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Ganier C. Unlocking Skin's Symphony: Single-Cell and Spatial Transcriptomics Reveal the Harmonious Interplay among Diverse Cell Populations. J Invest Dermatol 2024; 144:1917-1920. [PMID: 38678464 DOI: 10.1016/j.jid.2024.01.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 05/01/2024]
Affiliation(s)
- Clarisse Ganier
- Centre for Gene Therapy and Regenerative Medicine, Guy's Hospital, King's College London, London, United Kingdom.
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2
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Dainese-Marque O, Garcia V, Andrieu-Abadie N, Riond J. Contribution of Keratinocytes in Skin Cancer Initiation and Progression. Int J Mol Sci 2024; 25:8813. [PMID: 39201498 DOI: 10.3390/ijms25168813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 08/10/2024] [Accepted: 08/11/2024] [Indexed: 09/02/2024] Open
Abstract
Keratinocytes are major cellular components of the skin and are strongly involved in its homeostasis. Oncogenic events, starting mainly from excessive sun exposure, lead to the dysregulation of their proliferation and differentiation programs and promote the initiation and progression of non-melanoma skin cancers (NMSCs). Primary melanomas, which originate from melanocytes, initiate and develop in close interaction with keratinocytes, whose role in melanoma initiation, progression, and immune escape is currently being explored. Recent studies highlighted, in particular, unexpected modes of communication between melanocytic cells and keratinocytes, which may be of interest as sources of new biomarkers in melanomagenesis or potential therapeutic targets. This review aims at reporting the various contributions of keratinocytes in skin basal cell carcinoma (BCC), cutaneous squamous cell carcinoma (cSCC), and melanoma, with a greater focus on the latter in order to highlight some recent breakthrough findings. The readers are referred to recent reviews when contextual information is needed.
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Affiliation(s)
- Océane Dainese-Marque
- Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, 31037 Toulouse, France
| | - Virginie Garcia
- Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, 31037 Toulouse, France
| | - Nathalie Andrieu-Abadie
- Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, 31037 Toulouse, France
| | - Joëlle Riond
- Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, 31037 Toulouse, France
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3
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Kwak Y, Nam SK, Park Y, Suh YS, Ahn SH, Kong SH, Park DJ, Lee HJ, Kim HH, Yang HK, Lee HS. Distinctive Phenotypic and Microenvironmental Characteristics of Neuroendocrine Carcinoma and Adenocarcinoma Components in Gastric Mixed Adenoneuroendocrine Carcinoma. Mod Pathol 2024; 37:100568. [PMID: 39029904 DOI: 10.1016/j.modpat.2024.100568] [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: 04/02/2024] [Revised: 06/30/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024]
Abstract
This study aimed to conduct an in-depth examination of gene expression and microenvironmental profiles of gastric neuroendocrine carcinoma (NEC) and mixed adeno-NEC (MANEC). Tissue microarrays from 55 patients with gastric MANEC (N = 32) or NEC (N = 23) were analyzed using digital spatial profiling (GeoMx DSP, NanoString Technologies). Representative regions of interest were selected from the adenocarcinoma (ADC) portion (ADC-MANEC) and the NEC portion (NEC-MANEC) of the MANEC cores, and pure NEC (pNEC) cores. All regions of interest were separated into epithelial components and stromal components using the masking procedure in the GeoMx platform, followed by transcriptome analysis. Comparison of gene expression between ADC-MANEC and NEC-MANEC/pNEC identified several differentially expressed genes in the epithelial (including PEG10, MAP1B, STMN3, and AKT3) and stromal (FN1, COL1A1, SPARC, and BGN) components. Gene set enrichment analysis revealed that pathways related to the E2F target and G2M checkpoint were more enriched in NEC-MANEC and pNEC than in ADC-MANEC. Deconvolution analysis showed that the microenvironmental profile varied according to histologic differentiation. In ADC-MANEC, intraepithelial infiltrating immune cells were relatively more numerous, whereas fibroblasts in the stroma were more abundant in NEC-MANEC and pNEC. This study confirmed the distinct expression profile of each histologic component of MANEC according to its tumor vs stromal compartment using the DSP platform. Although each component of MANEC shares the same genetic origin, distinctive phenotypes should not be overlooked when managing patients with MANEC. This study provides a useful validation data set for future studies.
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Affiliation(s)
- Yoonjin Kwak
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Soo Kyung Nam
- Department of Interdisciplinary Program in Cancer Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Yujun Park
- Department of Pathology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam, Korea
| | - Yun-Suhk Suh
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Sang-Hoon Ahn
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Seong-Ho Kong
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Do Joong Park
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hyuk-Joon Lee
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hyung-Ho Kim
- Department of Surgery, Chung-Ang University College of Medicine, Seoul, Korea
| | - Han-Kwang Yang
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hye Seung Lee
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea.
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4
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Łuszczyński K, Soszyńska M, Komorowski M, Lewandowska P, Zdanowski R, Sobiepanek A, Brytan M, Malejczyk J, Lutyńska A, Ścieżyńska A. Markers of Dermal Fibroblast Subpopulations for Viable Cell Isolation via Cell Sorting: A Comprehensive Review. Cells 2024; 13:1206. [PMID: 39056788 PMCID: PMC11274970 DOI: 10.3390/cells13141206] [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: 06/06/2024] [Revised: 07/04/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Fibroblasts are among the most abundant cell types in the human body, playing crucial roles in numerous physiological processes, including the structural maintenance of the dermis, production of extracellular matrix components, and mediation of inflammatory responses. Despite their importance, fibroblasts remain one of the least characterized cell populations. The advent of single-cell analysis techniques, particularly single-cell RNA sequencing (scRNA-seq) and fluorescence-activated cell sorting (FACS), has enabled detailed investigations into fibroblast biology. In this study, we present an extensive analysis of fibroblast surface markers suitable for cell sorting and subsequent functional studies. We reviewed over three thousand research articles describing fibroblast populations and their markers, characterizing and comparing subtypes based on their surface markers, as well as their intra- and extracellular proteins. Our detailed analysis identified a variety of distinct fibroblast subpopulations, each with unique markers, characteristics dependent on their location, and the physiological or pathophysiological environment. These findings underscore the diversity of fibroblasts as a cellular population and could lead to the development of novel diagnostic and therapeutic tools.
