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Lee T, Oka T, Demehri S. High-Risk Non-Melanoma Skin Cancers: Biological and Therapeutic Advances. Hematol Oncol Clin North Am 2024:S0889-8588(24)00053-4. [PMID: 38908957 DOI: 10.1016/j.hoc.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
Nonmelanoma skin cancers (NMSCs) are the most common cancers, with high-risk NMSCs sharing features such as poor histologic differentiation, invasion into deeper layers, and anatomic location. NMSC includes basal cell carcinoma, cutaneous squamous cell carcinoma, and Merkel cell carcinoma. Herein, the authors describe advances in understanding the genetic mechanisms of malignant transformation and the composition of tumor microenvironment for these cancers. They summarize recent therapeutic advances, including targeted therapy and immunotherapy for NMSCs. Effective skin protection against ultraviolet radiation-induced carcinogenesis remains an urgent unmet need for NMSC prevention. The authors highlight immune-based interventions as novel strategies to address this need.
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Affiliation(s)
| | - Tomonori Oka
- Center for Cancer Immunology, Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Dermatology, Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Shadmehr Demehri
- Harvard Medical School, Boston, MA 02115, USA; Center for Cancer Immunology, Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Dermatology, Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, MA 02114, USA.
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2
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Pong A, Mah CK, Yeo GW, Lewis NE. Computational cell-cell interaction technologies drive mechanistic and biomarker discovery in the tumor microenvironment. Curr Opin Biotechnol 2024; 85:103048. [PMID: 38142648 PMCID: PMC11168798 DOI: 10.1016/j.copbio.2023.103048] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 11/11/2023] [Accepted: 11/25/2023] [Indexed: 12/26/2023]
Abstract
Complex networks of cell-cell interactions (CCIs) within the tumor microenvironment (TME) play a crucial role in cancer persistence. These communication axes represent prime targets for therapeutic intervention, but our incomplete understanding of the cellular heterogeneity and interacting partners within the TME remains a stubborn barrier to complete drug responses. This review outlines recent advances in the study of CCIs that leverage single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) technologies that can clarify TME dynamics. We anticipate that these strategies will promote discovery of CCIs critical to the tumor-immune interface and will, by extension, expand the repertoire of druggable tumor biomarkers.
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Affiliation(s)
- Avery Pong
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Clarence K Mah
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA; Division of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Nathan E Lewis
- Departments of Pediatrics and Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
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3
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Li S, Zhang P, Chen W, Ye L, Brannan KW, Le NT, Abe JI, Cooke JP, Wang G. A relay velocity model infers cell-dependent RNA velocity. Nat Biotechnol 2024; 42:99-108. [PMID: 37012448 PMCID: PMC10545816 DOI: 10.1038/s41587-023-01728-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 02/28/2023] [Indexed: 04/05/2023]
Abstract
RNA velocity provides an approach for inferring cellular state transitions from single-cell RNA sequencing (scRNA-seq) data. Conventional RNA velocity models infer universal kinetics from all cells in an scRNA-seq experiment, resulting in unpredictable performance in experiments with multi-stage and/or multi-lineage transition of cell states where the assumption of the same kinetic rates for all cells no longer holds. Here we present cellDancer, a scalable deep neural network that locally infers velocity for each cell from its neighbors and then relays a series of local velocities to provide single-cell resolution inference of velocity kinetics. In the simulation benchmark, cellDancer shows robust performance in multiple kinetic regimes, high dropout ratio datasets and sparse datasets. We show that cellDancer overcomes the limitations of existing RNA velocity models in modeling erythroid maturation and hippocampus development. Moreover, cellDancer provides cell-specific predictions of transcription, splicing and degradation rates, which we identify as potential indicators of cell fate in the mouse pancreas.
