1
|
Li Y, Wang Y, Wu R, Li P, Cheng Z. HTR2B as a novel biomarker of chronic obstructive pulmonary disease with lung squamous cell carcinoma. Sci Rep 2024; 14:13206. [PMID: 38851806 PMCID: PMC11162446 DOI: 10.1038/s41598-024-63896-x] [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: 01/30/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is often associated with lung squamous cell carcinoma (LUSC), which has the same etiology (smoking, inflammation, oxidative stress, microenvironmental changes, and genetics). Smoking, inflammation, and airway remodeling are the most important and classical mechanisms of COPD comorbidity in LUSC patients. Cancer can occur during repeated airway damage and repair (airway remodeling). Changes in the inflammatory and immune microenvironments, which can cause malignant transformation of some cells, are currently being revealed in both LUSC and COPD patients. We obtained the GSE76925 dataset from the Gene Expression Omnibus database. Screening for possible COPD biomarkers was performed using the LASSO regression model and a random forest classifier. The compositional patterns of the immune cell fraction in COPD patients were determined using CIBERSORT. HTR2B expression was analyzed using validation datasets (GSE47460, GSE106986, and GSE1650). HTR2B expression in COPD cell models was determined via real-time quantitative PCR. Epithelial-mesenchymal transition (EMT) marker expression levels were determined after knocking down or overexpressing HTR2B. HTR2B function and mechanism in LUSC were analyzed with the Kaplan‒Meier plotter database. HTR2B expression was inhibited to detect changes in LUSC cell proliferation. A total of 1082 differentially expressed genes (DEGs) were identified in the GSE76925 dataset (371 genes were significantly upregulated, and 711 genes were significantly downregulated). Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis indicated that the DEGs were mainly enriched in the p53 signaling and β-alanine metabolism pathways. Gene Ontology enrichment analysis indicated that the DEGs were largely related to transcription initiation from the RNA polymerase I promoter and to the regulation of mononuclear cell proliferation. The LASSO regression model and random forest classifier results revealed that HTR2B, DPYS, FRY, and CD19 were key COPD genes. Immune cell infiltration analysis indicated that these genes were closely associated with immune cells. Analysis of the validation sets suggested that HTR2B was upregulated in COPD patients. HTR2B was significantly upregulated in COPD cell models, and its upregulation was associated with increased EMT marker expression. Compared with that in bronchial epithelial cells, HTR2B expression was upregulated in LUSC cells, and inhibiting HTR2B expression led to the inhibition of LUSC cell proliferation. In conclusions, HTR2B might be a new biomarker and therapeutic target in COPD patients with LUSC.
Collapse
MESH Headings
- Humans
- Pulmonary Disease, Chronic Obstructive/genetics
- Pulmonary Disease, Chronic Obstructive/metabolism
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Lung Neoplasms/metabolism
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/pathology
- Carcinoma, Squamous Cell/metabolism
- Epithelial-Mesenchymal Transition/genetics
- Receptor, Serotonin, 5-HT2B/genetics
- Receptor, Serotonin, 5-HT2B/metabolism
- Gene Expression Regulation, Neoplastic
- Cell Proliferation/genetics
- Cell Line, Tumor
Collapse
Affiliation(s)
- Yue Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Yu Wang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Ruhao Wu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Pengfei Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
| | - Zhe Cheng
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
| |
Collapse
|
2
|
Abstract
All cancers arise from normal cells whose progeny acquire the cancer-initiating mutations and epigenetic modifications leading to frank tumorigenesis. The identity of those "cells-of-origin" has historically been a source of controversy across tumor types, as it has not been possible to witness the dynamic events giving rise to human tumors. Genetically engineered mouse models (GEMMs) of cancer provide an invaluable substitute, enabling researchers to interrogate the competence of various naive cellular compartments to initiate tumors in vivo. Researchers using these models have relied on lineage-specific promoters, knowledge of preneoplastic disease states in humans, and technical advances allowing more precise manipulations of the mouse germline. These approaches have given rise to the emerging view that multiple lineages within a given organ may generate tumors with similar histopathology. Here, we review some of the key studies leading to this conclusion in solid tumors and highlight the biological and clinical ramifications.
Collapse
Affiliation(s)
- Jason R Pitarresi
- Division of Hematology and Oncology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01655, USA
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01655, USA
| | - Ben Z Stanger
- Division of Gastroenterology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| |
Collapse
|
3
|
Lin H, Wang J, Shi Q, Wu M. Significance of NKX2-1 as a biomarker for clinical prognosis, immune infiltration, and drug therapy in lung squamous cell carcinoma. PeerJ 2024; 12:e17338. [PMID: 38708353 PMCID: PMC11069361 DOI: 10.7717/peerj.17338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 04/15/2024] [Indexed: 05/07/2024] Open
Abstract
Background This study was performed to determine the biological processes in which NKX2-1 is involved and thus its role in the development of lung squamous cell carcinoma (LUSC) toward improving the prognosis and treatment of LUSC. Methods Raw RNA sequencing (RNA-seq) data of LUSC from The Cancer Genome Atlas (TCGA) were used in bioinformatics analysis to characterize NKX2-1 expression levels in tumor and normal tissues. Survival analysis of Kaplan-Meier curve, the time-dependent receiver operating characteristic (ROC) curve, and a nomogram were used to analyze the prognosis value of NKX2-1 for LUSC in terms of overall survival (OS) and progression-free survival (PFS). Then, differentially expressed genes (DEGs) were identified, and Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and Gene Set Enrichment Analysis (GSEA) were used to clarify the biological mechanisms potentially involved in the development of LUSC. Moreover, the correlation between the NKX2-1 expression level and tumor mutation burden (TMB), tumor microenvironment (TME), and immune cell infiltration revealed that NKX2-1 participates in the development of LUSC. Finally, we studied the effects of NKX2-1 on drug therapy. To validate the protein and gene expression levels of NKX2-1 in LUSC, we employed immunohistochemistry(IHC) datasets, The Gene Expression Omnibus (GEO) database, and qRT-PCR analysis. Results NKX2-1 expression levels were significantly lower in LUSC than in normal lung tissue. It significantly differed in gender, stage and N classification. The survival analysis revealed that high expression of NKX2-1 had shorter OS and PFS in LUSC. The multivariate Cox regression hazard model showed the NKX2-1 expression as an independent prognostic factor. Then, the nomogram predicted LUSC prognosis. There are 51 upregulated DEGs and 49 downregulated DEGs in the NKX2-1 high-level groups. GO, KEGG and GSEA analysis revealed that DEGs were enriched in cell cycle and DNA replication.The TME results show that NKX2-1 expression was positively associated with mast cells resting, neutrophils, monocytes, T cells CD4 memory resting, and M2 macrophages but negatively associated with M1 macrophages. The TMB correlated negatively with NKX2-1 expression. The pharmacotherapy had great sensitivity in the NKX2-1 low-level group, the immunotherapy is no significant difference in the NKX2-1 low-level and high-level groups. The analysis of GEO data demonstrated concurrence with TCGA results. IHC revealed NKX2-1 protein expression in tumor tissues of both LUAD and LUSC. Meanwhile qRT-PCR analysis indicated a significantly lower NKX2-1 expression level in LUSC compared to LUAD. These qRT-PCR findings were consistent with co-expression analysis of NKX2-1. Conclusion We conclude that NKX2-1 is a potential biomarker for prognosis and treatment LUSC. A new insights of NKX2-1 in LUSC is still needed further research.
