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Chen F, Li J, Li L, Tong L, Wang G, Zou X. Multidimensional biological characteristics of ground glass nodules. Front Oncol 2024; 14:1380527. [PMID: 38841161 PMCID: PMC11150621 DOI: 10.3389/fonc.2024.1380527] [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: 02/01/2024] [Accepted: 05/07/2024] [Indexed: 06/07/2024] Open
Abstract
The detection rate of ground glass nodules (GGNs) has increased in recent years because of their malignant potential but relatively indolent biological behavior; thus, correct GGN recognition and management has become a research focus. Many scholars have explored the underlying mechanism of the indolent progression of GGNs from several perspectives, such as pathological type, genomic mutational characteristics, and immune microenvironment. GGNs have different major mutated genes at different stages of development; EGFR mutation is the most common mutation in GGNs, and p53 mutation is the most abundant mutation in the invasive stage of GGNs. Pure GGNs have fewer genomic alterations and a simpler genomic profile and exhibit a gradually evolving genomic mutation profile as the pathology progresses. Compared to advanced lung adenocarcinoma, GGN lung adenocarcinoma has a higher immune cell percentage, is under immune surveillance, and has less immune escape. However, as the pathological progression and solid component increase, negative immune regulation and immune escape increase gradually, and a suppressive immune environment is established gradually. Currently, regular computer tomography monitoring and surgery are the main treatment strategies for persistent GGNs. Stereotactic body radiotherapy and radiofrequency ablation are two local therapeutic alternatives, and systemic therapy has been progressively studied for lung cancer with GGNs. In the present review, we discuss the characterization of the multidimensional molecular evolution of GGNs that could facilitate more precise differentiation of such highly heterogeneous lesions, laying a foundation for the development of more effective individualized treatment plans.
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Affiliation(s)
- Furong Chen
- Department of Oncology, The First People’s Hospital of Shuangliu District/West China (Airport) Hospital, Sichuan University, Chengdu, China
| | - Jiangtao Li
- Department of Oncology, The First People’s Hospital of Shuangliu District/West China (Airport) Hospital, Sichuan University, Chengdu, China
| | - Lei Li
- Department of Respiratory and Critical Care Medicine, Clinical Research Center for Respiratory Disease, West China Hospital, Sichuan University, Chengdu, China
- Department of State Key Laboratory of Respiratory Health and Multimobidity, West China Hospital, Sichuan University, Chengdu, China
| | - Lunbing Tong
- Department of Respiratory Medicine, Chengdu Seventh People’s Hospital/Affiliated Cancer Hospital of Chengdu Medical College, Chengdu, China
| | - Gang Wang
- Department of Respiratory and Critical Care Medicine, Clinical Research Center for Respiratory Disease, West China Hospital, Sichuan University, Chengdu, China
- Department of State Key Laboratory of Respiratory Health and Multimobidity, West China Hospital, Sichuan University, Chengdu, China
| | - Xuelin Zou
- Department of Respiratory Medicine, Chengdu Seventh People’s Hospital/Affiliated Cancer Hospital of Chengdu Medical College, Chengdu, China
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2
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Hu X, Zhu B, Vokes N, Fujimoto J, Rojas Alvarez FR, Heeke S, Moreira AL, Solis LM, Haymaker C, Velcheti V, Sterman DH, Pass HI, Cheng C, Lee JJ, Zhang J, Wei Z, Wu J, Le X, Ostrin E, Toumazis I, Gibbons D, Su D, Fukuoka J, Antonoff MB, Gerber DE, Li C, Kadara H, Wang L, Davis M, Heymach JV, Hannash S, Wistuba I, Dubinett S, Alexandrov L, Lippman S, Spira A, Futreal AP, Reuben A, Zhang J. The evolution of lung adenocarcinoma precursors is associated with chromosomal instability and transition from innate to adaptive immune response/evasion. RESEARCH SQUARE 2024:rs.3.rs-4396272. [PMID: 38798564 PMCID: PMC11118701 DOI: 10.21203/rs.3.rs-4396272/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Studying lung adenocarcinoma (LUAD) early carcinogenesis is challenging, primarily due to the lack of LUAD precursors specimens. We amassed multi-omics data from 213 LUAD and LUAD precursors to identify molecular features underlying LUAD precancer evolution. We observed progressively increasing mutations, chromosomal aberrations, whole genome doubling and genomic instability from precancer to invasive LUAD, indicating aggravating chromosomal instability (CIN). Telomere shortening, a crucial genomic alteration linked to CIN, emerged at precancer stage. Moreover, later-stage lesions demonstrated increasing cancer stemness and decreasing alveolar identity, suggesting epithelial de-differentiation during early LUAD carcinogenesis. The innate immune cells progressively diminished from precancer to invasive LUAD, concomitant with a gradual recruitment of adaptive immune cells (except CD8+ and gamma-delta T cells that decreased in later stages) and upregulation of numerous immune checkpoints, suggesting LUAD precancer evolution is associated with a shift from innate to adaptive immune response and immune evasion mediated by various mechanisms.
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Affiliation(s)
- Xin Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Bo Zhu
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Natalie Vokes
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | | | - Frank R. Rojas Alvarez
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Simon Heeke
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Andre L. Moreira
- Department of Pathology, New York University Langone Medical Center, New York, 10012, USA
| | - Luisa M. Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Cara Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Vamsidhar Velcheti
- Department of Medical oncology, New York University, New York, 10012, USA
| | | | - Harvey I. Pass
- Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, 10016, USA
| | - Chao Cheng
- Department of Medicine, Epidemiology and Population Science, Baylor College of Medicine. Houston, TX, 77030, USA
| | - Jack J. Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Zhubo Wei
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jia Wu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xiuning Le
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Edwin Ostrin
- Department of General Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Iakovos Toumazis
- Department of Health Services Research, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Don Gibbons
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Dan Su
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
- Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Junya Fukuoka
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 8528523, Japan
| | - Mara B. Antonoff
- Department of Thoracic & Cardiovasc Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - David E. Gerber
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Chenyang Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mark Davis
- Moores Cancer Center, UC San Diego School of Medicine, San Diego, CA, 92037, USA
| | - John V. Heymach
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Samir Hannash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ignacio Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Steven Dubinett
- Departments of Medicine and Pathology, University of California Los Angeles and Greater Los Angeles Healthcare System, Los Angeles, CA, 90095, USA
| | - Ludmil Alexandrov
- Moores Cancer Center, UC San Diego School of Medicine, San Diego, CA, 92037, USA
| | - Scott Lippman
- Moores Cancer Center, UC San Diego School of Medicine, San Diego, CA, 92037, USA
| | - Avrum Spira
- Pathology & Laboratory Medicine, and Bioinformatics, Boston University, Boston, MA, 02215, USA
| | - Andrew P. Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Alexandre Reuben
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Lead contact
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Wang Y, Huang Z, Li B, Xue J, Guo C, Bing Z, Zheng Z, Song Y, Xu Y, Huang G, Li H, Yu X, Xia Y, Li R, Si X, Zhang L, Li J, Song L, Xiong Y, Gu D, Song M, Zhou Z, Chen R, Feng Z, Bie Z, Li X, Yang H, Li S, Liang N. Clonal expansion of shared T cell receptors reveals the existence of immune commonality among different lesions of synchronous multiple primary lung cancer. Cancer Immunol Immunother 2024; 73:111. [PMID: 38668781 PMCID: PMC11052747 DOI: 10.1007/s00262-024-03703-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/14/2024] [Indexed: 04/29/2024]
Abstract
The increase in the detection rate of synchronous multiple primary lung cancer (MPLC) has posed remarkable clinical challenges due to the limited understanding of its pathogenesis and molecular features. Here, comprehensive comparisons of genomic and immunologic features between MPLC and solitary lung cancer nodule (SN), as well as different lesions of the same patient, were performed. Compared with SN, MPLC displayed a lower rate of EGFR mutation but higher rates of BRAF, MAP2K1, and MTOR mutation, which function exactly in the upstream and downstream of the same signaling pathway. Considerable heterogeneity in T cell receptor (TCR) repertoire exists among not only different patients but also among different lesions of the same patient. Invasive lesions of MPLC exhibited significantly higher TCR diversity and lower TCR expansion than those of SN. Intriguingly, different lesions of the same patient always shared a certain proportion of TCR clonotypes. Significant clonal expansion could be observed in shared TCR clonotypes, particularly in those existing in all lesions of the same patient. In conclusion, this study provided evidences of the distinctive mutational landscape, activation of oncogenic signaling pathways, and TCR repertoire in MPLC as compared with SN. The significant clonal expansion of shared TCR clonotypes demonstrated the existence of immune commonality among different lesions of the same patient and shed new light on the individually tailored precision therapy for MPLC.
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Affiliation(s)
- Yadong Wang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhicheng Huang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bowen Li
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianchao Xue
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chao Guo
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhongxing Bing
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhibo Zheng
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Song
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuan Xu
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guanghua Huang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haochen Li
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoqing Yu
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yankai Xia
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ruirui Li
- Department of Cardiothoracic Surgery, Civil Aviation General Hospital, Beijing, China
| | - Xiaoyan Si
- Department of Pulmonary and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li Zhang
- Department of Pulmonary and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ji Li
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lan Song
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | | | | | | | | | - Zhe Feng
- Department of Cardiothoracic Surgery, The Sixth Hospital of Beijing, Beijing, China
| | - Zhixin Bie
- Minimally Invasive Tumor Therapies Center, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoguang Li
- Minimally Invasive Tumor Therapies Center, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Huaxia Yang
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
- Department of Rheumatology and Clinical Immunology, National Clinical Research Center for Dermatologic and Immunologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, The Ministry of Education Key Laboratory, Beijing, China.
| | - Shanqing Li
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Naixin Liang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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4
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Parra ER, Zhang J, Duose DY, Gonzalez-Kozlova E, Redman MW, Chen H, Manyam GC, Kumar G, Zhang J, Song X, Lazcano R, Marques-Piubelli ML, Laberiano-Fernandez C, Rojas F, Zhang B, Taing L, Jhaveri A, Geisberg J, Altreuter J, Michor F, Provencher J, Yu J, Cerami E, Moravec R, Kannan K, Luthra R, Alatrash G, Huang HH, Xie H, Patel M, Nie K, Harris J, Argueta K, Lindsay J, Biswas R, Van Nostrand S, Kim-Schulze S, Gray JE, Herbst RS, Wistuba II, Gettinger S, Kelly K, Bazhenova L, Gnjatic S, Lee JJ, Zhang J, Haymaker C. Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial. Clin Cancer Res 2024; 30:1655-1668. [PMID: 38277235 PMCID: PMC11016892 DOI: 10.1158/1078-0432.ccr-23-0251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/06/2023] [Accepted: 01/24/2024] [Indexed: 01/28/2024]
Abstract
PURPOSE Identifying molecular and immune features to guide immune checkpoint inhibitor (ICI)-based regimens remains an unmet clinical need. EXPERIMENTAL DESIGN Tissue and longitudinal blood specimens from phase III trial S1400I in patients with metastatic squamous non-small cell carcinoma (SqNSCLC) treated with nivolumab monotherapy (nivo) or nivolumab plus ipilimumab (nivo+ipi) were subjected to multi-omics analyses including multiplex immunofluorescence (mIF), nCounter PanCancer Immune Profiling Panel, whole-exome sequencing, and Olink. RESULTS Higher immune scores from immune gene expression profiling or immune cell infiltration by mIF were associated with response to ICIs and improved survival, except regulatory T cells, which were associated with worse overall survival (OS) for patients receiving nivo+ipi. Immune cell density and closer proximity of CD8+GZB+ T cells to malignant cells were associated with superior progression-free survival and OS. The cold immune landscape of NSCLC was associated with a higher level of chromosomal copy-number variation (CNV) burden. Patients with LRP1B-mutant tumors had a shorter survival than patients with LRP1B-wild-type tumors. Olink assays revealed soluble proteins such as LAMP3 increased in responders while IL6 and CXCL13 increased in nonresponders. Upregulation of serum CXCL13, MMP12, CSF-1, and IL8 were associated with worse survival before radiologic progression. CONCLUSIONS The frequency, distribution, and clustering of immune cells relative to malignant ones can impact ICI efficacy in patients with SqNSCLC. High CNV burden may contribute to the cold immune microenvironment. Soluble inflammation/immune-related proteins in the blood have the potential to monitor therapeutic benefit from ICI treatment in patients with SqNSCLC.
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Affiliation(s)
- Edwin Roger Parra
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jiexin Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dzifa Yawa Duose
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Edgar Gonzalez-Kozlova
- Department of Oncological Sciences, Mount Sinai, New York, New York
- Tisch Cancer Institute, Mount Sinai, New York, New York
- Precision Immunology Institute, Mount Sinai, New York, New York
- Icahn School of Medicine at Mount Sinai, New York, New York
| | - Mary W. Redman
- SWOG Statistical Center, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Hong Chen
- Department of Thoracic-Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ganiraju C. Manyam
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gayatri Kumar
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rossana Lazcano
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mario L. Marques-Piubelli
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Caddie Laberiano-Fernandez
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Frank Rojas
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Baili Zhang
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Len Taing
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Aashna Jhaveri
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jacob Geisberg
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jennifer Altreuter
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Franziska Michor
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - James Provencher
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Joyce Yu
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ethan Cerami
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Radim Moravec
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, NCI, Bethesda, Maryland
| | - Kasthuri Kannan
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gheath Alatrash
- Department of Stem Cell Transplantation, The University of Texas MD Anderson Cancer, Houston, Texas
| | - Hsin-Hui Huang
- Precision Immunology Institute, Mount Sinai, New York, New York
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Hui Xie
- Precision Immunology Institute, Mount Sinai, New York, New York
| | | | - Kai Nie
- Precision Immunology Institute, Mount Sinai, New York, New York
| | - Jocelyn Harris
- Precision Immunology Institute, Mount Sinai, New York, New York
| | | | - James Lindsay
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Roshni Biswas
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Stephen Van Nostrand
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Seunghee Kim-Schulze
- Department of Oncological Sciences, Mount Sinai, New York, New York
- Tisch Cancer Institute, Mount Sinai, New York, New York
- Precision Immunology Institute, Mount Sinai, New York, New York
- Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Roy S. Herbst
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Ignacio I. Wistuba
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Karen Kelly
- International Association for the Study of Lung Cancer, Denver, Colorado
| | - Lyudmila Bazhenova
- University of California San Diego Moores Cancer Center, La Jolla, California
| | - Sacha Gnjatic
- Department of Oncological Sciences, Mount Sinai, New York, New York
- Tisch Cancer Institute, Mount Sinai, New York, New York
- Precision Immunology Institute, Mount Sinai, New York, New York
- Icahn School of Medicine at Mount Sinai, New York, New York
| | - J. Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianjun Zhang
- Department of Thoracic-Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cara Haymaker
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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5
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Wang X, Shi J, Liu Z. Advancements in the diagnosis and treatment of sub‑centimeter lung cancer in the era of precision medicine (Review). Mol Clin Oncol 2024; 20:28. [PMID: 38414512 PMCID: PMC10895471 DOI: 10.3892/mco.2024.2726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 01/10/2024] [Indexed: 02/29/2024] Open
Abstract
Lung cancer is the malignancy with the highest global mortality rate and imposes a substantial burden on society. The increasing popularity of lung cancer screening has led to increasing number of patients being diagnosed with pulmonary nodules due to their potential for malignancy, causing considerable distress in the affected population. However, the diagnosis and treatment of sub-centimeter grade pulmonary nodules remain controversial. The evolution of genetic detection technology and the development of targeted drugs have positioned the diagnosis and treatment of lung cancer in the precision medicine era, leading to a marked improvement in the survival rate of patients with lung cancer. It has been established that lung cancer driver genes serve a key role in the development and progression of sub-centimeter lung cancer. The present review aimed to consolidate the findings on genes associated with sub-centimeter lung cancer, with the intent of serving as a reference for future studies and the personalized management of sub-centimeter lung cancer through genetic testing.
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Affiliation(s)
- Xiao Wang
- Department of Thoracic Surgery, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
| | - Jingwei Shi
- Department of Thoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu 210008, P.R. China
| | - Zhengcheng Liu
- Department of Thoracic Surgery, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
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6
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Wang Q, Xie B, Sun J, Li Z, Xiao D, Tao Y, She X. An Investigation of the Immune Microenvironment and Genome during Lung Adenocarcinoma Development. J Cancer 2024; 15:1687-1700. [PMID: 38370388 PMCID: PMC10869965 DOI: 10.7150/jca.92101] [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: 11/10/2023] [Accepted: 01/09/2024] [Indexed: 02/20/2024] Open
Abstract
Background: Adenocarcinoma in situ (AIS) and minimally invasive adenocarcinoma (MIA) are two consecutive pathological processes that occur before invasive lung adenocarcinoma (LUAD). However, our understanding of the immune editing patterns during the progression of LUAD remains limited. Furthermore, we know very little about whether alterations in driver genes are involved in forming the tumor microenvironment (TME). Therefore, it is necessary to elucidate the regulatory role of TME in LUAD development from multiple dimensions, including immune cell infiltration, molecular mutation events, and oncogenic signaling pathways. Methods: We collected 145 surgically resected pulmonary nodule specimens, including 28 cases of AIS, 52 cases of MIA, and 65 cases of LUAD. Immunohistochemistry (IHC) was used to detect the expression of immune markers CD3, CD4, CD8, CD68 and programmed death ligand 1 (PD-L1). Genomic data and TMB generated by targeted next-generation sequencing (NGS). Results: LUAD exhibited higher levels of immune cell infiltration, tumor mutation burden (TMB), and activation of oncogenic pathways compared to AIS and MIA. In LUAD, compared to epidermal growth factor receptor (EGFR) single mutation and wild-type (WT) samples, cases with EGFR co-mutations showed a more pronounced rise in the CD4/CD8 ratio and CD68 infiltration. Patients with low-density lipoprotein (LDL) receptor-related protein 1B (LRP1B) mutation have higher TMB and PD-L1 expression. The transition from AIS to LUAD tends to shift the TME towards the PD-L1+CD8+ subtype (adaptive resistance). Progression-associated mutations (PAMs) were enriched in the lymphocyte differentiation pathway and related to exhausted cells' phenotype. Conclusion: Tumor-infiltrating immune cells tend to accumulate as the depth of LUAD invasion increases, but subsequently develop into an immune exhaustion and immune escape state. Mutations in EGFR and LRP1B could potentially establish an immune niche that fosters tumor growth. PAMs in LUAD may accelerate disease progression by promoting T cell differentiation into an exhausted state.