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Affiliation(s)
- Shengyu Li
- Center for Bioinformatics and Computational Biology, Houston Methodist Research Institute, Houston, TX, USA
- Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX, USA
- Center for RNA Therapeutics, Houston Methodist Research Institute, Houston, TX, USA
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Pengzhi Zhang
- Center for Bioinformatics and Computational Biology, Houston Methodist Research Institute, Houston, TX, USA
- Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX, USA
- Center for RNA Therapeutics, Houston Methodist Research Institute, Houston, TX, USA
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Weiqing Chen
- Center for Bioinformatics and Computational Biology, Houston Methodist Research Institute, Houston, TX, USA
- Department of Physiology, Biophysics & Systems Biology, Weill Cornell Graduate School of Medical Science, Weill Cornell Medicine, Cornell University, Ithaca, NY, USA
| | - Lingqun Ye
- Center for Bioinformatics and Computational Biology, Houston Methodist Research Institute, Houston, TX, USA
- Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX, USA
- Center for RNA Therapeutics, Houston Methodist Research Institute, Houston, TX, USA
| | - Kristopher W Brannan
- Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX, USA
- Center for RNA Therapeutics, Houston Methodist Research Institute, Houston, TX, USA
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Nhat-Tu Le
- Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX, USA
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Jun-Ichi Abe
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John P Cooke
- Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX, USA
| | - Guangyu Wang
- Center for Bioinformatics and Computational Biology, Houston Methodist Research Institute, Houston, TX, USA.
- Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX, USA.
- Center for RNA Therapeutics, Houston Methodist Research Institute, Houston, TX, USA.
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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4
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Peri SS, Narayanaa Y K, Hubert TD, Rajaraman R, Arfuso F, Sundaram S, Archana B, Warrier S, Dharmarajan A, Perumalsamy LR. Navigating Tumour Microenvironment and Wnt Signalling Crosstalk: Implications for Advanced Cancer Therapeutics. Cancers (Basel) 2023; 15:5847. [PMID: 38136392 PMCID: PMC10741643 DOI: 10.3390/cancers15245847] [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: 10/27/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Cancer therapeutics face significant challenges due to drug resistance and tumour recurrence. The tumour microenvironment (TME) is a crucial contributor and essential hallmark of cancer. It encompasses various components surrounding the tumour, including intercellular elements, immune system cells, the vascular system, stem cells, and extracellular matrices, all of which play critical roles in tumour progression, epithelial-mesenchymal transition, metastasis, drug resistance, and relapse. These components interact with multiple signalling pathways, positively or negatively influencing cell growth. Abnormal regulation of the Wnt signalling pathway has been observed in tumorigenesis and contributes to tumour growth. A comprehensive understanding and characterisation of how different cells within the TME communicate through signalling pathways is vital. This review aims to explore the intricate and dynamic interactions, expressions, and alterations of TME components and the Wnt signalling pathway, offering valuable insights into the development of therapeutic applications.
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Affiliation(s)
- Shraddha Shravani Peri
- Department of Biomedical Sciences, Faculty of Biomedical Sciences, Technology and Research, Sri Ramachandra Institute of Higher Education and Research, Chennai 600116, India; (S.S.P.); (K.N.Y.); (T.D.H.); (R.R.)
| | - Krithicaa Narayanaa Y
- Department of Biomedical Sciences, Faculty of Biomedical Sciences, Technology and Research, Sri Ramachandra Institute of Higher Education and Research, Chennai 600116, India; (S.S.P.); (K.N.Y.); (T.D.H.); (R.R.)
| | - Therese Deebiga Hubert
- Department of Biomedical Sciences, Faculty of Biomedical Sciences, Technology and Research, Sri Ramachandra Institute of Higher Education and Research, Chennai 600116, India; (S.S.P.); (K.N.Y.); (T.D.H.); (R.R.)
| | - Roshini Rajaraman
- Department of Biomedical Sciences, Faculty of Biomedical Sciences, Technology and Research, Sri Ramachandra Institute of Higher Education and Research, Chennai 600116, India; (S.S.P.); (K.N.Y.); (T.D.H.); (R.R.)
| | - Frank Arfuso
- School of Human Sciences, The University of Western Australia, Nedlands, WA 6009, Australia;
| | - Sandhya Sundaram
- Department of Pathology, Sri Ramachandra Institute of Higher Education and Research, Chennai 600116, India; (S.S.); (B.A.)
| | - B. Archana
- Department of Pathology, Sri Ramachandra Institute of Higher Education and Research, Chennai 600116, India; (S.S.); (B.A.)
| | - Sudha Warrier
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research, Chennai 600116, India;
| | - Arun Dharmarajan
- Department of Biomedical Sciences, Faculty of Biomedical Sciences, Technology and Research, Sri Ramachandra Institute of Higher Education and Research, Chennai 600116, India; (S.S.P.); (K.N.Y.); (T.D.H.); (R.R.)
- School of Human Sciences, The University of Western Australia, Nedlands, WA 6009, Australia;
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
| | - Lakshmi R. Perumalsamy
- Department of Biomedical Sciences, Faculty of Biomedical Sciences, Technology and Research, Sri Ramachandra Institute of Higher Education and Research, Chennai 600116, India; (S.S.P.); (K.N.Y.); (T.D.H.); (R.R.)
