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Danielsen M, Emmanuel T, Nielsen MM, Lindahl LM, Gluud M, Ødum N, Raaby L, Steiniche T, Iversen L, Bech R, Buus TB, Johansen C. RUNX2 as a novel biomarker for early identification of patients progressing to advanced-stage mycosis fungoides. Front Oncol 2024; 14:1421443. [PMID: 39435287 PMCID: PMC11491341 DOI: 10.3389/fonc.2024.1421443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 09/04/2024] [Indexed: 10/23/2024] Open
Abstract
Introduction The majority of patients with mycosis fungoides (MF) have an indolent disease course, but a substantial fraction (20-30%) of patients progress to advanced stages - usually with a grave prognosis. Early differentiation between indolent and aggressive types of MF is important for the choice of treatment regimen and monitoring of the individual patient. Good biomarkers are therefore desired. Methods Here, we used spatial transcriptomics on skin samples at time-of-diagnosis to enable prediction of patients who later progressed to advanced stages of MF. Formalin-fixed, paraffin-embedded skin biopsies at time of diagnosis from six patients with MF who progressed to advanced stages of disease within 4 months to 12 years after diagnosis, and nine patients who remained in early-stage disease over 9 to 27 years were analyzed using the GeoMx Digital Spatial Profiler to capture spatially resolved high-plex RNA gene expression data. Five different regions of interest (the epidermis, the basal layer of epidermis, CD4+ T-cells and neighboring cells, and Pautrier's microabscesses) were profiled for further assessment. Results and discussion Interestingly, RUNX2, SHMT2, and MCM7 were upregulated in the enriched population of malignant T-cells in Pautrier's microabscesses in patients who later developed advanced stages of disease. Expression of RUNX2, SHMT2 and MCM7 in malignant T-cells was confirmed in a subset of patients in MF skin using scRNA-seq datasets across multiple studies and correlating with stage of disease. Taken together, we provide first evidence that RUNX2 has potential as a biomarker to identify MF patients progressing to advanced stage disease. As RUNX2 has not previously been linked to MF, our data also shows the analytical strength of combining spatial transcriptomics with scRNA-seq analysis.
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Affiliation(s)
- Maria Danielsen
- Department of Dermatology, Aarhus University Hospital, Aarhus, Denmark
| | - Thomas Emmanuel
- Department of Dermatology, Aarhus University Hospital, Aarhus, Denmark
| | - Morten Muhlig Nielsen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | | | - Maria Gluud
- Skin Immunology Research Center, Department of Immunology & Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Niels Ødum
- Skin Immunology Research Center, Department of Immunology & Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Line Raaby
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Torben Steiniche
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Iversen
- Department of Dermatology, Aarhus University Hospital, Aarhus, Denmark
| | - Rikke Bech
- Department of Dermatology, Aarhus University Hospital, Aarhus, Denmark
| | - Terkild Brink Buus
- Skin Immunology Research Center, Department of Immunology & Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Claus Johansen
- Department of Dermatology, Aarhus University Hospital, Aarhus, Denmark
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2
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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; 62:1880-1891. [PMID: 38656304 DOI: 10.1515/cclm-2023-1245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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3
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Raybould MIJ, Greenshields-Watson A, Agarwal P, Aguilar-Sanjuan B, Olsen TH, Turnbull OM, Quast NP, Deane CM. The Observed T Cell Receptor Space database enables paired-chain repertoire mining, coherence analysis, and language modeling. Cell Rep 2024; 43:114704. [PMID: 39216000 DOI: 10.1016/j.celrep.2024.114704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 08/05/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024] Open
Abstract
T cell activation is governed through T cell receptors (TCRs), heterodimers of two sequence-variable chains (often an α and β chain) that synergistically recognize antigen fragments presented on cell surfaces. Despite this, there only exist repositories dedicated to collecting single-chain, not paired-chain, TCR sequence data. We addressed this gap by creating the Observed TCR Space (OTS) database, a source of consistently processed and annotated, full-length, paired-chain TCR sequences. Currently, OTS contains 5.35 million redundant (1.63 million non-redundant), predominantly human sequences from across 50 studies and at least 75 individuals. Using OTS, we identify pairing biases, public TCRs, and distinct chain coherence patterns relative to antibodies. We also release a paired-chain TCR language model, providing paired embedding representations and a method for residue in-filling conditional on the partner chain. OTS will be updated as a central community resource and is freely downloadable and available as a web application.
