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Boutzen H, Murison A, Oriecuia A, Bansal S, Arlidge C, Wang JCY, Lupien M, Kaufmann KB, Dick JE. Identification of leukemia stem cell subsets with distinct transcriptional, epigenetic and functional properties. Leukemia 2024; 38:2090-2101. [PMID: 39169113 PMCID: PMC11436360 DOI: 10.1038/s41375-024-02358-9] [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: 01/03/2024] [Revised: 07/02/2024] [Accepted: 07/17/2024] [Indexed: 08/23/2024]
Abstract
The leukemia stem cell (LSC) compartment is a complex reservoir fueling disease progression in acute myeloid leukemia (AML). The existence of heterogeneity within this compartment is well documented but prior studies have focused on genetic heterogeneity without being able to address functional heterogeneity. Understanding this heterogeneity is critical for the informed design of therapies targeting LSC, but has been hampered by LSC scarcity and the lack of reliable cell surface markers for viable LSC isolation. To overcome these challenges, we turned to the patient-derived OCI-AML22 cell model. This model includes functionally, transcriptionally and epigenetically characterized LSC broadly representative of LSC found in primary AML samples. Focusing on the pool of LSC, we used an integrated approach combining xenograft assays with single-cell analysis to identify two LSC subtypes with distinct transcriptional, epigenetic and functional properties. These LSC subtypes differed in depth of quiescence, differentiation potential, repopulation capacity, sensitivity to chemotherapy and could be isolated based on CD112 expression. A majority of AML patient samples had transcriptional signatures reflective of either LSC subtype, and some even showed coexistence within an individual sample. This work provides a framework for investigating the LSC compartment and designing combinatorial therapeutic strategies in AML.
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Affiliation(s)
- Héléna Boutzen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 0A3, Canada.
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 0A3, Canada
| | - Alexa Oriecuia
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 0A3, Canada
| | - Suraj Bansal
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 0A3, Canada
| | - Christopher Arlidge
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 0A3, Canada
| | - Jean C Y Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 0A3, Canada
- Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 0A3, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5S 1A4, Canada
| | - Kerstin B Kaufmann
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 0A3, Canada.
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 0A3, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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2
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Jia R, Liang X, Tu J, Yang H. A scoring model for the expression of genes related to programmed cell death predicts immunotherapy response and prognosis in lung adenocarcinoma. Discov Oncol 2024; 15:435. [PMID: 39264392 PMCID: PMC11393378 DOI: 10.1007/s12672-024-01319-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Accepted: 09/05/2024] [Indexed: 09/13/2024] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) continues to be the leading cause of cancer death worldwide, driven by environmental factors like smoking and genetic predispositions. LUAD has a high mortality rate, and new biomarkers are urgently needed to improve treatment strategies and patient management. Programmed cell death (PCD) is involved in tumor progression and response to treatment. Therefore, there is a need for an extensive study of the role and functions of PCD-related genes (PCDRGs) in lung adenocarcinoma so as to understand the pathophysiologic features of lung adenocarcinoma. METHODS Based on TCGA and GEO databases, this research is aimed at screening differentially expressed PCD-related genes in lung adenocarcinoma. We conducted GO, and KEGG analysis to establish the link between these genes and biological processes. By applying various machine learning algorithms such as CoxBoost analysis, we developed PCD-related indices (PCDI) that were used to verify their ability to predict prognosis with the use of other datasets. This was done in addition to exploring the biological functions of PCD genes associated with lung adenocarcinoma by assessing the relationship between immune cell components of tumor microenvironment and PCD genes together with examining how they affect drug sensitivity. RESULTS The research presented in this article offers significant insights into LUAD. The authors identified 113 PCDRGs that were differentially expressed in LUAD. These genes are implicated in various biological functions, including High risk ing apoptosis, ferroptosis, and pathways specific to non-small cell lung cancer. Notably, the PCDI proved effective in distinguishing between High risk and Low risk LUAD patients, demonstrating a higher accuracy in prognosis prediction compared to traditional clinical indicators such as age and gender. This high prediction accuracy was validated in both test and validation cohorts. Additionally, these genes showed significant correlations with immune cell infiltration and drug sensitivity in LUAD patients. CONCLUSION We analysed the expression and function of PCDRGs in LUAD and revealed their correlation with patient survival, the immune microenvironment and drug sensitivity. The constructed PCDI model provides a scientific basis for the personalised treatment of lung adenocarcinoma, and future optimisation of treatment strategies based on these genes may improve patient clinical outcomes.
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Affiliation(s)
- Runan Jia
- Cancer Center, Lishui Central Hospital, The Fifth Affiliated Hospital of Wenzhou Medical College, Zhejiang University Lishui Hospital, Lishui Central Hospital, 289 Kuangcang Road, Lishui City, 323000, Zhejiang Province, China
| | - Xiaolong Liang
- Pharmacy Department, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, No.150 Ximen Street, Linhai City, Taizhou City, 317000, Zhejiang Province, China
| | - Jianfei Tu
- Cancer Center, Lishui Central Hospital, The Fifth Affiliated Hospital of Wenzhou Medical College, Zhejiang University Lishui Hospital, Lishui Central Hospital, 289 Kuangcang Road, Lishui City, 323000, Zhejiang Province, China.
| | - Hongyuan Yang
- Cancer Center, Lishui Central Hospital, The Fifth Affiliated Hospital of Wenzhou Medical College, Zhejiang University Lishui Hospital, Lishui Central Hospital, 289 Kuangcang Road, Lishui City, 323000, Zhejiang Province, China.
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Hlady RA, Zhao X, El Khoury LY, Wagner RT, Luna A, Pham K, Pyrosopoulos NT, Jain D, Wang L, Liu C, Robertson KD. Epigenetic heterogeneity hotspots in human liver disease progression. Hepatology 2024:01515467-990000000-00966. [PMID: 39028883 DOI: 10.1097/hep.0000000000001023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 06/30/2024] [Indexed: 07/21/2024]
Abstract
BACKGROUND AND AIMS Disruption of the epigenome is a hallmark of human disease, including liver cirrhosis and HCC. While genetic heterogeneity is an established effector of pathologic phenotypes, epigenetic heterogeneity is less well understood. Environmental exposures alter the liver-specific DNA methylation landscape and influence the onset of liver cancer. Given that currently available treatments are unable to target frequently mutated genes in HCC, there is an unmet need for novel therapeutics to prevent or reverse liver damage leading to hepatic tumorigenesis, which the epigenome may provide. APPROACH AND RESULTS We performed genome-wide profiling of DNA methylation, copy number, and gene expression from multiple liver regions from 31 patients with liver disease to examine their crosstalk and define the individual and combinatorial contributions of these processes to liver disease progression. We identified epigenetic heterogeneity hotspots that are conserved across patients. Elevated epigenetic heterogeneity is associated with increased gene expression heterogeneity. Cirrhotic regions comprise 2 distinct cohorts-one exclusively epigenetic, and the other where epigenetic and copy number variations collaborate. Epigenetic heterogeneity hotspots are enriched for genes central to liver function (eg, HNF1A ) and known tumor suppressors (eg, RASSF1A ). These hotspots encompass genes including ACSL1 , ACSL5 , MAT1A , and ELFN1 , which have phenotypic effects in functional screens, supporting their relevance to hepatocarcinogenesis. Moreover, epigenetic heterogeneity hotspots are linked to clinical measures of outcome. CONCLUSIONS Substantial epigenetic heterogeneity arises early in liver disease development, targeting key pathways in the progression and initiation of both cirrhosis and HCC. Integration of epigenetic and transcriptional heterogeneity unveils putative epigenetic regulators of hepatocarcinogenesis.
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Affiliation(s)
- Ryan A Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Xia Zhao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Louis Y El Khoury
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Ryan T Wagner
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Aesis Luna
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Kien Pham
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | | | - Dhanpat Jain
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Liguo Wang
- Division of Computational Biology, Mayo Clinic, Department of Quantitative Health Sciences, Rochester, Minnesota, USA
| | - Chen Liu
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
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Peng W, Fu J, Zhou L, Duan H. METTL1/FOXM1 promotes lung adenocarcinoma progression and gefitinib resistance by inhibiting PTPN13 expression. Cancer Med 2024; 13:e7420. [PMID: 38967523 PMCID: PMC11225164 DOI: 10.1002/cam4.7420] [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: 02/01/2024] [Revised: 05/17/2024] [Accepted: 06/07/2024] [Indexed: 07/06/2024] Open
Abstract
INTRODUCTION Lung adenocarcinoma (LUAD) is the most common malignant tumor in respiratory system. Methyltransferase-like 1 (METTL1) is a driver of m7G modification in mRNA. This study aimed to demonstrate the role of METTL1 in the proliferation, invasion and Gefitinib-resistance of LUAD. METHODS Public datasets were downloaded from the Gene Expression Profiling Interactive Analysis (GEPIA) and GSE31210 datasets. Malignant tumor phenotypes were tested in vitro and in vivo through biological function assays and nude mouse with xenograft tumors. RNA immunoprecipitation assays were conducted to determine the interaction between METTL1 protein and FOXM1 mRNA. Public transcriptional database, Chromatin immunoprecipitation and luciferase report assays were conducted to detect the downstream target of a transcriptional factor FOXM1. Half maximal inhibitory concentration (IC50) was calculated to evaluate the sensitivity to Gefitinib in LUAD cells. RESULTS The results showed that METTL1 was upregulated in LUAD, and the high expression of METTL1 was associated with unfavorable prognosis. Through the m7G-dependent manner, METTL1 improved the RNA stability of FOXM1, leading to the up-regulation of FOXM1. FOXM1 transcriptionally suppressed PTPN13 expression. The METTL1/FOXM1/PTPN13 axis reduced the sensitivity of LUAD cells to Gefitinib. Taken together, our data suggested that METTL1 plays oncogenic role in LUAD through inducing the m7G modification of FOXM1, therefore METTL1 probably is a new potential therapeutic target to counteract Gefitinib resistance in LUAD.
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Affiliation(s)
- Wei Peng
- Department of Oncology, Hunan Provincial People's HospitalThe First Affiliated of Human Normal UniversityChangshaHunanChina
- Key Laboratory of Study and Discovey of Small Targeted Molecules of Hunan ProvinceHunan Normal UniversityChangshaHunanChina
- Laboratory of Oncology, Institute of Translational MedicineHunan Procincial People's HospitalChangshaHunanChina
| | - Jia Fu
- Department of Oncology, Hunan Provincial People's HospitalThe First Affiliated of Human Normal UniversityChangshaHunanChina
| | - Lijun Zhou
- Department of Oncology, Hunan Provincial People's HospitalThe First Affiliated of Human Normal UniversityChangshaHunanChina
| | - Huaxin Duan
- Department of Oncology, Hunan Provincial People's HospitalThe First Affiliated of Human Normal UniversityChangshaHunanChina
- Key Laboratory of Study and Discovey of Small Targeted Molecules of Hunan ProvinceHunan Normal UniversityChangshaHunanChina
- Laboratory of Oncology, Institute of Translational MedicineHunan Procincial People's HospitalChangshaHunanChina
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Yang M, Shulkin N, Gonzalez E, Castillo J, Yan C, Zhang K, Arvanitis L, Borok Z, Wallace WD, Raz D, Torres ETR, Marconett CN. Cell of origin alters myeloid-mediated immunosuppression in lung adenocarcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.19.599651. [PMID: 38948812 PMCID: PMC11213232 DOI: 10.1101/2024.06.19.599651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Solid carcinomas are often highly heterogenous cancers, arising from multiple epithelial cells of origin. Yet, how the cell of origin influences the response of the tumor microenvironment is poorly understood. Lung adenocarcinoma (LUAD) arises in the distal alveolar epithelium which is populated primarily by alveolar epithelial type I (AT1) and type II (AT2) cells. It has been previously reported that Gramd2 + AT1 cells can give rise to a histologically-defined LUAD that is distinct in pathology and transcriptomic identity from that arising from Sftpc + AT2 cells1,2. To determine how cells of origin influence the tumor immune microenvironment (TIME) landscape, we comprehensively characterized transcriptomic, molecular, and cellular states within the TIME of Gramd2 + AT1 and Sftpc + AT2-derived LUAD using KRASG12D oncogenic driver mouse models. Myeloid cells within the Gramd2 + AT1-derived LUAD TIME were increased, specifically, immunoreactive monocytes and tumor associated macrophages (TAMs). In contrast, the Sftpc + AT2 LUAD TIME was enriched for Arginase-1+ myeloid derived suppressor cells (MDSC) and TAMs expressing profiles suggestive of immunosuppressive function. Validation of immune infiltration was performed using flow cytometry, and intercellular interaction analysis between the cells of origin and major myeloid cell populations indicated that cell-type specific markers SFTPD in AT2 cells and CAV1 in AT1 cells mediated unique interactions with myeloid cells of the differential immunosuppressive states within each cell of origin mouse model. Taken together, Gramd2 + AT1-derived LUAD presents with an anti-tumor, immunoreactive TIME, while the TIME of Sftpc + AT2-derived LUAD has hallmarks of immunosuppression. This study suggests that LUAD cell of origin influences the composition and suppression status of the TIME landscape and may hold critical implications for patient response to immunotherapy.
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Affiliation(s)
- Minxiao Yang
- Department of Integrative Translational Sciences, Beckman Research Institute, City of Hope, Duarte, CA USA 91010
- Department of Surgery, University of Southern California, Los Angeles, CA USA 90089
- Department of Translational Genomics, University of Southern California, Los Angeles, CA USA 90089
| | - Noah Shulkin
- Department of Integrative Translational Sciences, Beckman Research Institute, City of Hope, Duarte, CA USA 91010
| | - Edgar Gonzalez
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA USA 90089
| | - Jonathan Castillo
- Department of Integrative Translational Sciences, Beckman Research Institute, City of Hope, Duarte, CA USA 91010
| | - Chunli Yan
- Department of Surgery, University of Southern California, Los Angeles, CA USA 90089
| | - Keqiang Zhang
- Division of Thoracic Surgery, Department of Surgery, City of Hope National Medical Center, City of Hope, Duarte, CA USA 91010
| | - Leonidas Arvanitis
- Department of Pathology, City of Hope National Medical Center, City of Hope, Duarte, CA USA 91010
| | - Zea Borok
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA USA 92093
| | - W. Dean Wallace
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA USA 90089
| | - Dan Raz
- Division of Thoracic Surgery, Department of Surgery, City of Hope National Medical Center, City of Hope, Duarte, CA USA 91010
| | - Evanthia T. Roussos Torres
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA USA 90089
| | - Crystal N. Marconett
- Department of Integrative Translational Sciences, Beckman Research Institute, City of Hope, Duarte, CA USA 91010
- Department of Surgery, University of Southern California, Los Angeles, CA USA 90089
- Department of Translational Genomics, University of Southern California, Los Angeles, CA USA 90089
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Cheng J, Xiao M, Meng Q, Zhang M, Zhang D, Liu L, Jin Q, Fu Z, Li Y, Chen X, Xie H. Decoding temporal heterogeneity in NSCLC through machine learning and prognostic model construction. World J Surg Oncol 2024; 22:156. [PMID: 38872167 PMCID: PMC11170806 DOI: 10.1186/s12957-024-03435-0] [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: 03/11/2024] [Accepted: 06/01/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) is a prevalent and heterogeneous disease with significant genomic variations between the early and advanced stages. The identification of key genes and pathways driving NSCLC tumor progression is critical for improving the diagnosis and treatment outcomes of this disease. METHODS In this study, we conducted single-cell transcriptome analysis on 93,406 cells from 22 NSCLC patients to characterize malignant NSCLC cancer cells. Utilizing cNMF, we classified these cells into distinct modules, thus identifying the diverse molecular profiles within NSCLC. Through pseudotime analysis, we delineated temporal gene expression changes during NSCLC evolution, thus demonstrating genes associated with disease progression. Using the XGBoost model, we assessed the significance of these genes in the pseudotime trajectory. Our findings were validated by using transcriptome sequencing data from The Cancer Genome Atlas (TCGA), supplemented via LASSO regression to refine the selection of characteristic genes. Subsequently, we established a risk score model based on these genes, thus providing a potential tool for cancer risk assessment and personalized treatment strategies. RESULTS We used cNMF to classify malignant NSCLC cells into three functional modules, including the metabolic reprogramming module, cell cycle module, and cell stemness module, which can be used for the functional classification of malignant tumor cells in NSCLC. These findings also indicate that metabolism, the cell cycle, and tumor stemness play important driving roles in the malignant evolution of NSCLC. We integrated cNMF and XGBoost to select marker genes that are indicative of both early and advanced NSCLC stages. The expression of genes such as CHCHD2, GAPDH, and CD24 was strongly correlated with the malignant evolution of NSCLC at the single-cell data level. These genes have been validated via histological data. The risk score model that we established (represented by eight genes) was ultimately validated with GEO data. CONCLUSION In summary, our study contributes to the identification of temporal heterogeneous biomarkers in NSCLC, thus offering insights into disease progression mechanisms and potential therapeutic targets. The developed workflow demonstrates promise for future applications in clinical practice.