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Affiliation(s)
- Qingyi Wang
- Department of Pathology, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410078 China
| | - Bin Xie
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410078 China
| | - Jingyue Sun
- Department of Pathology, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410078 China
| | - Zisheng Li
- Department of Pathology, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410078 China
| | - Desheng Xiao
- Department of Pathology, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410078 China
| | - Yongguang Tao
- Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
- Key Laboratory of Carcinogenesis and Cancer Invasion (Central South University), Ministry of Education, Hunan, 410078, China
| | - Xiaoling She
- Department of Pathology, The Second Xiangya Hospital, Central South University Changsha, Hunan, 410011, China
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7
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Zhang Y, Fu F, Zhang Q, Li L, Liu H, Deng C, Xue Q, Zhao Y, Sun W, Han H, Gao Z, Guo C, Zheng Q, Hu H, Sun Y, Li Y, Ding C, Chen H. Evolutionary proteogenomic landscape from pre-invasive to invasive lung adenocarcinoma. Cell Rep Med 2024; 5:101358. [PMID: 38183982 PMCID: PMC10829798 DOI: 10.1016/j.xcrm.2023.101358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 08/29/2023] [Accepted: 12/11/2023] [Indexed: 01/08/2024]
Abstract
Lung adenocarcinoma follows a stepwise progression from pre-invasive to invasive. However, there remains a knowledge gap regarding molecular events from pre-invasive to invasive. Here, we conduct a comprehensive proteogenomic analysis comprising whole-exon sequencing, RNA sequencing, and proteomic and phosphoproteomic profiling on 98 pre-invasive and 99 invasive lung adenocarcinomas. The deletion of chr4q12 contributes to the progression from pre-invasive to invasive adenocarcinoma by downregulating SPATA18, thus suppressing mitophagy and promoting cell invasion. Proteomics reveals diverse enriched pathways in normal lung tissues and pre-invasive and invasive adenocarcinoma. Proteomic analyses identify three proteomic subtypes, which represent different stages of tumor progression. We also illustrate the molecular characterization of four immune clusters, including endothelial cells, B cells, DCs, and immune depression subtype. In conclusion, this comprehensive proteogenomic study characterizes the molecular architecture and hallmarks from pre-invasive to invasive lung adenocarcinoma, guiding the way to a deeper understanding of the tumorigenesis and progression of this disease.
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Affiliation(s)
- Yang Zhang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Fangqiu Fu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Qiao Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Lingling Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Hui Liu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai 200433, China; State Key Laboratory Cell Differentiation and Regulation, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Chaoqiang Deng
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Qianqian Xue
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Yue Zhao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Wenrui Sun
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Han Han
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Zhendong Gao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Chunmei Guo
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Qiang Zheng
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Hong Hu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yihua Sun
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yuan Li
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China.
| | - Chen Ding
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai 200433, China.
| | - Haiquan Chen
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Institute of Thoracic Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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8
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Yang Z, Zhang Y, Tang L, Yang X, Song L, Shen C, Zvyagin AV, Li Y, Yang B, Lin Q. "All in one" nanoprobe Au-TTF-1 for target FL/CT bioimaging, machine learning technology and imaging-guided photothermal therapy against lung adenocarcinoma. J Nanobiotechnology 2024; 22:22. [PMID: 38184620 PMCID: PMC10770976 DOI: 10.1186/s12951-023-02280-9] [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: 11/04/2023] [Accepted: 12/19/2023] [Indexed: 01/08/2024] Open
Abstract
The accurate preoperative diagnosis and tracking of lung adenocarcinoma is hindered by non-targeting and diffusion of dyes used for marking tumors. Hence, there is an urgent need to develop a practical nanoprobe for tracing lung adenocarcinoma precisely even treating them noninvasively. Herein, Gold nanoclusters (AuNCs) conjugate with thyroid transcription factor-1 (TTF-1) antibody, then multifunctional nanoprobe Au-TTF-1 is designed and synthesized, which underscores the paramount importance of advancing the machine learning diagnosis and bioimaging-guided treatment of lung adenocarcinoma. Bright fluorescence (FL) and strong CT signal of Au-TTF-1 set the stage for tracking. Furthermore, the high specificity of TTF-1 antibody facilitates selective targeting of lung adenocarcinoma cells as compared to common lung epithelial cells, so machine learning software Lung adenocarcinoma auxiliary detection system was designed, which combined with Au-TTF-1 to assist the intelligent recognition of lung adenocarcinoma jointly. Besides, Au-TTF-1 not only contributes to intuitive and targeted visualization, but also guides the following noninvasive photothermal treatment. The boundaries of tumor are light up by Au-TTF-1 for navigation, it penetrates into tumor and implements noninvasive photothermal treatment, resulting in ablating tumors in vivo locally. Above all, Au-TTF-1 serves as a key platform for target bio-imaging navigation, machine learning diagnosis and synergistic PTT as a single nanoprobe, which demonstrates attractive performance on lung adenocarcinoma.
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Affiliation(s)
- Zhe Yang
- State Key Laboratory of Supramolecular Structure and Material, College of Chemistry, Jilin University, Changchun, 130012, China
| | - Yujia Zhang
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, 130021, China
| | - Lu Tang
- Department of Breast, China-Japan Union Hospital of Jilin University, Changchun, 130031, China
| | - Xiao Yang
- College of Computer Science and Technology Jilin University, Changchun, 130012, China
| | - Lei Song
- Department of Breast, China-Japan Union Hospital of Jilin University, Changchun, 130031, China
| | - Chun Shen
- College of Computer Science and Technology Jilin University, Changchun, 130012, China
| | - Andrei V Zvyagin
- Australian Research Council Centre of Excellence for Nanoscale Biophotonics, Macquarie University, Sydney, NSW, 2109, Australia
| | - Yang Li
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, 130021, China.
| | - Bai Yang
- State Key Laboratory of Supramolecular Structure and Material, College of Chemistry, Jilin University, Changchun, 130012, China
| | - Quan Lin
- State Key Laboratory of Supramolecular Structure and Material, College of Chemistry, Jilin University, Changchun, 130012, China.
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9
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Zhang J, Li Y, Yang Y, Huang J, Sun Y, Zhang X, Kong X. A novel iTreg-related signature for prognostic prediction in lung adenocarcinoma. Cancer Sci 2024; 115:109-124. [PMID: 38015097 PMCID: PMC10823293 DOI: 10.1111/cas.16015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/09/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is the most common subtype of lung cancer. Most patients are diagnosed at an advanced stage, therefore it is crucial to identify novel prognostic biomarkers for LUAD. As important regulatory cells, inducible regulatory T cells (iTregs) play a vital role in immune suppression and are important for the maintenance of immune homeostasis. This study explored the prognostic value and therapeutic effects of iTreg-related genes in LUAD. Data for LUAD patients, including immune infiltration data, RNA sequencing data, and clinical features, were acquired from The Cancer Genome Atlas, Gene Expression Omnibus, and Tumor Immune Single-cell Hub 2 databases. Immune-related subgroups with different infiltration patterns and iTreg-related genes were identified through univariate and multivariate Cox regression analyses and weighted correlation network analysis. Functional enrichment analyses were performed to explore the underlying mechanisms of iTreg-related genes. A prognostic risk signature was constructed using Cox regression analysis with the least absolute shrinkage and selection operator penalty. The ESTIMATE algorithm was applied to determine the immune status of LUAD patients. We applied the constructed signature to predict chemosensitivity and performed single-cell RNA sequencing analysis. The infiltration of iTregs was identified as an independent factor for predicting patient outcomes. We constructed a prognostic signature based on seven iTreg-related genes (GIMAP5, SLA, MS4A7, ZNF366, POU2AF1, MRPL12, and COL5A1), which was applied to subdivide patients into high- and low-risk subgroups. Our results revealed that patients in the iTreg-related low-risk subgroup had a better prognosis and possibly greater sensitivity to traditional chemotherapy. Our study provides a novel iTreg-related signature to elucidate the mechanisms underlying LUAD prognosis and promote individualized chemotherapy treatment.
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Affiliation(s)
- Jian Zhang
- Department of Thoracic SurgeryHarbin Medical University Cancer HospitalHarbinHeilongjiangChina
| | - Yan Li
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiangChina
| | - Yue Yang
- Institute of Cancer Prevention and Treatment, Harbin Medical UniversityHarbinHeilongjiangChina
| | - Jian Huang
- The Fourth Department of Medical OncologyHarbin Medical University Cancer HospitalHarbinHeilongjiangChina
| | - Yue Sun
- The Academic Department of Science and TechnologyHarbin Medical University Cancer HospitalHarbinHeilongjiangChina
| | - Xi Zhang
- Department of AnaesthesiologyHarbin Medical University Cancer HospitalHarbinHeilongjiangChina
| | - Xianglong Kong
- Department of Thoracic SurgeryHarbin Medical University Cancer HospitalHarbinHeilongjiangChina
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10
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Haga Y, Sakamoto Y, Kajiya K, Kawai H, Oka M, Motoi N, Shirasawa M, Yotsukura M, Watanabe SI, Arai M, Zenkoh J, Shiraishi K, Seki M, Kanai A, Shiraishi Y, Yatabe Y, Matsubara D, Suzuki Y, Noguchi M, Kohno T, Suzuki A. Whole-genome sequencing reveals the molecular implications of the stepwise progression of lung adenocarcinoma. Nat Commun 2023; 14:8375. [PMID: 38102134 PMCID: PMC10724178 DOI: 10.1038/s41467-023-43732-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
The mechanism underlying the development of tumors, particularly at early stages, still remains mostly elusive. Here, we report whole-genome long and short read sequencing analysis of 76 lung cancers, focusing on very early-stage lung adenocarcinomas such as adenocarcinoma in situ (AIS) and minimally invasive adenocarcinoma. The obtained data is further integrated with bulk and spatial transcriptomic data and epigenomic data. These analyses reveal key events in lung carcinogenesis. Minimal somatic mutations in pivotal driver mutations and essential proliferative factors are the only detectable somatic mutations in the very early-stage of AIS. These initial events are followed by copy number changes and global DNA hypomethylation. Particularly, drastic changes are initiated at the later AIS stage, i.e., in Noguchi type B tumors, wherein cancer cells are exposed to the surrounding microenvironment. This study sheds light on the pathogenesis of lung adenocarcinoma from integrated pathological and molecular viewpoints.
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Affiliation(s)
- Yasuhiko Haga
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Yoshitaka Sakamoto
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Keiko Kajiya
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Hitomi Kawai
- Department of Diagnostic Pathology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Miho Oka
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
- Ono Pharmaceutical Co., Ltd., Ibaraki, Japan
| | - Noriko Motoi
- Department of Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Department of Pathology, Saitama Cancer Center, 780 Komuro, Ina, Kita-Adachi-gun, Saitama, 362-0806, Japan
| | - Masayuki Shirasawa
- Department of Thoracic Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Division of Genome Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Masaya Yotsukura
- Department of Thoracic Surgery, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Shun-Ichi Watanabe
- Department of Thoracic Surgery, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Miyuki Arai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Junko Zenkoh
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Department of Clinical Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Akinori Kanai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yasushi Yatabe
- Department of Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Daisuke Matsubara
- Department of Diagnostic Pathology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.
| | - Masayuki Noguchi
- Department of Diagnostic Pathology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
- Clinical Cancer Research Division, Shonan Research Institute of Innovative Medicine, Shonan Kamakura General Hospital, 1370-1 Okamoto, Kamakura, Kanagawa, 247-8533, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Ayako Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.
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11
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Chen P, Rojas FR, Hu X, Serrano A, Zhu B, Chen H, Hong L, Bandyoyadhyay R, Aminu M, Kalhor N, Lee JJ, El Hussein S, Khoury JD, Pass HI, Moreira AL, Velcheti V, Sterman DH, Fukuoka J, Tabata K, Su D, Ying L, Gibbons DL, Heymach JV, Wistuba II, Fujimoto J, Solis Soto LM, Zhang J, Wu J. Pathomic Features Reveal Immune and Molecular Evolution From Lung Preneoplasia to Invasive Adenocarcinoma. Mod Pathol 2023; 36:100326. [PMID: 37678674 PMCID: PMC10841057 DOI: 10.1016/j.modpat.2023.100326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 08/12/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023]
Abstract
Recent statistics on lung cancer, including the steady decline of advanced diseases and the dramatically increasing detection of early-stage diseases and indeterminate pulmonary nodules, mark the significance of a comprehensive understanding of early lung carcinogenesis. Lung adenocarcinoma (ADC) is the most common histologic subtype of lung cancer, and atypical adenomatous hyperplasia is the only recognized preneoplasia to ADC, which may progress to adenocarcinoma in situ (AIS) and minimally invasive adenocarcinoma (MIA) and eventually to invasive ADC. Although molecular evolution during early lung carcinogenesis has been explored in recent years, the progress has been significantly hindered, largely due to insufficient materials from ADC precursors. Here, we employed state-of-the-art deep learning and artificial intelligence techniques to robustly segment and recognize cells on routinely used hematoxylin and eosin histopathology images and extracted 9 biology-relevant pathomic features to decode lung preneoplasia evolution. We analyzed 3 distinct cohorts (Japan, China, and United States) covering 98 patients, 162 slides, and 669 regions of interest, including 143 normal, 129 atypical adenomatous hyperplasia, 94 AIS, 98 MIA, and 205 ADC. Extracted pathomic features revealed progressive increase of atypical epithelial cells and progressive decrease of lymphocytic cells from normal to AAH, AIS, MIA, and ADC, consistent with the results from tissue-consuming and expensive molecular/immune profiling. Furthermore, pathomics analysis manifested progressively increasing cellular intratumor heterogeneity along with the evolution from normal lung to invasive ADC. These findings demonstrated the feasibility and substantial potential of pathomics in studying lung cancer carcinogenesis directly from the low-cost routine hematoxylin and eosin staining.
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Affiliation(s)
- Pingjun Chen
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Frank R Rojas
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xin Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alejandra Serrano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bo Zhu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hong Chen
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lingzhi Hong
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rukhmini Bandyoyadhyay
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Muhammad Aminu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Neda Kalhor
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Siba El Hussein
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York
| | - Joseph D Khoury
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Harvey I Pass
- Department of Surgery, NYU Langone Health, New York, New York
| | - Andre L Moreira
- Department of Pathology, NYU Langone Health, New York, New York
| | - Vamsidhar Velcheti
- Department of Medicine, NYU Grossman School of Medicine, New York, New York
| | - Daniel H Sterman
- Department of Medicine, NYU Grossman School of Medicine, New York, New York; Department of Cardiothoracic Surgery, NYU Grossman School of Medicine, New York, New York
| | - Junya Fukuoka
- Department of Pathology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Kazuhiro Tabata
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Dan Su
- Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| | - Lisha Ying
- Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Luisa M Solis Soto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Jia Wu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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12
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Zhang X, Liang B, Huang Y, Meng H, Li Z, Du J, Zhou L, Zhong Y, Wang B, Lin X, Yu G, Chen X, Lu W, Chen Z, Yang X, Huang Z. Behind the Indolent Facade: Uncovering the Molecular Features and Malignancy Potential in Lung Minimally Invasive Adenocarcinoma by Single-Cell Transcriptomics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303753. [PMID: 37991139 PMCID: PMC10754125 DOI: 10.1002/advs.202303753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 10/28/2023] [Indexed: 11/23/2023]
Abstract
The increased use of low-dose computed tomography screening has led to more frequent detection of early stage lung tumors, including minimally invasive adenocarcinoma (MIA). To unravel the intricacies of tumor cells and the immune microenvironment in MIA, this study performs a comprehensive single-cell transcriptomic analysis and profiles the transcriptomes of 156,447 cells from fresh paired MIA and invasive adenocarcinoma (IA) tumor samples, peripheral blood mononuclear cells, and adjacent normal tissue samples from three patients with synchronous multiple primary lung adenocarcinoma. This study highlights a connection and heterogeneity between the tumor ecosystem of MIA and IA. MIA tumor cells exhibited high expression of aquaporin-1 and angiotensin II receptor type 2 and a basal-like molecular character. Furthermore, it identifies that cathepsin B+ tumor-associated macrophages may over-activate CD8+ T cells in MIA, leading to an enrichment of granzyme K+ senescent CD8+ T cells, indicating the possibility of malignant progression behind the indolent appearance of MIA. These findings are further validated in 34 MIA and 35 IA samples by multiplexed immunofluorescence. These findings provide valuable insights into the mechanisms that maintain the indolent nature and prompt tumor progression of MIA and can be used to develop more effective therapeutic targets and strategies for MIA patients.