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Affiliation(s)
- Matthew I J Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', OX1 3LB Oxford, UK.
| | - Alexander Greenshields-Watson
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', OX1 3LB Oxford, UK
| | - Parth Agarwal
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', OX1 3LB Oxford, UK
| | - Broncio Aguilar-Sanjuan
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', OX1 3LB Oxford, UK
| | - Tobias H Olsen
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', OX1 3LB Oxford, UK
| | - Oliver M Turnbull
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', OX1 3LB Oxford, UK
| | - Nele P Quast
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', OX1 3LB Oxford, UK
| | - Charlotte M Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', OX1 3LB Oxford, UK.
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4
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Chennareddy S, Rindler K, Ruggiero JR, Alkon N, Cohenour ER, Tran S, Weninger W, Griss J, Jonak C, Brunner PM. Single-cell RNA sequencing comparison of CD4+, CD8+ and TCR-γδ+ cutaneous T-cell lymphomas reveals subset-specific molecular phenotypes. Br J Dermatol 2024:ljae313. [PMID: 39133553 DOI: 10.1093/bjd/ljae313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/17/2024] [Accepted: 08/09/2024] [Indexed: 09/15/2024]
Abstract
BACKGROUND Malignant clones of primary cutaneous T-cell lymphomas (CTCL) can show a CD4, CD8 or TCR-γδ phenotype, but their individual impact on tumor biology and skin lesion formation remains ill-defined. OBJECTIVES To perform a comprehensive molecular characterization of CD4+ vs. CD8+ and TCR-γ/δ+ CTCL lesions. METHODS We performed scRNA-seq of 18 CTCL skin biopsies to compare classic CD4+ advanced-stage mycosis fungoides (MF) with TCR-γ/δ+MF and primary cutaneous CD8+ aggressive epidermotropic cytotoxic T-cell lymphoma (Berti's lymphoma). RESULTS Malignant clones of TCR-γ/δ+MF and Berti's lymphoma showed similar clustering patterns distinct from CD4+MF, along with increased expression of cytotoxic markers such as NKG7, CTSW, GZMA, and GZMM. Only advanced-stage CD4+MF clones expressed central memory T-cell markers (SELL, CCR7, LEF1), alongside B1/B2 blood involvement, whereas TCR-γ/δ+MF and Berti's lymphoma harbored a more tissue-resident phenotype (CD69, CXCR4, NR4A1) without detectable cells in the blood. CD4+MF and TCR-γ/δ+MF skin lesions harbored strong type 2 immune activation across myeloid cells, while Berti's lymphoma was more skewed towards type 1 immune responses. Both CD4+MF and TCR-γ/δ+MF lesions showed upregulation of keratinocyte hyperactivation markers such as S100As and KRT16 genes. This increase was entirely absent in Berti's lymphoma, possibly reflecting an aberrant keratinocyte response to invading tumor cells, that could contribute to the formation of the typical ulcero-necrotic lesions within this entity. CONCLUSIONS Our scRNAseq profiling study reveals specific molecular patterns associated with distinct CTCL subtypes.
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Affiliation(s)
- Sumanth Chennareddy
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - John R Ruggiero
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Natalia Alkon
- Department of Dermatology, Medical University of Vienna, Austria
| | - Emry R Cohenour
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sophia Tran
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Johannes Griss
- Department of Dermatology, Medical University of Vienna, Austria
| | - Constanze Jonak
- Department of Dermatology, Medical University of Vienna, Austria
| | - Patrick M Brunner
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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5
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De Masson A, Lazaridou I, Moins-Teisserenc H, Ram-Wolff C, Giustiniani J, Bagot M, Battistella M, Bensussan A. Pathophysiology of cutaneous T-cell lymphomas: Perspective from a French referral centre. Immunol Lett 2024; 268:106871. [PMID: 38801999 DOI: 10.1016/j.imlet.2024.106871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/13/2024] [Accepted: 05/22/2024] [Indexed: 05/29/2024]
Abstract
Cutaneous T-cell lymphomas (CTCL) are a diverse group of malignant blood disorders characterized by initial skin infiltration, and sometimes, tumor spreading to lymph nodes, blood, and viscera. Mycosis fungoides is the most common form. Sézary syndrome is a distinctive form of CTCL marked by a significant presence of circulating tumor cells in peripheral blood. These diseases are characterized by the plasticity and heterogeneity of the tumor cells in the different tissue compartments, and a difficulty in identifying these tumor cells for diagnostic purposes and therapeutic monitoring. Progress has been made in the understanding of the pathophysiology of these diseases in recent years, and we provide here a review of these advancements.
