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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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2
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Taylor MA, El Kurdi A, Hailer A, Wang S, Yuan M, Mukhopadhyay S, Bhutani T, North JP, Cho RJ, Cheng JB. Optimizing Single T-Cell Transcriptomic Discrimination of Atopic Dermatitis Versus Psoriasis Vulgaris. J Invest Dermatol 2024; 144:898-901.e3. [PMID: 37879399 DOI: 10.1016/j.jid.2023.09.283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/09/2023] [Accepted: 09/12/2023] [Indexed: 10/27/2023]
Affiliation(s)
- Mark A Taylor
- Department of Dermatology, University of California San Francisco, San Francisco, California, USA
| | - Abdullah El Kurdi
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Ashley Hailer
- Department of Dermatology, University of California San Francisco, San Francisco, California, USA; Dermatology, Veterans Affairs Medical Center, San Francisco, California, USA
| | - Sijia Wang
- Department of Dermatology, University of California San Francisco, San Francisco, California, USA; Dermatology, Veterans Affairs Medical Center, San Francisco, California, USA; Department of Dermatology, The Second Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Michelle Yuan
- Department of Dermatology, University of California San Francisco, San Francisco, California, USA
| | | | - Tina Bhutani
- Department of Dermatology, University of California San Francisco, San Francisco, California, USA
| | - Jeffrey P North
- Dermatopathology Service, University of California San Francisco, San Francisco, California, USA
| | - Raymond J Cho
- Department of Dermatology, University of California San Francisco, San Francisco, California, USA.
| | - Jeffrey B Cheng
- Department of Dermatology, University of California San Francisco, San Francisco, California, USA; Dermatology, Veterans Affairs Medical Center, San Francisco, California, USA.
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3
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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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Chen L, Chang D, Tandukar B, Deivendran D, Pozniak J, Cruz-Pacheco N, Cho RJ, Cheng J, Yeh I, Marine C, Bastian BC, Ji AL, Shain AH. STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer. Genome Biol 2023; 24:273. [PMID: 38037084 PMCID: PMC10688493 DOI: 10.1186/s13059-023-03121-6] [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: 01/08/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023] Open
Abstract
Spatial transcriptomic technologies, such as the Visium platform, measure gene expression in different regions of tissues. Here, we describe new software, STmut, to visualize somatic point mutations, allelic imbalance, and copy number alterations in Visium data. STmut is tested on fresh-frozen Visium data, formalin-fixed paraffin-embedded (FFPE) Visium data, and tumors with and without matching DNA sequencing data. Copy number is inferred on all conditions, but the chemistry of the FFPE platform does not permit analyses of single nucleotide variants. Taken together, we propose solutions to add the genetic dimension to spatial transcriptomic data and describe the limitations of different datatypes.
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Affiliation(s)
- Limin Chen
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
| | - Darwin Chang
- Department of Immunology, H. Lee Moffitt Cancer Center, Tampa, USA
| | - Bishal Tandukar
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
| | - Delahny Deivendran
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
| | - Joanna Pozniak
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Louvain, Belgium
- Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Louvain, Belgium
| | - Noel Cruz-Pacheco
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
| | - Jeffrey Cheng
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
| | - Iwei Yeh
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
- Department of Pathology, University of California, San Francisco, San Francisco, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA
| | - Chris Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Louvain, Belgium
- Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Louvain, Belgium
| | - Boris C Bastian
- Department of Dermatology, University of California, San Francisco, San Francisco, USA
- Department of Pathology, University of California, San Francisco, San Francisco, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA
| | - Andrew L Ji
- Department of Dermatology, Department of Oncological Sciences, Black Family Stem Cell Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, USA
| | - A Hunter Shain
- Department of Dermatology, University of California, San Francisco, San Francisco, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA.
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6
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Yu DM, Zhao J, Lee EE, Kim D, Mahapatra R, Rose EK, Zhou Z, Hosler C, El Kurdi A, Choe JY, Abel ED, Hoxhaj G, Westover KD, Cho RJ, Cheng JB, Wang RC. GLUT3 promotes macrophage signaling and function via RAS-mediated endocytosis in atopic dermatitis and wound healing. J Clin Invest 2023; 133:e170706. [PMID: 37721853 PMCID: PMC10617774 DOI: 10.1172/jci170706] [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: 03/20/2023] [Accepted: 09/08/2023] [Indexed: 09/20/2023] Open
Abstract
The facilitative GLUT1 and GLUT3 hexose transporters are expressed abundantly in macrophages, but whether they have distinct functions remains unclear. We confirmed that GLUT1 expression increased after M1 polarization stimuli and found that GLUT3 expression increased after M2 stimulation in macrophages. Conditional deletion of Glut3 (LysM-Cre Glut3fl/fl) impaired M2 polarization of bone marrow-derived macrophages. Alternatively activated macrophages from the skin of patients with atopic dermatitis showed increased GLUT3 expression, and a calcipotriol-induced model of atopic dermatitis was rescued in LysM-Cre Glut3fl/fl mice. M2-like macrophages expressed GLUT3 in human wound tissues as assessed by transcriptomics and costaining, and GLUT3 expression was significantly decreased in nonhealing, compared with healing, diabetic foot ulcers. In an excisional wound healing model, LysM-Cre Glut3fl/fl mice showed significantly impaired M2 macrophage polarization and delayed wound healing. GLUT3 promoted IL-4/STAT6 signaling, independently of its glucose transport activity. Unlike plasma membrane-localized GLUT1, GLUT3 was localized primarily to endosomes and was required for the efficient endocytosis of IL-4Rα subunits. GLUT3 interacted directly with GTP-bound RAS in vitro and in vivo through its intracytoplasmic loop domain, and this interaction was required for efficient STAT6 activation and M2 polarization. PAK activation and macropinocytosis were also impaired without GLUT3, suggesting broader roles for GLUT3 in the regulation of endocytosis. Thus, GLUT3 is required for efficient alternative macrophage polarization and function, through a glucose transport-independent, RAS-mediated role in the regulation of endocytosis and IL-4/STAT6 activation.
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Affiliation(s)
- Dong-Min Yu
- Department of Dermatology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Jiawei Zhao
- Division of Hematology/Oncology, Boston Children’s Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Eunice E. Lee
- Department of Dermatology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Dohun Kim
- Children’s Medical Center Research Institute and
| | - Ruchika Mahapatra
- Department of Dermatology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Elysha K. Rose
- Department of Dermatology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Zhiwei Zhou
- Departments of Biochemistry and Radiation Oncology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Calvin Hosler
- Department of Dermatology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Abdullah El Kurdi
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Jun-Yong Choe
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - E. Dale Abel
- Department of Medicine, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Gerta Hoxhaj
- Children’s Medical Center Research Institute and
| | - Kenneth D. Westover
- Departments of Biochemistry and Radiation Oncology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Raymond J. Cho
- Department of Dermatology, UCSF, San Francisco, California, USA
| | | | - Richard C. Wang
- Department of Dermatology, UT Southwestern Medical Center, Dallas, Texas, USA
- Harold C. Simmons Cancer Center, UT Southwestern Medical Center, Dallas, Texas, USA
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7
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Hailer AA, Wu D, El Kurdi A, Yuan M, Cho RJ, Cheng JB. Isolation of human cutaneous immune cells for single-cell RNA sequencing. STAR Protoc 2023; 4:102239. [PMID: 37120815 PMCID: PMC10173011 DOI: 10.1016/j.xpro.2023.102239] [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: 01/04/2023] [Revised: 02/21/2023] [Accepted: 03/23/2023] [Indexed: 05/01/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) allows for high-resolution analysis of transcriptionally dysregulated cell subpopulations in inflammatory diseases. However, it can be challenging to properly isolate viable immune cells from human skin for scRNA-seq due to its barrier properties. Here, we present a protocol to isolate high-viability human cutaneous immune cells. We describe steps for obtaining and enzymatically dissociating a skin biopsy specimen and isolating immune cells using flow cytometry. We then provide an overview of downstream computational techniques to analyze sequencing data. For complete details on the use and execution of this protocol, please refer to Cook et al. (2022)1 and Liu et al. (2022).2.
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Affiliation(s)
- Ashley A Hailer
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA; Dermatology, Veterans Affairs Medical Center, San Francisco, CA 94121, USA
| | - David Wu
- Department of Dermatology, 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
| | - Michelle Yuan
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA; Dermatology, Veterans Affairs Medical Center, San Francisco, CA 94121, USA
| | - Raymond J Cho
- Department of Dermatology, 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, Veterans Affairs Medical Center, San Francisco, CA 94121, USA.
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8
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Hakimi M, North JP, Taylor MA, Hailer A, Liu Y, Kim E, Morehead K, Shinkai K, Bhutani T, Cheng JB, Cho RJ. Transcriptomics aids differentiation of IL-23 overactivity in a patient with atypical skin and joint disease. Lancet 2023; 401:1381. [PMID: 37087172 DOI: 10.1016/s0140-6736(23)00455-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 01/30/2023] [Accepted: 02/28/2023] [Indexed: 04/24/2023]
Affiliation(s)
- Marwa Hakimi
- Department of Dermatology, University of California, San Francisco, CA, USA
| | - Jeffrey P North
- Department of Dermatology, University of California, San Francisco, CA, USA
| | - Mark A Taylor
- Department of Dermatology, University of California, San Francisco, CA, USA
| | - Ashley Hailer
- Department of Dermatology, University of California, San Francisco, CA, USA
| | - Yale Liu
- Department of Dermatology, University of California, San Francisco, CA, USA
| | - Esther Kim
- Division of Plastic and Reconstructive Surgery, University of California, San Francisco, CA, USA
| | - Kerstin Morehead
- Department of Rheumatology, University of California, San Francisco, CA, USA
| | - Kanade Shinkai
- Department of Dermatology, University of California, San Francisco, CA, USA
| | - Tina Bhutani
- Department of Dermatology, University of California, San Francisco, CA, USA
| | - Jeffrey B Cheng
- Department of Dermatology, University of California, San Francisco, CA, USA; Department of Dermatology, Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, CA, USA.
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9
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Cook CP, Taylor M, Liu Y, Schmidt R, Sedgewick A, Kim E, Hailer A, North JP, Harirchian P, Wang H, Kashem SW, Shou Y, McCalmont TC, Benz SC, Choi J, Purdom E, Marson A, Ramos SB, Cheng JB, Cho RJ. A single-cell transcriptional gradient in human cutaneous memory T cells restricts Th17/Tc17 identity. Cell Rep Med 2022; 3:100715. [PMID: 35977472 PMCID: PMC9418858 DOI: 10.1016/j.xcrm.2022.100715] [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: 01/04/2022] [Revised: 05/21/2022] [Accepted: 07/14/2022] [Indexed: 11/29/2022]
Abstract
The homeostatic mechanisms that fail to restrain chronic tissue inflammation in diseases, such as psoriasis vulgaris, remain incompletely understood. We profiled transcriptomes and epitopes of single psoriatic and normal skin-resident T cells, revealing a gradated transcriptional program of coordinately regulated inflammation-suppressive genes. This program, which is sharply suppressed in lesional skin, strikingly restricts Th17/Tc17 cytokine and other inflammatory mediators on the single-cell level. CRISPR-based deactivation of two core components of this inflammation-suppressive program, ZFP36L2 and ZFP36, replicates the interleukin-17A (IL-17A), granulocyte macrophage-colony-stimulating factor (GM-CSF), and interferon gamma (IFNγ) elevation in psoriatic memory T cells deficient in these transcripts, functionally validating their influence. Combinatoric expression analysis indicates the suppression of specific inflammatory mediators by individual program members. Finally, we find that therapeutic IL-23 blockade reduces Th17/Tc17 cell frequency in lesional skin but fails to normalize this inflammatory-suppressive program, suggesting how treated lesions may be primed for recurrence after withdrawal of treatment.
