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Senosain MF, Zou Y, Patel K, Zhao S, Coullomb A, Rowe DJ, Lehman JM, Irish JM, Maldonado F, Kammer MN, Pancaldi V, Lopez CF. Integrated Multi-omics Analysis of Early Lung Adenocarcinoma Links Tumor Biological Features with Predicted Indolence or Aggressiveness. CANCER RESEARCH COMMUNICATIONS 2023; 3:1350-1365. [PMID: 37501683 PMCID: PMC10370362 DOI: 10.1158/2767-9764.crc-22-0373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 05/01/2023] [Accepted: 06/30/2023] [Indexed: 07/29/2023]
Abstract
Lung adenocarcinoma (LUAD) is a heterogeneous group of tumors associated with different survival rates, even when detected at an early stage. Here, we aim to investigate the biological determinants of early LUAD indolence or aggressiveness using radiomics as a surrogate of behavior. We present a set of 92 patients with LUAD with data collected across different methodologies. Patients were risk-stratified using the CT-based Score Indicative of Lung cancer Aggression (SILA) tool (0 = least aggressive, 1 = most aggressive). We grouped the patients as indolent (x ≤ 0.4, n = 14), intermediate (0.4 > x ≤ 0.6, n = 27), and aggressive (0.6 > x ≤ 1, n = 52). Using Cytometry by time of flight (CyTOF), we identified subpopulations with high HLA-DR expression that were associated with indolent behavior. In the RNA sequencing (RNA-seq) dataset, pathways related to immune response were associated with indolent behavior, while pathways associated with cell cycle and proliferation were associated with aggressive behavior. We extracted quantitative radiomics features from the CT scans of the patients. Integrating these datasets, we identified four feature signatures and four patient clusters that were associated with survival. Using single-cell RNA-seq, we found that indolent tumors had significantly more T cells and less B cells than aggressive tumors, and that the latter had a higher abundance of regulatory T cells and Th cells. In conclusion, we were able to uncover a correspondence between radiomics and tumor biology, which could improve the discrimination between indolent and aggressive LUAD tumors, enhance our knowledge in the biology of these tumors, and offer novel and personalized avenues for intervention. Significance This study provides a comprehensive profiling of LUAD indolence and aggressiveness at the biological bulk and single-cell levels, as well as at the clinical and radiomics levels. This hypothesis generating study uncovers several potential future research avenues. It also highlights the importance and power of data integration to improve our systemic understanding of LUAD and to help reduce the gap between basic science research and clinical practice.
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Affiliation(s)
- Maria-Fernanda Senosain
- Cancer Biology Graduate Program, Vanderbilt University, Nashville, Tennessee
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Cancer Early Detection and Prevention Initiative, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical. Center, Nashville, Tennessee
| | - Yong Zou
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Cancer Early Detection and Prevention Initiative, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical. Center, Nashville, Tennessee
| | - Khushbu Patel
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Cancer Early Detection and Prevention Initiative, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical. Center, Nashville, Tennessee
| | - Shilin Zhao
- Vanderbilt Ingram Cancer Center, Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Alexis Coullomb
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - Dianna J. Rowe
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Cancer Early Detection and Prevention Initiative, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical. Center, Nashville, Tennessee
| | - Jonathan M. Lehman
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jonathan M. Irish
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Fabien Maldonado
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Michael N. Kammer
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Cancer Early Detection and Prevention Initiative, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical. Center, Nashville, Tennessee
| | - Vera Pancaldi
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Barcelona Supercomputing Center, Carrer de Jordi Girona, 29, 31, 08034 Barcelona, Spain
| | - Carlos F. Lopez
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
- Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee
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Peng H, Wu X, Liu S, He M, Tang C, Wen Y, Xie C, Zhong R, Li C, Xiong S, Liu J, Zheng H, He J, Lu X, Liang W. Cellular dynamics in tumour microenvironment along with lung cancer progression underscore spatial and evolutionary heterogeneity of neutrophil. Clin Transl Med 2023; 13:e1340. [PMID: 37491740 PMCID: PMC10368809 DOI: 10.1002/ctm2.1340] [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: 04/13/2023] [Revised: 06/21/2023] [Accepted: 07/12/2023] [Indexed: 07/27/2023] Open
Abstract
BACKGROUND The cellular dynamics in the tumour microenvironment (TME) along with non-small cell lung cancer (NSCLC) progression remain unclear. METHODS Multiplex immunofluorescence test detecting 10 immune-related markers on 553 primary tumour (PT) samples of NSCLC was conducted and spatial information in TME was assessed by the StarDist depth learning model. The single-cell transcriptomic atlas of PT (n = 4) and paired tumour-draining lymph nodes (TDLNs) (n = 5 for tumour-invaded, n = 3 for tumour-free) microenvironment was profiled. Various bioinformatics analyses based on Gene Expression Omnibus, TCGA and Array-Express databases were also used to validate the discoveries. RESULTS Spatial distances of CD4+ T cells-CD38+ T cells, CD4+ T cells-neutrophils and CD38+ T cells-neutrophils prolonged and they were replaced by CD163+ macrophages in PT along with tumour progression. Neutrophils showed unique stage and location-dependent prognostic effects. A high abundance of stromal neutrophils improved disease-free survival in the early-stage, whereas high intratumoural neutrophil infiltrates predicted poor prognosis in the mid-to-late-stage. Significant molecular and functional reprogramming in PT and TDLN microenvironments was observed. Diverse interaction networks mediated by neutrophils were found between positive and negative TDLNs. Five phenotypically and functionally heterogeneous subtypes of tumour-associated neutrophil (TAN) were further identified by pseudotime analysis, including TAN-0 with antigen-presenting function, TAN-1 with strong expression of interferon (IFN)-stimulated genes, the pro-tumour TAN-2 subcluster, the classical subset (TAN-3) and the pro-inflammatory subtype (TAN-4). Loss of IFN-stimulated signature and growing angiogenesis activity were discovered along the transitional trajectory. Eventually, a robust six neutrophil differentiation relevant genes-based model was established, showing that low-risk patients had longer overall survival time and may respond better to immunotherapy. CONCLUSIONS The cellular composition, spatial location, molecular and functional changes in PT and TDLN microenvironments along with NSCLC progression were deciphered, highlighting the immunoregulatory roles and evolutionary heterogeneity of TANs.
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Affiliation(s)
- Haoxin Peng
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Diseasethe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Deparment of Clinical MedicineNanshan SchoolGuangzhou Medical UniversityGuangzhouChina
- Department of OncologyPeking University Cancer Hospital & InstitutePeking University Health Science Center, Peking UniversityBeijingChina
| | - Xiangrong Wu
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Diseasethe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Deparment of Clinical MedicineNanshan SchoolGuangzhou Medical UniversityGuangzhouChina
- Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
| | - Shaopeng Liu
- Department of Computer ScienceGuangdong Polytechnic Normal UniversityGuangzhouChina
- Department of Artificial Intelligence ResearchPazhou LabGuangzhouChina
| | - Miao He
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Diseasethe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Deparment of Clinical MedicineNanshan SchoolGuangzhou Medical UniversityGuangzhouChina
| | - Chenshuo Tang
- Department of Computer ScienceGuangdong Polytechnic Normal UniversityGuangzhouChina
| | - Yaokai Wen
- Deparment of Clinical MedicineTongji UniversityShanghaiChina
- Department of Medical OncologyShanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University, School of MedicineShanghaiChina
| | - Chao Xie
- Department of Computer ScienceGuangdong Polytechnic Normal UniversityGuangzhouChina
| | - Ran Zhong
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Diseasethe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Caichen Li
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Diseasethe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Shan Xiong
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Diseasethe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Jun Liu
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Diseasethe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Hongbo Zheng
- Medical DepartmentGenecast Biotechnology Co., LtdBeijingChina
| | - Jianxing He
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Diseasethe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Xu Lu
- Department of Computer ScienceGuangdong Polytechnic Normal UniversityGuangzhouChina
- Department of Artificial Intelligence ResearchPazhou LabGuangzhouChina
| | - Wenhua Liang
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Diseasethe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Medical OncologyThe First People's Hospital of ZhaoqingZhaoqingChina
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Hirayama A, Tanaka K, Tsutsumi H, Nakanishi T, Yamashita S, Mizusaki S, Ishii Y, Ota K, Yoneshima Y, Iwama E, Okamoto I. Regulation of PD-L1 expression in non-small cell lung cancer by interleukin-1β. Front Immunol 2023; 14:1192861. [PMID: 37441079 PMCID: PMC10333574 DOI: 10.3389/fimmu.2023.1192861] [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: 03/24/2023] [Accepted: 06/12/2023] [Indexed: 07/15/2023] Open
Abstract
Introduction Programmed cell death-ligand 1 (PD-L1) is a biomarker for prediction of the clinical efficacy of immune checkpoint inhibitors in various cancer types. The role of cytokines in regulation of PD-L1 expression in tumor cells has not been fully characterized, however. Here we show that interleukin-1β (IL-1β) plays a key role in regulation of PD-L1 expression in non-small cell lung cancer (NSCLC). Methods We performed comprehensive screening of cytokine gene expression in NSCLC tissue using available single-cell RNA-Sequence data. Then we examined the role of IL-1β in vitro to elucidate its induction of PD-L1 on NSCLC cells. Results The IL-1β gene is highly expressed in the tumor microenvironment, particularly in macrophages. The combination of IL-1β and interferon-γ (IFN-γ) induced a synergistic increase in PD-L1 expression in NSCLC cell lines. IL-1β and IFN-γ also cooperatively activated mitogen-activated protein kinase (MAPK) signaling and promoted the binding of downstream transcription factors to the PD-L1 gene promoter. Furthermore, inhibitors of MAPK signaling blocked upregulation of PD-L1 by IL-1β and IFN-γ. Discussion Our study reports high levels of IL-1β in the tumor microenvironment may cooperate with IFN-γ to induce maximal PD-L1 expression in tumor cells via activation of MAPK signaling, with the IL-1β-MAPK axis being a promising therapeutic target for attenuation of PD-L1-mediated suppression of antitumor immunity.
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Fang H, Sun Q, Zhou J, Zhang H, Song Q, Zhang H, Yu G, Guo Y, Huang C, Mou Y, Jia C, Song Y, Liu A, Song K, Lu C, Tian R, Wei S, Yang D, Chen Y, Li T, Wang K, Yu Y, Lv Y, Mo K, Sun P, Yu X, Song X. m 6A methylation reader IGF2BP2 activates endothelial cells to promote angiogenesis and metastasis of lung adenocarcinoma. Mol Cancer 2023; 22:99. [PMID: 37353784 PMCID: PMC10288689 DOI: 10.1186/s12943-023-01791-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 05/16/2023] [Indexed: 06/25/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is a common type of lung cancer with a high risk of metastasis, but the exact molecular mechanisms of metastasis are not yet understood. METHODS This study acquired single-cell transcriptomics profiling of 11 distal normal lung tissues, 11 primary LUAD tissues, and 4 metastatic LUAD tissues from the GSE131907 dataset. The lung multicellular ecosystems were characterized at a single-cell resolution, and the potential mechanisms underlying angiogenesis and metastasis of LUAD were explored. RESULTS We constructed a global single-cell landscape of 93,610 cells from primary and metastatic LUAD and found that IGF2BP2 was specifically expressed both in a LUAD cell subpopulation (termed as LUAD_IGF2BP2), and an endothelial cell subpopulation (termed as En_IGF2BP2). The LUAD_IGF2BP2 subpopulation progressively formed and dominated the ecology of metastatic LUAD during metastatic evolution. IGF2BP2 was preferentially secreted by exosomes in the LUAD_IGF2BP2 subpopulation, which was absorbed by the En_IGF2BP2 subpopulation in the tumor microenvironment. Subsequently, IGF2BP2 improved the RNA stability of FLT4 through m6A modification, thereby activating the PI3K-Akt signaling pathway, and eventually promoting angiogenesis and metastasis. Analysis of clinical data showed that IGF2BP2 was linked with poor overall survival and relapse-free survival for LUAD patients. CONCLUSIONS Overall, these findings provide a novel insight into the multicellular ecosystems of primary and metastatic LUAD, and demonstrate that a specific LUAD_IGF2BP2 subpopulation is a key orchestrator promoting angiogenesis and metastasis, with implications for the gene regulatory mechanisms of LUAD metastatic evolution, representing themselves as potential antiangiogenic targets.
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Affiliation(s)
- Han Fang
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
- Key Laboratory of Spatiotemporal Single-Cell Technologies and Translational Medicine, Yantai, 264000, Shandong, China
| | - Qi Sun
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
- Key Laboratory of Spatiotemporal Single-Cell Technologies and Translational Medicine, Yantai, 264000, Shandong, China
| | - Jin Zhou
- Key Laboratory of Spatiotemporal Single-Cell Technologies and Translational Medicine, Yantai, 264000, Shandong, China
- Department of Endocrinology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
| | - Huijuan Zhang
- Department of Oncology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
| | - Qiong Song
- Key Laboratory of Spatiotemporal Single-Cell Technologies and Translational Medicine, Yantai, 264000, Shandong, China
| | - Hua Zhang
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
- Key Laboratory of Spatiotemporal Single-Cell Technologies and Translational Medicine, Yantai, 264000, Shandong, China
| | - Guohua Yu
- Department of Pathology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
| | - Ying Guo
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
- Key Laboratory of Spatiotemporal Single-Cell Technologies and Translational Medicine, Yantai, 264000, Shandong, China
| | - Chengyu Huang
- Key Laboratory of Spatiotemporal Single-Cell Technologies and Translational Medicine, Yantai, 264000, Shandong, China
| | - Yakui Mou
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
- Key Laboratory of Spatiotemporal Single-Cell Technologies and Translational Medicine, Yantai, 264000, Shandong, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai, 264000, Shandong, China
| | - Chuanliang Jia
- Key Laboratory of Spatiotemporal Single-Cell Technologies and Translational Medicine, Yantai, 264000, Shandong, China
| | - Yingjian Song
- Department of Thoracic Surgery, Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
| | - Aina Liu
- Department of Oncology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
| | - Kaiyu Song
- Key Laboratory of Spatiotemporal Single-Cell Technologies and Translational Medicine, Yantai, 264000, Shandong, China
- Department of Endocrinology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
| | - Congxian Lu
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
- Key Laboratory of Spatiotemporal Single-Cell Technologies and Translational Medicine, Yantai, 264000, Shandong, China
| | - Ruxian Tian
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
- Key Laboratory of Spatiotemporal Single-Cell Technologies and Translational Medicine, Yantai, 264000, Shandong, China
| | - Shizhuang Wei
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
- Key Laboratory of Spatiotemporal Single-Cell Technologies and Translational Medicine, Yantai, 264000, Shandong, China
| | - Dengfeng Yang
- Biology Institute, Guangxi Academy of Sciences, Nanning, 530007, Guangxi, China
| | - Yixuan Chen
- Key Laboratory of Spatiotemporal Single-Cell Technologies and Translational Medicine, Yantai, 264000, Shandong, China
- Department Of Basic Science, YuanDong Life California Ivy Research Institute, West Hollywood, CA, 90069, USA
| | - Ting Li
- Key Laboratory of Spatiotemporal Single-Cell Technologies and Translational Medicine, Yantai, 264000, Shandong, China
- Department Of Basic Science, YuanDong Life California Ivy Research Institute, West Hollywood, CA, 90069, USA
| | - Kejian Wang
- Biology Institute, Guangxi Academy of Sciences, Nanning, 530007, Guangxi, China
- Experimental Center of BIOQGene, YuanDong International Academy Of Life Sciences, Hong Kong, 999077, China
| | - Yilan Yu
- Biology Institute, Guangxi Academy of Sciences, Nanning, 530007, Guangxi, China
- Experimental Center of BIOQGene, YuanDong International Academy Of Life Sciences, Hong Kong, 999077, China
| | - Yufeng Lv
- Department Of Basic Science, YuanDong Life California Ivy Research Institute, West Hollywood, CA, 90069, USA
| | - Ke Mo
- Key Laboratory of Spatiotemporal Single-Cell Technologies and Translational Medicine, Yantai, 264000, Shandong, China.