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Affiliation(s)
- Adèle De Masson
- Service de Dermatologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Centre coordinateur national du réseau de cancers rares INCa Lymphomes Cutanés, France; INSERM U976, Institut de Recherche Saint-Louis, Paris, France; Université Paris Cité, Paris, France.
| | | | - Hélène Moins-Teisserenc
- Université Paris Cité, Paris, France; INSERM U1160, Institut de Recherche Saint-Louis, Paris, France; Laboratoire d'Hématologie Biologique, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, France
| | - Caroline Ram-Wolff
- Service de Dermatologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Centre coordinateur national du réseau de cancers rares INCa Lymphomes Cutanés, France
| | | | - Martine Bagot
- Service de Dermatologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Centre coordinateur national du réseau de cancers rares INCa Lymphomes Cutanés, France; INSERM U976, Institut de Recherche Saint-Louis, Paris, France; Université Paris Cité, Paris, France
| | - Maxime Battistella
- INSERM U976, Institut de Recherche Saint-Louis, Paris, France; Université Paris Cité, Paris, France; Laboratoire de Pathologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, France
| | - Armand Bensussan
- INSERM U976, Institut de Recherche Saint-Louis, Paris, France; Université Paris Cité, Paris, France; Mohammed VI Polytechnic University, Benguerir, Morocco
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6
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Cherfan C, Chebly A, Rezvani HR, Beylot-Barry M, Chevret E. Delving into the Metabolism of Sézary Cells: A Brief Review. Genes (Basel) 2024; 15:635. [PMID: 38790264 PMCID: PMC11121102 DOI: 10.3390/genes15050635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Primary cutaneous lymphomas (PCLs) are a heterogeneous group of lymphoproliferative disorders caused by the accumulation of neoplastic T or B lymphocytes in the skin. Sézary syndrome (SS) is an aggressive and rare form of cutaneous T cell lymphoma (CTCL) characterized by an erythroderma and the presence of atypical cerebriform T cells named Sézary cells in skin and blood. Most of the available treatments for SS are not curative, which means there is an urgent need for the development of novel efficient therapies. Recently, targeting cancer metabolism has emerged as a promising strategy for cancer therapy. This is due to the accumulating evidence that metabolic reprogramming highly contributes to tumor progression. Genes play a pivotal role in regulating metabolic processes, and alterations in these genes can disrupt the delicate balance of metabolic pathways, potentially contributing to cancer development. In this review, we discuss the importance of targeting energy metabolism in tumors and the currently available data on the metabolism of Sézary cells, paving the way for potential new therapeutic approaches aiming to improve clinical outcomes for patients suffering from SS.
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Affiliation(s)
- Carel Cherfan
- BRIC, BoRdeaux Institute of onCology, UMR 1312, Inserm, Université de Bordeaux, 33000 Bordeaux, France; (C.C.); (H.R.R.); (M.B.-B.)
| | - Alain Chebly
- Center Jacques Loiselet for Medical Genetics and Genomics (CGGM), Faculty of Medicine, Saint Joseph University, Beirut P.O. Box 17-5208, Lebanon;
| | - Hamid Reza Rezvani
- BRIC, BoRdeaux Institute of onCology, UMR 1312, Inserm, Université de Bordeaux, 33000 Bordeaux, France; (C.C.); (H.R.R.); (M.B.-B.)
| | - Marie Beylot-Barry
- BRIC, BoRdeaux Institute of onCology, UMR 1312, Inserm, Université de Bordeaux, 33000 Bordeaux, France; (C.C.); (H.R.R.); (M.B.-B.)
- Dermatology Department, Centre Hospitalier Universitaire de Bordeaux, 33075 Bordeaux, France
| | - Edith Chevret
- BRIC, BoRdeaux Institute of onCology, UMR 1312, Inserm, Université de Bordeaux, 33000 Bordeaux, France; (C.C.); (H.R.R.); (M.B.-B.)