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Affiliation(s)
- Xin Zhang
- Department of Thoracic SurgeryThe First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory HealthGuangzhou510140China
| | - Boxuan Liang
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Yuji Huang
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Hao Meng
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Zhiming Li
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Jiaxin Du
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Lang Zhou
- Department of BioinformaticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Yizhou Zhong
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Bo Wang
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Xi Lin
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Guangchuang Yu
- Department of BioinformaticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Xuewei Chen
- Department of Thoracic SurgeryThe First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory HealthGuangzhou510140China
| | - Weixiang Lu
- Department of Thoracic SurgeryThe First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory HealthGuangzhou510140China
| | - Zhe‐Sheng Chen
- College of Pharmacy and Health SciencesSt. John's UniversityQueensNY11439USA
| | - Xingfen Yang
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Zhenlie Huang
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical UniversityGuangzhou510515China
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13
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Wang Z, Yang L, Wang W, Zhou H, Chen J, Ma Z, Wang X, Zhang Q, Liu H, Zhou C, Guo Z, Zhang X. Comparative immunological landscape between pre- and early-stage LUAD manifested as ground-glass nodules revealed by scRNA and scTCR integrated analysis. Cell Commun Signal 2023; 21:325. [PMID: 37957625 PMCID: PMC10644515 DOI: 10.1186/s12964-023-01322-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 09/16/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Mechanism underlying the malignant progression of precancer to early-stage lung adenocarcinoma (LUAD) as well as their indolence nature remains elusive. METHODS Single-cell RNA sequencing (scRNA) with simultaneous T cell receptor (TCR) sequencing on 5 normal lung tissues, 3 precancerous and 4 early-stage LUAD manifested as pulmonary ground-glass nodules (GGNs) were performed. RESULTS Through this integrated analysis, we have delineated five key modules that drive the malignant progression of early-stage LUAD in a disease stage-dependent manner. These modules are related to cell proliferation and metabolism, immune response, mitochondria, cilia, and cell adhesion. We also find that the tumor micro-environment (TME) of early-stage LUAD manifested as GGN are featured with regulatory T (Tregs) cells accumulation with three possible origins, and loss-functional state (decreased clonal expansion and cytotoxicity) of CD8 + T cells. Instead of exhaustion, the CD8 + T cells are featured with a shift to memory phenotype, which is significantly different from the late stage LUAD. Furthermore, we have identified monocyte-derived macrophages that undergo a lipid-phenotype transition and may contribute to the suppressive TME. Intense interaction between stromal cells, myeloid cells including lipid associated macrophages and LAMP3 + DCs, and lymphocytes were also characterized. CONCLUSIONS Our work provides new insight into the molecular and cellular mechanism underlying malignant progression of LUAD manifested as GGN, and pave way for novel immunotherapies for GGN. Video Abstract.
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Affiliation(s)
- Ziqi Wang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Li Yang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Wenqiang Wang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Huanhuan Zhou
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Juan Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zeheng Ma
- Department of Thoracic Surgery Department, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Xiaoyan Wang
- Department of Pathological Department, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Quncheng Zhang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Haiyang Liu
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Chao Zhou
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Zhiping Guo
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China.
- Henan Provincial Key Laboratory of Chronic Diseases and Health Management, Zhengzhou, 450003, Henan, China.
| | - Xiaoju Zhang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China.
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14
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Hu X, Ren J, Xue Q, Luan R, Ding D, Tan J, Su X, Yang J. Anti‑PD‑1/PD‑L1 and anti‑CTLA‑4 associated checkpoint inhibitor pneumonitis in non‑small cell lung cancer: Occurrence, pathogenesis and risk factors (Review). Int J Oncol 2023; 63:122. [PMID: 37681488 PMCID: PMC10552702 DOI: 10.3892/ijo.2023.5570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/22/2023] [Indexed: 09/09/2023] Open
Abstract
Immune checkpoint inhibitors (ICIs) play a significant anti‑tumor role in the management of non‑small cell lung cancer. The most broadly used ICIs are anti‑programmed death 1 (PD‑1), anti‑programmed cell death‑ligand 1, and anti‑cytotoxic T lymphocyte‑associated antigen‑4 monoclonal antibody. Compared with traditional chemotherapy, ICIs have the advantages of greater efficiency and more specific targeting. However, the resulting immune‑related adverse events limit the clinical application of ICIs, especially checkpoint inhibitor pneumonitis (CIP). CIP chiefly occurs within 6 months of administration of ICIs. Excessive activation and amplification of cytotoxic T lymphocytes, helper T cells, downregulation of regulatory T cells, and over‑secretion of pro‑inflammatory cytokines are the dominant mechanisms underlying the pathophysiology of CIP. The dysregulation of innate immune cells, such as an increase in inflammatory monocytes, dendritic cells, neutrophils and M1 polarization of macrophages, an increase in IL‑10 and IL‑35, and a decrease in eosinophils, may underlie CIP. Although contested, several factors may accelerate CIP, such as a history of previous respiratory disease, radiotherapy, chemotherapy, administration of epidermal growth factor receptor tyrosine kinase inhibitors, PD‑1 blockers, first‑line application of ICIs, and combined immunotherapy. Interestingly, first‑line ICIs plus chemotherapy may reduce CIP. Steroid hormones remain the primary treatment strategy against grade ≥2 CIP, although cytokine blockers are promising therapeutic agents. Herein, the current research on CIP occurrence, clinical and radiological characteristics, pathogenesis, risk factors, and management is summarized to further expand our understanding, clarify the prognosis, and guide treatment.
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Affiliation(s)
- Xiao Hu
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Jilin University, Changchun, Jilin 130041
| | - Jin Ren
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Jilin University, Changchun, Jilin 130041
| | - Qianfei Xue
- Department of Respiratory Medicine, Hospital of Jilin University, Changchun, Jilin 130012,
P.R. China
| | - Rumei Luan
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Jilin University, Changchun, Jilin 130041
| | - Dongyan Ding
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Jilin University, Changchun, Jilin 130041
| | - Jie Tan
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Jilin University, Changchun, Jilin 130041
| | - Xin Su
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Jilin University, Changchun, Jilin 130041
| | - Junling Yang
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Jilin University, Changchun, Jilin 130041
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15
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Liu Y, Wang H, Zhao X, Zhang J, Zhao Z, Lian X, Zhang J, Kong F, Hu T, Wang T, Li X, Wang L, Wang D, Li C, Luan H, Liu X, Wang C, Jiang Y, Li X, Li F, Ji S, Wang Y, Li Z. Targeting the Immunoglobulin IGSF9 Enhances Antitumor T-cell Activity and Sensitivity to Anti-PD-1 Immunotherapy. Cancer Res 2023; 83:3385-3399. [PMID: 37506192 DOI: 10.1158/0008-5472.can-22-3115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 02/14/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023]
Abstract
Immune checkpoints modulate the immune response and represent important immunotherapy targets for cancer treatment. However, as many tumors are resistant to current immune checkpoint inhibitors, the discovery of novel immune checkpoints could facilitate the development of additional immunotherapeutic strategies to improve patient responses. Here, we identified increased expression of the adhesion molecule immunoglobulin superfamily member 9 (IGSF9) in tumor cells and tumor-infiltrating immune cells across multiple cancer types. IGSF9 overexpression or knockout in tumor cells did not alter cell proliferation in vitro or tumor growth in immunocompromised mice. Alternatively, IGSF9 deficient tumor cells lost the ability to suppress T-cell proliferation and exhibited reduced growth in immunocompetent mice. Similarly, growth of tumor cells was reduced in IGSF9 knockout syngeneic and humanized mice, accompanied by increased tumor-infiltrating T cells. Mechanistically, the extracellular domain (ECD) of IGSF9 bound to T cells and inhibited their proliferation and activation, and the tumor-promoting effect of IGSF9 ECD was reversed by CD3+ T-cell depletion. Anti-IGSF9 antibody treatment inhibited tumor growth and enhanced the antitumor efficacy of anti-programmed cell death protein 1 immunotherapy. Single-cell RNA sequencing revealed tumor microenvironment remodeling from tumor promoting to tumor suppressive following anti-IGSF9 treatment. Together, these results indicate that IGSF9 promotes tumor immune evasion and is a candidate immune checkpoint target. SIGNIFICANCE IGSF9 is an immune checkpoint regulator that suppresses T-cell activation in cancer and can be targeted to stimulate antitumor immunity and inhibit tumor growth.
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Affiliation(s)
- Yifan Liu
- Department of Biochemistry and Molecular Biology, Shandong Tumor Immunotherapy Research Innovation Team, Binzhou Medical University, Yantai, Shandong, P.R. China
| | - Hongying Wang
- Department of Biochemistry and Molecular Biology, Shandong Tumor Immunotherapy Research Innovation Team, Binzhou Medical University, Yantai, Shandong, P.R. China
| | - Xinyu Zhao
- Department of Biochemistry and Molecular Biology, Shandong Tumor Immunotherapy Research Innovation Team, Binzhou Medical University, Yantai, Shandong, P.R. China
| | - Jiashen Zhang
- Department of Biochemistry and Molecular Biology, Shandong Tumor Immunotherapy Research Innovation Team, Binzhou Medical University, Yantai, Shandong, P.R. China
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Shandong Agricultural University, Taian, Shandong, P.R. China
| | - Zhiling Zhao
- Department of Biochemistry and Molecular Biology, Shandong Tumor Immunotherapy Research Innovation Team, Binzhou Medical University, Yantai, Shandong, P.R. China
| | - Xia Lian
- Department of Biochemistry and Molecular Biology, Shandong Tumor Immunotherapy Research Innovation Team, Binzhou Medical University, Yantai, Shandong, P.R. China
| | - Juan Zhang
- Department of Biochemistry and Molecular Biology, Shandong Tumor Immunotherapy Research Innovation Team, Binzhou Medical University, Yantai, Shandong, P.R. China
| | - Feng Kong
- Shandong Institute of Clinical Medicine, Shandong Provincial Hospital, Jinan, Shandong, P.R. China
| | - Tao Hu
- Department of thoracic surgery, Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, Shandong, P.R. China
| | - Ting Wang
- Department of Pathology, Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, Shandong, P.R. China
| | - Xiaohua Li
- Yantai Central Blood Station, Yantai, Shandong, P.R. China
| | - Lei Wang
- Department of Biochemistry and Molecular Biology, Shandong Tumor Immunotherapy Research Innovation Team, Binzhou Medical University, Yantai, Shandong, P.R. China
| | - Dapeng Wang
- Department of Biochemistry and Molecular Biology, Shandong Tumor Immunotherapy Research Innovation Team, Binzhou Medical University, Yantai, Shandong, P.R. China
| | - Chunling Li
- Department of Biochemistry and Molecular Biology, Shandong Tumor Immunotherapy Research Innovation Team, Binzhou Medical University, Yantai, Shandong, P.R. China
| | - Huiwen Luan
- Department of Biochemistry and Molecular Biology, Shandong Tumor Immunotherapy Research Innovation Team, Binzhou Medical University, Yantai, Shandong, P.R. China
| | - Xiaoli Liu
- Department of Biochemistry and Molecular Biology, Shandong Tumor Immunotherapy Research Innovation Team, Binzhou Medical University, Yantai, Shandong, P.R. China
| | - Chunyan Wang
- Department of Biochemistry and Molecular Biology, Shandong Tumor Immunotherapy Research Innovation Team, Binzhou Medical University, Yantai, Shandong, P.R. China
| | - Yun Jiang
- Department of Biochemistry and Molecular Biology, Shandong Tumor Immunotherapy Research Innovation Team, Binzhou Medical University, Yantai, Shandong, P.R. China
| | - Xiaomin Li
- Department of Biochemistry and Molecular Biology, Shandong Tumor Immunotherapy Research Innovation Team, Binzhou Medical University, Yantai, Shandong, P.R. China
| | - Fangmin Li
- Department of Biochemistry and Molecular Biology, Shandong Tumor Immunotherapy Research Innovation Team, Binzhou Medical University, Yantai, Shandong, P.R. China
| | - Shuhao Ji
- Department of Biochemistry and Molecular Biology, Shandong Tumor Immunotherapy Research Innovation Team, Binzhou Medical University, Yantai, Shandong, P.R. China
| | - Yaopeng Wang
- Department of thoracic surgery, Qingdao Hospital, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, Shandong, P.R. China
| | - Zunling Li
- Department of Biochemistry and Molecular Biology, Shandong Tumor Immunotherapy Research Innovation Team, Binzhou Medical University, Yantai, Shandong, P.R. China
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16
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Ying L, Zhang C, Reuben A, Tian Y, Jin J, Wang C, Bai J, Liu X, Fang J, Feng T, Xu C, Zhu R, Huang M, Lyu Y, Lu T, Pan X, Zhang J, Su D. Immune-active tumor-adjacent tissues are associated with favorable prognosis in stage I lung squamous cell carcinoma. iScience 2023; 26:107732. [PMID: 37694148 PMCID: PMC10483046 DOI: 10.1016/j.isci.2023.107732] [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: 03/05/2023] [Revised: 07/07/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023] Open
Abstract
The immunogenomic features of tumor-adjacent lungs (TALs) in stage I lung squamous cell carcinoma (LUSC) are not clear. Multiomics analyses of tumor tissues and paired TALs from 59 stage I LUSC patients were performed. Compared to tumors, TALs exhibited a better-preserved immune contexture indicated by upregulation of immune pathways, increased immune infiltration, and higher expression of immune effector molecules. Notably, TALs had no mutations in PTEN and KEAP1, a lower incidence of human leukocyte antigen (HLA) loss and higher expression of HLA class I genes, major histocompatibility complex (MHC) I chaperones, and interferon (IFN)-γ-associated genes. Digital spatial profiling validated the generally higher immune infiltration in TALs and revealed a higher level of immune heterogeneity in LUSC tumors. Importantly, patients with higher immune infiltration in TALs had significantly longer survival, while high immune heterogeneity was associated with inferior patient survival. Our work can be considered in the selection of patients for adjuvant therapy, especially immunotherapy.
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Affiliation(s)
- Lisha Ying
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | | | - Alexandre Reuben
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yiping Tian
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Jiaoyue Jin
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Canming Wang
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Jing Bai
- Geneplus-Beijing Institute, Beijing, China
| | - Xinyuan Liu
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- The Second Clinical Medical College, Zhejiang Chinese Medicine University, Hangzhou, Zhejiang 310053, China
| | - Jianfei Fang
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Tingting Feng
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Chenyang Xu
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Rui Zhu
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Minran Huang
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yingqi Lyu
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Department of Oncology, The First Clinical Medical College of Wenzhou Medical University, Wenzhou, Zhejiang 325015, China
| | - Tingting Lu
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Department of Oncology, The First Clinical Medical College of Wenzhou Medical University, Wenzhou, Zhejiang 325015, China
| | - Xiaodan Pan
- Human Tissue Bank, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Jianjun Zhang
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dan Su
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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17
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Bowen MB, Helmink BA, Wargo JA, Yates MS. TIME for Bugs: The Immune Microenvironment and Microbes in Precancer. Cancer Prev Res (Phila) 2023; 16:497-505. [PMID: 37428011 PMCID: PMC10542944 DOI: 10.1158/1940-6207.capr-23-0087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/14/2023] [Accepted: 07/07/2023] [Indexed: 07/11/2023]
Abstract
Major advances in our understanding of the tumor immune microenvironment (TIME) in established cancer have been made, including the influence of host-intrinsic (host genomics) and -extrinsic factors (such as diet and the microbiome) on treatment response. Nonetheless, the immune and microbiome milieu across the spectrum of precancerous tissue and early neoplasia is a growing area of interest. There are emerging data describing the contribution of the immune microenvironment and microbiota on benign and premalignant tissues, with opportunities to target these factors in cancer prevention and interception. Throughout this review, we provide rationale for not only the critical need to further elucidate the premalignant immune microenvironment, but also for the utility of pharmacologic and lifestyle interventions to alter the immune microenvironment of early lesions to reverse carcinogenesis. Novel research methodologies, such as implementing spatial transcriptomics and proteomics, in combination with innovative sampling methods will advance precision targeting of the premalignant immune microenvironment. Additional studies defining the continuum of immune and microbiome evolution, which emerges in parallel with tumor development, will provide novel opportunities for cancer interception at the earliest steps in carcinogenesis.
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Affiliation(s)
- Mikayla Borthwick Bowen
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Beth A Helmink
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Jennifer A Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Melinda S Yates
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
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18
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Xiang C, Zhang M, Shang Z, Chen S, Zhao J, Ding B, Jiang D, Zhu Q, Teng H, Zhu L, Shao J, Zhao R, Ye M, Yu Y, Han Y. Single-cell profiling reveals the trajectory of FOLR2-expressing tumor-associated macrophages to regulatory T cells in the progression of lung adenocarcinoma. Cell Death Dis 2023; 14:493. [PMID: 37532692 PMCID: PMC10397223 DOI: 10.1038/s41419-023-06021-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 07/17/2023] [Accepted: 07/25/2023] [Indexed: 08/04/2023]
Abstract
An immunosuppressive microenvironment enriched with regulatory CD4+ T lymphocytes (Tregs) facilitates the progression of lung adenocarcinoma (LUAD). This study aims to investigate the cellular mechanism underlying the formation of the immunosuppressive microenvironment in LUAD. LUAD samples (n = 12) and normal lung samples (n = 3) were obtained from patients with different pathological stages of LUAD. Single-cell RNA sequencing was performed to classify cellular components and analyze the transcriptomes, including transcription factors/targets and chemokine ligands/receptors, followed by bioinformatics study such as pseudotime analysis. Myeloid cells and T cells were the most abundant cell types in tumors and normal lung tissues, while tumor-associated macrophage-folate receptor 2 (TAM-FOLR2) and CD4+ nuclear receptor subfamily 4 group A member 3 (NR4A3) exhibited sharp increases in invasive adenocarcinoma (IA). The enrichment of TAM-FOLR2 in IA might result from alveolar resident macrophage-resistin (ARM-RETN) transformation and recruitment of dendritic cells (DCs) and other TAMs, as evidenced by temporal trajectories and differential expression profiles of chemokine ligands/receptors versus those in the early stages of tumors. High expression of CCL17/19/22 was observed in IA as well as in DCs, along with the strong interaction of TAM-FOLR2 with DCs. The results of pseudotime analysis suggested that CD4+NR4A3 might potentially convert to CD4+FOXP3, further supported by the high expression of NR4A3 target genes in CD4+FOXP3 cells. This study provides a single-cell transcriptome atlas from preinvasive to invasive LUAD and reveals a potential ARM-RETN/TAM-FOLR2/DCs/CD4+NR4A3/CD4+FOXP3 trajectory in shaping the immune suppressive microenvironment along the pathogenesis of LUAD.