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Affiliation(s)
- Krzysztof Łuszczyński
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine National Research Institute, 128 Szaserów Street, 04-141 Warsaw, Poland; (K.Ł.); (R.Z.); (A.L.)
| | - Marta Soszyńska
- Department of Histology and Embryology, Medical University of Warsaw, 02-004 Warsaw, Poland; (M.S.); (M.K.); (P.L.); (J.M.)
| | - Michał Komorowski
- Department of Histology and Embryology, Medical University of Warsaw, 02-004 Warsaw, Poland; (M.S.); (M.K.); (P.L.); (J.M.)
| | - Paulina Lewandowska
- Department of Histology and Embryology, Medical University of Warsaw, 02-004 Warsaw, Poland; (M.S.); (M.K.); (P.L.); (J.M.)
| | - Robert Zdanowski
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine National Research Institute, 128 Szaserów Street, 04-141 Warsaw, Poland; (K.Ł.); (R.Z.); (A.L.)
| | - Anna Sobiepanek
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland;
| | - Marek Brytan
- Department of Pharmacology and Toxicology, Military Institute of Hygiene and Epidemiology, 01-163 Warsaw, Poland;
| | - Jacek Malejczyk
- Department of Histology and Embryology, Medical University of Warsaw, 02-004 Warsaw, Poland; (M.S.); (M.K.); (P.L.); (J.M.)
| | - Anna Lutyńska
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine National Research Institute, 128 Szaserów Street, 04-141 Warsaw, Poland; (K.Ł.); (R.Z.); (A.L.)
| | - Aneta Ścieżyńska
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine National Research Institute, 128 Szaserów Street, 04-141 Warsaw, Poland; (K.Ł.); (R.Z.); (A.L.)
- Department of Histology and Embryology, Medical University of Warsaw, 02-004 Warsaw, Poland; (M.S.); (M.K.); (P.L.); (J.M.)
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5
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Moutafi MK, Bates KM, Aung TN, Milian RG, Xirou V, Vathiotis IA, Gavrielatou N, Angelakis A, Schalper KA, Salichos L, Rimm DL. High-throughput transcriptome profiling indicates ribosomal RNAs to be associated with resistance to immunotherapy in non-small cell lung cancer (NSCLC). J Immunother Cancer 2024; 12:e009039. [PMID: 38857914 PMCID: PMC11168162 DOI: 10.1136/jitc-2024-009039] [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] [Accepted: 05/27/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Despite the impressive outcomes with immune checkpoint inhibitor (ICI) in non-small cell lung cancer (NSCLC), only a minority of the patients show long-term benefits from ICI. In this study, we used retrospective cohorts of ICI treated patients with NSCLC to discover and validate spatially resolved protein markers associated with resistance to programmed cell death protein-1 (PD-1) axis inhibition. METHODS Pretreatment samples from 56 patients with NSCLC treated with ICI were collected and analyzed in a tissue microarray (TMA) format in including four different tumor regions per patient using the GeoMx platform for spatially informed transcriptomics. 34 patients had assessable tissue with tumor compartment in all 4 TMA spots, 22 with leukocyte compartment and 12 with CD68 compartment. The patients' tissue that was not assessable in fourfold redundancy in each compartment was designated as the validation cohort; cytokeratin (CK) (N=22), leukocytes CD45 (N=31), macrophages, CD68 (N=43). The human whole transcriptome, represented by~18,000 individual genes assessed by oligonucleotide-tagged in situ hybridization, was sequenced on the NovaSeq platform to quantify the RNAs present in each region of interest. RESULTS 54,000 gene variables were generated per case, from them 25,740 were analyzed after removing targets with expression lower than a prespecified frequency. Cox proportional-hazards model analysis was performed for overall and progression-free survival (OS, PFS, respectively). After identifying genes significantly associated with limited survival benefit (HR>1)/progression per spot per patient, we used the intersection of them across the four TMA spots per patient. This resulted in a list of 12 genes in the tumor-cell compartment (RPL13A, GNL3, FAM83A, CYBA, ACSL4, SLC25A6, EPAS1, RPL5, APOL1, HSPD1, RPS4Y1, ADI1). RPL13A, GNL3 in tumor-cell compartment were also significantly associated with OS and PFS, respectively, in the validation cohort (CK: HR, 2.48; p=0.02 and HR, 5.33; p=0.04). In CD45 compartment, secreted frizzled-related protein 2, was associated with OS in the discovery cohort but not in the validation cohort. Similarly, in the CD68 compartment ARHGAP and PNN interacting serine and arginine rich protein were significantly associated with PFS and OS, respectively, in the majority but not all four spots per patient. CONCLUSION This work highlights RPL13A and GNL3 as potential indicative biomarkers of resistance to PD-1 axis blockade that might help to improve precision immunotherapy strategies for lung cancer.