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7
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Zeng Z, Vadivel CK, Gluud M, Namini MRJ, Yan L, Ahmad S, Hansen MB, Coquet J, Mustelin T, Koralov SB, Bonefeld CM, Woetmann A, Geisler C, Guenova E, Kamstrup MR, Litman T, Gjerdrum LMR, Buus TB, Ødum N. Keratinocytes Present Staphylococcus aureus Enterotoxins and Promote Malignant and Nonmalignant T Cell Proliferation in Cutaneous T-Cell Lymphoma. J Invest Dermatol 2024:S0022-202X(24)00377-4. [PMID: 38762064 DOI: 10.1016/j.jid.2024.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/06/2024] [Accepted: 04/09/2024] [Indexed: 05/20/2024]
Abstract
Cutaneous T-cell lymphoma is characterized by malignant T cells proliferating in a unique tumor microenvironment dominated by keratinocytes (KCs). Skin colonization and infection by Staphylococcus aureus are a common cause of morbidity and are suspected of fueling disease activity. In this study, we show that expression of HLA-DRs, high-affinity receptors for staphylococcal enterotoxins (SEs), by KCs correlates with IFN-γ expression in the tumor microenvironment. Importantly, IFN-γ induces HLA-DR, SE binding, and SE presentation by KCs to malignant T cells from patients with Sézary syndrome and malignant and nonmalignant T-cell lines derived from patients with Sézary syndrome and mycosis fungoides. Likewise, preincubation of KCs with supernatant from patient-derived SE-producing S aureus triggers proliferation in malignant T cells and cytokine release (including IL-2), when cultured with nonmalignant T cells. This is inhibited by pretreatment with engineered bacteriophage S aureus-specific endolysins. Furthermore, alteration in the HLA-DR-binding sites of SE type A and small interfering RNA-mediated knockdown of Jak3 and IL-2Rγ block induction of malignant T-cell proliferation. In conclusion, we show that upon exposure to patient-derived S aureus and SE, KCs stimulate IL-2Rγ/Jak3-dependent proliferation of malignant and nonmalignant T cells in an environment with nonmalignant T cells. These findings suggest that KCs in the tumor microenvironment play a key role in S aureus-mediated disease activity in cutaneous T-cell lymphoma.
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Affiliation(s)
- Ziao Zeng
- LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Chella Krishna Vadivel
- LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Maria Gluud
- LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Martin R J Namini
- LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Lang Yan
- LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Sana Ahmad
- LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Morten Bagge Hansen
- Blood Bank, Department of Clinical Immunology, State University Hospital (Rigshospitalet), Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan Coquet
- LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Tomas Mustelin
- Department of Rheumatology, University of Washington, Seattle, Washington, USA
| | - Sergei B Koralov
- Department of Pathology, New York University School of Medicine, New York, New York, USA
| | - Charlotte Menne Bonefeld
- LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Anders Woetmann
- LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Carsten Geisler
- LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Emmanuella Guenova
- University Hospital Lausanne (CHUV), Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Maria R Kamstrup
- Department of Dermatology, Bispebjerg and Frederiksberg University Hospital, Copenhagen, Denmark
| | - Thomas Litman
- LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Lise-Mette R Gjerdrum
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Pathology, Zealand University Hospital, Roskilde, Roskilde, Denmark
| | - Terkild B Buus
- LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.
| | - Niels Ødum
- LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.
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8
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Goldner Kabeli R, Zevin S, Abargel A, Zilberberg A, Efroni S. Self-supervised learning of T cell receptor sequences exposes core properties for T cell membership. SCIENCE ADVANCES 2024; 10:eadk4670. [PMID: 38669334 DOI: 10.1126/sciadv.adk4670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
The T cell receptor (TCR) repertoire is an extraordinarily diverse collection of TCRs essential for maintaining the body's homeostasis and response to threats. In this study, we compiled an extensive dataset of more than 4200 bulk TCR repertoire samples, encompassing 221,176,713 sequences, alongside 6,159,652 single-cell TCR sequences from over 400 samples. From this dataset, we then selected a representative subset of 5 million bulk sequences and 4.2 million single-cell sequences to train two specialized Transformer-based language models for bulk (CVC) and single-cell (scCVC) TCR repertoires, respectively. We show that these models successfully capture TCR core qualities, such as sharing, gene composition, and single-cell properties. These qualities are emergent in the encoded TCR latent space and enable classification into TCR-based qualities such as public sequences. These models demonstrate the potential of Transformer-based language models in TCR downstream applications.