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Affiliation(s)
- Christopher P. Cook
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA,Dermatology, Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Mark Taylor
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA,Clinical Research Centre, Medical University of Białystok, Białystok, Poland
| | - Yale Liu
- Dermatology, Veterans Affairs Medical Center, San Francisco, CA, USA,Department of Dermatology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, ShaanXi 710004, P.R. China
| | - Ralf Schmidt
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | | | - Esther Kim
- Division of Plastic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Ashley Hailer
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey P. North
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Paymann Harirchian
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA,Dermatology, Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Hao Wang
- Department of Statistics, University of California, Berkeley, Berkeley, CA, USA
| | - Sakeen W. Kashem
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA,Dermatology, Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Yanhong Shou
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Timothy C. McCalmont
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA,Department of Pathology, University of California, San Francisco, San Francisco, CA, USA,Golden State Dermatology Associates, Walnut Creek, CA, USA
| | | | - Jaehyuk Choi
- Department of Dermatology, Northwestern University, Evanston, IL, USA
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, Berkeley, CA, USA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Silvia B.V. Ramos
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeffrey B. Cheng
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA,Dermatology, Veterans Affairs Medical Center, San Francisco, CA, USA,Corresponding author
| | - Raymond J. Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA,Corresponding author
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10
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Liu Y, Wang H, Cook C, Taylor MA, North JP, Hailer A, Shou Y, Sadik A, Kim E, Purdom E, Cheng JB, Cho RJ. Defining Patient-Level Molecular Heterogeneity in Psoriasis Vulgaris Based on Single-Cell Transcriptomics. Front Immunol 2022; 13:842651. [PMID: 35958578 PMCID: PMC9360479 DOI: 10.3389/fimmu.2022.842651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Identifying genetic variation underlying human diseases establishes targets for therapeutic development and helps tailor treatments to individual patients. Large-scale transcriptomic profiling has extended the study of such molecular heterogeneity between patients to somatic tissues. However, the lower resolution of bulk RNA profiling, especially in a complex, composite tissue such as the skin, has limited its success. Here we demonstrate approaches to interrogate patient-level molecular variance in a chronic skin inflammatory disease, psoriasis vulgaris, leveraging single-cell RNA-sequencing of CD45+ cells isolated from active lesions. Highly psoriasis-specific transcriptional abnormalities display greater than average inter-individual variance, nominating them as potential sources of clinical heterogeneity. We find that one of these chemokines, CXCL13, demonstrates significant correlation with severity of lesions within our patient series. Our analyses also establish that genes elevated in psoriatic skin-resident memory T cells are enriched for programs orchestrating chromatin and CDC42-dependent cytoskeleton remodeling, specific components of which are distinctly correlated with and against Th17 identity on a single-cell level. Collectively, these analyses describe systematic means to dissect cell type- and patient-level differences in cutaneous psoriasis using high-resolution transcriptional profiles of human inflammatory disease.
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Affiliation(s)
- Yale Liu
- Department of Dermatology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Dermatology, Veterans Affairs Medical Center, San Francisco, CA, United States
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, United States
| | - Hao Wang
- Department of Statistics, University of California, Berkeley, Berkeley, CA, United States
| | - Christopher Cook
- Department of Dermatology, Veterans Affairs Medical Center, San Francisco, CA, United States
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, United States
| | - Mark A. Taylor
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, United States
- Clinical Research Centre, Medical University of Białystok, Białystok, Poland
| | - Jeffrey P. North
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, United States
| | - Ashley Hailer
- Department of Dermatology, Veterans Affairs Medical Center, San Francisco, CA, United States
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, United States
| | - Yanhong Shou
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Arsil Sadik
- Department of Dermatology, Veterans Affairs Medical Center, San Francisco, CA, United States
| | - Esther Kim
- Department of Plastic Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, Berkeley, CA, United States
| | - Jeffrey B. Cheng
- Department of Dermatology, Veterans Affairs Medical Center, San Francisco, CA, United States
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, United States
- *Correspondence: Raymond J. Cho, ; Jeffrey B. Cheng,
| | - Raymond J. Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, United States
- *Correspondence: Raymond J. Cho, ; Jeffrey B. Cheng,
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11
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Zhang S, Leistico JR, Cho RJ, Cheng JB, Song JS. Spectral clustering of single-cell multi-omics data on multilayer graphs. Bioinformatics 2022; 38:3600-3608. [PMID: 35652725 DOI: 10.1093/bioinformatics/btac378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/20/2022] [Accepted: 05/30/2022] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Single-cell sequencing technologies that simultaneously generate multimodal cellular profiles present opportunities for improved understanding of cell heterogeneity in tissues. How the multimodal information can be integrated to obtain a common cell type identification, however, poses a computational challenge. Multilayer graphs provide a natural representation of multi-omic single-cell sequencing datasets, and finding cell clusters may be understood as a multilayer graph partition problem. RESULTS We introduce two spectral algorithms on multilayer graphs, spectral clustering on multilayer graphs (SCML) and the weighted locally linear (WLL) method, to cluster cells in multi-omic single-cell sequencing datasets. We connect these algorithms through a unifying mathematical framework that represents each layer using a Hamiltonian operator and a mixture of its eigenstates to integrate the multiple graph layers, demonstrating in the process that the WLL method is a rigorous multilayer spectral graph theoretic reformulation of the popular Seurat weighted nearest neighbor (WNN) algorithm. Implementing our algorithms and applying them to a CITE-seq dataset of cord blood mononuclear cells yields results similar to the Seurat WNN analysis. Our work thus extends spectral methods to multimodal single-cell data analysis. AVAILABILITY The code used in this study can be found at https://github.com/jssong-lab/sc-spectrum. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Shuyi Zhang
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jacob R Leistico
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey B Cheng
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Jun S Song
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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12
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Liu Y, Wang H, Taylor M, Cook C, Martínez-Berdeja A, North JP, Harirchian P, Hailer AA, Zhao Z, Ghadially R, Ricardo-Gonzalez RR, Grekin RC, Mauro TM, Kim E, Choi J, Purdom E, Cho RJ, Cheng JB. Classification of human chronic inflammatory skin disease based on single-cell immune profiling. Sci Immunol 2022; 7:eabl9165. [PMID: 35427179 PMCID: PMC9301819 DOI: 10.1126/sciimmunol.abl9165] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [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] [Indexed: 01/17/2023]
Abstract
Inflammatory conditions represent the largest class of chronic skin disease, but the molecular dysregulation underlying many individual cases remains unclear. Single-cell RNA sequencing (scRNA-seq) has increased precision in dissecting the complex mixture of immune and stromal cell perturbations in inflammatory skin disease states. We single-cell-profiled CD45+ immune cell transcriptomes from skin samples of 31 patients (7 atopic dermatitis, 8 psoriasis vulgaris, 2 lichen planus (LP), 1 bullous pemphigoid (BP), 6 clinical/histopathologically indeterminate rashes, and 7 healthy controls). Our data revealed active proliferative expansion of the Treg and Trm components and universal T cell exhaustion in human rashes, with a relative attenuation of antigen-presenting cells. Skin-resident memory T cells showed the greatest transcriptional dysregulation in both atopic dermatitis and psoriasis, whereas atopic dermatitis also demonstrated recurrent abnormalities in ILC and CD8+ cytotoxic lymphocytes. Transcript signatures differentiating these rash types included genes previously implicated in T helper cell (TH2)/TH17 diatheses, segregated in unbiased functional networks, and accurately identified disease class in untrained validation data sets. These gene signatures were able to classify clinicopathologically ambiguous rashes with diagnoses consistent with therapeutic response. Thus, we have defined major classes of human inflammatory skin disease at the molecular level and described a quantitative method to classify indeterminate instances of pathologic inflammation. To make this approach accessible to the scientific community, we created a proof-of-principle web interface (RashX), where scientists and clinicians can visualize their patient-level rash scRNA-seq-derived data in the context of our TH2/TH17 transcriptional framework.
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Affiliation(s)
- Yale Liu
- Department of Dermatology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, ShaanXi 710004, P. R. China
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA
- Dermatology, Veterans Affairs Medical Center, San Francisco, CA 94121, USA
| | - Hao Wang
- Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mark Taylor
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Christopher Cook
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA
- Dermatology, Veterans Affairs Medical Center, San Francisco, CA 94121, USA
| | | | - Jeffrey P North
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Paymann Harirchian
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA
- Dermatology, Veterans Affairs Medical Center, San Francisco, CA 94121, USA
| | - Ashley A Hailer
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA
- Dermatology, Veterans Affairs Medical Center, San Francisco, CA 94121, USA
| | - Zijun Zhao
- Santa Clara Valley Medical Center, Santa Clara, CA 95128, USA
| | - Ruby Ghadially
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA
- Dermatology, Veterans Affairs Medical Center, San Francisco, CA 94121, USA
| | - Roberto R Ricardo-Gonzalez
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA
- Department of Immunology and Microbiology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Roy C Grekin
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Theodora M Mauro
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94107, USA
- Dermatology, Veterans Affairs Medical Center, San Francisco, CA 94121, USA
| | - Esther Kim
- Department of Plastic Surgery, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Jaehyuk Choi
- Department of Dermatology, Northwestern School of Medicine, Chicago, IL 60611, USA
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Raymond J Cho
- Department of Dermatology, 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, Veterans Affairs Medical Center, San Francisco, CA 94121, USA
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13
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Patel J, den Breems NY, Tuluc M, Johnson J, Curry JM, South AP, Cho RJ. Elevated APOBEC mutational signatures implicate chronic injury in etiology of an aggressive head-and-neck squamous cell carcinoma: a case report. J Med Case Rep 2021; 15:252. [PMID: 33926553 PMCID: PMC8086066 DOI: 10.1186/s13256-021-02685-w] [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: 03/24/2020] [Accepted: 01/18/2021] [Indexed: 12/02/2022] Open
Abstract
Background Aggressive squamous cell carcinomas (SCCs) present frequently in the context of chronic skin injury occurring in patients with the congenital blistering disease recessive dystrophic epidermolysis bullosa. Recently, these cancers were shown to harbor mutation signatures associated with endogenous deaminases of the active polynucleotide cytosine deaminase family, collectively termed APOBEC, and clock-like COSMIC [Catalogue of Somatic Mutations in Cancer] signatures, which are associated with normal aging and might result from cumulative DNA replication errors. We present a case of a nasal septal SCC arising in the context of recurrent injury, but also modest past tobacco use. Our genetic analysis of this tumor reveals unusually high APOBEC and clock-like but low tobacco-related COSMIC signatures, suggesting that chronic injury may have played a primary role in somatic mutation. This case report demonstrates how signature-based analyses may implicate key roles for certain mutagenic forces in individual malignancies such as head-and-neck SCC, with multiple etiological origins. Case presentation We report the case of a 43-year-old male former smoker who presented with congestion and swelling following a traumatic nasal fracture. During surgery, the mucosa surrounding the right nasal valve appeared abnormal, and biopsies revealed invasive keratinizing SCC. Frozen section biopsies revealed multiple areas to be positive for SCC. Gene sequencing showed loss of PTEN (exons 2–8), CDKN2A/B and TP53 (exons 8–9), MYC amplification, and BLM S338*. Exome sequencing data also revealed that 36% of mutations matched an APOBEC mutational signature (COSMIC signatures 2 and 13) and 53% of mutations matched the clock-like mutation signature (COSMIC signature 5). These proportions place this tumor in the 90th percentile bearing each signature, independently, in a reference data set combining cutaneous and The Cancer Genome Atlas (TCGA) head and neck SCC data. In contrast, few mutations harbored a tobacco-related COSMIC signature 4, representing about the 10th percentile in our reference SCC data set. The patient was treated with partial rhinectomy with local flap reconstruction, bilateral neck dissection, and adjuvant radiation therapy; the patient remains disease-free to date. Conclusion Based on comparative mutational signature analysis, we propose that the history of tobacco use and traumatic injury may have collaborated in activating APOBEC enzymes and the clock-like mutational process, ultimately leading to cancer formation. Clinical awareness of the relationship between epithelial injury and tumorigenesis should enhance earlier detection of this particularly aggressive type of cancer.
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Affiliation(s)
- Jena Patel
- Department of Otolaryngology-Head and Neck Surgery, Thomas Jefferson University, 925 Chestnut St, Philadelphia, PA, 19801, USA.
| | - Nicoline Y den Breems
- Centre for Advanced Computational Solutions (C-fACS), Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, 7647, Canterbury, New Zealand
| | - Madalina Tuluc
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Jennifer Johnson
- Department of Oncology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Joseph M Curry
- Department of Otolaryngology-Head and Neck Surgery, Thomas Jefferson University, 925 Chestnut St, Philadelphia, PA, 19801, USA
| | - Andrew P South
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, CA, 94115, USA
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14
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Vergara IA, Mintoff CP, Sandhu S, McIntosh L, Young RJ, Wong SQ, Colebatch A, Cameron DL, Kwon JL, Wolfe R, Peng A, Ellul J, Dou X, Fedele C, Boyle S, Arnau GM, Raleigh J, Hatzimihalis A, Szeto P, Mooi J, Widmer DS, Cheng PF, Amann V, Dummer R, Hayward N, Wilmott J, Scolyer RA, Cho RJ, Bowtell D, Thorne H, Alsop K, Cordner S, Woodford N, Leditschke J, O'Brien P, Dawson SJ, McArthur GA, Mann GJ, Levesque MP, Papenfuss AT, Shackleton M. Evolution of late-stage metastatic melanoma is dominated by aneuploidy and whole genome doubling. Nat Commun 2021; 12:1434. [PMID: 33664264 PMCID: PMC7933255 DOI: 10.1038/s41467-021-21576-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 01/26/2021] [Indexed: 12/24/2022] Open
Abstract
Although melanoma is initiated by acquisition of point mutations and limited focal copy number alterations in melanocytes-of-origin, the nature of genetic changes that characterise lethal metastatic disease is poorly understood. Here, we analyze the evolution of human melanoma progressing from early to late disease in 13 patients by sampling their tumours at multiple sites and times. Whole exome and genome sequencing data from 88 tumour samples reveals only limited gain of point mutations generally, with net mutational loss in some metastases. In contrast, melanoma evolution is dominated by whole genome doubling and large-scale aneuploidy, in which widespread loss of heterozygosity sculpts the burden of point mutations, neoantigens and structural variants even in treatment-naïve and primary cutaneous melanomas in some patients. These results imply that dysregulation of genomic integrity is a key driver of selective clonal advantage during melanoma progression.