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Affiliation(s)
- Myrto K Moutafi
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Katherine M Bates
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Thazin Nwe Aung
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
- Yale School of Medicine, New Haven, Connecticut, USA
| | - Rolando Garcia Milian
- Bioinformatics Support Program, Cushing/Whitney Medical Library, Yale School of Medicine, New Haven, Connecticut, USA
| | - Vasiliki Xirou
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
- Yale School of Medicine, New Haven, Connecticut, USA
| | - Ioannis A Vathiotis
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Niki Gavrielatou
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
- Yale School of Medicine, New Haven, Connecticut, USA
| | - Athanasios Angelakis
- Epidemiology and Data Science, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
- Department of Methodology, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Kurt A Schalper
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Leonidas Salichos
- Biomedical Data Science Center Director, Center for Cancer Research, Department of Computational Biology at New York Institute of Technology, New York Institute of Technology, Old Westbury, New York, USA
| | - David L Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
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6
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Mori Y, Okimoto Y, Sakai H, Kanda Y, Ohata H, Shiokawa D, Suzuki M, Yoshida H, Ueda H, Sekizuka T, Tamura R, Yamawaki K, Ishiguro T, Mateos RN, Shiraishi Y, Yatabe Y, Hamada A, Yoshihara K, Enomoto T, Okamoto K. Targeting PDGF signaling of cancer-associated fibroblasts blocks feedback activation of HIF-1α and tumor progression of clear cell ovarian cancer. Cell Rep Med 2024; 5:101532. [PMID: 38670097 PMCID: PMC11149410 DOI: 10.1016/j.xcrm.2024.101532] [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: 02/22/2023] [Revised: 01/04/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024]
Abstract
Ovarian clear cell carcinoma (OCCC) is a gynecological cancer with a dismal prognosis; however, the mechanism underlying OCCC chemoresistance is not well understood. To explore the intracellular networks associated with the chemoresistance, we analyze surgical specimens by performing integrative analyses that combine single-cell analyses and spatial transcriptomics. We find that a chemoresistant OCCC subpopulation with elevated HIF activity localizes mainly in areas populated by cancer-associated fibroblasts (CAFs) with a myofibroblastic phenotype, which is corroborated by quantitative immunostaining. CAF-enhanced chemoresistance and HIF-1α induction are recapitulated in co-culture assays, which show that cancer-derived platelet-derived growth factor (PDGF) contributes to the chemoresistance and HIF-1α induction via PDGF receptor signaling in CAFs. Ripretinib is identified as an effective receptor tyrosine kinase inhibitor against CAF survival. In the co-culture system and xenograft tumors, ripretinib prevents CAF survival and suppresses OCCC proliferation in the presence of carboplatin, indicating that combination of conventional chemotherapy and CAF-targeted agents is effective against OCCC.
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MESH Headings
- Female
- Humans
- Cancer-Associated Fibroblasts/metabolism
- Cancer-Associated Fibroblasts/pathology
- Cancer-Associated Fibroblasts/drug effects
- Hypoxia-Inducible Factor 1, alpha Subunit/metabolism
- Hypoxia-Inducible Factor 1, alpha Subunit/genetics
- Ovarian Neoplasms/pathology
- Ovarian Neoplasms/metabolism
- Ovarian Neoplasms/drug therapy
- Ovarian Neoplasms/genetics
- Platelet-Derived Growth Factor/metabolism
- Signal Transduction/drug effects
- Animals
- Mice
- Cell Line, Tumor
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Disease Progression
- Coculture Techniques
- Cell Proliferation/drug effects
- Mice, Nude
- Adenocarcinoma, Clear Cell/metabolism
- Adenocarcinoma, Clear Cell/pathology
- Adenocarcinoma, Clear Cell/drug therapy
- Adenocarcinoma, Clear Cell/genetics
- Feedback, Physiological/drug effects
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Yutaro Mori
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo 173-0003, Japan; Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8520, Japan
| | - Yoshie Okimoto
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo 173-0003, Japan
| | - Hiroaki Sakai
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo 173-0003, Japan
| | - Yusuke Kanda
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo 173-0003, Japan
| | - Hirokazu Ohata
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo 173-0003, Japan
| | - Daisuke Shiokawa
- Ehime University Hospital Translational Research Center, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Mikiko Suzuki
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Hiroshi Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Haruka Ueda
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8520, Japan
| | - Tomoyuki Sekizuka
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8520, Japan
| | - Ryo Tamura
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8520, Japan
| | - Kaoru Yamawaki
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8520, Japan
| | - Tatsuya Ishiguro
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8520, Japan
| | - Raul Nicolas Mateos
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Yasushi Yatabe
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Akinobu Hamada
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8520, Japan
| | - Takayuki Enomoto
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8520, Japan
| | - Koji Okamoto
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo 173-0003, Japan.
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7
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Sosa J, Oyelakin A, Sinha S. The Reign of Follistatin in Tumors and Their Microenvironment: Implications for Drug Resistance. BIOLOGY 2024; 13:130. [PMID: 38392348 PMCID: PMC10887188 DOI: 10.3390/biology13020130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/10/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024]
Abstract
Follistatin (FST) is a potent neutralizer of the transforming growth factor-β superfamily and is associated with normal cellular programs and various hallmarks of cancer, such as proliferation, migration, angiogenesis, and immune evasion. The aberrant expression of FST by solid tumors is a well-documented observation, yet how FST influences tumor progression and therapy response remains unclear. The recent surge in omics data has revealed new insights into the molecular foundation underpinning tumor heterogeneity and its microenvironment, offering novel precision medicine-based opportunities to combat cancer. In this review, we discuss these recent FST-centric studies, thereby offering an updated perspective on the protean role of FST isoforms in shaping the complex cellular ecosystem of tumors and in mediating drug resistance.