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Affiliation(s)
- Romi Goldner Kabeli
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Sarit Zevin
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Avital Abargel
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Alona Zilberberg
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Sol Efroni
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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9
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Chang YT, Prompsy P, Kimeswenger S, Tsai YC, Ignatova D, Pavlova O, Iselin C, French LE, Levesque MP, Kuonen F, Bobrowicz M, Brunner PM, Pascolo S, Hoetzenecker W, Guenova E. MHC-I upregulation safeguards neoplastic T cells in the skin against NK cell-mediated eradication in mycosis fungoides. Nat Commun 2024; 15:752. [PMID: 38272918 PMCID: PMC10810852 DOI: 10.1038/s41467-024-45083-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
Cancer-associated immune dysfunction is a major challenge for effective therapies. The emergence of antibodies targeting tumor cell-surface antigens led to advancements in the treatment of hematopoietic malignancies, particularly blood cancers. Yet their impact is constrained against tumors of hematopoietic origin manifesting in the skin. In this study, we employ a clonality-supervised deep learning methodology to dissect key pathological features implicated in mycosis fungoides, the most common cutaneous T-cell lymphoma. Our investigations unveil the prominence of the IL-32β-major histocompatibility complex (MHC)-I axis as a critical determinant in tumor T-cell immune evasion within the skin microenvironment. In patients' skin, we find MHC-I to detrimentally impact the functionality of natural killer (NK) cells, diminishing antibody-dependent cellular cytotoxicity and promoting resistance of tumor skin T-cells to cell-surface targeting therapies. Through murine experiments in female mice, we demonstrate that disruption of the MHC-I interaction with NK cell inhibitory Ly49 receptors restores NK cell anti-tumor activity and targeted T-cell lymphoma elimination in vivo. These findings underscore the significance of attenuating the MHC-I-dependent immunosuppressive networks within skin tumors. Overall, our study introduces a strategy to reinvigorate NK cell-mediated anti-tumor responses to overcome treatment resistance to existing cell-surface targeted therapies for skin lymphoma.
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Affiliation(s)
- Yun-Tsan Chang
- Department of Dermatology, Lausanne University Hospital (CHUV) and Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Pacôme Prompsy
- Department of Dermatology, Lausanne University Hospital (CHUV) and Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Susanne Kimeswenger
- Department of Dermatology and Venerology, Medical Faculty, Johannes Kepler University, Linz, Austria
| | - Yi-Chien Tsai
- Department of Dermatology, Lausanne University Hospital (CHUV) and Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Desislava Ignatova
- Department of Dermatology, University Hospital of Zurich and Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Olesya Pavlova
- Department of Dermatology, Lausanne University Hospital (CHUV) and Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Christoph Iselin
- Department of Dermatology, Lausanne University Hospital (CHUV) and Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Lars E French
- Department of Dermatology and Allergology, Ludwig-Maximilians-University of Munich, Munich, Germany
- Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mitchell P Levesque
- Department of Dermatology, University Hospital of Zurich and Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - François Kuonen
- Department of Dermatology, Lausanne University Hospital (CHUV) and Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | | | - Patrick M Brunner
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Steve Pascolo
- Department of Dermatology, University Hospital of Zurich and Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Wolfram Hoetzenecker
- Department of Dermatology and Venerology, Medical Faculty, Johannes Kepler University, Linz, Austria.
| | - Emmanuella Guenova
- Department of Dermatology, Lausanne University Hospital (CHUV) and Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
- Department of Dermatology, University Hospital of Zurich and Faculty of Medicine, University of Zurich, Zurich, Switzerland.
- Department of Dermatology, Hospital 12 de Octubre, Medical School, University Complutense, Madrid, Spain.
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10
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Gaydosik AM, Stonesifer CJ, Tabib T, Lafyatis R, Geskin LJ, Fuschiotti P. The mycosis fungoides cutaneous microenvironment shapes dysfunctional cell trafficking, antitumor immunity, matrix interactions, and angiogenesis. JCI Insight 2023; 8:e170015. [PMID: 37669110 PMCID: PMC10619438 DOI: 10.1172/jci.insight.170015] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/31/2023] [Indexed: 09/07/2023] Open
Abstract
Malignant T lymphocyte proliferation in mycosis fungoides (MF) is largely restricted to the skin, implying that malignant cells are dependent on their specific cutaneous tumor microenvironment (TME), including interactions with non-malignant immune and stromal cells, cytokines, and other immunomodulatory factors. To explore these interactions, we performed a comprehensive transcriptome analysis of the TME in advanced-stage MF skin tumors by single-cell RNA sequencing. Our analysis identified cell-type compositions, cellular functions, and cell-to-cell interactions in the MF TME that were distinct from those from healthy skin and benign dermatoses. While patterns of gene expression were common among patient samples, high transcriptional diversity was also observed in immune and stromal cells, with dynamic interactions and crosstalk between these cells and malignant T lymphocytes. This heterogeneity mapped to processes such as cell trafficking, matrix interactions, angiogenesis, immune functions, and metabolism that affect cancer cell growth, migration, and invasion, as well as antitumor immunity. By comprehensively characterizing the transcriptomes of immune and stromal cells within the cutaneous microenvironment of individual MF tumors, we have identified patterns of dysfunction common to all tumors that represent a resource for identifying candidates with therapeutic potential as well as patient-specific heterogeneity that has important implications for personalized disease management.