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5
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Liu W, Zhang F, Quan B, Yao F, Chen R, Ren Z, Yin X. NLRP3/IL-1β induced myeloid-derived suppressor cells recruitment and PD-L1 upregulation promotes oxaliplatin resistance of hepatocellular carcinoma. MedComm (Beijing) 2023; 4:e447. [PMID: 38116060 PMCID: PMC10728756 DOI: 10.1002/mco2.447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 12/21/2023] Open
Abstract
Oxaliplatin is commonly used as the first-line chemotherapeutic agent for advanced hepatocellular carcinoma (HCC). Unfortunately, the acquired resistance, limits the effectiveness of oxaliplatin and the underlying mechanisms remain unknown. Therefore, we explored the role of NOD-like receptor protein 3 (NLRP3)/IL-1β in mediating oxaliplatin resistance in HCC. We observed that NLRP3/IL-1β expression was much higher in oxaliplatin-resistant HCC cells. To further understand its impact on drug resistance, we knocked down NLRP3 and observed that it sensitized HCC cells to the growth-inhibitory effects of oxaliplatin and induced cell apoptosis. NLRP3/IL-1β overexpressing tumor cells also attracted polymorphonuclear myeloid-derived suppressor cells. Using mouse models, we demonstrated that NLRP3/IL-1β inhibition by short hairpin RNA or MCC950 effectively overcame oxaliplatin resistance. Furthermore, NLRP3/IL-1β inhibition resulted in reduced expression of PD-L1. We also found that PD-L1 antibody combined with NLRP3/IL-1β blockade displayed significant antitumor effect in HCC. Overall, our study provides compelling evidence supporting the essential role of NLRP3/IL-1β in conferring resistance to oxaliplatin and reshaping the immunosuppressive microenvironment in HCC. Targeting NLRP3/IL-1β presents a potential therapeutic target for overcoming oxaliplatin resistance and reshaping microenvironment of HCC.
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Affiliation(s)
- Wenfeng Liu
- Department of Hepatic Oncology, Liver Cancer Institute, Zhongshan HospitalFudan UniversityShanghaiChina
- Department of National Clinical Research Center for Interventional MedicineZhongshan hospital, Fudan universityShanghaiChina
| | - Feng Zhang
- Department of Hepatic Oncology, Liver Cancer Institute, Zhongshan HospitalFudan UniversityShanghaiChina
- Department of National Clinical Research Center for Interventional MedicineZhongshan hospital, Fudan universityShanghaiChina
| | - Bing Quan
- Department of Hepatic Oncology, Liver Cancer Institute, Zhongshan HospitalFudan UniversityShanghaiChina
- Department of National Clinical Research Center for Interventional MedicineZhongshan hospital, Fudan universityShanghaiChina
| | - Fan Yao
- Department of Hepatic Oncology, Liver Cancer Institute, Zhongshan HospitalFudan UniversityShanghaiChina
- Department of National Clinical Research Center for Interventional MedicineZhongshan hospital, Fudan universityShanghaiChina
| | - Rongxin Chen
- Department of Hepatic Oncology, Liver Cancer Institute, Zhongshan HospitalFudan UniversityShanghaiChina
- Department of National Clinical Research Center for Interventional MedicineZhongshan hospital, Fudan universityShanghaiChina
| | - Zhenggang Ren
- Department of Hepatic Oncology, Liver Cancer Institute, Zhongshan HospitalFudan UniversityShanghaiChina
- Department of National Clinical Research Center for Interventional MedicineZhongshan hospital, Fudan universityShanghaiChina
| | - Xin Yin
- Department of Hepatic Oncology, Liver Cancer Institute, Zhongshan HospitalFudan UniversityShanghaiChina
- Department of National Clinical Research Center for Interventional MedicineZhongshan hospital, Fudan universityShanghaiChina
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Iglesia MD, Jayasinghe RG, Chen S, Terekhanova NV, Herndon JM, Storrs E, Karpova A, Zhou DC, Al Deen NN, Shinkle AT, Lu RJH, Caravan W, Houston A, Zhao Y, Sato K, Lal P, Street C, Rodrigues FM, Southard-Smith AN, Targino da Costa ALN, Zhu H, Mo CK, Crowson L, Fulton RS, Wyczalkowski MA, Fronick CC, Fulton LA, Sun H, Davies SR, Appelbaum EL, Chasnoff SE, Carmody M, Brooks C, Liu R, Wendl MC, Oh C, Bender D, Cruchaga C, Harari O, Bredemeyer A, Lavine K, Bose R, Margenthaler J, Held JM, Achilefu S, Ademuyiwa F, Aft R, Ma C, Colditz GA, Ju T, Oh ST, Fitzpatrick J, Hwang ES, Shoghi KI, Chheda MG, Veis DJ, Chen F, Fields RC, Gillanders WE, Ding L. Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.565031. [PMID: 37961519 PMCID: PMC10634973 DOI: 10.1101/2023.10.31.565031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Breast cancer is a heterogeneous disease, and treatment is guided by biomarker profiles representing distinct molecular subtypes. Breast cancer arises from the breast ductal epithelium, and experimental data suggests breast cancer subtypes have different cells of origin within that lineage. The precise cells of origin for each subtype and the transcriptional networks that characterize these tumor-normal lineages are not established. In this work, we applied bulk, single-cell (sc), and single-nucleus (sn) multi-omic techniques as well as spatial transcriptomics and multiplex imaging on 61 samples from 37 breast cancer patients to show characteristic links in gene expression and chromatin accessibility between breast cancer subtypes and their putative cells of origin. We applied the PAM50 subtyping algorithm in tandem with bulk RNA-seq and snRNA-seq to reliably subtype even low-purity tumor samples and confirm promoter accessibility using snATAC. Trajectory analysis of chromatin accessibility and differentially accessible motifs clearly connected progenitor populations with breast cancer subtypes supporting the cell of origin for basal-like and luminal A and B tumors. Regulatory network analysis of transcription factors underscored the importance of BHLHE40 in luminal breast cancer and luminal mature cells, and KLF5 in basal-like tumors and luminal progenitor cells. Furthermore, we identify key genes defining the basal-like ( PRKCA , SOX6 , RGS6 , KCNQ3 ) and luminal A/B ( FAM155A , LRP1B ) lineages, with expression in both precursor and cancer cells and further upregulation in tumors. Exhausted CTLA4-expressing CD8+ T cells were enriched in basal-like breast cancer, suggesting altered means of immune dysfunction among breast cancer subtypes. We used spatial transcriptomics and multiplex imaging to provide spatial detail for key markers of benign and malignant cell types and immune cell colocation. These findings demonstrate analysis of paired transcription and chromatin accessibility at the single cell level is a powerful tool for investigating breast cancer lineage development and highlight transcriptional networks that define basal and luminal breast cancer lineages.
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Huang L, Wang X, Pei S, Li X, Dong L, Bian X, Sun H, Jin L, Hou H, Shi W, Zhang X, Zhang L, Zhao S, Chen X, Yin M. Single-Cell Profiling Reveals Sustained Immune Infiltration, Surveillance, and Tumor Heterogeneity in Infiltrative Basal Cell Carcinoma. J Invest Dermatol 2023; 143:2283-2294.e17. [PMID: 37201777 DOI: 10.1016/j.jid.2023.04.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 03/31/2023] [Accepted: 04/10/2023] [Indexed: 05/20/2023]
Abstract
Infiltrative basal cell carcinoma (iBCC) is a particularly aggressive subtype of basal cell carcinoma that tends to progress and recur after surgery, and its malignancy is closely related to the tumor microenvironment. In this study, we performed a comprehensive single-cell RNA analysis to profile 29,334 cells from iBCC and adjacent normal skin. We found active immune collaborations enriched in iBCC. Specifically, SPP1+CXCL9/10high macrophage 1 had strong BAFF signaling with plasma cells, and T follicular helper-like cells highly expressed the B-cell chemokine CXCL13. Heterogeneous proinflammatory SPP1+CXCL9/10high macrophage 1 and angiogenesis-related SPP1+CCL2high macrophage 1 were identified within the tumor microenvironment. Interestingly, we found an upregulation of major histocompatibility complex I molecules in fibroblasts in iBCC compared with those in adjacent normal skin. Moreover, MDK signals derived from malignant basal cells were markedly increased, and their expression was an independent factor in predicting the infiltration depth of iBCC, emphasizing its role in driving malignancy and remodeling the tumor microenvironment. In addition, we identified differentiation-associated SOSTDC1+IGFBP5+CTSV+ malignant basal subtype 1 and epithelial-mesenchymal transition-associated TNC+SFRP1+CHGA+ malignant basal subtype 2 cells. The high expression of malignant basal 2 cell markers was associated with the invasion and recurrence of iBCC. Altogether, our study helps to elucidate the cellular heterogeneity in iBCC and provides potential therapeutic targets for clinical research.