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Affiliation(s)
- Junpeng Cheng
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, P. R. China
| | - Meizhu Xiao
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, P. R. China
| | - Qingkang Meng
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, P. R. China
| | - Min Zhang
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, P. R. China
| | - Denan Zhang
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, P. R. China
| | - Lei Liu
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, P. R. China
| | - Qing Jin
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, P. R. China
| | - Zhijin Fu
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, P. R. China
| | - Yanjiao Li
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, P. R. China
| | - Xiujie Chen
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, P. R. China.
| | - Hongbo Xie
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, P. R. China.
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Sun L, Guo W, Guo L, Chen X, Zhou H, Yan S, Zhao G, Bao H, Wu X, Shao Y, Ying J, Lin L. Molecular landscape and multi-omic measurements of heterogeneity in fetal adenocarcinoma of the lung. NPJ Precis Oncol 2024; 8:99. [PMID: 38831114 PMCID: PMC11148097 DOI: 10.1038/s41698-024-00569-y] [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: 08/22/2023] [Accepted: 02/26/2024] [Indexed: 06/05/2024] Open
Abstract
Fetal adenocarcinoma of the lung (FLAC) is a rare form of lung adenocarcinoma and was divided into high-grade (H-FLAC) and low-grade (L-FLAC) subtypes. Despite the existence of some small case series studies, a comprehensive multi-omics study of FLAC has yet to be undertaken. In this study, we depicted the multi-omics landscapes of this rare lung cancer type by performing multi-regional sampling on 20 FLAC cases. A comparison of multi-omics profiles revealed significant differences between H-FLAC and L-FLAC in a multi-omic landscape. Two subtypes also showed distinct relationships between multi-layer intratumor heterogeneity (ITH). We discovered that a lower genetic ITH was significantly associated with worse recurrence-free survival and overall survival in FLAC patients, whereas higher methylation ITH in H-FLAC patients suggested a short survival. Our findings highlight the complex interplay between genetic and transcriptional heterogeneity in FLAC and suggest that different types of ITH may have distinct implications for patient prognosis.
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Affiliation(s)
- Li Sun
- 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, People's Republic of China
| | - Wei Guo
- 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, People's Republic of China.
- Key Laboratory of Minimally Invasive Therapy Research for Lung Cancer, Chinese Academy of Medical Sciences, Beijing, China.
| | - Lei Guo
- 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, People's Republic of China
| | - Xiaoxi Chen
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, Nanjing, China
| | - Haitao Zhou
- Department of Thoracic Surgery, Peking University Cancer Hospital and Institute, Beijing, China
| | - Shi Yan
- Department of Thoracic Surgery, Peking University Cancer Hospital and Institute, Beijing, China
| | - Gang Zhao
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Hua Bao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, Nanjing, China
| | - Xue Wu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, Nanjing, China
| | - Yang Shao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, Nanjing, China
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jianming Ying
- 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, People's Republic of China.
| | - Lin Lin
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.
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El-Tanani M, Rabbani SA, Babiker R, Rangraze I, Kapre S, Palakurthi SS, Alnuqaydan AM, Aljabali AA, Rizzo M, El-Tanani Y, Tambuwala MM. Unraveling the tumor microenvironment: Insights into cancer metastasis and therapeutic strategies. Cancer Lett 2024; 591:216894. [PMID: 38626856 DOI: 10.1016/j.canlet.2024.216894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/29/2024] [Accepted: 04/11/2024] [Indexed: 05/03/2024]
Abstract
This comprehensive review delves into the pivotal role of the tumor microenvironment (TME) in cancer metastasis and therapeutic response, offering fresh insights into the intricate interplay between cancer cells and their surrounding milieu. The TME, a dynamic ecosystem comprising diverse cellular and acellular elements, not only fosters tumor progression but also profoundly affects the efficacy of conventional and emerging cancer therapies. Through nuanced exploration, this review illuminates the multifaceted nature of the TME, elucidating its capacity to engender drug resistance via mechanisms such as hypoxia, immune evasion, and the establishment of physical barriers to drug delivery. Moreover, it investigates innovative therapeutic approaches aimed at targeting the TME, including stromal reprogramming, immune microenvironment modulation, extracellular matrix (ECM)-targeting agents, and personalized medicine strategies, highlighting their potential to augment treatment outcomes. Furthermore, this review critically evaluates the challenges posed by the complexity and heterogeneity of the TME, which contribute to variable therapeutic responses and potentially unintended consequences. This underscores the need to identify robust biomarkers and advance predictive models to anticipate treatment outcomes, as well as advocate for combination therapies that address multiple facets of the TME. Finally, the review emphasizes the necessity of an interdisciplinary approach and the integration of cutting-edge technologies to unravel the intricacies of the TME, thereby facilitating the development of more effective, adaptable, and personalized cancer treatments. By providing critical insights into the current state of TME research and its implications for the future of oncology, this review highlights the dynamic and evolving landscape of this field.
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Affiliation(s)
- Mohamed El-Tanani
- College of Pharmacy, Ras Al Khaimah Medical and Health Sciences University, Ras Al Khaimah, United Arab Emirates.
| | - Syed Arman Rabbani
- College of Pharmacy, Ras Al Khaimah Medical and Health Sciences University, Ras Al Khaimah, United Arab Emirates
| | - Rasha Babiker
- Physiology Department, RAK College of Medical Sciences, RAK Medical and Health Sciences University, Ras-al-Khaimah, United Arab Emirates
| | - Imran Rangraze
- Internal Medicine Department, RAK College of Medical Sciences, RAK Medical and Health Sciences University, Ras-al-Khaimah, United Arab Emirates
| | - Sumedha Kapre
- Department of Pharmaceutical Sciences, Irma Lerma Rangel School of Pharmacy, Texas A&M University, Kingsville, TX, 78363, USA
| | - Sushesh Srivastsa Palakurthi
- Department of Pharmaceutical Sciences, Irma Lerma Rangel School of Pharmacy, Texas A&M University, Kingsville, TX, 78363, USA
| | - Abdullah M Alnuqaydan
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia.
| | - Alaa A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University, Irbid, 21163, Jordan
| | - Manfredi Rizzo
- (D)epartment of Health Promotion, Mother and Childcare, Internal Medicine and Medical Specialties, School of Medicine, University of Palermo, Palermo, Italy
| | - Yahia El-Tanani
- Medical School, St George's University of London, Cranmer Terrace, Tooting, London, SW17 0RE, UK.
| | - Murtaza M Tambuwala
- College of Pharmacy, Ras Al Khaimah Medical and Health Sciences University, Ras Al Khaimah, United Arab Emirates; Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln, LN6 7TS, UK.
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Xu J, Zhang Y, Li M, Shao Z, Dong Y, Li Q, Bai H, Duan J, Zhong J, Wan R, Bai J, Yi X, Tang F, Wang J, Wang Z. A single-cell characterised signature integrating heterogeneity and microenvironment of lung adenocarcinoma for prognostic stratification. EBioMedicine 2024; 102:105092. [PMID: 38547579 PMCID: PMC10990706 DOI: 10.1016/j.ebiom.2024.105092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND The high heterogeneity of tumour and the complexity of tumour microenvironment (TME) greatly impacted the tumour development and the prognosis of cancer in the era of immunotherapy. In this study, we aimed to portray the single cell-characterised landscape of lung adenocarcinoma (LUAD), and develop an integrated signature incorporating both tumour heterogeneity and TME for prognosis stratification. METHODS Single-cell tagged reverse transcription sequencing (STRT-seq) was performed on tumour tissues and matched normal tissues from 14 patients with LUAD for immune landscape depiction and candidate key genes selection for signature construction. Kaplan-Meier survival analyses and in-vitro cell experiments were conducted to confirm the gene functions. The transcriptomic profile of 1949 patients from 11 independent cohorts including nine public datasets and two in-house cohorts were obtained for validation. FINDINGS We selected 11 key genes closely related to cell-to-cell interaction, tumour development, T cell phenotype transformation, and Ma/Mo cell distribution, including HLA-DPB1, FAM83A, ITGB4, OAS1, FHL2, S100P, FSCN1, SFTPD, SPP1, DBH-AS1, CST3, and established an integrated 11-gene signature, stratifying patients to High-Score or Low-Score group for better or worse prognosis. Moreover, the prognostically-predictive potency of the signature was validated by 11 independent cohorts, and the immunotherapeutic predictive potency was also validated by our in-house cohort treated by immunotherapy. Additionally, the in-vitro cell experiments and drug sensitivity prediction further confirmed the gene function and generalizability of this signature across the entire RNA profile spectrum. INTERPRETATION This single cell-characterised 11-gene signature might offer insights for prognosis stratification and potential guidance for treatment selection. FUNDING Support for the study was provided by National key research and development project (2022YFC2505004, 2022YFC2505000 to Z.W. and J.W.), Beijing Natural Science Foundation (7242114 to J.X.), National Natural Science Foundation of China of China (82102886 to J.X., 81871889 and 82072586 to Z.W.), Beijing Nova Program (20220484119 to J.X.), NSFC general program (82272796 to J.W.), NSFC special program (82241229 to J.W.), CAMS Innovation Fund for Medical Sciences (2021-1-I2M-012, 2022-I2M-1-009 to Z.W. and J.W.), Beijing Natural Science Foundation (7212084 to Z.W.), CAMS Key lab of translational research on lung cancer (2018PT31035 to J.W.), Aiyou Foundation (KY201701 to J.W.). Medical Oncology Key Foundation of Cancer Hospital Chinese Academy of Medical Sciences (CICAMS-MOCP2022003 to J.X.).
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Affiliation(s)
- Jiachen Xu
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yundi Zhang
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Man Li
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhuo Shao
- Geneplus-Beijing Institute, Changping District, Beijing, China
| | - Yiting Dong
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qingqing Li
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China; Beijing Advanced Innovation Center for Genomics & Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Hua Bai
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianchun Duan
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Medical Oncology, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Jia Zhong
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rui Wan
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Bai
- Geneplus-Beijing Institute, Changping District, Beijing, China
| | - Xin Yi
- Geneplus-Beijing Institute, Changping District, Beijing, China
| | - Fuchou Tang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China; Beijing Advanced Innovation Center for Genomics & Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Jie Wang
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Zhijie Wang
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, 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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10
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Liu M, Yang L, Sun X, Liang X, Li C, Feng Q, Li M, Zhang L. Evaluation of Prognosis in Patients with Lung Adenocarcinoma with Atypical Solid Nodules on Thin-Section CT Images. Radiol Cardiothorac Imaging 2024; 6:e220234. [PMID: 38206165 PMCID: PMC10912885 DOI: 10.1148/ryct.220234] [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: 10/13/2022] [Revised: 04/03/2023] [Accepted: 08/23/2023] [Indexed: 01/12/2024]
Abstract
Purpose To evaluate the clinicopathologic characteristics and prognosis of patients with clinical stage IA lung adenocarcinoma with atypical solid nodules (ASNs) on thin-section CT images. Materials and Methods Data from patients with clinical stage IA lung adenocarcinoma who underwent resection between January 2005 and December 2012 were retrospectively reviewed. According to their manifestations on thin-section CT images, nodules were classified as ASNs, subsolid nodules (SSNs), and typical solid nodules (TSNs). The clinicopathologic characteristics of the ASNs were investigated, and the differences across the three groups were analyzed. The Kaplan-Meier method and multivariable Cox analysis were used to evaluate survival differences among patients with ASNs, SSNs, and TSNs. Results Of the 254 patients (median age, 58 years [IQR, 53-66]; 152 women) evaluated, 49 had ASNs, 123 had SSNs, and 82 had TSNs. Compared with patients with SSNs, those with ASNs were more likely to have nonsmall adenocarcinoma (P < .001), advanced-stage adenocarcinoma (P = .004), nonlepidic growth adenocarcinoma (P < .001), and middle- or low-grade differentiation tumors (P < .001). Compared with patients with TSNs, those with ASNs were more likely to have no lymph node involvement (P = .009) and epidermal growth factor receptor mutation positivity (P = .018). Average disease-free survival in patients with ASNs was significantly longer than that in patients with TSNs (P < .001) but was not distinguishable from that in patients with SSNs (P = .051). Conclusion ASNs were associated with better clinical outcomes than TSNs in patients with clinical stage IA lung adenocarcinoma. Keywords: Adenocarcinoma, Atypical Solid Nodules, CT, Disease-free Survival, Lung, Prognosis, Pulmonary Supplemental material is available for this article. Published under a CC BY 4.0 license.