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Affiliation(s)
- Chan Xiang
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Min Zhang
- Novogene Co., Ltd., Beijing, 100015, China
| | - Zhanxian Shang
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Shengnan Chen
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Jikai Zhao
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Bowen Ding
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Dong Jiang
- Novogene Co., Ltd., Beijing, 100015, China
| | - Qian Zhu
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Haohua Teng
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Lei Zhu
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Jinchen Shao
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Ruiying Zhao
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Min Ye
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Yang Yu
- Novogene Co., Ltd., Beijing, 100015, China.
| | - Yuchen Han
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
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19
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Chen Z, Lau KS. Advances in Mapping Tumor Progression from Precancer Atlases. Cancer Prev Res (Phila) 2023; 16:439-447. [PMID: 37167978 PMCID: PMC10523872 DOI: 10.1158/1940-6207.capr-22-0473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/22/2023] [Accepted: 04/11/2023] [Indexed: 05/13/2023]
Abstract
Tissue profiling technologies present opportunities for understanding transition from precancerous lesions to malignancy, which may impact risk stratification, prevention, and even cancer treatment. A human precancer atlas building effort is ongoing to tackle the significant challenge of decoding the heterogeneity among cells, specimens, and patients. Here, we discuss the findings resulting from atlases built across precancer types, including those found in colon, breast, lung, stomach, cervix, and skin, using bulk, single-cell, and spatial profiling strategies. We highlight two main themes that emerge across precancer types: the ordering of molecular events that occur during tumor progression and the fluctuation of microenvironmental response during precancer progression. We further highlight the key challenges of data integration across large cohorts of patients, and the need for computational tools to reliably annotate and quality control high-volume, high-dimensional data.
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Affiliation(s)
- Zhengyi Chen
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ken S. Lau
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
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20
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Shang J, Jiang H, Zhao Y, Lai J, Shi L, Yang J, Chen H, Zheng Y. Differences of molecular events driving pathological and radiological progression of lung adenocarcinoma. EBioMedicine 2023; 94:104728. [PMID: 37506543 PMCID: PMC10406962 DOI: 10.1016/j.ebiom.2023.104728] [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: 02/10/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Ground-glass opacity (GGO)-like lung adenocarcinoma (LUAD) has been detected increasingly in the clinic and its inert property and superior survival indicate unique biological characteristics. However, we do not know much about them, which hampers identification of key reasons for the inert property of GGO-like LUAD. METHODS Using whole-exome sequencing and RNA sequencing, taking into account both radiological and pathological classifications of the same 197 patients concomitantly, we systematically interrogate genes driving the progression from GGO to solid nodule and potential reasons for the inertia of GGO. Using flow cytometry and IHC, we validated the abundance of immune cells and activity of cell proliferation. FINDINGS Identifying the differences between GGO and solid nodule, we found adenocarcinoma in situ/minimally invasive adenocarcinoma (AIS/MIA) and GGO-like LUAD exhibited lower TP53 mutation frequency and less active cell proliferation-related pathways than solid nodule in LUAD. Identifying the differences in GGO between AIS/MIA and LUAD, we noticed that EGFR mutation frequency and CNV load were significantly higher in LUAD than in AIS/MIA. Regulatory T cell was also higher in LUAD, while CD8+ T cell decreased from AIS/MIA to LUAD. Finally, we constructed a transcriptomic signature to quantify the development from GGO to solid nodule, which was an independent predictor of patients' prognosis in 11 external LUAD datasets. INTERPRETATION Our results provide deeper insights into the indolent nature of GGO and provide a molecular basis for the treatment of GGO-like LUAD. FUNDING This study was supported in part by the National Natural Science Foundation of China (32170657), the National Natural Science Foundation of China (82203037), and Shanghai Sailing Program (22YF1408900).
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Affiliation(s)
- Jun Shang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - He Jiang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yue Zhao
- Department of Thoracic Surgery, Shanghai Cancer Center, Fudan University, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China
| | - Jinglei Lai
- Department of Thoracic Surgery, Shanghai Cancer Center, Fudan University, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China
| | - Jingcheng Yang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China; Greater Bay Area Institute of Precision Medicine, 115 Jiaoxi Road, Guangzhou, China.
| | - Haiquan Chen
- Department of Thoracic Surgery, Shanghai Cancer Center, Fudan University, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China.
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21
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Harms PW, Frankel TL, Moutafi M, Rao A, Rimm DL, Taube JM, Thomas D, Chan MP, Pantanowitz L. Multiplex Immunohistochemistry and Immunofluorescence: A Practical Update for Pathologists. Mod Pathol 2023; 36:100197. [PMID: 37105494 DOI: 10.1016/j.modpat.2023.100197] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 03/07/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023]
Abstract
Our understanding of the biology and management of human disease has undergone a remarkable evolution in recent decades. Improved understanding of the roles of complex immune populations in the tumor microenvironment has advanced our knowledge of antitumor immunity, and immunotherapy has radically improved outcomes for many advanced cancers. Digital pathology has unlocked new possibilities for the assessment and discovery of the tumor microenvironment, such as quantitative and spatial image analysis. Despite these advances, tissue-based evaluations for diagnosis and prognosis continue to rely on traditional practices, such as hematoxylin and eosin staining, supplemented by the assessment of single biomarkers largely using chromogenic immunohistochemistry (IHC). Such approaches are poorly suited to complex quantitative analyses and the simultaneous evaluation of multiple biomarkers. Thus, multiplex staining techniques have significant potential to improve diagnostic practice and immuno-oncology research. The different approaches to achieve multiplexed IHC and immunofluorescence are described in this study. Alternatives to multiplex immunofluorescence/IHC include epitope-based tissue mass spectrometry and digital spatial profiling (DSP), which require specialized platforms not available to most clinical laboratories. Virtual multiplexing, which involves digitally coregistering singleplex IHC stains performed on serial sections, is another alternative to multiplex staining. Regardless of the approach, analysis of multiplexed stains sequentially or simultaneously will benefit from standardized protocols and digital pathology workflows. Although this is a complex and rapidly advancing field, multiplex staining is now technically feasible for most clinical laboratories and may soon be leveraged for routine diagnostic use. This review provides an update on the current state of the art for tissue multiplexing, including the capabilities and limitations of different techniques, with an emphasis on potential relevance to clinical diagnostic practice.
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Affiliation(s)
- Paul W Harms
- Department of Pathology, Michigan Medicine/University of Michigan, Ann Arbor, Michigan; Department of Dermatology, Michigan Medicine/University of Michigan, Ann Arbor, Michigan; Rogel Cancer Center, Michigan Medicine/University of Michigan, Ann Arbor, Michigan.
| | - Timothy L Frankel
- Rogel Cancer Center, Michigan Medicine/University of Michigan, Ann Arbor, Michigan; Department of Surgery, Michigan Medicine/University of Michigan, Ann Arbor, Michigan
| | - Myrto Moutafi
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Arvind Rao
- Department of Computational Medicine and Bioinformatics, Michigan Medicine/University of Michigan, Ann Arbor, Michigan; Department of Radiation Oncology, Michigan Medicine/University of Michigan, Ann Arbor, Michigan; Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan
| | - David L Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Janis M Taube
- Department of Oncology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center, and Johns Hopkins Bloomberg-Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland; Department of Dermatology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center, and Johns Hopkins Bloomberg-Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center, and Johns Hopkins Bloomberg-Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland
| | - Dafydd Thomas
- Department of Pathology, Michigan Medicine/University of Michigan, Ann Arbor, Michigan; Rogel Cancer Center, Michigan Medicine/University of Michigan, Ann Arbor, Michigan
| | - May P Chan
- Department of Pathology, Michigan Medicine/University of Michigan, Ann Arbor, Michigan; Department of Dermatology, Michigan Medicine/University of Michigan, Ann Arbor, Michigan
| | - Liron Pantanowitz
- Department of Pathology, Michigan Medicine/University of Michigan, Ann Arbor, Michigan
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22
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Saad MB, Hong L, Aminu M, Vokes NI, Chen P, Salehjahromi M, Qin K, Sujit SJ, Lu X, Young E, Al-Tashi Q, Qureshi R, Wu CC, Carter BW, Lin SH, Lee PP, Gandhi S, Chang JY, Li R, Gensheimer MF, Wakelee HA, Neal JW, Lee HS, Cheng C, Velcheti V, Lou Y, Petranovic M, Rinsurongkawong W, Le X, Rinsurongkawong V, Spelman A, Elamin YY, Negrao MV, Skoulidis F, Gay CM, Cascone T, Antonoff MB, Sepesi B, Lewis J, Wistuba II, Hazle JD, Chung C, Jaffray D, Gibbons DL, Vaporciyan A, Lee JJ, Heymach JV, Zhang J, Wu J. Predicting benefit from immune checkpoint inhibitors in patients with non-small-cell lung cancer by CT-based ensemble deep learning: a retrospective study. Lancet Digit Health 2023; 5:e404-e420. [PMID: 37268451 PMCID: PMC10330920 DOI: 10.1016/s2589-7500(23)00082-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/28/2023] [Accepted: 04/04/2023] [Indexed: 06/04/2023]
Abstract
BACKGROUND Only around 20-30% of patients with non-small-cell lung cancer (NCSLC) have durable benefit from immune-checkpoint inhibitors. Although tissue-based biomarkers (eg, PD-L1) are limited by suboptimal performance, tissue availability, and tumour heterogeneity, radiographic images might holistically capture the underlying cancer biology. We aimed to investigate the application of deep learning on chest CT scans to derive an imaging signature of response to immune checkpoint inhibitors and evaluate its added value in the clinical context. METHODS In this retrospective modelling study, 976 patients with metastatic, EGFR/ALK negative NSCLC treated with immune checkpoint inhibitors at MD Anderson and Stanford were enrolled from Jan 1, 2014, to Feb 29, 2020. We built and tested an ensemble deep learning model on pretreatment CTs (Deep-CT) to predict overall survival and progression-free survival after treatment with immune checkpoint inhibitors. We also evaluated the added predictive value of the Deep-CT model in the context of existing clinicopathological and radiological metrics. FINDINGS Our Deep-CT model demonstrated robust stratification of patient survival of the MD Anderson testing set, which was validated in the external Stanford set. The performance of the Deep-CT model remained significant on subgroup analyses stratified by PD-L1, histology, age, sex, and race. In univariate analysis, Deep-CT outperformed the conventional risk factors, including histology, smoking status, and PD-L1 expression, and remained an independent predictor after multivariate adjustment. Integrating the Deep-CT model with conventional risk factors demonstrated significantly improved prediction performance, with overall survival C-index increases from 0·70 (clinical model) to 0·75 (composite model) during testing. On the other hand, the deep learning risk scores correlated with some radiomics features, but radiomics alone could not reach the performance level of deep learning, indicating that the deep learning model effectively captured additional imaging patterns beyond known radiomics features. INTERPRETATION This proof-of-concept study shows that automated profiling of radiographic scans through deep learning can provide orthogonal information independent of existing clinicopathological biomarkers, bringing the goal of precision immunotherapy for patients with NSCLC closer. FUNDING National Institutes of Health, Mark Foundation Damon Runyon Foundation Physician Scientist Award, MD Anderson Strategic Initiative Development Program, MD Anderson Lung Moon Shot Program, Andrea Mugnaini, and Edward L C Smith.
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Affiliation(s)
- Maliazurina B Saad
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lingzhi Hong
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Muhammad Aminu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Natalie I Vokes
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pingjun Chen
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Morteza Salehjahromi
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kang Qin
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sheeba J Sujit
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xuetao Lu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Elliana Young
- Department of Enterprise Data Engineering and Analytics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Qasem Al-Tashi
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rizwan Qureshi
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carol C Wu
- Department of Thoracic Imaging, 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
| | - Steven H Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Percy P Lee
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Radiation Oncology, City of Hope National Medical Center, Los Angeles, CA, USA
| | - Saumil Gandhi
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joe Y Chang
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ruijiang Li
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Michael F Gensheimer
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Heather A Wakelee
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA; Stanford Cancer Institute, Stanford, CA, USA
| | - Joel W Neal
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA; Stanford Cancer Institute, Stanford, CA, USA
| | - Hyun-Sung Lee
- Systems Onco-Immunology Laboratory, David J Sugarbaker Division of Thoracic Surgery, Michael E DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX, USA
| | - Chao Cheng
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Vamsidhar Velcheti
- Department of Hematology and Oncology, New York University Langone Health, New York, NY, USA
| | - Yanyan Lou
- Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, USA
| | - Milena Petranovic
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Waree Rinsurongkawong
- Department of Biostatistics, 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
| | - Vadeerat Rinsurongkawong
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Amy Spelman
- 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
| | - Marcelo V Negrao
- 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
| | - Carl M Gay
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tina Cascone
- Department of Thoracic/Head and Neck Medical Oncology, 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
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jeff Lewis
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John D Hazle
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Caroline Chung
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Neuroradiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David Jaffray
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Radiation Physics, 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
| | - Ara Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, 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
| | - John V Heymach
- 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; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Jia Wu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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23
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Liu J, Ji Y, Weng X, Shao W, Zhao J, Chen H, Shen L, Wang F, Meng Q, Wu X, Wang X, Ou Q, Ke H. Immune microenvironment analysis and novel biomarkers of early-stage lung adenocarcinoma evolution. Front Oncol 2023; 13:1150098. [PMID: 37427097 PMCID: PMC10328385 DOI: 10.3389/fonc.2023.1150098] [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: 01/23/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023] Open
Abstract
Background Lung cancer is the deadliest and most diagnosed type of cancer worldwide. The 5-year survival rate of lung adenocarcinoma (LUAD) dropped significantly when tumor stages advanced. Patients who received surgically resecting at the pre-invasive stage had a 5-year survival rate of nearly 100%. However, the study on the differences in gene expression profiles and immune microenvironment among pre-invasive LUAD patients is still lacking. Methods In this study, the gene expression profiles of three pre-invasive LUAD stages were compared using the RNA-sequencing data of 10 adenocarcinoma in situ (AIS) samples, 12 minimally invasive adenocarcinoma (MIA) samples, and 10 invasive adenocarcinoma (IAC) samples. Results The high expression levels of PTGFRN (Hazard Ratio [HR] = 1.45; 95% Confidence Interval [CI]: 1.08-1.94; log-rank P = 0.013) and SPP1 (HR = 1.44; 95% CI: 1.07-1.93; log-rank P = 0.015) were identified to be associated with LUAD prognosis. Moreover, the early LUAD invasion was accompanied by the enhancement of antigen presentation ability, reflected by the increase of myeloid dendritic cells infiltration rate (Cuzick test P < 0.01) and the upregulation of seven important genes participating in the antigen presentation, including HLA-A (Cuzick test P = 0.03), MICA (Cuzick test P = 0.01), MICB (Cuzick test P = 0.01), HLA-DPA1 (Cuzick test P = 0.04), HLA-DQA2 (Cuzick test P < 0.01), HLA-DQB1 (Cuzick test P = 0.03), and HLA-DQB2 (Cuzick test P < 0.01). However, the tumor-killing ability of the immune system was inhibited during this process, as there were no rising cytotoxic T cell activity (Cuzick test P = 0.20) and no increasing expression in genes encoding cytotoxic proteins. Conclusion In all, our research elucidated the changes in the immune microenvironment during early-stage LUAD evolution and may provide a theoretical basis for developing novel early-stage lung cancer therapeutic targets.
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Affiliation(s)
- Jun Liu
- Department of Chemotherapy, Affiliated Hospital of Nantong University, Nantong, China
| | - Yaxin Ji
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Xiaodan Weng
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Wei Shao
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Jiaping Zhao
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Hanlin Chen
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Lu Shen
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Fufeng Wang
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Qi Meng
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Xue Wu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Xiaonan Wang
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Qiuxiang Ou
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Honggang Ke
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, China
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24
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Li R, Altan M, Reuben A, Lin R, Heymach JV, Tran H, Chen R, Little L, Hubert S, Zhang J, Li Z. A novel statistical method for decontaminating T-cell receptor sequencing data. Brief Bioinform 2023:bbad230. [PMID: 37337757 PMCID: PMC10359082 DOI: 10.1093/bib/bbad230] [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: 12/29/2022] [Revised: 05/16/2023] [Accepted: 05/30/2023] [Indexed: 06/21/2023] Open
Abstract
The T-cell receptor (TCR) repertoire is highly diverse among the population and plays an essential role in initiating multiple immune processes. TCR sequencing (TCR-seq) has been developed to profile the T cell repertoire. Similar to other high-throughput experiments, contamination can happen during several steps of TCR-seq, including sample collection, preparation and sequencing. Such contamination creates artifacts in the data, leading to inaccurate or even biased results. Most existing methods assume 'clean' TCR-seq data as the starting point with no ability to handle data contamination. Here, we develop a novel statistical model to systematically detect and remove contamination in TCR-seq data. We summarize the observed contamination into two sources, pairwise and cross-cohort. For both sources, we provide visualizations and summary statistics to help users assess the severity of the contamination. Incorporating prior information from 14 existing TCR-seq datasets with minimum contamination, we develop a straightforward Bayesian model to statistically identify contaminated samples. We further provide strategies for removing the impacted sequences to allow for downstream analysis, thus avoiding any need to repeat experiments. Our proposed model shows robustness in contamination detection compared with a few off-the-shelf detection methods in simulation studies. We illustrate the use of our proposed method on two TCR-seq datasets generated locally.