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Affiliation(s)
- Lingjuan Huang
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, China
| | - Xianggui Wang
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, China; Eye Center of Xiangya Hospital, Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China
| | - Shiyao Pei
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, China
| | - Xin Li
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, China
| | - Liang Dong
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, China
| | - Xiaohui Bian
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, China
| | - Hongyin Sun
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, China
| | - Liping Jin
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, China
| | - Huihui Hou
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, China
| | - Wensheng Shi
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, China; Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Xiyuan Zhang
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, China
| | - Lining Zhang
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, China
| | - Shuang Zhao
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, China
| | - Xiang Chen
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, China
| | - Mingzhu Yin
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, China.
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8
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Li J, Xia Y, Kong S, Yang K, Chen H, Zhang Y, Liu D, Chen L, Sun X. Single-cell RNA-seq reveals actinic keratosis-specific keratinocyte subgroups and their crosstalk with secretory-papillary fibroblasts. J Eur Acad Dermatol Venereol 2023; 37:2273-2283. [PMID: 37357444 DOI: 10.1111/jdv.19289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/09/2023] [Indexed: 06/27/2023]
Abstract
BACKGROUND AND AIM Actinic keratosis (AK) represents an intraepidermal malignant neoplasm with the proliferation of atypical keratinocytes. AK lesions are regarded as early in situ squamous cell carcinomas (SCCs) having the potential to progress into invasive SCC (iSCC) and metastasize, causing death. This study aimed to investigate the heterogeneity of keratinocytes and how this heterogeneity promoted AK development and progression. METHODS We employed single-cell RNA sequencing (scRNA-seq) to examine the heterogeneity of keratinocytes and dermal fibroblast clusters in AKs and adjacent normal skins. Cell clustering, pseudotime trajectory construction, gene ontology enrichment analysis, transcription factor network analysis, and cell-cell communication were used to investigate the heterogeneity of keratinocytes in AK. The cellular identity and function were verified by immunohistochemical and immunofluorescence staining. RESULTS Using scRNA-seq, we revealed 13 keratinocyte subgroups (clusters 0-12) in AK tissues and characterized 2 AK-specific clusters. Cluster 9 displayed high levels of IL1R2 and WFDC2, and cluster 11 showed high levels of FADS2 and FASN. The percentages of cells in these two clusters significantly increased in AK compared with normal tissues. The existence and spatial localization of AK-specific IL1R2+WFDC2+ cluster were verified by immunohistochemical and immunofluorescence staining. Functional studies indicated that the genes identified in the IL1R2+WFDC2+ cluster were crucial for epithelial cell proliferation, migration, and angiogenesis. Further immunofluorescent staining revealed the interactions between AK-specific keratinocytes and secretory-papillary fibroblasts mainly through ANGPTL4-ITGA5 signalling pathway rarely seen in normal tissues. CONCLUSION The findings of this study might help better understand AK pathogenesis.
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Affiliation(s)
- Jun Li
- Department of Dermatology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Ying Xia
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Shumin Kong
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Kun Yang
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Hui Chen
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Yong Zhang
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Dongxian Liu
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Lan Chen
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Xiaoyan Sun
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
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9
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Wang X, Almet AA, Nie Q. The promising application of cell-cell interaction analysis in cancer from single-cell and spatial transcriptomics. Semin Cancer Biol 2023; 95:42-51. [PMID: 37454878 PMCID: PMC10627116 DOI: 10.1016/j.semcancer.2023.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 03/02/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Cell-cell interactions instruct cell fate and function. These interactions are hijacked to promote cancer development. Single-cell transcriptomics and spatial transcriptomics have become powerful new tools for researchers to profile the transcriptional landscape of cancer at unparalleled genetic depth. In this review, we discuss the rapidly growing array of computational tools to infer cell-cell interactions from non-spatial single-cell RNA-sequencing and the limited but growing number of methods for spatial transcriptomics data. Downstream analyses of these computational tools and applications to cancer studies are highlighted. We finish by suggesting several directions for further extensions that anticipate the increasing availability of multi-omics cancer data.
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Affiliation(s)
- Xinyi Wang
- Department of Mathematics, University of California, Irvine, Irvine, CA, United States
| | - Axel A Almet
- Department of Mathematics, University of California, Irvine, Irvine, CA, United States; The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, United States.