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Affiliation(s)
- Jennifer Sosa
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Akinsola Oyelakin
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle Children's Hospital, Seattle, WA 98101, USA
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle Children's Hospital, Seattle, WA 98101, USA
| | - Satrajit Sinha
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
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8
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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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9
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Pinjusic K, Ambrosini G, Lourenco J, Fournier N, Iseli C, Guex N, Egorova O, Nassiri S, Constam DB. Inhibition of anti-tumor immunity by melanoma cell-derived Activin-A depends on STING. Front Immunol 2024; 14:1335207. [PMID: 38304252 PMCID: PMC10830842 DOI: 10.3389/fimmu.2023.1335207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/22/2023] [Indexed: 02/03/2024] Open
Abstract
The transforming growth factor-β (TGF-β) family member activin A (hereafter Activin-A) is overexpressed in many cancer types, often correlating with cancer-associated cachexia and poor prognosis. Activin-A secretion by melanoma cells indirectly impedes CD8+ T cell-mediated anti-tumor immunity and promotes resistance to immunotherapies, even though Activin-A can be proinflammatory in other contexts. To identify underlying mechanisms, we here analyzed the effect of Activin-A on syngeneic grafts of Braf mutant YUMM3.3 mouse melanoma cells and on their microenvironment using single-cell RNA sequencing. We found that the Activin-A-induced immune evasion was accompanied by a proinflammatory interferon signature across multiple cell types, and that the associated increase in tumor growth depended at least in part on pernicious STING activity within the melanoma cells. Besides corroborating a role for proinflammatory signals in facilitating immune evasion, our results suggest that STING holds considerable potential as a therapeutic target to mitigate tumor-promoting Activin-A signaling at least in melanoma.
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Affiliation(s)
- Katarina Pinjusic
- Ecole Polytechnique Fédérale de Lausanne (EPFL), SV ISREC, Lausanne, Switzerland
| | - Giovanna Ambrosini
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Université de Lausanne, Lausanne, Switzerland
| | - Joao Lourenco
- Translational Data Science Facility, Swiss Institute of Bioinformatics, AGORA Cancer Research Center, Lausanne, Switzerland
| | - Nadine Fournier
- Translational Data Science Facility, Swiss Institute of Bioinformatics, AGORA Cancer Research Center, Lausanne, Switzerland
| | - Christian Iseli
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Université de Lausanne, Lausanne, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Université de Lausanne, Lausanne, Switzerland
| | - Olga Egorova
- Ecole Polytechnique Fédérale de Lausanne (EPFL), SV ISREC, Lausanne, Switzerland
| | - Sina Nassiri
- Translational Data Science Facility, Swiss Institute of Bioinformatics, AGORA Cancer Research Center, Lausanne, Switzerland
| | - Daniel B Constam
- Ecole Polytechnique Fédérale de Lausanne (EPFL), SV ISREC, Lausanne, Switzerland
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10
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Ganier C, Mazin P, Herrera-Oropeza G, Du-Harpur X, Blakeley M, Gabriel J, Predeus AV, Cakir B, Prete M, Harun N, Darrigrand JF, Haiser A, Wyles S, Shaw T, Teichmann SA, Haniffa M, Watt FM, Lynch MD. Multiscale spatial mapping of cell populations across anatomical sites in healthy human skin and basal cell carcinoma. Proc Natl Acad Sci U S A 2024; 121:e2313326120. [PMID: 38165934 PMCID: PMC10786309 DOI: 10.1073/pnas.2313326120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 11/13/2023] [Indexed: 01/04/2024] Open
Abstract
Our understanding of how human skin cells differ according to anatomical site and tumour formation is limited. To address this, we have created a multiscale spatial atlas of healthy skin and basal cell carcinoma (BCC), incorporating in vivo optical coherence tomography, single-cell RNA sequencing, spatial global transcriptional profiling, and in situ sequencing. Computational spatial deconvolution and projection revealed the localisation of distinct cell populations to specific tissue contexts. Although cell populations were conserved between healthy anatomical sites and in BCC, mesenchymal cell populations including fibroblasts and pericytes retained signatures of developmental origin. Spatial profiling and in silico lineage tracing support a hair follicle origin for BCC and demonstrate that cancer-associated fibroblasts are an expansion of a POSTN+ subpopulation associated with hair follicles in healthy skin. RGS5+ pericytes are also expanded in BCC suggesting a role in vascular remodelling. We propose that the identity of mesenchymal cell populations is regulated by signals emanating from adjacent structures and that these signals are repurposed to promote the expansion of skin cancer stroma. The resource we have created is publicly available in an interactive format for the research community.
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Affiliation(s)
- Clarisse Ganier
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, LondonSE1 9RT, United Kingdom
| | - Pavel Mazin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CambridgeCB10 1SA, United Kingdom
| | - Gabriel Herrera-Oropeza
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, LondonSE1 1UL, United Kingdom
| | - Xinyi Du-Harpur
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, LondonSE1 9RT, United Kingdom
- The Francis Crick Institute, LondonNW1 1AT, United Kingdom
| | - Matthew Blakeley
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, LondonSE1 9RT, United Kingdom
| | - Jeyrroy Gabriel
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, LondonSE1 9RT, United Kingdom
| | - Alexander V. Predeus
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CambridgeCB10 1SA, United Kingdom
| | - Batuhan Cakir
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CambridgeCB10 1SA, United Kingdom
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CambridgeCB10 1SA, United Kingdom
| | - Nasrat Harun
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, LondonSE1 9RT, United Kingdom
| | - Jean-Francois Darrigrand
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, LondonSE1 9RT, United Kingdom
| | - Alexander Haiser
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, LondonSE1 9RT, United Kingdom
| | - Saranya Wyles
- Department of Dermatology, Mayo Clinic, Rochester, MN55905
| | - Tanya Shaw
- Centre for Inflammation Biology and Cancer Immunology, King’s College London, LondonSE1 1UL, United Kingdom
| | - Sarah A. Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CambridgeCB10 1SA, United Kingdom
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, CambridgeCB3 0HE, United Kingdom
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CambridgeCB10 1SA, United Kingdom
- Biosciences Institute, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
- National Institute for Health Research Newcastle Biomedical Research Centre, Newcastle Hospitals National Health Service Foundation Trust, Newcastle upon TyneNE1 4LP, United Kingdom
| | - Fiona M. Watt
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, LondonSE1 9RT, United Kingdom