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Affiliation(s)
- Ruoxing Li
- Department of Biostatistics and Data Science, The University of Texas Health Science Center at Houston, 77030, Texas, Houston, USA
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 77030, Texas, Houston, USA
| | - Mehmet Altan
- Department of Thoracic-Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 77030, Texas, Houston, USA
| | - Alexandre Reuben
- Department of Thoracic-Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 77030, Texas, Houston, USA
| | - Ruitao Lin
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 77030, Texas, Houston, USA
| | - John V Heymach
- Department of Thoracic-Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 77030, Texas, Houston, USA
| | - Hai Tran
- Department of Thoracic-Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 77030, Texas, Houston, USA
| | - Runzhe Chen
- Department of Thoracic-Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 77030, Texas, Houston, USA
| | - Latasha Little
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 77030, Texas, Houston, USA
| | - Shawna Hubert
- Department of Thoracic-Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 77030, Texas, Houston, USA
| | - Jianjun Zhang
- Department of Thoracic-Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 77030, Texas, Houston, USA
| | - Ziyi Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 77030, Texas, Houston, USA
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25
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Cui Y, Li J, Zhang P, Yin D, Wang Z, Dai J, Wang W, Zhang E, Guo R. B4GALT1 promotes immune escape by regulating the expression of PD-L1 at multiple levels in lung adenocarcinoma. J Exp Clin Cancer Res 2023; 42:146. [PMID: 37303063 DOI: 10.1186/s13046-023-02711-3] [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: 01/17/2023] [Accepted: 05/15/2023] [Indexed: 06/13/2023] Open
Abstract
BACKGROUND Invasive adenocarcinoma (IAC), which is typically preceded by minimally invasive adenocarcinoma (MIA), is the dominant pathological subtype of early-stage lung adenocarcinoma (LUAD). Identifying the molecular events underlying the progression from MIA to IAC may provide a crucial perspective and boost the exploration of novel strategies for early-stage LUAD diagnosis and treatment. METHODS Transcriptome sequencing of four pairs of MIA and IAC tumours obtained from four multiple primary lung cancer patients was performed to screen out beta-1,4-galactosyltransferase1 (B4GALT1). Function and mechanism experiments in vitro and in vivo were performed to explore the regulatory mechanism of B4GALT1-mediated immune evasion by regulating programmed cell death ligand 1 (PD-L1). RESULTS B4GALT1, a key gene involved in N-glycan biosynthesis, was highly expressed in IAC samples. Further experiments revealed that B4GALT1 regulated LUAD cell proliferation and invasion both in vitro and in vivo and was related to the impaired antitumour capacity of CD8 + T cells. Mechanistically, B4GALT1 directly mediates the N-linked glycosylation of PD-L1 protein, thus preventing PD-L1 degradation at the posttranscriptional level. In addition, B4GALT1 stabilized the TAZ protein via glycosylation, which activated CD274 at the transcriptional level. These factors lead to lung cancer immune escape. Importantly, inhibition of B4GALT1 increased CD8 + T-cell abundance and activity and enhanced the antitumour immunity of anti-PD-1 therapy in vivo. CONCLUSION B4GALT1 is a critical molecule in the development of early-stage LUAD and may be a novel target for LUAD intervention and immunotherapy.
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Affiliation(s)
- Yanan Cui
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P. R. China
| | - Jun Li
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P. R. China
| | - Pengpeng Zhang
- Department of Thoracic Surgery, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P. R. China
| | - Dandan Yin
- Clinical Research Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Zhong Fu Road, Gulou District, Nanjing, Jiangsu, 210003, P. R. China
| | - Ziyu Wang
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Jiali Dai
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P. R. China
| | - Wei Wang
- Department of Thoracic Surgery, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P. R. China.
| | - Erbao Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China.
| | - Renhua Guo
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P. R. China.
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26
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Otegui N, Houry M, Arozarena I, Serrano D, Redin E, Exposito F, Leon S, Valencia K, Montuenga L, Calvo A. Cancer Cell-Intrinsic Alterations Associated with an Immunosuppressive Tumor Microenvironment and Resistance to Immunotherapy in Lung Cancer. Cancers (Basel) 2023; 15:3076. [PMID: 37370686 PMCID: PMC10295869 DOI: 10.3390/cancers15123076] [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: 05/01/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Despite the great clinical success of immunotherapy in lung cancer patients, only a small percentage of them (<40%) will benefit from this therapy alone or combined with other strategies. Cancer cell-intrinsic and cell-extrinsic mechanisms have been associated with a lack of response to immunotherapy. The present study is focused on cancer cell-intrinsic genetic, epigenetic, transcriptomic and metabolic alterations that reshape the tumor microenvironment (TME) and determine response or refractoriness to immune checkpoint inhibitors (ICIs). Mutations in KRAS, SKT11(LKB1), KEAP1 and TP53 and co-mutations of these genes are the main determinants of ICI response in non-small-cell lung cancer (NSCLC) patients. Recent insights into metabolic changes in cancer cells that impose restrictions on cytotoxic T cells and the efficacy of ICIs indicate that targeting such metabolic restrictions may favor therapeutic responses. Other emerging pathways for therapeutic interventions include epigenetic modulators and DNA damage repair (DDR) pathways, especially in small-cell lung cancer (SCLC). Therefore, the many potential pathways for enhancing the effect of ICIs suggest that, in a few years, we will have much more personalized medicine for lung cancer patients treated with immunotherapy. Such strategies could include vaccines and chimeric antigen receptor (CAR) cells.
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Affiliation(s)
- Nerea Otegui
- CCUN Cancer Center and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (N.O.); (M.H.); (D.S.); (S.L.); (K.V.); (L.M.)
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Maeva Houry
- CCUN Cancer Center and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (N.O.); (M.H.); (D.S.); (S.L.); (K.V.); (L.M.)
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Imanol Arozarena
- Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain;
- Cancer Signaling Unit, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), 31008 Pamplona, Spain
| | - Diego Serrano
- CCUN Cancer Center and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (N.O.); (M.H.); (D.S.); (S.L.); (K.V.); (L.M.)
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Esther Redin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Francisco Exposito
- Yale Cancer Center, New Haven, CT 06519, USA;
- Department of Pathology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sergio Leon
- CCUN Cancer Center and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (N.O.); (M.H.); (D.S.); (S.L.); (K.V.); (L.M.)
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Karmele Valencia
- CCUN Cancer Center and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (N.O.); (M.H.); (D.S.); (S.L.); (K.V.); (L.M.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), ISCIII, 28029 Madrid, Spain
| | - Luis Montuenga
- CCUN Cancer Center and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (N.O.); (M.H.); (D.S.); (S.L.); (K.V.); (L.M.)
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain;
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), ISCIII, 28029 Madrid, Spain
| | - Alfonso Calvo
- CCUN Cancer Center and Program in Solid Tumors, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (N.O.); (M.H.); (D.S.); (S.L.); (K.V.); (L.M.)
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain;
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), ISCIII, 28029 Madrid, Spain
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27
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Xiao F, Zeng J, Wang H, Zhu H, Guo Y, Zhang Z, Xiao Y, Hu G, Huang K, Yang Q, Guo H. MGME1 associates with poor prognosis and is vital for cell proliferation in lower-grade glioma. Aging (Albany NY) 2023; 15:3690-3714. [PMID: 37166417 PMCID: PMC10449294 DOI: 10.18632/aging.204705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/18/2023] [Indexed: 05/12/2023]
Abstract
OBJECTIVE Mitochondrial genome maintenance exonuclease 1 (MGME1) is associated with DNA depletion, deletion, duplication, and rearrangement. However, the function of MGME1 in tumors, especially lower-grade gliomas (LGGs), has not been established. METHODS Pan-cancer analysis was used to define the expression patterns and prognostic value of MGME1 in various cancers. Subsequently, we systematically determined the associations between MGME1 expression and clinicopathological characteristics, prognosis, biological functions, immune characteristics, genomic mutations, and therapeutic responses of LGGs based on their expression patterns. The expression level and specific functions of MGME1 in LGGs was detected by conducting in vitro experiments. RESULTS Abnormally enhanced and high MGME1 expressions were associated with poor prognoses of various tumors, including LGG. Multivariate and univariate Cox regression analyses manifested that MGME1 expression was an independent prognostic biomarker for LGG. The immune-related signatures, infiltration of immune cells, immune checkpoint genes (ICPGs), copy number alteration (CNA), tumor mutation burden (TMB), and treatment responses of LGG patients were associated with the expression of MGME1. The in vitro experiments affirmed that MGME1 was elevated and tightly connected with the cell proliferation and cell cycle in LGG. CONCLUSIONS MGME1 is an independent prognostic biomarker and closely related to the cell proliferation in LGG.
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Affiliation(s)
- Feng Xiao
- Departments of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, China
| | - Jie Zeng
- Departments of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, China
| | - Haiyan Wang
- Department of Operation, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
| | - Hong Zhu
- Departments of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, China
| | - Yun Guo
- Departments of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, China
| | - Zhe Zhang
- Departments of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, China
| | - Yao Xiao
- Departments of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, China
| | - Guowen Hu
- Departments of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
| | - Kai Huang
- Departments of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, China
| | - Qing Yang
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330030, Jiangxi, China
| | - Hua Guo
- Departments of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, China
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28
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Weeden CE, Gayevskiy V, Marceaux C, Batey D, Tan T, Yokote K, Ribera NT, Clatch A, Christo S, Teh CE, Mitchell AJ, Trussart M, Rankin LC, Obers A, McDonald JA, Sutherland KD, Sharma VJ, Starkey G, D'Costa R, Antippa P, Leong T, Steinfort D, Irving L, Swanton C, Gordon CL, Mackay LK, Speed TP, Gray DHD, Asselin-Labat ML. Early immune pressure initiated by tissue-resident memory T cells sculpts tumor evolution in non-small cell lung cancer. Cancer Cell 2023; 41:837-852.e6. [PMID: 37086716 DOI: 10.1016/j.ccell.2023.03.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 02/05/2023] [Accepted: 03/24/2023] [Indexed: 04/24/2023]
Abstract
Tissue-resident memory T (TRM) cells provide immune defense against local infection and can inhibit cancer progression. However, it is unclear to what extent chronic inflammation impacts TRM activation and whether TRM cells existing in tissues before tumor onset influence cancer evolution in humans. We performed deep profiling of healthy lungs and lung cancers in never-smokers (NSs) and ever-smokers (ESs), finding evidence of enhanced immunosurveillance by cells with a TRM-like phenotype in ES lungs. In preclinical models, tumor-specific or bystander TRM-like cells present prior to tumor onset boosted immune cell recruitment, causing tumor immune evasion through loss of MHC class I protein expression and resistance to immune checkpoint inhibitors. In humans, only tumors arising in ES patients underwent clonal immune evasion, unrelated to tobacco-associated mutagenic signatures or oncogenic drivers. These data demonstrate that enhanced TRM-like activity prior to tumor development shapes the evolution of tumor immunogenicity and can impact immunotherapy outcomes.
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Affiliation(s)
- Clare E Weeden
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Velimir Gayevskiy
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Claire Marceaux
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Daniel Batey
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Tania Tan
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Kenta Yokote
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Nina Tubau Ribera
- Advanced Technology and Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Allison Clatch
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Susan Christo
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Charis E Teh
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Andrew J Mitchell
- Materials Characterisation and Fabrication Platform, Department of Chemical Engineering, the University of Melbourne, Parkville, VIC, Australia
| | - Marie Trussart
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Lucille C Rankin
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Andreas Obers
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Jackson A McDonald
- ACRF Stem Cells and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Kate D Sutherland
- ACRF Stem Cells and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Varun J Sharma
- Department of Surgery, University of Melbourne, Parkville, VIC, Australia; Liver and Intestinal Transplant Unit, Austin Health, Heidelberg, VIC, Australia; Department of Cardiothoracic Surgery, Austin Health, Heidelberg, VIC, Australia
| | - Graham Starkey
- Department of Surgery, University of Melbourne, Parkville, VIC, Australia; Liver and Intestinal Transplant Unit, Austin Health, Heidelberg, VIC, Australia
| | - Rohit D'Costa
- DonateLife Victoria, Carlton, VIC, Australia; Department of Intensive Care Medicine, Melbourne Health, Melbourne, VIC, Australia
| | - Phillip Antippa
- Department of Surgery, University of Melbourne, Parkville, VIC, Australia; The Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Tracy Leong
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia; Department of Respiratory and Sleep Medicine, Austin Health, Heidelberg, VIC, Australia
| | - Daniel Steinfort
- Department of Medicine, the University of Melbourne, Parkville, VIC, Australia; The Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Louis Irving
- Department of Medicine, the University of Melbourne, Parkville, VIC, Australia; The Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute, London, UK; Department of Oncology, University College London Hospitals, London, UK
| | - Claire L Gordon
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, VIC, Australia; North Eastern Public Health Unit, Austin Health, Heidelberg, VIC, Australia
| | - Laura K Mackay
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Terence P Speed
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; School of Mathematics and Statistics, the University of Melbourne, Parkville, VIC, Australia
| | - Daniel H D Gray
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia.
| | - Marie-Liesse Asselin-Labat
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia.
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29
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Frank ML, Lu K, Erdogan C, Han Y, Hu J, Wang T, Heymach JV, Zhang J, Reuben A. T-Cell Receptor Repertoire Sequencing in the Era of Cancer Immunotherapy. Clin Cancer Res 2023; 29:994-1008. [PMID: 36413126 PMCID: PMC10011887 DOI: 10.1158/1078-0432.ccr-22-2469] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/07/2022] [Accepted: 11/14/2022] [Indexed: 11/23/2022]
Abstract
T cells are integral components of the adaptive immune system, and their responses are mediated by unique T-cell receptors (TCR) that recognize specific antigens from a variety of biological contexts. As a result, analyzing the T-cell repertoire offers a better understanding of immune responses and of diseases like cancer. Next-generation sequencing technologies have greatly enabled the high-throughput analysis of the TCR repertoire. On the basis of our extensive experience in the field from the past decade, we provide an overview of TCR sequencing, from the initial library preparation steps to sequencing and analysis methods and finally to functional validation techniques. With regards to data analysis, we detail important TCR repertoire metrics and present several computational tools for predicting antigen specificity. Finally, we highlight important applications of TCR sequencing and repertoire analysis to understanding tumor biology and developing cancer immunotherapies.
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Affiliation(s)
- Meredith L Frank
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,The University of Texas MD Anderson Cancer Center UT Health Houston Graduate School of Biomedical Sciences, Houston, Texas
| | - Kaylene Lu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,The University of Texas MD Anderson Cancer Center UT Health Houston Graduate School of Biomedical Sciences, Houston, Texas.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Can Erdogan
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Rice University, Houston, Texas
| | - Yi Han
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jian Hu
- The University of Texas MD Anderson Cancer Center UT Health Houston Graduate School of Biomedical Sciences, Houston, Texas.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tao Wang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas.,Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,The University of Texas MD Anderson Cancer Center UT Health Houston Graduate School of Biomedical Sciences, Houston, Texas
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,The University of Texas MD Anderson Cancer Center UT Health Houston Graduate School of Biomedical Sciences, Houston, Texas.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,The University of Texas MD Anderson Cancer Center UT Health Houston Graduate School of Biomedical Sciences, Houston, Texas
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30
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DeLuca VJ, Saleh T. Insights into the role of senescence in tumor dormancy: mechanisms and applications. Cancer Metastasis Rev 2023; 42:19-35. [PMID: 36681750 DOI: 10.1007/s10555-023-10082-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 01/12/2023] [Indexed: 01/23/2023]
Abstract
One of the most formidable challenges in oncology and tumor biology research is to provide an accurate understanding of tumor dormancy mechanisms. Dormancy refers to the ability of tumor cells to go undetected in the body for a prolonged period, followed by "spontaneous" escape. Various models of dormancy have been postulated, including angiogenic, immune-mediated, and cellular dormancy. While the former two propose mechanisms by which tumor growth may remain static at a population level, cellular dormancy refers to molecular processes that restrict proliferation at the cell level. Senescence is a form of growth arrest, during which cells undergo distinct phenotypic, epigenetic, and metabolic changes. Senescence is also associated with the development of a robust secretome, comprised of various chemokines and cytokines that interact with the surrounding microenvironment, including other tumor cells, stromal cells, endothelial cells, and immune cells. Both tumor and non-tumor cells can undergo senescence following various stressors, many of which are present during tumorigenesis and therapy. As such, senescent cells are present within forming tumors and in residual tumors post-treatment and therefore play a major role in tumor biology. However, the contributions of senescence to dormancy are largely understudied. Here, we provide an overview of multiple processes that have been well established as being involved in tumor dormancy, and we speculate on how senescence may contribute to these mechanisms.
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Affiliation(s)
- Valerie J DeLuca
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Tareq Saleh
- Department of Pharmacology and Public Health, Faculty of Medicine, The Hashemite University, Zarqa, 13133, Jordan.