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Affiliation(s)
- Alyxzandria M. Gaydosik
- Department of Medicine, Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | | | - Tracy Tabib
- Department of Medicine, Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Robert Lafyatis
- Department of Medicine, Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | | | - Patrizia Fuschiotti
- Department of Medicine, Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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11
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Feng Y, Wang S, Xie J, Ding B, Wang M, Zhang P, Mi P, Wang C, Liu R, Zhang T, Yu X, Yuan D, Zhang C. Spatial transcriptomics reveals heterogeneity of macrophages in the tumor microenvironment of granulomatous slack skin. J Pathol 2023; 261:105-119. [PMID: 37550813 DOI: 10.1002/path.6151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/30/2023] [Accepted: 06/01/2023] [Indexed: 08/09/2023]
Abstract
Granulomatous slack skin (GSS) is an extremely rare subtype of cutaneous T-cell lymphoma accompanied by an abundant number of macrophages and is clinically characterized by the development of pendulous skin folds. However, the characteristics of these macrophages in GSS remain unclear. Here, we conducted a spatial transcriptomic study on one frozen GSS sample and drew transcriptomic maps of GSS for the first time. Gene expression analysis revealed the enrichment of three clusters with macrophage transcripts, each exhibiting distinct characteristics suggesting that their primary composition consists of different subpopulations of macrophages. The CD163+ /CD206+ cluster showed a tumor-associated macrophage (TAM) M2-like phenotype and highly expressed ZFP36, CCL2, TNFAIP6, and KLF2, which are known to be involved in T-cell interaction and tumor progression. The APOC1+ /APOE+ cluster presented a non-M1 or -M2 phenotype and may be related to lipid metabolism. The CD11c+ /LYZ+ cluster exhibited an M1-like phenotype. Notably, these cells strongly expressed MMP9, MMP12, CHI3L1, CHIT1, COL1A1, TIMP1, and SPP1, which are responsible for extracellular matrix (ECM) degradation and tissue remodeling. This may partially explain the symptoms of cutaneous relaxation in GSS. Further immunohistochemistry on four GSS cases demonstrated that CD11c predominantly marked granulomas and multinucleated giant cells, whereas CD163 was mainly expressed on scattered macrophages, appearing as a mutually exclusive pattern. The expression pattern of MMP9 overlapped with that of CD11c, implying that CD11c+ macrophages may be a source of MMP9. Our data shed light on the characteristics of macrophages in the GSS microenvironment and provide a theoretical basis for the application of MMP9 inhibitors to prevent cutaneous relaxation of GSS. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Yawei Feng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Shiguan Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Jianjun Xie
- Department of Pathology, Qingdao Chengyang People's Hospital, Qingdao, PR China
| | - Bin Ding
- Department of Pathology, Affiliated Qingdao Central Hospital, Qingdao University, Qingdao, PR China
| | - Min Wang
- Department of Pathology, The Second People's Hospital of Liaocheng, Linqing, PR China
| | - Peng Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Ping Mi
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Chunxue Wang
- Institute of Pathology and Pathophysiology, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Ruirui Liu
- Institute of Pathology and Pathophysiology, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Tingguo Zhang
- Institute of Pathology and Pathophysiology, Cheeloo College of Medicine, Shandong University, Jinan, PR China
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, PR China
| | - Xiaojing Yu
- Department of Dermatology, Qilu Hospital of Shandong University, Jinan, PR China
| | - Detian Yuan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Cuijuan Zhang
- Institute of Pathology and Pathophysiology, Cheeloo College of Medicine, Shandong University, Jinan, PR China
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, PR China
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12
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Huang D, Ma N, Li X, Gou Y, Duan Y, Liu B, Xia J, Zhao X, Wang X, Li Q, Rao J, Zhang X. Advances in single-cell RNA sequencing and its applications in cancer research. J Hematol Oncol 2023; 16:98. [PMID: 37612741 PMCID: PMC10463514 DOI: 10.1186/s13045-023-01494-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023] Open
Abstract
Cancers are a group of heterogeneous diseases characterized by the acquisition of functional capabilities during the transition from a normal to a neoplastic state. Powerful experimental and computational tools can be applied to elucidate the mechanisms of occurrence, progression, metastasis, and drug resistance; however, challenges remain. Bulk RNA sequencing techniques only reflect the average gene expression in a sample, making it difficult to understand tumor heterogeneity and the tumor microenvironment. The emergence and development of single-cell RNA sequencing (scRNA-seq) technologies have provided opportunities to understand subtle changes in tumor biology by identifying distinct cell subpopulations, dissecting the tumor microenvironment, and characterizing cellular genomic mutations. Recently, scRNA-seq technology has been increasingly used in cancer studies to explore tumor heterogeneity and the tumor microenvironment, which has increased the understanding of tumorigenesis and evolution. This review summarizes the basic processes and development of scRNA-seq technologies and their increasing applications in cancer research and clinical practice.