- Department Of Basic Science, YuanDong Life California Ivy Research Institute, West Hollywood, CA, 90069, USA.
- Experimental Center of BIOQGene, YuanDong International Academy Of Life Sciences, Hong Kong, 999077, China.
| | - Ping Sun
- Department of Oncology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China.
| | - Xiaofeng Yu
- Department of Thoracic Surgery, Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China.
| | - Xicheng Song
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China.
- Key Laboratory of Spatiotemporal Single-Cell Technologies and Translational Medicine, Yantai, 264000, Shandong, China.
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Zeng Q, Mousa M, Nadukkandy AS, Franssens L, Alnaqbi H, Alshamsi FY, Safar HA, Carmeliet P. Understanding tumour endothelial cell heterogeneity and function from single-cell omics. Nat Rev Cancer 2023:10.1038/s41568-023-00591-5. [PMID: 37349410 DOI: 10.1038/s41568-023-00591-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/22/2023] [Indexed: 06/24/2023]
Abstract
Anti-angiogenic therapies (AATs) are used to treat different types of cancers. However, their success is limited owing to insufficient efficacy and resistance. Recently, single-cell omics studies of tumour endothelial cells (TECs) have provided new mechanistic insight. Here, we overview the heterogeneity of human TECs of all tumour types studied to date, at the single-cell level. Notably, most human tumour types contain varying numbers but only a small population of angiogenic TECs, the presumed targets of AATs, possibly contributing to the limited efficacy of and resistance to AATs. In general, TECs are heterogeneous within and across all tumour types, but comparing TEC phenotypes across tumours is currently challenging, owing to the lack of a uniform nomenclature for endothelial cells and consistent single-cell analysis protocols, urgently raising the need for a more consistent approach. Nonetheless, across most tumour types, universal TEC markers (ACKR1, PLVAP and IGFBP3) can be identified. Besides angiogenesis, biological processes such as immunomodulation and extracellular matrix organization are among the most commonly predicted enriched signatures of TECs across different tumour types. Although angiogenesis and extracellular matrix targets have been considered for AAT (without the hoped success), the immunomodulatory properties of TECs have not been fully considered as a novel anticancer therapeutic approach. Therefore, we also discuss progress, limitations, solutions and novel targets for AAT development.
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Affiliation(s)
- Qun Zeng
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven and Center for Cancer Biology, VIB, Leuven, Belgium
| | - Mira Mousa
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, UAE
| | - Aisha Shigna Nadukkandy
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven and Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Angiogenesis and Vascular Heterogeneity, Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Lies Franssens
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven and Center for Cancer Biology, VIB, Leuven, Belgium
| | - Halima Alnaqbi
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, UAE
| | - Fatima Yousif Alshamsi
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, UAE
| | - Habiba Al Safar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, UAE.
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, UAE.
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven and Center for Cancer Biology, VIB, Leuven, Belgium.
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, UAE.
- Laboratory of Angiogenesis and Vascular Heterogeneity, Department of Biomedicine, Aarhus University, Aarhus, Denmark.
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Liu X, Zhang X, Yao C, Liang J, Noble PW, Jiang D. A transcriptional cell atlas identifies the decline in the AT2 niche in aged human lungs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545378. [PMID: 37398304 PMCID: PMC10312782 DOI: 10.1101/2023.06.16.545378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Aging poses a global public health challenge, associated with molecular and physiological changes in the lungs. It increases susceptibility to acute and chronic lung diseases, yet the underlying molecular and cellular drivers in aged populations are not fully appreciated. To systematically profile the genetic changes associated with age, we present a single-cell transcriptional atlas comprising nearly half a million cells from the healthy lungs of human subjects spanning various ages, sexes, and smoking statuses. Most annotated cell lineages in aged lungs exhibit dysregulated genetic programs. Specifically, the aged alveolar epithelial cells, including both alveolar type II (AT2) and type I (AT1) cells, demonstrate loss of epithelial identities, heightened inflammaging characterized by increased expression of AP-1 transcription factor and chemokine genes, and significantly increased cellular senescence. Furthermore, the aged mesenchymal cells display a remarkable decrease in Collagen and Elastin transcription. The decline of the AT2 niche is further exacerbated by a weakened endothelial cell phenotype and a dysregulated genetic program in macrophages. These findings highlight the dysregulation observed in both AT2 stem cells and their supportive niche cells, potentially contributing to the increased susceptibility of aged populations to lung diseases.
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207
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Scortegagna M, Du Y, Bradley LM, Wang K, Molinolo A, Ruppin E, Murad R, Ronai ZA. Ubiquitin Ligases Siah1a/2 Control Alveolar Macrophage Functions to Limit Carcinogen-Induced Lung Adenocarcinoma. Cancer Res 2023; 83:2016-2033. [PMID: 37078793 PMCID: PMC10330299 DOI: 10.1158/0008-5472.can-23-0258] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/22/2023] [Accepted: 04/17/2023] [Indexed: 04/21/2023]
Abstract
Cellular components of the tumor microenvironment, including myeloid cells, play important roles in the progression of lung adenocarcinoma (LUAD) and its response to therapy. Here, we characterize the function of the ubiquitin ligases Siah1a/2 in regulating the differentiation and activity of alveolar macrophages (AM) and assess the implication of Siah1a/2 control of AMs for carcinogen-induced LUAD. Macrophage-specific genetic ablation of Siah1a/2 promoted accumulation of AMs with an immature phenotype and increased expression of protumorigenic and pro-inflammatory Stat3 and β-catenin gene signatures. Administration of urethane to wild-type mice promoted enrichment of immature-like AMs and lung tumor development, which was enhanced by macrophage-specific Siah1a/2 ablation. The profibrotic gene signature seen in Siah1a/2-ablated immature-like macrophages was associated with increased tumor infiltration of CD14+ myeloid cells and poorer survival of patients with LUAD. Single-cell RNA-seq confirmed the presence of a cluster of immature-like AMs expressing a profibrotic signature in lungs of patients with LUAD, a signature enhanced in smokers. These findings identify Siah1a/2 in AMs as gatekeepers of lung cancer development. SIGNIFICANCE The ubiquitin ligases Siah1a/2 control proinflammatory signaling, differentiation, and profibrotic phenotypes of alveolar macrophages to suppress lung carcinogenesis.
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Affiliation(s)
- Marzia Scortegagna
- NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla CA
| | - Yuanning Du
- NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla CA
| | - Linda M. Bradley
- NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla CA
| | - Kun Wang
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | - Eytan Ruppin
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Rabi Murad
- NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla CA
| | - Ze’ev A. Ronai
- NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla CA
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Geissler M, Jia W, Kiraz EN, Kulacz I, Liu X, Rombach A, Prinz V, Jussen D, Kokkaliaris KD, Medyouf H, Sevenich L, Czabanka M, Broggini T. The Brain Pre-Metastatic Niche: Biological and Technical Advancements. Int J Mol Sci 2023; 24:10055. [PMID: 37373202 DOI: 10.3390/ijms241210055] [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: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Metastasis, particularly brain metastasis, continues to puzzle researchers to this day, and exploring its molecular basis promises to break ground in developing new strategies for combatting this deadly cancer. In recent years, the research focus has shifted toward the earliest steps in the formation of metastasis. In this regard, significant progress has been achieved in understanding how the primary tumor affects distant organ sites before the arrival of tumor cells. The term pre-metastatic niche was introduced for this concept and encompasses all influences on sites of future metastases, ranging from immunological modulation and ECM remodeling to the softening of the blood-brain barrier. The mechanisms governing the spread of metastasis to the brain remain elusive. However, we begin to understand these processes by looking at the earliest steps in the formation of metastasis. This review aims to present recent findings on the brain pre-metastatic niche and to discuss existing and emerging methods to further explore the field. We begin by giving an overview of the pre-metastatic and metastatic niches in general before focusing on their manifestations in the brain. To conclude, we reflect on the methods usually employed in this field of research and discuss novel approaches in imaging and sequencing.
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Affiliation(s)
- Maximilian Geissler
- Department of Neurosurgery, University Hospital, Goethe-University, 60528 Frankfurt am Main, Germany
| | - Weiyi Jia
- Department of Neurosurgery, University Hospital, Goethe-University, 60528 Frankfurt am Main, Germany
| | - Emine Nisanur Kiraz
- Department of Neurosurgery, University Hospital, Goethe-University, 60528 Frankfurt am Main, Germany
| | - Ida Kulacz
- Department of Neurosurgery, University Hospital, Goethe-University, 60528 Frankfurt am Main, Germany
| | - Xiao Liu
- Department of Neurosurgery, University Hospital, Goethe-University, 60528 Frankfurt am Main, Germany
| | - Adrian Rombach
- Department of Neurosurgery, University Hospital, Goethe-University, 60528 Frankfurt am Main, Germany
| | - Vincent Prinz
- Department of Neurosurgery, University Hospital, Goethe-University, 60528 Frankfurt am Main, Germany
| | - Daniel Jussen
- Department of Neurosurgery, University Hospital, Goethe-University, 60528 Frankfurt am Main, Germany
| | - Konstantinos D Kokkaliaris
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, 60528 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60528 Frankfurt am Main, Germany
- Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, 60528 Frankfurt am Main, Germany
| | - Hind Medyouf
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60528 Frankfurt am Main, Germany
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60528 Frankfurt am Main, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Lisa Sevenich
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60528 Frankfurt am Main, Germany
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60528 Frankfurt am Main, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marcus Czabanka
- Department of Neurosurgery, University Hospital, Goethe-University, 60528 Frankfurt am Main, Germany
- Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, 60528 Frankfurt am Main, Germany
| | - Thomas Broggini
- Department of Neurosurgery, University Hospital, Goethe-University, 60528 Frankfurt am Main, Germany
- Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, 60528 Frankfurt am Main, Germany
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209
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Herzog BH, Baer JM, Borcherding N, Kingston NL, Belle JI, Knolhoff BL, Hogg GD, Ahmad F, Kang LI, Petrone J, Lin CY, Govindan R, DeNardo DG. Tumor-associated fibrosis impairs immune surveillance and response to immune checkpoint blockade in non-small cell lung cancer. Sci Transl Med 2023; 15:eadh8005. [PMID: 37285399 DOI: 10.1126/scitranslmed.adh8005] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/17/2023] [Indexed: 06/09/2023]
Abstract
Non-small cell lung cancer (NSCLC) is a leading cause of cancer-related deaths. Immune checkpoint blockade has improved survival for many patients with NSCLC, but most fail to obtain long-term benefit. Understanding the factors leading to reduced immune surveillance in NSCLC is critical in improving patient outcomes. Here, we show that human NSCLC harbors large amounts of fibrosis that correlates with reduced T cell infiltration. In murine NSCLC models, the induction of fibrosis led to increased lung cancer progression, impaired T cell immune surveillance, and failure of immune checkpoint blockade efficacy. Associated with these changes, we observed that fibrosis leads to numerically and functionally impaired dendritic cells and altered macrophage phenotypes that likely contribute to immunosuppression. Within cancer-associated fibroblasts, distinct changes within the Col13a1-expressing population suggest that these cells produce chemokines to recruit macrophages and regulatory T cells while limiting recruitment of dendritic cells and T cells. Targeting fibrosis through transforming growth factor-β receptor signaling overcame the effects of fibrosis to enhance T cell responses and improved the efficacy of immune checkpoint blockade but only in the context of chemotherapy. Together, these data suggest that fibrosis in NSCLC leads to reduced immune surveillance and poor responsiveness to checkpoint blockade and highlight antifibrotic therapies as a candidate strategy to overcome immunotherapeutic resistance.
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Affiliation(s)
- Brett H Herzog
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - John M Baer
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicholas Borcherding
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Natalie L Kingston
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jad I Belle
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brett L Knolhoff
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Graham D Hogg
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Faiz Ahmad
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Liang-I Kang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jessica Petrone
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chieh-Yu Lin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ramaswamy Govindan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David G DeNardo
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
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210
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Luo W, Zeng Z, Jin Y, Yang L, Fan T, Wang Z, Pan Y, Yang Y, Yao M, Li Y, Xiao X, Wang G, Wang C, Chang S, Che G, Zhang L, Li Y, Peng Y, Li W. Distinct immune microenvironment of lung adenocarcinoma in never-smokers from smokers. Cell Rep Med 2023:101078. [PMID: 37301197 DOI: 10.1016/j.xcrm.2023.101078] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/19/2023] [Accepted: 05/15/2023] [Indexed: 06/12/2023]
Abstract
Lung cancer in never-smokers (LCINS) presents clinicopathological and molecular features distinct from that in smokers. Tumor microenvironment (TME) plays important roles in cancer progression and therapeutic response. To decipher the difference in TME between never-smoker and smoker lung cancers, we conduct single-cell RNA sequencing on 165,753 cells from 22 treatment-naive lung adenocarcinoma (LUAD) patients. We find that the dysfunction of alveolar cells induced by cigarette smoking contributes more to the aggressiveness of smoker LUADs, while the immunosuppressive microenvironment exerts more effects on never-smoker LUADs' aggressiveness. Moreover, the SPP1hi pro macrophage is identified to be another independent source of monocyte-derived macrophage. Importantly, higher expression of immune checkpoint CD47 and lower expression of major histocompatibility complex (MHC)-I in cancer cells of never-smoker LUADs imply that CD47 may be a better immunotherapy target for LCINS. Therefore, this study reveals the difference of tumorigenesis between never-smoker and smoker LUADs and provides a potential immunotherapy strategy for LCINS.
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Affiliation(s)
- Wenxin Luo
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhen Zeng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yang Jin
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lan Yang
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ting Fan
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhoufeng Wang
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yitong Pan
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ying Yang
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Menglin Yao
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yangqian Li
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xue Xiao
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Gang Wang
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Chengdi Wang
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Shuai Chang
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Guowei Che
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Li Zhang
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yalun Li
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yong Peng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
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211
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Timperi E, Romano E. Stromal circuits involving tumor-associated macrophages and cancer-associated fibroblasts. Front Immunol 2023; 14:1194642. [PMID: 37342322 PMCID: PMC10277481 DOI: 10.3389/fimmu.2023.1194642] [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: 03/27/2023] [Accepted: 05/19/2023] [Indexed: 06/22/2023] Open
Abstract
The tumor associated macrophages (TAM) represent one of most abundant subpopulations across several solid cancers and their number/frequency is associated with a poor clinical outcome. It has been clearly demonstrated that stromal cells, such as the cancer associated fibroblasts (CAFs), may orchestrate TAM recruitment, survival and reprogramming. Today, single cell-RNA sequencing (sc-RNA seq) technologies allowed a more granular knowledge about TAMs and CAFs phenotypical and functional programs. In this mini-review we discuss the recent discoveries in the sc-RNA seq field focusing on TAM and CAF identity and their crosstalk in the tumor microenvironment (TME) of solid cancers.
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Affiliation(s)
- Eleonora Timperi
- Department of Immunology, INSERM U932, Université Paris Sciences et Lettres (PSL) Research University, Institut Curie, Paris, France
| | - Emanuela Romano
- Department of Immunology, INSERM U932, Université Paris Sciences et Lettres (PSL) Research University, Institut Curie, Paris, France
- Department of Medical Oncology, Center for Cancer Immunotherapy, Institut Curie, Paris, France
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212
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Martínez-Jiménez F, Movasati A, Brunner SR, Nguyen L, Priestley P, Cuppen E, Van Hoeck A. Pan-cancer whole-genome comparison of primary and metastatic solid tumours. Nature 2023; 618:333-341. [PMID: 37165194 PMCID: PMC10247378 DOI: 10.1038/s41586-023-06054-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 04/05/2023] [Indexed: 05/12/2023]
Abstract
Metastatic cancer remains an almost inevitably lethal disease1-3. A better understanding of disease progression and response to therapies therefore remains of utmost importance. Here we characterize the genomic differences between early-stage untreated primary tumours and late-stage treated metastatic tumours using a harmonized pan-cancer analysis (or reanalysis) of two unpaired primary4 and metastatic5 cohorts of 7,108 whole-genome-sequenced tumours. Metastatic tumours in general have a lower intratumour heterogeneity and a conserved karyotype, displaying only a modest increase in mutations, although frequencies of structural variants are elevated overall. Furthermore, highly variable tumour-specific contributions of mutational footprints of endogenous (for example, SBS1 and APOBEC) and exogenous mutational processes (for example, platinum treatment) are present. The majority of cancer types had either moderate genomic differences (for example, lung adenocarcinoma) or highly consistent genomic portraits (for example, ovarian serous carcinoma) when comparing early-stage and late-stage disease. Breast, prostate, thyroid and kidney renal clear cell carcinomas and pancreatic neuroendocrine tumours are clear exceptions to the rule, displaying an extensive transformation of their genomic landscape in advanced stages. Exposure to treatment further scars the tumour genome and introduces an evolutionary bottleneck that selects for known therapy-resistant drivers in approximately half of treated patients. Our data showcase the potential of pan-cancer whole-genome analysis to identify distinctive features of late-stage tumours and provide a valuable resource to further investigate the biological basis of cancer and resistance to therapies.