- Directors’ Unit, European Molecular Biology Laboratory, Heidelberg69117, Germany
| | - Magnus D. Lynch
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, LondonSE1 9RT, United Kingdom
- St. John’s Institute of Dermatology, King’s College London, Guy’s Hospital, LondonSE1 9RT, United Kingdom
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11
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Wang Q, Zhi Y, Zi M, Mo Y, Wang Y, Liao Q, Zhang S, Gong Z, Wang F, Zeng Z, Guo C, Xiong W. Spatially Resolved Transcriptomics Technology Facilitates Cancer Research. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302558. [PMID: 37632718 PMCID: PMC10602551 DOI: 10.1002/advs.202302558] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/16/2023] [Indexed: 08/28/2023]
Abstract
Single cell RNA sequencing (scRNA-seq) provides a great convenience for studying tumor occurrence and development for its ability to study gene expression at the individual cell level. However, patient-derived tumor tissues are composed of multiple types of cells including tumor cells and adjacent non-malignant cells such as stromal cells and immune cells. The spatial locations of various cells in situ tissues plays a pivotal role in the occurrence and development of tumors, which cannot be elucidated by scRNA-seq alone. Spatially resolved transcriptomics (SRT) technology emerges timely to explore the unrecognized relationship between the spatial background of a particular cell and its functions, and is increasingly used in cancer research. This review provides a systematic overview of the SRT technologies that are developed, in particular the more widely used cutting-edge SRT technologies based on next-generation sequencing (NGS). In addition, the main achievements by SRT technologies in precisely unveiling the underappreciated spatial locations on gene expression and cell function with unprecedented high-resolution in cancer research are emphasized, with the aim of developing more effective clinical therapeutics oriented to a deeper understanding of the interaction between tumor cells and surrounding non-malignant cells.
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Affiliation(s)
- Qian Wang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer MetabolismHunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaHunan410008P. R. China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
| | - Yuan Zhi
- Department of Oral and Maxillofacial SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaHunan410012P. R. China
| | - Moxin Zi
- Department of Oral and Maxillofacial SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaHunan410012P. R. China
| | - Yongzhen Mo
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
- Department of Otolaryngology Head and Neck SurgeryXiangya HospitalCentral South UniversityChangshaHunan410008P. R. China
| | - Yumin Wang
- Department of Otolaryngology Head and Neck SurgeryXiangya HospitalCentral South UniversityChangshaHunan410008P. R. China
| | - Qianjin Liao
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer MetabolismHunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaHunan410008P. R. China
| | - Shanshan Zhang
- Department of Otolaryngology Head and Neck SurgeryXiangya HospitalCentral South UniversityChangshaHunan410008P. R. China
| | - Zhaojian Gong
- Department of Oral and Maxillofacial SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaHunan410012P. R. China
| | - Fuyan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer MetabolismHunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaHunan410008P. R. China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
| | - Can Guo
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer MetabolismHunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaHunan410008P. R. China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer MetabolismHunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityChangshaHunan410008P. R. China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of EducationCancer Research InstituteCentral South UniversityChangshaHunan410008P. R. China
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12
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Ramakrishnan A, Symeonidi A, Hanel P, Schmid KT, Richter ML, Schubert M, Colomé-Tatché M. epiAneufinder identifies copy number alterations from single-cell ATAC-seq data. Nat Commun 2023; 14:5846. [PMID: 37730813 PMCID: PMC10511508 DOI: 10.1038/s41467-023-41076-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/23/2023] [Indexed: 09/22/2023] Open
Abstract
Single-cell open chromatin profiling via scATAC-seq has become a mainstream measurement of open chromatin in single-cells. Here we present epiAneufinder, an algorithm that exploits the read count information from scATAC-seq data to extract genome-wide copy number alterations (CNAs) for individual cells, allowing the study of CNA heterogeneity present in a sample at the single-cell level. Using different cancer scATAC-seq datasets, we show that epiAneufinder can identify intratumor clonal heterogeneity in populations of single cells based on their CNA profiles. We demonstrate that these profiles are concordant with the ones inferred from single-cell whole genome sequencing data for the same samples. EpiAneufinder allows the inference of single-cell CNA information from scATAC-seq data, without the need of additional experiments, unlocking a layer of genomic variation which is otherwise unexplored.
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Affiliation(s)
- Akshaya Ramakrishnan
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Aikaterini Symeonidi
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany.
| | - Patrick Hanel
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
| | - Katharina T Schmid
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
| | - Maria L Richter
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
| | - Michael Schubert
- Oncode Institute, Division of Cell Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Maria Colomé-Tatché
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany.
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13
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Azimi A, Fernandez-Peñas P. Molecular Classifiers in Skin Cancers: Challenges and Promises. Cancers (Basel) 2023; 15:4463. [PMID: 37760432 PMCID: PMC10526380 DOI: 10.3390/cancers15184463] [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: 04/23/2023] [Revised: 08/29/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Skin cancers are common and heterogenous malignancies affecting up to two in three Australians before age 70. Despite recent developments in diagnosis and therapeutic strategies, the mortality rate and costs associated with managing patients with skin cancers remain high. The lack of well-defined clinical and histopathological features makes their diagnosis and classification difficult in some cases and the prognostication difficult in most skin cancers. Recent advancements in large-scale "omics" studies, including genomics, transcriptomics, proteomics, metabolomics and imaging-omics, have provided invaluable information about the molecular and visual landscape of skin cancers. On many occasions, it has refined tumor classification and has improved prognostication and therapeutic stratification, leading to improved patient outcomes. Therefore, this paper reviews the recent advancements in omics approaches and appraises their limitations and potential for better classification and stratification of skin cancers.