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Affiliation(s)
- Ismael A Vergara
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Melanoma Institute of Australia, Sydney, Australia
| | | | | | - Lachlan McIntosh
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | | | - Stephen Q Wong
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | | | - Daniel L Cameron
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Julia Lai Kwon
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Rory Wolfe
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Angela Peng
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Australia
| | - Jason Ellul
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Xuelin Dou
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Clare Fedele
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Samantha Boyle
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | | | | | | | - Pacman Szeto
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Australia
| | - Jennifer Mooi
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Daniel S Widmer
- Department of Dermatology, University of Zürich Hospital, Zürich, Switzerland
| | - Phil F Cheng
- Department of Dermatology, University of Zürich Hospital, Zürich, Switzerland
| | - Valerie Amann
- Department of Dermatology, University of Zürich Hospital, Zürich, Switzerland
| | - Reinhard Dummer
- Department of Dermatology, University of Zürich Hospital, Zürich, Switzerland
| | - Nicholas Hayward
- Melanoma Institute of Australia, Sydney, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - Richard A Scolyer
- Melanoma Institute of Australia, Sydney, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, Australia
- Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, CA, USA
| | - David Bowtell
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Heather Thorne
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Kathryn Alsop
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Stephen Cordner
- The Victorian Institute of Forensic Medicine, Melbourne, Australia
| | - Noel Woodford
- The Victorian Institute of Forensic Medicine, Melbourne, Australia
| | - Jodie Leditschke
- The Victorian Institute of Forensic Medicine, Melbourne, Australia
| | - Patricia O'Brien
- The Victorian Institute of Forensic Medicine, Melbourne, Australia
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Centre of Cancer Research, The University of Melbourne, Parkville, VIC, Australia
| | - Grant A McArthur
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Graham J Mann
- Melanoma Institute of Australia, Sydney, Australia
- Centre for Cancer Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Mitchell P Levesque
- Department of Dermatology, University of Zürich Hospital, Zürich, Switzerland
| | - Anthony T Papenfuss
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- Department of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.
| | - Mark Shackleton
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.
- Department of Oncology, Alfred Health, Melbourne, Australia.
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15
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Watkins TBK, Lim EL, Petkovic M, Elizalde S, Birkbak NJ, Wilson GA, Moore DA, Grönroos E, Rowan A, Dewhurst SM, Demeulemeester J, Dentro SC, Horswell S, Au L, Haase K, Escudero M, Rosenthal R, Bakir MA, Xu H, Litchfield K, Lu WT, Mourikis TP, Dietzen M, Spain L, Cresswell GD, Biswas D, Lamy P, Nordentoft I, Harbst K, Castro-Giner F, Yates LR, Caramia F, Jaulin F, Vicier C, Tomlinson IPM, Brastianos PK, Cho RJ, Bastian BC, Dyrskjøt L, Jönsson GB, Savas P, Loi S, Campbell PJ, Andre F, Luscombe NM, Steeghs N, Tjan-Heijnen VCG, Szallasi Z, Turajlic S, Jamal-Hanjani M, Van Loo P, Bakhoum SF, Schwarz RF, McGranahan N, Swanton C. Pervasive chromosomal instability and karyotype order in tumour evolution. Nature 2020; 587:126-132. [PMID: 32879494 PMCID: PMC7611706 DOI: 10.1038/s41586-020-2698-6] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [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: 04/01/2019] [Accepted: 06/24/2020] [Indexed: 12/13/2022]
Abstract
Chromosomal instability in cancer consists of dynamic changes to the number and structure of chromosomes1,2. The resulting diversity in somatic copy number alterations (SCNAs) may provide the variation necessary for tumour evolution1,3,4. Here we use multi-sample phasing and SCNA analysis of 1,421 samples from 394 tumours across 22 tumour types to show that continuous chromosomal instability results in pervasive SCNA heterogeneity. Parallel evolutionary events, which cause disruption in the same genes (such as BCL9, MCL1, ARNT (also known as HIF1B), TERT and MYC) within separate subclones, were present in 37% of tumours. Most recurrent losses probably occurred before whole-genome doubling, that was found as a clonal event in 49% of tumours. However, loss of heterozygosity at the human leukocyte antigen (HLA) locus and loss of chromosome 8p to a single haploid copy recurred at substantial subclonal frequencies, even in tumours with whole-genome doubling, indicating ongoing karyotype remodelling. Focal amplifications that affected chromosomes 1q21 (which encompasses BCL9, MCL1 and ARNT), 5p15.33 (TERT), 11q13.3 (CCND1), 19q12 (CCNE1) and 8q24.1 (MYC) were frequently subclonal yet appeared to be clonal within single samples. Analysis of an independent series of 1,024 metastatic samples revealed that 13 focal SCNAs were enriched in metastatic samples, including gains in chromosome 8q24.1 (encompassing MYC) in clear cell renal cell carcinoma and chromosome 11q13.3 (encompassing CCND1) in HER2+ breast cancer. Chromosomal instability may enable the continuous selection of SCNAs, which are established as ordered events that often occur in parallel, throughout tumour evolution.
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Affiliation(s)
- Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Emilia L Lim
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Marina Petkovic
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Sergi Elizalde
- Department of Mathematics, Dartmouth College, Hanover, NH, USA
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
- Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Eva Grönroos
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Sally M Dewhurst
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Jonas Demeulemeester
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Stefan C Dentro
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Oxford Big Data Institute, University of Oxford, Oxford, UK
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Stuart Horswell
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Lewis Au
- Renal and Skin Units, The Royal Marsden Hospital NHS Foundation Trust, London, UK
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Kerstin Haase
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Mickael Escudero
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Rachel Rosenthal
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Hang Xu
- Stanford Cancer Institute, Stanford, CA, USA
| | - Kevin Litchfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Wei Ting Lu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Thanos P Mourikis
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, University College London Cancer Institute, University College London, London, UK
| | - Michelle Dietzen
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, University College London Cancer Institute, University College London, London, UK
| | - Lavinia Spain
- Renal and Skin Units, The Royal Marsden Hospital NHS Foundation Trust, London, UK
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - George D Cresswell
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London, UK
| | - Dhruva Biswas
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Philippe Lamy
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Katja Harbst
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
- Lund University Cancer Centre, Lund University, Lund, Sweden
| | - Francesc Castro-Giner
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Lucy R Yates
- Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Clinical Oncology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Franco Caramia
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Cécile Vicier
- Department of Medical Oncology, Institut Paoli-Calmettes, Aix-Marseille University, Marseille, France
| | - Ian P M Tomlinson
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Priscilla K Brastianos
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Boris C Bastian
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Lars Dyrskjøt
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Göran B Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
- Lund University Cancer Centre, Lund University, Lund, Sweden
| | - Peter Savas
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Sherene Loi
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Fabrice Andre
- INSERM U981, PRISM Institute, Gustave Roussy, Villejuif, France
- Department of Medical Oncology, Gustave Roussy, Villejuif, France
- Medical School, Université Paris Saclay, Kremlin Bicetre, France
| | - Nicholas M Luscombe
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London, UK
- UCL Genetics Institute, Department of Genetics, Evolution & Environment, University College London, London, UK
- Okinawa Institute of Science & Technology, Okinawa, Japan
| | - Neeltje Steeghs
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Vivianne C G Tjan-Heijnen
- Department of Medical Oncology, School of GROW, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Zoltan Szallasi
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- 2nd Department of Pathology, SE-NAP Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
| | - Samra Turajlic
- Renal and Skin Units, The Royal Marsden Hospital NHS Foundation Trust, London, UK
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals, London, UK
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, University College London Cancer Institute, University College London, London, UK.
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Department of Medical Oncology, University College London Hospitals, London, UK.
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16
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Liu Y, Cook C, Sedgewick AJ, Zhang S, Fassett MS, Ricardo-Gonzalez RR, Harirchian P, Kashem SW, Hanakawa S, Leistico JR, North JP, Taylor MA, Zhang W, Man MQ, Charruyer A, Beliakova-Bethell N, Benz SC, Ghadially R, Mauro TM, Kaplan DH, Kabashima K, Choi J, Song JS, Cho RJ, Cheng JB. Single-Cell Profiling Reveals Divergent, Globally Patterned Immune Responses in Murine Skin Inflammation. iScience 2020; 23:101582. [PMID: 33205009 PMCID: PMC7648132 DOI: 10.1016/j.isci.2020.101582] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/12/2020] [Accepted: 09/16/2020] [Indexed: 01/01/2023] Open
Abstract
Inflammatory response heterogeneity has impeded high-resolution dissection of diverse immune cell populations during activation. We characterize mouse cutaneous immune cells by single-cell RNA sequencing, after inducing inflammation using imiquimod and oxazolone dermatitis models. We identify 13 CD45+ subpopulations, which broadly represent most functionally characterized immune cell types. Oxazolone pervasively upregulates Jak2/Stat3 expression across T cells and antigen-presenting cells (APCs). Oxazolone also induces Il4/Il13 expression in newly infiltrating basophils, and Il4ra and Ccl24, most prominently in APCs. In contrast, imiquimod broadly upregulates Il17/Il22 and Ccl4/Ccl5. A comparative analysis of single-cell inflammatory transcriptional responses reveals that APC response to oxazolone is tightly restricted by cell identity, whereas imiquimod enforces shared programs on multiple APC populations in parallel. These global molecular patterns not only contrast immune responses on a systems level but also suggest that the mechanisms of new sources of inflammation can eventually be deduced by comparison to known signatures. Oxazolone pervasively upregulates Jak2/Stat3 expression across T cells and APCs Il4/Il13 induction in skin by oxazolone is dominated by infiltrating basophils Imiquimod broadly increases Il17/Il22 and Ccl4/Ccl5, extending to non-T cells Oxazolone induces more highly compartmentalized immune cell responses than imiquimod
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Affiliation(s)
- Yale Liu
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Dermatology Service, San Francisco Veterans Administration Health Care System, San Francisco, CA, USA
- Department of Dermatology, the Second Affiliated Hospital of Xi'an Jiaotong University, ShaanXi, China
| | - Christopher Cook
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Dermatology Service, San Francisco Veterans Administration Health Care System, San Francisco, CA, USA
| | | | - Shuyi Zhang
- Department of Physics, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Marlys S. Fassett
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Department of Immunology and Microbiology, University of California, San Francisco, San Francisco, CA, USA
| | - Roberto R. Ricardo-Gonzalez
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Department of Immunology and Microbiology, University of California, San Francisco, San Francisco, CA, USA
| | - Paymann Harirchian
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Dermatology Service, San Francisco Veterans Administration Health Care System, San Francisco, CA, USA
| | - Sakeen W. Kashem
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Sho Hanakawa
- Department of Dermatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Jacob R. Leistico
- Department of Physics, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Jeffrey P. North
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Mark A. Taylor
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Wei Zhang
- Dermatology Service, San Francisco Veterans Administration Health Care System, San Francisco, CA, USA
| | - Mao-Qiang Man
- Dermatology Service, San Francisco Veterans Administration Health Care System, San Francisco, CA, USA
| | - Alexandra Charruyer
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Dermatology Service, San Francisco Veterans Administration Health Care System, San Francisco, CA, USA
| | - Nadejda Beliakova-Bethell
- Department of Medicine, University of California San Diego, La Jolla, CA 92093-0679, USA
- Veterans Affairs Medical Center, San Diego, CA, USA
| | | | - Ruby Ghadially
- Dermatology Service, San Francisco Veterans Administration Health Care System, San Francisco, CA, USA
| | - Theodora M. Mauro
- Dermatology Service, San Francisco Veterans Administration Health Care System, San Francisco, CA, USA
| | - Daniel H. Kaplan
- Departments of Dermatology and Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kenji Kabashima
- Department of Dermatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Singapore Immunology Network (SIgN) and Skin Research Institute of Singapore (SRIS), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Jaehyuk Choi
- Department of Dermatology, Northwestern School of Medicine, Chicago, IL, USA
| | - Jun S. Song
- Department of Physics, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Raymond J. Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Corresponding author
| | - Jeffrey B. Cheng
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Dermatology Service, San Francisco Veterans Administration Health Care System, San Francisco, CA, USA
- Corresponding author
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17
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Fuentes I, Guttmann-Gruber C, Tockner B, Diem A, Klausegger A, Cofré-Araneda G, Figuera O, Hidalgo Y, Morandé P, Palisson F, Rebolledo-Jaramillo B, Yubero MJ, Cho RJ, Rishel HI, Marinkovich MP, Teng JMC, Webster TG, Prisco M, Eraso LH, Piñon Hofbauer J, South AP. Cells from discarded dressings differentiate chronic from acute wounds in patients with Epidermolysis Bullosa. Sci Rep 2020; 10:15064. [PMID: 32934247 PMCID: PMC7492213 DOI: 10.1038/s41598-020-71794-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/22/2020] [Indexed: 02/06/2023] Open
Abstract
Impaired wound healing complicates a wide range of diseases and represents a major cost to healthcare systems. Here we describe the use of discarded wound dressings as a novel, cost effective, accessible, and non-invasive method of isolating viable human cells present at the site of skin wounds. By analyzing 133 discarded wound dressings from 51 patients with the inherited skin-blistering disease epidermolysis bullosa (EB), we show that large numbers of cells, often in excess of 100 million per day, continually infiltrate wound dressings. We show, that the method is able to differentiate chronic from acute wounds, identifying significant increases in granulocytes in chronic wounds, and we show that patients with the junctional form of EB have significantly more cells infiltrating their wounds compared with patients with recessive dystrophic EB. Finally, we identify subsets of granulocytes and T lymphocytes present in all wounds paving the way for single cell profiling of innate and adaptive immune cells with relevance to wound pathologies. In summary, our study delineates findings in EB that have potential relevance for all chronic wounds, and presents a method of cellular isolation that has wide reaching clinical application.
