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Kang J, Lee JH, Cha H, An J, Kwon J, Lee S, Kim S, Baykan MY, Kim SY, An D, Kwon AY, An HJ, Lee SH, Choi JK, Park JE. Systematic dissection of tumor-normal single-cell ecosystems across a thousand tumors of 30 cancer types. Nat Commun 2024; 15:4067. [PMID: 38744958 PMCID: PMC11094150 DOI: 10.1038/s41467-024-48310-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
The complexity of the tumor microenvironment poses significant challenges in cancer therapy. Here, to comprehensively investigate the tumor-normal ecosystems, we perform an integrative analysis of 4.9 million single-cell transcriptomes from 1070 tumor and 493 normal samples in combination with pan-cancer 137 spatial transcriptomics, 8887 TCGA, and 1261 checkpoint inhibitor-treated bulk tumors. We define a myriad of cell states constituting the tumor-normal ecosystems and also identify hallmark gene signatures across different cell types and organs. Our atlas characterizes distinctions between inflammatory fibroblasts marked by AKR1C1 or WNT5A in terms of cellular interactions and spatial co-localization patterns. Co-occurrence analysis reveals interferon-enriched community states including tertiary lymphoid structure (TLS) components, which exhibit differential rewiring between tumor, adjacent normal, and healthy normal tissues. The favorable response of interferon-enriched community states to immunotherapy is validated using immunotherapy-treated cancers (n = 1261) including our lung cancer cohort (n = 497). Deconvolution of spatial transcriptomes discriminates TLS-enriched from non-enriched cell types among immunotherapy-favorable components. Our systematic dissection of tumor-normal ecosystems provides a deeper understanding of inter- and intra-tumoral heterogeneity.
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Affiliation(s)
- Junho Kang
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Jun Hyeong Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Hongui Cha
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jinhyeon An
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Joonha Kwon
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- Division of Cancer Data Science, National Cancer Center, Bioinformatics Branch, Goyang, Republic of Korea
| | - Seongwoo Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Seongryong Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Mert Yakup Baykan
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - So Yeon Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Dohyeon An
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Ah-Young Kwon
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam-si, Republic of Korea
| | - Hee Jung An
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam-si, Republic of Korea
| | - Se-Hoon Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
- Department of Health Sciences and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
- Penta Medix Co., Ltd., Seongnam-si, Gyeonggi-do, Republic of Korea.
| | - Jong-Eun Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
- Biomedical Research Center, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
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Al-Attar R, Storey KB. RAGE management: ETS1- EGR1 mediated transcriptional networks regulate angiogenic factors in wood frogs. Cell Signal 2022; 98:110408. [PMID: 35842171 DOI: 10.1016/j.cellsig.2022.110408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 07/02/2022] [Accepted: 07/11/2022] [Indexed: 11/03/2022]
Abstract
Freeze-tolerant species, such as wood frogs (Rana sylvatica), are susceptible to multiple co-occurring stresses that they must overcome to survive. Freezing is accompanied by mechanical stress and dehydration due to ice crystal formation in the extracellular space, ischemia/anoxia due to interruption in blood flood, and hyperglycemia due to cryoprotective measures. Wood frogs can survive dehydration, anoxia, and high glucose stress independently of freezing, thereby creating a multifactorial model for studying freeze-tolerance. Oxidative stress and high glucose levels favors the production of pro-oxidant molecules and advanced glycation end product (AGE) adducts that could cause substantial cellular damage. In this study, the involvement of the high mobility group box 1 (HMGB1)-AGE/RAGE (receptor for AGE) axis and the regulation of ETS1 and EGR1-mediated angiogenic responses were investigated in liver of wood frogs expose to freeze/thaw, anoxia/reoxygenation and dehydration/rehydration treatments. HMGB1 and not AGE-adducts are likely to induce the activation of ETS1 and EGR1 via the RAGE pathway. The increase in nuclear localization of both ETS1 and EGR1, but not DNA binding activity in response to stress hints to a potential spatial and temporal regulation in inducing angiogenic factors. Freeze/thaw and dehydration/rehydration treatments increase the levels of both pro- and anti-angiogenic factors, perhaps to prepare for the distribution of cryoprotectants or enable the repair of damaged capillaries and wounds when needed. Overall, wood frogs appear to anticipate the need for angiogenesis in response to freezing and dehydration but not anoxic treatments, probably due to mechanical stress associated with the two former conditions.