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Affiliation(s)
- Mengwen Liu
- From the Department of Diagnostic Radiology (M. Liu, Q.F., M. Li,
L.Z.), Department of Pathology (L.Y., X.S.), Medical Statistics Office (X.L.),
and Medical Records Room (C.L.), National Cancer Center/National Clinical
Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences
and Peking Union Medical College, No. 17 Panjiayuan Nanli, Chaoyang District,
Beijing 100021, China
| | - Lin Yang
- From the Department of Diagnostic Radiology (M. Liu, Q.F., M. Li,
L.Z.), Department of Pathology (L.Y., X.S.), Medical Statistics Office (X.L.),
and Medical Records Room (C.L.), National Cancer Center/National Clinical
Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences
and Peking Union Medical College, No. 17 Panjiayuan Nanli, Chaoyang District,
Beijing 100021, China
| | - Xujie Sun
- From the Department of Diagnostic Radiology (M. Liu, Q.F., M. Li,
L.Z.), Department of Pathology (L.Y., X.S.), Medical Statistics Office (X.L.),
and Medical Records Room (C.L.), National Cancer Center/National Clinical
Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences
and Peking Union Medical College, No. 17 Panjiayuan Nanli, Chaoyang District,
Beijing 100021, China
| | - Xin Liang
- From the Department of Diagnostic Radiology (M. Liu, Q.F., M. Li,
L.Z.), Department of Pathology (L.Y., X.S.), Medical Statistics Office (X.L.),
and Medical Records Room (C.L.), National Cancer Center/National Clinical
Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences
and Peking Union Medical College, No. 17 Panjiayuan Nanli, Chaoyang District,
Beijing 100021, China
| | - Cong Li
- From the Department of Diagnostic Radiology (M. Liu, Q.F., M. Li,
L.Z.), Department of Pathology (L.Y., X.S.), Medical Statistics Office (X.L.),
and Medical Records Room (C.L.), National Cancer Center/National Clinical
Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences
and Peking Union Medical College, No. 17 Panjiayuan Nanli, Chaoyang District,
Beijing 100021, China
| | - Qianqian Feng
- From the Department of Diagnostic Radiology (M. Liu, Q.F., M. Li,
L.Z.), Department of Pathology (L.Y., X.S.), Medical Statistics Office (X.L.),
and Medical Records Room (C.L.), National Cancer Center/National Clinical
Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences
and Peking Union Medical College, No. 17 Panjiayuan Nanli, Chaoyang District,
Beijing 100021, China
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11
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Wang Z, Li J, Wang L, Liu Y, Wang W, Chen J, Liang H, Chen YQ, Zhu S. FFAR4 activation inhibits lung adenocarcinoma via blocking respiratory chain complex assembly associated mitochondrial metabolism. Cell Mol Biol Lett 2024; 29:17. [PMID: 38243188 PMCID: PMC10799372 DOI: 10.1186/s11658-024-00535-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/08/2024] [Indexed: 01/21/2024] Open
Abstract
Despite notable advancements in the investigation and management of lung adenocarcinoma (LUAD), the mortality rate for individuals afflicted with LUAD remains elevated, and attaining an accurate prognosis is challenging. LUAD exhibits intricate genetic and environmental components, and it is plausible that free fatty acid receptors (FFARs) may bridge the genetic and dietary aspects. The objective of this study is to ascertain whether a correlation exists between FFAR4, which functions as the primary receptor for dietary fatty acids, and various characteristics of LUAD, while also delving into the potential underlying mechanism. The findings of this study indicate a decrease in FFAR4 expression in LUAD, with a positive correlation (P < 0.01) between FFAR4 levels and overall patient survival (OS). Receiver operating characteristic (ROC) curve analysis demonstrated a significant diagnostic value [area under the curve (AUC) of 0.933] associated with FFAR4 expression. Functional investigations revealed that the FFAR4-specific agonist (TUG891) effectively suppressed cell proliferation and induced cell cycle arrest. Furthermore, FFAR4 activation resulted in significant metabolic shifts, including a decrease in oxygen consumption rate (OCR) and an increase in extracellular acidification rate (ECAR) in A549 cells. In detail, the activation of FFAR4 has been observed to impact the assembly process of the mitochondrial respiratory chain complex and the malate-aspartate shuttle process, resulting in a decrease in the transition of NAD+ to NADH and the inhibition of LUAD. These discoveries reveal a previously unrecognized function of FFAR4 in the negative regulation of mitochondrial metabolism and the inhibition of LUAD, indicating its potential as a promising therapeutic target for the treatment and diagnosis of LUAD.
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Affiliation(s)
- Zhe Wang
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Jinyou Li
- Department of Thoracic Surgery, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - LongFei Wang
- The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Yaowei Liu
- State Key Lab of Food Science and Resources, Jiangnan University, Wuxi, China
| | - Wei Wang
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - JiaYao Chen
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - HuiJun Liang
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Y Q Chen
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - ShengLong Zhu
- Wuxi School of Medicine, Jiangnan University, Wuxi, China.
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12
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Kahraman DT, Bozgeyik E, Guven H, Guler S, Saglam E, Cangi S, Oztuzcu S, Bozgeyik I, Isik AF. Long non-coding RNA signatures in non-small cell lung cancer and their clinicopathological significance. Pathol Res Pract 2024; 253:154946. [PMID: 37995424 DOI: 10.1016/j.prp.2023.154946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023]
Abstract
Lung cancer is the most common type of cancer in our country and worldwide, and it is a leading cause of cancer-related deaths. According to the latest global cancer statistics, lung cancer was identified as the second most common type of cancer, and the leading cause of cancer-related deaths. Long non-coding RNAs (lncRNAs) are a highly heterogeneous class of RNA molecules sharing many characteristics with mRNAs, except for the protein-coding potential. Accumulating mass of evidence suggest that lncRNAs play key regulatory roles during the multistep formation of human cancers including lung cancer. In previous studies, it has been shown that many lncRNA molecules play significant roles in the formation and progression of lung cancer. However, there are still numerous lncRNA molecules in lung cancer whose roles remain unknown. Accordingly, here we sought to ascertain the diagnostic and prognostic value of lncRNAs by analyzing the expression profiles of THRIL, NEAT1, and LOC105376095 in lung cancer. Remarkably, NEAT1 and LOC105376095 but not THRIL were identified to be differentially expressed in tissues of lung tumors. More importantly, LOC105376095, a yet uncharacterized lncRNA molecule, was significantly associated with the disease severity. Collectively, NEAT1 and LOC105376095 hold promise as potential diagnostic and prognostic biomarkers for lung cancer, presenting opportunities for targeted therapeutic interventions in the future.
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Affiliation(s)
- Demet Tasdemir Kahraman
- Department of Medical Biochemistry, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey; Department of Respiratory Biology, Institute of Health Sciences, Gaziantep University, Gaziantep, Turkey.
| | - Esra Bozgeyik
- Department of Medical Services and Techniques, Vocational School of Health Services, Adiyaman University, Adiyaman, Turkey
| | - Hulya Guven
- Department of Respiratory Biology, Institute of Health Sciences, Gaziantep University, Gaziantep, Turkey
| | - Semih Guler
- Department of Respiratory Biology, Institute of Health Sciences, Gaziantep University, Gaziantep, Turkey
| | - Ebru Saglam
- Department of Respiratory Biology, Institute of Health Sciences, Gaziantep University, Gaziantep, Turkey
| | - Sibel Cangi
- Department of Pathology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Serdar Oztuzcu
- Department of Medical Biology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Ibrahim Bozgeyik
- Department of Medical Biology, Faculty of Medicine, Adiyaman University, Adiyaman, Turkey
| | - Ahmet Ferudun Isik
- Department of Respiratory Biology, Institute of Health Sciences, Gaziantep University, Gaziantep, Turkey; Department of Thoracic Surgery, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
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13
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Kurkalang S, Roy S, Acharya A, Mazumder P, Mazumder S, Patra S, Ghosh S, Sarkar S, Kundu S, Biswas NK, Ghose S, Majumder PP, Maitra A. Single-cell transcriptomic analysis of gingivo-buccal oral cancer reveals two dominant cellular programs. Cancer Sci 2023; 114:4732-4746. [PMID: 37792582 PMCID: PMC10728019 DOI: 10.1111/cas.15979] [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: 06/23/2023] [Revised: 09/02/2023] [Accepted: 09/13/2023] [Indexed: 10/06/2023] Open
Abstract
Oral squamous cell carcinoma of the gingivo-buccal region (OSCC-GB) is the most common cancer among men in India, and is associated with poor prognosis and frequent recurrence. Cellular heterogeneity in OSCC-GB was investigated by single-cell RNA sequencing of tumors derived from the oral cavity of 12 OSCC-GB patients, 3 of whom had concomitant presence of a precancerous lesion (oral submucous fibrosis [OSMF]). Unique malignant cell types, features, and phenotypic shifts in the stromal cell population were identified in oral tumors with associated submucous fibrosis. Expression levels of FOS, ATP1A, and DUSP1 provided robust discrimination between tumors with or without the concomitant presence of OSMF. Malignant cell populations shared between tumors with and without OSMF were enriched with the expression of partial epithelial-mesenchymal transition (pEMT) or fetal cell type signatures indicative of two dominant cellular programs in OSCC-GB-pEMT and fetal cellular reprogramming. Malignant cells exhibiting fetal cellular and pEMT programs were enriched with the expression of immune-related pathway genes known to be involved in antitumor immune response. In the tumor microenvironment, higher infiltration of immune cells than the stromal cells was observed. The T cell population was large in tumors and diverse subtypes of T cells with varying levels of infiltration were found. We also detected double-negative PLCG2+ T cells and cells with intermediate M1-M2 macrophage polarization. Our findings shed light on unique aspects of cellular heterogeneity and cell states in OSCC-GB.
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Affiliation(s)
| | - Sumitava Roy
- National Institute of Biomedical GenomicsKalyaniIndia
- Regional Centre for BiotechnologyFaridabadIndia
| | - Arunima Acharya
- National Institute of Biomedical GenomicsKalyaniIndia
- Regional Centre for BiotechnologyFaridabadIndia
| | - Paramita Mazumder
- Department of Oral PathologyDr. R. Ahmed Dental College and HospitalKolkataIndia
| | | | - Subrata Patra
- National Institute of Biomedical GenomicsKalyaniIndia
| | - Shekhar Ghosh
- National Institute of Biomedical GenomicsKalyaniIndia
| | | | - Sudip Kundu
- National Institute of Biomedical GenomicsKalyaniIndia
| | | | - Sandip Ghose
- Department of Oral PathologyDr. R. Ahmed Dental College and HospitalKolkataIndia
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14
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Su GH, Xiao Y, You C, Zheng RC, Zhao S, Sun SY, Zhou JY, Lin LY, Wang H, Shao ZM, Gu YJ, Jiang YZ. Radiogenomic-based multiomic analysis reveals imaging intratumor heterogeneity phenotypes and therapeutic targets. SCIENCE ADVANCES 2023; 9:eadf0837. [PMID: 37801493 PMCID: PMC10558123 DOI: 10.1126/sciadv.adf0837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
Intratumor heterogeneity (ITH) profoundly affects therapeutic responses and clinical outcomes. However, the widespread methods for assessing ITH based on genomic sequencing or pathological slides, which rely on limited tissue samples, may lead to inaccuracies due to potential sampling biases. Using a newly established multicenter breast cancer radio-multiomic dataset (n = 1474) encompassing radiomic features extracted from dynamic contrast-enhanced magnetic resonance images, we formulated a noninvasive radiomics methodology to effectively investigate ITH. Imaging ITH (IITH) was associated with genomic and pathological ITH, predicting poor prognosis independently in breast cancer. Through multiomic analysis, we identified activated oncogenic pathways and metabolic dysregulation in high-IITH tumors. Integrated metabolomic and transcriptomic analyses highlighted ferroptosis as a vulnerability and potential therapeutic target of high-IITH tumors. Collectively, this work emphasizes the superiority of radiomics in capturing ITH. Furthermore, we provide insights into the biological basis of IITH and propose therapeutic targets for breast cancers with elevated IITH.
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Affiliation(s)
- Guan-Hua Su
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center and Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yi Xiao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center and Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Chao You
- Department of Radiology, Fudan University Shanghai Cancer Center and Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ren-Cheng Zheng
- Institute of Science and Technology for Brain-inspired Intelligence, Fudan University, Shanghai 201203, China
| | - Shen Zhao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center and Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Shi-Yun Sun
- Department of Radiology, Fudan University Shanghai Cancer Center and Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jia-Yin Zhou
- Department of Radiology, Fudan University Shanghai Cancer Center and Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lu-Yi Lin
- Department of Radiology, Fudan University Shanghai Cancer Center and Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - He Wang
- Institute of Science and Technology for Brain-inspired Intelligence, Fudan University, Shanghai 201203, China
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center and Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ya-Jia Gu
- Department of Radiology, Fudan University Shanghai Cancer Center and Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center and Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
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15
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Ashouri A, Zhang C, Gaiti F. Decoding Cancer Evolution: Integrating Genetic and Non-Genetic Insights. Genes (Basel) 2023; 14:1856. [PMID: 37895205 PMCID: PMC10606072 DOI: 10.3390/genes14101856] [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: 09/01/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
The development of cancer begins with cells transitioning from their multicellular nature to a state akin to unicellular organisms. This shift leads to a breakdown in the crucial regulators inherent to multicellularity, resulting in the emergence of diverse cancer cell subpopulations that have enhanced adaptability. The presence of different cell subpopulations within a tumour, known as intratumoural heterogeneity (ITH), poses challenges for cancer treatment. In this review, we delve into the dynamics of the shift from multicellularity to unicellularity during cancer onset and progression. We highlight the role of genetic and non-genetic factors, as well as tumour microenvironment, in promoting ITH and cancer evolution. Additionally, we shed light on the latest advancements in omics technologies that allow for in-depth analysis of tumours at the single-cell level and their spatial organization within the tissue. Obtaining such detailed information is crucial for deepening our understanding of the diverse evolutionary paths of cancer, allowing for the development of effective therapies targeting the key drivers of cancer evolution.
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Affiliation(s)
- Arghavan Ashouri
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Chufan Zhang
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Federico Gaiti
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
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16
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Wang Y, Liu B, Min Q, Yang X, Yan S, Ma Y, Li S, Fan J, Wang Y, Dong B, Teng H, Lin D, Zhan Q, Wu N. Spatial transcriptomics delineates molecular features and cellular plasticity in lung adenocarcinoma progression. Cell Discov 2023; 9:96. [PMID: 37723144 PMCID: PMC10507052 DOI: 10.1038/s41421-023-00591-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 07/27/2023] [Indexed: 09/20/2023] Open
Abstract
Indolent (lepidic) and aggressive (micropapillary, solid, and poorly differentiated acinar) histologic subtypes often coexist within a tumor tissue of lung adenocarcinoma (LUAD), but the molecular features associated with different subtypes and their transitions remain elusive. Here, we combine spatial transcriptomics and multiplex immunohistochemistry to elucidate molecular characteristics and cellular plasticity of distinct histologic subtypes of LUAD. We delineate transcriptional reprogramming and dynamic cell signaling that determine subtype progression, especially hypoxia-induced regulatory network. Different histologic subtypes exhibit heterogeneity in dedifferentiation states. Additionally, our results show that macrophages are the most abundant cell type in LUAD, and identify different tumor-associated macrophage subpopulations that are unique to each histologic subtype, which might contribute to an immunosuppressive microenvironment. Our results provide a systematic landscape of molecular profiles that drive LUAD subtype progression, and demonstrate potentially novel therapeutic strategies and targets for invasive lung adenocarcinoma.
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Affiliation(s)
- Yan Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Bing Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Qingjie Min
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xin Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Shi Yan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yuanyuan Ma
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Shaolei Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Jiawen Fan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yaqi Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Bin Dong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Central Laboratory, Peking University Cancer Hospital and Institute, Beijing, China
| | - Huajing Teng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Dongmei Lin
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Qimin Zhan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China.
- State Key Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China.
- Cancer Institute, Peking University Shenzhen Hospital, Shenzhen Peking University-Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, Guangdong, China.
- Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, China.
- International Cancer Institute, Peking University Health Science Center, Beijing, China.
- Soochow University Cancer institute, Suzhou, Jiangsu, China.
| | - Nan Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China.