Collapse
Affiliation(s)
- Huiyue Lin
- Oncology Department, Longhua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Juyong Wang
- Oncology Department, Longhua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qing Shi
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Minmin Wu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| |
Collapse
|
4
|
Hao B, Dong H, Xiong R, Song C, Xu C, Li N, Geng Q. Identification of SLC2A1 as a predictive biomarker for survival and response to immunotherapy in lung squamous cell carcinoma. Comput Biol Med 2024; 171:108183. [PMID: 38422959 DOI: 10.1016/j.compbiomed.2024.108183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 01/20/2024] [Accepted: 02/18/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND As one of the common subtypes of non-small lung cancer, lung squamous cell carcinoma (LUSC) patients with advanced stage have few choices of treatment strategies. Therefore, it is urgent to discover genes that are associated with the survival and efficacy of immunotherapies. METHOD Differential gene expression analyses were conducted using TCGA LUSC bulk-sequencing and single-cell RNA-sequencing data. Prognostic genes were identified from the TCGA LUSC cohort. Protein expression validation and survival analyses were performed. Experiments were conducted to explore the underlying mechanisms. In addition, the correlation between gene expression and pathological response to adjuvant immunochemotherapy was also investigated. RESULTS After a series of bioinformatic analyses, solute carrier family 2 member 1(SLC2A1), encoding glucose transporter-1 (GLUT1), was found to be differentially expressed between tumor and normal tissues. GLUT1 was subsequently identified as an independent prognostic factor for LUSC. GSEA analysis revealed the glycolysis metabolism pathway of KEGG enriched in SLC2A1high tumor tissues. LASSO analyses revealed that tumor tissues with high expression of SLC2A1 were associated with high levels of protein lactylation. We found that SLC2A1 was preferentially expressed by SPP1+ macrophages in the tumor microenvironment, and the expression of SLC2A1 was associated with the abundance of SPP1+ macrophages. Immunofluorescence demonstrated GLUT1 and HIF1α colocalization in tumor-infiltrating macrophages. In vitro experiments showed HIF-1α-induced macrophage polarization under hypoxia, and GLUT1 inhibition blocked this polarization. In addition, SLC2A1 was negatively associated with the common immune checkpoint molecules, such as programmed cell death 1(PD-1), T cell immunoreceptor with Ig and ITIM domains (TIGIT), cytotoxic T-lymphocyte associated protein 4 (CTLA4) and lymphocyte activating 3 (LAG3), while showed a positive association with CD44. Finally, we observed that there was a significant correlation between pre-adjuvant-treatment GLUT1 expression and the pathological response. CONCLUSION SLC2A1 expression was differentially upregulated in tumor tissues, and elevated GLUT1 expression was associated with worse survival and poor pathological response to adjuvant immunochemotherapy. Upregulation of GLUT1 promoted macrophage polarization into the M2 phenotype. The findings will contribute to guiding the treatment selection for LUSC patients and providing personalized immunotherapy strategies.
Collapse
Affiliation(s)
- Bo Hao
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, No.238 Jiefang Road, Wuchang District, Wuhan 430060, China.
| | - Huixing Dong
- Department of Pulmonary and Critical Care Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111 XianXia Road, Shanghai 200336, China.
| | - Rui Xiong
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, No.238 Jiefang Road, Wuchang District, Wuhan 430060, China.
| | - Congkuan Song
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, No.238 Jiefang Road, Wuchang District, Wuhan 430060, China.
| | - Chenzhen Xu
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, No.238 Jiefang Road, Wuchang District, Wuhan 430060, China.
| | - Ning Li
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, No.238 Jiefang Road, Wuchang District, Wuhan 430060, China.
| | - Qing Geng
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, No.238 Jiefang Road, Wuchang District, Wuhan 430060, China.
| |
Collapse
|
5
|
Kwon J, Zhang J, Mok B, Allsup S, Kim C, Toretsky J, Han C. USP13 drives lung squamous cell carcinoma by switching lung club cell lineage plasticity. Mol Cancer 2023; 22:204. [PMID: 38093367 PMCID: PMC10717271 DOI: 10.1186/s12943-023-01892-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/27/2023] [Indexed: 12/17/2023] Open
Abstract
Lung squamous cell carcinoma (LUSC) is associated with high mortality and limited targeted therapies. USP13 is one of the most amplified genes in LUSC, yet its role in lung cancer is largely unknown. Here, we established a novel mouse model of LUSC by overexpressing USP13 on KrasG12D/+; Trp53flox/flox background (KPU). KPU-driven lung squamous tumors faithfully recapitulate key pathohistological, molecular features, and cellular pathways of human LUSC. We found that USP13 altered lineage-determining factors such as NKX2-1 and SOX2 in club cells of the airway and reinforced the fate of club cells to squamous carcinoma development. We showed a strong molecular association between USP13 and c-MYC, leading to the upregulation of squamous programs in murine and human lung cancer cells. Collectively, our data demonstrate that USP13 is a molecular driver of lineage plasticity in club cells and provide mechanistic insight that may have potential implications for the treatment of LUSC.
Collapse
Affiliation(s)
- Juntae Kwon
- Department of Oncology, Georgetown University School of Medicine, Washington D.C, USA
| | - Jinmin Zhang
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University School of Medicine, Washington D.C, USA
| | - Boram Mok
- Department of Oncology, Georgetown University School of Medicine, Washington D.C, USA
| | - Samuel Allsup
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University School of Medicine, Washington D.C, USA
| | - Chul Kim
- Division of Hematology and Oncology, Georgetown University School of Medicine, Washington D.C, USA
- MedStar Georgetown University Hospital, Washington D.C, USA
- Lombardi Comprehensive Cancer Center, Washington D.C, USA
| | - Jeffrey Toretsky
- Department of Oncology, Georgetown University School of Medicine, Washington D.C, USA
- Lombardi Comprehensive Cancer Center, Washington D.C, USA
- Departments of Pediatrics, Washington D.C, USA
| | - Cecil Han
- Department of Oncology, Georgetown University School of Medicine, Washington D.C, USA.
- Lombardi Comprehensive Cancer Center, Washington D.C, USA.
| |
Collapse
|
6
|
Zhang L, Liu J, Wang H, Xu Z, Wang Y, Chen Y, Peng H. MYH16 upregulation is associated with lung adenocarcinoma aggressiveness and immune infiltration. J Biochem Mol Toxicol 2023; 37:e23490. [PMID: 37589445 DOI: 10.1002/jbt.23490] [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: 01/18/2023] [Revised: 06/11/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023]
Abstract
Myosin heavy chain 16 (MYH16) may significantly affect cell cycle progression. Nevertheless, there is a lack of evidence about the clinical relevance of MYH16 upregulation in pan cancers, including lung adenocarcinoma (LUAD). MYH16 expression patterns were evaluated in various bioinformatics databases using The Cancer Genome Atlas data set. Clinical and pathological factor data were employed to risk-stratify patients. The Kaplan-Meier plotter approach was used to estimate survival rates. Tumor immune infiltration was explored via the TIMER tool, and gene set enrichment analysis (GSEA) was used to identify the pathways involved in MYH16 upregulation. The results showed that MYH16 was abnormally upregulated in pan cancers, including LUAD. MYH16 expression induction in LUAD was found to be related to the tumor stage. Furthermore, MYH16 upregulation was correlated with LUAD development and worse overall survival, particularly in women. Notably, MYH16 overexpression in LUAD tissues corresponded to the amount of immune infiltration in the tumor. Additionally, univariate Cox hazard regression analysis revealed that MYH16 may be an independent prognostic indicator for LUAD. Furthermore, a nomogram was constructed according to MYH16 expression and clinical characteristics. BMP6 expression deficiency may be a key factor contributing to MYH16 upregulation in LUAD. Finally, GSEA demonstrated that MYH16 might mediate meiosis and gene silencing through RNA signaling pathways. This study, for the first time, showed that MYH16 upregulation in LUAD is associated with various risk factors, increased cancer aggressiveness, enhanced infiltration of tumor immune cells, and reduced survival rates.