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, Irvine, CA, United States; The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, United States; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, United States.
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10
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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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11
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Polito MP, Marini G, Palamenghi M, Enzo E. Decoding the Human Epidermal Complexity at Single-Cell Resolution. Int J Mol Sci 2023; 24:ijms24108544. [PMID: 37239891 DOI: 10.3390/ijms24108544] [Citation(s) in RCA: 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: 04/27/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
The epidermis is one of the largest tissues in the human body, serving as a protective barrier. The basal layer of the epidermis, which consists of epithelial stem cells and transient amplifying progenitors, represents its proliferative compartment. As keratinocytes migrate from the basal layer to the skin surface, they exit the cell cycle and initiate terminal differentiation, ultimately generating the suprabasal epidermal layers. A deeper understanding of the molecular mechanisms and pathways driving keratinocytes' organization and regeneration is essential for successful therapeutic approaches. Single-cell techniques are valuable tools for studying molecular heterogeneity. The high-resolution characterization obtained with these technologies has identified disease-specific drivers and new therapeutic targets, further promoting the advancement of personalized therapies. This review summarizes the latest findings on the transcriptomic and epigenetic profiling of human epidermal cells, analyzed from human biopsy or after in vitro cultivation, focusing on physiological, wound healing, and inflammatory skin conditions.
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Affiliation(s)
- Maria Pia Polito
- Centre for Regenerative Medicine ''Stefano Ferrari'', University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Grazia Marini
- Centre for Regenerative Medicine ''Stefano Ferrari'', University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Michele Palamenghi
- Centre for Regenerative Medicine ''Stefano Ferrari'', University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Elena Enzo
- Centre for Regenerative Medicine ''Stefano Ferrari'', University of Modena and Reggio Emilia, 41125 Modena, Italy
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12
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Chiang E, Stafford H, Buell J, Ramesh U, Amit M, Nagarajan P, Migden M, Yaniv D. Review of the Tumor Microenvironment in Basal and Squamous Cell Carcinoma. Cancers (Basel) 2023; 15:2453. [PMID: 37173918 PMCID: PMC10177565 DOI: 10.3390/cancers15092453] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
It is widely known that tumor cells of basal and squamous cell carcinoma interact with the cellular and acellular components of the tumor microenvironment to promote tumor growth and progression. While this environment differs for basal and squamous cell carcinoma, the cellular players within both create an immunosuppressed environment by downregulating effector CD4+ and CD8+ T cells and promoting the release of pro-oncogenic Th2 cytokines. Understanding the crosstalk that occurs within the tumor microenvironment has led to the development of immunotherapeutic agents, including vismodegib and cemiplimab to treat BCC and SCC, respectively. However, further investigation of the TME will provide the opportunity to discover novel treatment options.
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Affiliation(s)
- Elizabeth Chiang
- School of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Haleigh Stafford
- School of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jane Buell
- School of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Uma Ramesh
- School of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Moran Amit
- Head and Neck Surgery Department, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
- Graduate School of Biomedical Sciences, The University of Texas, Houston, TX 77030, USA
| | - Priyadharsini Nagarajan
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael Migden
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dan Yaniv
- Head and Neck Surgery Department, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
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13
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Zhao K, Zhou G, Liu Y, Zhang J, Chen Y, Liu L, Zhang G. HSP70 Family in Cancer: Signaling Mechanisms and Therapeutic Advances. Biomolecules 2023; 13:601. [PMID: 37189349 PMCID: PMC10136146 DOI: 10.3390/biom13040601] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/10/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023] Open
Abstract
The 70 kDa heat shock proteins (HSP70s) are a group of highly conserved and inducible heat shock proteins. One of the main functions of HSP70s is to act as molecular chaperones that are involved in a large variety of cellular protein folding and remodeling processes. HSP70s are found to be over-expressed and may serve as prognostic markers in many types of cancers. HSP70s are also involved in most of the molecular processes of cancer hallmarks as well as the growth and survival of cancer cells. In fact, many effects of HSP70s on cancer cells are not only related to their chaperone activities but rather to their roles in regulating cancer cell signaling. Therefore, a number of drugs directly or indirectly targeting HSP70s, and their co-chaperones have been developed aiming to treat cancer. In this review, we summarized HSP70-related cancer signaling pathways and corresponding key proteins regulated by the family of HSP70s. In addition, we also summarized various treatment approaches and progress of anti-tumor therapy based on targeting HSP70 family proteins.