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17
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Andrade JR, Gallagher AD, Maharaj J, McClelland SE. Disentangling the roles of aneuploidy, chromosomal instability and tumour heterogeneity in developing resistance to cancer therapies. Chromosome Res 2023; 31:28. [PMID: 37721639 PMCID: PMC10506951 DOI: 10.1007/s10577-023-09737-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/26/2023] [Accepted: 08/29/2023] [Indexed: 09/19/2023]
Abstract
Aneuploidy is defined as the cellular state of having a number of chromosomes that deviates from a multiple of the normal haploid chromosome number of a given organism. Aneuploidy can be present in a static state: Down syndrome individuals stably maintain an extra copy of chromosome 21 in their cells. In cancer cells, however, aneuploidy is usually present in combination with chromosomal instability (CIN) which leads to a continual generation of new chromosomal alterations and the development of intratumour heterogeneity (ITH). The prevalence of cells with specific chromosomal alterations is further shaped by evolutionary selection, for example, during the administration of cancer therapies. Aneuploidy, CIN and ITH have each been individually associated with poor prognosis in cancer, and a wealth of evidence suggests they contribute, either alone or in combination, to cancer therapy resistance by providing a reservoir of potential resistant states, or the ability to rapidly evolve resistance. A full understanding of the contribution and interplay between aneuploidy, CIN and ITH is required to tackle therapy resistance in cancer patients. However, these characteristics often co-occur and are intrinsically linked, presenting a major challenge to defining their individual contributions. Moreover, their accurate measurement in both experimental and clinical settings is a technical hurdle. Here, we attempt to deconstruct the contribution of the individual and combined roles of aneuploidy, CIN and ITH to therapy resistance in cancer, and outline emerging approaches to measure and disentangle their roles as a step towards integrating these principles into cancer therapeutic strategy.
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Affiliation(s)
- Joana Reis Andrade
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M6BQ, England
| | - Annie Dinky Gallagher
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M6BQ, England
| | - Jovanna Maharaj
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M6BQ, England
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18
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Mu J, Huang J, Ao M, Li W, Jiang L, Yang L. Advances in diagnosis and prediction for aggression of pure solid T1 lung cancer. PRECISION CLINICAL MEDICINE 2023; 6:pbad020. [PMID: 38025970 PMCID: PMC10680022 DOI: 10.1093/pcmedi/pbad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/07/2023] [Indexed: 12/01/2023] Open
Abstract
A growing number of early-stage lung cancers presenting as malignant pulmonary nodules have been diagnosed because of the increased adoption of low-dose spiral computed tomography. But pure solid T1 lung cancer with ≤3 cm in the greatest dimension is not always at an early stage, despite its small size. This type of cancer can be highly aggressive and is associated with pathological involvement, metastasis, postoperative relapse, and even death. However, it is easily misdiagnosed or delay diagnosed in clinics and thus poses a serious threat to human health. The percentage of nodal or extrathoracic metastases has been reported to be >20% in T1 lung cancer. As such, understanding and identifying the aggressive characteristics of pure solid T1 lung cancer is crucial for prevention, diagnosis, and therapeutic strategies, and beneficial to improving the prognosis. With the widespread of lung cancer screening, these highly invasive pure solid T1 lung cancer will become the main advanced lung cancer in future. However, there is limited information regarding precision medicine on how to identify these "early-stage" aggressive lung cancers. To provide clinicians with new insights into early recognition and intervention of the highly invasive pure solid T1 lung cancer, this review summarizes its clinical characteristics, imaging, pathology, gene alterations, immune microenvironment, multi-omics, and current techniques for diagnosis and prediction.
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Affiliation(s)
- Junhao Mu
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Jing Huang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Min Ao
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Weiyi Li
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Li Jiang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Li Yang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
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19
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He X, Zhao D, Zhang X, Ma Y, Zhang R, Huang Z, Wang G, Guo G, Wang W, Wen Y, Zhang L. Intrinsic Immunogenic Tumor Cell Death Subtypes Delineate Prognosis and Responsiveness to Immunotherapy in Lung Adenocarcinoma. BIOLOGY 2023; 12:808. [PMID: 37372093 DOI: 10.3390/biology12060808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023]
Abstract
Recent studies have highlighted the combination of activation of host immunogenic cell death (ICD) and tumor-directed cytotoxic strategies. However, overall multiomic analysis of the intrinsic ICD property in lung adenocarcinoma (LUAD) has not been performed. Therefore, the aim of this study was to develop an ICD-based risk scoring system to predict overall survival (OS) and immunotherapeutic efficacy in patients. In our study, both weighted gene co-expression network analysis (WGCNA) and LASSO-Cox analysis were utilized to identify ICDrisk subtypes (ICDrisk). Moreover, we identify genomic alterations and differences in biological processes, analyze the immune microenvironment, and predict the response to immunotherapy in patients with pan-cancer. Importantly, immunogenicity subgroup typing was performed based on the immune score (IS) and microenvironmental tumor neoantigens (meTNAs). Our results demonstrate that ICDrisk subtypes were identified based on 16 genes. Furthermore, high ICDrisk was proved to be a poor prognostic factor in LUAD patients and indicated poor efficacy of immune checkpoint inhibitor (ICI) treatment in patients with pan-cancer. The two ICDrisk subtypes displayed distinct clinicopathologic features, tumor-infiltrating immune cell patterns, and biological processes. The ISlowmeTNAhigh subtype showed low intratumoral heterogeneity (ITH) and immune-activated phenotypes and correlated with better survival than the other subtypes within the high ICDrisk group. This study suggests effective biomarkers for the prediction of OS in LUAD patients and immunotherapeutic response across Pan-cancer and contributes to enhancing our understanding of intrinsic immunogenic tumor cell death.
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Affiliation(s)
- Xiaotian He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Dechang Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xuewen Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yiyang Ma
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Rusi Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Zirui Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Gongming Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Guangran Guo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Weidong Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yingsheng Wen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Lanjun Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
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20
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Xu J, Yang Z, Xie W, Wan R, Li C, Fei K, Sun B, Yang X, Chen P, Meng F, Wang G, Zhao J, Han Y, Cai S, Wang J, Wang Z. A prognostic and immunotherapeutic predictive model based on the cell-originated characterization of tumor microenvironment in lung adenocarcinoma. iScience 2023; 26:106616. [PMID: 37168563 PMCID: PMC10165414 DOI: 10.1016/j.isci.2023.106616] [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: 01/06/2023] [Revised: 02/24/2023] [Accepted: 04/04/2023] [Indexed: 05/13/2023] Open
Abstract
Tumor microenvironment (TME) plays a crucial role in predicting prognosis and response to therapy in lung cancer. Our study established a prognostic and immunotherapeutic predictive model, the tumor immune cell score (TICS), by differentiating cell origins in lung adenocarcinoma (LUAD) based on the transcriptomic data of 2,510 patients in 14 independent cohorts, including 12 public datasets and two in-house cohorts. The high TICS was associated with prolonged overall survival (OS), especially in the early-stage LUAD. For the advanced-stage LUAD, high TICS predicted a superior OS in patients who were treated with immunotherapy instead of chemotherapy or TKI. The result suggested that TICS could serve as an indicator for the prognostic stratification management of patients in the early-stage LUAD, and as a potential guide for therapeutic decision-marking in the advanced-stage LUAD. Our findings provided an insight into prognosis stratification and potential guidance for treatment strategy selection.
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Affiliation(s)
- Jiachen Xu
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
- Guangdong Provincial People’s Hospital/Guangdong Provincial Academy of Medical Sciences, Guangdong Provincial Key Lab of Translational Medicine in Lung Cancer, Guangdong 510317, P.R. China
| | - Zhenlin Yang
- Department of Thoracic Surgery, National Cancer Center/ National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
| | - Wenchuan Xie
- Burning Rock Biotech, Guangdong 510300, P.R. China
| | - Rui Wan
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
| | | | - Kailun Fei
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
| | - Boyang Sun
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
| | - Xu Yang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
| | - Ping Chen
- Department of Oncology, Yancheng First Hospital, Affiliated Hospital of Nanjing University Medical School, The First People’s Hospital of Yancheng; Jiangsu 224001, P.R. China
| | - Fanqi Meng
- Burning Rock Biotech, Guangdong 510300, P.R. China
| | | | - Jing Zhao
- Burning Rock Biotech, Guangdong 510300, P.R. China
| | - Yusheng Han
- Burning Rock Biotech, Guangdong 510300, P.R. China
| | - Shangli Cai
- Burning Rock Biotech, Guangdong 510300, P.R. China
| | - Jie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
| | - Zhijie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
- Corresponding author
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21
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Liu N, Chen HG, Li Y, Zhang G, Zhang J, Qu G, He B, Meng TQ, Xiong CL, Pan A, Yin Y, Liang Y, Shi J, Wang YX, Hu L, Jiang G. Exogenous Metals Atlas in Spermatozoa at Single-Cell Resolution in Relation to Human Semen Quality. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:7358-7369. [PMID: 37144275 DOI: 10.1021/acs.est.2c08838] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
While exogenous metal/metalloid (metal) exposure has been associated with reduced human semen quality, no study has assessed the associations of exogenous metals in human spermatozoa with semen quality. Here, we developed a strategy to explore the associations between exogenous metals in spermatozoa at single-cell resolution and human semen quality among 84 men screened as sperm donors, who provided 266 semen samples within 90 days. A cellular atlas of exogenous metals at the single-cell level was created with mass cytometry (CyTOF) technology, which concurrently displayed 18 metals in more than 50 000 single sperm. Exogenous metals in spermatozoa at single-cell resolution were extremely heterogeneous and diverse. Further analysis using multivariable linear regression and linear mixed-effects models revealed that the heterogeneity and prevalence of the exogenous metals at single-cell resolution were associated with semen quality. The heterogeneity of lead (Pb), tin (Sn), yttrium (Y), and zirconium (Zr) was negatively associated with sperm concentration and count, while their prevalence showed positive associations. These findings revealed that the heterogeneous properties of exogenous metals in spermatozoa were associated with human semen quality, highlighting the importance of assessing exogenous metals in spermatozoa at single-cell resolution to evaluate male reproductive health risk precisely.
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Affiliation(s)
- Nian Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing 100085, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310042, China
| | - Heng-Gui Chen
- Clinical Research and Translation Center, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Yu Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing 100085, China
| | - Guohuan Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing 100085, China
| | - Jie Zhang
- School of Public Health, Xiamen University, Xiamen 361102, China
| | - Guangbo Qu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing 100085, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310042, China
| | - Bin He
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing 100085, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310042, China
| | - Tian-Qing Meng
- Center of Reproductive Medicine, Wuhan Tongji Reproductive Medicine Hospital, Wuhan 430030, China
- Hubei Province Human Sperm Bank, Wuhan 430030, China
| | - Cheng-Liang Xiong
- Center of Reproductive Medicine, Wuhan Tongji Reproductive Medicine Hospital, Wuhan 430030, China
- Hubei Province Human Sperm Bank, Wuhan 430030, China
| | - An Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yongguang Yin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing 100085, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310042, China
| | - Yong Liang
- Institute of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Jianbo Shi
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing 100085, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310042, China
| | - Yi-Xin Wang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Ligang Hu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing 100085, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310042, China
- Institute of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing 100085, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310042, China
- Institute of Environment and Health, Jianghan University, Wuhan 430056, China
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22
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El Khoury LY, Pan X, Hlady RA, Wagner RT, Shaikh S, Wang L, Humphreys MR, Castle EP, Stanton ML, Ho TH, Robertson KD. Extensive intratumor regional epigenetic heterogeneity in clear cell renal cell carcinoma targets kidney enhancers and is associated with poor outcome. Clin Epigenetics 2023; 15:71. [PMID: 37120552 PMCID: PMC10149001 DOI: 10.1186/s13148-023-01471-3] [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: 12/09/2022] [Accepted: 03/21/2023] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND Clear cell renal cell cancer (ccRCC), the 8th leading cause of cancer-related death in the US, is challenging to treat due to high level intratumoral heterogeneity (ITH) and the paucity of druggable driver mutations. CcRCC is unusual for its high frequency of epigenetic regulator mutations, such as the SETD2 histone H3 lysine 36 trimethylase (H3K36me3), and low frequency of traditional cancer driver mutations. In this work, we examined epigenetic level ITH and defined its relationships with pathologic features, aspects of tumor biology, and SETD2 mutations. RESULTS A multi-region sampling approach coupled with EPIC DNA methylation arrays was conducted on a cohort of normal kidney and ccRCC. ITH was assessed using DNA methylation (5mC) and CNV-based entropy and Euclidian distances. We found elevated 5mC heterogeneity and entropy in ccRCC relative to normal kidney. Variable CpGs are highly enriched in enhancer regions. Using intra-class correlation coefficient analysis, we identified CpGs that segregate tumor regions according to clinical phenotypes related to tumor aggressiveness. SETD2 wild-type tumors overall possess greater 5mC and copy number ITH than SETD2 mutant tumor regions, suggesting SETD2 loss contributes to a distinct epigenome. Finally, coupling our regional data with TCGA, we identified a 5mC signature that links regions within a primary tumor with metastatic potential. CONCLUSION Taken together, our results reveal marked levels of epigenetic ITH in ccRCC that are linked to clinically relevant tumor phenotypes and could translate into novel epigenetic biomarkers.
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Affiliation(s)
- Louis Y El Khoury
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Xiaoyu Pan
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Ryan A Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Ryan T Wagner
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Shafiq Shaikh
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Liguo Wang
- Division of Biomedical Statistics and Informatics, Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | | | - Erik P Castle
- Department of Urology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Melissa L Stanton
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Phoenix, AZ, USA
| | - Thai H Ho
- Division of Hematology and Medical Oncology, Mayo Clinic Arizona, Scottsdale, AZ, USA.
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.
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23
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Ji XY, Li H, Chen HH, Lin J. Diagnostic performance of RASSF1A and SHOX2 methylation combined with EGFR mutations for differentiation between small pulmonary nodules. J Cancer Res Clin Oncol 2023:10.1007/s00432-023-04745-8. [PMID: 37097393 DOI: 10.1007/s00432-023-04745-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 04/03/2023] [Indexed: 04/26/2023]
Abstract
BACKGROUND AND AIM Aberrant methylation of Ras association domain family 1, isoform A (RASSF1A), and short-stature homeobox gene 2 (SHOX2) promoters has been validated as a pair of valuable biomarkers for diagnosing early lung adenocarcinomas (LUADs). Epidermal growth factor receptor (EGFR) is the key driver mutation in lung carcinogenesis. This study aimed to investigate the aberrant promoter methylation of RASSF1A and SHOX2, and the genetic mutation of EGFR in 258 specimens of early LUADs. METHODS We retrospectively selected 258 paraffin-embedded samples of pulmonary nodules measuring 2 cm or less in diameter and evaluated the diagnostic performance of individual biomarker assays and multiple panels between noninvasive (group 1) and invasive lesions (groups 2A and 2B). Then, we investigated the interaction between genetic and epigenetic alterations. RESULTS The degree of RASSF1A and SHOX2 promoter methylation and EGFR mutation was significantly higher in invasive lesions than in noninvasive lesions. The three biomarkers distinguished between noninvasive and invasive lesions with reliable sensitivity and specificity: 60.9% sensitivity [95% confidence interval (CI) 52.41-68.78] and 80.0% specificity (95% CI 72.14-86.07). The novel panel biomarkers could further discriminate among three invasive pathological subtypes (area under the curve value > 0.6). The distribution of RASSF1A methylation and EGFR mutation was considerably exclusive in early LUAD (P = 0.002). CONCLUSION DNA methylation of RASSF1A and SHOX2 is a pair of promising biomarkers, which may be used in combination with other driver alterations, such as EGFR mutation, to support the differential diagnosis of LUADs, especially for stage I.