Collapse
Affiliation(s)
- Libin Zhang
- Thoracic Surgery Department, Yan'an Hospital Affiliated to Kunming Medical University, Kunming City, Yunnan Province, China
| | - Jun Liu
- Department of Thoracic Surgery, The First People's Hospital of Yunnan Province, Kunming City, Yunnan Province, China
| | - Han Wang
- Department of Thoracic Surgery, The First People's Hospital of Yunnan Province, Kunming City, Yunnan Province, China
| | - Zheyuan Xu
- Department of Thoracic Surgery, The First People's Hospital of Yunnan Province, Kunming City, Yunnan Province, China
| | - Yang Wang
- Department of Thoracic Surgery, The First People's Hospital of Yunnan Province, Kunming City, Yunnan Province, China
| | - Yun Chen
- Department of Thoracic Surgery, The First People's Hospital of Yunnan Province, Kunming City, Yunnan Province, China
| | - Hao Peng
- Department of Thoracic Surgery, The First People's Hospital of Yunnan Province, Kunming City, Yunnan Province, China
| |
Collapse
|
7
|
Cui Y, Wu Y, Zhang M, Zhu Y, Su X, Kong W, Zheng X, Sun G. Identification of prognosis-related lncRNAs and cell validation in lung squamous cell carcinoma based on TCGA data. Front Oncol 2023; 13:1240868. [PMID: 37965447 PMCID: PMC10642190 DOI: 10.3389/fonc.2023.1240868] [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: 06/15/2023] [Accepted: 10/12/2023] [Indexed: 11/16/2023] Open
Abstract
Objective To discern long non-coding RNAs (lncRNAs) with prognostic relevance in the context of lung squamous cell carcinoma (LUSC), we intend to predict target genes by leveraging The Cancer Genome Atlas (TCGA) repository. Subsequently, we aim to investigate the proliferative potential of critical lncRNAs within the LUSC milieu. Methods DESeq2 was employed to identify differentially expressed genes within the TCGA database. Following this, we utilized both univariate and multivariate Cox regression analyses to identify lncRNAs with prognostic relevance. Noteworthy lncRNAs were selected for validation in cell lines. The intracellular localization of these lncRNAs was ascertained through nucleocytoplasmic isolation experiments. Additionally, the impact of these lncRNAs on cellular proliferation, invasion, and migration capabilities was investigated using an Antisense oligonucleotides (ASO) knockdown system. Results Multivariate Cox regression identified a total of 12 candidate genes, consisting of seven downregulated lncRNAs (BRE-AS1, CCL15-CCL14, DNMBP-AS1, LINC00482, LOC100129034, MIR22HG, PRR26) and five upregulated lncRNAs (FAM83A-AS1, LINC00628, LINC00923, LINC01341, LOC100130691). The target genes associated with these lncRNAs exhibit significant enrichment within diverse biological pathways, including metabolic processes, cancer pathways, MAPK signaling, PI3K-Akt signaling, protein binding, cellular components, cellular transformation, and other functional categories. Furthermore, nucleocytoplasmic fractionation experiments demonstrated that LINC00923 and LINC01341 are predominantly localized within the cellular nucleus. Subsequent investigations utilizing CCK-8 assays and colony formation assays revealed that the knockdown of LINC00923 and LINC01341 effectively suppressed the proliferation of H226 and H1703 cells. Additionally, transwell assays showed that knockdown of LINC00923 and LINC01341 significantly attenuated the invasive and migratory capacities of H226 and H1703 cells. Conclusion This study has identified 12 candidate lncRNA associated with prognostic implications, among which LINC00923 and LINC01341 exhibit potential as markers for the prediction of LUSC outcomes.
Collapse
Affiliation(s)
- Yishuang Cui
- School of Public Health, North China University of Science and Technology, Department of Hebei Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei, China
| | - Yanan Wu
- School of Public Health, North China University of Science and Technology, Department of Hebei Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei, China
| | - Mengshi Zhang
- School of Public Health, North China University of Science and Technology, Department of Hebei Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei, China
| | - Yingze Zhu
- School of Public Health, North China University of Science and Technology, Department of Hebei Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei, China
| | - Xin Su
- School of Public Health, North China University of Science and Technology, Department of Hebei Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei, China
| | - Wenyue Kong
- School of Public Health, North China University of Science and Technology, Department of Hebei Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei, China
| | - Xuan Zheng
- School of Public Health, North China University of Science and Technology, Department of Hebei Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei, China
| | - Guogui Sun
- Department of Hebei Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei, China
| |
Collapse
|
8
|
Joon HK, Thalor A, Gupta D. Machine learning analysis of lung squamous cell carcinoma gene expression datasets reveals novel prognostic signatures. Comput Biol Med 2023; 165:107430. [PMID: 37703712 DOI: 10.1016/j.compbiomed.2023.107430] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/06/2023] [Accepted: 08/28/2023] [Indexed: 09/15/2023]
Abstract
BACKGROUND Lung squamous cell carcinoma (LUSC) patients are often diagnosed at an advanced stage and have poor prognoses. Thus, identifying novel biomarkers for the LUSC is of utmost importance. METHODS Multiple datasets from the NCBI-GEO repository were obtained and merged to construct the complete dataset. We also constructed a subset from this complete dataset with only known cancer driver genes. Further, machine learning classifiers were employed to obtain the best features from both datasets. Simultaneously, we perform differential gene expression analysis. Furthermore, survival and enrichment analyses were performed. RESULTS The kNN classifier performed comparatively better on the complete and driver datasets' top 40 and 50 gene features, respectively. Out of these 90 gene features, 35 were found to be differentially regulated. Lasso-penalized Cox regression further reduced the number of genes to eight. The median risk score of these eight genes significantly stratified the patients, and low-risk patients have significantly better overall survival. We validated the robust performance of these eight genes on the TCGA dataset. Pathway enrichment analysis identified that these genes are associated with cell cycle, cell proliferation, and migration. CONCLUSION This study demonstrates that an integrated approach involving machine learning and system biology may effectively identify novel biomarkers for LUSC.
Collapse
Affiliation(s)
- Hemant Kumar Joon
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India; Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Anamika Thalor
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| |
Collapse
|
9
|
Yang Q, Zhu W, Gong H. Subtype classification based on t cell proliferation-related regulator genes and risk model for predicting outcomes of lung adenocarcinoma. Front Immunol 2023; 14:1148483. [PMID: 37077919 PMCID: PMC10106713 DOI: 10.3389/fimmu.2023.1148483] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
BackgroundLung adenocarcinoma (LUAD), the major lung cancer histotype, represents 40% lung cancers. Currently, outcomes are remarkably different in LUAD patients with similar AJCC/UICC-TNM features. T cell proliferation-related regulator genes (TPRGs) relate to the proliferation, activity and function of T cells and tumor progression. The values of TPRGs in classifying LUAD patients and predicting outcomes remain unknown.MethodsGene expression profile and corresponding clinical data were downloaded from TCGA and the GEO databases. We systematically analyzed the expression profile characteristics of 35 TPRGs in LUAD patients and investigated the differences in overall survival (OS), biology pathway, immunity and somatic mutation between different TPRGs-related subtypes. Subsequently, we constructed a TPRGs-related risk model in TCGA cohort to quantify risk scores using LASSO cox regression analysis and then validated this risk model in two GEO cohorts. LUAD patients were divided into high- and low-risk subtypes according to the median risk score. We systematically compared the biology pathway, immunity, somatic mutation and drug susceptibility between the two risk subtypes. Finally, we validate biological functions of two TPRGs-encoded proteins (DCLRE1B and HOMER1) in LUAD cells A549.ResultsWe identified different TPRGs-related subtypes (including cluster 1/cluster A and its counterpart cluster 2/cluster B). Compared to the cluster 1/cluster A subtype, cluster 2/cluster B subtype tended to have a prominent survival advantage with an immunosuppressive microenvironment and a higher somatic mutation frequency. Then, we constructed a TPRGs-related 6-gene risk model. The high-risk subtype characterized by higher somatic mutation frequency and lower immunotherapy response had a worse prognosis. This risk model was an independent prognostic factor and showed to be reliable and accurate for LUAD classification. Furthermore, subtypes with different risk scores were significantly associated with drug sensitivity. DCLRE1B and HOMER1 suppressed cell proliferation, migration and invasion in LUAD cells A549, which was in line with their prognostic values.ConclusionWe construed a novel stratification model of LUAD based on TPRGs, which can accurately and reliably predict the prognosis and might be used as a predictive tool for LUAD patients.