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Affiliation(s)
- Kejia Zhao
- Department of Thoracic Surgery and Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
- Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Chengdu 610041, China
| | - Guanyu Zhou
- Department of Thoracic Surgery and Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
- Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Chengdu 610041, China
- Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yu Liu
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong 999077, China
| | - Jian Zhang
- Department of Thoracic Surgery and Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
- Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Chengdu 610041, China
| | - Yaohui Chen
- Department of Thoracic Surgery and Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
- Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Chengdu 610041, China
| | - Lunxu Liu
- Department of Thoracic Surgery and Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
- Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Chengdu 610041, China
| | - Gao Zhang
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong 999077, China
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14
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Liu HT, Chen SY, Peng LL, Zhong L, Zhou L, Liao SQ, Chen ZJ, Wang QL, He S, Zhou ZH. Spatially resolved transcriptomics revealed local invasion-related genes in colorectal cancer. Front Oncol 2023; 13:1089090. [PMID: 36816947 PMCID: PMC9928961 DOI: 10.3389/fonc.2023.1089090] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/16/2023] [Indexed: 02/04/2023] Open
Abstract
Objective Local invasion is the first step of metastasis, the main cause of colorectal cancer (CRC)-related death. Recent studies have revealed extensive intertumoral and intratumoral heterogeneity. Here, we focused on revealing local invasion-related genes in CRC. Methods We used spatial transcriptomic techniques to study the process of local invasion in four CRC tissues. First, we compared the pre-cancerous, cancer center, and invasive margin in one section (S115) and used pseudo-time analysis to reveal the differentiation trajectories from cancer center to invasive margin. Next, we performed immunohistochemical staining for RPL5, STC1, AKR1B1, CD47, and HLA-A on CRC samples. Moreover, we knocked down AKR1B1 in CRC cell lines and performed CCK-8, wound healing, and transwell assays to assess cell proliferation, migration, and invasion. Results We demonstrated that 13 genes were overexpressed in invasive clusters, among which the expression of CSTB and TM4SF1 was correlated with poor PFS in CRC patients. The ribosome pathway was increased, while the antigen processing and presentation pathway was decreased along CRC progression. RPL5 was upregulated, while HLA-A was downregulated along cancer invasion in CRC samples. Pseudo-time analysis revealed that STC1, AKR1B1, SIRPA, C4orf3, EDNRA, CES1, PRRX1, EMP1, PPIB, PLTP, SULF2, and EGFL6 were unpregulated along the trajectories. Immunohistochemic3al staining showed the expression of STC1, AKR1B1, and CD47 was increased along cancer invasion in CRC samples. Knockdown of AKR1B1 inhibited CRC cells' proliferation, migration, and invasion. Conclusions We revealed the spatial heterogeneity within CRC tissues and uncovered some novel genes that were associated with CRC invasion.
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Affiliation(s)
- Hong-Tao Liu
- Department of Gastroenterology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Si-Yuan Chen
- Department of Gastroenterology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China,Centre for Lipid Research & Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Ling-Long Peng
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Li Zhong
- Department of Gastroenterology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Li Zhou
- Department of Gastroenterology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Si-Qi Liao
- Department of Gastroenterology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhi-Ji Chen
- Department of Gastroenterology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qing-Liang Wang
- Department of Pathology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Song He
- Department of Gastroenterology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China,*Correspondence: Zhi-Hang Zhou, ; Song He,
| | - Zhi-Hang Zhou
- Department of Gastroenterology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China,*Correspondence: Zhi-Hang Zhou, ; Song He,
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15
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Srivastava A, Bencomo T, Das I, Lee CS. Unravelling the landscape of skin cancer through single-cell transcriptomics. Transl Oncol 2022; 27:101557. [PMID: 36257209 PMCID: PMC9576539 DOI: 10.1016/j.tranon.2022.101557] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 11/15/2022] Open
Abstract
The human skin is a complex organ that forms the first line of defense against pathogens and external injury. It is composed of a wide variety of cells that work together to maintain homeostasis and prevent disease, such as skin cancer. The exponentially rising incidence of skin malignancies poses a growing public health challenge, particularly when the disease course is complicated by metastasis and therapeutic resistance. Recent advances in single-cell transcriptomics have provided a high-resolution view of gene expression heterogeneity that can be applied to skin cancers to define cell types and states, understand disease evolution, and develop new therapeutic concepts. This approach has been particularly valuable in characterizing the contribution of immune cells in skin cancer, an area of great clinical importance given the increasing use of immunotherapy in this setting. In this review, we highlight recent skin cancer studies utilizing bulk RNA sequencing, introduce various single-cell transcriptomics approaches, and summarize key findings obtained by applying single-cell transcriptomics to skin cancer.