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Affiliation(s)
- Xiang-Yu Ji
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Hong Li
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Hui-Hui Chen
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Jie Lin
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China.
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China.
- National Virtual and Reality Experimental Education Center for Medical Morphology, Southern Medical University, Guangzhou, People's Republic of China.
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24
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Ito Y, Usui G, Seki M, Fukuyo M, Matsusaka K, Hoshii T, Sata Y, Morimoto J, Hata A, Nakajima T, Rahmutulla B, Kaiho T, Inage T, Tanaka K, Sakairi Y, Suzuki H, Yoshino I, Kaneda A. Association of frequent hypermethylation with high grade histological subtype in lung adenocarcinoma. Cancer Sci 2023. [PMID: 37082886 DOI: 10.1111/cas.15817] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 04/22/2023] Open
Abstract
Lung adenocarcinoma is classified morphologically into five histological subtypes according to the WHO classification. While each histological subtype correlates with a distinct prognosis, the molecular basis has not been fully elucidated. Here we conducted DNA methylation analysis of 30 lung adenocarcinoma cases annotated with the predominant histological subtypes and three normal lung cases using the Infinium BeadChip. Unsupervised hierarchical clustering analysis revealed three subgroups with different methylation levels: high-, intermediate-, and low-methylation epigenotypes (HME, IME, and LME). Micropapillary pattern (MPP)-predominant cases and those with MPP components were significantly enriched in HME (p = 0.02 and p = 0.03, respectively). HME cases showed a significantly poor prognosis for recurrence-free survival (p < 0.001) and overall survival (p = 0.006). We identified 365 HME marker genes specifically hypermethylated in HME cases with enrichment of "cell morphogenesis" related genes; 305 IME marker genes hypermethylated in HME and IME, but not in LME, with enrichment "embryonic organ morphogenesis"-related genes; 257 Common marker genes hypermethylated commonly in all cancer cases, with enrichment of "regionalization"-related genes. We extracted surrogate markers for each epigenotype and designed pyrosequencing primers for five HME markers (TCERG1L, CXCL12, FAM181B, HOXA11, GAD2), three IME markers (TBX18, ZNF154, NWD2) and three Common markers (SCT, GJD2, BARHL2). DNA methylation profiling using Infinium data was validated by pyrosequencing, and HME cases defined by pyrosequencing results also showed the worse recurrence-free survival. In conclusion, lung adenocarcinomas are stratified into subtypes with distinct DNA methylation levels, and the high-methylation subtype correlated with MPP-predominant cases and those with MPP components and showed a poor prognosis.
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Affiliation(s)
- Yuki Ito
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Genki Usui
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Motoaki Seki
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Keisuke Matsusaka
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Pathology, Chiba University Hospital, Chiba, Japan
| | - Takayuki Hoshii
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yuki Sata
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Junichi Morimoto
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Hata
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takahiro Nakajima
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Taisuke Kaiho
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Terunaga Inage
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kazuhisa Tanaka
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yuichi Sakairi
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hidemi Suzuki
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ichiro Yoshino
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
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Cui S, McGranahan N, Gao J, Chen P, Jiang W, Yang L, Ma L, Liao J, Xie T, Xie C, Enver T, Wu S. Tracking the evolution of esophageal squamous cell carcinoma under dynamic immune selection by multi-omics sequencing. Nat Commun 2023; 14:892. [PMID: 36807354 PMCID: PMC9938262 DOI: 10.1038/s41467-023-36558-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
Intratumoral heterogeneity (ITH) has been linked to decreased efficacy of clinical treatments. However, although genomic ITH has been characterized in genetic, transcriptomic and epigenetic alterations are hallmarks of esophageal squamous cell carcinoma (ESCC), the extent to which these are heterogeneous in ESCC has not been explored in a unified framework. Further, the extent to which tumor-infiltrated T lymphocytes are directed against cancer cells, but how the immune infiltration acts as a selective force to shape the clonal evolution of ESCC is unclear. In this study, we perform multi-omic sequencing on 186 samples from 36 primary ESCC patients. Through multi-omics analyses, it is discovered that genomic, epigenomic, and transcriptomic ITH are underpinned by ongoing chromosomal instability. Based on the RNA-seq data, we observe diverse levels of immune infiltrate across different tumor sites from the same tumor. We reveal genetic mechanisms of neoantigen evasion under distinct selection pressure from the diverse immune microenvironment. Overall, our work offers an avenue of dissecting the complex contribution of the multi-omics level to the ITH in ESCC and thereby enhances the development of clinical therapy.
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Affiliation(s)
- Sijia Cui
- Department of Radiation and Medical Oncology, Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | | | - Jing Gao
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Peng Chen
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Wei Jiang
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Lingrong Yang
- Hangzhou Cancer Institution, Hangzhou Cancer Hospital, Hangzhou, China
| | - Li Ma
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Junfang Liao
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Tian Xie
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Congying Xie
- Department of Radiation and Medical Oncology, Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
| | - Tariq Enver
- Cancer Institute, University College London, London, UK.
| | - Shixiu Wu
- Department of Radiation and Medical Oncology, Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China. .,National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China.
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26
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Al-Hamaly MA, Turner LT, Rivera-Martinez A, Rodriguez A, Blackburn JS. Zebrafish Cancer Avatars: A Translational Platform for Analyzing Tumor Heterogeneity and Predicting Patient Outcomes. Int J Mol Sci 2023; 24:2288. [PMID: 36768609 PMCID: PMC9916713 DOI: 10.3390/ijms24032288] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
The increasing number of available anti-cancer drugs presents a challenge for oncologists, who must choose the most effective treatment for the patient. Precision cancer medicine relies on matching a drug with a tumor's molecular profile to optimize the therapeutic benefit. However, current precision medicine approaches do not fully account for intra-tumoral heterogeneity. Different mutation profiles and cell behaviors within a single heterogeneous tumor can significantly impact therapy response and patient outcomes. Patient-derived avatar models recapitulate a patient's tumor in an animal or dish and provide the means to functionally assess heterogeneity's impact on drug response. Mouse xenograft and organoid avatars are well-established, but the time required to generate these models is not practical for clinical decision-making. Zebrafish are emerging as a time-efficient and cost-effective cancer avatar model. In this review, we highlight recent developments in zebrafish cancer avatar models and discuss the unique features of zebrafish that make them ideal for the interrogation of cancer heterogeneity and as part of precision cancer medicine pipelines.
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Affiliation(s)
- Majd A. Al-Hamaly
- Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40356, USA
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Logan T. Turner
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
- Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40356, USA
| | | | - Analiz Rodriguez
- Department of Neurosurgery, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jessica S. Blackburn
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
- Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40356, USA
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Jie Y, Wu J, An D, Li M, He H, Wang D, Gu A, E M. Molecular characterization based on tumor microenvironment-related signatures for guiding immunotherapy and therapeutic resistance in lung adenocarcinoma. Front Pharmacol 2023; 14:1099927. [PMID: 36726580 PMCID: PMC9884810 DOI: 10.3389/fphar.2023.1099927] [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: 11/16/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023] Open
Abstract
Background: Although the role of tumor microenvironment in lung adenocarcinoma (LUAD) has been explored in a number of studies, the value of TME-related signatures in immunotherapy has not been comprehensively characterized. Materials and Methods: Consensus clustering was conducted to characterize TME-based molecular subtypes using transcription data of LUAD samples. The biological pathways and immune microenvironment were assessed by CIBERSORT, ESTIMATE, and gene set enrichment analysis. A TME-related risk model was established through the algorithms of least absolute shrinkage and selection operator (Lasso) and stepwise Akaike information criterion (stepAIC). Results: Four TME-based molecular subtypes including C1, C2, C3, and C4 were identified, and they showed distinct overall survival, genomic characteristics, DNA methylation pattern, immune microenvironment, and biological pathways. C1 had the worst prognosis and high tumor proliferation rate. C3 and C4 had higher enrichment of anti-tumor signatures compared to C1 and C2. C4 had evidently low enrichment of epithelial-mesenchymal transition (EMT) signature and tumor proliferation rate. C3 was predicted to be more sensitive to immunotherapy compared with other subtypes. C1 is more sensitive to chemotherapy drugs, including Docetaxel, Vinorelbine and Cisplatin, while C3 is more sensitive to Paclitaxel. A five-gene risk model was constructed, which showed a favorable performance in three independent datasets. Low-risk group showed a longer overall survival, more infiltrated immune cells, and higher response to immunotherapy than high-risk group. Conclusion: This study comprehensively characterized the molecular features of LUAD patients based on TME-related signatures, demonstrating the potential of TME-based signatures in exploring the mechanisms of LUAD development. The TME-related risk model was of clinical value to predict LUAD prognosis and guide immunotherapy.
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Affiliation(s)
- Yamin Jie
- Department of Radiation Oncology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jianing Wu
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Dongxue An
- Department of Radiation Oncology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Man Li
- Department of Endoscopy, Harbin Medical University Cancer Hospital, Harbin, China
| | - Hongjiang He
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Duo Wang
- Department of Neurology, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Anxin Gu
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Mingyan E
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin, China
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28
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Yang D, Liu M, Jiang J, Luo Y, Wang Y, Chen H, Li D, Wang D, Yang Z, Chen H. Comprehensive Analysis of DMRT3 as a Potential Biomarker Associated with the Immune Infiltration in a Pan-Cancer Analysis and Validation in Lung Adenocarcinoma. Cancers (Basel) 2022; 14:cancers14246220. [PMID: 36551704 PMCID: PMC9777283 DOI: 10.3390/cancers14246220] [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: 11/17/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Doublesex and Mab-3 related Transcription Factor 3 (DMRT3) is associated with the prognosis of some tumors. It is possible to explore the role of DMRT3 in the cancer process using bioinformatic approaches and experimental validation. We comprehensively explored the clinical and immunological characteristics of DMRT3. The DMRT3 expression is abnormal in human cancers and correlates with clinical staging. A high DMRT3 expression is significantly associated with poor overall survival (OS) in KIRC, KIRP, LUAD, and UCEC. Amplification was the greatest frequency of the DMRT3 alterations in pan-cancer. The OS was significantly lower in the DMRT3 altered group than in the DMRT3 unaltered group (P = 0.0276). The DMRT3 expression was significantly associated with MSI in three cancer types and TMB in six cancer types. The DMRT3 expression was significantly correlated with the level of the immune cell infiltration and the immune checkpoint genes. The DMRT3 was involved in some pathways in pan-cancer. DMRT3 may play a role in chemotherapy and may be associated with chemoresistance. A ceRNA network of KCNQ1OT1/miR-335-5p/DMRT3 was constructed in LUAD. DMRT3 was significantly upregulated in the LUAD cell lines. DMRT3 was aberrantly expressed in pan-cancer and may promote tumorigenesis and progression via different mechanisms. DMRT3 can be used as a therapeutic target to treat cancer in humans.
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Affiliation(s)
- Donghong Yang
- Department of Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524000, China
| | - Meilian Liu
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524000, China
| | - Junhong Jiang
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524000, China
| | - Yiping Luo
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524000, China
| | - Yongcun Wang
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524000, China
| | - Huoguang Chen
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524000, China
| | - Dongbing Li
- Department of Medicine, ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Dongliang Wang
- Department of Medicine, ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Zhixiong Yang
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524000, China
- Correspondence: (Z.Y.); (H.C.); Tel.: +86-0759-2387458 (Z.Y.); +86-0759-2387458 (H.C.)
| | - Hualin Chen
- Department of Pulmonary Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524000, China
- Correspondence: (Z.Y.); (H.C.); Tel.: +86-0759-2387458 (Z.Y.); +86-0759-2387458 (H.C.)
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29
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Xie B, Chen X, Deng Q, Shi K, Xiao J, Zou Y, Yang B, Guan A, Yang S, Dai Z, Xie H, He S, Chen Q. Development and Validation of a Prognostic Nomogram for Lung Adenocarcinoma: A Population-Based Study. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:5698582. [PMID: 36536690 PMCID: PMC9759395 DOI: 10.1155/2022/5698582] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 01/22/2024]
Abstract
PURPOSE To establish an effective and accurate prognostic nomogram for lung adenocarcinoma (LUAD). Patients and Methods. 62,355 LUAD patients from 1975 to 2016 enrolled in the Surveillance, Epidemiology, and End Results (SEER) database were randomly and equally divided into the training cohort (n = 31,179) and the validation cohort (n = 31,176). Univariate and multivariate Cox regression analyses screened the predictive effects of each variable on survival. The concordance index (C-index), calibration curves, receiver operating characteristic (ROC) curve, and area under the ROC curve (AUC) were used to examine and validate the predictive accuracy of the nomogram. Kaplan-Meier curves were used to estimate overall survival (OS). RESULTS 10 prognostic factors associated with OS were identified, including age, sex, race, marital status, American Joint Committee on Cancer (AJCC) TNM stage, tumor size, grade, and primary site. A nomogram was established based on these results. C-indexes of the nomogram model reached 0.777 (95% confidence interval (CI), 0.773 to 0.781) and 0.779 (95% CI, 0.775 to 0.783) in the training and validation cohorts, respectively. The calibration curves were well-fitted for both cohorts. The AUC for the 3- and 5-year OS presented great prognostic accuracy in the training cohort (AUC = 0.832 and 0.827, respectively) and validation cohort (AUC = 0.835 and 0.828, respectively). The Kaplan-Meier curves presented significant differences in OS among the groups. CONCLUSION The nomogram allows accurate and comprehensive prognostic prediction for patients with LUAD.
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Affiliation(s)
- Bin Xie
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Geriatrics,Respiratory Medicine, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xi Chen
- Department of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Qi Deng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Ke Shi
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Jian Xiao
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Geriatrics,Respiratory Medicine, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yong Zou
- Department of Emergency Medicine, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Baishuang Yang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Geriatrics,Respiratory Medicine, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Anqi Guan
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Geriatrics,Respiratory Medicine, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Shasha Yang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Geriatrics,Respiratory Medicine, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Ziyu Dai
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Geriatrics,Respiratory Medicine, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Huayan Xie
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Geriatrics,Respiratory Medicine, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Shuya He
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang 421001, China
| | - Qiong Chen
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Geriatrics,Respiratory Medicine, Xiangya Hospital, Central South University, Changsha 410008, China
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30
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Yang Y, Cui H, Li D, Gao Y, Chen L, Zhou C, Feng M, Tu W, Li S, Chen X, Hao B, Li L, Cao Y. Prognosis and Immunological Characteristics of PGK1 in Lung Adenocarcinoma: A Systematic Analysis. Cancers (Basel) 2022; 14:5228. [PMID: 36358653 PMCID: PMC9653683 DOI: 10.3390/cancers14215228] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/13/2022] [Accepted: 10/21/2022] [Indexed: 01/30/2024] Open
Abstract
Background: Aerobic glycolysis plays a key role in tumor metabolic reprogramming to reshape the immune microenvironment. The phosphoglycerate kinase 1 (PGK1) gene codes a glycolytic enzyme that converts 1,3-diphosphoglycerate to 3-phosphoglycerate. However, in lung adenocarcinoma (LUAD), the role of PGK1 in altering the tumor microenvironment (TME) has not yet been determined. Methods: Raw data, including bulk DNA and mRNA-seq data, methylation modification data, single-cell RNA-seq data, proteomics data, clinical case characteristics survival, immunotherapy data, and so on, were obtained from multiple independent public data sets. These data were reanalyzed to uncover the prognosis and immunological characteristics of PGK1 in LUAD. Results: We found that PGK1 mRNA and protein were considerably over-expressed in LUAD compared to normal tissue and that high PGK1 expression is associated with poorer prognostic outcomes in LUAD. The enrichment analysis of PGK1 co-expressed genes in lung adenocarcinoma revealed that PGK1 may be involved in hypoxia, metabolism, DNA synthesis, cell cycle, PI3K/AKT, and various immune and inflammatory signaling pathways. Furthermore, PGK1 is also linked to the recruitment of numerous immune cells, including aDC (dendritic cells), macrophages, and neutrophils. More importantly, PGK1 was highly expressed in immunosuppressive cells, including M2 macrophages, Tregs, and exhausted T cells, among others. Finally, higher PGK1 expression indicated significant correlations to immune checkpoints, TMB (tumor mutation burden), and high response to immunotherapy. Conclusions: The presented findings imply that PGK1, as a glycolysis core gene, may be important for the modification of the immune microenvironment by interacting with the tumor metabolism. The results of this study provide clues for a potential immunometabolic combination therapy strategy in LUAD, for which more experimental and clinical translational research is needed.