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Affiliation(s)
- Dezhi Huang
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Naya Ma
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Xinlei Li
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Yang Gou
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Yishuo Duan
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Bangdong Liu
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Jing Xia
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Xianlan Zhao
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Xiaoqi Wang
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Qiong Li
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China.
- Jinfeng Laboratory, Chongqing, 401329, China.
| | - Jun Rao
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China.
- Jinfeng Laboratory, Chongqing, 401329, China.
- National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 215006, China.
| | - Xi Zhang
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, China.
- Jinfeng Laboratory, Chongqing, 401329, China.
- National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 215006, China.
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13
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Lefebvre MN, Borcherding N, Reis RJ, Mou E, Liu V, Jabbari A. Molecular techniques drive cutting edge advancements in management of cutaneous T cell lymphoma. Front Immunol 2023; 14:1228563. [PMID: 37654486 PMCID: PMC10465366 DOI: 10.3389/fimmu.2023.1228563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/27/2023] [Indexed: 09/02/2023] Open
Abstract
Cutaneous 5T cell lymphoma (CTCL), characterized by malignant T cells infiltrating the skin with potential for dissemination, remains a challenging disease to diagnose and treat due to disease heterogeneity, treatment resistance, and lack of effective and standardized diagnostic and prognostic clinical tools. Currently, diagnosis of CTCL practically relies on clinical presentation, histopathology, and immunohistochemistry. These methods are collectively fraught with limitations in sensitivity and specificity. Fortunately, recent advances in flow cytometry, polymerase chain reaction, high throughput sequencing, and other molecular techniques have shown promise in improving diagnosis and treatment of CTCL. Examples of these advances include T cell receptor clonotyping via sequencing to detect CTCL earlier in the disease course and single-cell RNA sequencing to identify gene expression patterns that commonly drive CTCL pathogenesis. Experience with these techniques has afforded novel insights which may translate into enhanced diagnostic and therapeutic approaches for CTCL.
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Affiliation(s)
- Mitchell N. Lefebvre
- University of Iowa Carver College of Medicine, Iowa City, IA, United States
- Department of Dermatology, University of Iowa, University of Iowa Hospitals and Clinics, Iowa City, IA, United States
| | - Nicholas Borcherding
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Ryan J. Reis
- University of Iowa Carver College of Medicine, Iowa City, IA, United States
- Cancer Biology Graduate Program, University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - Eric Mou
- Department of Hematology and Oncology, University of Iowa Hospitals and Clinics, Iowa City, IA, United States
| | - Vincent Liu
- University of Iowa Carver College of Medicine, Iowa City, IA, United States
- Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, IA, United States
| | - Ali Jabbari
- University of Iowa Carver College of Medicine, Iowa City, IA, United States
- Iowa City Veterans Affairs Medical Center, Iowa City, IA, United States
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14
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Strobl J, Haniffa M. Functional heterogeneity of human skin-resident memory T cells in health and disease. Immunol Rev 2023; 316:104-119. [PMID: 37144705 PMCID: PMC10952320 DOI: 10.1111/imr.13213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/11/2023] [Accepted: 04/15/2023] [Indexed: 05/06/2023]
Abstract
The human skin is populated by a diverse pool of memory T cells, which can act rapidly in response to pathogens and cancer antigens. Tissue-resident memory T cells (TRM ) have been implicated in range of allergic, autoimmune and inflammatory skin diseases. Clonal expansion of cells with TRM properties is also known to contribute to cutaneous T-cell lymphoma. Here, we review the heterogeneous phenotypes, transcriptional programs, and effector functions of skin TRM . We summarize recent studies on TRM formation, longevity, plasticity, and retrograde migration and contextualize the findings to skin TRM and their role in maintaining skin homeostasis and altered functions in skin disease.