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Affiliation(s)
- Francisco Martínez-Jiménez
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | - Ali Movasati
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sascha Remy Brunner
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Luan Nguyen
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
- Hartwig Medical Foundation Australia, Sydney, New South Wales, Australia
| | - Peter Priestley
- Hartwig Medical Foundation Australia, Sydney, New South Wales, Australia
| | - Edwin Cuppen
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands.
- Hartwig Medical Foundation, Amsterdam, The Netherlands.
| | - Arne Van Hoeck
- Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
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213
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Theodoris CV, Xiao L, Chopra A, Chaffin MD, Al Sayed ZR, Hill MC, Mantineo H, Brydon EM, Zeng Z, Liu XS, Ellinor PT. Transfer learning enables predictions in network biology. Nature 2023; 618:616-624. [PMID: 37258680 PMCID: PMC10949956 DOI: 10.1038/s41586-023-06139-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/27/2023] [Indexed: 06/02/2023]
Abstract
Mapping gene networks requires large amounts of transcriptomic data to learn the connections between genes, which impedes discoveries in settings with limited data, including rare diseases and diseases affecting clinically inaccessible tissues. Recently, transfer learning has revolutionized fields such as natural language understanding1,2 and computer vision3 by leveraging deep learning models pretrained on large-scale general datasets that can then be fine-tuned towards a vast array of downstream tasks with limited task-specific data. Here, we developed a context-aware, attention-based deep learning model, Geneformer, pretrained on a large-scale corpus of about 30 million single-cell transcriptomes to enable context-specific predictions in settings with limited data in network biology. During pretraining, Geneformer gained a fundamental understanding of network dynamics, encoding network hierarchy in the attention weights of the model in a completely self-supervised manner. Fine-tuning towards a diverse panel of downstream tasks relevant to chromatin and network dynamics using limited task-specific data demonstrated that Geneformer consistently boosted predictive accuracy. Applied to disease modelling with limited patient data, Geneformer identified candidate therapeutic targets for cardiomyopathy. Overall, Geneformer represents a pretrained deep learning model from which fine-tuning towards a broad range of downstream applications can be pursued to accelerate discovery of key network regulators and candidate therapeutic targets.
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Affiliation(s)
- Christina V Theodoris
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School Genetics Training Program, Boston, USA.
| | - Ling Xiao
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Anant Chopra
- Precision Cardiology Laboratory, Bayer US LLC, Cambridge, MA, USA
| | - Mark D Chaffin
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zeina R Al Sayed
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew C Hill
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Helene Mantineo
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | | | - Zexian Zeng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
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214
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Yin X, Wang H, Li R, Song X, Zhang T, Liang Y, Chen YZ, Yu X, Mao Q, Xia W, Chen B, Xu L, Dong G, Jiang F. Tobacco exposure primes the secretion of CCL21 positively associated with tertiary lymphoid structure and response to immunotherapy. J Immunother Cancer 2023; 11:e006939. [PMID: 37369391 PMCID: PMC10410842 DOI: 10.1136/jitc-2023-006939] [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] [Accepted: 06/11/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND It has been reported that smoking history as a predictor of immunotherapy efficacy in patients with advanced lung cancer, however, the underlying mechanisms of this phenomenon remain largely unknown. METHODS The patients with lung adenocarcinoma's (LUAD) cohort and the orthotopical transplanted mouse model were used to explore the correlation between smoking status and tertiary lymphoid structure (TLS) and chemokine CCL21, respectively. Cell adhesion and co-immunoprecipitation assays were performed to explore the interaction between CD4+T cells and CD20+B cells under tobacco exposure. Chromatin immunoprecipitation-PCR was used to dissect the mechanism of upregulated CCL21 secretion in tobacco treatment. Serum CCL21 level was recorded in patients with LUAD treated with immunotherapy. RESULTS Here we observed that individuals with a smoking history exhibit an increased quantity and maturation level of TLS compared with non-smokers, along with higher levels of CCL21 secretion. Tobacco exposure promoted CCL21 expression in an epithelial cell-intrinsic manner, of which BaP, the main component of tobacco, facilitated the nuclear retention of the aryl hydrocarbon receptor that occupied the promoter of CCL21. Additionally, the activated CCL21/CCR7 axis increased the CD11a expression of CD4+T cells, boosting the interaction with CD20+B cells dependent on ICAM1, which potentially induced the TLSs formation. Patients with elevated serum levels of CCL21 benefited more from immunotherapy. CONCLUSIONS Patients with a smoking history exhibited higher levels of TLS via the CCL21-dependent mechanism, serum CCL21 was identified as a reliable biomarker for predicting the efficacy of immunotherapy.
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Affiliation(s)
- Xuewen Yin
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, People's Republic of China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, People's Republic of China
- Department of Pharmacy, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Hui Wang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, People's Republic of China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, People's Republic of China
- The Fourth Clinical College of Nanjing Medical University, Nanjing, People's Republic of China
| | - Rutao Li
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, People's Republic of China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, People's Republic of China
- The Fourth Clinical College of Nanjing Medical University, Nanjing, People's Republic of China
| | - Xuming Song
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, People's Republic of China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, People's Republic of China
- The Fourth Clinical College of Nanjing Medical University, Nanjing, People's Republic of China
| | - Te Zhang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, People's Republic of China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, People's Republic of China
- The Fourth Clinical College of Nanjing Medical University, Nanjing, People's Republic of China
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Yingkuan Liang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, People's Republic of China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, People's Republic of China
| | - Yu-Zhong Chen
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, People's Republic of China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, People's Republic of China
- The Fourth Clinical College of Nanjing Medical University, Nanjing, People's Republic of China
| | - Xinnian Yu
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, People's Republic of China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, People's Republic of China
- The Fourth Clinical College of Nanjing Medical University, Nanjing, People's Republic of China
| | - Qixing Mao
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, People's Republic of China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, People's Republic of China
| | - Wenjie Xia
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, People's Republic of China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, People's Republic of China
| | - Bing Chen
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, People's Republic of China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, People's Republic of China
| | - Lin Xu
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, People's Republic of China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, People's Republic of China
- The Fourth Clinical College of Nanjing Medical University, Nanjing, People's Republic of China
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, People's Republic of China
| | - Gaochao Dong
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, People's Republic of China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, People's Republic of China
| | - Feng Jiang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, People's Republic of China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, People's Republic of China
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Zhong H, Lu W, Tang Y, Wiel C, Wei Y, Cao J, Riedlinger G, Papagiannakopoulos T, Guo JY, Bergo MO, Kang Y, Ganesan S, Sabaawy HE, Pine SR. SOX9 drives KRAS-induced lung adenocarcinoma progression and suppresses anti-tumor immunity. Oncogene 2023:10.1038/s41388-023-02715-5. [PMID: 37258742 DOI: 10.1038/s41388-023-02715-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 04/25/2023] [Accepted: 05/04/2023] [Indexed: 06/02/2023]
Abstract
The SOX9 transcription factor ensures proper tissue development and homeostasis and has been implicated in promoting tumor progression. However, the role of SOX9 as a driver of lung adenocarcinoma (LUAD), or any cancer, remains unclear. Using CRISPR/Cas9 and Cre-LoxP gene knockout approaches in the KrasG12D-driven mouse LUAD model, we found that loss of Sox9 significantly reduces lung tumor development, burden and progression, contributing to significantly longer overall survival. SOX9 consistently drove organoid growth in vitro, but SOX9-promoted tumor growth was significantly attenuated in immunocompromised mice compared to syngeneic mice. We demonstrate that SOX9 suppresses immune cell infiltration and functionally suppresses tumor associated CD8+ T, natural killer and dendritic cells. These data were validated by flow cytometry, gene expression, RT-qPCR, and immunohistochemistry analyses in KrasG12D-driven murine LUAD, then confirmed by interrogating bulk and single-cell gene expression repertoires and immunohistochemistry in human LUAD. Notably, SOX9 significantly elevates collagen-related gene expression and substantially increases collagen fibers. We propose that SOX9 increases tumor stiffness and inhibits tumor-infiltrating dendritic cells, thereby suppressing CD8+ T cell and NK cell infiltration and activity. Thus, SOX9 drives KrasG12D-driven lung tumor progression and inhibits anti-tumor immunity at least partly by modulating the tumor microenvironment.
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Affiliation(s)
- Hua Zhong
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Wen Lu
- Howard Hughes Medical Institute, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, Department of Microbiology and Immunology, University of California, San Francisco, CA, 94143-0795, USA
| | - Yong Tang
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
- Ludwig Institute for Cancer Research Princeton Branch, Princeton, NJ, 08544, USA
| | - Clotilde Wiel
- Sahlgrenska Center for Cancer Research, Department of Surgery, Institute of Clinical Sciences, University of Gothenburg, 405 30, Gothenburg, Sweden
- Sahlgrenska Cancer Center, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Yong Wei
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
- Ludwig Institute for Cancer Research Princeton Branch, Princeton, NJ, 08544, USA
| | - Jian Cao
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Gregory Riedlinger
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Department of Pathology and Laboratory Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Thales Papagiannakopoulos
- Perlmutter NYU Cancer Center, Department of Pathology, New York University School of Medicine, New York, NY, 10016, USA
| | - Jessie Yanxiang Guo
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Department of Chemical Biology, Rutgers Ernest Mario School of Pharmacy, Piscataway, NJ, 08854, USA
| | - Martin O Bergo
- Sahlgrenska Cancer Center, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Yibin Kang
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
- Ludwig Institute for Cancer Research Princeton Branch, Princeton, NJ, 08544, USA
| | - Shridar Ganesan
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Hatim E Sabaawy
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Department of Pathology and Laboratory Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Sharon R Pine
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
- Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
- Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
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Yang J, Liu K, Yang L, Ji J, Qin J, Deng H, Wang Z. Identification and validation of a novel cuproptosis-related stemness signature to predict prognosis and immune landscape in lung adenocarcinoma by integrating single-cell and bulk RNA-sequencing. Front Immunol 2023; 14:1174762. [PMID: 37287976 PMCID: PMC10242006 DOI: 10.3389/fimmu.2023.1174762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/11/2023] [Indexed: 06/09/2023] Open
Abstract
Background Cancer stem cells (CSCs) play vital roles in lung adenocarcinoma (LUAD) recurrence, metastasis, and drug resistance. Cuproptosis has provided a novel insight into the treatment of lung CSCs. However, there is a lack of knowledge regarding the cuproptosis-related genes combined with the stemness signature and their roles in the prognosis and immune landscape of LUAD. Methods Cuproptosis-related stemness genes (CRSGs) were identified by integrating single-cell and bulk RNA-sequencing data in LUAD patients. Subsequently, cuproptosis-related stemness subtypes were classified using consensus clustering analysis, and a prognostic signature was constructed by univariate and least absolute shrinkage operator (LASSO) Cox regression. The association between signature with immune infiltration, immunotherapy, and stemness features was also investigated. Finally, the expression of CRSGs and the functional roles of target gene were validated in vitro. Results We identified six CRSGs that were mainly expressed in epithelial and myeloid cells. Three distinct cuproptosis-related stemness subtypes were identified and associated with the immune infiltration and immunotherapy response. Furthermore, a prognostic signature was constructed to predict the overall survival (OS) of LUAD patients based on eight differently expressed genes (DEGs) with cuproptosis-related stemness signature (KLF4, SCGB3A1, COL1A1, SPP1, C4BPA, TSPAN7, CAV2, and CTHRC1) and confirmed in validation cohorts. We also developed an accurate nomogram to improve clinical applicability. Patients in the high-risk group showed worse OS with lower levels of immune cell infiltration and higher stemness features. Ultimately, further cellular experiments were performed to verify the expression of CRSGs and prognostic DEGs and demonstrate that SPP1 could affect the proliferation, migration, and stemness of LUAD cells. Conclusion This study developed a novel cuproptosis-related stemness signature that can be used to predict the prognosis and immune landscape of LUAD patients, and provided potential therapeutic targets for lung CSCs in the future.
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Affiliation(s)
- Jia Yang
- *Correspondence: Zhongqi Wang, ; Jia Yang,
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Naito Y, Koyama S, Masuhiro K, Hirai T, Uenami T, Inoue T, Osa A, Machiyama H, Watanabe G, Sax N, Villa J, Kinugasa-Katayama Y, Nojima S, Yaga M, Hosono Y, Okuzaki D, Satoh S, Tsuda T, Nakanishi Y, Suga Y, Morita T, Fukushima K, Nishide M, Shiroyama T, Miyake K, Iwahori K, Hirata H, Nagatomo I, Yano Y, Tamiya M, Kumagai T, Takemoto N, Inohara H, Yamasaki S, Yamashita K, Aoshi T, Akbay EA, Hosen N, Shintani Y, Takamatsu H, Mori M, Takeda Y, Kumanogoh A. Tumor-derived semaphorin 4A improves PD-1-blocking antibody efficacy by enhancing CD8 + T cell cytotoxicity and proliferation. SCIENCE ADVANCES 2023; 9:eade0718. [PMID: 37205755 DOI: 10.1126/sciadv.ade0718] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 04/14/2023] [Indexed: 05/21/2023]
Abstract
Immune checkpoint inhibitors (ICIs) have caused revolutionary changes in cancer treatment, but low response rates remain a challenge. Semaphorin 4A (Sema4A) modulates the immune system through multiple mechanisms in mice, although the role of human Sema4A in the tumor microenvironment remains unclear. This study demonstrates that histologically Sema4A-positive non-small cell lung cancer (NSCLC) responded significantly better to anti-programmed cell death 1 (PD-1) antibody than Sema4A-negative NSCLC. Intriguingly, SEMA4A expression in human NSCLC was mainly derived from tumor cells and was associated with T cell activation. Sema4A promoted cytotoxicity and proliferation of tumor-specific CD8+ T cells without terminal exhaustion by enhancing mammalian target of rapamycin complex 1 and polyamine synthesis, which led to improved efficacy of PD-1 inhibitors in murine models. Improved T cell activation by recombinant Sema4A was also confirmed using isolated tumor-infiltrating T cells from patients with cancer. Thus, Sema4A might be a promising therapeutic target and biomarker for predicting and promoting ICI efficacy.