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Affiliation(s)
- Ignacia Fuentes
- DEBRA Chile, Francisco de Villagra 392, Ñuñoa, Santiago, Chile. .,Centro de Genética Y Genómica, Facultad de Medicina Clínica Alemana, Universidad de Desarrollo, Santiago, Chile.
| | - Christina Guttmann-Gruber
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Birgit Tockner
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Anja Diem
- EB House Austria, Outpatient Unit, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Alfred Klausegger
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | | | - Olga Figuera
- DEBRA Chile, Francisco de Villagra 392, Ñuñoa, Santiago, Chile
| | - Yessia Hidalgo
- Consorcio Regenero, Chilean Consortium for Regenerative Medicine, 7620157, Santiago, Chile.,Cells for Cells, 7620157, Santiago, Chile.,Faculty of Medicine, Universidad de Los Andes, 7620001, Santiago, Las Condes, Chile
| | - Pilar Morandé
- DEBRA Chile, Francisco de Villagra 392, Ñuñoa, Santiago, Chile
| | - Francis Palisson
- DEBRA Chile, Francisco de Villagra 392, Ñuñoa, Santiago, Chile.,Facultad de Medicina Clínica Alemana, Universidad de Desarrollo, Santiago, Chile
| | - Boris Rebolledo-Jaramillo
- Centro de Genética Y Genómica, Facultad de Medicina Clínica Alemana, Universidad de Desarrollo, Santiago, Chile
| | - María Joao Yubero
- DEBRA Chile, Francisco de Villagra 392, Ñuñoa, Santiago, Chile.,Facultad de Medicina Clínica Alemana, Universidad de Desarrollo, Santiago, Chile
| | | | - Heather I Rishel
- Dermatology Department, Stanford University School of Medicine, Stanford, CA, USA
| | - M Peter Marinkovich
- Dermatology Department, Stanford University School of Medicine, Stanford, CA, USA.,Dermatology Service, VA Medical Center, Palo Alto, CA, USA
| | - Joyce M C Teng
- Dermatology Department, Stanford University School of Medicine, Stanford, CA, USA
| | - Timothy G Webster
- Dermatology and Cutaneous Biology, Thomas Jefferson University, Bluemle Life Sciences Building, Room 406, 233 South Tenth Street, Philadelphia, PA, 19107, USA
| | - Marco Prisco
- Dermatology and Cutaneous Biology, Thomas Jefferson University, Bluemle Life Sciences Building, Room 406, 233 South Tenth Street, Philadelphia, PA, 19107, USA
| | - Luis H Eraso
- Vascular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Josefina Piñon Hofbauer
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Andrew P South
- Dermatology and Cutaneous Biology, Thomas Jefferson University, Bluemle Life Sciences Building, Room 406, 233 South Tenth Street, Philadelphia, PA, 19107, USA. .,Joel and Joan Center for Fibrotic Diseases Research, Thomas Jefferson University, Philadelphia, PA, USA. .,Sydney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA.
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18
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Zhang S, Leistico JR, Cook C, Liu Y, Cho RJ, Cheng JB, Song JS. Riemannian geometry and statistical modeling correct for batch effects and control false discoveries in single-cell surface protein count data. Phys Rev E 2020; 102:012409. [PMID: 32794969 DOI: 10.1103/physreve.102.012409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/10/2020] [Indexed: 01/26/2023]
Abstract
Recent advances in next generation sequencing-based single-cell technologies have allowed high-throughput quantitative detection of cell-surface proteins along with the transcriptome in individual cells, extending our understanding of the heterogeneity of cell populations in diverse tissues that are in different diseased states or under different experimental conditions. Count data of surface proteins from the cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) technology pose new computational challenges, and there is currently a dearth of rigorous mathematical tools for analyzing the data. This work utilizes concepts and ideas from Riemannian geometry to remove batch effects between samples and develops a statistical framework for distinguishing positive signals from background noise. The strengths of these approaches are demonstrated on two independent CITE-seq data sets in mouse and human.
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Affiliation(s)
- Shuyi Zhang
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, USA
| | - Jacob R Leistico
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, USA
| | - Christopher Cook
- Department of Dermatology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Yale Liu
- Department of Dermatology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Jeffrey B Cheng
- Department of Dermatology, University of California, San Francisco, San Francisco, California 94143, USA.,Dermatology, Veterans Affairs Medical Center, San Francisco, California 94121, USA
| | - Jun S Song
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, USA
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19
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Heskett MB, Sanborn JZ, Boniface C, Goode B, Chapman J, Garg K, Rabban JT, Zaloudek C, Benz SC, Spellman PT, Solomon DA, Cho RJ. Multiregion exome sequencing of ovarian immature teratomas reveals 2N near-diploid genomes, paucity of somatic mutations, and extensive allelic imbalances shared across mature, immature, and disseminated components. Mod Pathol 2020; 33:1193-1206. [PMID: 31911616 PMCID: PMC7286805 DOI: 10.1038/s41379-019-0446-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 10/18/2019] [Revised: 11/30/2019] [Accepted: 12/15/2019] [Indexed: 01/31/2023]
Abstract
Immature teratoma is a subtype of malignant germ cell tumor of the ovary that occurs most commonly in the first three decades of life, frequently with bilateral ovarian disease. Despite being the second most common malignant germ cell tumor of the ovary, little is known about its genetic underpinnings. Here we performed multiregion whole-exome sequencing to interrogate the genetic zygosity, clonal relationship, DNA copy number, and mutational status of 52 pathologically distinct tumor components from ten females with ovarian immature teratomas, with bilateral tumors present in five cases and peritoneal dissemination in seven cases. We found that ovarian immature teratomas are genetically characterized by 2N near-diploid genomes with extensive loss of heterozygosity and an absence of genes harboring recurrent somatic mutations or known oncogenic variants. All components within a single ovarian tumor (immature teratoma, mature teratoma with different histologic patterns of differentiation, and yolk sac tumor) were found to harbor an identical pattern of loss of heterozygosity across the genome, indicating a shared clonal origin. In contrast, the four analyzed bilateral teratomas showed distinct patterns of zygosity changes in the right versus left sided tumors, indicating independent clonal origins. All disseminated teratoma components within the peritoneum (including gliomatosis peritonei) shared a clonal pattern of loss of heterozygosity with either the right or left primary ovarian tumor. The observed genomic loss of heterozygosity patterns indicate that diverse meiotic errors contribute to the formation of ovarian immature teratomas, with 11 out of the 15 genetically distinct clones determined to result from nondisjunction errors during meiosis I or II. Overall, these findings suggest that copy-neutral loss of heterozygosity resulting from meiotic abnormalities may be sufficient to generate ovarian immature teratomas from germ cells.
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Affiliation(s)
- Michael B. Heskett
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | | | - Christopher Boniface
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Benjamin Goode
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Jocelyn Chapman
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Francisco, CA, USA
| | - Karuna Garg
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Joseph T. Rabban
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Charles Zaloudek
- Department of Pathology, University of California, San Francisco, CA, USA
| | | | - Paul T. Spellman
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - David A. Solomon
- Department of Pathology, University of California, San Francisco, CA, USA,To whom correspondence should be addressed: David A. Solomon, MD, PhD, Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA 94143, United States, Ph: (415) 514-9761, , Raymond J. Cho, MD, PhD, Department of Dermatology, University of California, San Francisco, 1701 Divisadero Street, 3rd floor, San Francisco, CA 94115, United States, Ph: (415) 650-5208,
| | - Raymond J. Cho
- Department of Dermatology, University of California, San Francisco, CA, USA,To whom correspondence should be addressed: David A. Solomon, MD, PhD, Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA 94143, United States, Ph: (415) 514-9761, , Raymond J. Cho, MD, PhD, Department of Dermatology, University of California, San Francisco, 1701 Divisadero Street, 3rd floor, San Francisco, CA 94115, United States, Ph: (415) 650-5208,
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20
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Cheng JB, Sedgewick AJ, Finnegan AI, Harirchian P, Lee J, Kwon S, Fassett MS, Golovato J, Gray M, Ghadially R, Liao W, Perez White BE, Mauro TM, Mully T, Kim EA, Sbitany H, Neuhaus IM, Grekin RC, Yu SS, Gray JW, Purdom E, Paus R, Vaske CJ, Benz SC, Song JS, Cho RJ. Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution. Cell Rep 2019; 25:871-883. [PMID: 30355494 PMCID: PMC6367716 DOI: 10.1016/j.celrep.2018.09.006] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/28/2018] [Accepted: 09/04/2018] [Indexed: 11/28/2022] Open
Abstract
Perturbations in the transcriptional programs specifying epidermal differentiation cause diverse skin pathologies ranging from impaired barrier function to inflammatory skin disease. However, the global scope and organization of this complex cellular program remain undefined. Here we report single-cell RNA sequencing profiles of 92,889 human epidermal cells from 9 normal and 3 inflamed skin samples. Transcriptomics-derived keratinocyte subpopulations reflect classic epidermal strata but also sharply compartmentalize epithelial functions such as cell-cell communication, inflammation, and WNT pathway modulation. In keratinocytes, ~12% of assessed transcript expression varies in coordinate patterns, revealing undescribed gene expression programs governing epidermal homeostasis. We also identify molecular fingerprints of inflammatory skin states, including S100 activation in the interfollicular epidermis of normal scalp, enrichment of a CD1C+CD301A+ myeloid dendritic cell population in psoriatic epidermis, and IL1βhiCCL3hiCD14+ monocyte-derived macrophages enriched in foreskin. This compendium of RNA profiles provides a critical step toward elucidating epidermal diseases of development, differentiation, and inflammation. Cheng et al. report single-cell RNA sequencing of normal and inflamed human epidermis, revealing a discrete set of specialized keratinocytes that exhibit a distinct composition at different anatomic sites. Myeloid dendritic cells and macrophages also vary sharply with epidermal anatomic site and inflammation, indicating dynamic programming of antigen-presenting cells.
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Affiliation(s)
- Jeffrey B Cheng
- Department of Dermatology, University of California, San Francisco and Veterans Affairs Medical Center, San Francisco, CA, USA
| | | | - Alex I Finnegan
- Department of Physics, Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Paymann Harirchian
- Department of Dermatology, University of California, San Francisco and Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Jerry Lee
- Department of Dermatology, University of California, San Francisco and Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Sunjong Kwon
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, Portland, OR, USA
| | - Marlys S Fassett
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Ruby Ghadially
- Department of Dermatology, University of California, San Francisco and Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Wilson Liao
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Bethany E Perez White
- Department of Dermatology and Skin Tissue Engineering Core, Northwestern University, Chicago, IL, USA
| | - Theodora M Mauro
- Department of Dermatology, University of California, San Francisco and Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Thaddeus Mully
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Esther A Kim
- Department of Plastic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Hani Sbitany
- Department of Plastic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Isaac M Neuhaus
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Roy C Grekin
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Siegrid S Yu
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Joe W Gray
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, Portland, OR, USA
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, Berkeley, CA, USA
| | - Ralf Paus
- Centre for Dermatology Research, University of Manchester, Manchester Academic Health Science Centre and NIHR Manchester Biomedical Research Centre, Manchester, UK; Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | | | - Jun S Song
- Department of Physics, Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA.