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Affiliation(s)
- Yuechao Yang
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Huanhuan Cui
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Deheng Li
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yang Gao
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lei Chen
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Changshuai Zhou
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Mingtao Feng
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Wenjing Tu
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Sen Li
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xin Chen
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Bin Hao
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Liangdong Li
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yiqun Cao
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
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31
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[Consensus on Postoperative Recurrence Prediction of Non-small Cell Lung Cancer
Based on Molecular Markers]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2022; 25:701-714. [PMID: 36285390 PMCID: PMC9619343 DOI: 10.3779/j.issn.1009-3419.2022.102.44] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Significant progress has been made in lung cancer screening, surgery, chemoradiation, targeted therapy, and immunotherapy recently. Surgical resection is the most important treatment for localized non-small cell lung cancer (NSCLC) so far, but there are still many patients who develop local recurrence or distant metastases within 5 years of surgery. Currently, the risk factors of recurrence in patients with NSCLC are mainly based on clinical and pathological features, which hardly identify patients at high risk of recurrence accurately. With the development of new detection technologies, a number of molecular markers that may have a predictive risk of recurrence in NSCLC have been discovered over the years. In order to summarize the molecular markers related to postoperative recurrence in NSCLC patients, we have formulated a consensus on the prediction of postoperative recurrence of NSCLC based on molecular markers. This consensus mainly focuses on the early stage NSCLC patients, discusses and summarizes the risk factors of disease recurrence from the molecular level. It is hoped that more and more valuable information can be provided for the management of patients, so as to provide more guidance for the perioperative management of the patients with early stage NSCLC in the future.
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32
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Chen Y, Xia L, Peng Y, Wang G, Bi L, Xiao X, Li C, Li W. Development and validation of a m 6A -regulated prognostic signature in lung adenocarcinoma. Front Oncol 2022; 12:947808. [PMID: 36303829 PMCID: PMC9593055 DOI: 10.3389/fonc.2022.947808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is the most frequent subtype of lung cancer, with a 5-year survival rate of less than 20%. N6-methyladenosine (m6A) is the most prevalent RNA epigenetic modification in eukaryotic cells, and post-transcriptionally regulates gene expression and function by affecting RNA metabolism. The alterations of functionally important m6A sites have been previously shown to play vital roles in tumor initiation and progression, but little is known about the extent to which m6A-regulated genes play in prognostic performance for patients with LUAD. Here, we presented an overview of the m6A methylome in LUAD tissues using transcriptome-wide m6A methylation profiles, and found that differentially methylated transcripts were significantly enriched in tumor-related processes, including immune response, angiogenesis and cell-substrate adhesion. Joint analysis of m6A modification and gene expression suggested that 300 genes were regulated by m6A. Furthermore, we developed a m6A-regulated prognosis-associated signature (m6A-PPS) by performing a multi-step process. The m6A-PPS model, a 15-gene set, was qualified for prognosis prediction for LUAD patients. By regrouping the patients with this model, the OS of the high-risk group was shorter than that of the low-risk group across all datasets. Importantly, patients with high m6A-PPS scores respond better to immunotherapeutic. Our results provide a valuable resource for understanding the important role of epitranscriptomic modifications in the pathogenesis of LUAD, and obtain potential prognostic biomarkers.
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Affiliation(s)
- Yaxin Chen
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Lei Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yuxuan Peng
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Gang Wang
- Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Liyun Bi
- Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xue Xiao
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Cui Li
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Weimin Li
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
- The Research Units of West China, Chinese Academy of Medical Sciences, West China Hospital, Chengdu, China
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33
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Song X, Zhang T, Ding H, Feng Y, Yang W, Yin X, Chen B, Liang Y, Mao Q, Xia W, Yu G, Xu L, Dong G, Jiang F. Non-genetic stratification reveals epigenetic heterogeneity and identifies vulnerabilities of glycolysis addiction in lung adenocarcinoma subtype. Oncogenesis 2022; 11:61. [PMID: 36216804 PMCID: PMC9550819 DOI: 10.1038/s41389-022-00436-0] [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: 04/15/2022] [Revised: 09/12/2022] [Accepted: 09/26/2022] [Indexed: 11/12/2022] Open
Abstract
Lung adenocarcinoma (LUAD) exhibits high heterogeneity and is well known for its high genetic variation. Recently, the understanding of non-genetic variation provides a new perspective to study the heterogeneity of LUAD. Little is known about whether super-enhancers (SEs) may be primarily responsible for the inter-tumor heterogeneity of LUAD. We used super-enhancer RNA (seRNA) levels of a large-scale clinical well-annotated LUAD cohort to stratify patients into three clusters with different prognosis and other malignant characteristics. Mechanistically, estrogen-related receptor alpha (ERRα) in cluster 3-like cell lines acts as a cofactor of BRD4 to assist SE-promoter loops to activate glycolysis-related target gene expression, thereby promoting glycolysis and malignant progression, which confers a therapeutic vulnerability to glycolytic inhibitors. Our study identified three groups of patients according to seRNA levels, among which patients in cluster 3 have the worst prognosis and vulnerability of glycolysis dependency. We also proposed a 3-TF index model to stratify patients with glycolysis-addicted tumors according to tumor SE stratification.
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Affiliation(s)
- Xuming Song
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, P. R. China
| | - Te Zhang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, P. R. China
| | - Hanlin Ding
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, P. R. China
| | - Yipeng Feng
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, P. R. China
| | - Wenmin Yang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, P. R. China
| | - Xuewen Yin
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, 211198, Nanjing, P. R. China
| | - Bing Chen
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, P. R. China
| | - Yingkuan Liang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China
| | - Qixing Mao
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China
| | - Wenjie Xia
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China
| | - Guiping Yu
- Department of Cardiothoracic Surgery, The affiliated Jiangyin Hospital of Southeast University Medical College, 214400, Jiangyin, P. R. China
| | - Lin Xu
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China. .,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China. .,The Fourth Clinical College of Nanjing Medical University, Nanjing, P. R. China. .,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, 211116, Nanjing, P. R. China.
| | - Gaochao Dong
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China. .,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China.
| | - Feng Jiang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 210009, Nanjing, P. R. China. .,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, P. R. China. .,The Fourth Clinical College of Nanjing Medical University, Nanjing, P. R. China.
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Ashrafi A, Akter Z, Modareszadeh P, Modareszadeh P, Berisha E, Alemi PS, Chacon Castro MDC, Deese AR, Zhang L. Current Landscape of Therapeutic Resistance in Lung Cancer and Promising Strategies to Overcome Resistance. Cancers (Basel) 2022; 14:4562. [PMID: 36230484 PMCID: PMC9558974 DOI: 10.3390/cancers14194562] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 02/06/2023] Open
Abstract
Lung cancer is one of the leading causes of cancer-related deaths worldwide with a 5-year survival rate of less than 18%. Current treatment modalities include surgery, chemotherapy, radiation therapy, targeted therapy, and immunotherapy. Despite advances in therapeutic options, resistance to therapy remains a major obstacle to the effectiveness of long-term treatment, eventually leading to therapeutic insensitivity, poor progression-free survival, and disease relapse. Resistance mechanisms stem from genetic mutations and/or epigenetic changes, unregulated drug efflux, tumor hypoxia, alterations in the tumor microenvironment, and several other cellular and molecular alterations. A better understanding of these mechanisms is crucial for targeting factors involved in therapeutic resistance, establishing novel antitumor targets, and developing therapeutic strategies to resensitize cancer cells towards treatment. In this review, we summarize diverse mechanisms driving resistance to chemotherapy, radiotherapy, targeted therapy, and immunotherapy, and promising strategies to help overcome this therapeutic resistance.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Li Zhang
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX 75080, USA
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35
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Cheng T, Wu Y, Liu Z, Yu Y, Sun S, Guo M, Sun B, Huang C. CDKN2A-mediated molecular subtypes characterize the hallmarks of tumor microenvironment and guide precision medicine in triple-negative breast cancer. Front Immunol 2022; 13:970950. [PMID: 36052076 PMCID: PMC9424905 DOI: 10.3389/fimmu.2022.970950] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Currently, breast cancer (BRCA) has become the most common cancer in the world, whose pathological mechanism is complex. Among its subtypes, triple-negative breast cancer (TNBC) has the worst prognosis. With the increasing number of diagnosed TNBC patients, the urgent need of novel biomarkers is also rising. Cyclin-dependent kinase inhibitor 2A (CDKN2A) has recently emerged as a key regulator associated with ferroptosis and cuproptosis (FAC) and has exhibited a significant effect on BRCA, but its detailed mechanism remains elusive. Herein, we conducted the first converge comprehensive landscape analysis of FAC-related gene CDKN2A in BRCA and disclosed its prognostic value in BRCA. Then, an unsupervised cluster analysis based on CDKN2A-correlated genes unveiled three subtypes, namely cold-immune subtype, IFN-γ activated subtype and FTL-dominant subtype. Subsequent analyses depicting hallmarks of tumor microenvironment (TME) among three subtypes suggested strong association between TNBC and CDKN2A. Given the fact that the most clinically heterogeneous TNBC always displayed the most severe outcomes and lacked relevant drug targets, we further explored the potential of immunotherapy for TNBC by interfering CDKN2A and constructed the CDKN2A-derived prognostic model for TNBC patients by Lasso-Cox. The 21-gene–based prognostic model showed high accuracy and was verified in external independent validation cohort. Moreover, we proposed three drugs for TNBC patients based on our model via targeting epidermal growth factor receptor. In summary, our study indicated the potential of CDKN2A as a pioneering prognostic predictor for TNBC and provided a rationale of immunotherapy for TNBC, and offered fresh perspectives and orientations for cancer treatment via inducing ferroptosis and cuproptosis to develop novel anti-cancer treatment strategies.
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Affiliation(s)
- Tianyi Cheng
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macao, Macao SAR, China
| | - Yingyi Wu
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macao, Macao SAR, China
- Dr. Neher’s Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macao, Macao SAR, China
| | - Zhiyu Liu
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macao, Macao SAR, China
| | - Yi Yu
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macao, Macao SAR, China
| | - Shixue Sun
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target and Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Min Guo
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Baoqing Sun
- Department of Allergy and Clinical Immunology, Department of Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Baoqing Sun, ; Chen Huang,
| | - Chen Huang
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macao, Macao SAR, China
- Dr. Neher’s Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macao, Macao SAR, China
- *Correspondence: Baoqing Sun, ; Chen Huang,
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Liu B, Wang C, Fang Z, Bai J, Qian Y, Ma Y, Ruan X, Yan S, Li S, Wang Y, Dong B, Yang X, Li M, Xia X, Qu H, Fang X, Wu N. Single-cell RNA sequencing reveals the cellular and molecular changes that contribute to the progression of lung adenocarcinoma. Front Cell Dev Biol 2022; 10:927300. [PMID: 36046337 PMCID: PMC9420948 DOI: 10.3389/fcell.2022.927300] [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: 04/24/2022] [Accepted: 07/04/2022] [Indexed: 11/20/2022] Open
Abstract
Pure ground glass nodules (GGNs) and solid nodules (SNs) represent early and relatively late stages of lung adenocarcinoma (LUAD) in radiology, respectively. The cellular and molecular characteristics of pure GGNs and SNs have not been comprehensively elucidated. Additionally, the mechanism driving the progression of lung adenocarcinoma from pure GGN to SN in radiology is also elusive. In this study, by analyzing the single-cell transcriptomic profiles of 76,762 cells from four pure GGNs, four SNs, and four normal tissues, we found that anti-tumor immunity mediated by NK and CD8+T cells gradually weakened with the progression of LUAD and humoral immunity mediated by plasma B cells was more active in SNs. Additionally, the proliferation ability of some special epithelial cell increased during the progression process from pure GGN to SN. Furthermore, stromal cells and M2 macrophages could assist the progression of LUAD. Through comprehensive analyses, we revealed dynamic changes in cellular components and intercellular interactions during the progression of LUAD. These findings could facilitate our understanding of LUAD and discovery of novel therapeutic targets.
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Affiliation(s)
- Bing Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Chen Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhanjie Fang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Bai
- Geneplus-Beijing Institution, Peking University Medical Industrial Park, Zhongguancun Life Science Park, Beijing, China
| | - Ying Qian
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuanyuan Ma
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiuyan Ruan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
| | - Shi Yan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Shaolei Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yaqi Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Bin Dong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Central Laboratory, Peking University Cancer Hospital and Institute, Beijing, China
| | - Xin Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Meng Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
| | - Xuefeng Xia
- Geneplus-Beijing Institution, Peking University Medical Industrial Park, Zhongguancun Life Science Park, Beijing, China
| | - Hongzhu Qu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Hongzhu Qu, ; Xiangdong Fang, ; Nan Wu,
| | - Xiangdong Fang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Hongzhu Qu, ; Xiangdong Fang, ; Nan Wu,
| | - Nan Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
- *Correspondence: Hongzhu Qu, ; Xiangdong Fang, ; Nan Wu,
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Preoperative Prediction Value of Pelvic Lymph Node Metastasis of Endometrial Cancer: Combining of ADC Value and Radiomics Features of the Primary Lesion and Clinical Parameters. JOURNAL OF ONCOLOGY 2022; 2022:3335048. [PMID: 35813867 PMCID: PMC9262528 DOI: 10.1155/2022/3335048] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/08/2022] [Indexed: 01/17/2023]
Abstract
Objective To investigate the value of apparent diffusion coefficient (ADC) value of endometrial cancer (EC) primary lesion and magnetic resonance imaging (MRI) three-dimensional (3D) radiomics features combined with clinical parameters for preoperative prediction of pelvic lymph node metastasis (PLNM). Methods A total of 136 patients with EC confirmed by postoperative pathology were retrospectively reviewed and analyzed. Patients were randomly divided into training set (n = 95) and test set (n = 41) at a ratio of 7 : 3. Radiomics features based on T2WI, DWI, and contrast-enhanced T1WI (CE-T1WI) sequence were extracted and screened, and then radiomics score (Rads-score) was calculated. Clinical parameters and ADC value of EC primary lesion were measured and collected, and their correlation with PLNM was analyzed. Receiver operating characteristic (ROC) curve was plotted to assess the diagnostic efficacy of the model. A nomogram for PLNM was created based on the multivariate logistic regression model. Results The ADC value of the EC primary lesion showed inverse correlation with PLNM, while CA125 and Rads-score were positively associated with PLNM. A predictive model was proposed based on ADC value, Rads-score, CA125, and MR-reported pelvic lymph node status (PLNS) for PLNM in EC. The area under the curve (AUC) of the model is 0.940; the sensitivity and specificity (87.1% and 90.6%) of the model were significantly higher than that of the MRI morphological signs. Conclusion A combination of ADC value, MRI 3D radiomics features of the EC primary lesion, and clinical parameters generated a prediction model for PLNM in EC and had a good diagnostic performance; it was a useful supplement to MR-reported PLNS based on MRI morphological signs.