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Affiliation(s)
- Ali Azimi
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
- Department of Dermatology, Westmead Hospital, Westmead, NSW 2145, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia
| | - Pablo Fernandez-Peñas
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
- Department of Dermatology, Westmead Hospital, Westmead, NSW 2145, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia
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14
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Schütz S, Solé-Boldo L, Lucena-Porcel C, Hoffmann J, Brobeil A, Lonsdorf AS, Rodríguez-Paredes M, Lyko F. Functionally distinct cancer-associated fibroblast subpopulations establish a tumor promoting environment in squamous cell carcinoma. Nat Commun 2023; 14:5413. [PMID: 37669956 PMCID: PMC10480447 DOI: 10.1038/s41467-023-41141-9] [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: 11/04/2022] [Accepted: 08/24/2023] [Indexed: 09/07/2023] Open
Abstract
Cutaneous squamous cell carcinoma (cSCC) is a serious public health problem due to its high incidence and metastatic potential. It may progress from actinic keratosis (AK), a precancerous lesion, or the in situ carcinoma, Bowen's disease (BD). During this progression, malignant keratinocytes activate dermal fibroblasts into tumor promoting cancer-associated fibroblasts (CAFs), whose origin and emergence remain largely unknown. Here, we generate and analyze >115,000 single-cell transcriptomes from healthy skin, BD and cSCC of male donors. Our results reveal immunoregulatory and matrix-remodeling CAF subtypes that may derive from pro-inflammatory and mesenchymal fibroblasts, respectively. These CAF subtypes are largely absent in AK and interact with different cell types to establish a pro-tumorigenic microenvironment. These findings are cSCC-specific and could not be recapitulated in basal cell carcinomas. Our study provides important insights into the potential origin and functionalities of dermal CAFs that will be highly beneficial for the specific targeting of the cSCC microenvironment.
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Affiliation(s)
- Sabrina Schütz
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120, Heidelberg, Germany
| | - Llorenç Solé-Boldo
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120, Heidelberg, Germany
| | - Carlota Lucena-Porcel
- Institute of Pathology, Ruprecht-Karls University of Heidelberg, 69120, Heidelberg, Germany
- Tissue Bank of the National Center for Tumor Diseases (NCT), 69120, Heidelberg, Germany
| | - Jochen Hoffmann
- Department of Dermatology, University Hospital, Ruprecht-Karls University of Heidelberg, 69120, Heidelberg, Germany
| | - Alexander Brobeil
- Institute of Pathology, Ruprecht-Karls University of Heidelberg, 69120, Heidelberg, Germany
- Tissue Bank of the National Center for Tumor Diseases (NCT), 69120, Heidelberg, Germany
| | - Anke S Lonsdorf
- Department of Dermatology, University Hospital, Ruprecht-Karls University of Heidelberg, 69120, Heidelberg, Germany
| | - Manuel Rodríguez-Paredes
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120, Heidelberg, Germany.
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120, Heidelberg, Germany.
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15
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Li M, Wu B, Li L, Lv C, Tian Y. Reprogramming of cancer-associated fibroblasts combined with immune checkpoint inhibitors: A potential therapeutic strategy for cancers. Biochim Biophys Acta Rev Cancer 2023; 1878:188945. [PMID: 37356739 DOI: 10.1016/j.bbcan.2023.188945] [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: 03/28/2023] [Revised: 06/21/2023] [Accepted: 06/21/2023] [Indexed: 06/27/2023]
Abstract
Activated fibroblasts, namely cancer-associated fibroblasts (CAFs), are highly heterogeneous in phenotypes, functions, and origins. CAFs originated from varieties of cell types, including local resident fibroblasts, epithelial cells, mesenchymal stromal cells, or others. These cells participate in tumor angiogenesis, mechanics, drug access, and immune suppression, with the latter being particularly important. It was difficult to distinguish CAFs by subsets due to their complex origins until the use of scRNA-seq. Reprogramming CAFs with TGFβ-RI inhibitor, a CXCR4 blocker, or other methods increases T cells activation and infiltration, together with a decrease in CAFs recruitment, thus improving the prognosis. As depletion of CAFs can't bring clinical benefit, the combination of reprogramming CAFs and immune checkpoint inhibitors (ICIs) come into consideration. It has shown better outcomes compared with monotherapy respectively in basic/preclinical researches, and needs more data on clinical trials. Combination therapy may be a promising and expecting method for treatment of cancer.
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Affiliation(s)
- Min Li
- Department of Mammary Gland, Dalian Women and Children's Medical Center(Group), No. 1 Dunhuang Road, Dalian 116000, Liaoning Province, China; Department of General Surgery, Shengjing Hospital of China Medical University, No.36.Sanhao Street, Shenyang 110004, Liaoning Province, China
| | - Baokang Wu
- Department of General Surgery, Shengjing Hospital of China Medical University, No.36.Sanhao Street, Shenyang 110004, Liaoning Province, China
| | - Lunxu Li
- Department of General Surgery, Shengjing Hospital of China Medical University, No.36.Sanhao Street, Shenyang 110004, Liaoning Province, China
| | - Chao Lv
- Department of General Surgery, Shengjing Hospital of China Medical University, No.36.Sanhao Street, Shenyang 110004, Liaoning Province, China
| | - Yu Tian
- Department of General Surgery, Shengjing Hospital of China Medical University, No.36.Sanhao Street, Shenyang 110004, Liaoning Province, China.