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Affiliation(s)
- Johanna Strobl
- Department of DermatologyMedical University of ViennaViennaAustria
- CeMM Research Center for Molecular MedicineViennaAustria
| | - Muzlifah Haniffa
- Wellcome Sanger InstituteCambridgeUK
- Department of Dermatology and NIHR Newcastle Biomedical Research CentreNewcastle Hospitals NHS Foundation TrustNewcastle upon TyneUK
- Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
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15
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Sant P, Rippe K, Mallm JP. Approaches for single-cell RNA sequencing across tissues and cell types. Transcription 2023; 14:127-145. [PMID: 37062951 PMCID: PMC10807473 DOI: 10.1080/21541264.2023.2200721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/30/2023] [Indexed: 04/18/2023] Open
Abstract
Single-cell sequencing of RNA (scRNA-seq) has advanced our understanding of cellular heterogeneity and signaling in developmental biology and disease. A large number of complementary assays have been developed to profile transcriptomes of individual cells, also in combination with other readouts, such as chromatin accessibility or antibody-based analysis of protein surface markers. As scRNA-seq technologies are advancing fast, it is challenging to establish robust workflows and up-to-date protocols that are best suited to address the large range of research questions. Here, we review scRNA-seq techniques from mRNA end-counting to total RNA in relation to their specific features and outline the necessary sample preparation steps and quality control measures. Based on our experience in dealing with the continuously growing portfolio from the perspective of a central single-cell facility, we aim to provide guidance on how workflows can be best automatized and share our experience in coping with the continuous expansion of scRNA-seq techniques.
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Affiliation(s)
- Pooja Sant
- Single-cell Open Lab, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Karsten Rippe
- Division Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Jan-Philipp Mallm
- Single-cell Open Lab, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
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16
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Atilla PA, Atilla E. Are we there yet? cellular therapies for cutaneous T cell lymphoma. Curr Res Transl Med 2023; 71:103390. [PMID: 37062252 DOI: 10.1016/j.retram.2023.103390] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 03/08/2023] [Accepted: 04/04/2023] [Indexed: 04/18/2023]
Abstract
Cutaneous T cell lymphomas (CTCLs) are a heterogenous group of skin-involved T-cell non-Hodgkin lymphoma which Mycosis Fungoides and Sezary Syndrome are the most common variants. Despite considerable progress in distinguishing the pathophysiology, the treatment options are still limited for advanced-stage disease. Recent approval of novel agents such as vorinostat, brentuximab vedotin and mogamulizumab paved a way. Allogeneic hematopoietic stem cell transplantation has been shown to be a feasible option in selected advanced-stage CTCL patients. Chimeric antigen receptor (CAR) T cells have been promising for the treatment of B-cell tumors and have been approved for second-line treatment in non-Hodgkin's lymphoma. Although several obstacles still need to be addressed, CAR T cell treatment for CTCLs seems not far off. This review discusses new discoveries in pathophysiology, the state of cellular therapies in current practice, challenges for cellular treatment in advanced CTCL, and how to overcome these challenges.
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Affiliation(s)
- Pinar Ataca Atilla
- Ankara University Stem Cell Institute, Ankara, Turkey; Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA
| | - Erden Atilla
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA; Genyo Centre for Genomics and Oncological Research, Genomic Medicine Department, Pfizer/University of Gradana/Andalusian Regional Government, Health Sciences Technnology Park, Granada, Spain.
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17
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Charli-Joseph Y, Pincus LB, Ai WZ. Prognostic Relevance of Dominant Blood T-Cell Clones in Early Mycosis Fungoides-Reply. JAMA Dermatol 2023; 159:116-117. [PMID: 36416842 DOI: 10.1001/jamadermatol.2022.4854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Yann Charli-Joseph
- Cutaneous Hematopathology Clinic, Department of Dermatology, National Institute of Health Sciences and Nutrition, Mexico City, Mexico
| | - Laura Beth Pincus
- Departments of Pathology and Dermatology, University of California, San Francisco
| | - Weiyun Z Ai
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco
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