproliferative skin disorders, e. g., psoriasis. Psoriasis is a multifactorial inflammatory disease, caused by alteration of keratinocytes homeostasis. The imbalanced differentiation state, triggered by the infiltration of immune cells, represents one of the events responsible for this pathology. In the present work, we explore the role of uc.291 and its interactor ACTL6A in psoriasis skin, using quantitative real-time PCR (RT-qPCR), immunohistochemistry and bioinformatic analysis of publicly available datasets. Our data suggest that the expression of the uc.291 and of EDC genes loricrin and filaggrin (LOR, FLG) is reduced in lesional skin compared to nonlesional skin of psoriatic patients; conversely, the mRNA and protein level of ACTL6A are up-regulated. Furthermore, we provide evidence that the expression of uc.291, FLG and LOR is reduced, while ACTL6A mRNA is up-regulated, in an in vitro psoriasis-like model obtained by treating differentiated keratinocytes with interleukin 22 (IL-22). Furthermore, analysis of a publicly available dataset of human epidermal keratinocytes treated with IL-22 (GSE7216) confirmed our in vitro results. Taken together, our data reveal a novel role of uc.291 and its functional axis with ACTL6A in psoriasis disorder and a proof of concept that biological inhibition of this molecular axis could have a potential pharmacological effect against psoriasis and, in general, in skin diseases with a suppressed differentiation programme.
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Affiliation(s)
- Mara Mancini
- Istituto Dermopatico Dell'Immacolata, IDI-IRCCS, 00167, Rome, Italy
- Department of Experimental Medicine, University of Rome "Tor Vergata", 00133, Rome, Italy
| | - Simone Sergio
- Department of Experimental Medicine, University of Rome "Tor Vergata", 00133, Rome, Italy
| | - Angela Cappello
- Interdisciplinary Department of Medicine, University of Bari "Aldo Moro", 70121, Bari, Italy
| | - Timea Farkas
- Istituto Dermopatico Dell'Immacolata, IDI-IRCCS, 00167, Rome, Italy
| | - Francesca Bernassola
- Department of Experimental Medicine, University of Rome "Tor Vergata", 00133, Rome, Italy
| | - Claudia Scarponi
- Istituto Dermopatico Dell'Immacolata, IDI-IRCCS, 00167, Rome, Italy
| | | | - Gerry Melino
- Department of Experimental Medicine, University of Rome "Tor Vergata", 00133, Rome, Italy
| | - Eleonora Candi
- Istituto Dermopatico Dell'Immacolata, IDI-IRCCS, 00167, Rome, Italy.
- Department of Experimental Medicine, University of Rome "Tor Vergata", 00133, Rome, Italy.
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6
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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] [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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7
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Filipp FV. Spatial Cancer Systems Biology Resolves Heterotypic Interactions and Identifies Disruption of Spatial Hierarchy as a Pathological Driver Event. J Invest Dermatol 2023; 143:1342-1347. [PMID: 37455062 DOI: 10.1016/j.jid.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 02/07/2023] [Indexed: 07/18/2023]
Affiliation(s)
- Fabian V Filipp
- Cancer Systems Biology, Institute of Diabetes and Cancer, Helmholtz Zentrum München, München, Germany; School of Life Sciences Weihenstephan, Technical University München, Maximus-von-Imhof-Forum 3, Freising, Germany; Institute for Advanced Study, Technical University München, Maximus-von-Imhof-Forum 3, Freising, Germany; Metaflux, San Diego, California, USA.
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8
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Houser AE, Kazmi A, Nair AK, Ji AL. The Use of Single-Cell RNA-Sequencing and Spatial Transcriptomics in Understanding the Pathogenesis and Treatment of Skin Diseases. JID INNOVATIONS 2023; 3:100198. [PMID: 37205302 PMCID: PMC10186616 DOI: 10.1016/j.xjidi.2023.100198] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/15/2023] [Accepted: 02/27/2023] [Indexed: 05/21/2023] Open
Abstract
The development of multiomic profiling tools has rapidly expanded in recent years, along with their use in profiling skin tissues in various contexts, including dermatologic diseases. Among these tools, single-cell RNA-sequencing (scRNA-seq) and spatial transcriptomics (ST) have emerged as widely adopted and powerful assays for elucidating key cellular components and their spatial arrangement within skin disease. In this paper, we review the recent biological insights gained from the use of scRNA-seq and ST and the advantages of combining both for profiling skin diseases, including aberrant wound healing, inflammatory skin diseases, and cancer. We discuss the role of scRNA-seq and ST in improving skin disease treatments and moving toward the goal of achieving precision medicine in dermatology, whereby patients can be optimally matched to treatments that maximize therapeutic response.