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16
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Pich-Bavastro C, Yerly L, Di Domizio J, Tissot-Renaud S, Gilliet M, Kuonen F. Activin A-Mediated Polarization of Cancer-Associated Fibroblasts and Macrophages Confers Resistance to Checkpoint Immunotherapy in Skin Cancer. Clin Cancer Res 2023; 29:3498-3513. [PMID: 37327314 PMCID: PMC10472111 DOI: 10.1158/1078-0432.ccr-23-0219] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 05/05/2023] [Accepted: 06/14/2023] [Indexed: 06/18/2023]
Abstract
PURPOSE Cemiplimab is approved for the treatment of locally advanced basal cell carcinomas (BCC), although with mitigated results. We sought to interrogate the cellular and molecular transcriptional reprogramming underlying BCC resistance to immunotherapy. EXPERIMENTAL DESIGN Here, we combined spatial and single-cell transcriptomics to deconvolute the spatial heterogeneity of the tumor microenvironment in regard with response to immunotherapy, in a cohort of both naïve and resistant BCCs. RESULTS We identified subsets of intermingled cancer-associated fibroblasts (CAF) and macrophages contributing the most to CD8 T-cell exclusion and immunosuppression. Within this spatially resolved peritumoral immunosuppressive niche, CAFs and adjacent macrophages were found to display Activin A-mediated transcriptional reprogramming towards extracellular matrix remodeling, suggesting active participation to CD8 T-cell exclusion. In independent datasets of human skin cancers, Activin A-conditioned CAFs and macrophages were associated with resistance to immune checkpoint inhibitors (ICI). CONCLUSIONS Altogether, our data identify the cellular and molecular plasticity of tumor microenvironment (TME) and the pivotal role of Activin A in polarizing the TME towards immune suppression and ICI resistance.
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Affiliation(s)
- Christine Pich-Bavastro
- Department of Dermatology and Venereology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Laura Yerly
- Department of Dermatology and Venereology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Jeremy Di Domizio
- Department of Dermatology and Venereology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Stéphanie Tissot-Renaud
- Department of Oncology, Immune Landscape Laboratory, Center of Experimental Therapeutics, Lausanne University Hospital, Lausanne, Switzerland
- Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Switzerland
| | - Michel Gilliet
- Department of Dermatology and Venereology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - François Kuonen
- Department of Dermatology and Venereology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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17
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Houser AE, Kazmi A, Nair AK, Ji AL. The Use of Single-Cell RNA-Sequencing and Spatial Transcriptomics in Understanding the Pathogenesis and Treatment of Skin Diseases. JID INNOVATIONS 2023; 3:100198. [PMID: 37205302 PMCID: PMC10186616 DOI: 10.1016/j.xjidi.2023.100198] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/15/2023] [Accepted: 02/27/2023] [Indexed: 05/21/2023] Open
Abstract
The development of multiomic profiling tools has rapidly expanded in recent years, along with their use in profiling skin tissues in various contexts, including dermatologic diseases. Among these tools, single-cell RNA-sequencing (scRNA-seq) and spatial transcriptomics (ST) have emerged as widely adopted and powerful assays for elucidating key cellular components and their spatial arrangement within skin disease. In this paper, we review the recent biological insights gained from the use of scRNA-seq and ST and the advantages of combining both for profiling skin diseases, including aberrant wound healing, inflammatory skin diseases, and cancer. We discuss the role of scRNA-seq and ST in improving skin disease treatments and moving toward the goal of achieving precision medicine in dermatology, whereby patients can be optimally matched to treatments that maximize therapeutic response.
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Affiliation(s)
- Aubrey E. Houser
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Abiha Kazmi
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Arjun K. Nair
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Andrew L. Ji
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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18
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Wiley MB, Bauer J, Mehrotra K, Zessner-Spitzenberg J, Kolics Z, Cheng W, Castellanos K, Nash MG, Gui X, Kone L, Maker AV, Qiao G, Reddi D, Church DN, Kerr RS, Kerr DJ, Grippo PJ, Jung B. Non-Canonical Activin A Signaling Stimulates Context-Dependent and Cellular-Specific Outcomes in CRC to Promote Tumor Cell Migration and Immune Tolerance. Cancers (Basel) 2023; 15:3003. [PMID: 37296966 PMCID: PMC10252122 DOI: 10.3390/cancers15113003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
We have shown that activin A (activin), a TGF-β superfamily member, has pro-metastatic effects in colorectal cancer (CRC). In lung cancer, activin activates pro-metastatic pathways to enhance tumor cell survival and migration while augmenting CD4+ to CD8+ communications to promote cytotoxicity. Here, we hypothesized that activin exerts cell-specific effects in the tumor microenvironment (TME) of CRC to promote anti-tumoral activity of immune cells and the pro-metastatic behavior of tumor cells in a cell-specific and context-dependent manner. We generated an Smad4 epithelial cell specific knockout (Smad4-/-) which was crossed with TS4-Cre mice to identify SMAD-specific changes in CRC. We also performed IHC and digital spatial profiling (DSP) of tissue microarrays (TMAs) obtained from 1055 stage II and III CRC patients in the QUASAR 2 clinical trial. We transfected the CRC cells to reduce their activin production and injected them into mice with intermittent tumor measurements to determine how cancer-derived activin alters tumor growth in vivo. In vivo, Smad4-/- mice displayed elevated colonic activin and pAKT expression and increased mortality. IHC analysis of the TMA samples revealed increased activin was required for TGF-β-associated improved outcomes in CRC. DSP analysis identified that activin co-localization in the stroma was coupled with increases in T-cell exhaustion markers, activation markers of antigen presenting cells (APCs), and effectors of the PI3K/AKT pathway. Activin-stimulated PI3K-dependent CRC transwell migration, and the in vivo loss of activin lead to smaller CRC tumors. Taken together, activin is a targetable, highly context-dependent molecule with effects on CRC growth, migration, and TME immune plasticity.