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Affiliation(s)
- Rasha Al-Attar
- Institude of Biochemistry and Department of Biology, Carleton University, Ottawa, ON K1S-5B6, Canada; McEwen Stem Cell Institute, University Health Network, Toronto, Ontario, Canada
| | - Kenneth B Storey
- Institude of Biochemistry and Department of Biology, Carleton University, Ottawa, ON K1S-5B6, Canada.
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Chai GR, Liu S, Yang HW, Chen XL. Quercetin protects against diabetic retinopathy in rats by inducing heme oxygenase-1 expression. Neural Regen Res 2021; 16:1344-1350. [PMID: 33318415 PMCID: PMC8284280 DOI: 10.4103/1673-5374.301027] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Quercetin is a widely-occurring flavonoid that protects against cancer, and improves memory and cardiovascular functions. However, whether quercetin exhibits therapeutic effects in diabetic retinopathy remains unclear. In this study, we established a rat model of streptozocin-induced diabetic retinopathy. Seventy-two hours later, the rats were intraperitoneally administered 150 mg/kg quercetin for 16 successive weeks. Quercetin markedly increased the thickness of the retinal cell layer, increased the number of ganglion cells, and decreased the overexpression of the pro-inflammatory factors interleukin-1β, interleukin-18, interleukin-6 and tumor necrosis factor-α in the retinal tissue as well as the overexpression of high mobility group box-1 and the overactivation of the NLRP3 inflammasome. Furthermore, quercetin inhibited the overexpression of TLR4 and NF-κBp65, reduced the expression of the pro-angiogenic vascular endothelial growth factor and soluble intercellular adhesion molecule-1, and upregulated the neurotrophins brain-derived neurotrophic factor and nerve growth factor. Intraperitoneal injection of the heme oxygenase-1 inhibitor zinc protoporphyrin blocked the protective effect of quercetin. These findings suggest that quercetin exerts therapeutic effects in diabetic retinopathy possibly by inducing heme oxygenase-1 expression. This study was approved by the Animal Ethics Committee of China Medical University, China (approval No. 2016PS229K) on April 8, 2016.
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Affiliation(s)
- Guang-Rui Chai
- Department of Ophthalmology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Shu Liu
- Department of Geratology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Hong-Wei Yang
- Department of Ophthalmology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Xiao-Long Chen
- Department of Ophthalmology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, China
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Liang WJ, Yang HW, Liu HN, Qian W, Chen XL. HMGB1 upregulates NF-kB by inhibiting IKB-α and associates with diabetic retinopathy. Life Sci 2019; 241:117146. [PMID: 31816325 DOI: 10.1016/j.lfs.2019.117146] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/30/2019] [Accepted: 11/02/2019] [Indexed: 01/05/2023]
Abstract
AIMS Diabetic retinopathy (DR) is the main cause of blindness in adults and investigating new therapeutic targets for DR is necessary. This study aimed to investigate the effect of high-mobility group box 1 (HMGB1) protein and its mechanism in diabetic retinopathy (DR) were investigated. MAIN METHODS Human retinal endothelial cells (HREC) were uesd for chip-seq. Sprague Dawley (SD) rats were randomly divided into control group, HMGB1 group, diabetes mellitus (DM) combined with HMGB1 siRNA group, and DM group. Next, eyeballs were removed and retinas were detached for western blot. The DM model of cell was built by increasing the glucose concentration in cell culture medium. The regulation of HMGB1 was achieved by short hairpin (sh)-HMGB1 transfection, then, the transfected cells were harvested for luciferase assay, western blot and qRT-PCR analyses as well as proliferation and apoptosis detection. KEY FINDINGS Chip-seq and luciferase assay showed the possible transcription factor functions of HMGB1 and IKB-α was one of the HMGB1 binding sites. In vivo and in vitro results indicated high expression of HMGB1 and NF-kB and low expression of IKB-α in DR and the expression of IKB-α and NF-kB was regulated by HMGB1. Moreover, cell assays showed that HMGB1 inhibited cell proliferation and promoted apoptosis. SIGNIFICANCE The results from the present study showed that HMGB1 may be involved in the pathogenesis of DR as a transcription factor through NF-kB pathway. Therefore, blockade of HMGB1 may be a new method for the treatment of DR.