Collapse
Affiliation(s)
- Qin Yang
- School of Basic Medicine, Shaoyang University, the First Affiliated Hospital of Shaoyang University, Shaoyang, Hunan, China
| | - Weiyuan Zhu
- School of Basic Medicine, Shaoyang University, the First Affiliated Hospital of Shaoyang University, Shaoyang, Hunan, China
| | - Han Gong
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| |
Collapse
|
10
|
Wang HM, Zhang CY, Peng KC, Chen ZX, Su JW, Li YF, Li WF, Gao QY, Zhang SL, Chen YQ, Zhou Q, Xu C, Xu CR, Wang Z, Su J, Yan HH, Zhang XC, Chen HJ, Wu YL, Yang JJ. Using patient-derived organoids to predict locally advanced or metastatic lung cancer tumor response: A real-world study. Cell Rep Med 2023; 4:100911. [PMID: 36657446 PMCID: PMC9975107 DOI: 10.1016/j.xcrm.2022.100911] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/23/2022] [Accepted: 12/22/2022] [Indexed: 01/19/2023]
Abstract
Predicting the clinical response to chemotherapeutic or targeted treatment in patients with locally advanced or metastatic lung cancer requires an accurate and affordable tool. Tumor organoids are a potential approach in precision medicine for predicting the clinical response to treatment. However, their clinical application in lung cancer has rarely been reported because of the difficulty in generating pure tumor organoids. In this study, we have generated 214 cancer organoids from 107 patients, of which 212 are lung cancer organoids (LCOs), primarily derived from malignant serous effusions. LCO-based drug sensitivity tests (LCO-DSTs) for chemotherapy and targeted therapy have been performed in a real-world study to predict the clinical response to the respective treatment. LCO-DSTs accurately predict the clinical response to treatment in this cohort of patients with advanced lung cancer. In conclusion, LCO-DST is a promising precision medicine tool in treating of advanced lung cancer.
Collapse
Affiliation(s)
- Han-Min Wang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Chan-Yuan Zhang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China; The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Kai-Cheng Peng
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China; School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Ze-Xin Chen
- Guangdong Research Center of Organoid Engineering and Technology, Guangzhou 510530, China
| | - Jun-Wei Su
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Yu-Fa Li
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Wen-Feng Li
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Qing-Yun Gao
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Shi-Ling Zhang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China; The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Yu-Qing Chen
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China; School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Qing Zhou
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Cong Xu
- Guangdong Research Center of Organoid Engineering and Technology, Guangzhou 510530, China
| | - Chong-Rui Xu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Zhen Wang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Jian Su
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Hong-Hong Yan
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Xu-Chao Zhang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Hua-Jun Chen
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China.
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China.
| | - Jin-Ji Yang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China; The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China; School of Medicine, South China University of Technology, Guangzhou 510006, China.
| |
Collapse
|
11
|
Pan Y, Han H, Hu H, Wang H, Song Y, Hao Y, Tong X, Patel AS, Misirlioglu S, Tang S, Huang HY, Geng K, Chen T, Karatza A, Sherman F, Labbe KE, Yang F, Chafitz A, Peng C, Guo C, Moreira AL, Velcheti V, Lau SCM, Sui P, Chen H, Diehl JA, Rustgi AK, Bass AJ, Poirier JT, Zhang X, Ji H, Zhang H, Wong KK. KMT2D deficiency drives lung squamous cell carcinoma and hypersensitivity to RTK-RAS inhibition. Cancer Cell 2023; 41:88-105.e8. [PMID: 36525973 PMCID: PMC10388706 DOI: 10.1016/j.ccell.2022.11.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 09/06/2022] [Accepted: 11/22/2022] [Indexed: 12/16/2022]
Abstract
Lung squamous cell carcinoma (LUSC) represents a major subtype of lung cancer with limited treatment options. KMT2D is one of the most frequently mutated genes in LUSC (>20%), and yet its role in LUSC oncogenesis remains unknown. Here, we identify KMT2D as a key regulator of LUSC tumorigenesis wherein Kmt2d deletion transforms lung basal cell organoids to LUSC. Kmt2d loss increases activation of receptor tyrosine kinases (RTKs), EGFR and ERBB2, partly through reprogramming the chromatin landscape to repress the expression of protein tyrosine phosphatases. These events provoke a robust elevation in the oncogenic RTK-RAS signaling. Combining SHP2 inhibitor SHP099 and pan-ERBB inhibitor afatinib inhibits lung tumor growth in Kmt2d-deficient LUSC murine models and in patient-derived xenografts (PDXs) harboring KMT2D mutations. Our study identifies KMT2D as a pivotal epigenetic modulator for LUSC oncogenesis and suggests that KMT2D loss renders LUSC therapeutically vulnerable to RTK-RAS inhibition.
Collapse
Affiliation(s)
- Yuanwang Pan
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Han Han
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Hai Hu
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Hua Wang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Yueqiang Song
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuan Hao
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA; Applied Bioinformatics Laboratories, Office of Science and Research, New York University Grossman School of Medicine, New York, NY, USA
| | - Xinyuan Tong
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Ayushi S Patel
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Selim Misirlioglu
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Sittinon Tang
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Hsin-Yi Huang
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Ke Geng
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Ting Chen
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Angeliki Karatza
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Fiona Sherman
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Kristen E Labbe
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Fan Yang
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Alison Chafitz
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Chengwei Peng
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Chenchen Guo
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Andre L Moreira
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Vamsidhar Velcheti
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Sally C M Lau
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Pengfei Sui
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Haiquan Chen
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - J Alan Diehl
- Department of Biochemistry, Case Western Reserve University and Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - Anil K Rustgi
- Herbert Irving Comprehensive Cancer Center, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Adam J Bass
- Herbert Irving Comprehensive Cancer Center, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - John T Poirier
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Xiaoyang Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hongbin Ji
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Hua Zhang
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA; Hillman Cancer Center, UPMC, Pittsburgh, PA 15232, USA; Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Kwok-Kin Wong
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
| |
Collapse
|
12
|
Lu J, Duan Y, Liu P, He X, Yang Y, Zhang R, Weng L. Identification of tumour-infiltrating myeloid subsets associated with overall survival in lung squamous cell carcinoma. J Pathol 2023; 259:21-34. [PMID: 36178315 PMCID: PMC10100161 DOI: 10.1002/path.6015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/02/2022] [Accepted: 09/28/2022] [Indexed: 11/08/2022]
Abstract
Lung squamous cell carcinoma (LUSC) is a primary subtype of lung cancer with limited therapeutic options and poor prognosis, and tumour-infiltrating myeloid cells (TIMs) are key regulators of LUSC. However, the correlation between the abundance of TIM subtypes and clinical outcomes of LUSC remains unexplored. This study aimed to develop and validate a prognostic model for low- and high-risk patients with LUSC based on myeloid cell microenvironments. TIM markers in the tumoural (T) and stromal (S) regions were quantified using immunohistochemistry for 502 LUSC patients. L1-penalized Cox regression was used to develop a myeloid survival score (MSS) model based on the training cohort, followed by validation in distinct cohorts from multiple centres. RNA sequencing and immunostaining were used to examine the mechanisms of myeloid cells in LUSC progression and predict potential drug targets and therapeutic agents. Of the 12 myeloid markers, CD163T, CD163S, and S100A12T were highly associated with overall survival (OS) in LUSC patients. The MSS of the three myeloid signatures accurately categorized LUSC patients into risk categories, with an observable difference in OS between the training and validation cohorts. Tumours with high MSS were associated with enhanced antioxidative ability and hedgehog signalling and a shift to a more pro-tumorigenic microenvironment, accompanied by a reduced tumour cell immunogenicity and increased CD8+ T cell exhaustion patterns. Additionally, in high-risk patients, potential drug targets and compounds regulating hedgehog signalling were identified. Our study provides the first prognostic myeloid signature for LUSC, which may help advance precision medicine. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Jun Lu