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31
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Tani Y, Kaneda H, Koh Y, Tamiya A, Isa S, Kubo A, Ogawa K, Matsumoto Y, Sawa K, Yoshimoto N, Mitsuoka S, Kawaguchi T. The Impact of Estrogen Receptor Expression on Mutational Status in the Evolution of Non-Small Cell Lung Cancer. Clin Lung Cancer 2023; 24:165-174. [PMID: 36646585 DOI: 10.1016/j.cllc.2022.12.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/15/2022] [Accepted: 12/14/2022] [Indexed: 01/01/2023]
Abstract
BACKGROUND The role of estrogen receptor (ER) status in the carcinogenesis of lung cancer and its impact on prognosis remain unclear. MATERIALS AND METHODS We previously reported a prospective, multicenter, molecular epidemiology study (Japan Molecular Epidemiology for Lung Cancer Study [JME]). We examined the relationship of ER status with reproductive and hormonal factors, mutational profile, and survival using JME study data. Patients were enrolled between July 2012 and December 2013, with follow-up until November, 2017. RESULTS Among 441 ever- and 435 never-smokers, ER expression was observed in 46.4% and 53.5%, respectively (P = .022). Hormone use and reproductive history of female patients were not associated with ER status. Mutations in EGFR (P = .003), TP53 (P = .007), and CTNNB1 (P = .027) were significantly associated with ER expression. Multivariate analysis showed that mutations in EGFR (P = .032) and CTNNB1 (P = .026) were significantly associated with ER expression, whereas TP53 mutations exhibited a trend toward significance (P = .059). Relapse-free survival (RFS) was longer in all the patients with ER-positive tumors than those with ER-negative tumors (P = .021). RFS and overall survival were longer (P = .024, P = .011, respectively) in the stage I patients with ER-positive tumors than those with ER-negative tumors. CONCLUSION ERβ expression is positively associated with EGFR mutations and negatively with TP53 and CTNNB1 mutations. ER-positive tumors can be associated with better prognosis of the patients, suggesting that ER expression with coexisting EGFR mutations and wild-type TP53 contribute to the biology of non-small cell lung cancer.
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Affiliation(s)
- Yoko Tani
- Department of Clinical Oncology, Osaka Metropolitan University Graduate School of Medicine, Osaka City, Osaka Prefecture, Japan
| | - Hiroyasu Kaneda
- Department of Clinical Oncology, Osaka Metropolitan University Graduate School of Medicine, Osaka City, Osaka Prefecture, Japan.
| | - Yasuhiro Koh
- Center for Biomedical Sciences, Wakayama Medical University, Wakayama City, Wakayama Prefecture, Japan; Department of Internal Medicine III, Wakayama Medical University, Wakayama City, Wakayama Prefecture, Japan
| | - Akihiro Tamiya
- Department of Internal Medicine, National Hospital Organization Kinki-Chuo Chest Medical Center, Sakai City, Osaka Prefecture, Japan
| | - Shunichi Isa
- Department of Thoracic Oncology, Clinical Research Center, National Hospital Organization Kinki-Chuo Chest Medical Center, Sakai City, Osaka Prefecture, Japan
| | - Akihito Kubo
- Department of Medical Oncology, Oncology Center, Aichi Medical University Hospital, Nagakute City, Aichi Prefecture, Japan
| | - Koichi Ogawa
- Department of Respiratory Medicine, Osaka Metropolitan University, Graduate School of Medicine, Osaka City, Osaka Prefecture, Japan
| | - Yoshiya Matsumoto
- Department of Respiratory Medicine, Osaka Metropolitan University, Graduate School of Medicine, Osaka City, Osaka Prefecture, Japan
| | - Kenji Sawa
- Department of Respiratory Medicine, Osaka Metropolitan University, Graduate School of Medicine, Osaka City, Osaka Prefecture, Japan
| | - Naoki Yoshimoto
- Department of Clinical Oncology, Osaka Metropolitan University Graduate School of Medicine, Osaka City, Osaka Prefecture, Japan; Department of Respiratory Medicine, Ishikiri Seiki Hospital, Osaka City, Osaka Prefecture, Japan
| | - Shigeki Mitsuoka
- Department of Clinical Oncology, Osaka Metropolitan University Graduate School of Medicine, Osaka City, Osaka Prefecture, Japan
| | - Tomoya Kawaguchi
- Department of Clinical Oncology, Osaka Metropolitan University Graduate School of Medicine, Osaka City, Osaka Prefecture, Japan; Department of Respiratory Medicine, Osaka Metropolitan University, Graduate School of Medicine, Osaka City, Osaka Prefecture, Japan
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32
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Upregulation of NDUFAF2 in Lung Adenocarcinoma Is a Novel Independent Prognostic Biomarker. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2023; 2023:2912968. [PMID: 36703939 PMCID: PMC9873462 DOI: 10.1155/2023/2912968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/31/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023]
Abstract
Background NADH dehydrogenase (ubiquinone) 1 alpha subcomplex assembly factor 2 (NDUFAF2) acts as a molecular chaperone for the assembly of complex I on the mitochondrial membrane, which is involved in the transfer of electrons in the respiratory chain. However, whether NDUFAF2 plays a role in lung adenocarcinoma (LUAD) is largely unexplored. Methods Expression profiles were obtained from the TCGA and GEO databases and integrated via R3.6.3 and several bioinformatics platforms. Western blotting analysis and immunohistochemistry staining were used to examine the expressions of NDUFAF2 in clinical samples. Moreover, the diagnostic and prognostic value of NDUFAF2 expression level was also assessed. GO, KEGG, and gene set enrichment analysis (GSEA) were adopted to investigate NDUFAF2-related molecular functions, signaling pathways, and life activity processes. Results NDUFAF2 was predominantly expressed in LUAD, and it is identified as a promising biomarker in the diagnosis of LUAD and its prognostic prediction. Overexpression of NDUFAF2 was correlated with N stage, T stage, and pathologic stage in LUAD, leading to worse overall survival (OS). Besides, the level of NDUFAF2 was independently associated with OS through a multivariate Cox analysis (HR = 1.538, 95% (1.086-2.177), P = 0.015). GO analysis revealed enrichment in innate immune response in mucosa and mucosal immune response, and GSEA indicated enrichment in G2_M_checkpoints, DNA replication, diseases of mitotic cell cycle, retinoblastoma gene in cancer, cell cycle pathway, and cell cycle. Furthermore, the expression level of NDUFAF2 was negatively correlated with infiltration levels of Tem, Tcm, NK CD56bright cells, and B cells. In contrast, the expression level of NDUFAF2 was positively correlated with the infiltration level of DCs and Th2 cells in LUAD patients. Conclusions Collectively, NDUFAF2 is a promising independent prognostic biomarker and target in LUAD. In addition, NDUFAF2 might affect the prognosis of LUAD via DNA replication, diseases of mitotic cell cycle, cell cycle pathway, and cell cycle.
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Zhang LL, Lin S, Zhang Y, Yao DM, Du X. Serum Spondin-2 expression, tumor invasion, and antitumor immune response in patients with cervical cancer. World J Clin Cases 2022; 10:13304-13312. [PMID: 36683629 PMCID: PMC9851009 DOI: 10.12998/wjcc.v10.i36.13304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/19/2022] [Accepted: 11/28/2022] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Cervical cancer is a gynecological malignancy common in middle-aged and older patients, with a high mortality rate. Spondin-2 is an extracellular matrix protein that involved in innate and acquired immune responses. Herein, we investigated the relationship between serum Spondin-2 expression, tumor invasion and infiltration, and immune response in patients with cervical cancer and provided a theoretical basis for clinical practice.
AIM To investigate the relationship between serum Spondin-2 expression and cervical cancer-related indicators.
METHODS Overall, 147 patients with cervical cancer who were admitted to our institution between January 2019 and August 2019 were assigned to the cervical cancer group, and 92 patients with benign uterine lesions and 86 healthy individuals were assigned to the benign and control groups, respectively. In each group, serum Spondin-2 expression was measured, and the receiver operating characteristic (ROC) curve was determined. Patients with cervical cancer were classified into high or low Spondin-2 groups depending on the Spondin-2 threshold value used for diagnosing cervical cancer. Patient’s clinical data were collected to compare the clinicopathologic characteristics, immune cytokine levels, and prognosis of patients with varying Spondin-2 expression levels.
RESULTS The expression level of serum Spondin-2 was significantly higher in the cervical cancer group than in the benign and control groups (P < 0.05). According to the ROC curve, the cutoff value of Spondin-2 used in the diagnosis of cervical carcinoma was 25.68 ± 7.11 μg/L. The proportion of patients with Federation of Gynecology and Obstetrics stage III, nerve invasion, vascular invasion, and lymph node metastasis was higher in the high Spondin-2 group than in the low Spondin-2 group (P < 0.05). Interleukin-5 (IL-5) and IL-4 Levels were higher in the high Spondin-2 group than in the low Spondin-2 group. In contrast, IL-2 and tumor necrosis factor-α levels were lower in the high Spondin-2 group than in the low Spondin-2 group (P < 0.05). After 3 years of follow-up, progression-free survival and overall survival were significantly shorter in the high Spondin-2 group than in the low Spondin-2 group (P < 0.05).
CONCLUSION The expression of serum Spondin-2 is upregulated in patients with cervical carcinoma and is related to tumor invasion and infiltration, antitumor immune response, and prognosis.
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Affiliation(s)
- Ling-Li Zhang
- Department of Gynecology, Maternal and Child Health Hospital of Hubei Province, Wuhan 430070, Hubei Province, China
| | - Song Lin
- Department of Surgery, Maternal and Child Health Hospital of Hubei Province, Wuhan 430070, Hubei Province, China
| | - Yan Zhang
- Department of Women’s Health, Maternal and Child Health Hospital of Hubei Province, Wuhan 430070, Hubei Province, China
| | - Dong-Mei Yao
- Department of Gynecology, Maternal and Child Health Hospital of Hubei Province, Wuhan 430070, Hubei Province, China
| | - Xin Du
- Department of Gynecology, Maternal and Child Health Hospital of Hubei Province, Wuhan 430070, Hubei Province, China
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Chen R, Li J, Fujimoto J, Hong L, Hu X, Quek K, Tang M, Mitra A, Behrens C, Chow CW, Jiang P, Little LD, Gumbs C, Song X, Zhang J, Tan D, Heymach JV, Wistuba I, Futreal PA, Gibbons DL, Byers LA, Zhang J, Reuben A. Immunogenomic intertumor heterogeneity across primary and metastatic sites in a patient with lung adenocarcinoma. J Exp Clin Cancer Res 2022; 41:172. [PMID: 35546239 PMCID: PMC9092788 DOI: 10.1186/s13046-022-02361-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 04/10/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Lung cancer is the leading cause of cancer death, partially owing to its extensive heterogeneity. The analysis of intertumor heterogeneity has been limited by an inability to concurrently obtain tissue from synchronous metastases unaltered by multiple prior lines of therapy.
Methods
In order to study the relationship between genomic, epigenomic and T cell repertoire heterogeneity in a rare autopsy case from a 32-year-old female never-smoker with left lung primary late-stage lung adenocarcinoma (LUAD), we did whole-exome sequencing (WES), DNA methylation and T cell receptor (TCR) sequencing to characterize the immunogenomic landscape of one primary and 19 synchronous metastatic tumors.
Results
We observed heterogeneous mutation, methylation, and T cell patterns across distinct metastases. Only TP53 mutation was detected in all tumors suggesting an early event while other cancer gene mutations were later events which may have followed subclonal diversification. A set of prevalent T cell clonotypes were completely excluded from left-side thoracic tumors indicating distinct T cell repertoire profiles between left-side and non left-side thoracic tumors. Though a limited number of predicted neoantigens were shared, these were associated with homology of the T cell repertoire across metastases. Lastly, ratio of methylated neoantigen coding mutations was negatively associated with T-cell density, richness and clonality, suggesting neoantigen methylation may partially drive immunosuppression.
Conclusions
Our study demonstrates heterogeneous genomic and T cell profiles across synchronous metastases and how restriction of unique T cell clonotypes within an individual may differentially shape the genomic and epigenomic landscapes of synchronous lung metastases.
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Yu F, Peng M, Bai J, Zhu X, Zhang B, Tang J, Liu W, Chen C, Wang X, Chen M, Tan S, Sun Y, Liang Q, Li J, Hu Y, Liao A, Hu H, He Y, Xiao X, Wang B, Xing G, Xu Y, Chen R, Xia X, Chen X. Comprehensive characterization of genomic and radiologic features reveals distinct driver patterns of RTK/RAS pathway in ground-glass opacity pulmonary nodules. Int J Cancer 2022; 151:2020-2030. [PMID: 36029220 PMCID: PMC9805018 DOI: 10.1002/ijc.34238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 06/12/2022] [Accepted: 06/13/2022] [Indexed: 01/09/2023]
Abstract
Ground-glass opacity (GGO)-associated pulmonary nodules have been known as a radiologic feature of early-stage lung cancers and exhibit an indolent biological behavior. However, the correlation between driver genes and radiologic features as well as the immune microenvironment remains poorly understood. We performed a custom 1021-gene panel sequencing of 334 resected pulmonary nodules presenting as GGO from 262 Chinese patients. A total of 130 multiple pulmonary nodules were sampled from 58 patients. Clinical-pathologic and radiologic parameters of these pulmonary nodules were collected. Immunohistochemistry (IHC) and multiplex immunofluorescent staining (mIF) were applied to analyze proliferation and immune cell markers of GGO-associated pulmonary nodules. Compared with pure GGO nodules, mixed GGO nodules were enriched for invasive adenocarcinoma (IAC) (182/216 vs 73/118, P < .001). Eighty-eight percent (294/334) of GGO-associated nodules carried at least one mutation in EGFR/ERBB2/BRAF/KRAS/MAP2K1 of the RTK/RAS signaling pathway, and the alterations in these driver genes were mutually exclusive. The analysis of multifocal pulmonary nodules from the same patient revealed evidence of functional convergence on RTK/RAS pathways. Nodules with ERBB2/BRAF/MAP2K1 mutations tended to be more indolent than those with EGFR and KRAS mutations. IHC and mIF staining showed that KRAS-mutant GGO nodules displayed higher infiltration of CD4+ T cell and CD8+ T cell as well as stronger proliferation and immune inhibitory signals. Our study demonstrates a driver landscape of radiologically detectable GGO-associated pulmonary nodules in Chinese patients and supports that different driver patterns in RTK/RAS pathway are corresponding to different radiologic features.
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Affiliation(s)
- Fenglei Yu
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Muyun Peng
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Jing Bai
- Geneplus‐Beijing InstitutePeking University Medical Industrial ParkBeijingChina
| | - Xiuli Zhu
- Geneplus‐Beijing InstitutePeking University Medical Industrial ParkBeijingChina
| | - Bingyu Zhang
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Jingqun Tang
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Wenliang Liu
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Chen Chen
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Xiang Wang
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Mingjiu Chen
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Sichuang Tan
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Yi Sun
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of PathologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Qingchun Liang
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of PathologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Jina Li
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Yan Hu
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Aihui Liao
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of General SurgeryHunan Geological and Mineral HospitalChangshaChina
| | - Huali Hu
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of General SurgeryHunan Geological and Mineral HospitalChangshaChina
| | - Yu He
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Xiao Xiao
- Geneplus‐ShenzhenShenzhenGuangdong ProvinceChina
| | - Bin Wang
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Guanlan Xing
- Geneplus‐Beijing InstitutePeking University Medical Industrial ParkBeijingChina
| | - Yaping Xu
- Geneplus‐Beijing InstitutePeking University Medical Industrial ParkBeijingChina
| | - Rongrong Chen
- Geneplus‐Beijing InstitutePeking University Medical Industrial ParkBeijingChina
| | - Xuefeng Xia
- Geneplus‐Beijing InstitutePeking University Medical Industrial ParkBeijingChina
| | - Xiaofeng Chen
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of AnesthesiaThe Second Xiangya Hospital of Central South UniversityChangshaChina
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Insight into the Prospects for Tumor Therapy Based on Photodynamic Immunotherapy. Pharmaceuticals (Basel) 2022; 15:ph15111359. [DOI: 10.3390/ph15111359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 10/30/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Malignancy is one of the common diseases with high mortality worldwide and the most important obstacle to improving the overall life expectancy of the population in the 21st century. Currently, single or combined treatments, including surgery, chemotherapy, and radiotherapy, are still the mainstream regimens for tumor treatment, but they all present significant side effects on normal tissues and organs, such as organ hypofunction, energy metabolism disorders, and various concurrent diseases. Based on this, theranostic measures for the highly selective killing of tumor cells have always been a hot area in cancer-related fields, among which photodynamic therapy (PDT) is expected to be an ideal candidate for practical clinical application due to its precise targeting and excellent safety performance, so-called PDT refers to a therapeutic method mainly composed of photosensitizers (PSs), laser light, and reactive oxygen species (ROS). Photoimmunotherapy (PIT), a combination of PDT and immunotherapy, can induce systemic antitumor immune responses and inhibit continuing growth and distant metastasis of residual tumor cells, demonstrating a promising application prospect. This article reviews the types of immune responses that occur in the host after PDT treatment, including innate and adaptive immunity. To further help PIT-related drugs improve their pharmacokinetic properties and bioavailability, we highlight the potential improvement of photodynamic immunotherapy from three aspects: immunostimulatory agents, tumor-associated antigens (TAAs) as well as different immune cells. Finally, we focus on recent advances in various strategies and shed light on their corresponding mechanisms of immune activation and possible clinical applications such as cancer vaccines. Having discovered the inherent potential of PDT and the mechanisms that PDT triggers host immune responses, a variety of immunotherapeutic strategies have been investigated in parallel with approaches to improve PDT efficiency. However, it remains to be further elucidated under what conditions the immune effect induced by PDT can achieve tumor immunosuppression and to what extent PDT-induced antitumor immunity will lead to complete tumor rejection. Currently, PIT presents several outstanding intractable challenges, such as the aggregation ability of PSs locally in tumors, deep tissue penetration ability of laser light, immune escape, and biological toxicity, and it is hoped that these issues raised will help to point out the direction of preclinical research on PIT and accelerate its transition to clinical practice.