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Zhao H, Lu G. Prognostic Implication and Immunological Role of PSMD2 in Lung Adenocarcinoma. Front Genet 2022; 13:905581. [PMID: 35754829 PMCID: PMC9214243 DOI: 10.3389/fgene.2022.905581] [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: 03/27/2022] [Accepted: 05/23/2022] [Indexed: 12/01/2022] Open
Abstract
Background: Although previous studies reported that 26S proteasome non-ATPase regulatory subunit 2 (PSMD2) is involved in many human cancers. However, its clinical significance and function in lung adenocarcinoma remain unclear. Here, we examined the prognostic and immunological role of PSMD2 in lung adenocarcinoma. Methods: The Cancer Genome Atlas (TCGA) was conducted to analyze PSMD2 expression and verified using UALCAN. PrognoScan and Kaplan-Meier curves were utilized to assess the effect of PSMD2 on survival. cBioPortal database was conducted to identify the mutation characteristics of PSMD2. Functional enrichment was performed to determine PSMD2-related function. Cancer Single-cell State Atlas (CancerSEA) was used to explore the cancer functional status of PSMD2 at single-cell resolution. PSMD2-related immune infiltration analysis was conducted. Tumor-Immune system interaction database (TISIDB) was performed to verify the correlation between PSMD2 expression and tumor-infiltrating lymphocytes (TILs). Results: Both mRNA and protein expression of PSMD2 were significantly elevated in lung adenocarcinoma. High expression of PSMD2 was significantly correlated with high T stage (p = 0.014), lymph node metastases (p < 0.001), and TNM stage p = 0.005). Kaplan-Meier curves indicated that high expression of PSMD2 was correlated with poor overall survival (38.2 vs. 59.7 months, p < 0.001) and disease-specific survival (59.9 months vs. not available, p = 0.004). Multivariate analysis suggested that PSMD2 was an independent biomarker for poor overall survival (HR 1.471, 95%CI, 1.024–2.114, p = 0.037). PSMD2 had a high mutation frequency of 14% in lung adenocarcinoma. The genetic mutation of PSMD2 was also correlated with poor overall survival, disease-specific survival, and progression-free survival in lung adenocarcinoma. Functional enrichment suggested PSMD2 expression was involved in the cell cycle, RNA transport, and cellular senescence. CancerSEA analysis indicated PSMD2 expression was positively correlated with cell cycle, DNA damage, and DNA repair. Immune infiltration analysis suggested that PSMD2 expression was correlated with immune cell infiltration levels and abundance of TILs. Conclusion: The upregulation of PSMD2 is significantly correlated with poor prognosis and immune infiltration levels in lung adenocarcinoma. Our findings suggest that PSMD2 is a potential biomarker for poor prognosis and immune therapeutic target in lung adenocarcinoma.
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Affiliation(s)
- Huihui Zhao
- Department of Oncology, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Guojun Lu
- Department of Respiratory Medicine, Nanjing Chest Hospital, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, China
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Tang Y, Guo Y. A Ubiquitin-Proteasome Gene Signature for Predicting Prognosis in Patients With Lung Adenocarcinoma. Front Genet 2022; 13:893511. [PMID: 35711913 PMCID: PMC9194557 DOI: 10.3389/fgene.2022.893511] [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: 03/18/2022] [Accepted: 05/05/2022] [Indexed: 11/29/2022] Open
Abstract
Background: Dysregulation of the ubiquitin-proteasome system (UPS) can lead to instability in the cell cycle and may act as a crucial factor in both tumorigenesis and tumor progression. However, there is no established prognostic signature based on UPS genes (UPSGs) for lung adenocarcinoma (LUAD) despite their value in other cancers. Methods: We retrospectively evaluated a total of 703 LUAD patients through multivariate Cox and Lasso regression analyses from two datasets, the Cancer Genome Atlas (n = 477) and GSE31210 (n = 226). An independent dataset (GSE50081) containing 128 LUAD samples were used for validation. Results: An eight-UPSG signature, including ARIH2, FBXO9, KRT8, MYLIP, PSMD2, RNF180, TRIM28, and UBE2V2, was established. Kaplan-Meier survival analysis and time-receiver operating characteristic curves for the training and validation datasets revealed that this risk signature presented with good performance in predicting overall and relapsed-free survival. Based on the signature and its associated clinical features, a nomogram and corresponding web-based calculator for predicting survival were established. Calibration plot and decision curve analyses showed that this model was clinically useful for both the training and validation datasets. Finally, a web-based calculator (https://ostool.shinyapps.io/lungcancer) was built to facilitate convenient clinical application of the signature. Conclusion: An UPSG based model was developed and validated in this study, which may be useful as a novel prognostic predictor for LUAD.
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Affiliation(s)
- Yunliang Tang
- Department of Rehabilitation Medicine, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yinhong Guo
- Department of Oncology, Zhuji People's Hospital of Zhejiang Province, Zhuji, China
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40
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Lu F, Gao J, Hou Y, Cao K, Xia Y, Chen Z, Yu H, Chang L, Li W. Construction of a Novel Prognostic Model in Lung Adenocarcinoma Based on 7-Methylguanosine-Related Gene Signatures. Front Oncol 2022; 12:876360. [PMID: 35785179 PMCID: PMC9243265 DOI: 10.3389/fonc.2022.876360] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Increasing evidence has implicated the modification of 7-methylguanosine (m7G), a type of RNA modification, in tumor progression. However, no comprehensive analysis to date has summarized the predicted role of m7G-related gene signatures in lung adenocarcinoma (LUAD). Herein, we aimed to develop a novel prognostic model in LUAD based on m7G-related gene signatures. The LUAD transcriptome profiling data and corresponding clinical data were acquired from the Cancer Genome Atlas (TCGA) and two Gene Expression Omnibus datasets. After screening, we first obtained 29 m7G-related genes, most of which were upregulated in tumor tissues and negatively associated with overall survival (OS). According to the expression similarity of m7G-related genes, the combined samples from the TCGA-LUAD and GSE68465 datasets were further classified as two clusters that exhibit distinct OS rates and genetic heterogeneity. Then, we constructed a novel prognostic model involving four genes by using 130 differentially expressed genes among the two clusters. The combined samples were randomly divided into a training cohort and an internal validation cohort in a 1:1 ratio, and the GSE72094 dataset was used as an external validation cohort. The samples were divided into high- and low-risk groups. We demonstrated that a higher risk score was an independent negative prognostic factor and predicted poor OS. A nomogram was further constructed to better predict the survival of LUAD patients. Functional enrichment analyses indicated that cell cycle and DNA replication-related biological processes and pathways were enriched in the high-risk group. More importantly, the low-risk group had greater infiltration and enrichment of most immune cells, as well as higher ESTIMATE, immune, and stromal scores. In addition, the high-risk group had a lower TIDE score and higher expressions of most immune checkpoint-related genes. We finally noticed that patients in the high-risk group were more sensitive to chemotherapeutic agents commonly used in LUAD. In conclusion, we herein summarized for the first time the alterations and prognostic role of m7G-related genes in LUAD and then constructed a prognostic model based on m7G-related gene signatures that could accurately and stably predict survival and guide individualized treatment decision-making in LUAD patients.
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Affiliation(s)
- Fei Lu
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
- Department of Oncology and Hematology, Southern Central Hospital of Yunnan Province, The First People’s Hospital of Honghe State, Mengzi, China
| | - Jingyan Gao
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Yu Hou
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Ke Cao
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Yaoxiong Xia
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Zhengting Chen
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Hui Yu
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Li Chang
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
- *Correspondence: Wenhui Li, ; Li Chang,
| | - Wenhui Li
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
- *Correspondence: Wenhui Li, ; Li Chang,
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Wang C, Lu T, Xu R, Chang X, Luo S, Peng B, Wang J, Yao L, Wang K, Shen Z, Zhao J, Zhang L. A bioinformatics-based immune-related prognostic index for lung adenocarcinoma that predicts patient response to immunotherapy and common treatments. J Thorac Dis 2022; 14:2131-2146. [PMID: 35813746 PMCID: PMC9264088 DOI: 10.21037/jtd-22-494] [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: 03/22/2022] [Accepted: 05/27/2022] [Indexed: 12/25/2022]
Abstract
Background There is increasing evidence of the effectiveness of immune checkpoint blockade (ICB) therapy for the treatment of lung adenocarcinoma (LUAD). However, the benefits of ICB therapy vary among LUAD patients. Due to the research dimension, existing biomarkers, such as programmed death-ligand 1 (PD-L1) expression and tumor mutation burden (TMB), could not reflect the complex tumor environment, and had low prediction accuracy of ICB. Therefore, we aimed to uncover a prognostic biomarker that could also predict whether a patient would benefit from ICB therapy and other common treatments from multiple dimensions, so as to improve the prediction accuracy of pre-treatment patients. Methods Based on the LUAD dataset retrieved from The Cancer Genome Atlas (TCGA) database, 50 immune-related hub genes were identified using weighted gene co-expression network analysis and univariate Cox regression analyses. An immune-related gene prognostic index (IRGPI) was constructed using a Cox proportional-hazards model based on 15 genes and validated using GSE72094 dataset. We tested its prognostic accuracy by Kaplan-Meier (K-M) survival curves of the two datasets and assessed its predictive power by comparing area under curve (AUC) of IRGPI with existing biomarkers. Subsequently, we analyzed the molecular and immune characteristics, and evaluated the benefits of ICB by PD-L1 expression and Tumor Immune Dysfunction and Exclusion (TIDE) analysis, predicted the inhibitory concentration 50 of common treatments drugs for two IRGPI score-related subgroups. Results Patients in the IRGPI-high subgroup had lower overall survival (OS) than patients in the IRGPI-low subgroup in K-M survival curve in two cohorts. And IRGPI has AUC values of 0.715, 0.724, and 0.743 in 1, 2, and 3 years, respectively. A higher tumor mutation burden and PD-L1 expression and the tumor microenvironment (TME) landscape demonstrated that IRGPI-high subgroup patients may respond better to ICB therapy. Genomics of Drug Sensitivity in Cancer (GDSC) analysis indicated that the IRGPI-high subgroup showed greater sensitivity to chemotherapy. Conclusions IRGPI is a prospective biomarker for evaluating whether a patient will benefit from ICB therapy and other treatments, and distinguishing patients with different molecular and immune characteristics.
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Affiliation(s)
- Chenghao Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Tong Lu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Ran Xu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaoyan Chang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shan Luo
- Second Clinical College of Medicine, Harbin Medical University, Harbin, China
| | - Bo Peng
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jun Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lingqi Yao
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Kaiyu Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhiping Shen
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiaying Zhao
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Linyou Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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Next-Generation Sequencing in Lung Cancer Patients: A Comparative Approach in NSCLC and SCLC Mutational Landscapes. J Pers Med 2022; 12:jpm12030453. [PMID: 35330454 PMCID: PMC8955273 DOI: 10.3390/jpm12030453] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 02/04/2023] Open
Abstract
Background: Lung cancer remains one of the most diagnosed malignancies, being the second most diagnosed cancer, while still being the leading cause of cancer-related deaths. Late diagnosis remains a problem, alongside the high mutational burden encountered in lung cancer. Methods: We assessed the genetic profile of cancer genes in lung cancer using The Cancer Genome Atlas (TCGA) datasets for mutations and validated the results in a separate cohort of 32 lung cancer patients using tumor tissue and whole blood samples for next-generation sequencing (NGS) experiments. Another separate cohort of 32 patients was analyzed to validate some of the molecular alterations depicted in the NGS experiment. Results: In the TCGA analysis, we identified the most commonly mutated genes in each lung cancer dataset, with differences among the three histotypes analyzed. NGS analysis revealed TP53, CSF1R, PIK3CA, FLT3, ERBB4, and KDR as being the genes most frequently mutated. We validated the c.1621A>C mutation in KIT. The correlation analysis indicated negative correlation between adenocarcinoma and altered PIK3CA (r = −0.50918; p = 0.0029). TCGA survival analysis indicated that NRAS and IDH2 (LUAD), STK11 and TP53 (LUSC), and T53 (SCLC) alterations are correlated with the survival of patients. Conclusions: The study revealed differences in the mutational landscape of lung cancer histotypes.
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43
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Deciphering Tumour Heterogeneity: From Tissue to Liquid Biopsy. Cancers (Basel) 2022; 14:cancers14061384. [PMID: 35326534 PMCID: PMC8946040 DOI: 10.3390/cancers14061384] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/04/2022] [Accepted: 03/05/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Most malignant tumours are highly heterogeneous at molecular and phenotypic levels. Tumour variability poses challenges for the management of patients, as it arises between patients and even evolves in space and time within a single patient. Currently, treatment-decision making usually relies on the molecular characteristics of a limited tumour tissue sample at the time of diagnosis or disease progression but does not take into account the complexity of the bulk tumours and their constant evolution over time. In this review, we explore the extent of tumour heterogeneity and report the mechanisms that promote and sustain this diversity in cancers. We summarise the clinical strikes of tumour diversity in the management of patients with cancer. Finally, we discuss the current material and technological approaches that are relevant to adequately appreciate tumour heterogeneity. Abstract Human solid malignancies harbour a heterogeneous set of cells with distinct genotypes and phenotypes. This heterogeneity is installed at multiple levels. A biological diversity is commonly observed between tumours from different patients (inter-tumour heterogeneity) and cannot be fully captured by the current consensus molecular classifications for specific cancers. To extend the complexity in cancer, there are substantial differences from cell to cell within an individual tumour (intra-tumour heterogeneity, ITH) and the features of cancer cells evolve in space and time. Currently, treatment-decision making usually relies on the molecular characteristics of a limited tumour tissue sample at the time of diagnosis or disease progression but does not take into account the complexity of the bulk tumours and their constant evolution over time. In this review, we explore the extent of tumour heterogeneity with an emphasis on ITH and report the mechanisms that promote and sustain this diversity in cancers. We summarise the clinical strikes of ITH in the management of patients with cancer. Finally, we discuss the current material and technological approaches that are relevant to adequately appreciate ITH.