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Affiliation(s)
- Yujiro Naito
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunology and Molecular Medicine, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
| | - Shohei Koyama
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunology and Molecular Medicine, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research and Clinical Trial Center (EPOC), National Cancer Center, Kashiwa,Chiba, and Tokyo, Japan
| | - Kentaro Masuhiro
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
| | - Takashi Hirai
- Department of Immunopathology, World Premier International Research Center (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Takeshi Uenami
- Department of Thoracic Oncology, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | - Takako Inoue
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Akio Osa
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Hirotomo Machiyama
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Go Watanabe
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research and Clinical Trial Center (EPOC), National Cancer Center, Kashiwa,Chiba, and Tokyo, Japan
| | - Nicolas Sax
- KOTAI Biotechnologies Inc., Suita, Osaka, Japan
| | | | - Yumi Kinugasa-Katayama
- Department of Cellular Immunology, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Satoshi Nojima
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Moto Yaga
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
| | - Yuki Hosono
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Laboratory of Molecular Immunology, WPI, IFReC, Osaka University, Suita, Osaka, Japan
- Department of Molecular Immunology, RIMD, Osaka University, Suita, Osaka, Japan
| | - Daisuke Okuzaki
- Single Cell Genomics, Human Immunology, WPI, IFReC, Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
- Center for Infectious Diseases for Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
| | - Shingo Satoh
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
| | - Takeshi Tsuda
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Yoshimitsu Nakanishi
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
| | - Yasuhiko Suga
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Takayoshi Morita
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
| | - Kiyoharu Fukushima
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Laboratory of Host Defense, WPI, IFReC, Osaka University, Suita, Osaka, Japan
| | - Masayuki Nishide
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
| | - Takayuki Shiroyama
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Kotaro Miyake
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Kota Iwahori
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Haruhiko Hirata
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Izumi Nagatomo
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Yukihiro Yano
- Department of Thoracic Oncology, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | - Motohiro Tamiya
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Toru Kumagai
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Norihiko Takemoto
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Hidenori Inohara
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Sho Yamasaki
- Laboratory of Molecular Immunology, WPI, IFReC, Osaka University, Suita, Osaka, Japan
- Department of Molecular Immunology, RIMD, Osaka University, Suita, Osaka, Japan
| | | | - Taiki Aoshi
- Department of Cellular Immunology, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Esra A Akbay
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Naoki Hosen
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Laboratory of Cellular Immunotherapy, WPI, IFReC, Osaka University, Suita, Osaka, Japan
| | - Yasushi Shintani
- Department of General Thoracic Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Hyota Takamatsu
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
| | - Masahide Mori
- Department of Thoracic Oncology, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | - Yoshito Takeda
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunology and Molecular Medicine, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
- Center for Infectious Diseases for Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
- Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology (AMED-CREST), Osaka University, Suita, Osaka, Japan
- Center for Advanced Modalities and DDS (CAMaD), Osaka University, Suita, Osaka, Japan
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Yang X, Bai Q, Chen W, Liang J, Wang F, Gu W, Liu L, Li Q, Chen Z, Zhou A, Long J, Tian H, Wu J, Ding X, Zhou N, Li M, Yang Y, Cai J. m 6 A-Dependent Modulation via IGF2BP3/MCM5/Notch Axis Promotes Partial EMT and LUAD Metastasis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023:e2206744. [PMID: 37171793 PMCID: PMC10369244 DOI: 10.1002/advs.202206744] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/21/2023] [Indexed: 05/13/2023]
Abstract
The importance of mRNA N6-methyladenosine (m6 A) modification during tumor metastasis is controversial as it plays distinct roles in different biological contexts. Moreover, how cancer cell plasticity is shaped by m6 A modification is interesting but remains uncharacterized. Here, this work shows that m6 A reader insulin like growth factor 2 mRNA binding protein 3 (IGF2BP3) is remarkably upregulated in metastatic lung adenocarcinoma (LUAD) and indicates worse prognosis of patients. Interestingly, IGF2BP3 induces partial epithelial-mesenchymal-transition (EMT) and confers LUAD cells plasticity to metastasize through m6 A-dependent overactivation of Notch signaling. Mechanistically, IGF2BP3 recognized m6 A-modified minichromosome maintenance complex component (MCM5) mRNAs to prolong stability of them, subsequently upregulating MCM5 protein, which competitively inhibits SIRT1-mediated deacetylation of Notch1 intracellular domain (NICD1), stabilizes NICD1 protein and contributes to m6 A-dependent IGF2BP3-mediated cellular plasticity. Notably, a tight correlation of the IGF2BP3/MCM5/Notch axis is evidenced in clinical LUAD specimens. Therefore, this study elucidates a critical role of m6 A modification on LUAD cell plasticity in fostering tumor metastasis via the above axis, providing potential targets for metastatic LUAD.
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Affiliation(s)
- Xia Yang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Qiaorui Bai
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Weizhong Chen
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Jiaer Liang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Fang Wang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Weiqi Gu
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Lei Liu
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Quanfeng Li
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 518033, China
| | - Zishuo Chen
- Cancer Institute, Southern Medical University, Shenzhen, 510515, China
| | - Anni Zhou
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Jianting Long
- Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Han Tian
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Jueheng Wu
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Xiaofan Ding
- Faculty of Health Sciences Building University of Macau, Macau, 999078, China
| | - Ningning Zhou
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Mengfeng Li
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Cancer Institute, Southern Medical University, Shenzhen, 510515, China
| | - Yi Yang
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Junchao Cai
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China
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Ferrena A, Wang J, Zhang R, Karadal-Ferrena B, Al-Hardan W, Singh S, Borjihan H, Schwartz E, Zhao H, Yang R, Geller D, Hoang B, Zheng D. SKP2 knockout in Rb1/p53 deficient mouse models of osteosarcoma induces immune infiltration and drives a transcriptional program with a favorable prognosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540053. [PMID: 37214958 PMCID: PMC10197654 DOI: 10.1101/2023.05.09.540053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Purpose Osteosarcoma (OS) is an aggressive bone malignancy with a poor prognosis. One putative proto-oncogene in OS is SKP2, encoding a substrate recognition factor of the SCF E3 ubiquitin ligase. We previously demonstrated that SKP2 knockout in murine OS improved survival and delayed tumorigenesis. Here we aim to define the SKP2 drives transcriptional program and its clinical implication in OS. Experimental Design We performed RNA-sequencing (RNA-seq) on tumors from a transgenic OS mouse model with conditional Trp53 and Rb1 knockouts in the osteoblast lineage ("DKO": Osx1-Cre;Rb1lox/lox;p53lox/lox) and a triple-knockout model with additional Skp2 germline knockout ("TKO": Osx1-Cre;Rb1lox/lox;p53lox/lox;SKP2-/-). We validated our RNA-seq findings using qPCR and immunohistochemistry. To investigate the clinical implications of our results, we analyzed a human OS patient cohort ("NCI-TARGET OS") with RNA-seq and clinical data. Results We found large differences in gene expression after SKP2 knockout. Strikingly, we observed increased expression of genes related to immune microenvironment infiltration in TKO tumors. We observed significant increases in signature genes for macrophages and to a lesser extent, T cells, B cells and vascular cells. We also uncovered a set of relevant transcription factors that may mediate the changes. In OS patient cohorts, high expression of genes upregulated in TKO was correlated with favorable overall survival, which was largely explained by the macrophage gene signatures. This relationship was further supported by our finding that SKP2 expression was negatively correlated with macrophage infiltration in the NCI-TARGET OS and the TCGA Sarcoma cohort. Conclusion Our findings indicate that SKP2 may mediate immune exclusion from the OS tumor microenvironment, suggesting that SKP2 modulation in OS may induce anti-tumor immune activation.
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Affiliation(s)
- Alexander Ferrena
- Institute for Clinical and Translational Research, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jichuan Wang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ranxin Zhang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Waleed Al-Hardan
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Swapnil Singh
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Hasibagan Borjihan
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Edward Schwartz
- Department of Oncology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Hongling Zhao
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rui Yang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - David Geller
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bang Hoang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
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Cui X, Liu C, Dong P, Liu C, Bai Y. The combination therapy of isomucronulatol 7-O-beta-glucoside (IMG) and CEP-9722 targeting ferroptosis-related biomarkers in non-small cell lung cancer (NSCLC). BMC Pulm Med 2023; 23:162. [PMID: 37165402 PMCID: PMC10173508 DOI: 10.1186/s12890-023-02445-0] [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: 12/19/2022] [Accepted: 04/18/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND NSCLC is a malignant tumor with a high incidence. Ferroptosis presents an essential function in regulating carcinogenesis and tumor progression. However, the ferroptosis-associated prognostic model based on single-cell sequencing of NSCLC remains unexplored. Our study aims to establish a potential predictive model for NSCLC patients and provide available targeted drugs for clinical treatment. METHODS The data on NSCLC patients were collected from TCGA and GEO databases to analyze their gene expression profiles. ConsensusCluster was adopted to divide the patients into different groups based on ferroptosis-related genes. Then, the univariable Cox and LASSO analyses were applied to data analysis and model establishment. Single-cell analysis was used to explore the risk score genes in different cell populations and states. The protein levels of these genes were also investigated through the HPA database. Drug sensitivity was evaluated in CellMiner database. CCK8 and colony formation assays were performed to validate potential drugs' effects on lung cancer cell lines. RESULTS A ferroptosis-related prognostic model involving 14 genes in NSCLC patients was established. The risk score model was developed in training set GSE31210 and validated in the test set TCGA. The low-risk score group showed a better prognosis than the high-risk score group. The single-cell analysis revealed that the risk score genes were mainly derived from lung tumor cells. Most risk score genes were more highly expressed in tumor tissue than in normal tissue, according to the HPA database. Besides, these genes were associated with 106 drugs in CellMiner database. Finally, the drug effects on NSCLC cell growth were evaluated by cck8 and colony formation. CONCLUSIONS We identified an effective ferroptosis-related prognostic model based on single-cell sequencing. The potential prediction model is devoted to exploring clinical therapeutic targets for NSCLC.
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Affiliation(s)
- Xiaofei Cui
- Department of EICU, the Second Affiliated Hospital of Dalian Medical University, Dalian, 116027, Liaoning, China
| | - Chang Liu
- Department of Thoracic Surgery, Shenyang Tenth People's Hospital, Shenyang Chest Hospital, Shenyang, 110044, Liaoning, China
| | - Penghua Dong
- Dalian Medical University, Dalian, Liaoning, China
| | - Chao Liu
- Dalian Medical University, Dalian, Liaoning, China
| | - Yu Bai
- Department of Thoracic Surgery, the Second Affiliated Hospital of Dalian Medical University, Dalian, 116027, Liaoning, China.
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221
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Wu S, Sun Z, Guo Z, Li P, Mao Q, Tang Y, Chen H, Peng H, Wang S, Cao Y. The effectiveness of blood-activating and stasis-transforming traditional Chinese medicines (BAST) in lung cancer progression-a comprehensive review. JOURNAL OF ETHNOPHARMACOLOGY 2023; 314:116565. [PMID: 37172918 DOI: 10.1016/j.jep.2023.116565] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/20/2023] [Accepted: 04/29/2023] [Indexed: 05/15/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Blood-activating and stasis-transforming traditional Chinese medicines (BAST) are a class of herbs that have the effect of dilating blood vessels and dispersing stagnation. Modern pharmaceutical research has demonstrated that they are capable of improving hemodynamics and micro-flow, resist thrombosis and promote blood flow. BAST contain numerous active ingredients, which can theoretically regulate multiple targets at the same time and have a wide range of pharmacological effects in the treatment of diseases including human cancers. Clinically, BAST have minimal side effects and can be used in combination with Western medicine to improve patients' quality of life, lessen adverse effects and minimize the risk of recurrence and metastasis of cancers. AIM OF THE REVIEW We aimed to summarize the research progression of BAST on lung cancer in the past five years and present a prospect for the future. Particularly, this review further analyzes the effects and molecular mechanisms that BAST inhibit the invasion and metastasis of lung cancer. MATERIALS AND METHODS Relevant studies about BSAT were collected from PubMed and Web of science. RESULTS Lung cancer is one of the malignant tumors with the highest mortality rate. Most patients with lung cancer are diagnosed at an advanced stage and are highly susceptible to metastasis. Recent studies have shown that BAST, a class of traditional Chinese medicine (TCM) with the function of opening veins and dispersing blood stasis, significantly improve hemodynamics and microcirculation, prevent thrombosis and promote blood flow, and thereby inhibiting the invasion and metastasis of lung cancer. In the current review, we analyzed 51 active ingredients extracted from BAST. It was found that BAST and their active ingredients contribute to the prevention of invasion and metastasis of lung cancer through multiple mechanisms, such as regulation of EMT process, specific signaling pathway and metastasis-related genes, tumor blood vessel formation, immune microenvironment and inflammatory response of tumors. CONCLUSIONS BSAT and its active ingredients have showed promising anticancer activity and significantly inhibit the invasion and metastasis of lung cancer. A growing number of studies have realized their potential clinical significance in the therapy of lung cancer, which will provide substantial evidences for the development of new TCM for lung cancer therapy.
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Affiliation(s)
- Siqi Wu
- The First Clinical School of Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Zhe Sun
- The First Clinical School of Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Zehuai Guo
- The First Clinical School of Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Peiqin Li
- The First Clinical School of Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Qianqian Mao
- The First Clinical School of Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Yang Tang
- The First Clinical School of Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Hongyu Chen
- The First Clinical School of Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Huiting Peng
- The First Clinical School of Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Sisi Wang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Yang Cao
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
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Villemin JP, Bassaganyas L, Pourquier D, Boissière F, Cabello-Aguilar S, Crapez E, Tanos R, Cornillot E, Turtoi A, Colinge J. Inferring ligand-receptor cellular networks from bulk and spatial transcriptomic datasets with BulkSignalR. Nucleic Acids Res 2023:7152875. [PMID: 37144485 DOI: 10.1093/nar/gkad352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/24/2023] [Accepted: 04/22/2023] [Indexed: 05/06/2023] Open
Abstract
The study of cellular networks mediated by ligand-receptor interactions has attracted much attention recently owing to single-cell omics. However, rich collections of bulk data accompanied with clinical information exists and continue to be generated with no equivalent in single-cell so far. In parallel, spatial transcriptomic (ST) analyses represent a revolutionary tool in biology. A large number of ST projects rely on multicellular resolution, for instance the Visium™ platform, where several cells are analyzed at each location, thus producing localized bulk data. Here, we describe BulkSignalR, a R package to infer ligand-receptor networks from bulk data. BulkSignalR integrates ligand-receptor interactions with downstream pathways to estimate statistical significance. A range of visualization methods complement the statistics, including functions dedicated to spatial data. We demonstrate BulkSignalR relevance using different datasets, including new Visium liver metastasis ST data, with experimental validation of protein colocalization. A comparison with other ST packages shows the significantly higher quality of BulkSignalR inferences. BulkSignalR can be applied to any species thanks to its built-in generic ortholog mapping functionality.
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Affiliation(s)
- Jean-Philippe Villemin
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
| | - Laia Bassaganyas
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
| | - Didier Pourquier
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
| | | | - Simon Cabello-Aguilar
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
| | - Evelyne Crapez
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
| | - Rita Tanos
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
| | - Emmanuel Cornillot
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
- Faculté de Pharmacie, Université de Montpellier, Montpellier, France
| | - Andrei Turtoi
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
| | - Jacques Colinge
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm U 1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Institut régional du Cancer Montpellier (ICM), Montpellier, France
- Faculté de Médecine, Université de Montpellier, Montpellier, France
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223
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Wei W, Su Y. Function of CD8 +, conventional CD4 +, and regulatory CD4 + T cell identification in lung cancer. Comput Biol Med 2023; 160:106933. [PMID: 37156220 DOI: 10.1016/j.compbiomed.2023.106933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/06/2023] [Accepted: 04/13/2023] [Indexed: 05/10/2023]
Abstract
Lung cancer is the malignant tumor with the highest mortality rate in the world. There is obvious heterogeneity within the tumor. Single cell sequencing technology enables scholars to obtain information about the cell type, status, subpopulation distribution and communication behavior between cells in the tumor microenvironment from the cellular level. However, due to the problem of sequencing depth, some genes with low expression cannot be detected, which results in that most of the specific genes of immune cells cannot be recognized, and lead to defects in the functional identification of immune cells. In this paper, we used single cell sequencing data of 12346 T cells in 14 treatment-naïve non-small-cell lung cancer patients to identify immune cell-specific genes and infer the function of three types of T cells. The method, named GRAPH-LC, implemented this function by gene interaction network and graph learning methods. Graph learning methods are used to extract genes feature and dense neural network is used to identify immune cell-specific genes. The experiments on 10-cross validation shows that the AUROC and AUPR reached at least 0.802, 0.815 on identifying cell-specific genes of three types of T cells. And we did functional enrichment analysis on the top 15 expressed genes. By functional enrichment analysis, we got 95 GO terms and 39 KEGG pathways that related to three types of T cells. The use of this technology will help to deeply understand the mechanism of the occurrence and development of lung cancer, find new diagnostic markers and therapeutic targets, and provide a theoretical reference for the precise treatment of lung cancer patients in the future.