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Affiliation(s)
- Wen-Jing Liang
- Department of Ophthalmology, Shengjing Hospital, China Medical University, No.36 Sanhao Street, Heping District Shenyang, Liaoning Zip, China.
| | - Hong-Wei Yang
- Department of Ophthalmology, Shengjing Hospital, China Medical University, No.36 Sanhao Street, Heping District Shenyang, Liaoning Zip, China.
| | - He-Nan Liu
- Department of Ophthalmology, Shengjing Hospital, China Medical University, No.36 Sanhao Street, Heping District Shenyang, Liaoning Zip, China.
| | - Wei Qian
- Medical Imaging Informatics Laboratory College of Engineering, University of Texas, El Paso 500 West University Avenue El Paso, TX 79968, United States of America.
| | - Xiao-Long Chen
- Department of Ophthalmology, Shengjing Hospital, China Medical University, No.36 Sanhao Street, Heping District Shenyang, Liaoning Zip, China.
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Di X, He G, Chen H, Zhu C, Qin Q, Yan J, Zhang X, Sun X. High-mobility group box 1 protein modulated proliferation and radioresistance in esophageal squamous cell carcinoma. J Gastroenterol Hepatol 2019; 34:728-735. [PMID: 29968320 DOI: 10.1111/jgh.14371] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/14/2018] [Accepted: 06/23/2018] [Indexed: 01/08/2023]
Abstract
BACKGROUND AND AIM The high-mobility group box 1 (HMGB1) protein plays an important role in a lot of biological behaviors, including DNA damage repair, gene transcription, cell replication, and cell death, and its expression is higher in many solid tumors tissues than in their adjacent normal tissues, and it is always involved in tumor proliferation, metastasis, therapeutic tolerance, and poor prognosis. However, HMGB1 in proliferation and radioresistance of esophageal squamous cell carcinoma (ESCC) remains poorly understood. In this study, the effect of HMGB1 on proliferation, cell death, DNA damage repair and radioresistance, and its underlying mechanism was investigated in human ESCC. METHODS The immunohistochemistry scores of tumor and adjacent normal tissues in ESCC tissue microarray were analyzed. Stable HMGB1 knockdown cell lines were constructed using Kyse150 and Kyse450 cells. Cell viability, radioresistance, apoptosis, autophagy, and DNA damage were determined using CCK-8, 5-ethynyl-2'-deoxyuridine, clonogenic survival assay, immunofluorescence, flow cytometry, and western blot assays. RESULTS Differential analyses showed that the expression of HMGB1 in esophageal cancer tissue was significantly higher than that in adjacent normal tissues. The downregulation of HMGB1 could effectively inhibit proliferation, increase radiosensitivity, impair DNA damage repair abilities, reduce autophagy, and increase apoptosis rates in ESCC cells after irradiation. CONCLUSIONS HMGB1 is expected to be a potential target for ESCC therapy and radiosensitization.
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Affiliation(s)
- Xiaoke Di
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Guofeng He
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hui Chen
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Caiqiang Zhu
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qin Qin
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jingjing Yan
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaowen Zhang
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xinchen Sun
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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