- Department of Oncology, Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, PR China.,Hunan Normal University School of Medicine, Changsha, PR China
| | - Yumei Duan
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, PR China.,Department of Pathology, Xiangya Hospital, Central South University, Changsha, PR China
| | - Pinbo Liu
- Center of Clinical Pharmacology, Third Xiangya Hospital, Central South University, Changsha, PR China
| | - Xiang He
- Department of Oncology, Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, PR China
| | - Yiping Yang
- Center of Clinical Pharmacology, Third Xiangya Hospital, Central South University, Changsha, PR China
| | - Ran Zhang
- Hunan Normal University School of Medicine, Changsha, PR China
| | - Liang Weng
- Department of Oncology, Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, PR China.,Key Laboratory of Molecular Radiation Oncology, Hunan Province, Xiangya Hospital, Central South University, Changsha, PR China.,Hunan International Science and Technology Collaboration Base of Precision Medicine for Cancer, Xiangya Hospital, Central South University, Changsha, PR China.,Hunan Provincial Clinical Research Center for Respiratory Diseases, Xiangya Hospital, Central South University, Changsha, PR China.,Institute of Gerontological Cancer Research, National Clinical Research Center for Gerontology, Xiangya Hospital, Central South University, Changsha, PR China.,Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha, PR China
| |
Collapse
|
13
|
Zhang F, Zhang M, Yuan X, Tao Y, Wang J. Involvement of CHRNA6 in the Immune Response in Lung Squamous Cell Carcinoma and its Potential as a Drug Target for the Disease. Curr Pharm Des 2023; 29:2091-2100. [PMID: 37680128 DOI: 10.2174/1381612829666230901143203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/12/2023] [Accepted: 07/24/2023] [Indexed: 09/09/2023]
Abstract
BACKGROUND Lung squamous cell carcinoma (LUSC) is a subtype of lung cancer with a poor prognosis and limited treatment options. Previous studies show that some components of the cholinergic pathway may play important roles in the tumorigenesis of lung cancer, including LUSC. OBJECTIVE The purpose of this study is to investigate the involvement of cholinergic genes in immune infiltration in LUSC, and identify the key genes in the pathway and analyze their potential as targets for LUSC treatment and novel drugs. METHODS We first screened the cholinergic genes associated with immune infiltration in LUSC based on transcriptomic samples and explored the correlation between the key genes and immune infiltrating cells and immune pathways. Then, we assessed the effect of immunotherapeutic response in the high and low-expression groups of key genes in vitro. And finally, we screened potential drugs for the treatment of LUSC. RESULTS We found that the expression of CHRNA6, the gene encoding the α6 subunit of nicotinic acetylcholine receptors (nAChR), was significantly correlated with the proportion of immune infiltrating cells in LUSC, and the high expression level of the gene was associated with poor prognosis of the disease. Also, the proportion of Tregs, M1 macrophages, and resting mast cells was correlated with the expression of CHRNA6. In addition, LUSC patients with higher CHRNA6 expression levels had better immunotherapy responses. Furthermore, we found that the drugs, i.e., adavosertib, varbulin and pyrazoloacridine, had a strong affinity with CHRNA6, with adavosertib binding most stably with the protein. CONCLUSION CHRNA6 may be associated with immune infiltration in LUSC and affects patient prognosis and immunotherapeutic response by regulating immune cells and immune pathways. In addition, adavosertib may be a potential drug for the treatment of LUSC.
Collapse
Affiliation(s)
- Fengyu Zhang
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, 300070, China
| | - Meidi Zhang
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, 300070, China
| | - Xin Yuan
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, 300070, China
| | - Yulian Tao
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, 300070, China
| | - Ju Wang
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, 300070, China
| |
Collapse
|
14
|
Gao B, Li R, Song X, Hu S, Yang F. miR-139-5p and miR-451a as a Diagnostic Biomarker in LUSC. Pharmgenomics Pers Med 2023; 16:313-323. [PMID: 37063774 PMCID: PMC10093518 DOI: 10.2147/pgpm.s402750] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/31/2023] [Indexed: 04/18/2023] Open
Abstract
Background Lung squamous cell carcinoma (LUSC) is a type of lung cancer that originates from segmental or subsegmental bronchial mucosa. There is evidence that miRNA plays an important role in the occurrence and progression of tumors. Methods In this study, plasma samples of patients with early LUSC and healthy volunteers were subjected to miRNA sequencing, and the levels of differentially expressed miRNAs (DEMs) in LUSC tissues were analyzed using R language. Cox regression and Kaplan-Meier (K-M) survival curve analyses were performed to determine the relationship between DEMs and prognosis in LUSC, and PCR method was verified for the plasma expression level of DEMs in patients with LUSC. The levels of CYFRA21-1 and SCC-Ag in plasma were measured, and area under curve (AUC) was used to evaluate the diagnostic value of the DEMs. Results A total of 21 DEMs were screened out by sequencing. The expression levels of DEMs in tissue samples in the TCGA database were analyzed, and four DEMs with consistent expression levels were further screened from plasma and tissue samples. Regression analysis and K-M curve were performed to select two DEMs (miR-139-5p, miR-451a) that were correlated with the prognosis. PCR verification results showed that the levels of miR-451a and miR-139-5p were low in patients, and the level of miR-139-5p in late stages III & IV with the patients of LUSC was higher than that in stages I & II. The AUC values of the four indicators (SCC-Ag, CYFRA21-1, miR-451a and miR-139-5p) in the diagnosis of LUSC, early and late cases were 0.884, 0.935 and 0.778, respectively. Conclusion The detection of miR-139-5p and miR-451a levels in plasma has a certain potential in the non-invasive diagnosis, especially in patients with early stages of LUSC.
Collapse
Affiliation(s)
- Bo Gao
- Departments of Laboratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, People’s Republic of China
| | - Rui Li
- Departments of Medical office, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, People’s Republic of China
| | - Xiaojia Song
- Shiyan Prefecture Center for Disease Control and Prevention, Shiyan, Hubei, 442000, People’s Republic of China
| | - Shan Hu
- Departments of Obstetrics and Gynecology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, People’s Republic of China
| | - Fengmei Yang
- Departments of Obstetrics and Gynecology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, People’s Republic of China
- Correspondence: Fengmei Yang, Email
| |
Collapse
|
15
|
Xu D, Liu S, Wu X, Marti TM, Dorn P, Schmid RA, Peng RW, Shu Y. Dissecting the Immunological Profiles in NSD3-Amplified LUSC through Integrative Multi-Scale Analyses. Cancers (Basel) 2022; 14:cancers14204997. [PMID: 36291782 PMCID: PMC9599511 DOI: 10.3390/cancers14204997] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/03/2022] [Accepted: 10/10/2022] [Indexed: 11/28/2022] Open
Abstract
Simple Summary Although cancer immunotherapy has become a “game changer” in treating LUSC patients, challenges still prevail due to the heterogeneous response and insufficient predictive biomarkers. Recently, NSD3, a neighbor gene of FGFR1, was identified as a key genetic driver of LUSC tumorigenesis. While previous studies have reported the relevance of NSD3 in innate antiviral immunity, the association of NSD3 with the TIME remains an open question requiring further investigation. We first show that NSD3 gene amplification is associated with an immune-desert phenotype and correlated with a worse immunotherapy outcome. Further molecular characterizations pinpoint that the high activity of UPR signaling might be a pivotal mediator for the non-inflamed TME phenotype of NSD3-amplified LUSC. Concordantly, the pharmaco-transcriptomic correlation analysis indicated that the intervention of UPR signaling could be a promising synthetic lethality target for NSD3-amplified LUSC. Our findings reveal a previously unappreciated immunological role for NSD3 in LUSC pathobiology and provide therapeutic rationales for this daunting disease. Abstract The histone H3 lysine 36 (H3K36) methyltransferase NSD3, a neighboring gene of FGFR1, has been identified as a critical genetic driver of lung squamous cell carcinoma (LUSC). However, the molecular characteristics, especially the immunological roles of NSD3 in driving carcinogenesis, are poorly understood. In this study, we systematically integrated multi-omics data (e.g., genome, transcriptome, proteome, and TMA array) to dissect the immunological profiles in NSD3-amplified LUSC. Next, pharmaco-transcriptomic correlation analysis was implemented to identify the molecular underpinnings and therapeutic vulnerabilities in LUSC. We revealed that NSD3-amplified LUSC presents a non-inflamed tumor immune microenvironment (TIME) state in multiple independent LUSC patient cohorts. Predictably, elevated NSD3 expression was correlated with a worse immunotherapy outcome. Further molecular characterizations revealed that the high activity of unfolded protein response (UPR) signaling might be a pivotal mediator for the non-immunogenic phenotype of NSD3-amplified LUSC. Concordantly, we showed that NSD3-amplified LUSCs exhibited a more sensitive phenotype to compounds targeting UPR branches than the wild-type group. In brief, our multi-level analyses point to a previously unappreciated immunological role for NSD3 and provide therapeutic rationales for NSD3-amplified squamous lung cancer.