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Affiliation(s)
- Wei Wei
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, tianjin, China
| | - Yanjun Su
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, tianjin, China.
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Kuhlmann-Hogan A, Cordes T, Xu Z, Traina KA, Robles-Oteíza C, Ayeni D, Kwong EM, Levy SR, Nobari M, Cheng GZ, Shaw R, Leibel SL, Metallo CM, Politi K, Kaech SM. EGFR + lung adenocarcinomas coopt alveolar macrophage metabolism and function to support EGFR signaling and growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.15.536974. [PMID: 37131637 PMCID: PMC10153136 DOI: 10.1101/2023.04.15.536974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The limited efficacy of currently approved immunotherapies in EGFR-mutant lung adenocarcinoma (LUAD) underscores the need to better understand mechanisms governing local immunosuppression. Elevated surfactant and GM-CSF secretion from the transformed epithelium induces tumor-associated alveolar macrophages (TA-AM) to proliferate and support tumor growth by rewiring inflammatory functions and lipid metabolism. TA-AM properties are driven by increased GM-CSF-PPARγ signaling and inhibition of airway GM-CSF or PPARγ in TA-AMs suppresses cholesterol efflux to tumor cells, which impairs EGFR phosphorylation and restrains LUAD progression. In the absence of TA-AM metabolic support, LUAD cells compensate by increasing cholesterol synthesis, and blocking PPARγ in TA-AMs simultaneous with statin therapy further suppresses tumor progression and increases T cell effector functions. These results reveal new therapeutic combinations for immunotherapy resistant EGFR-mutant LUADs and demonstrate how such cancer cells can metabolically co-opt TA-AMs through GM-CSF-PPARγ signaling to provide nutrients that promote oncogenic signaling and growth.
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225
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Guo M, Abd-Rabbo D, Bertol B, Carew M, Lukhele S, Snell LM, Xu W, Boukhaled GM, Elsaesser H, Halaby MJ, Hirano N, McGaha TL, Brooks DG. Molecular, metabolic and functional CD4 T cell paralysis impedes tumor control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.15.536946. [PMID: 37131587 PMCID: PMC10153152 DOI: 10.1101/2023.04.15.536946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
CD4 T cells are important effectors of anti-tumor immunity, yet the regulation of CD4 tumor-specific T (T TS ) cells during cancer development is still unclear. We demonstrate that CD4 T TS cells are initially primed in the tumor draining lymph node and begin to divide following tumor initiation. Distinct from CD8 T TS cells and previously defined exhaustion programs, CD4 T TS cell proliferation is rapidly frozen in place and differentiation stunted by a functional interplay of T regulatory cells and both intrinsic and extrinsic CTLA4 signaling. Together these mechanisms paralyze CD4 T TS cell differentiation, redirecting metabolic and cytokine production circuits, and reducing CD4 T TS cell accumulation in the tumor. Paralysis is actively maintained throughout cancer progression and CD4 T TS cells rapidly resume proliferation and functional differentiation when both suppressive reactions are alleviated. Strikingly, Treg depletion alone reciprocally induced CD4 T TS cells to themselves become tumor-specific Tregs, whereas CTLA4 blockade alone failed to promote T helper differentiation. Overcoming their paralysis established long-term tumor control, demonstrating a novel immune evasion mechanism that specifically cripples CD4 T TS cells to favor tumor progression.
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226
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Yu D, Zhang S, Liu Z, Xu L, Chen L, Xie L. Single-Cell RNA Sequencing Analysis of Gene Regulatory Network Changes in the Development of Lung Adenocarcinoma. Biomolecules 2023; 13:671. [PMID: 37189418 PMCID: PMC10135828 DOI: 10.3390/biom13040671] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/31/2023] [Accepted: 04/09/2023] [Indexed: 05/17/2023] Open
Abstract
Lung cancer is a highly heterogeneous disease. Cancer cells and other cells within the tumor microenvironment interact to determine disease progression, as well as response to or escape from treatment. Understanding the regulatory relationship between cancer cells and their tumor microenvironment in lung adenocarcinoma is of great significance for exploring the heterogeneity of the tumor microenvironment and its role in the genesis and development of lung adenocarcinoma. This work uses public single-cell transcriptome data (distant normal, nLung; early LUAD, tLung; advanced LUAD, tL/B), to draft a cell map of lung adenocarcinoma from onset to progression, and provide a cell-cell communication view of lung adenocarcinoma in the different disease stages. Based on the analysis of cell populations, it was found that the proportion of macrophages was significantly reduced in the development of lung adenocarcinoma, and patients with lower proportions of macrophages exhibited poor prognosis. We therefore constructed a process to screen an intercellular gene regulatory network that reduces any error generated by single cell communication analysis and increases the credibility of selected cell communication signals. Based on the key regulatory signals in the macrophage-tumor cell regulatory network, we performed a pseudotime analysis of the macrophages and found that signal molecules (TIMP1, VEGFA, SPP1) are highly expressed in immunosuppression-associated macrophages. These molecules were also validated using an independent dataset and were significantly associated with poor prognosis. Our study provides an effective method for screening the key regulatory signals in the tumor microenvironment and the selected signal molecules may serve as a reference to guide the development of diagnostic biomarkers for risk stratification and therapeutic targets for lung adenocarcinoma.
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Affiliation(s)
- Dongshuo Yu
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China;
- Shanghai-MOST Key Laboratory of Health and Disease Genomics (Chinese National Human Genome Center at Shanghai), Institute of Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200037, China; (S.Z.); (Z.L.); (L.X.)
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Siwen Zhang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics (Chinese National Human Genome Center at Shanghai), Institute of Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200037, China; (S.Z.); (Z.L.); (L.X.)
| | - Zhenhao Liu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics (Chinese National Human Genome Center at Shanghai), Institute of Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200037, China; (S.Z.); (Z.L.); (L.X.)
| | - Linfeng Xu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics (Chinese National Human Genome Center at Shanghai), Institute of Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200037, China; (S.Z.); (Z.L.); (L.X.)
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China;
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Lu Xie
- Shanghai-MOST Key Laboratory of Health and Disease Genomics (Chinese National Human Genome Center at Shanghai), Institute of Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200037, China; (S.Z.); (Z.L.); (L.X.)
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227
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Pai JA, Hellmann MD, Sauter JL, Mattar M, Rizvi H, Woo HJ, Shah N, Nguyen EM, Uddin FZ, Quintanal-Villalonga A, Chan JM, Manoj P, Allaj V, Baine MK, Bhanot UK, Jain M, Linkov I, Meng F, Brown D, Chaft JE, Plodkowski AJ, Gigoux M, Won HH, Sen T, Wells DK, Donoghue MTA, de Stanchina E, Wolchok JD, Loomis B, Merghoub T, Rudin CM, Chow A, Satpathy AT. Lineage tracing reveals clonal progenitors and long-term persistence of tumor-specific T cells during immune checkpoint blockade. Cancer Cell 2023; 41:776-790.e7. [PMID: 37001526 PMCID: PMC10563767 DOI: 10.1016/j.ccell.2023.03.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 11/21/2022] [Accepted: 03/07/2023] [Indexed: 04/12/2023]
Abstract
Paired single-cell RNA and T cell receptor sequencing (scRNA/TCR-seq) has allowed for enhanced resolution of clonal T cell dynamics in cancer. Here, we report a scRNA/TCR-seq analysis of 187,650 T cells from 31 tissue regions, including tumor, adjacent normal tissues, and lymph nodes (LN), from three patients with non-small cell lung cancer after immune checkpoint blockade (ICB). Regions with viable cancer cells are enriched for exhausted CD8+ T cells, regulatory CD4+ T cells (Treg), and follicular helper CD4+ T cells (TFH). Tracking T cell clonotypes across tissues, combined with neoantigen specificity assays, reveals that TFH and tumor-specific exhausted CD8+ T cells are clonally linked to TCF7+SELL+ progenitors in tumor draining LNs, and progressive exhaustion trajectories of CD8+ T, Treg, and TFH cells with proximity to the tumor microenvironment. Finally, longitudinal tracking of tumor-specific CD8+ and CD4+ T cell clones reveals persistence in the peripheral blood for years after ICB therapy.
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Affiliation(s)
- Joy A Pai
- Department of Pathology, Stanford University, Stanford, CA, USA; Immunology Program, Stanford University, Stanford, CA, USA
| | - Matthew D Hellmann
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA; Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jennifer L Sauter
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marissa Mattar
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hira Rizvi
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hyung Jun Woo
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nisargbhai Shah
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Evelyn M Nguyen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Cancer Biology Program, Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fathema Z Uddin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Joseph M Chan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Parvathy Manoj
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Viola Allaj
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marina K Baine
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Umesh K Bhanot
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mala Jain
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irina Linkov
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fanli Meng
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David Brown
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jamie E Chaft
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA
| | - Andrew J Plodkowski
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mathieu Gigoux
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Helen H Won
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Triparna Sen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA
| | - Daniel K Wells
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Santa Ana Bio, Alameda, CA, USA
| | - Mark T A Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jedd D Wolchok
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA; Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brian Loomis
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Taha Merghoub
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA; Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew Chow
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA; Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA; Immunology Program, Stanford University, Stanford, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, Stanford University, Stanford, CA, USA.
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228
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Chen JH, Nieman LT, Spurrell M, Jorgji V, Richieri P, Xu KH, Madhu R, Parikh M, Zamora I, Mehta A, Nabel CS, Freeman SS, Pirl JD, Lu C, Meador CB, Barth JL, Sakhi M, Tang AL, Sarkizova S, Price C, Fernandez NF, Emanuel G, He J, Raay KV, Reeves JW, Yizhak K, Hofree M, Shih A, Sade-Feldman M, Boland GM, Pelka K, Aryee M, Korsunsky I, Mino-Kenudson M, Gainor JF, Hacohen N. Spatial analysis of human lung cancer reveals organized immune hubs enriched for stem-like CD8 T cells and associated with immunotherapy response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.04.535379. [PMID: 37066412 PMCID: PMC10104028 DOI: 10.1101/2023.04.04.535379] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The organization of immune cells in human tumors is not well understood. Immunogenic tumors harbor spatially-localized multicellular 'immunity hubs' defined by expression of the T cell-attracting chemokines CXCL10/CXCL11 and abundant T cells. Here, we examined immunity hubs in human pre-immunotherapy lung cancer specimens, and found that they were associated with beneficial responses to PD-1-blockade. Immunity hubs were enriched for many interferon-stimulated genes, T cells in multiple differentiation states, and CXCL9/10/11 + macrophages that preferentially interact with CD8 T cells. Critically, we discovered the stem-immunity hub, a subtype of immunity hub strongly associated with favorable PD-1-blockade outcomes, distinct from mature tertiary lymphoid structures, and enriched for stem-like TCF7+PD-1+ CD8 T cells and activated CCR7 + LAMP3 + dendritic cells, as well as chemokines that organize these cells. These results elucidate the spatial organization of the human intratumoral immune response and its relevance to patient immunotherapy outcomes.
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Li M, Zhou B, Zheng C. An integrated bioinformatic analysis of bulk and single-cell sequencing clarifies immune microenvironment and metabolic profiles of lung adenocarcinoma to predict immunotherapy efficacy. Front Cell Dev Biol 2023; 11:1163314. [PMID: 37091977 PMCID: PMC10113470 DOI: 10.3389/fcell.2023.1163314] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/24/2023] [Indexed: 04/08/2023] Open
Abstract
Targeting the tumor microenvironment is increasingly recognized as an effective treatment of advanced lung adenocarcinoma (LUAD). However, few studies have addressed the efficacy of immunotherapy for LUAD. Here, a novel method for predicting immunotherapy efficacy has been proposed, which combines single-cell and bulk sequencing to characterize the immune microenvironment and metabolic profile of LUAD. TCGA bulk dataset was used to cluster two immune subtypes: C1 with “cold” tumor characteristics and C2 with “hot” tumor characteristics, with different prognosis. The Scissor algorithm, which is based on these two immune subtypes, identified GSE131907 single cell dataset into two groups of epithelial cells, labeled as Scissor_C1 and Scissor_C2. The enrichment revealed that Scissor_C1 was characterized by hypoxia, and a hypoxic microenvironment is a potential inducing factor for tumor invasion, metastasis, and immune therapy non-response. Furthermore, single cell analysis was performed to investigate the molecular mechanism of hypoxic microenvironment-induced invasion, metastasis, and immune therapy non-response in LUAD. Notably, Scissor_C1 cells significantly interacted with T cells and cancer-associated fibroblasts (CAF), and exhibited epithelial–mesenchymal transition and immunosuppressive features. CellChat analysis revealed that a hypoxic microenvironment in Scissor_C1elevated TGFβ signaling and induced ANGPTL4 and SEMA3C secretion. Interaction with endothelial cells with ANGPTL4, which increases vascular permeability and achieves distant metastasis across the vascular endothelium. Additionally, interaction of tumor-associated macrophages (TAM) and Scissor_C1 via the EREG/EFGR pathway induces tyrosine kinase inhibitor drug-resistance in patients with LAUD. Thereafter, a subgroup of CAF cells that exhibited same features as those of Scissor_C1 that exert immunosuppressive functions in the tumor microenvironment were identified. Moreover, the key genes (EPHB2 and COL1A1) in the Scissor_C1 gene network were explored and their expressions were verified using immunohistochemistry. Finally, the metabolism dysfunction in cells crosstalk was determined, which is characterized by glutamine secretion by TAM and uptake by Scissor_C1 via SLC38A2 transporter, which may induce glutamine addiction in LUAD cells. Overall, single-cell sequencing clarifies how the tumor microenvironment affects immunotherapy efficacy via molecular mechanisms and biological processes, whereas bulk sequencing explains immunotherapy efficacy based on clinical information.
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He M, He Q, Cai X, Liu J, Deng H, Li F, Zhong R, Lu Y, Peng H, Wu X, Chen Z, Lao S, Li C, Li J, He J, Liang W. Intratumoral tertiary lymphoid structure (TLS) maturation is influenced by draining lymph nodes of lung cancer. J Immunother Cancer 2023; 11:jitc-2022-005539. [PMID: 37072348 PMCID: PMC10124324 DOI: 10.1136/jitc-2022-005539] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND Tertiary lymphoid structure (TLS) is an organized infiltration of immune cells, showing features of germinal center (GC) commonly seen in secondary lymphoid organs. However, its relationship with tumor-draining lymph nodes (TDLNs) has not been studied and we hypothesized that TDLN may influence maturation of intratumoral TLS in non-small cell lung cancer (NSCLC). METHODS Tissue slides of 616 patients that had undergone surgeries were examined. Cox proportional hazard regression model was used to assess risk factors of patients' survival, and logistic regression model was used for their relationship with TLS. Single-cell RNA-sequencing (scRNA-seq) was employed to explore transcriptomic features of TDLNs. Immunohistochemistry, multiplex immunofluorescence and flow cytometry were performed to analyze cellular composition. Cellular components of NSCLC samples from The Cancer Genome Atlas database were inferred with Microenvironment Cell Populations-counter (MCP-counter) method. Murine NSCLC models were used to dissect underlying mechanisms for relationship between TDLN and TLS maturation. RESULTS While GC+ TLS was associated with better prognosis, GC- TLS was not. TDLN metastasis reduced the prognostic relevance of TLS, and was associated with less GC formation. Primary tumor sites showed reduced B cell infiltration in TDLN-positive patients, and scRNA-seq revealed diminished memory B cell formation in tumor-invaded TDLNs, together with an emphasis on weakened interferon (IFN)-γ response. Murine NSCLC models revealed that IFN-γ signaling is involved in memory B cell differentiation in TDLNs and GC formation in primary tumors. CONCLUSIONS Our research emphasizes the influence of TDLN on intratumoral TLS maturation and suggests a role of memory B cells and IFN-γ signaling in this communication.