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Affiliation(s)
- Ankit Srivastava
- Stanford Program in Epithelial Biology, Stanford University, Stanford, CA 94305 United States of America,Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institute, Stockholm 17177, Sweden
| | - Tomas Bencomo
- Stanford Program in Epithelial Biology, Stanford University, Stanford, CA 94305 United States of America
| | - Ishani Das
- Division of Oncology, School of Medicine, Stanford University, Stanford, CA 94305 United States of America
| | - Carolyn S. Lee
- Stanford Program in Epithelial Biology, Stanford University, Stanford, CA 94305 United States of America,Stanford Cancer Institute, Stanford University, Stanford, CA 94305 United States of America,Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA 94304 United States of America,Corresponding author at: 269 Campus Drive, Room 2160, Stanford, CA 94305.
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16
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Kazakova AN, Anufrieva KS, Ivanova OM, Shnaider PV, Malyants IK, Aleshikova OI, Slonov AV, Ashrafyan LA, Babaeva NA, Eremeev AV, Boichenko VS, Lukina MM, Lagarkova MA, Govorun VM, Shender VO, Arapidi GP. Deeper insights into transcriptional features of cancer-associated fibroblasts: An integrated meta-analysis of single-cell and bulk RNA-sequencing data. Front Cell Dev Biol 2022; 10:825014. [PMID: 36263012 PMCID: PMC9574913 DOI: 10.3389/fcell.2022.825014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
Cancer-associated fibroblasts (CAFs) have long been known as one of the most important players in tumor initiation and progression. Even so, there is an incomplete understanding of the identification of CAFs among tumor microenvironment cells as the list of CAF marker genes varies greatly in the literature, therefore it is imperative to find a better way to identify reliable markers of CAFs. To this end, we summarized a large number of single-cell RNA-sequencing data of multiple tumor types and corresponding normal tissues. As a result, for 9 different types of cancer, we identified CAF-specific gene expression signatures and found 10 protein markers that showed strongly positive staining of tumor stroma according to the analysis of IHC images from the Human Protein Atlas database. Our results give an insight into selecting the most appropriate combination of cancer-associated fibroblast markers. Furthermore, comparison of different approaches for studying differences between cancer-associated and normal fibroblasts (NFs) illustrates the superiority of transcriptome analysis of fibroblasts obtained from fresh tissue samples. Using single-cell RNA sequencing data, we identified common differences in gene expression patterns between normal and cancer-associated fibroblasts, which do not depend on the type of tumor.
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Affiliation(s)
- Anastasia N. Kazakova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- *Correspondence: Anastasia N. Kazakova, ; Ksenia S. Anufrieva,
| | - Ksenia S. Anufrieva
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- *Correspondence: Anastasia N. Kazakova, ; Ksenia S. Anufrieva,
| | - Olga M. Ivanova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Polina V. Shnaider
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Faculty of biology, Lomonosov Moscow State University, Moscow, Russia
| | - Irina K. Malyants
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Faculty of Chemical-Pharmaceutical Technologies and Biomedical Drugs, Mendeleev University of Chemical Technology of Russia, Moscow, Russia
| | - Olga I. Aleshikova
- National Medical Scientific Centre of Obstetrics, Gynecology and Perinatal Medicine named after V.I. Kulakov, Moscow, Russia
| | - Andrey V. Slonov
- National Medical Scientific Centre of Obstetrics, Gynecology and Perinatal Medicine named after V.I. Kulakov, Moscow, Russia
| | - Lev A. Ashrafyan
- National Medical Scientific Centre of Obstetrics, Gynecology and Perinatal Medicine named after V.I. Kulakov, Moscow, Russia
| | - Nataliya A. Babaeva
- National Medical Scientific Centre of Obstetrics, Gynecology and Perinatal Medicine named after V.I. Kulakov, Moscow, Russia
| | - Artem V. Eremeev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, Russia
| | - Veronika S. Boichenko
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Faculty of biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria M. Lukina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Maria A. Lagarkova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Vadim M. Govorun
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Scientific Research Institute for Systems Biology and Medicine, Moscow, Russia
| | - Victoria O. Shender
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Georgij P. Arapidi
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
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