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21
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Cho RJ, Alexandrov LB, den Breems NY, Atanasova VS, Farshchian M, Purdom E, Nguyen TN, Coarfa C, Rajapakshe K, Prisco M, Sahu J, Tassone P, Greenawalt EJ, Collisson EA, Wu W, Yao H, Su X, Guttmann-Gruber C, Hofbauer JP, Hashmi R, Fuentes I, Benz SC, Golovato J, Ehli EA, Davis CM, Davies GE, Covington KR, Murrell DF, Salas-Alanis JC, Palisson F, Bruckner AL, Robinson W, Has C, Bruckner-Tuderman L, Titeux M, Jonkman MF, Rashidghamat E, Lwin SM, Mellerio JE, McGrath JA, Bauer JW, Hovnanian A, Tsai KY, South AP. APOBEC mutation drives early-onset squamous cell carcinomas in recessive dystrophic epidermolysis bullosa. Sci Transl Med 2019; 10:10/455/eaas9668. [PMID: 30135250 DOI: 10.1126/scitranslmed.aas9668] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/09/2018] [Accepted: 08/01/2018] [Indexed: 01/05/2023]
Abstract
Recessive dystrophic epidermolysis bullosa (RDEB) is a rare inherited skin and mucous membrane fragility disorder complicated by early-onset, highly malignant cutaneous squamous cell carcinomas (SCCs). The molecular etiology of RDEB SCC, which arises at sites of sustained tissue damage, is unknown. We performed detailed molecular analysis using whole-exome, whole-genome, and RNA sequencing of 27 RDEB SCC tumors, including multiple tumors from the same patient and multiple regions from five individual tumors. We report that driver mutations were shared with spontaneous, ultraviolet (UV) light-induced cutaneous SCC (UV SCC) and head and neck SCC (HNSCC) and did not explain the early presentation or aggressive nature of RDEB SCC. Instead, endogenous mutation processes associated with apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) deaminases dominated RDEB SCC. APOBEC mutation signatures were enhanced throughout RDEB SCC tumor evolution, relative to spontaneous UV SCC and HNSCC mutation profiles. Sixty-seven percent of RDEB SCC driver mutations was found to emerge as a result of APOBEC and other endogenous mutational processes previously associated with age, potentially explaining a >1000-fold increased incidence and the early onset of these SCCs. Human papillomavirus-negative basal and mesenchymal subtypes of HNSCC harbored enhanced APOBEC mutational signatures and transcriptomes similar to those of RDEB SCC, suggesting that APOBEC deaminases drive other subtypes of SCC. Collectively, these data establish specific mutagenic mechanisms associated with chronic tissue damage. Our findings reveal a cause for cancers arising at sites of persistent inflammation and identify potential therapeutic avenues to treat RDEB SCC.
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Affiliation(s)
- Raymond J Cho
- Department of Dermatology, University of California, San Francisco, CA 94115, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Velina S Atanasova
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Mehdi Farshchian
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Tran N Nguyen
- Departments of Anatomic Pathology and Tumor Biology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Cristian Coarfa
- Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Kimal Rajapakshe
- Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Marco Prisco
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Joya Sahu
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Patrick Tassone
- Department of Otolaryngology-Head and Neck Surgery, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Evan J Greenawalt
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Eric A Collisson
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94115, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Wei Wu
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94115, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Translational Medical Center, Central Hospital, Zhengzhou University, Zhengzhou, China
| | - Hui Yao
- Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaoping Su
- Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christina Guttmann-Gruber
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology, University Hospital Salzburg, Paracelsus Medical University, A-5020 Salzburg, Austria
| | - Josefina Piñón Hofbauer
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology, University Hospital Salzburg, Paracelsus Medical University, A-5020 Salzburg, Austria
| | - Raabia Hashmi
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Ignacia Fuentes
- Fundación DEBRA Chile, Santiago 7760099, Chile.,Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago 7710162, Chile
| | | | | | - Erik A Ehli
- Avera Institute for Human Genetics, Sioux Falls, SD 57108, USA
| | | | - Gareth E Davies
- Avera Institute for Human Genetics, Sioux Falls, SD 57108, USA
| | | | - Dedee F Murrell
- St. George Hospital, University of New South Wales, Sydney, New South Wales 2217, Australia
| | - Julio C Salas-Alanis
- Escuela de Medicina y Ciencias de la Salud TecSalud del Tecnologico de Monterrey, Morones Prieto 3000, Los doctores, Monterrey, Nuevo León 64710, Mexico
| | - Francis Palisson
- Fundación DEBRA Chile, Santiago 7760099, Chile.,Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 7710162, Chile
| | - Anna L Bruckner
- Departments of Dermatology and Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - William Robinson
- Cutaneous Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Cristina Has
- Department of Dermatology, Medical Center-University of Freiburg, 79104 Freiburg, Germany
| | | | - Matthias Titeux
- INSERM UMR 1163, Paris, France.,Imagine Institute, 75015 Paris, France
| | - Marcel F Jonkman
- Center for Blistering Diseases, Department of Dermatology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, Netherlands
| | - Elham Rashidghamat
- St. John's Institute of Dermatology, King's College London (Guy's Campus), London SE1 9RT, UK
| | - Su M Lwin
- St. John's Institute of Dermatology, King's College London (Guy's Campus), London SE1 9RT, UK
| | - Jemima E Mellerio
- St. John's Institute of Dermatology, King's College London (Guy's Campus), London SE1 9RT, UK
| | - John A McGrath
- St. John's Institute of Dermatology, King's College London (Guy's Campus), London SE1 9RT, UK
| | - Johann W Bauer
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology, University Hospital Salzburg, Paracelsus Medical University, A-5020 Salzburg, Austria
| | - Alain Hovnanian
- INSERM UMR 1163, Paris, France.,Imagine Institute, 75015 Paris, France
| | - Kenneth Y Tsai
- Departments of Anatomic Pathology and Tumor Biology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Andrew P South
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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22
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Finnegan A, Cho RJ, Luu A, Harirchian P, Lee J, Cheng JB, Song JS. Single-Cell Transcriptomics Reveals Spatial and Temporal Turnover of Keratinocyte Differentiation Regulators. Front Genet 2019; 10:775. [PMID: 31552090 PMCID: PMC6733986 DOI: 10.3389/fgene.2019.00775] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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: 04/17/2019] [Accepted: 07/23/2019] [Indexed: 01/07/2023] Open
Abstract
Keratinocyte differentiation requires intricately coordinated spatiotemporal expression changes that specify epidermis structure and function. This article utilizes single-cell RNA-seq data from 22,338 human foreskin keratinocytes to reconstruct the transcriptional regulation of skin development and homeostasis genes, organizing them by differentiation stage and also into transcription factor (TF)–associated modules. We identify groups of TFs characterized by coordinate expression changes during progression from the undifferentiated basal to the differentiated state and show that these TFs also have concordant differential predicted binding enrichment in the super-enhancers previously reported to turn over between the two states. The identified TFs form a core subset of the regulators controlling gene modules essential for basal and differentiated keratinocyte functions, supporting their nomination as master coordinators of keratinocyte differentiation. Experimental depletion of the TFs ZBED2 and ETV4, both predicted to promote the basal state, induces differentiation. Furthermore, our single-cell RNA expression analysis reveals preferential expression of antioxidant genes in the basal state, suggesting keratinocytes actively suppress reactive oxygen species to maintain the undifferentiated state. Overall, our work demonstrates diverse computational methods to advance our understanding of dynamic gene regulation in development.
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Affiliation(s)
- Alex Finnegan
- Department of Physics, Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, United States
| | - Alan Luu
- Department of Physics, Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Paymann Harirchian
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, United States.,Veterans Affairs Medical Center, San Francisco, CA, United States
| | - Jerry Lee
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, United States.,Veterans Affairs Medical Center, San Francisco, CA, United States
| | - Jeffrey B Cheng
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, United States.,Veterans Affairs Medical Center, San Francisco, CA, United States
| | - Jun S Song
- Department of Physics, Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
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23
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North JP, Solomon DA, Golovato J, Bloomer M, Benz SC, Cho RJ. Loss of ZNF750 in ocular and cutaneous sebaceous carcinoma. J Cutan Pathol 2019; 46:736-741. [PMID: 31148199 DOI: 10.1111/cup.13516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 01/08/2019] [Revised: 05/24/2019] [Accepted: 05/28/2019] [Indexed: 01/13/2023]
Abstract
BACKGROUND Sebaceous carcinoma (SeC) is an uncommon malignancy arising from sebaceous glands of the conjunctiva and skin. Recurrent mutations in the ZNF750 were recently identified in ocular SeC. We assessed whether ZNF750 loss is a specific feature of ocular SeC or a general feature of sebaceous tumors. METHODS Immunostaining for ZNF750 expression was performed in 54 benign and malignant sebocytic proliferations. Staining for ZNF750 was scored on a three-tier scale: positive (>75%), partially positive (5%-74%), and negative (<5%). RESULTS ZNF750 expression was negative in 4/11 ocular SeC, and partially positive in 4/11 ocular SeC and 6/13 cutaneous SeC. No extraocular tumors were negative. No loss was found in sebaceous adenoma or sebaceous hyperplasia. In nine previously sequenced ocular SeCs, two lacked detectable somatic mutations in ZNF750, but showed complete loss of staining, indicating non-mutational inactivation of ZNF750. CONCLUSION We show complete loss of the ZNF750 epidermal differentiation regulator in about half of ocular SeC, highlighting the most common genetic defect in this cancer type. Loss of ZNF750 expression is seen even in tumors without truncating mutations and reduced in many of the remaining ocular and cutaneous SeC. In contrast, no ZNF750 loss was detected in benign sebaceous proliferations.
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Affiliation(s)
- Jeffrey P North
- Department of Dermatology, University of California, San Francisco, San Francisco, California.,Department of Pathology, University of California, San Francisco, San Francisco, California
| | - David A Solomon
- Department of Pathology, University of California, San Francisco, San Francisco, California
| | | | - Michele Bloomer
- Department of Pathology, University of California, San Francisco, San Francisco, California.,Department of Ophthalmology, University of California, San Francisco, San Francisco, California
| | | | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, California
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24
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Chiang A, Tan CZ, Kuonen F, Hodgkinson LM, Chiang F, Cho RJ, South AP, Tang JY, Chang ALS, Rieger KE, Oro AE, Sarin KY. Genetic Mutations Underlying Phenotypic Plasticity in Basosquamous Carcinoma. J Invest Dermatol 2019; 139:2263-2271.e5. [PMID: 31207229 DOI: 10.1016/j.jid.2019.03.1163] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 03/02/2019] [Accepted: 03/19/2019] [Indexed: 12/30/2022]
Abstract
Basosquamous carcinoma (BSC) is an aggressive skin neoplasm with the features of both basal cell carcinoma (BCC) and squamous cell carcinoma (SCC). While genetic drivers of BCC and SCC development have been extensively characterized, BSC has not been well studied, and it remains unclear whether these tumors originally derive from BCC or SCC. In addition, it is unknown which molecular pathways mediate the reprogramming of tumor keratinocytes toward basaloid or squamatized phenotypes. We sought to characterize the genomic alterations underlying sporadic BSC to elucidate the derivation of these mixed tumors. We identifed frequent Hedgehog (Hh) pathway mutations in BSCs, implicating Hh deregulation as the primary driving event in BSC. Principal component analysis of BCC and SCC driver genes further demonstrate the genetic similarity between BCC and BSC. In addition, 45% of the BSCs harbor recurrent mutations in the SWI/SNF complex gene, ARID1A, and evolutionary analysis revealed that ARID1A mutations occur after PTCH1 but before SCC driver mutations, indicating that ARID1A mutations may bestow plasticity enabling squamatization. Finally, we demonstrate mitogen-activated protein kinase pathway activation and the loss of Hh signaling associated with the squamatization of BSCs. Overall, these results support the genetic derivation of BSCs from BCCs and highlight potential factors involved in modulating tumor reprogramming between basaloid and squamatized phenotypes.
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Affiliation(s)
- Audris Chiang
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA; University of California, Irvine School of Medicine, Irvine, California, USA
| | - Caroline Z Tan
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - François Kuonen
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Luqman M Hodgkinson
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Felicia Chiang
- Department of Civil and Environmental Engineering, University of California, Irvine, Irvine, California, USA
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | - Andrew P South
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Jean Y Tang
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Anne Lynn S Chang
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Kerri E Rieger
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA; Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Anthony E Oro
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Kavita Y Sarin
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA.