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Affiliation(s)
- Miao He
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, Guangdong, China
| | - Qihua He
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, Guangdong, China
| | - Xiuyu Cai
- Department of General Internal Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Jun Liu
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, Guangdong, China
| | - Hongshen Deng
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, Guangdong, China
| | - Feng Li
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, Guangdong, China
| | - Ran Zhong
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, Guangdong, China
| | - Yi Lu
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, Guangdong, China
| | - Haoxin Peng
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, Guangdong, China
| | - Xiangrong Wu
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, Guangdong, China
| | - Zisheng Chen
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, Guangdong, China
| | - Shen Lao
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, Guangdong, China
| | - Caichen Li
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, Guangdong, China
| | - Jianfu Li
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, Guangdong, China
| | - Jianxing He
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, Guangdong, China
- Department of surgery, Southern Medical University, Guangzhou, Guangdong, China
| | - Wenhua Liang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, Guangdong, China
- Department of Medical Oncology, The First People Hospital of Zhaoqing, Zhaoqing, Guangdong, China
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Puram SV, Mints M, Pal A, Qi Z, Reeb A, Gelev K, Barrett TF, Gerndt S, Liu P, Parikh AS, Ramadan S, Law T, Mroz EA, Rocco JW, Adkins D, Thorstad WL, Gay HA, Ding L, Paniello RC, Pipkorn P, Jackson RS, Wang X, Mazul A, Chernock R, Zevallos JP, Silva-Fisher J, Tirosh I. Cellular states are coupled to genomic and viral heterogeneity in HPV-related oropharyngeal carcinoma. Nat Genet 2023; 55:640-650. [PMID: 37012457 PMCID: PMC10191634 DOI: 10.1038/s41588-023-01357-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/27/2023] [Indexed: 04/05/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) includes a subset of cancers driven by human papillomavirus (HPV). Here we use single-cell RNA-seq to profile both HPV-positive and HPV-negative oropharyngeal tumors, uncovering a high level of cellular diversity within and between tumors. First, we detect diverse chromosomal aberrations within individual tumors, suggesting genomic instability and enabling the identification of malignant cells even at pathologically negative margins. Second, we uncover diversity with respect to HNSCC subtypes and other cellular states such as the cell cycle, senescence and epithelial-mesenchymal transitions. Third, we find heterogeneity in viral gene expression within HPV-positive tumors. HPV expression is lost or repressed in a subset of cells, which are associated with a decrease in HPV-associated cell cycle phenotypes, decreased response to treatment, increased invasion and poor prognosis. These findings suggest that HPV expression diversity must be considered during diagnosis and treatment of HPV-positive tumors, with important prognostic ramifications.
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Affiliation(s)
- Sidharth V Puram
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA.
| | - Michael Mints
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Ananya Pal
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Zongtai Qi
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Ashley Reeb
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Kyla Gelev
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Thomas F Barrett
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Sophie Gerndt
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Ping Liu
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Anuraag S Parikh
- Department of Otolaryngology-Head and Neck Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Salma Ramadan
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Travis Law
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Edmund A Mroz
- Department of Otolaryngology-Head and Neck Surgery, Ohio State University, Columbus, OH, USA
| | - James W Rocco
- Department of Otolaryngology-Head and Neck Surgery, Ohio State University, Columbus, OH, USA
| | - Doug Adkins
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Wade L Thorstad
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Hiram A Gay
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Li Ding
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Randal C Paniello
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Patrik Pipkorn
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Ryan S Jackson
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Xiaowei Wang
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Angela Mazul
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Rebecca Chernock
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jose P Zevallos
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Jessica Silva-Fisher
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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Qiu J, Qu X, Wang Y, Guo C, Lv B, Jiang Q, Su W, Wang L, Hua K. Single-Cell Landscape Highlights Heterogenous Microenvironment, Novel Immune Reaction Patterns, Potential Biomarkers and Unique Therapeutic Strategies of Cervical Squamous Carcinoma, Human Papillomavirus-Associated (HPVA) and Non-HPVA Adenocarcinoma. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2204951. [PMID: 36725337 PMCID: PMC10074047 DOI: 10.1002/advs.202204951] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 12/09/2022] [Indexed: 06/18/2023]
Abstract
Cervical adenocarcinomas (ADCs), including human papillomavirus (HPV)-associated (HPVA) and non-HPVA (NHPVA), though exhibiting a more malignant phenotype and poorer prognosis, are treated identically to squamous cell carcinoma (SCC). This clinical dilemma requires a deeper investigation into their differences. Herein a transcriptomic atlas of SCC, HPVA, and NHPVA-ADC using single-cell RNA (scRNA) and T-cell receptor sequencing (TCR-seq) is presented. Regarding structural cells, the malignancy origin of epithelial cells, angiogenic tip cells and two subtypes of fibroblasts is revealed. The promalignant properties of the structural cells using organoids are further confirmed. Regarding immune cells, myeloid cells with multiple functions other than antigen presentation and exhausted T lymphocytes contribute to immunosuppression. From the perspective of HPV infection, not only is HPV-dependent and independent cervical cancer oncogenesis proposed but also three immune reaction patterns mediated by T cells (coordinated/inactive/imbalanced) are identified. Strikingly, diagnostic biomarkers to distinguish ADC from SCC are discovered and prognostic biomarkers with marker genes for malignant epithelial cells, tip cells, and SPP1/C1QC macrophages are generated. Importantly, the efficacy of anti-CD96 and anti-TIGIT, not inferior to anti-PD1, in animal experiments is confirmed and targeted therapies specifically for HPV-positive SCC, HPVA and NHPVA-ADC, providing essential clues for further clinical trials, are proposed.
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Affiliation(s)
- Junjun Qiu
- Department of GynecologyObstetrics and Gynecology HospitalFudan University419 Fangxie RoadShanghai200011China
- Shanghai Key Laboratory of Female Reproductive Endocrine‐Related Diseases413 Zhaozhou RoadShanghai200011China
| | - Xinyu Qu
- Department of GynecologyObstetrics and Gynecology HospitalFudan University419 Fangxie RoadShanghai200011China
- Shanghai Key Laboratory of Female Reproductive Endocrine‐Related Diseases413 Zhaozhou RoadShanghai200011China
| | - Yumeng Wang
- Department of GynecologyObstetrics and Gynecology HospitalFudan University419 Fangxie RoadShanghai200011China
- Shanghai Key Laboratory of Female Reproductive Endocrine‐Related Diseases413 Zhaozhou RoadShanghai200011China
| | - Chenyan Guo
- Department of GynecologyObstetrics and Gynecology HospitalFudan University419 Fangxie RoadShanghai200011China
- Shanghai Key Laboratory of Female Reproductive Endocrine‐Related Diseases413 Zhaozhou RoadShanghai200011China
| | - Bin Lv
- Department of GynecologyObstetrics and Gynecology HospitalFudan University419 Fangxie RoadShanghai200011China
- Shanghai Key Laboratory of Female Reproductive Endocrine‐Related Diseases413 Zhaozhou RoadShanghai200011China
| | - Qian Jiang
- Department of GynecologyObstetrics and Gynecology HospitalFudan University419 Fangxie RoadShanghai200011China
- Shanghai Key Laboratory of Female Reproductive Endocrine‐Related Diseases413 Zhaozhou RoadShanghai200011China
| | - Wentao Su
- School of Food Science and TechnologyDalian Polytechnic UniversityDalian116034China
| | - Li Wang
- Institutes of Biomedical SciencesFudan UniversityNo. 130 Dongan RoadShanghai200032China
- Center for Medical Research and InnovationShanghai Pudong HospitalFudan University Pudong Medical Center2800 Gongwei Road, PudongShanghai201399China
| | - Keqin Hua
- Department of GynecologyObstetrics and Gynecology HospitalFudan University419 Fangxie RoadShanghai200011China
- Shanghai Key Laboratory of Female Reproductive Endocrine‐Related Diseases413 Zhaozhou RoadShanghai200011China
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233
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Matsuda S, Revandkar A, Dubash TD, Ravi A, Wittner BS, Lin M, Morris R, Burr R, Guo H, Seeger K, Szabolcs A, Che D, Nieman L, Getz GA, Ting DT, Lawrence MS, Gainor J, Haber DA, Maheswaran S. TGF-β in the microenvironment induces a physiologically occurring immune-suppressive senescent state. Cell Rep 2023; 42:112129. [PMID: 36821441 PMCID: PMC10187541 DOI: 10.1016/j.celrep.2023.112129] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 12/06/2022] [Accepted: 01/31/2023] [Indexed: 02/24/2023] Open
Abstract
TGF-β induces senescence in embryonic tissues. Whether TGF-β in the hypoxic tumor microenvironment (TME) induces senescence in cancer and how the ensuing senescence-associated secretory phenotype (SASP) remodels the cellular TME to influence immune checkpoint inhibitor (ICI) responses are unknown. We show that TGF-β induces a deeper senescent state under hypoxia than under normoxia; deep senescence correlates with the degree of E2F suppression and is marked by multinucleation, reduced reentry into proliferation, and a distinct 14-gene SASP. Suppressing TGF-β signaling in tumors in an immunocompetent mouse lung cancer model abrogates endogenous senescent cells and suppresses the 14-gene SASP and immune infiltration. Untreated human lung cancers with a high 14-gene SASP display immunosuppressive immune infiltration. In a lung cancer clinical trial of ICIs, elevated 14-gene SASP is associated with increased senescence, TGF-β and hypoxia signaling, and poor progression-free survival. Thus, TME-induced senescence may represent a naturally occurring state in cancer, contributing to an immune-suppressive phenotype associated with immune therapy resistance.
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Affiliation(s)
- Satoru Matsuda
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Ajinkya Revandkar
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Taronish D Dubash
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Arvind Ravi
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02139, USA; Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ben S Wittner
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Maoxuan Lin
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Robert Morris
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Risa Burr
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Hongshan Guo
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Karsen Seeger
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Annamaria Szabolcs
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Dante Che
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Linda Nieman
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Gad A Getz
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - David T Ting
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Michael S Lawrence
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Justin Gainor
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Daniel A Haber
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Howard Hughes Medical Institute, Bethesda, MD 20815, USA.
| | - Shyamala Maheswaran
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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234
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Prazanowska KH, Lim SB. An integrated single-cell transcriptomic dataset for non-small cell lung cancer. Sci Data 2023; 10:167. [PMID: 36973297 PMCID: PMC10042991 DOI: 10.1038/s41597-023-02074-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
As single-cell RNA sequencing (scRNA-seq) has emerged as a great tool for studying cellular heterogeneity within the past decade, the number of available scRNA-seq datasets also rapidly increased. However, reuse of such data is often problematic due to a small cohort size, limited cell types, and insufficient information on cell type classification. Here, we present a large integrated scRNA-seq dataset containing 224,611 cells from human primary non-small cell lung cancer (NSCLC) tumors. Using publicly available resources, we pre-processed and integrated seven independent scRNA-seq datasets using an anchor-based approach, with five datasets utilized as reference and the remaining two, as validation. We created two levels of annotation based on cell type-specific markers conserved across the datasets. To demonstrate usability of the integrated dataset, we created annotation predictions for the two validation datasets using our integrated reference. Additionally, we conducted a trajectory analysis on subsets of T cells and lung cancer cells. This integrated data may serve as a resource for studying NSCLC transcriptome at the single cell level.
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Affiliation(s)
- Karolina Hanna Prazanowska
- Department of Biochemistry & Molecular Biology, Ajou University School of Medicine, Suwon, 16499, Korea
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, 16499, Korea
| | - Su Bin Lim
- Department of Biochemistry & Molecular Biology, Ajou University School of Medicine, Suwon, 16499, Korea.
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, 16499, Korea.
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235
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Landais Y, Vallot C. Multi-modal quantification of pathway activity with MAYA. Nat Commun 2023; 14:1668. [PMID: 36966153 PMCID: PMC10039856 DOI: 10.1038/s41467-023-37410-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 03/16/2023] [Indexed: 03/27/2023] Open
Abstract
Signaling pathways can be activated through various cascades of genes depending on cell identity and biological context. Single-cell atlases now provide the opportunity to inspect such complexity in health and disease. Yet, existing reference tools for pathway scoring resume activity of each pathway to one unique common metric across cell types. Here, we present MAYA, a computational method that enables the automatic detection and scoring of the diverse modes of activation of biological pathways across cell populations. MAYA improves the granularity of pathway analysis by detecting subgroups of genes within reference pathways, each characteristic of a cell population and how it activates a pathway. Using multiple single-cell datasets, we demonstrate the biological relevance of identified modes of activation, the robustness of MAYA to noisy pathway lists and batch effect. MAYA can also predict cell types starting from lists of reference markers in a cluster-free manner. Finally, we show that MAYA reveals common modes of pathway activation in tumor cells across patients, opening the perspective to discover shared therapeutic vulnerabilities.
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Affiliation(s)
| | - Céline Vallot
- CNRS UMR3244, Institut Curie, PSL University, Paris, France.
- Translational Research Department, Institut Curie, PSL University, Paris, France.
- Single Cell Initiative, Institut Curie, PSL University, Paris, France.
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236
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Nguyen HCT, Baik B, Yoon S, Park T, Nam D. Benchmarking integration of single-cell differential expression. Nat Commun 2023; 14:1570. [PMID: 36944632 PMCID: PMC10030080 DOI: 10.1038/s41467-023-37126-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 03/03/2023] [Indexed: 03/23/2023] Open
Abstract
Integration of single-cell RNA sequencing data between different samples has been a major challenge for analyzing cell populations. However, strategies to integrate differential expression analysis of single-cell data remain underinvestigated. Here, we benchmark 46 workflows for differential expression analysis of single-cell data with multiple batches. We show that batch effects, sequencing depth and data sparsity substantially impact their performances. Notably, we find that the use of batch-corrected data rarely improves the analysis for sparse data, whereas batch covariate modeling improves the analysis for substantial batch effects. We show that for low depth data, single-cell techniques based on zero-inflation model deteriorate the performance, whereas the analysis of uncorrected data using limmatrend, Wilcoxon test and fixed effects model performs well. We suggest several high-performance methods under different conditions based on various simulation and real data analyses. Additionally, we demonstrate that differential expression analysis for a specific cell type outperforms that of large-scale bulk sample data in prioritizing disease-related genes.
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Affiliation(s)
- Hai C T Nguyen
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Bukyung Baik
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Sora Yoon
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Taesung Park
- Department of Statistics, Seoul National University, Seoul, 08826, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dougu Nam
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
- Department of Mathematical Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
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Jin X, Wang Q, Luo F, Pan J, Lu T, Zhao Y, Zhang X, Xiang E, Zhou C, Huang B, Lu G, Chen P, Shao Y. Single-cell transcriptomic analysis of tumor heterogeneity and intercellular networks in human urothelial carcinoma. Chin Med J (Engl) 2023; 136:690-706. [PMID: 36939254 PMCID: PMC10129232 DOI: 10.1097/cm9.0000000000002573] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Indexed: 03/21/2023] Open
Abstract
BACKGROUND Heterogeneity of tumor cells and the tumor microenvironment (TME) is significantly associated with clinical outcomes and treatment responses in patients with urothelial carcinoma (UC). Comprehensive profiling of the cellular diversity and interactions between malignant cells and TME may clarify the mechanisms underlying UC progression and guide the development of novel therapies. This study aimed to extend our understanding of intra-tumoral heterogeneity and the immunosuppressive TME in UC and provide basic support for the development of novel UC therapies. METHODS Seven patients with UC were included who underwent curative surgery at our hospital between July 2020 and October 2020. We performed single-cell RNA sequencing (scRNA-seq) analysis in seven tumors with six matched adjacent normal tissues and integrated the results with two public scRNA-seq datasets. The functional properties and intercellular interactions between single cells were characterized, and the results were validated using multiplex immunofluorescence staining, flow cytometry, and bulk transcriptomic datasets. All statistical analyses were performed using the R package with two-sided tests. Wilcoxon-rank test, log-rank test, one-way analysis of variance test, and Pearson correlation analysis were used properly. RESULTS Unsupervised t-distributed stochastic neighbor embedding clustering analysis identified ten main cellular subclusters in urothelial tissues. Of them, seven urothelial subtypes were noted, and malignant urothelial cells were characterized with enhanced cellular proliferation and reduced immunogenicity. CD8 + T cell subclusters exhibited enhanced cellular cytotoxicity activities along with increased exhaustion signature in UC tissues, and the recruitment of CD4 + T regulatory cells was also increased in tumor tissues. Regarding myeloid cells, coordinated reprogramming of infiltrated neutrophils, M2-type polarized macrophages, and LAMP3 + dendritic cells contribute to immunosuppressive TME in UC tissues. Tumor tissues demonstrated enhanced angiogenesis mediated by KDR + endothelial cells and RGS5 + /ACTA2 + pericytes. Through deconvolution analysis, we identified multiple cellular subtypes may influence the programmed death-ligand 1 (PD-L1) immunotherapy response in patients with UC. CONCLUSION Our scRNA-seq analysis clarified intra-tumoral heterogeneity and delineated the pro-tumoral and immunosuppressive microenvironment in UC tissues, which may provide novel therapeutic targets.