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Affiliation(s)
- Aubrey E. Houser
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Abiha Kazmi
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Arjun K. Nair
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Andrew L. Ji
- Department of Dermatology, 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
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Correspondence: Andrew L. Ji, Department of Dermatology, Icahn School of Medicine at Mount Sinai, 1428 Madison Avenue, Atran 7-10F, Box 1048, New York, New York 10029, USA.
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9
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Fries A, Saidoune F, Kuonen F, Dupanloup I, Fournier N, Guerra de Souza AC, Haniffa M, Ma F, Gudjonsson JE, Roesner L, Li Y, Werfel T, Conrad C, Gottardo R, Modlin RL, Di Domizio J, Gilliet M. Differentiation of IL-26 + T H17 intermediates into IL-17A producers via epithelial crosstalk in psoriasis. Nat Commun 2023; 14:3878. [PMID: 37391412 PMCID: PMC10313793 DOI: 10.1038/s41467-023-39484-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/15/2023] [Indexed: 07/02/2023] Open
Abstract
Interleukin (IL)-26 is a TH17 cytokine with known antimicrobial and pro-inflammatory functions. However, the precise role of IL-26 in the context of pathogenic TH17 responses is unknown. Here we identify a population of blood TH17 intermediates that produce high levels of IL-26 and differentiate into IL-17A-producing TH17 cells upon TGF-β1 exposure. By combining single cell RNA sequencing, TCR sequencing and spatial transcriptomics we show that this process occurs in psoriatic skin. In fact, IL-26+ TH17 intermediates infiltrating psoriatic skin induce TGF-β1 expression in basal keratinocytes and thereby promote their own differentiation into IL-17A-producing cells. Thus, our study identifies IL-26-producing cells as an early differentiation stage of TH17 cells that infiltrates psoriatic skin and controls its own maturation into IL17A-producing TH17 cells, via epithelial crosstalk involving paracrine production of TGF-β1.
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Affiliation(s)
- Anissa Fries
- Department of Dermatology, CHUV University Hospital and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Fanny Saidoune
- Department of Dermatology, CHUV University Hospital and University of Lausanne (UNIL), Lausanne, Switzerland
| | - François Kuonen
- Department of Dermatology, CHUV University Hospital and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Isabelle Dupanloup
- Translational Data Science Facility, Agora Cancer Research Center, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nadine Fournier
- Translational Data Science Facility, Agora Cancer Research Center, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ana Cristina Guerra de Souza
- Translational Data Science Facility, Agora Cancer Research Center, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Muzlifah Haniffa
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE2 4LP, UK
| | - Feiyang Ma
- Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Johann E Gudjonsson
- Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Lennart Roesner
- Department of Dermatology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Yang Li
- Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine (CiiM), Helmholtz Centre for Infection Research (HZI), Hannover Medical School (MHH), Hannover, Germany
| | - Thomas Werfel
- Department of Dermatology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Curdin Conrad
- Department of Dermatology, CHUV University Hospital and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Raphael Gottardo
- Biomedical Data Sciences Center, CHUV, UNIL, and SIB, Lausanne, Switzerland
| | - Robert L Modlin
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Jeremy Di Domizio
- Department of Dermatology, CHUV University Hospital and University of Lausanne (UNIL), Lausanne, Switzerland.
| | - Michel Gilliet
- Department of Dermatology, CHUV University Hospital and University of Lausanne (UNIL), Lausanne, Switzerland.
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10
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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] [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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11
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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] [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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12
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Tekkela S, Theocharidis G, McGrath JA, Onoufriadis A. Spatial transcriptomics in human skin research. Exp Dermatol 2023. [PMID: 37150587 DOI: 10.1111/exd.14827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/17/2023] [Accepted: 04/21/2023] [Indexed: 05/09/2023]
Abstract
Spatial transcriptomics is a revolutionary technique that enables researchers to characterise tissue architecture and localisation of gene expression. A plethora of technologies that map gene expression are currently being developed, aiming to facilitate spatially resolved, high-dimensional assessment of gene transcription in the context of human skin research. Knowing which gene is expressed by which cell and in which location within skin, facilitates understanding of skin function and dysfunction in both health and disease. In this review, we summarise the available spatial transcriptomic methods and we describe their application to a broad spectrum of dermatological diseases.