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25
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Cheng JB, Cho RJ. Emergence and Evolution of Mutational Hotspots in Sun-Damaged Skin. J Invest Dermatol 2019; 138:16-17. [PMID: 29273145 DOI: 10.1016/j.jid.2017.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 09/11/2017] [Accepted: 09/13/2017] [Indexed: 10/18/2022]
Abstract
In this issue, Albibas et al. investigate the mutational nature of p53-immunopositive patches, commonly observed in sun-damaged skin. p53-immunopositive patches have long been suspected to be lineal precursors to actinic keratoses and cutaneous squamous cell carcinomas. However, the mutations actually giving rise to p53-immunopositive patches, and their relationship to skin cancer, have never been defined. The considerable clinical and economic costs of monitoring and treating sun-damaged skin demand we better understand the evolution of these common premalignancies.
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Affiliation(s)
- Jeffrey B Cheng
- Department of Dermatology, University of California, San Francisco, California, USA; Veterans Affairs Medical Center, San Francisco, California, USA
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, California, USA.
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26
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Harirchian P, Lee J, Hilz S, Sedgewick AJ, Perez White BE, Kesling MJ, Mully T, Golovato J, Gray M, Mauro TM, Purdom E, Kim EA, Sbitany H, Bhutani T, Vaske CJ, Benz SC, Cho RJ, Cheng JB. A20 and ABIN1 Suppression of a Keratinocyte Inflammatory Program with a Shared Single-Cell Expression Signature in Diverse Human Rashes. J Invest Dermatol 2018; 139:1264-1273. [PMID: 30543901 DOI: 10.1016/j.jid.2018.10.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 10/17/2018] [Accepted: 10/26/2018] [Indexed: 02/06/2023]
Abstract
Genetic variation in the NF-κB inhibitors, ABIN1 and A20, increase risk for psoriasis. While critical for hematopoietic immune cell function, these genes are believed to additionally inhibit psoriasis by dampening inflammatory signaling in keratinocytes. We dissected ABIN1 and A20's regulatory role in human keratinocyte inflammation using an RNA sequencing-based comparative genomic approach. Here we show subsets of the IL-17 and tumor necrosis factor-α signaling pathways are robustly restricted by A20 overexpression. In contrast, ABIN1 overexpression inhibits these genes more modestly for IL-17, and weakly for tumor necrosis factor-α. Our genome-scale analysis also indicates that inflammatory program suppression appears to be the major transcriptional influence of A20/ABIN1 overexpression, without obvious influence on keratinocyte viability genes. Our findings thus enable dissection of the differing anti-inflammatory mechanisms of two distinct psoriasis modifiers, which may be directly exploited for therapeutic purposes. Importantly, we report that IL-17-induced targets of A20 show similar aberrant epidermal layer-specific transcriptional upregulation in keratinocytes from diseases as diverse as psoriasis, atopic dermatitis, and erythrokeratodermia variabilis, suggesting a contributory role for epidermal inflammation in a broad spectrum of rashes.
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Affiliation(s)
- Paymann Harirchian
- Department of Dermatology, University of California, San Francisco and Veterans Affairs Medical Center, San Francisco, California, USA
| | - Jerry Lee
- Department of Dermatology, University of California, San Francisco and Veterans Affairs Medical Center, San Francisco, California, USA
| | - Stephanie Hilz
- Department of Neurological Surgery, University of California, San Francisco, California
| | | | - Bethany E Perez White
- Skin Tissue Engineering Core and Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | | | - Thaddeus Mully
- Department of Pathology, University of California, San Francisco, California
| | | | | | - Theodora M Mauro
- Department of Dermatology, University of California, San Francisco and Veterans Affairs Medical Center, San Francisco, California, USA
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, California
| | - Esther A Kim
- Department of Plastic Surgery, University of California, San Francisco, California
| | - Hani Sbitany
- Department of Plastic Surgery, University of California, San Francisco, California
| | - Tina Bhutani
- Department of Dermatology, University of California, San Francisco, California
| | | | | | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, California
| | - Jeffrey B Cheng
- Department of Dermatology, University of California, San Francisco and Veterans Affairs Medical Center, San Francisco, California, USA.
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27
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Cheng JB, Harirchian P, Greer J, Parsons M, Heiser LM, Mauro T, Cho RJ. Image-based transcription factor siRNA screen reveals novel regulators of epidermal differentiation. J Dermatol Sci 2017. [DOI: 10.1016/j.jdermsci.2017.02.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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28
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Fong K, Bailey CV, Tuttle P, Cunningham B, McGrath JA, Cho RJ. Questioning the Clinical Utility of Exome Sequencing in Developing Countries. Pediatr Dermatol 2017; 34:e32-e34. [PMID: 27874213 DOI: 10.1111/pde.13029] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The availability of whole-exome sequencing has revolutionized the study of genetic disease in recent years, particularly in dermatology, where clinical phenotypes are readily recognized. As this technology becomes increasingly affordable and accessible, questions are emerging regarding the clinical and ethical responsibilities of physicians who determine variants underlying disease, especially with regard to children, for whom treatment may be warranted and clinical course improved based on a known genotype. These responsibilities are accentuated in the developing countries, which harbor most consanguineous populations and thus bear the brunt of monogenic genodermatoses. Although many genetic disorders are identified in these populations, limited educational and clinical infrastructure rarely offers opportunities to improve the course of disease. Here we report a genetic study that illustrates these challenges.
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Affiliation(s)
- Kenneth Fong
- National Skin Centre, Singapore, Singapore.,St. John's Institute of Dermatology, King's College London, London, UK
| | - Celeste V Bailey
- College of Medicine, Pennsylvania State University, State College, Pennsylvania
| | - Peggy Tuttle
- Good Samaritan International, Seattle, Washington
| | | | - John A McGrath
- St. John's Institute of Dermatology, King's College London, London, UK
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, California
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29
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Schulman JM, Oh DH, Sanborn JZ, Pincus L, McCalmont TH, Cho RJ. Multiple Hereditary Infundibulocystic Basal Cell Carcinoma Syndrome Associated With a Germline SUFU Mutation. JAMA Dermatol 2016; 152:323-7. [PMID: 26677003 DOI: 10.1001/jamadermatol.2015.4233] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
IMPORTANCE Multiple hereditary infundibulocystic basal cell carcinoma syndrome (MHIBCC) is a rare genodermatosis in which numerous indolent, well-differentiated basal cell carcinomas develop primarily on the face and genitals, without other features characteristic of basal cell nevus syndrome. The cause is unknown. The purpose of the study was to identify a genetic basis for the syndrome and a mechanism by which the associated tumors develop. OBSERVATIONS Whole-exome sequencing of 5 tumors and a normal buccal mucosal sample from a patient with MHIBCC was performed. A conserved splice-site mutation in 1 copy of the suppressor of fused gene (SUFU) was identified in all tumor and normal tissue samples. Additional distinct deletions of the trans SUFU allele were identified in all tumor samples, none of which were present in the normal sample. CONCLUSIONS AND RELEVANCE A germline SUFU mutation was present in a patient with MHIBCC, and additional acquired SUFU mutations underlie the development of infundibulocystic basal cell carcinomas. The downstream location of the SUFU gene within the sonic hedgehog pathway may explain why its loss is associated with relatively well-differentiated tumors and suggests that MHIBCC will not respond to therapeutic strategies, such as smoothened inhibitors, that target upstream components of this pathway.
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Affiliation(s)
- Joshua M Schulman
- Department of Dermatology, University of California, San Francisco2Department of Pathology, University of California, San Francisco
| | - Dennis H Oh
- Department of Dermatology, University of California, San Francisco3Dermatology Research Unit, San Francisco Veterans Affairs Medical Center, San Francisco, California
| | | | - Laura Pincus
- Department of Dermatology, University of California, San Francisco2Department of Pathology, University of California, San Francisco
| | - Timothy H McCalmont
- Department of Dermatology, University of California, San Francisco2Department of Pathology, University of California, San Francisco
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco
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30
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Cho RJ, Collisson EA. Election 2016: Voting on Variants. Cancer Discov 2016; 6:694-6. [DOI: 10.1158/2159-8290.cd-16-0559] [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] [Indexed: 11/16/2022]
Abstract
Abstract
Summary: Genome sequencing studies increasingly identify variants of unknown significance in provocative genes. Kim and colleagues present a system with which to functionally annotate such variants in a high-throughput, biologically relevant series of assays. Cancer Discov; 6(7); 694–6. ©2016 AACR.
See related article by Kim et al., p. 714.
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Affiliation(s)
- Raymond J. Cho
- 1Department of Dermatology, University of California, San Francisco, San Francisco, California
| | - Eric A. Collisson
- 2Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
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Shain AH, Garrido M, Botton T, Talevich E, Yeh I, Sanborn JZ, Chung J, Wang NJ, Kakavand H, Mann GJ, Thompson JF, Wiesner T, Roy R, Olshen AB, Gagnon A, Gray JW, Huh N, Hur JS, Busam KJ, Scolyer RA, Cho RJ, Murali R, Bastian BC. Exome sequencing of desmoplastic melanoma identifies recurrent NFKBIE promoter mutations and diverse activating mutations in the MAPK pathway. Nat Genet 2015; 47:1194-9. [PMID: 26343386 PMCID: PMC4589486 DOI: 10.1038/ng.3382] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 07/22/2015] [Indexed: 12/16/2022]
Abstract
Desmoplastic melanoma is an uncommon variant of melanoma with sarcomatous histology, distinct clinical behavior and unknown pathogenesis. We performed low-coverage genome and high-coverage exome sequencing of 20 desmoplastic melanomas, followed by targeted sequencing of 293 genes in a validation cohort of 42 cases. A high mutation burden (median of 62 mutations/Mb) ranked desmoplastic melanoma among the most highly mutated cancers. Mutation patterns strongly implicate ultraviolet radiation as the dominant mutagen, indicating a superficially located cell of origin. Newly identified alterations included recurrent promoter mutations of NFKBIE, encoding NF-κB inhibitor ɛ (IκBɛ), in 14.5% of samples. Common oncogenic mutations in melanomas, in particular in BRAF (encoding p.Val600Glu) and NRAS (encoding p.Gln61Lys or p.Gln61Arg), were absent. Instead, other genetic alterations known to activate the MAPK and PI3K signaling cascades were identified in 73% of samples, affecting NF1, CBL, ERBB2, MAP2K1, MAP3K1, BRAF, EGFR, PTPN11, MET, RAC1, SOS2, NRAS and PIK3CA, some of which are candidates for targeted therapies.
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Affiliation(s)
- A Hunter Shain
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | - Maria Garrido
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | - Thomas Botton
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | - Eric Talevich
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | - Iwei Yeh
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | | | - Jongsuk Chung
- Samsung Advanced Institute of Technology, Seoul, Korea
| | - Nicholas J Wang
- Department of Biomedical Engineering, Oregon Health and Sciences University, Portland, Oregon, USA
- Knight Cancer Institute, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Hojabr Kakavand
- Melanoma Institute Australia, Sydney, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Graham J Mann
- Melanoma Institute Australia, Sydney, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - John F Thompson
- Melanoma Institute Australia, Sydney, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Thomas Wiesner
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ritu Roy
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
| | - Adam B Olshen
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - Alexander Gagnon
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | - Joe W Gray
- Department of Biomedical Engineering, Oregon Health and Sciences University, Portland, Oregon, USA
- Knight Cancer Institute, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Nam Huh
- Samsung Advanced Institute of Technology, Seoul, Korea
| | - Joe S Hur
- Samsung Electronics Headquarters, Seoul, Korea
| | - Klaus J Busam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Richard A Scolyer
- Melanoma Institute Australia, Sydney, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | - Rajmohan Murali
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Boris C Bastian
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
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32
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Daemen A, Griffith OL, Heiser LM, Wang NJ, Enache OM, Sanborn Z, Pepin F, Durinck S, Korkola JE, Griffith M, Hur JS, Huh N, Chung J, Cope L, Fackler MJ, Umbricht C, Sukumar S, Seth P, Sukhatme VP, Jakkula LR, Lu Y, Mills GB, Cho RJ, Collisson EA, Van't Veer LJ, Spellman PT, Gray JW. Erratum to: Modeling precision treatment of breast cancer. Genome Biol 2015; 16:95. [PMID: 25962591 PMCID: PMC4426644 DOI: 10.1186/s13059-015-0658-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 04/09/2015] [Indexed: 12/01/2022] Open
Abstract
During the type-setting of the final version of the article [1] some of the additional files were swapped. The correct files are republished in this Erratum.