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Fortunato O, Huber V, Segale M, Cova A, Vallacchi V, Squarcina P, Rivoltini L, Suatoni P, Sozzi G, Pastorino U, Boeri M. Development of a Molecular Blood-Based Immune Signature Classifier as Biomarker for Risks Assessment in Lung Cancer Screening. Cancer Epidemiol Biomarkers Prev 2022; 31:2020-2029. [PMID: 36112827 PMCID: PMC9627262 DOI: 10.1158/1055-9965.epi-22-0689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/15/2022] [Accepted: 08/23/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Low-dose CT (LDCT) screening trials have shown that lung cancer early detection saves lives. However, a better stratification of the screening population is still needed. In this respect, we generated and prospectively validated a plasma miRNA signature classifier (MSC) able to categorize screening participants according to lung cancer risk. Here, we aimed to deeply characterize the peripheral immune profile and develop a diagnostic immune signature classifier to further implement blood testing in lung cancer screening. METHODS Peripheral blood mononuclear cell (PBMC) samples collected from 20 patients with LDCT-detected lung cancer and 20 matched cancer-free screening volunteers were analyzed by flow cytometry using multiplex panels characterizing both lymphoid and myeloid immune subsets. Data were validated in PBMC from 40 patients with lung cancer and 40 matched controls and in a lung cancer specificity set including 27 subjects with suspicious lung nodules. A qPCR-based gene expression signature was generated resembling selected immune subsets. RESULTS Monocytic myeloid-derived suppressor cell (MDSC), polymorphonuclear MDSC, intermediate monocytes and CD8+PD-1+ T cells distinguished patients with lung cancer from controls with AUCs values of 0.94/0.72/0.88 in the training, validation, and lung cancer specificity set, respectively. AUCs raised up to 1.00/0.84/0.92 in subgroup analysis considering only MSC-negative subjects. A 14-immune genes expression signature distinguished patients from controls with AUC values of 0.76 in the validation set and 0.83 in MSC-negative subjects. CONCLUSIONS An immune-based classifier can enhance the accuracy of blood testing, thus supporting the contribution of systemic immunity to lung carcinogenesis. IMPACT Implementing LDCT screening trials with minimally invasive blood tests could help reduce unnecessary procedures and optimize cost-effectiveness.
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Affiliation(s)
- Orazio Fortunato
- Tumor Genomics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Veronica Huber
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Miriam Segale
- Tumor Genomics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Agata Cova
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Viviana Vallacchi
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paola Squarcina
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Licia Rivoltini
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paola Suatoni
- Thoracic Surgery Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Gabriella Sozzi
- Tumor Genomics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.,Corresponding Author: Gabriella Sozzi, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, Milan 20133, Italy. Phone: 223-903-775; E-mail:
| | - Ugo Pastorino
- Thoracic Surgery Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Mattia Boeri
- Tumor Genomics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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Zhan X, Feng S, Zhou X, Liao W, Zhao B, Yang Q, Tan Q, Shen J. Immunotherapy response and microenvironment provide biomarkers of immunotherapy options for patients with lung adenocarcinoma. Front Genet 2022; 13:1047435. [PMID: 36386793 PMCID: PMC9640754 DOI: 10.3389/fgene.2022.1047435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 10/17/2022] [Indexed: 11/30/2022] Open
Abstract
Background: Immunotherapy has been a promising approach option for lung cancer. Method: All the open-accessed data was obtained from the Cancer Genome Atlas (TCGA) database. All the analysis was conducted using the R software analysis. Results: Firstly, the genes differentially expressed in lung cancer immunotherapy responders and non-responders were identified. Then, the lung adenocarcinoma immunotherapy-related genes were determined by LASSO logistic regression and SVM-RFE, respectively. A total of 18 immunotherapy response-related genes were included in our investigation. Subsequently, we constructed the logistics score model. Patients with high logistics score had a better clinical effect on immunotherapy, with 63.2% of patients responding to immunotherapy, while only 12.1% of patients in the low logistics score group responded to immunotherapy. Moreover, we found that pathways related to immunotherapy were mainly enriched in metabolic pathways such as fatty acid metabolism, bile acid metabolism, oxidative phosphorylation, and carcinogenic pathways such as KRAS signaling. Logistics score was positively correlated with NK cells activated, Mast cells resting, Monocytes, Macrophages M2, dendritic cells resting, dendritic cells activated and eosinophils, while was negatively related to Tregs, macrophages M0, macrophages M1, and mast cells activated. In addition, ERVH48-1 was screened for single-cell exploration. The expression of ERVH48-1 increased in patients with distant metastasis, and ERVH48-1 was associated with pathways such as pancreas beta cells, spermatogenesis, G2M checkpoints and KRAS signaling. The result of quantitative real-time PCR showed that ERVH48-1 was upregulated in lung cancer cells. Conclusion: Our study developed an effective signature to predict the immunotherapy response of lung cancer patients.
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Affiliation(s)
- Xue Zhan
- Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing, China
| | - Shihan Feng
- Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing, China
| | - Xutao Zhou
- Department of Oncology, Jiulongpo Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Wei Liao
- Department of Oncology, Jiulongpo Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Bin Zhao
- Department of Oncology, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Qian Yang
- Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing, China
| | - Qi Tan
- Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing, China
| | - Jian Shen
- Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing, China
- *Correspondence: Jian Shen,
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Yao Y, Gu L, Zuo Z, Wang D, Zhou T, Xu X, Yang L, Huang X, Wang L. Necroptosis-related lncRNAs: Combination of bulk and single-cell sequencing reveals immune landscape alteration and a novel prognosis stratification approach in lung adenocarcinoma. Front Oncol 2022; 12:1010976. [PMID: 36605426 PMCID: PMC9808398 DOI: 10.3389/fonc.2022.1010976] [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: 08/03/2022] [Accepted: 09/26/2022] [Indexed: 01/07/2023] Open
Abstract
Necroptosis, which is recently recognized as a form of programmed cell death, plays a critical role in cancer biology, including tumorigenesis and cancer immunology. It was recognized not only to defend against tumor progression by suppressing adaptive immune responses but also to promote tumorigenesis and cancer metastasis after recruiting inflammatory responses. Thus the crucial role of necrosis in tumorigenesis has attracted increasing attention. Due to the heterogeneity of the tumor immune microenvironment (TIME) in lung adenocarcinoma (LUAD), the prognosis and the response to immunotherapy vary distinctly across patients, underscoring the need for a stratification algorithm for clinical practice. Although previous studies have formulated the crucial role of lncRNAs in tumorigenicity, the relationship between necroptosis-related lncRNAs, TIME, and the prognosis of patients with LUAD was still elusive. In the current study, a robust and novel prognostic stratification model based on Necroptosis-related LncRNA Risk Scoring (NecroLRS) and clinicopathological parameters was constructed and systemically validated in both internal and external validation cohorts. The expression profile of four key lncRNAs was further validated by qRT-PCR in 4 human LUAD cell lines. And a novel immune landscape alteration was observed between NecroLRS-High and -Low patients. To further elucidate the mechanism of necroptosis in the prognosis of LUAD from a single-cell perspective, a novel stratification algorithm based on K-means clustering was introduced to extract both malignant and NecroLRS-High subsets from epithelial cells. And the necroptosis-related immune infiltration landscape and developmental trajectory were investigated respectively. Critically, NecroLRS was found to be positively correlated with neutrophil enrichment, inflammatory immune response, and malignant phenotypes of LUAD. In addition, novel ligand-receptor pairs between NecroLRS-High cells and other immunocytes were investigated and optimal therapeutic compounds were screened to provide potential targets for future studies. Taken together, our findings reveal emerging mechanisms of necroptosis-induced immune microenvironment alteration on the deteriorative prognosis and may contribute to improved prognosis and individualized precision therapy for patients with LUAD.
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Affiliation(s)
| | | | | | | | | | | | - Lehe Yang
- *Correspondence: Lehe Yang, ; Xiaoying Huang, ; Liangxing Wang,
| | - Xiaoying Huang
- *Correspondence: Lehe Yang, ; Xiaoying Huang, ; Liangxing Wang,
| | - Liangxing Wang
- *Correspondence: Lehe Yang, ; Xiaoying Huang, ; Liangxing Wang,
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Zhao H, Collet C, Peng D, Sinha UK, Lin DC. Investigation of early neoplastic transformation and premalignant biology using genetically engineered organoid models. Comput Struct Biotechnol J 2022; 20:5309-5315. [PMID: 36212534 PMCID: PMC9513696 DOI: 10.1016/j.csbj.2022.09.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/19/2022] [Accepted: 09/19/2022] [Indexed: 11/24/2022] Open
Abstract
Organoid modeling is a powerful, robust and efficient technology faithfully preserving physiological and pathological characteristics of tissues of origin. Recently, substantial advances have been made in applying genetically engineered organoid models to study early tumorigenesis and premalignant biology. These efforts promise to identify novel avenues for early cancer detection, intervention and prevention. Here, we highlight significant advancements in the functional characterization of early genomic and epigenomic events during neoplastic evolution using organoid modeling, discuss the application of the lineage-tracing methodology in organoids to study cancer cells-of-origin, and review future opportunities for further development and improvement of organoid modeling of cancer precursors.
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Affiliation(s)
- Hua Zhao
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Casey Collet
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Dongzi Peng
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - Uttam K. Sinha
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - De-Chen Lin
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
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Distinct cellular immune profiles in lung adenocarcinoma manifesting as pure ground glass opacity versus solid nodules. J Cancer Res Clin Oncol 2022:10.1007/s00432-022-04289-3. [DOI: 10.1007/s00432-022-04289-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/14/2022] [Indexed: 10/15/2022]
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Zhang S, Pang K, Feng X, Zeng Y. Transcriptomic data exploration of consensus genes and molecular mechanisms between chronic obstructive pulmonary disease and lung adenocarcinoma. Sci Rep 2022; 12:13214. [PMID: 35918384 PMCID: PMC9345949 DOI: 10.1038/s41598-022-17552-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/27/2022] [Indexed: 11/09/2022] Open
Abstract
Most current research has focused on chronic obstructive pulmonary disease (COPD) and lung adenocarcinoma (LUAD) alone; however, it is important to understand the complex mechanism of COPD progression to LUAD. This study is the first to explore the unique and jointly molecular mechanisms in the pathogenesis of COPD and LUAD across several datasets based on a variety of analysis methods. We used weighted correlation network analysis to search hub genes in two datasets from public databases: GSE10072 and GSE76925. We explored the unique and jointly molecular mechanistic signatures of the two diseases in pathogenesis through enrichment analysis, immune infiltration analysis, and therapeutic targets analysis. Finally, the results were confirmed using real-time quantitative reverse transcription PCR. Fifteen hub genes were identified: GPI, EZH2, EFNA4, CFB, ENO1, SH3PXD2B, SELL, CORIN, MAD2L1, CENPF, TOP2A, ASPM, IGFBP2, CDKN2A, and ELF3. For the first time, SELL, CORIN, GPI, and EFNA4 were found to play a role in the etiology of COPD and LUAD. The LUAD genes identified were primarily involved in the cell cycle and DNA replication processes; COPD genes we found were related to ubiquitin-mediated proteolysis, ribosome, and T/B-cell receptor signaling pathways. The tumor microenvironment of LUAD pathogenesis was influenced by CD4 + T cells, type 1 regulatory T cells, and T helper 1 cells. T follicular helper cells, natural killer T cells, and B cells all impact the immunological inflammation in COPD. The results of drug targets analysis suggest that cisplatin and tretinoin, as well as bortezomib and metformin may be potential targeted therapy for patients with COPD combined LUAD. These signatures may be provided a new direction for developing early interventions and treatments to improve the prognosis of COPD and LUAD.
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Affiliation(s)
- Siyu Zhang
- Department of Respiratory Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 39 Yanhu Avenue, Wuchang District, Wuhan, 430000, Hubei, China
| | - Kun Pang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Xinyu Feng
- Department of Respiratory Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 39 Yanhu Avenue, Wuchang District, Wuhan, 430000, Hubei, China
| | - Yulan Zeng
- Department of Respiratory Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 39 Yanhu Avenue, Wuchang District, Wuhan, 430000, Hubei, China.
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Zheng Y, Zhou Z, Wei R, Xiao C, Zhang H, Fan T, Zheng B, Li C, He J. The RNA-binding protein PCBP1 represses lung adenocarcinoma progression by stabilizing DKK1 mRNA and subsequently downregulating β-catenin. J Transl Med 2022; 20:343. [PMID: 35907982 PMCID: PMC9338556 DOI: 10.1186/s12967-022-03552-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/24/2022] [Indexed: 12/02/2022] Open
Abstract
Background PolyC-RNA-binding protein 1 (PCBP1) functions as a tumour suppressor and RNA regulator that is downregulated in human cancers. Here, we aimed to reveal the biological function of PCBP1 in lung adenocarcinoma (LUAD). Methods First, PCBP1 was identified as an important biomarker that maintains LUAD through The Cancer Genome Atlas (TCGA) project screening and confirmed by immunohistochemistry and qPCR. Via colony formation, CCK8, IncuCyte cell proliferation, wound healing and Transwell assays, we confirmed that PCBP1 was closely related to the proliferation and migration of LUAD cells. The downstream gene DKK1 was discovered by RNA sequencing of PCBP1 knockdown cells. The underlying mechanisms were further investigated using western blot, qPCR, RIP, RNA pulldown and mRNA stability assays. Results We demonstrate that PCBP1 is downregulated in LUAD tumour tissues. The reduction in PCBP1 promotes the proliferation, migration and invasion of LUAD in vitro and in vivo. Mechanistically, the RNA-binding protein PCBP1 represses LUAD by stabilizing DKK1 mRNA. Subsequently, decreased expression of the DKK1 protein relieves the inhibitory effect on the Wnt/β-catenin signalling pathway. Taken together, these results show that PCBP1 acts as a tumour suppressor gene, inhibiting the tumorigenesis of LUAD. Conclusions We found that PCBP1 inhibits LUAD development by upregulating DKK1 to inactivate the Wnt/β-catenin pathway. Our findings highlight the potential of PCBP1 as a promising therapeutic target. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03552-y.
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Affiliation(s)
- Yujia Zheng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zheng Zhou
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ran Wei
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chu Xiao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hao Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tao Fan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bo Zheng
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chunxiang Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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Hu Y, Ding J, Wu C, Gao H, Ge M, Shao Q, Liu Y, Ye Q. Differential Expression and Prognostic Correlation of Immune Related Factors Between Right and Left Side Colorectal Cancer. Front Oncol 2022; 12:845765. [PMID: 35936748 PMCID: PMC9353740 DOI: 10.3389/fonc.2022.845765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Background Growing evidence suggests that colorectal cancer (CRC) should be considered a heterogeneous disease. The right side (RCC) and left side (LCC) colorectal cancer have different clinical characteristics and immune landscapes. The aim of this study was to analyze differential expression and prognostic correlation of immune-related factors between RCC and LCC. Methods The gene expression profile and clinical characteristics of CRC patients were retrieved from The Cancer Genome Atlas data portal (n=525). Using a deconvolution algorithm, immune cell infiltration in RCC and LCC based on the RNA-seq data was analyzed. Differentially expressed genes (DEGs) were obtained by performing differential gene expression analysis. Immune-related DEGs were derived by the intersection with immune-related factors downloaded from the IMMPORT database. To further validate the findings, we applied immunohistochemical (IHC) staining of a CRC tissue microarray (TMA). The distribution of immune cells in RCC and LCC and changes in the expression of immune molecules on their membranes were verified. The expression levels of circulating cytokines were measured by flow cytometry to detect the cytokines secreted by immune cells in RCC and LCC. Furthermore, to reveal the prognostic value of differential immune factors on RCC and LCC patients, survival analysis based on mRNA levels using TCGA cohort and survival analysis using protein levels was performed using our CRC patients. Results The infiltration of immune cells differed between RCC and LCC, the infiltration degree of macrophages M0 was significantly higher in LCC, while the infiltration degree of differentiated macrophages M1 and M2, CD4+ T and CD8+ T cells was significantly higher in RCC. The expression of related molecules by immune cells also differed between RCC and LCC. The expression of 7 genes in RCC was higher than that in LCC, which were CCR5, CD209, CD8A, HCK, HLA-DPB1, HLA-DQA1, HLA-DRA, respectively. Meanwhile, the expression of 2 genes in LCC was higher than in RCC, which were IL-34 and PROCR. Patients with RCC having high expression of HLA-DQA1 mRNA or proteins had better survival and LCC patients with high expression of IL 34 mRNA or protein had better survival. Conclusions In this study, we comprehensively compared differences in immune cells and regulating factors between left and right colorectal cancer. Different expression patterns and their effects on survival were identified. The analysis of immune-related factors may provide a theoretical basis for precise immunotherapy of RCC and LCC.