Collapse
Affiliation(s)
- Duo Xu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Shengchen Liu
- Department of Cardio-Thoracic Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Xi Wu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Thomas M. Marti
- Division of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
- Department for BioMedical Research (DBMR), Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Patrick Dorn
- Division of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
- Department for BioMedical Research (DBMR), Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Ralph A. Schmid
- Division of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
- Department for BioMedical Research (DBMR), Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Ren-Wang Peng
- Division of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
- Department for BioMedical Research (DBMR), Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Yongqian Shu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
- Correspondence: ; Tel.: +86-025-83714511
| |
Collapse
|
16
|
Mei J, Cai Y, Mussafi O, Zheng M, Xu Y, Chen R, Jiang G, Mao W, Xia W, Wan Y. Identification of adenoid subtype characterized with immune-escaped phenotype in lung squamous carcinoma based on transcriptomics. Exp Hematol Oncol 2022; 11:70. [PMID: 36224612 PMCID: PMC9555124 DOI: 10.1186/s40164-022-00327-5] [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: 09/18/2022] [Accepted: 09/21/2022] [Indexed: 11/24/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is a heterogeneous disease, and its demarcation contributes to various therapeutic outcomes. However, a small subset of tumors shows different molecular features that are in contradiction with pathological classification. Unsupervised clustering was performed to subtype NSCLC using the transcriptome data from the TCGA database. Next, immune microenvironment features of lung adenocarcinoma (LUAD), lung squamous carcinoma (LUSC), and lung adenoid squamous carcinoma (LASC) were characterized. In addition, diagnostic biomarkers to demarcate LASC among LUSC were screened using weighted gene co-expression network analysis (WGCNA) and validated by the in-house cohort. LASC was identified as a novel subtype with adenoid transcriptomic features in LUSC, which exhibited the most immuno-escaped phenotype among all NSCLC subtypes. In addition, FOLR1 was identified as a biomarker for LASC discrimination using the WGCNA analysis, and its diagnostic value was validated by the in-house cohort. Moreover, FOLR1 was related to immuno-escaped tumors in LUSC but not in LUAD. Overall, we proposed a novel typing strategy in NSCLC and identified FOLR1 as a biomarker for LASC discrimination.
Collapse
Affiliation(s)
- Jie Mei
- Department of Thoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, No. 299 Qingyang Road, Wuxi, 214023, China.,Department of Oncology, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, 214023, China.,Wuxi Clinical Medical College, Nanjing Medical University, Wuxi, 214023, China
| | - Yun Cai
- Wuxi Clinical Medical College, Nanjing Medical University, Wuxi, 214023, China
| | - Ofek Mussafi
- The Pq Laboratory of BiomeDx/Rx, Department of Biomedical Engineering, Binghamton University, 65 Murray Hill Road, Biotechnology Building BI2625, Binghamton, NY, 13850, USA
| | - Mingfeng Zheng
- Department of Thoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, No. 299 Qingyang Road, Wuxi, 214023, China
| | - Yongrui Xu
- Department of Thoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, No. 299 Qingyang Road, Wuxi, 214023, China
| | - Ruo Chen
- Department of Thoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, No. 299 Qingyang Road, Wuxi, 214023, China
| | - Guanyu Jiang
- Department of Thoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, No. 299 Qingyang Road, Wuxi, 214023, China
| | - Wenjun Mao
- Department of Thoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, No. 299 Qingyang Road, Wuxi, 214023, China.
| | - Wei Xia
- Department of Intensive Care Unit, The Affiliated Wuxi People's Hospital of Nanjing Medical University, No. 299 Qingyang Road, Wuxi, 214023, China.
| | - Yuan Wan
- The Pq Laboratory of BiomeDx/Rx, Department of Biomedical Engineering, Binghamton University, 65 Murray Hill Road, Biotechnology Building BI2625, Binghamton, NY, 13850, USA.
| |
Collapse
|
17
|
Li Y, Dong Y, Zhao S, Gao J, Hao X, Wang Z, Li M, Wang M, Liu Y, Yu X, Xu W. Serum-derived piR-hsa-164586 of extracellular vesicles as a novel biomarker for early diagnosis of non-small cell lung cancer. Front Oncol 2022; 12:850363. [PMID: 36249068 PMCID: PMC9559724 DOI: 10.3389/fonc.2022.850363] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is a major cause of death in those with malignant tumors. To achieve the early diagnosis of NSCLC, we investigated serum-derived Piwi-interacting RNA (piRNA) of extracellular vesicles to filter diagnostic biomarkers for NSCLC. High-throughput sequencing from cancerous tissues and adjacent noncancerous tissues in patients with NSCLC was first applied to recognize candidate piRNAs as diagnostic biomarkers. These screened piRNAs were further validated in 115 patients (including 95 cases in stage I) and 47 healthy individuals using quantitative real-time PCR (qRT-PCR). We showed that piR-hsa-164586 was significantly upregulated compared with paracancerous tissues and extracellular vesicles from the serum samples of healthy individuals. Moreover, the area under the curve (AUC) value of piR-hsa-164586 was 0.623 and 0.624 to distinguish patients with all stages or stage I of NSCLC, respectively, from healthy individuals. The diagnostic performance of piR-hsa-164586 was greatly improved compared with the cytokeratin-19-fragment (CYFRA21-1). Additionally, piR-hs-164586 was associated with the clinical characteristics of patients with NSCLC. Its expression was associated with the age and TNM stage of patients with NSCLC, indicating that it can serve as an effective and promising biomarker for the early diagnosis of NSCLC.