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Affiliation(s)
- Anneleen Daemen
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94115, USA. .,Present address: Department of Bioinformatics & Computational Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA.
| | - Obi L Griffith
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, 97239, USA. .,The Genome Institute, Washington University School of Medicine, St Louis, MO, 63105, USA.
| | - Laura M Heiser
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Biomedical Engineering, Center for Spatial Systems Biomedicine, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97239, USA.
| | - Nicholas J Wang
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Biomedical Engineering, Center for Spatial Systems Biomedicine, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97239, USA.
| | - Oana M Enache
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | | | - Francois Pepin
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Present address: Sequenta Inc, South San Francisco, CA, 94080, USA.
| | - Steffen Durinck
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - James E Korkola
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Biomedical Engineering, Center for Spatial Systems Biomedicine, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97239, USA.
| | - Malachi Griffith
- The Genome Institute, Washington University School of Medicine, St Louis, MO, 63105, USA.
| | - Joe S Hur
- Samsung Electronics Headquarters, Seocho-gu, Seoul, 137-857, Korea.
| | - Nam Huh
- Emerging Technology Research Center, Samsung Advanced Institute of Technology, Kyunggi-do, 446-712, Korea.
| | - Jongsuk Chung
- Emerging Technology Research Center, Samsung Advanced Institute of Technology, Kyunggi-do, 446-712, Korea.
| | - Leslie Cope
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Mary Jo Fackler
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Christopher Umbricht
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Saraswati Sukumar
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Pankaj Seth
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
| | - Vikas P Sukhatme
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
| | - Lakshmi R Jakkula
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Yiling Lu
- Department of Systems Biology, MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Gordon B Mills
- Department of Systems Biology, MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, CA, 94115, USA.
| | - Eric A Collisson
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94115, USA.
| | - Laura J Van't Veer
- Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94115, USA.
| | - Paul T Spellman
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, 97239, USA.
| | - Joe W Gray
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Biomedical Engineering, Center for Spatial Systems Biomedicine, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97239, USA.
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33
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Zheng CL, Wang NJ, Chung J, Moslehi H, Sanborn JZ, Hur JS, Collisson EA, Vemula SS, Naujokas A, Chiotti KE, Cheng JB, Fassihi H, Blumberg AJ, Bailey CV, Fudem GM, Mihm FG, Cunningham BB, Neuhaus IM, Liao W, Oh DH, Cleaver JE, LeBoit PE, Costello JF, Lehmann AR, Gray JW, Spellman PT, Arron ST, Huh N, Purdom E, Cho RJ. Transcription restores DNA repair to heterochromatin, determining regional mutation rates in cancer genomes. Cell Rep 2014; 9:1228-34. [PMID: 25456125 DOI: 10.1016/j.celrep.2014.10.031] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 08/26/2014] [Accepted: 10/11/2014] [Indexed: 12/25/2022] Open
Abstract
Somatic mutations in cancer are more frequent in heterochromatic and late-replicating regions of the genome. We report that regional disparities in mutation density are virtually abolished within transcriptionally silent genomic regions of cutaneous squamous cell carcinomas (cSCCs) arising in an XPC(-/-) background. XPC(-/-) cells lack global genome nucleotide excision repair (GG-NER), thus establishing differential access of DNA repair machinery within chromatin-rich regions of the genome as the primary cause for the regional disparity. Strikingly, we find that increasing levels of transcription reduce mutation prevalence on both strands of gene bodies embedded within H3K9me3-dense regions, and only to those levels observed in H3K9me3-sparse regions, also in an XPC-dependent manner. Therefore, transcription appears to reduce mutation prevalence specifically by relieving the constraints imposed by chromatin structure on DNA repair. We model this relationship among transcription, chromatin state, and DNA repair, revealing a new, personalized determinant of cancer risk.
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Affiliation(s)
- Christina L Zheng
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Sciences University, Portland, OR 97239, USA; Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR 97239, USA
| | - Nicholas J Wang
- Department of Biomedical Engineering, Oregon Health & Sciences University, Portland, OR 97239, USA
| | - Jongsuk Chung
- Emerging Technology Research Center, Samsung Advanced Institute of Technology, Kyunggi-do 446-712, Korea
| | - Homayoun Moslehi
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Joseph S Hur
- Headquarters, Samsung Electronics, Seocho-gu, Seoul 137-857, Korea
| | - Eric A Collisson
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Swapna S Vemula
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Agne Naujokas
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kami E Chiotti
- Department of Molecular and Medical Genetics, Oregon Health & Sciences University, Portland, OR 97239, USA
| | - Jeffrey B Cheng
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Hiva Fassihi
- National Xeroderma Pigmentosum Service, St John's Institute of Dermatology, Guy's and St Thomas' NHS Trust, London SE1 9RT, UK
| | - Andrew J Blumberg
- Department of Mathematics, University of Texas, Austin, Austin, TX 78712, USA
| | - Celeste V Bailey
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA 94158, USA
| | - Gary M Fudem
- Department of Surgery, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Frederick G Mihm
- Department of Anesthesiology, Pain and Perioperative Medicine, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Bari B Cunningham
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Isaac M Neuhaus
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Wilson Liao
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dennis H Oh
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA; Dermatology Research Unit, Veterans Affairs Medical Center, San Francisco, San Francisco, CA 94121, USA
| | - James E Cleaver
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Philip E LeBoit
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
| | - Alan R Lehmann
- Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RH, UK
| | - Joe W Gray
- Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR 97239, USA; Department of Biomedical Engineering, Oregon Health & Sciences University, Portland, OR 97239, USA
| | - Paul T Spellman
- Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR 97239, USA; Department of Molecular and Medical Genetics, Oregon Health & Sciences University, Portland, OR 97239, USA
| | - Sarah T Arron
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nam Huh
- Emerging Technology Research Center, Samsung Advanced Institute of Technology, Kyunggi-do 446-712, Korea
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA.
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34
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Dimon MT, Wood HM, Rabbitts PH, Liao W, Cho RJ, Arron ST. No evidence for integrated viral DNA in the genome sequence of cutaneous squamous cell carcinoma. J Invest Dermatol 2014; 134:2055-2057. [PMID: 24480882 PMCID: PMC4057961 DOI: 10.1038/jid.2014.52] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Michelle T Dimon
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | - Henry M Wood
- Pre-Cancer Genomics, Leeds Institute of Cancer Studies and Pathology, Leeds, UK
| | - Pamela H Rabbitts
- Pre-Cancer Genomics, Leeds Institute of Cancer Studies and Pathology, Leeds, UK
| | - Wilson Liao
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | - Sarah T Arron
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA.
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35
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Abstract
Motivation: Tumors acquire many chromosomal amplifications, and those acquired early in the lifespan of the tumor may be not only important for tumor growth but also can be used for diagnostic purposes. Many methods infer the order of the accumulation of abnormalities based on their occurrence in a large cohort of patients. Recently, Durinck et al. (2011) and Greenman et al. (2012) developed methods to order a single tumor’s chromosomal amplifications based on the patterns of mutations accumulated within those regions. This method offers an unprecedented opportunity to assess the etiology of a single tumor sample, but has not been widely evaluated. Results: We show that the model for timing chromosomal amplifications is limited in scope, particularly for regions with high levels of amplification. We also show that the estimation of the order of events can be sensitive for events that occur early in the progression of the tumor and that the partial maximum likelihood method of Greenman et al. (2012) can give biased estimates, particularly for moderate read coverage or normal contamination. We propose a maximum-likelihood estimation procedure that fully accounts for sequencing variability and show that it outperforms the partial maximum-likelihood estimation method. We also propose a Bayesian estimation procedure that stabilizes the estimates in certain settings. We implement these methods on a small number of ovarian tumors, and the results suggest possible differences in how the tumors acquired amplifications. Availability and implementation: We provide implementation of these methods in an R package cancerTiming, which is available from the Comprehensive R Archive Network (CRAN) at http://CRAN.R-project.org/. Contact:epurdom@stat.Berkeley.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, 367 Evans Hall Berkeley, CA 94720-3860, USA, Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA and Department of Dermatology, University of California, San Francisco, CA 94115, USA
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36
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Kluk MJ, Ashworth T, Wang H, Knoechel B, Mason EF, Morgan EA, Dorfman D, Pinkus G, Weigert O, Hornick JL, Chirieac LR, Hirsch M, Oh DJ, South AP, Leigh IM, Pourreyron C, Cassidy AJ, Deangelo DJ, Weinstock DM, Krop IE, Dillon D, Brock JE, Lazar AJF, Peto M, Cho RJ, Stoeck A, Haines BB, Sathayanrayanan S, Rodig S, Aster JC. Gauging NOTCH1 Activation in Cancer Using Immunohistochemistry. PLoS One 2013; 8:e67306. [PMID: 23825651 PMCID: PMC3688991 DOI: 10.1371/journal.pone.0067306] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 05/16/2013] [Indexed: 12/12/2022] Open
Abstract
Fixed, paraffin-embedded (FPE) tissues are a potentially rich resource for studying the role of NOTCH1 in cancer and other pathologies, but tests that reliably detect activated NOTCH1 (NICD1) in FPE samples have been lacking. Here, we bridge this gap by developing an immunohistochemical (IHC) stain that detects a neoepitope created by the proteolytic cleavage event that activates NOTCH1. Following validation using xenografted cancers and normal tissues with known patterns of NOTCH1 activation, we applied this test to tumors linked to dysregulated Notch signaling by mutational studies. As expected, frequent NICD1 staining was observed in T lymphoblastic leukemia/lymphoma, a tumor in which activating NOTCH1 mutations are common. However, when IHC was used to gauge NOTCH1 activation in other human cancers, several unexpected findings emerged. Among B cell tumors, NICD1 staining was much more frequent in chronic lymphocytic leukemia than would be predicted based on the frequency of NOTCH1 mutations, while mantle cell lymphoma and diffuse large B cell lymphoma showed no evidence of NOTCH1 activation. NICD1 was also detected in 38% of peripheral T cell lymphomas. Of interest, NICD1 staining in chronic lymphocytic leukemia cells and in angioimmunoblastic lymphoma was consistently more pronounced in lymph nodes than in surrounding soft tissues, implicating factors in the nodal microenvironment in NOTCH1 activation in these diseases. Among carcinomas, diffuse strong NICD1 staining was observed in 3.8% of cases of triple negative breast cancer (3 of 78 tumors), but was absent from 151 non-small cell lung carcinomas and 147 ovarian carcinomas. Frequent staining of normal endothelium was also observed; in line with this observation, strong NICD1 staining was also seen in 77% of angiosarcomas. These findings complement insights from genomic sequencing studies and suggest that IHC staining is a valuable experimental tool that may be useful in selection of patients for clinical trials.
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Affiliation(s)
- Michael J Kluk
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
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37
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Collisson EA, Cho RJ. Histology, anatomy, or geography? Exome sequencing begins to delineate somatic mutational differences in esophageal cancer. Cancer Discov 2012; 2:870-1. [PMID: 23071029 DOI: 10.1158/2159-8290.cd-12-0393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Esophageal carcinoma is composed of squamous cell and adenocarcinoma types, each with geographically distinct incidence. The earliest exome sequences in this disease begin to illuminate the genetic demarcations of these anatomically related cancers.
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Affiliation(s)
- Eric A Collisson
- Department of Medicine, Division of Hematology and Oncology, University of California at San Francisco, San Francisco, California, USA.
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38
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Cho RJ, McCalmont TH, Ai WZ, Fox LP, Treseler P, Pincus LB. Use of an expanded immunohistochemical panel to distinguish cutaneous Hodgkin lymphoma from histopathologic imitators. J Cutan Pathol 2012; 39:651-8. [DOI: 10.1111/j.1600-0560.2012.01872.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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39
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Abstract
Recent deep sequencing of cancer genomes has produced an explosion of new data implicating Notch signaling in several human cancers. Unlike most other pathways, these data indicate that Notch signaling can be either oncogenic or tumor suppressive, depending on the cellular context. In some instances, these relationships were predicted from mouse models or presaged by developmental roles for Notch, but in other cases were unanticipated. This review discusses the pathogenic and translational significance of these new findings.
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Affiliation(s)
- Andrew P South
- Division of Cancer Research, Medical Research Institute, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
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40
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Abstract
Rapid advances in next-generation sequencing technology are revolutionizing approaches to genomic and epigenomic studies of skin. Deep sequencing of cutaneous malignancies reveals heavily mutagenized genomes with large numbers of low-prevalence mutations and multiple resistance mechanisms to targeted therapies. Next-generation sequencing approaches have already paid rich dividends in identifying the genetic causes of dermatologic disease, both in heritable mutations and the somatic aberrations that underlie cutaneous mosaicism. Although epigenetic alterations clearly influence tumorigenesis, pluripotent stem cell biology, and epidermal cell lineage decisions, labor and cost-intensive approaches long delayed a genome-scale perspective. New insights into epigenomic mechanisms in skin disease should arise from the accelerating assessment of histone modification, DNA methylation, and related gene expression signatures.