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Affiliation(s)
- Stavroula Tekkela
- St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Georgios Theocharidis
- Joslin-Beth Israel Deaconess Foot Center and The Rongxiang Xu, MD, Center for Regenerative Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - John A McGrath
- St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Alexandros Onoufriadis
- St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, UK
- Laboratory of Medical Biology and Genetics, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
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13
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Filipp FV. Spatial cancer systems biology resolves heterotypic interactions and identifies disruption of spatial hierarchy as a pathological driver event. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.01.530706. [PMID: 36993709 PMCID: PMC10054974 DOI: 10.1101/2023.03.01.530706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Spatially annotated single-cell datasets provide unprecedented opportunities to dissect cell-cell communication in development and disease. Heterotypic signaling includes interactions between different cell types and is well established in tissue development and spatial organization. Epithelial organization requires several different programs that are tightly regulated. Planar cell polarity (PCP) is the organization of epithelial cells along the planar axis, orthogonal to the apical-basal axis. Here, we investigate PCP factors and explore the implications of developmental regulators as malignant drivers. Utilizing cancer systems biology analysis, we derive a gene expression network for WNT-ligands (WNT) and their cognate frizzled (FZD) receptors in skin cutaneous melanoma. The profiles supported by unsupervised clustering of multiple-sequence alignments identify ligand-independent signaling and implications for metastatic progression based on the underpinning developmental spatial program. Omics studies and spatial biology connect developmental programs with oncological events and explain key spatial features of metastatic aggressiveness. Dysregulation of prominent PCP factors such as specific representatives of the WNT and FZD families in malignant melanoma recapitulates the development program of normal melanocytes but in an uncontrolled and disorganized fashion.
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Affiliation(s)
- Fabian V. Filipp
- Cancer Systems Biology, Institute of Diabetes and Cancer, Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764 München, Germany
- School of Life Sciences Weihenstephan, Technical University München, Maximus-von-Imhof-Forum 3, D-85354 Freising, Germany
- Institute for Advanced Study, Technical University München, Maximus-von-Imhof-Forum 3, D-85354 Freising, Germany
- Metaflux, San Diego, CA, 92105, United States of America
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14
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Filipp FV. Spatial cancer systems biology resolves heterotypic interactions and identifies disruption of spatial hierarchy as a pathological driver event. ARXIV 2023:2303.00933. [PMID: 36911273 PMCID: PMC10002759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Spatially annotated single-cell datasets provide unprecedented opportunities to dissect cell-cell communication in development and disease. Heterotypic signaling includes interactions between different cell types and is well established in tissue development and spatial organization. Epithelial organization requires several different programs that are tightly regulated. Planar cell polarity is the organization of epithelial cells along the planar axis orthogonal to the apical-basal axis. In this study, we investigate planar cell polarity factors and explore the implications of developmental regulators as malignant drivers. Utilizing cancer systems biology analysis, we derive gene expression network for WNT-ligands (WNT) and their cognate frizzled (FZD) receptors in skin cutaneous melanoma. The profiles supported by unsupervised clustering of multiple-sequence alignments identify ligand-independent signaling and implications for metastatic progression based on the underpinning developmental spatial program. Omics studies and spatial biology connect developmental programs with oncological events and explain key spatial features of metastatic aggressiveness. Dysregulation of prominent planar cell polarity factors such specific representative of the WNT and FZD families in malignant melanoma recapitulates the development program of normal melanocytes but in an uncontrolled and disorganized fashion.
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15
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Jung S, Lee JS. Single-Cell Genomics for Investigating Pathogenesis of Inflammatory Diseases. Mol Cells 2023; 46:120-129. [PMID: 36859476 PMCID: PMC9982059 DOI: 10.14348/molcells.2023.0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 03/03/2023] Open
Abstract
Recent technical advances have enabled unbiased transcriptomic and epigenetic analysis of each cell, known as "single-cell analysis". Single-cell analysis has a variety of technical approaches to investigate the state of each cell, including mRNA levels (transcriptome), the immune repertoire (immune repertoire analysis), cell surface proteins (surface proteome analysis), chromatin accessibility (epigenome), and accordance with genome variants (eQTLs; expression quantitative trait loci). As an effective tool for investigating robust immune responses in coronavirus disease 2019 (COVID-19), many researchers performed single-cell analysis to capture the diverse, unbiased immune cell activation and differentiation. Despite challenges elucidating the complicated immune microenvironments of chronic inflammatory diseases using existing experimental methods, it is now possible to capture the simultaneous immune features of different cell types across inflamed tissues using various single-cell tools. In this review, we introduce patient-based and experimental mouse model research utilizing single-cell analyses in the field of chronic inflammatory diseases, as well as multi-organ atlas targeting immune cells.
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Affiliation(s)
- Seyoung Jung
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jeong Seok Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
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