Collapse
Affiliation(s)
- Yanli Li
- Department of Pathology and Pathophysiology, The Medical Faculty of Qingdao University, Qingdao, China
| | - Yanhan Dong
- Institute of Translational Medicine, Qingdao University, Qingdao, China
| | - Shupeng Zhao
- Asset and Laboratory Management Office, Qingdao University, Qingdao, China
| | - Jinning Gao
- Institute of Translational Medicine, Qingdao University, Qingdao, China
| | - Xiaodan Hao
- Institute of Translational Medicine, Qingdao University, Qingdao, China
| | - Zibo Wang
- Department of Inspection, The Medical Faculty of Qingdao University, Qingdao, China
| | - Meng Li
- Department of Inspection, The Medical Faculty of Qingdao University, Qingdao, China
| | - Mengyuan Wang
- Department of Inspection, The Medical Faculty of Qingdao University, Qingdao, China
| | - Yiming Liu
- Department of Inspection, The Medical Faculty of Qingdao University, Qingdao, China
| | - Xiaoling Yu
- Department of Pathology and Pathophysiology, The Medical Faculty of Qingdao University, Qingdao, China
- *Correspondence: Xiaoling Yu, ; Wenhua Xu,
| | - Wenhua Xu
- Department of Inspection, The Medical Faculty of Qingdao University, Qingdao, China
- *Correspondence: Xiaoling Yu, ; Wenhua Xu,
| |
Collapse
|
18
|
Zhang M, Zhang J, Liu Y. Comprehensive analysis of molecular features, prognostic values, and immune landscape association of m6A-regulated immune-related lncRNAs in smoking-associated lung squamous cell carcinoma. Front Genet 2022; 13:887477. [PMID: 36035178 PMCID: PMC9399351 DOI: 10.3389/fgene.2022.887477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
Lung squamous cell carcinoma (LUSC) is the second most common histopathological subtype of lung cancer, and smoking is the leading cause of this type of cancer. However, the critical factors that directly affect the survival rate and sensitivity to immunotherapy of smoking LUSC patients are still unknown. Previous studies have highlighted the role of N6-methyladenosine (m6A) RNA modification, the most common epigenetic modification in eukaryotic species, together with immune-related long non-coding RNAs (lncRNAs) in promoting the development and progression of tumors. Thus, elucidating m6A-modified immune lncRNAs in LUSC patients with smoking history is vital. In this study, we described the expression and mutation features of the 24 m6A-related regulators in the smoking-associated LUSC cohort from The Cancer Genome Atlas (TCGA) database. Then, two distinct subtypes based on the expression levels of the prognostic m6A-regulated immune lncRNAs were defined, and differentially expressed genes (DEGs) between the subtypes were identified. The distributions of clinical characteristics and the tumor microenvironment (TME) between clusters were analyzed. Finally, we established a lncRNA-associated risk model and exhaustively clarified the clinical features, prognosis, immune landscape, and drug sensitivity on the basis of this scoring system. Our findings give insight into potential mechanisms of LUSC tumorigenesis and development and provide new ideas in offering LUSC patients with individual and effective immunotherapies.
Collapse
Affiliation(s)
- Meng Zhang
- School of Medicine, Nankai University, Tianjin, China
- Department of Thoracic Surgery, The First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Jian Zhang
- School of Medicine, Nankai University, Tianjin, China
- Department of Thoracic Surgery, The First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Yang Liu
- School of Medicine, Nankai University, Tianjin, China
- Department of Thoracic Surgery, The First Medical Centre, Chinese PLA General Hospital, Beijing, China
- *Correspondence: Yang Liu,
| |
Collapse
|
19
|
Ma DB, Liu XY, Jia H, Zhang Y, Jiang Q, Sun H, Li X, Sun F, Chai Y, Feng F, Liu L. A Novel Small-Molecule Inhibitor of SREBP-1 Based on Natural Product Monomers Upregulates the Sensitivity of Lung Squamous Cell Carcinoma Cells to Antitumor Drugs. Front Pharmacol 2022; 13:895744. [PMID: 35662712 PMCID: PMC9157598 DOI: 10.3389/fphar.2022.895744] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/26/2022] [Indexed: 12/16/2022] Open
Abstract
The transcription factor, sterol regulatory element binding protein 1 (SREBP-1), plays important roles in modulating the proliferation, metastasis, or resistance to antitumor agents by promoting cellular lipid metabolism and related cellular glucose-uptake/Warburg Effect. However, the underlying mechanism of SREBP-1 regulating the proliferation or drug-resistance in lung squamous cell carcinoma (LUSC) and the therapeutic strategies targeted to SREBP-1 in LUSC remain unclear. In this study, SREBP-1 was highly expressed in LUSC tissues, compared with the paired non-tumor tissues (the para-tumor tissues). A novel small-molecule inhibitor of SREBP-1, MSI-1 (Ma’s inhibitor of SREBP-1), based on natural product monomers, was identified by screening the database of natural products. Treatment with MSI-1 suppressed the activation of SREBP-1-related pathways and the Warburg effect of LUSC cells, as indicated by decreased glucose uptake or glycolysis. Moreover, treatment of MSI-1 enhanced the sensitivity of LUSC cells to antitumor agents. The specificity of MSI-1 on SREBP-1 was confirmed by molecular docking and point-mutation of SPEBP-1. Therefore, MSI-1 improved our understanding of SREBP-1 and provided additional options for the treatment of LUSC.
Collapse
Affiliation(s)
- De-Bin Ma
- Department of Respiratory and Critical Care Medicine, General Hospital of Northern Theater Command, Shenyang, China
| | - Xing-Yu Liu
- Department of General Internal Medicine, Central Medical Branch of PLA General Hospital, Beijing, China
| | - Hui Jia
- School of Traditional Chinese Medicine, Shenyang Medical College, Shenyang, China
| | - Yingshi Zhang
- Department of Clinical Pharmacy, Shenyang Pharmaceutical University, Shenyang, China
| | - Qiyu Jiang
- Institute of Infectious Diseases, Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Huiwei Sun
- Institute of Infectious Diseases, Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xiaojuan Li
- Institute of Infectious Diseases, Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Fang Sun
- Institute of Infectious Diseases, Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yantao Chai
- Department of Clinical Laboratory, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Fan Feng
- Department of Clinical Laboratory, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Lei Liu
- Department of Respiratory and Critical Care Medicine, General Hospital of Northern Theater Command, Shenyang, China
| |
Collapse
|
20
|
Xing J, Chen M, Han Y. Multiple datasets to explore the tumor microenvironment of cutaneous squamous cell carcinoma. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:5905-5924. [PMID: 35603384 DOI: 10.3934/mbe.2022276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND Cutaneous squamous cell carcinoma (cSCC) is one of the most frequent types of cutaneous cancer. The composition and heterogeneity of the tumor microenvironment significantly impact patient prognosis and the ability to practice precision therapy. However, no research has been conducted to examine the design of the tumor microenvironment and its interactions with cSCC. MATERIAL AND METHODS We retrieved the datasets GSE42677 and GSE45164 from the GEO public database, integrated them, and analyzed them using the SVA method. We then screened the core genes using the WGCNA network and LASSO regression and checked the model's stability using the ROC curve. Finally, we performed enrichment and correlation analyses on the core genes. RESULTS We identified four genes as core cSCC genes: DTYMK, CDCA8, PTTG1 and MAD2L1, and discovered that RORA, RORB and RORC were the primary regulators in the gene set. The GO semantic similarity analysis results indicated that CDCA8 and PTTG1 were the two most essential genes among the four core genes. The results of correlation analysis demonstrated that PTTG1 and HLA-DMA, CDCA8 and HLA-DQB2 were significantly correlated. CONCLUSIONS Examining the expression levels of four primary genes in cSCC aids in our understanding of the disease's pathophysiology. Additionally, the core genes were found to be highly related with immune regulatory genes, suggesting novel avenues for cSCC prevention and treatment.