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Affiliation(s)
- Mark B. Wiley
- Department of Medicine, University of Washington, Seattle, WA 98195, USA; (M.B.W.); (K.M.)
| | - Jessica Bauer
- Department of Medicine, University of Washington, Seattle, WA 98195, USA; (M.B.W.); (K.M.)
| | - Kunaal Mehrotra
- Department of Medicine, University of Washington, Seattle, WA 98195, USA; (M.B.W.); (K.M.)
| | - Jasmin Zessner-Spitzenberg
- Clinical Department for Gastroenterology and Hepatology, Medical University of Vienna, 1090 Vienna, Austria
| | - Zoe Kolics
- Department of Medicine, University of Washington, Seattle, WA 98195, USA; (M.B.W.); (K.M.)
| | - Wenxuan Cheng
- Department of Medicine, University of Washington, Seattle, WA 98195, USA; (M.B.W.); (K.M.)
| | - Karla Castellanos
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Michael G. Nash
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Xianyong Gui
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Lyonell Kone
- Department of Surgery, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Ajay V. Maker
- Department of Surgery, University of California-San Francisco, San Francisco, CA 94115, USA
| | - Guilin Qiao
- Department of Surgery, University of California-San Francisco, San Francisco, CA 94115, USA
| | - Deepti Reddi
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - David N. Church
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 4BH, UK
- NIHR Oxford Comprehensive Biomedical Research Center, Oxford University Hospitals NHS Foundation Trust, University of Oxford, Oxford OX1 4BH, UK
| | - Rachel S. Kerr
- Department of Oncology, University of Oxford, Oxford OX1 4BH, UK
| | - David J. Kerr
- Radcliffe Department of Medicine, University of Oxford, Oxford OX1 4BH, UK
| | - Paul J. Grippo
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Barbara Jung
- Department of Medicine, University of Washington, Seattle, WA 98195, USA; (M.B.W.); (K.M.)
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19
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Tekkela S, Theocharidis G, McGrath JA, Onoufriadis A. Spatial transcriptomics in human skin research. Exp Dermatol 2023. [PMID: 37150587 DOI: 10.1111/exd.14827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/17/2023] [Accepted: 04/21/2023] [Indexed: 05/09/2023]
Abstract
Spatial transcriptomics is a revolutionary technique that enables researchers to characterise tissue architecture and localisation of gene expression. A plethora of technologies that map gene expression are currently being developed, aiming to facilitate spatially resolved, high-dimensional assessment of gene transcription in the context of human skin research. Knowing which gene is expressed by which cell and in which location within skin, facilitates understanding of skin function and dysfunction in both health and disease. In this review, we summarise the available spatial transcriptomic methods and we describe their application to a broad spectrum of dermatological diseases.
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Affiliation(s)
- Stavroula Tekkela
- St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Georgios Theocharidis
- Joslin-Beth Israel Deaconess Foot Center and The Rongxiang Xu, MD, Center for Regenerative Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - John A McGrath
- St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Alexandros Onoufriadis
- St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, UK
- Laboratory of Medical Biology and Genetics, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
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20
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Yamazaki K, Maejima M, Saeki H, Osada SI. Recurrence or de novo? Intradermal Basal Cell Carcinoma of the Scrotum: A Report of Two Cases. Dermatopathology (Basel) 2023; 10:128-135. [PMID: 37092530 PMCID: PMC10123599 DOI: 10.3390/dermatopathology10020019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
Basal cell carcinoma (BCC) is the most common cutaneous malignancy, usually occurring in sun-exposed areas. Although BCC in the scrotal region is uncommon, it carries a higher risk of metastasis than BCC at other sites. Here, we report two cases of BCC that developed in the scrotal region: Case 1 presented as a superficial nodule and Case 2 as a subcutaneous nodule. Histopathologically, both tumors lacked continuity with the surface epidermis and formed an intradermal nodule. In Case 1, BCC occurred for the first time and presumably developed de novo. Case 2 underwent excision of a scrotal BCC 5 years previously, and the histopathological diagnosis at that time was nodular BCC. However, when the original specimen was re-examined, it was determined that, although the tumor had been completely resected, part of the lesion had moved away from the nodular area to represent a micronodular phenotype, an aggressive BCC subtype. We hypothesized that partial evolution from a nodular to a micronodular phenotype may have contributed to the recurrence of BCC in Case 2.
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21
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Zhu J, Shang L, Zhou X. SRTsim: spatial pattern preserving simulations for spatially resolved transcriptomics. Genome Biol 2023; 24:39. [PMID: 36869394 PMCID: PMC9983268 DOI: 10.1186/s13059-023-02879-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 02/16/2023] [Indexed: 03/05/2023] Open
Abstract
Spatially resolved transcriptomics (SRT)-specific computational methods are often developed, tested, validated, and evaluated in silico using simulated data. Unfortunately, existing simulated SRT data are often poorly documented, hard to reproduce, or unrealistic. Single-cell simulators are not directly applicable for SRT simulation as they cannot incorporate spatial information. We present SRTsim, an SRT-specific simulator for scalable, reproducible, and realistic SRT simulations. SRTsim not only maintains various expression characteristics of SRT data but also preserves spatial patterns. We illustrate the benefits of SRTsim in benchmarking methods for spatial clustering, spatial expression pattern detection, and cell-cell communication identification.
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Affiliation(s)
- Jiaqiang Zhu
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Lulu Shang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
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22
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Abstract
Historically, cancer research and therapy have focused on malignant cells and their tumor microenvironment. However, the vascular, lymphatic and nervous systems establish long-range communication between the tumor and the host. This communication is mediated by metabolites generated by the host or the gut microbiota, as well by systemic neuroendocrine, pro-inflammatory and immune circuitries-all of which dictate the trajectory of malignant disease through molecularly defined biological mechanisms. Moreover, aging, co-morbidities and co-medications have a major impact on the development, progression and therapeutic response of patients with cancer. In this Perspective, we advocate for a whole-body 'ecological' exploration of malignant disease. We surmise that accumulating knowledge on the intricate relationship between the host and the tumor will shape rational strategies for systemic, bodywide interventions that will eventually improve tumor control, as well as quality of life, in patients with cancer.
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