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Affiliation(s)
- Yue Hu
- Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Jie Ding
- Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Chengjiang Wu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Hong Gao
- Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Meiling Ge
- Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Qixiang Shao
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yanhong Liu
- Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- *Correspondence: Yanhong Liu, ; Qing Ye,
| | - Qing Ye
- Department of Pathology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Intelligent Pathology Institute, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- *Correspondence: Yanhong Liu, ; Qing Ye,
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Gao P, Zou K, Xiao L, Zhou H, Xu X, Zeng Z, Zhang W. High expression of PTGES3 is an independent predictive poor prognostic biomarker and correlates with immune infiltrates in lung adenocarcinoma. Int Immunopharmacol 2022; 110:108954. [PMID: 35820363 DOI: 10.1016/j.intimp.2022.108954] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/22/2022] [Accepted: 06/09/2022] [Indexed: 01/08/2023]
Abstract
BACKGROUND Immune-infiltration was positively relationship with overall survival in lung adenocarcinoma (LUAD). Nevertheless, the potential clinical value of PTGES3, especially in terms of prognosis and tumor immune-infiltration in LUAD had not been fully elucidated. METHODS Original data available from TCGA and GEO databases and integrated via R3.6.3. Kaplan-Meier and Cox regression methods were used to examine the effect of PTGES3 expression in overall survival, and nomogram was performed to illustrate the correlation between the PTGES3 expression and the risk of LUAD. The associate between PTGES3 and cancer immune characteristics were analyzed via the TISIDB databases. Western blot and RT-qPCR were used to analyze PTGES3 expression in the clinical lung adenocarcinoma tissue samples or non-small cell lung cancer cell lines. RESULTS PTGES3 mRNA and protein expression were significantly elevated in LUAD compared with normal lung tissues. Up-regulated PTGES3 was significantly associated with pathologic stage and TM stage. Kaplan-Meier survival analysis and subgroup analysis showed that up-regulated PTGES3 was associated with a worse overall survival of LUAD (HR = 1.71 (1.27-2.31), p < 0.001). Multivariate Cox analysis showed that high PTGES3 expression was an independent factor affecting overall survival (HR = 1.64 (1.14-2.37), p < 0.001). GO and KEGG analysis revealed that the cell cycle, regulation of DNA replication, and regulation of innate immune response were enriched. A positive correlation between PTGES3 expression and immune infiltrating levels of Th2 cells was found. CONCLUSION PTGES3 may play an important role in the cell cycle and as an independent predictive prognostic biomarker correlates with immune infiltrates in lung adenocarcinoma.
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Affiliation(s)
- Pengxiang Gao
- Department of Respiratory Medicine, the First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province 330006, China
| | - Kang Zou
- Department of Critical Care Medicine, the First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province 330006, China; Department of Critical Care Medicine, the First Affiliated Hospital of Gannan Medical College, Ganzhou City, Jiangxi Province 341000, China
| | - Li Xiao
- Department of Rehabilitation Medicine, the First Affiliated Hospital of Gannan Medical College, Ganzhou City, Jiangxi Province 341000, China
| | - Hongxia Zhou
- Department of Nephrology, No. 908 Hospital of People's Liberation Army, Nanchang 330000, Jiangxi, People's Republic of China
| | - Xinping Xu
- Jiangxi Institute of Respiratory Diseases, the First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province 330006, China; Jiangxi Clinical Research Center for Respiratory Diseases, the First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province 330006, China
| | - Zhenguo Zeng
- Department of Critical Care Medicine, the First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province 330006, China
| | - Wei Zhang
- Department of Respiratory Medicine, the First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province 330006, China; Jiangxi Institute of Respiratory Diseases, the First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province 330006, China; Jiangxi Clinical Research Center for Respiratory Diseases, the First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province 330006, China.
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Ono Y, Tagawa T, Kinoshita F, Haratake N, Takada K, Kohno M, Takenaka T, Kamitani T, Shimokawa M, Oda Y, Mori M, Yoshizumi T. Relationship between consolidation tumor ratio and tumor-infiltrating lymphocytes in small-sized lung adenocarcinoma. Thorac Cancer 2022; 13:2134-2141. [PMID: 35791738 PMCID: PMC9346188 DOI: 10.1111/1759-7714.14524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/09/2022] [Accepted: 05/14/2022] [Indexed: 11/30/2022] Open
Abstract
Background Consolidation tumor ratio (CTR) is associated with cancer progression and histological invasiveness in lung adenocarcinoma (LAD). However, little is known about the association between CTR and immune‐related factors, including tumor‐infiltrating lymphocytes (TILs) density or tumor expression of programmed death ligand 1 (PD‐L1) and indoleamine 2,3‐dioxygenase 1 (IDO1) in small‐sized LAD. Methods This study included 258 patients with LAD (<3 cm) who underwent surgery. Patients were assigned to four groups: CTR = 0; 0 < CTR <0.5; 0.5 ≤ CTR <1 (ground‐glass opacity [GGO] group); and CTR = 1 (pure‐solid group). CD4+, CD8+, and FoxP3+ TIL density and PD‐L1 and IDO1 tumor expression were assessed by immunohistochemistry. Results Among the GGO group, CD8+ and FoxP3+ TIL density increased significantly with increasing CTR (p < 0.001 and p < 0.001, respectively). Moreover, PD‐L1 and IDO1 expression was significantly higher in the pure‐solid group than in the GGO group (p < 0.001 and p < 0.001, respectively). Conclusions CTR was correlated with the abundance of CD8+ and FoxP3+ TILs in the GGO group. PD‐L1 and IDO1 positivity rates were significantly higher in the pure‐solid group than in the GGO group. Increased CTR may be correlated with immunosuppressive condition.
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Affiliation(s)
- Yuki Ono
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuzo Tagawa
- Department of Thoracic Surgery, Clinical Research Institute, National Hospital Organization, Kyushu Medical Center, Fukuoka, Japan
| | - Fumihiko Kinoshita
- Department of Thoracic Oncology, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Naoki Haratake
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kazuki Takada
- Department of Surgery, Saiseikai Fukuoka General Hospital, Fukuoka, Japan
| | - Mikihiro Kohno
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tomoyoshi Takenaka
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takeshi Kamitani
- Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Mototsugu Shimokawa
- Department of Biostatistics, Yamaguchi University Graduate School of Medicine, Yamaguchi, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masaki Mori
- Tokai University School of Medicine, Tokyo, Japan
| | - Tomoharu Yoshizumi
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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Wang Q, He Y, Li W, Xu X, Hu Q, Bian Z, Xu A, Tu H, Wu M, Wu X. Soluble Immune Checkpoint-Related Proteins in Blood Are Associated With Invasion and Progression in Non-Small Cell Lung Cancer. Front Immunol 2022; 13:887916. [PMID: 35874720 PMCID: PMC9296827 DOI: 10.3389/fimmu.2022.887916] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundImmune checkpoint inhibition therapy has been achieved significant success in the treatment of non-small cell lung cancer (NSCLC). However, the role of soluble immune checkpoint- related proteins in NSCLC remains obscure.MethodsWe evaluated the circulating levels of 14 immune checkpoint-related proteins panel (BTLA, LAG-3, GITR, IDO, PD-L2, PD-L1, PD-1, HVEM, Tim-3, CD28, CD27, CD80, CD137 and CTLA-4) and their associations with the risk of invasive disease and the risk of NSCLC in 43 pre-invasive (AIS), 81 invasive NSCLC (IAC) patients and matched 35 healthy donors using a multiplex Luminex assay. Gene expression in tumors from TCGA were analyzed to elucidate potential mechanisms. The multivariate logistic regression model was applied in the study. ROC(receiver operator characteristic) curve and calibration curve were used in the performance evaluation.ResultsWe found that sCD27, sCD80, CD137 and sPDL2 levels were significantly increased in IAC cases compared to AIS cases (P= 1.05E-06, 4.44E-05, 2.30E-05 and 1.16E-06, respectively), whereas sPDL1 and sPDL2 levels were significantly increased in NSCLC cases compared to healthy controls (P=3.25E-05 and 1.49E-05, respectively). Unconditional univariate logistic regression analysis indicated that increased sCD27, sCD80, sCD137, and sPDL2 were significantly correlated with the risk of invasive diseases. The model with clinical variables, sCD27 and sPDL2 demonstrated the best performance (AUC=0.845) in predicting the risk of IAC. CD27 and PDCD1LG2 (PDL2) showed significant association with cancer invasion signature in TCGA dataset.ConclusionOur study provides evidence that soluble immune checkpoint-related proteins may associate with the risk of IAC, and we further established an optimized multivariate predictive model, which highlights their potential application in the treatment of NSCLC patients. Future studies may apply these biomarkers to test their predictive value of survival and treatment outcome during immunotherapy in NSCLC patients.
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Affiliation(s)
- Qinchuan Wang
- Center for Biostatistics, Bioinformatics and Big Data, The Second Affiliated Hospital and School of Public Health, Zhejiang University School of Medicine, Hangzhou, China
- Department of Surgical Oncology, Affiliated Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Hangzhou, China
| | - Yue He
- Center for Biostatistics, Bioinformatics and Big Data, The Second Affiliated Hospital and School of Public Health, Zhejiang University School of Medicine, Hangzhou, China
- The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Hangzhou, China
| | - Wanlu Li
- Center for Biostatistics, Bioinformatics and Big Data, The Second Affiliated Hospital and School of Public Health, Zhejiang University School of Medicine, Hangzhou, China
- The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Hangzhou, China
| | - Xiaohang Xu
- Center for Biostatistics, Bioinformatics and Big Data, The Second Affiliated Hospital and School of Public Health, Zhejiang University School of Medicine, Hangzhou, China
- The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Hangzhou, China
| | - Qingfeng Hu
- Center for Biostatistics, Bioinformatics and Big Data, The Second Affiliated Hospital and School of Public Health, Zhejiang University School of Medicine, Hangzhou, China
- The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Hangzhou, China
| | - Zilong Bian
- Center for Biostatistics, Bioinformatics and Big Data, The Second Affiliated Hospital and School of Public Health, Zhejiang University School of Medicine, Hangzhou, China
- The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Hangzhou, China
| | - Andi Xu
- Center for Biostatistics, Bioinformatics and Big Data, The Second Affiliated Hospital and School of Public Health, Zhejiang University School of Medicine, Hangzhou, China
- The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Hangzhou, China
| | - Huakang Tu
- Center for Biostatistics, Bioinformatics and Big Data, The Second Affiliated Hospital and School of Public Health, Zhejiang University School of Medicine, Hangzhou, China
- The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Hangzhou, China
| | - Ming Wu
- Department of Thoracic Surgery, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Xifeng Wu, ; Ming Wu,
| | - Xifeng Wu
- Center for Biostatistics, Bioinformatics and Big Data, The Second Affiliated Hospital and School of Public Health, Zhejiang University School of Medicine, Hangzhou, China
- The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Hangzhou, China
- *Correspondence: Xifeng Wu, ; Ming Wu,
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Zhao Y, Shang J, Gao J, Han H, Gao Z, Yan Y, Zheng Q, Ye T, Fu F, Deng C, Ma Z, Zhang Y, Zheng D, Zheng S, Li Y, Cao Z, Shi L, Chen H. Increased Tumor Intrinsic Growth Potential and Decreased Immune Function Orchestrate the Progression of Lung Adenocarcinoma. Front Immunol 2022; 13:921761. [PMID: 35844495 PMCID: PMC9283781 DOI: 10.3389/fimmu.2022.921761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
Background The overall 5-year survival of lung cancer was reported to be only ~15%, with lung adenocarcinoma (LUAD) as the main pathological subtype. Before developing into invasive stages, LUAD undergoes pre-invasive stages of adenocarcinoma in situ (AIS) and minimally invasive adenocarcinoma (MIA), where surgical resection gives an excellent 5-year survival rate. Given the dramatic decline of prognosis from pre-invasive to invasive stages, a deeper understanding of key molecular changes driving the progression of LUAD is highly needed. Methods In this study, we performed whole-exome sequencing and RNA sequencing on surgically resected 24 AIS, 74 MIA, 99 LUAD specimens, and their adjacent paired normal tissues. Survival data were obtained by follow-up after surgery. Key molecular events were found by comparing the gene expression profiles of tumors with different stages. Finally, to measure the level of imbalance between tumor intrinsic growth potential and immune microenvironment, a tumor progressive (TP) index was developed to predict tumor progression and patients’ survival outcome and validated by external datasets. Results As tumors progressed to more invasive stages, they acquired higher growth potential, mutational frequency of tumor suppressor genes, somatic copy number alterations, and tumor mutation burden, along with suppressed immune function. To better predict tumor progression and patients’ outcome, TP index were built to measure the imbalance between tumor intrinsic growth potential and immune microenvironment. Patients with a higher TP index had significantly worse recurrence-free survival [Hazard ratio (HR), 10.47; 95% CI, 3.21–34.14; p < 0.0001] and overall survival (OS) [Hazard ratio (HR), 4.83e8; 95% CI, 0–Inf; p = 0.0013]. We used The Cancer Genome Atlas (TCGA)-LUAD dataset for validation and found that patients with a higher TP index had significantly worse OS (HR, 1.10; 95% CI, 0.83–1.45; p = 0.048), demonstrating the prognostic value of the TP index for patients with LUAD. Conclusions The imbalance of tumor intrinsic growth potential and immune function orchestrate the progression of LUAD, which can be measured by TP index. Our study provided new insights into predicting survival of patients with LUAD and new target discovery for LUAD through assessing the imbalance between tumor intrinsic growth potential and immune function.
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Affiliation(s)
- Yue Zhao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jun Shang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jian Gao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- International Human Phenome Institutes (Shanghai), Shanghai, China
| | - Han Han
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhendong Gao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yueren Yan
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qiang Zheng
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Ting Ye
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fangqiu Fu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chaoqiang Deng
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zelin Ma
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yang Zhang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Difan Zheng
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shanbo Zheng
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuan Li
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Zhiwei Cao
- School of Life Sciences, Fudan University, Shanghai, China
- *Correspondence: Haiquan Chen, ; Leming Shi, ; Zhiwei Cao,
| | - Leming Shi
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
- *Correspondence: Haiquan Chen, ; Leming Shi, ; Zhiwei Cao,
| | - Haiquan Chen
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- *Correspondence: Haiquan Chen, ; Leming Shi, ; Zhiwei Cao,
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Sun X, Huang X, Sun X, Chen S, Zhang Z, Yu Y, Zhang P. Oxidative Stress-Related lncRNAs Are Potential Biomarkers for Predicting Prognosis and Immune Responses in Patients With LUAD. Front Genet 2022; 13:909797. [PMID: 35754800 PMCID: PMC9214656 DOI: 10.3389/fgene.2022.909797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/04/2022] [Indexed: 12/24/2022] Open
Abstract
Lung adenocarcinoma is increasingly harmful to society and individuals as cancer with an inferior prognosis and insensitive to chemotherapy. Previous studies have demonstrated that oxidative stress and lncRNAs play a vital role in many biological processes. Therefore, we explored the role of lncRNAs associated with oxidative stress in the prognosis and survival of LUAD patients. We examined the expression profiles of lncRNAs and oxidative stress genes in this study. A prognosis prediction model and a nomogram were built based on oxidative stress-related lncRNAs. Functional and drug sensitivity analyses were also performed depending on oxidative stress-related lncRNA signature. Moreover, we investigated the relationship between immune response and immunotherapy. The results showed that a risk scoring model based on 16 critical oxidative stress lncRNAs was able to distinguish the clinical status of LUAD and better predict the prognosis and survival. Additionally, the model demonstrated a close correlation with the tumor immune system, and these key lncRNAs also revealed the relationship between LUAD and chemotherapeutic drug sensitivity. Our work aims to provide new perspectives and new ideas for the treatment and management of LUAD.
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Affiliation(s)
- Xinti Sun
- Department of Thoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Xingqi Huang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiaojuan Sun
- Department of Oncology, Qingdao University Affiliated Hospital, Qingdao, China
| | - Si Chen
- Department of Thoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Zeyang Zhang
- Department of Thoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Yao Yu
- Department of Thoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Peng Zhang
- Department of Thoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
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50
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Lin H, Pan X, Feng Z, Yan L, Hua J, Liang Y, Han C, Xu Z, Wang Y, Wu L, Cui Y, Huang X, Shi Z, Chen X, Chen X, Zhang Q, Liang C, Zhao K, Li Z, Liu Z. Automated whole-slide images assessment of immune infiltration in resected non-small-cell lung cancer: towards better risk-stratification. J Transl Med 2022; 20:261. [PMID: 35672787 PMCID: PMC9172185 DOI: 10.1186/s12967-022-03458-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/29/2022] [Indexed: 02/08/2023] Open
Abstract
Background High immune infiltration is associated with favourable prognosis in patients with non-small-cell lung cancer (NSCLC), but an automated workflow for characterizing immune infiltration, with high validity and reliability, remains to be developed. Methods We performed a multicentre retrospective study of patients with completely resected NSCLC. We developed an image analysis workflow for automatically evaluating the density of CD3+ and CD8+ T-cells in the tumour regions on immunohistochemistry (IHC)-stained whole-slide images (WSIs), and proposed an immune scoring system “I-score” based on the automated assessed cell density. Results A discovery cohort (n = 145) and a validation cohort (n = 180) were used to assess the prognostic value of the I-score for disease-free survival (DFS). The I-score (two-category) was an independent prognostic factor after adjusting for other clinicopathologic factors. Compared with a low I-score (two-category), a high I-score was associated with significantly superior DFS in the discovery cohort (adjusted hazard ratio [HR], 0.54; 95% confidence interval [CI] 0.33–0.86; P = 0.010) and validation cohort (adjusted HR, 0.57; 95% CI 0.36–0.92; P = 0.022). The I-score improved the prognostic stratification when integrating it into the Cox proportional hazard regression models with other risk factors (discovery cohort, C-index 0.742 vs. 0.728; validation cohort, C-index 0.695 vs. 0.685). Conclusion This automated workflow and immune scoring system would advance the clinical application of immune microenvironment evaluation and support the clinical decision making for patients with resected NSCLC. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03458-9.
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