Collapse
Affiliation(s)
- Jiahua Xing
- Department of Plastic and Reconstructive Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Muzi Chen
- Department of Plastic and Reconstructive Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Yan Han
- Department of Plastic and Reconstructive Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| |
Collapse
|
21
|
Zhang X, Zhang R, Liu P, Zhang R, Ning J, Ye Y, Yu W, Yu J. ATP8B1 Knockdown Activated the Choline Metabolism Pathway and Induced High-Level Intracellular REDOX Homeostasis in Lung Squamous Cell Carcinoma. Cancers (Basel) 2022; 14:cancers14030835. [PMID: 35159102 PMCID: PMC8834475 DOI: 10.3390/cancers14030835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/14/2022] [Accepted: 02/02/2022] [Indexed: 12/14/2022] Open
Abstract
Simple Summary We found that low expression of ATP8B1 was associated with poor prognosis, and involved in the dysregulation of glutathione (GSH) synthesis and choline metabolism in lung squamous cell carcinoma (LUSC) samples of The Cancer Genome Atlas (TCGA) and Tianjin Medical University Cancer Institute and Hospital (TJMUCH) cohort. We further constructed ATP8B1 knockdown of LUSC cell lines H520SH-ATP8B1 and SK-MES-1SH-ATP8B1 to investigate how ATP8B1 knockdown promoted cell proliferation, migration, and invasion in vitro and in vivo via upregulation of the CHKA-dependent choline metabolism pathway. We identified that ATP8B1 knockdown and CHKA upregulation can lead to mitochondrial dysfunction and high reduction-oxidation (REDOX) homeostasis, which may be involved in the roles of cardiolipin in maintaining mitochondrial dynamics and phospholipid homeostasis. Therefore, we proposed ATP8B1 as a novel predictive biomarker in LUSC and targeting ATP8B1-driven specific metabolic disorder might be a promising therapeutic strategy for LUSC. Abstract The flippase ATPase class I type 8b member 1 (ATP8B1) is essential for maintaining the stability and polarity of the epithelial membrane and can translocate specific phospholipids from the outer membrane to the inner membrane of the cell. Although ATP8B1 plays important roles in cell functions, ATP8B1 has been poorly studied in tumors and its prognostic value in patients with lung squamous cell carcinoma (LUSC) remains unclear. By investigating the whole genomic expression profiles of LUSC samples from The Cancer Genome Atlas (TCGA) database and Tianjin Medical University Cancer Institute and Hospital (TJMUCH) cohort, we found that low expression of ATP8B1 was associated with poor prognosis of LUSC patients. The results from cellular experiments and a xenograft-bearing mice model indicated that ATP8B1 knockdown firstly induced mitochondrial dysfunction and promoted ROS production. Secondly, ATP8B1 knockdown promoted glutathione synthesis via upregulation of the CHKA-dependent choline metabolism pathway, therefore producing and maintaining high-level intracellular REDOX homeostasis to aggravate carcinogenesis and progression of LUSC. In summary, we proposed ATP8B1 as a novel predictive biomarker in LUSC and targeting ATP8B1-driven specific metabolic disorder might be a promising therapeutic strategy for LUSC.
Collapse
Affiliation(s)
- Xiao Zhang
- Cancer Molecular Diagnostics Core, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China; (X.Z.); (R.Z.); (P.L.); (R.Z.); (J.N.); (Y.Y.)
- Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China
- National Clinical Research Center of Caner, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Immunology and Biotherapy, Department of Immunology, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China;
| | - Rui Zhang
- Cancer Molecular Diagnostics Core, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China; (X.Z.); (R.Z.); (P.L.); (R.Z.); (J.N.); (Y.Y.)
- Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China
| | - Pengpeng Liu
- Cancer Molecular Diagnostics Core, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China; (X.Z.); (R.Z.); (P.L.); (R.Z.); (J.N.); (Y.Y.)
- Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China
| | - Runjiao Zhang
- Cancer Molecular Diagnostics Core, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China; (X.Z.); (R.Z.); (P.L.); (R.Z.); (J.N.); (Y.Y.)
- Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China
- National Clinical Research Center of Caner, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Immunology and Biotherapy, Department of Immunology, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China;
| | - Junya Ning
- Cancer Molecular Diagnostics Core, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China; (X.Z.); (R.Z.); (P.L.); (R.Z.); (J.N.); (Y.Y.)
- Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China
- National Clinical Research Center of Caner, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Immunology and Biotherapy, Department of Immunology, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China;
| | - Yingnan Ye
- Cancer Molecular Diagnostics Core, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China; (X.Z.); (R.Z.); (P.L.); (R.Z.); (J.N.); (Y.Y.)
- Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China
| | - Wenwen Yu
- National Clinical Research Center of Caner, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Immunology and Biotherapy, Department of Immunology, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China;
| | - Jinpu Yu
- Cancer Molecular Diagnostics Core, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China; (X.Z.); (R.Z.); (P.L.); (R.Z.); (J.N.); (Y.Y.)
- Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China
- Correspondence: ; Tel.: +86-22-23340123; Fax: +86-22-23340123 (ext. 6325)
| |
Collapse
|
22
|
Acker F, Stratmann J, Aspacher L, Nguyen NTT, Wagner S, Serve H, Wild PJ, Sebastian M. KRAS Mutations in Squamous Cell Carcinomas of the Lung. Front Oncol 2022; 11:788084. [PMID: 34976827 PMCID: PMC8714661 DOI: 10.3389/fonc.2021.788084] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/22/2021] [Indexed: 12/13/2022] Open
Abstract
KRAS is one of the most commonly mutated oncogenes in cancer, enabling tumor proliferation and maintenance. After various approaches to target KRAS have failed over the past decades, the first specific inhibitor of the p.G12C mutation of KRAS was recently approved by the FDA after showing promising results in adenocarcinomas of the lung and other solid tumors. Lung cancer, the most common cancer worldwide, is a promising use case for these new therapies, as adenocarcinomas in particular frequently harbor KRAS mutations. However, in squamous cell carcinoma (SCC) of the lung, KRAS mutations are rare and their impact on clinical outcome is poorly understood. In this review, we discuss the current knowledge on the prevalence and prognostic and predictive significance of KRAS mutations in the context of SCC.
Collapse
Affiliation(s)
- Fabian Acker
- Medizinische Klinik II, University Hospital Frankfurt, Frankfurt, Germany
| | - Jan Stratmann
- Medizinische Klinik II, University Hospital Frankfurt, Frankfurt, Germany
| | - Lukas Aspacher
- Medizinische Klinik II, University Hospital Frankfurt, Frankfurt, Germany
| | | | - Sebastian Wagner
- Medizinische Klinik II, University Hospital Frankfurt, Frankfurt, Germany
| | - Hubert Serve
- Medizinische Klinik II, University Hospital Frankfurt, Frankfurt, Germany
| | - Peter J Wild
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt, Germany.,Wildlab, University Hospital MVZ GmbH, Frankfurt, Germany.,Frankfurt Institute for Advanced Studies (FIAS), Frankfurt, Germany
| | - Martin Sebastian
- Medizinische Klinik II, University Hospital Frankfurt, Frankfurt, Germany
| |
Collapse
|
23
|
Low-Coverage Whole Genome Sequencing Using Laser Capture Microscopy with Combined Digital Droplet PCR: An Effective Tool to Study Copy Number and Kras Mutations in Early Lung Adenocarcinoma Development. Int J Mol Sci 2021; 22:ijms222112034. [PMID: 34769463 PMCID: PMC8584993 DOI: 10.3390/ijms222112034] [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: 09/24/2021] [Revised: 10/22/2021] [Accepted: 10/31/2021] [Indexed: 11/17/2022] Open
Abstract
Defining detailed genomic characterization of early tumor progression is critical to identifying key regulators and pathways in carcinogenesis as potentially druggable targets. In human lung cancer, work to characterize early cancer development has mainly focused on squamous cancer, as the earliest lesions are more proximal in the airways and often accessible by repeated bronchoscopy. Adenocarcinomas are typically located distally in the lung, limiting accessibility for biopsy of pre-malignant and early stages. Mouse lung cancer models recapitulate many human genomic features and provide a model for tumorigenesis with pre-malignant atypical adenomatous hyperplasia and in situ adenocarcinomas often developing contemporaneously within the same animal. Here, we combined tissue characterization and collection by laser capture microscopy (LCM) with digital droplet PCR (ddPCR) and low-coverage whole genome sequencing (LC-WGS). ddPCR can be used to identify specific missense mutations in Kras (Kirsten rat sarcoma viral oncogene homolog, here focused on Kras Q61) and estimate the percentage of mutation predominance. LC-WGS is a cost-effective method to infer localized copy number alterations (CNAs) across the genome using low-input DNA. Combining these methods, the histological stage of lung cancer can be correlated with appearance of Kras mutations and CNAs. The utility of this approach is adaptable to other mouse models of human cancer.
Collapse
|