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Affiliation(s)
- Jeffrey B Cheng
- Department of Dermatology, University of California, San Francisco, San Francisco, California 94143, USA
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41
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Durinck S, Ho C, Wang NJ, Liao W, Jakkula LR, Collisson EA, Pons J, Chan SW, Lam ET, Chu C, Park K, Hong SW, Hur JS, Huh N, Neuhaus IM, Yu SS, Grekin RT, Mauro TM, Cleaver JE, Kwok PY, LeBoit PE, Getz G, Cibulskis K, Aster JC, Huang H, Purdom E, Li J, Bolund L, Arron ST, Gray JW, Spellman PT, Cho RJ. Temporal dissection of tumorigenesis in primary cancers. Cancer Discov 2011; 1:137-43. [PMID: 21984974 PMCID: PMC3187561 DOI: 10.1158/2159-8290.cd-11-0028] [Citation(s) in RCA: 207] [Impact Index Per Article: 15.9] [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] [Indexed: 01/12/2023]
Abstract
Timely intervention for cancer requires knowledge of its earliest genetic aberrations. Sequencing of tumors and their metastases reveals numerous abnormalities occurring late in progression. A means to temporally order aberrations in a single cancer, rather than inferring them from serially acquired samples, would define changes preceding even clinically evident disease. We integrate DNA sequence and copy number information to reconstruct the order of abnormalities as individual tumors evolve for 2 separate cancer types. We detect vast, unreported expansion of simple mutations sharply demarcated by recombinative loss of the second copy of TP53 in cutaneous squamous cell carcinomas (cSCC) and serous ovarian adenocarcinomas, in the former surpassing 50 mutations per megabase. In cSCCs, we also report diverse secondary mutations in known and novel oncogenic pathways, illustrating how such expanded mutagenesis directly promotes malignant progression. These results reframe paradigms in which TP53 mutation is required later, to bypass senescence induced by driver oncogenes.
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Affiliation(s)
- Steffen Durinck
- Life Sciences Division, Lawrence Berkeley National Laboratories, CA
| | - Christine Ho
- Department of Statistics, University of California, Berkeley, CA
| | - Nicholas J. Wang
- Life Sciences Division, Lawrence Berkeley National Laboratories, CA
| | - Wilson Liao
- Department of Dermatology, University of California, San Francisco, CA
| | | | | | - Jennifer Pons
- Department of Dermatology, University of California, San Francisco, CA
| | - Sai-Wing Chan
- Department of Dermatology, University of California, San Francisco, CA
| | - Ernest T. Lam
- Department of Dermatology, University of California, San Francisco, CA
| | - Catherine Chu
- Department of Dermatology, University of California, San Francisco, CA
| | - Kyunghee Park
- Emerging Technology Research Center, Samsung Advanced Institute of Technology, Seoul, Korea
| | - Sung-woo Hong
- Emerging Technology Research Center, Samsung Advanced Institute of Technology, Seoul, Korea
| | - Joe S. Hur
- Samsung Electronics Headquarters Seoul, Korea
| | - Nam Huh
- Emerging Technology Research Center, Samsung Advanced Institute of Technology, Seoul, Korea
| | - Isaac M. Neuhaus
- Department of Dermatology, University of California, San Francisco, CA
| | - Siegrid S. Yu
- Department of Dermatology, University of California, San Francisco, CA
| | - Roy T. Grekin
- Department of Dermatology, University of California, San Francisco, CA
| | - Theodora M. Mauro
- Department of Dermatology, University of California, San Francisco, CA
| | - James E. Cleaver
- Department of Dermatology, University of California, San Francisco, CA
| | - Pui-Yan Kwok
- Department of Dermatology, University of California, San Francisco, CA
| | | | - Gad Getz
- The Broad Institute of MIT and Harvard, MA
| | | | - Jon C. Aster
- Department of Pathology, Brigham and Women’s Hospital, MA
| | - Haiyan Huang
- Department of Statistics, University of California, Berkeley, CA
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, CA
| | - Jian Li
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
- Institute of Human Genetics, Aarhus University, Denmark
| | - Lars Bolund
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
- Institute of Human Genetics, Aarhus University, Denmark
| | - Sarah T. Arron
- Department of Dermatology, University of California, San Francisco, CA
| | - Joe W. Gray
- Life Sciences Division, Lawrence Berkeley National Laboratories, CA
- Biomedical Engineering Department, Oregon Health Sciences University, Oregon
| | - Paul T. Spellman
- Life Sciences Division, Lawrence Berkeley National Laboratories, CA
| | - Raymond J. Cho
- Department of Dermatology, University of California, San Francisco, CA
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42
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Abstract
Exponential advances in the quantitation of DNA variation and epigenetic states seem poised to convert much of biological research into a statistical exercise. But these developments also invite us to reimagine well-worn biological concepts on a grander scale. Somatic mosaicism refers to postzygotic mutations persisting in the individual, occasionally conspicuous to dermatologists as Blaschkoid, checkerboard, phylloid and patchy morphologies. A thoughtful examination of cutaneous mosaicism suggests, however, that virtually all of us may be somatic mosaics. Such genetic variability within individuals might explain localized presentations of disease and implies that some tissues literally evolve throughout life. We discuss here (i) the likely ubiquity of somatic mosaicism, (ii) the broad range of possible biological consequences and (iii) how experimentalists and clinicians may begin establishing genotype-to-phenotype correlates.
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Affiliation(s)
- Raymond J Cho
- Department of Dermatology, University of California, San Francisco, CA 94115, USA.
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Durinck S, Ho C, Wang NJ, Liao W, Jakkula LR, Collisson EA, Pons J, Chan SW, Lam ET, Chu C, Park K, Hong SW, Hur JS, Huh N, Neuhaus IM, Yu SS, Grekin RC, Mauro TM, Cleaver JE, Kwok PY, LeBoit PE, Getz G, Cibulskis K, Aster JC, Huang H, Purdom E, Li J, Bolund L, Arron ST, Gray JW, Spellman PT, Cho RJ. Timing chromosomal abnormalities using mutation data. Genome Biol 2011. [PMCID: PMC3439049 DOI: 10.1186/gb-2011-12-s1-p39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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44
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Pincus LB, LeBoit PE, Goddard DS, Cho RJ, McCalmont TH. Marked papillary dermal edema - an unreliable discriminator between polymorphous light eruption and lupus erythematosus or dermatomyositis. J Cutan Pathol 2010; 37:416-25. [DOI: 10.1111/j.1600-0560.2010.01516.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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45
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Calvano SE, Xiao W, Richards DR, Felciano RM, Baker HV, Cho RJ, Chen RO, Brownstein BH, Cobb JP, Tschoeke SK, Miller-Graziano C, Moldawer LL, Mindrinos MN, Davis RW, Tompkins RG, Lowry SF. A network-based analysis of systemic inflammation in humans. Nature 2005; 437:1032-7. [PMID: 16136080 DOI: 10.1038/nature03985] [Citation(s) in RCA: 1095] [Impact Index Per Article: 57.6] [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: 05/17/2005] [Accepted: 07/04/2005] [Indexed: 01/01/2023]
Abstract
Oligonucleotide and complementary DNA microarrays are being used to subclassify histologically similar tumours, monitor disease progress, and individualize treatment regimens. However, extracting new biological insight from high-throughput genomic studies of human diseases is a challenge, limited by difficulties in recognizing and evaluating relevant biological processes from huge quantities of experimental data. Here we present a structured network knowledge-base approach to analyse genome-wide transcriptional responses in the context of known functional interrelationships among proteins, small molecules and phenotypes. This approach was used to analyse changes in blood leukocyte gene expression patterns in human subjects receiving an inflammatory stimulus (bacterial endotoxin). We explore the known genome-wide interaction network to identify significant functional modules perturbed in response to this stimulus. Our analysis reveals that the human blood leukocyte response to acute systemic inflammation includes the transient dysregulation of leukocyte bioenergetics and modulation of translational machinery. These findings provide insight into the regulation of global leukocyte activities as they relate to innate immune system tolerance and increased susceptibility to infection in humans.
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Affiliation(s)
- Steve E Calvano
- Department of Surgery, UMDNJ-Robert Wood Johnson Medical School, New Brunswick, New Jersey 08903, USA
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46
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Ficenec D, Osborne M, Pradines J, Richards D, Felciano R, Cho RJ, Chen RO, Liefeld T, Owen J, Ruttenberg A, Reich C, Horvath J, Clark T. Computational knowledge integration in biopharmaceutical research. Brief Bioinform 2003; 4:260-78. [PMID: 14582520 DOI: 10.1093/bib/4.3.260] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An initiative to increase biopharmaceutical research productivity by capturing, sharing and computationally integrating proprietary scientific discoveries with public knowledge is described. This initiative involves both organisational process change and multiple interoperating software systems. The software components rely on mutually supporting integration techniques. These include a richly structured ontology, statistical analysis of experimental data against stored conclusions, natural language processing of public literature, secure document repositories with lightweight metadata, web services integration, enterprise web portals and relational databases. This approach has already begun to increase scientific productivity in our enterprise by creating an organisational memory (OM) of internal research findings, accessible on the web. Through bringing together these components it has also been possible to construct a very large and expanding repository of biological pathway information linked to this repository of findings which is extremely useful in analysis of DNA microarray data. This repository, in turn, enables our research paradigm to be shifted towards more comprehensive systems-based understandings of drug action.
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47
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Cho RJ. Deriving meaning from genomic information. Biotechnol Genet Eng Rev 2001; 17:91-107. [PMID: 11255683 DOI: 10.1080/02648725.2000.10647989] [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: 10/27/2022]
Affiliation(s)
- R J Cho
- Department of Genetics and Biochemistry, Stanford University School of Medicine, Stanford, CA 94035, USA.
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48
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Cho RJ, Huang M, Campbell MJ, Dong H, Steinmetz L, Sapinoso L, Hampton G, Elledge SJ, Davis RW, Lockhart DJ. Transcriptional regulation and function during the human cell cycle. Nat Genet 2001; 27:48-54. [PMID: 11137997 DOI: 10.1038/83751] [Citation(s) in RCA: 338] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We report here the transcriptional profiling of the cell cycle on a genome-wide scale in human fibroblasts. We identified approximately 700 genes that display transcriptional fluctuation with a periodicity consistent with that of the cell cycle. Systematic analysis of these genes revealed functional organization within groups of coregulated transcripts. A diverse set of cytoskeletal reorganization genes exhibit cell-cycle-dependent regulation, indicating that biological pathways are redirected for the execution of cell division. Many genes involved in cell motility and remodeling of the extracellular matrix are expressed predominantly in M phase, indicating a mechanism for balancing proliferative and invasive cellular behavior. Transcripts upregulated during S phase displayed extensive overlap with genes induced by DNA damage; cell-cycle-regulated transcripts may therefore constitute coherent programs used in response to external stimuli. Our data also provide clues to biological function for hundreds of previously uncharacterized human genes.
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Affiliation(s)
- R J Cho
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
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49
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Drenkard E, Richter BG, Rozen S, Stutius LM, Angell NA, Mindrinos M, Cho RJ, Oefner PJ, Davis RW, Ausubel FM. A simple procedure for the analysis of single nucleotide polymorphisms facilitates map-based cloning in Arabidopsis. Plant Physiol 2000; 124:1483-92. [PMID: 11115864 PMCID: PMC1539302 DOI: 10.1104/pp.124.4.1483] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We developed a modified allele-specific PCR procedure for assaying single nucleotide polymorphisms (SNPs) and used the procedure (called SNAP for single-nucleotide amplified polymorphisms) to generate 62 Arabidopsis mapping markers. SNAP primers contain a single base pair mismatch within three nucleotides from the 3' end of one allele (the specific allele) and in addition have a 3' mismatch with the nonspecific allele. A computer program called SNAPER was used to facilitate the design of primers that generate at least a 1,000-fold difference in the quantity of the amplification products from the specific and nonspecific SNP alleles. Because SNAP markers can be readily assayed by electrophoresis on standard agarose gels and because a public database of over 25,000 SNPs is available between the Arabidopsis Columbia and Landsberg erecta ecotypes, the SNAP method greatly facilitates the map-based cloning of Arabidopsis genes defined by a mutant phenotype.
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Affiliation(s)
- E Drenkard
- Department of Genetics, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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50
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Abstract
Large-scale studies of mRNA expression have displayed the unusual ability to both challenge traditional biological paradigms and enjoy rapid adoption among a wide range of researchers. The proliferating applications of this technology are poised to exert heavy influence on the very way biologists conceptualize problems and ask questions in the post-genome era.
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Affiliation(s)
- R J Cho
- aDepartments of Genetics and Biochemistry, Stanford University School of Medicine, Stanford, CA 94035, USA.
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