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Li C, Tian C, Zeng Y, Liang J, Yang Q, Gu F, Hu Y, Liu L. Integrated Analysis of MATH-Based Subtypes Reveals a Novel Screening Strategy for Early-Stage Lung Adenocarcinoma. Front Cell Dev Biol 2022; 10:769711. [PMID: 35211471 PMCID: PMC8861524 DOI: 10.3389/fcell.2022.769711] [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: 09/02/2021] [Accepted: 01/19/2022] [Indexed: 12/24/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is a frequently diagnosed cancer type, and many patients have already reached an advanced stage when diagnosed. Thus, it is crucial to develop a novel and efficient approach to diagnose and classify lung adenocarcinoma at an early stage. In our study, we combined in silico analysis and machine learning to develop a new five-gene–based diagnosis strategy, which was further verified in independent cohorts and in vitro experiments. Considering the heterogeneity in cancer, we used the MATH (mutant-allele tumor heterogeneity) algorithm to divide patients with early-stage LUAD into two groups (C1 and C2). Specifically, patients in C2 had lower intratumor heterogeneity and higher abundance of immune cells (including B cell, CD4 T cell, CD8 T cell, macrophage, dendritic cell, and neutrophil). In addition, patients in C2 had a higher likelihood of immunotherapy response and overall survival advantage than patients in C1. Combined drug sensitivity analysis (CTRP/PRISM/CMap/GDSC) revealed that BI-2536 might serve as a new therapeutic compound for patients in C1. In order to realize the application value of our study, we constructed the classifier (to classify early-stage LUAD patients into C1 or C2 groups) with multiple machine learning and bioinformatic analyses. The 21-gene–based classification model showed high accuracy and strong generalization ability, and it was verified in four independent validation cohorts. In summary, our research provided a new strategy for clinicians to make a quick preliminary assisting diagnosis of early-stage LUAD and make patient classification at the intratumor heterogeneity level. All data, codes, and study processes have been deposited to Github and are available online.
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Affiliation(s)
- Chang Li
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chen Tian
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yulan Zeng
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinyan Liang
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qifan Yang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Feifei Gu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yue Hu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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45
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Hoang PH, Landi MT. DNA Methylation in Lung Cancer: Mechanisms and Associations with Histological Subtypes, Molecular Alterations, and Major Epidemiological Factors. Cancers (Basel) 2022; 14:cancers14040961. [PMID: 35205708 PMCID: PMC8870477 DOI: 10.3390/cancers14040961] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/14/2021] [Accepted: 02/11/2022] [Indexed: 01/27/2023] Open
Abstract
Lung cancer is the major leading cause of cancer-related mortality worldwide. Multiple epigenetic factors-in particular, DNA methylation-have been associated with the development of lung cancer. In this review, we summarize the current knowledge on DNA methylation alterations in lung tumorigenesis, as well as their associations with different histological subtypes, common cancer driver gene mutations (e.g., KRAS, EGFR, and TP53), and major epidemiological risk factors (e.g., sex, smoking status, race/ethnicity). Understanding the mechanisms of DNA methylation regulation and their associations with various risk factors can provide further insights into carcinogenesis, and create future avenues for prevention and personalized treatments. In addition, we also highlight outstanding questions regarding DNA methylation in lung cancer to be elucidated in future studies.
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46
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Identification of Novel Subtypes in Lung Adenocarcinoma: Evidence from Gene Set Variation Analysis in Tumor and Adjacent Nontumor Samples. DISEASE MARKERS 2022; 2022:2602812. [PMID: 35096200 PMCID: PMC8793346 DOI: 10.1155/2022/2602812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 12/20/2021] [Indexed: 11/24/2022]
Abstract
In patients with lung adenocarcinoma (LUAD), the prognostic role of adjacent nontumor tissues is still unknown. Alterations in the activity of immunologic and hallmark gene sets in adjacent nontumor tissues may have a potential influence on cell proliferation of normal lung cell after pulmonary lobectomy. We sought to discover LUAD subgroups and prognostic gene sets based on changes in gene set activity in tumor and adjacent nontumor tissues. Firstly, we used gene set variation analysis (GSVA) to characterize the activity changes of 4922 gene sets in LUAD and nontumor samples. Luckily, we identified three novel LUAD subtypes using the nonnegative matrix factorization (NMF) algorithm. In detailed, patients with subtype-3 had a favorable prognosis, but subtypes 1 and 2 had a bad prognosis. In addition, patients with subtype-3 in the validation cohort also lived longer. Meanwhile, using the LASSO-Cox algorithm, we discovered 15 prognostic gene sets in tumors (T gene sets) and two prognostic gene sets in adjacent nontumors (N gene sets). Interestingly, genes from N gene sets were related with immune response in nontumor tissues, but genes from T gene sets were correlated with DNA damaging and repairing in tumor tissues. These findings highlighted the possibility of a stronger immune response in nearby nontumor tissues. In conclusion, our study established a theoretical foundation for selecting therapy strategy for LUAD patients that should be guided by changes in activity in tumor and adjacent nontumor tissues, particularly after pulmonary lobectomy.
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47
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Wang X, Wang Z, Huang R, Lu Z, Chen X, Huang D. UPP1 Promotes Lung Adenocarcinoma Progression through Epigenetic Regulation of Glycolysis. Aging Dis 2022; 13:1488-1503. [PMID: 36186123 PMCID: PMC9466982 DOI: 10.14336/ad.2022.0218] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/18/2022] [Indexed: 11/01/2022] Open
Affiliation(s)
- Xuan Wang
- Department of Thoracic Surgery Huashan Hospital & Cancer Metastasis Institute, Fudan University, Shanghai 200040, China.
- Correspondence should be addressed to: Dr. Dayu Huang (), Dr. Xiaofeng Chen (); Dr. Xuan Wang ().Department of Thoracic Surgery Huashan Hospital & Cancer Metastasis Institute, Fudan University, Shanghai 200040, China
| | - Zheng Wang
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Renhong Huang
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhouyi Lu
- Department of Thoracic Surgery Huashan Hospital & Cancer Metastasis Institute, Fudan University, Shanghai 200040, China.
| | - Xiaofeng Chen
- Department of Thoracic Surgery Huashan Hospital & Cancer Metastasis Institute, Fudan University, Shanghai 200040, China.
- Correspondence should be addressed to: Dr. Dayu Huang (), Dr. Xiaofeng Chen (); Dr. Xuan Wang ().Department of Thoracic Surgery Huashan Hospital & Cancer Metastasis Institute, Fudan University, Shanghai 200040, China
| | - Dayu Huang
- Department of Thoracic Surgery Huashan Hospital & Cancer Metastasis Institute, Fudan University, Shanghai 200040, China.
- Correspondence should be addressed to: Dr. Dayu Huang (), Dr. Xiaofeng Chen (); Dr. Xuan Wang ().Department of Thoracic Surgery Huashan Hospital & Cancer Metastasis Institute, Fudan University, Shanghai 200040, China
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48
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Flores-Téllez TDNJ, Baena E. Experimental challenges to modeling prostate cancer heterogeneity. Cancer Lett 2022; 524:194-205. [PMID: 34688843 DOI: 10.1016/j.canlet.2021.10.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/23/2021] [Accepted: 10/09/2021] [Indexed: 12/24/2022]
Abstract
Tumor heterogeneity plays a key role in prostate cancer prognosis, therapy selection, relapse, and acquisition of treatment resistance. Prostate cancer presents a heterogeneous diversity at inter- and intra-tumor and inter-patient levels which are influenced by multiple intrinsic and/or extrinsic factors. Recent studies have started to characterize the complexity of prostate tumors and these different tiers of heterogeneity. In this review, we discuss the most common factors that contribute to tumoral diversity. Moreover, we focus on the description of the in vitro and in vivo approaches, as well as high-throughput technologies, that help to model intra-tumoral diversity. Further understanding tumor heterogeneities and the challenges they present will guide enhanced patient risk stratification, aid the design of more precise therapies, and ultimately help beat this chameleon-like disease.
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Affiliation(s)
- Teresita Del N J Flores-Téllez
- Prostate Oncobiology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Alderley Edge, Macclesfield, SK10 4TG, UK
| | - Esther Baena
- Prostate Oncobiology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Alderley Edge, Macclesfield, SK10 4TG, UK; Belfast-Manchester Movember Centre of Excellence, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK10 4TG, UK.
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49
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Tan Z, Chen M, Wang Y, Peng F, Zhu X, Li X, Zhang L, Li Y, Liu Y. CHEK1: a hub gene related to poor prognosis for lung adenocarcinoma. Biomark Med 2021; 16:83-100. [PMID: 34882011 DOI: 10.2217/bmm-2021-0919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: The study aims to pinpoint hub genes and investigate their functions in order to gain insightful understandings of lung adenocarcinoma (LUAD). Methods: Bioinformatic approaches were adopted to investigate genes in databases including Gene Expression Omnibus, WebGestalt, STRING and Cytoscape, GEPIA2, Oncomine, Human Protein Atlas, TIMER2.0, UALCAN, cBioPortal, TargetScanHuman, OncomiR, ENCORI, Kaplan-Meier plotter, UCSC Xena, European Molecular Biology Laboratory - European Bioinformatics Institute Single Cell Expression Atlas and CancerSEA. Results: Five hub genes were ascertained. CHEK1 was overexpressed in a range of cancers, including LUAD. Promoter methylation, amplification and miRNA regulation might trigger CHEK1 upregulation, signaling poor prognosis. CHEK1 with its coexpressed genes were enriched in the cell cycle pathway. Intratumor heterogeneity of CHEK1 expression could be observed. Cell clusters with CHEK1 expression were more prone to metastasis and epithelial-to-mesenchymal transition. Conclusion: CHEK1 might potentially act as a prognostic biomarker for LUAD.
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Affiliation(s)
- Zhibo Tan
- Department of Radiation Oncology, Peking University Shenzhen Hospital, no. 1120, Lianhua Road, Futian District, Shenzhen, Guangdong Province, 518036, China.,Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Cancer Institute, Shenzhen-Peking University-Hong Kong University of Science & Technology Medical Center, Peking University Shenzhen Hospital, No. 1120, Lianhua Road, Futian District, Shenzhen, Guangdong Province, 518036, China
| | - Min Chen
- Department of Radiation Oncology, Peking University Shenzhen Hospital, no. 1120, Lianhua Road, Futian District, Shenzhen, Guangdong Province, 518036, China.,Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Cancer Institute, Shenzhen-Peking University-Hong Kong University of Science & Technology Medical Center, Peking University Shenzhen Hospital, No. 1120, Lianhua Road, Futian District, Shenzhen, Guangdong Province, 518036, China
| | - Ying Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 113, Baohe Avenue, Longgang District, Shenzhen, Guangdong Province, 518116, China
| | - Feng Peng
- Department of Radiation Oncology, Peking University Shenzhen Hospital, no. 1120, Lianhua Road, Futian District, Shenzhen, Guangdong Province, 518036, China.,Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Cancer Institute, Shenzhen-Peking University-Hong Kong University of Science & Technology Medical Center, Peking University Shenzhen Hospital, No. 1120, Lianhua Road, Futian District, Shenzhen, Guangdong Province, 518036, China
| | - Xiaopeng Zhu
- Department of Radiation Oncology, Peking University Shenzhen Hospital, no. 1120, Lianhua Road, Futian District, Shenzhen, Guangdong Province, 518036, China.,Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Cancer Institute, Shenzhen-Peking University-Hong Kong University of Science & Technology Medical Center, Peking University Shenzhen Hospital, No. 1120, Lianhua Road, Futian District, Shenzhen, Guangdong Province, 518036, China
| | - Xin Li
- Department of Radiation Oncology, Peking University Shenzhen Hospital, no. 1120, Lianhua Road, Futian District, Shenzhen, Guangdong Province, 518036, China.,Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Cancer Institute, Shenzhen-Peking University-Hong Kong University of Science & Technology Medical Center, Peking University Shenzhen Hospital, No. 1120, Lianhua Road, Futian District, Shenzhen, Guangdong Province, 518036, China
| | - Lei Zhang
- Department of Radiation Oncology, Peking University Shenzhen Hospital, no. 1120, Lianhua Road, Futian District, Shenzhen, Guangdong Province, 518036, China.,Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Cancer Institute, Shenzhen-Peking University-Hong Kong University of Science & Technology Medical Center, Peking University Shenzhen Hospital, No. 1120, Lianhua Road, Futian District, Shenzhen, Guangdong Province, 518036, China
| | - Ying Li
- Department of Radiation Oncology, Peking University Shenzhen Hospital, no. 1120, Lianhua Road, Futian District, Shenzhen, Guangdong Province, 518036, China.,Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Cancer Institute, Shenzhen-Peking University-Hong Kong University of Science & Technology Medical Center, Peking University Shenzhen Hospital, No. 1120, Lianhua Road, Futian District, Shenzhen, Guangdong Province, 518036, China
| | - Yajie Liu
- Department of Radiation Oncology, Peking University Shenzhen Hospital, no. 1120, Lianhua Road, Futian District, Shenzhen, Guangdong Province, 518036, China.,Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Cancer Institute, Shenzhen-Peking University-Hong Kong University of Science & Technology Medical Center, Peking University Shenzhen Hospital, No. 1120, Lianhua Road, Futian District, Shenzhen, Guangdong Province, 518036, China
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50
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Antonarelli G, Corti C, Tarantino P, Ascione L, Cortes J, Romero P, Mittendorf EA, Disis ML, Curigliano G. Therapeutic cancer vaccines revamping: technology advancements and pitfalls. Ann Oncol 2021; 32:1537-1551. [PMID: 34500046 PMCID: PMC8420263 DOI: 10.1016/j.annonc.2021.08.2153] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/21/2021] [Accepted: 08/29/2021] [Indexed: 12/12/2022] Open
Abstract
Cancer vaccines (CVs) represent a long-sought therapeutic and prophylactic immunotherapy strategy to obtain antigen (Ag)-specific T-cell responses and potentially achieve long-term clinical benefit. However, historically, most CV clinical trials have resulted in disappointing outcomes, despite promising signs of immunogenicity across most formulations. In the past decade, technological advances regarding vaccine delivery platforms, tools for immunogenomic profiling, and Ag/epitope selection have occurred. Consequently, the ability of CVs to induce tumor-specific and, in some cases, remarkable clinical responses have been observed in early-phase clinical trials. It is notable that the record-breaking speed of vaccine development in response to the coronavirus disease-2019 pandemic mainly relied on manufacturing infrastructures and technological platforms already developed for CVs. In turn, research, clinical data, and infrastructures put in place for the severe acute respiratory syndrome coronavirus 2 pandemic can further speed CV development processes. This review outlines the main technological advancements as well as major issues to tackle in the development of CVs. Possible applications for unmet clinical needs will be described, putting into perspective the future of cancer vaccinology.
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Affiliation(s)
- G Antonarelli
- Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Haematology (DIPO), University of Milan, Milan, Italy
| | - C Corti
- Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Haematology (DIPO), University of Milan, Milan, Italy
| | - P Tarantino
- Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Haematology (DIPO), University of Milan, Milan, Italy
| | - L Ascione
- Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Haematology (DIPO), University of Milan, Milan, Italy
| | - J Cortes
- International Breast Cancer Center (IBCC), Quironsalud Group, Barcelona, Spain; Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - P Romero
- Department of Fundamental Oncology, University of Lausanne, Lausanne, Switzerland
| | - E A Mittendorf
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, USA; Breast Oncology Program, Dana-Farber/Brigham and Women's Cancer Center, Boston, USA
| | - M L Disis
- UW Medicine Cancer Vaccine Institute, University of Washington, Seattle, USA
| | - G Curigliano
- Division of Early Drug Development for Innovative Therapy, European Institute of Oncology, IRCCS, Milan, Italy; Department of Oncology and Haematology (DIPO), University of Milan, Milan, Italy.
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