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Affiliation(s)
- Xingwei Jin
- Department of Urinary Cancer Multi-Disciplinary Treatment Clinic, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Qizhang Wang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Fangxiu Luo
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Junwei Pan
- Department of Urinary Cancer Multi-Disciplinary Treatment Clinic, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Tingwei Lu
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yang Zhao
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiang Zhang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Enfei Xiang
- Department of Central Laboratory, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chenghua Zhou
- Department of Central Laboratory, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Baoxing Huang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Guoliang Lu
- Department of Urinary Cancer Multi-Disciplinary Treatment Clinic, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Peizhan Chen
- Department of General Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yuan Shao
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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Becker LM, Chen SH, Rodor J, de Rooij LPMH, Baker AH, Carmeliet P. Deciphering endothelial heterogeneity in health and disease at single-cell resolution: progress and perspectives. Cardiovasc Res 2023; 119:6-27. [PMID: 35179567 PMCID: PMC10022871 DOI: 10.1093/cvr/cvac018] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/16/2021] [Accepted: 02/16/2022] [Indexed: 11/14/2022] Open
Abstract
Endothelial cells (ECs) constitute the inner lining of vascular beds in mammals and are crucial for homeostatic regulation of blood vessel physiology, but also play a key role in pathogenesis of many diseases, thereby representing realistic therapeutic targets. However, it has become evident that ECs are heterogeneous, encompassing several subtypes with distinct functions, which makes EC targeting and modulation in diseases challenging. The rise of the new single-cell era has led to an emergence of studies aimed at interrogating transcriptome diversity along the vascular tree, and has revolutionized our understanding of EC heterogeneity from both a physiological and pathophysiological context. Here, we discuss recent landmark studies aimed at teasing apart the heterogeneous nature of ECs. We cover driving (epi)genetic, transcriptomic, and metabolic forces underlying EC heterogeneity in health and disease, as well as current strategies used to combat disease-enriched EC phenotypes, and propose strategies to transcend largely descriptive heterogeneity towards prioritization and functional validation of therapeutically targetable drivers of EC diversity. Lastly, we provide an overview of the most recent advances and hurdles in single EC OMICs.
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Affiliation(s)
| | | | | | | | - Andrew H Baker
- Corresponding authors. Tel: +32 16 32 62 47, E-mail: (P.C.); Tel: +44 (0)131 242 6774, E-mail: (A.H.B.)
| | - Peter Carmeliet
- Corresponding authors. Tel: +32 16 32 62 47, E-mail: (P.C.); Tel: +44 (0)131 242 6774, E-mail: (A.H.B.)
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239
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Cascone T, Leung CH, Weissferdt A, Pataer A, Carter BW, Godoy MCB, Feldman H, William WN, Xi Y, Basu S, Sun JJ, Yadav SS, Rojas Alvarez FR, Lee Y, Mishra AK, Chen L, Pradhan M, Guo H, Sinjab A, Zhou N, Negrao MV, Le X, Gay CM, Tsao AS, Byers LA, Altan M, Glisson BS, Fossella FV, Elamin YY, Blumenschein G, Zhang J, Skoulidis F, Wu J, Mehran RJ, Rice DC, Walsh GL, Hofstetter WL, Rajaram R, Antonoff MB, Fujimoto J, Solis LM, Parra ER, Haymaker C, Wistuba II, Swisher SG, Vaporciyan AA, Lin HY, Wang J, Gibbons DL, Jack Lee J, Ajami NJ, Wargo JA, Allison JP, Sharma P, Kadara H, Heymach JV, Sepesi B. Neoadjuvant chemotherapy plus nivolumab with or without ipilimumab in operable non-small cell lung cancer: the phase 2 platform NEOSTAR trial. Nat Med 2023; 29:593-604. [PMID: 36928818 PMCID: PMC10033402 DOI: 10.1038/s41591-022-02189-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 12/15/2022] [Indexed: 03/18/2023]
Abstract
Neoadjuvant ipilimumab + nivolumab (Ipi+Nivo) and nivolumab + chemotherapy (Nivo+CT) induce greater pathologic response rates than CT alone in patients with operable non-small cell lung cancer (NSCLC). The impact of adding ipilimumab to neoadjuvant Nivo+CT is unknown. Here we report the results and correlates of two arms of the phase 2 platform NEOSTAR trial testing neoadjuvant Nivo+CT and Ipi+Nivo+CT with major pathologic response (MPR) as the primary endpoint. MPR rates were 32.1% (7/22, 80% confidence interval (CI) 18.7-43.1%) in the Nivo+CT arm and 50% (11/22, 80% CI 34.6-61.1%) in the Ipi+Nivo+CT arm; the primary endpoint was met in both arms. In patients without known tumor EGFR/ALK alterations, MPR rates were 41.2% (7/17) and 62.5% (10/16) in the Nivo+CT and Ipi+Nivo+CT groups, respectively. No new safety signals were observed in either arm. Single-cell sequencing and multi-platform immune profiling (exploratory endpoints) underscored immune cell populations and phenotypes, including effector memory CD8+ T, B and myeloid cells and markers of tertiary lymphoid structures, that were preferentially increased in the Ipi+Nivo+CT cohort. Baseline fecal microbiota in patients with MPR were enriched with beneficial taxa, such as Akkermansia, and displayed reduced abundance of pro-inflammatory and pathogenic microbes. Neoadjuvant Ipi+Nivo+CT enhances pathologic responses and warrants further study in operable NSCLC. (ClinicalTrials.gov registration: NCT03158129 .).
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Affiliation(s)
- Tina Cascone
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Cheuk H Leung
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Annikka Weissferdt
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Apar Pataer
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brett W Carter
- Department of Thoracic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Myrna C B Godoy
- Department of Thoracic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hope Feldman
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - William N William
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Hospital BP, a Beneficencia Portuguesa de Sao Paulo, Sao Paulo, Brazil
| | - Yuanxin Xi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sreyashi Basu
- The Immunotherapy Platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jing Jing Sun
- The Immunotherapy Platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shalini S Yadav
- The Immunotherapy Platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Frank R Rojas Alvarez
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Younghee Lee
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Aditya K Mishra
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lili Chen
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Monika Pradhan
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Haiping Guo
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ansam Sinjab
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nicolas Zhou
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marcelo V Negrao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiuning Le
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carl M Gay
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anne S Tsao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lauren Averett Byers
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mehmet Altan
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bonnie S Glisson
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Frank V Fossella
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yasir Y Elamin
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George Blumenschein
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ferdinandos Skoulidis
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jia Wu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Reza J Mehran
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David C Rice
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Garrett L Walsh
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wayne L Hofstetter
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ravi Rajaram
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mara B Antonoff
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luisa M Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edwin R Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cara Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio I Wistuba
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephen G Swisher
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ara A Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Heather Y Lin
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nadim J Ajami
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer A Wargo
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James P Allison
- The Immunotherapy Platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Padmanee Sharma
- The Immunotherapy Platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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240
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Single-cell RNA-seq Reveals Intratumoral Heterogeneity in Osteosarcoma Patients: A Review. J Bone Oncol 2023; 39:100475. [PMID: 37034356 PMCID: PMC10074210 DOI: 10.1016/j.jbo.2023.100475] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/22/2023] Open
Abstract
While primary bone malignancies make up just 0.2% of all cancers, osteosarcoma (OS) is the third most common cancer in adolescents. Due to its highly complex and heterogeneous tumor microenvironment (TME), OS has proven difficult to treat. There has been little to no improvement in therapy for this disease over the last 40 years. Even the recent success of immunotherapies in other blood-borne and solid malignancies has not translated to OS. With frequent recurrence and lung metastases continuing to pose a challenge in the clinic, recent advancements in molecular profiling, such as single-cell RNA sequencing (scRNA-seq), have proven useful in identifying novel biomarkers of OS tumors while providing new insight into this TME that could potentially lead to new therapeutic options. This review combines the analyses of over 150,000 cells from 18 lesions ranging from primary, recurrent, and metastatic OS lesions, revealing distinct cellular populations and gene signatures that exist between them. Here, we detail these previous findings and ultimately convey the intratumoral heterogeneity that exists within OS tumor specimens.
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241
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Zhang G, Xu X, Zhu L, Li S, Chen R, Lv N, Li Z, Wang J, Li Q, Zhou W, Yang P, Liu J. A Novel Molecular Classification Method for Glioblastoma Based on Tumor Cell Differentiation Trajectories. Stem Cells Int 2023; 2023:2826815. [PMID: 37964983 PMCID: PMC10643041 DOI: 10.1155/2023/2826815] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/29/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2023] Open
Abstract
The latest 2021 WHO classification redefines glioblastoma (GBM) as the hierarchical reporting standard by eliminating glioblastoma, IDH-mutant and only retaining the tumor entity of "glioblastoma, IDH-wild type." Knowing that subclassification of tumors based on molecular features is supposed to facilitate the therapeutic choice and increase the response rate in cancer patients, it is necessary to carry out molecular classification of the newly defined GBM. Although differentiation trajectory inference based on single-cell sequencing (scRNA-seq) data holds great promise for identifying cell heterogeneity, it has not been used in the study of GBM molecular classification. Single-cell transcriptome sequencing data from 10 GBM samples were used to identify molecular classification based on differentiation trajectories. The expressions of identified features were validated by public bulk RNA-sequencing data. Clinical feasibility of the classification system was examined in tissue samples by immunohistochemical (IHC) staining and immunofluorescence, and their clinical significance was investigated in public cohorts and clinical samples with complete clinical follow-up information. By analyzing scRNA-seq data of 10 GBM samples, four differentiation trajectories from the glioblastoma stem cell-like (GSCL) cluster were identified, based on which malignant cells were classified into five characteristic subclusters. Each cluster exhibited different potential drug sensitivities, pathways, functions, and transcriptional modules. The classification model was further examined in TCGA and CGGA datasets. According to the different abundance of five characteristic cell clusters, the patients were classified into five groups which we named Ac-G, Class-G, Neo-G, Opc-G, and Undiff-G groups. It was found that the Undiff-G group exhibited the worst overall survival (OS) in both TCGA and CGGA cohorts. In addition, the classification model was verified by IHC staining in 137 GBM samples to further clarify the difference in OS between the five groups. Furthermore, the novel biomarkers of glioblastoma stem cells (GSCs) were also described. In summary, we identified five classifications of GBM and found that they exhibited distinct drug sensitivities and different prognoses, suggesting that the new grouping system may be able to provide important prognostic information and have certain guiding significance for the treatment of GBM, and identified the GSCL cluster in GBM tissues and described its characteristic program, which may help develop new potential therapeutic targets for GSCs in GBM.
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Affiliation(s)
- Guanghao Zhang
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Xiaolong Xu
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Luojiang Zhu
- Neurosurgery Department, 922th Hospital of Joint Logistics Support Force, PLA, China
| | - Sisi Li
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Rundong Chen
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Nan Lv
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Zifu Li
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Jing Wang
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Qiang Li
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Wang Zhou
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Pengfei Yang
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Jianmin Liu
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
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242
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LncRNA PCAT6 promotes proliferation, migration, invasion, and epithelial-mesenchymal transition of lung adenocarcinoma cell by targeting miR-545-3p. Mol Biol Rep 2023; 50:3557-3568. [PMID: 36787056 PMCID: PMC10042954 DOI: 10.1007/s11033-023-08259-x] [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: 07/06/2022] [Accepted: 01/06/2023] [Indexed: 02/15/2023]
Abstract
BACKGROUND Lung cancer is a high incidence cancer on a worldwide basis and has become a major public health problem. Lung adenocarcinoma (LUAD) makes up approximately half of all lung cancers and is a threat to human health. Long non-coding RNAs (lncRNAs) is an important regulator of the development and progression of lung adenocarcinoma. In this manuscript we examined the role and potential mechanism of lncRNA PCAT6 in the development of LUAD. METHODS AND RESULTS Differences in lncRNA PCAT6 levels between LUAD samples and normal samples were first explored in the GEPIA database. We found that lncRNA PCAT6 expression was elevated, which was also validated in lung adenocarcinoma tissues and cell lines. Using western blotting, CCK-8, EdU, wound healing and transwell assays, we found that knockdown of lncRNA PCAT6 inhibited EMT, proliferation, migration, and invasion of LUAD cells. We noted a predicted a binding site for lncRNA PCAT6 and miR-545-3p through conducting bioinformatic analyses, and their binding was subsequently verified by a dual-luciferase reporter assay. Rescue experiments confirmed that miR-545-3p inhibitor partially abolished the inhibition function of lncRNA PCAT6 knockdown on LUAD cells. In addition, we predicted the downstream target genes of miR-545-3p and verified them by RT-qPCR. We found that EGFR was reduced in the silence of lncRNA PCAT6 and upregulated after miR-545-3p inhibition. CONCLUSION This study demonstrates that lncRNA PCAT6 promotes a more aggressive LUAD phenotype by sponging miR-545-3p. This finding may provide new ideas for the treatment of lung cancer.
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243
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Comprehensive analysis of BUBs gene family in lung adenocarcinoma with immunological analysis. Aging (Albany NY) 2023; 15:810-829. [PMID: 36787437 PMCID: PMC9970319 DOI: 10.18632/aging.204517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/05/2023] [Indexed: 02/16/2023]
Abstract
Lung adenocarcinoma (LUAD) is one of the most commonly malignant tumors, and major challenges remain in the treatment of LUAD. Budding uninhibited by benzimidazole 1/3 (BUB1/3) play significant roles in the process of spindle-assembly checkpoint (SAC) during mitosis. However, their roles in LUAD have not been established. Here, we performed an immunological analysis of BUB1/3 in LUAD using a comprehensive bioinformatics approach, quantitative real-time-PCR and Western blotting technique. Our results indicated that the expression levels of BUB1 and BUB3 in LUAD samples were higher than the expression levels in the control groups and were associated with some clinicopathologic parameters in patients with LUAD. BUB1/3 and their related genes were enriched in cell immune, and the immune infiltration analysis revealed that the BUB1/3 expression profile was significantly correlated with characteristics of immune cell infiltration. Survival analysis showed that the disease-free survival and overall survival of patients with LUAD decreased with an increase in the BUB1/3 expression levels. The mRNA and protein expression levels of BUB1 and BUB3 in each of the LUAD cell lines were upregulated to varying degrees. BUB1 and BUB3 are the potential immunological therapeutic intervention targets for patients with LUAD.
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244
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Werba G, Weissinger D, Kawaler EA, Zhao E, Kalfakakou D, Dhara S, Wang L, Lim HB, Oh G, Jing X, Beri N, Khanna L, Gonda T, Oberstein P, Hajdu C, Loomis C, Heguy A, Sherman MH, Lund AW, Welling TH, Dolgalev I, Tsirigos A, Simeone DM. Single-cell RNA sequencing reveals the effects of chemotherapy on human pancreatic adenocarcinoma and its tumor microenvironment. Nat Commun 2023; 14:797. [PMID: 36781852 PMCID: PMC9925748 DOI: 10.1038/s41467-023-36296-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 01/25/2023] [Indexed: 02/15/2023] Open
Abstract
The tumor microenvironment (TME) in pancreatic ductal adenocarcinoma (PDAC) is a complex ecosystem that drives tumor progression; however, in-depth single cell characterization of the PDAC TME and its role in response to therapy is lacking. Here, we perform single-cell RNA sequencing on freshly collected human PDAC samples either before or after chemotherapy. Overall, we find a heterogeneous mixture of basal and classical cancer cell subtypes, along with distinct cancer-associated fibroblast and macrophage subpopulations. Strikingly, classical and basal-like cancer cells exhibit similar transcriptional responses to chemotherapy and do not demonstrate a shift towards a basal-like transcriptional program among treated samples. We observe decreased ligand-receptor interactions in treated samples, particularly between TIGIT on CD8 + T cells and its receptor on cancer cells, and identify TIGIT as the major inhibitory checkpoint molecule of CD8 + T cells. Our results suggest that chemotherapy profoundly impacts the PDAC TME and may promote resistance to immunotherapy.
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Affiliation(s)
- Gregor Werba
- Department of Surgery, NYU Langone Health, New York, New York, 10016, USA
| | - Daniel Weissinger
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA
| | - Emily A Kawaler
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA
| | - Ende Zhao
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA
| | - Despoina Kalfakakou
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA
| | - Surajit Dhara
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA
| | - Lidong Wang
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA
| | - Heather B Lim
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA
| | - Grace Oh
- Department of Surgery, NYU Langone Health, New York, New York, 10016, USA.,Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA
| | - Xiaohong Jing
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA
| | - Nina Beri
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA.,Department of Medicine, NYU Langone Health, New York, New York, 10016, USA
| | - Lauren Khanna
- Department of Medicine, NYU Langone Health, New York, New York, 10016, USA
| | - Tamas Gonda
- Department of Medicine, NYU Langone Health, New York, New York, 10016, USA
| | - Paul Oberstein
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA.,Department of Medicine, NYU Langone Health, New York, New York, 10016, USA
| | - Cristina Hajdu
- Department of Pathology, NYU Langone Health, New York, New York, 10016, USA
| | - Cynthia Loomis
- Department of Pathology, NYU Langone Health, New York, New York, 10016, USA
| | - Adriana Heguy
- Department of Pathology, NYU Langone Health, New York, New York, 10016, USA
| | - Mara H Sherman
- Department of Cell, Developmental and Cancer Biology, Oregon Health Sciences University, Portland, Oregon, 97239, USA
| | - Amanda W Lund
- Department of Pathology, NYU Langone Health, New York, New York, 10016, USA.,Department of Dermatology, NYU Langone Health, New York, New York, 10016, USA
| | - Theodore H Welling
- Department of Surgery, NYU Langone Health, New York, New York, 10016, USA
| | - Igor Dolgalev
- Department of Pathology, NYU Langone Health, New York, New York, 10016, USA
| | - Aristotelis Tsirigos
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA. .,Department of Pathology, NYU Langone Health, New York, New York, 10016, USA.
| | - Diane M Simeone
- Department of Surgery, NYU Langone Health, New York, New York, 10016, USA. .,Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA. .,Department of Pathology, NYU Langone Health, New York, New York, 10016, USA.
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245
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Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data. Proc Natl Acad Sci U S A 2023; 120:e2217868120. [PMID: 36719923 PMCID: PMC9963017 DOI: 10.1073/pnas.2217868120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Single-cell RNA sequencing combined with genome-scale metabolic models (GEMs) has the potential to unravel the differences in metabolism across both cell types and cell states but requires new computational methods. Here, we present a method for generating cell-type-specific genome-scale models from clusters of single-cell RNA-Seq profiles. Specifically, we developed a method to estimate the minimum number of cells required to pool to obtain stable models, a bootstrapping strategy for estimating statistical inference, and a faster version of the task-driven integrative network inference for tissues algorithm for generating context-specific GEMs. In addition, we evaluated the effect of different RNA-Seq normalization methods on model topology and differences in models generated from single-cell and bulk RNA-Seq data. We applied our methods on data from mouse cortex neurons and cells from the tumor microenvironment of lung cancer and in both cases found that almost every cell subtype had a unique metabolic profile. In addition, our approach was able to detect cancer-associated metabolic differences between cancer cells and healthy cells, showcasing its utility. We also contextualized models from 202 single-cell clusters across 19 human organs using data from Human Protein Atlas and made these available in the web portal Metabolic Atlas, thereby providing a valuable resource to the scientific community. With the ever-increasing availability of single-cell RNA-Seq datasets and continuously improved GEMs, their combination holds promise to become an important approach in the study of human metabolism.
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246
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M2 macrophage-derived exosomal miR-1911-5p promotes cell migration and invasion in lung adenocarcinoma by down-regulating CELF2 -activated ZBTB4 expression. Anticancer Drugs 2023; 34:238-247. [PMID: 36730375 DOI: 10.1097/cad.0000000000001414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Lung adenocarcinoma (LUAD) is one of the most aggressive, lethal cancers, comprising around 40% of lung cancer cases. Metastases are the primary cause of LUAD deaths. The mechanism underlying metastatic LUAD and tumor microenvironment remain largely unknown. To explore the effect of M2 macrophage-derived exosomes on LUAD progression. Quantitative-PCR (q-PCR) and western blot were used to measure the expression of RNAs and proteins separately. Co-culture experiments wound healing and Transwell invasion assays were performed to evaluate the effect of M2 macrophage-derived exosomes on LUAD cell migration and invasion. RNA pulldown and luciferase reporter, RNA-binding immunoprecipitation (RIP), and mRNA stability assays were conducted to explore the downstream mechanism of exosomal microRNA-1911-5p (miR-1911-5p). M2 macrophage-derived exosomes accelerated the migration and invasion of LUAD cells. M2 macrophages-secreted exosomal miR-1911-5p enhanced cell migration and invasion in LUAD. Mechanically, miR-1911-5p targeted CUGBP- and ETR-3-like family 2 (CELF2) to downregulate zinc finger and BTB domain containing 4 (ZBTB4) in LUAD. Additionally, miR-1911-5p promoted LUAD progression via ZBTB4. The present study demonstrated that M2 macrophage-derived exosomal miR-1911-5p facilitates the migration and invasion of LUAD cells by inhibiting CELF2-activated ZBTB4, which might offer insight into LUAD treatment.
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247
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Juan H, Huang H. Quantitative analysis of high‐throughput biological data. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2023. [DOI: 10.1002/wcms.1658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Hsueh‐Fen Juan
- Department of Life Science, Institute of Biomedical Electronics and Bioinformatics, and Center for Systems Biology National Taiwan University Taipei Taiwan
- Taiwan AI Labs Taipei Taiwan
| | - Hsuan‐Cheng Huang
- Institute of Biomedical Informatics National Yang Ming Chiao Tung University Taipei Taiwan
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248
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Yi X, Zhang Q, Xie T, Feng S, Xu N, Lin JM. Microfluidic Mixer for In Situ Ammonia Analysis of Single Cells in Mass Spectrometry. Anal Chem 2023; 95:2321-2328. [PMID: 36656794 DOI: 10.1021/acs.analchem.2c04181] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Mass spectrometry (MS) is a powerful tool for exploring single-cell heterogeneity. However, due to the ultralow absolute content of most substances in a single cell, existing methods can only analyze high-content substances; conventional methods are incompetent for quantitative analysis of important trace-amount small-molecule metabolites such as ammonia and sulfide. Herein, a method integrating single-cell extraction, online derivatization, and MS for multifunctional and more accurate MS analysis is reported. For application, ammonia content in a single cell was analyzed, where the cellular heterogeneity in ammonia metabolism was revealed. First, the extraction room of a microfluidic probe was covered on the target single cell, and the extraction fluid was allowed to flow through a single cell and dissolve cellular ammonia. Then, the ammonia was mixed and reacted with the pretreatment reagent input from another inlet to achieve the derivatization and signal amplification, enhancing the analysis sensitivity on MS. Finally, the sample was sent to MS, and the ammonia content was successfully quantitatively evaluated by analyzing its derivative urotropine, demonstrating the potential of this method to advance single-cell mass spectrometry analysis to higher sensitivity.
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Affiliation(s)
- Xizhen Yi
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Qiang Zhang
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Tianze Xie
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Shuo Feng
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Ning Xu
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
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249
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Hanley CJ, Waise S, Ellis MJ, Lopez MA, Pun WY, Taylor J, Parker R, Kimbley LM, Chee SJ, Shaw EC, West J, Alzetani A, Woo E, Ottensmeier CH, Rose-Zerilli MJJ, Thomas GJ. Single-cell analysis reveals prognostic fibroblast subpopulations linked to molecular and immunological subtypes of lung cancer. Nat Commun 2023; 14:387. [PMID: 36720863 PMCID: PMC9889778 DOI: 10.1038/s41467-023-35832-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 01/04/2023] [Indexed: 02/01/2023] Open
Abstract
Fibroblasts are poorly characterised cells that variably impact tumour progression. Here, we use single cell RNA-sequencing, multiplexed immunohistochemistry and digital cytometry (CIBERSORTx) to identify and characterise three major fibroblast subpopulations in human non-small cell lung cancer: adventitial, alveolar and myofibroblasts. Alveolar and adventitial fibroblasts (enriched in control tissue samples) localise to discrete spatial niches in histologically normal lung tissue and indicate improved overall survival rates when present in lung adenocarcinomas (LUAD). Trajectory inference identifies three phases of control tissue fibroblast activation, leading to myofibroblast enrichment in tumour samples: initial upregulation of inflammatory cytokines, followed by stress-response signalling and ultimately increased expression of fibrillar collagens. Myofibroblasts correlate with poor overall survival rates in LUAD, associated with loss of epithelial differentiation, TP53 mutations, proximal molecular subtypes and myeloid cell recruitment. In squamous carcinomas myofibroblasts were not prognostic despite being transcriptomically equivalent. These findings have important implications for developing fibroblast-targeting strategies for cancer therapy.
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Affiliation(s)
- Christopher J Hanley
- School of Cancer Sciences, University of Southampton, Southampton, SO16 6YD, UK.
- Cancer Research UK and NIHR Southampton Experimental Cancer Medicine Centre, Southampton, SO16 6YD, UK.
| | - Sara Waise
- School of Cancer Sciences, University of Southampton, Southampton, SO16 6YD, UK
| | - Matthew J Ellis
- School of Cancer Sciences, University of Southampton, Southampton, SO16 6YD, UK
| | - Maria A Lopez
- Department of Histopathology, University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK
| | - Wai Y Pun
- Department of Histopathology, University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK
| | - Julian Taylor
- Department of Histopathology, University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK
| | - Rachel Parker
- School of Cancer Sciences, University of Southampton, Southampton, SO16 6YD, UK
| | - Lucy M Kimbley
- School of Cancer Sciences, University of Southampton, Southampton, SO16 6YD, UK
| | - Serena J Chee
- School of Cancer Sciences, University of Southampton, Southampton, SO16 6YD, UK
- Institute of Systems, Molecular and Integrative Biology (ISMIB) and Liverpool Experimental Cancer Medicines Centre, University of Liverpool, Liverpool, L69 7BE, UK
| | - Emily C Shaw
- Department of Histopathology, University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK
| | - Jonathan West
- School of Cancer Sciences, University of Southampton, Southampton, SO16 6YD, UK
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Aiman Alzetani
- Department of Thoracic surgery, University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK
| | - Edwin Woo
- Department of Thoracic surgery, University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK
| | - Christian H Ottensmeier
- School of Cancer Sciences, University of Southampton, Southampton, SO16 6YD, UK
- Cancer Research UK and NIHR Southampton Experimental Cancer Medicine Centre, Southampton, SO16 6YD, UK
- Institute of Systems, Molecular and Integrative Biology (ISMIB) and Liverpool Experimental Cancer Medicines Centre, University of Liverpool, Liverpool, L69 7BE, UK
| | - Matthew J J Rose-Zerilli
- School of Cancer Sciences, University of Southampton, Southampton, SO16 6YD, UK
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Gareth J Thomas
- School of Cancer Sciences, University of Southampton, Southampton, SO16 6YD, UK.
- Cancer Research UK and NIHR Southampton Experimental Cancer Medicine Centre, Southampton, SO16 6YD, UK.
- Department of Histopathology, University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK.
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250
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Liu Y, Jiang B, Lin C, Zhu W, Chen D, Sheng Y, Lou Z, Ji Z, Wu C, Wu M. m7G-related gene NUDT4 as a novel biomarker promoting cancer cell proliferation in lung adenocarcinoma. Front Oncol 2023; 12:1055605. [PMID: 36761423 PMCID: PMC9902657 DOI: 10.3389/fonc.2022.1055605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/29/2022] [Indexed: 01/25/2023] Open
Abstract
Background Lung cancer is the leading cause of mortality in cancer patients. N7-methylguanosine (m7G) modification as a translational regulation pattern has been reported to participate in multiple types of cancer progression, but little is known in lung cancer. This study attempts to explore the role of m7G-related proteins in genetic and epigenetic variations in lung adenocarcinoma, and its relationship with clinical prognosis, immune infiltration, and immunotherapy. Methods Sequencing data were obtained from the Genomic Data Commons (GDC) Data Portal and Gene Expression Omnibus (GEO) databases. Consensus clustering was utilized to distinguish m7G clusters, and responses to immunotherapy were also evaluated. Moreover, univariate and multivariate Cox and Least absolute shrinkage and selection operator LASSO Cox regression analyses were used to screen independent prognostic factors and generated risk scores for constructing a survival prediction model. Multiple cell types such as epithelial cells and immune cells were identified to verify the bulk RNA results. Short hairpin RNA (shRNA) Tet-on plasmids, Clustered Regularly Interspaced Short Palindromic Repeats CRISPR/Cas9 for knockout plasmids, and nucleoside diphosphate linked to moiety X-type motif 4 (NUDT4) overexpression plasmids were constructed to inhibit or promote tumor cell NUDT4 expression, then RT-qPCR, Cell Counting Kit-8 CCK8 proliferation assay, and Transwell assay were used to observe tumor cell biological functions. Results Fifteen m7G-related genes were highly expressed in tumor samples, and 12 genes were associated with poor prognosis. m7G cluster-B had lower immune infiltration level, worse survival, and samples that predicted poor responses to immunotherapy. The multivariate Cox model showed that NUDT4 and WDR4 (WD repeat domain 4) were independent risk factors. Single-cell m7G gene set variation analysis (GSVA) scores also had a negative correlation tendency with immune infiltration level and T-cell Programmed Death-1 PD-1 expression, but the statistics were not significant. Knocking down and knocking out the NUDT4 expression significantly inhibited cell proliferation capability in A549 and H1299 cells. In contrast, overexpressing NUDT4 promoted tumor cell proliferation. However, there was no difference in migration capability in the knockdown, knockout, or overexpression groups. Conclusions Our study revealed that m7G modification-related proteins are closely related to the tumor microenvironment, immune cell infiltration, responses to immunotherapy, and patients' prognosis in lung adenocarcinoma and could be useful biomarkers for the identification of patients who could benefit from immunotherapy. The m7G modification protein NUDT4 may be a novel biomarker in promoting the progression of lung cancer.
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Affiliation(s)
- Yafei Liu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine, Hang Zhou, China
| | - Bin Jiang
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine, Hang Zhou, China
| | - Chunjie Lin
- Life Sciences Institute, Zhejiang University, Hang Zhou, China
| | - Wanyinhui Zhu
- Life Sciences Institute, Zhejiang University, Hang Zhou, China
| | - Dingrui Chen
- Life Sciences Institute, Zhejiang University, Hang Zhou, China
| | - Yinuo Sheng
- Life Sciences Institute, Zhejiang University, Hang Zhou, China
| | - Zhiling Lou
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine, Hang Zhou, China
| | - Zhiheng Ji
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine, Hang Zhou, China
| | - Chuanqiang Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine, Hang Zhou, China
| | - Ming Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine, Hang Zhou, China,*Correspondence: Ming Wu,
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