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Zhang W, Zhou X, Lin L, Lin A, Cheng Q, Liu Z, Luo P, Zhang J. Development and validation of a novel immune‒metabolic-Based classifier for hepatocellular carcinoma. Heliyon 2024; 10:e37327. [PMID: 39296052 PMCID: PMC11407989 DOI: 10.1016/j.heliyon.2024.e37327] [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: 01/27/2024] [Revised: 08/04/2024] [Accepted: 09/01/2024] [Indexed: 09/21/2024] Open
Abstract
The heterogeneity of immune cells and metabolic pathways in hepatocellular carcinoma (HCC) patients has not been fully elucidated, leading to diverse clinical outcomes. Accurately distinguishing different HCC subtypes and recommending appropriate treatments is are highly important. In this study, we conducted a comprehensive analysis of 28 immune cells and 85 metabolic pathways in the TCGA-LIHC and GSE14520 datasets. Metabolism-related first principal component (MRPC1) and cytotoxic T lymphocyte (CTL) infiltration were used to assess the metabolic and immune infiltration levels of HCC patients, respectively. These two quantifiable indicators were then used to construct an immune‒metabolic classifier, which categorized HCC patients into three distinct groups. The potential biological mechanisms were explored through multiomics analysis, revealing that group S1 exhibited high metabolic activity and a high level of immune infiltration, that group S2 presented a low level of immune infiltration, and that group S3 presented low metabolic activity. This new immune‒metabolic classifier was well validated in a pancancer cohort of 9296 patients. The efficacy of multiple treatment approaches was assessed in relation to different immune‒metabolic groups, indicating that group S1 patients may benefit from immunotherapy, that group S2 patients are suitable for transcatheter arterial chemoembolization (TACE), and that group S3 patients are appropriate candidates for tyrosine kinase inhibitors. In conclusion, this immune‒metabolic classifier is anticipated to address the differences in treatment efficacy among HCC patients due to the heterogeneity of the tumor microenvironment, and to help refine the individualized treatment choices for clinical patients.
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Affiliation(s)
- Wenda Zhang
- Department of Oncology, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Xinyi Zhou
- Department of Oncology, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Lili Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Anqi Lin
- Department of Oncology, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zaoqu Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital of Southern Medical University, Guangzhou, China
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Chen R, Liu Y, Xie J. Construction of a pathomics model for predicting mRNAsi in lung adenocarcinoma and exploration of biological mechanism. Heliyon 2024; 10:e37100. [PMID: 39286147 PMCID: PMC11402732 DOI: 10.1016/j.heliyon.2024.e37100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 08/04/2024] [Accepted: 08/27/2024] [Indexed: 09/19/2024] Open
Abstract
Objective This study aimed to predict the level of stemness index (mRNAsi) and survival prognosis of lung adenocarcinoma (LUAD) using pathomics model. Methods From The Cancer Genome Atlas (TCGA) database, 327 LUAD patients were randomly assigned to a training set (n = 229) and a validation set (n = 98) for pathomics model development and evaluation. PyRadiomics was used to extract pathomics features, followed by feature selection using the mRMR-RFE algorithm. In the training set, Gradient Boosting Machine (GBM) was utilized to establish a model for predicting mRNAsi in LUAD. The model's predictive performance was evaluated using ROC curves, calibration curves, and decision curve analysis (DCA). Prognostic analysis was conducted using Kaplan-Meier curves and cox regression. Additionally, gene enrichment analysis, tumor microenvironment analysis, and tumor mutational burden (TMB) analysis were performed to explore the biological mechanisms underlying the pathomics prediction model. Results Multivariable cox analysis (HR = 1.488, 95 % CI 1.012-2.187, P = 0.043) identified mRNAsi as a prognostic risk factor for LUAD. A total of 465 pathomics features were extracted from TCGA-LUAD histopathological images, and ultimately, the most representative 8 features were selected to construct the predictive model. ROC curves demonstrated the significant predictive value of the model for mRNAsi in both the training set (AUC = 0.769) and the validation set (AUC = 0.757). Calibration curves and Hosmer-Lemeshow goodness-of-fit test showed good consistency between the model's prediction of mRNAsi levels and the actual values. DCA indicated a good net benefit of the model. The prediction of mRNAsi levels by the pathomics model is represented using the pathomics score (PS). PS was strongly associated with the prognosis of LUAD (HR = 1.496, 95 % CI 1.008-2.222, P = 0.046). Signaling pathways related to DNA replication and damage repair were significantly enriched in the high PS group. Prediction of immune therapy response indicated significantly reduced Dysfunction in the high PS group (P < 0.001). The high PS group exhibited higher TMB values (P < 0.001). Conclusions The predictive model constructed based on pathomics features can forecast the mRNAsi and survival risk of LUAD. This model holds promise to aid clinical practitioners in identifying high-risk patients and devising more optimized treatment plans for patients by jointly employing therapeutic strategies targeting cancer stem cells (CSCs).
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Affiliation(s)
- Rui Chen
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, No.1, Minde Road, Donghu District, Nanchang, Jiangxi, 330006, China
| | - Yuzhen Liu
- Department of Oncology, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
| | - Junping Xie
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, No.1, Minde Road, Donghu District, Nanchang, Jiangxi, 330006, China
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Mao T, Zhang M, Peng Z, Tang M, Li T, Liang C. Integrative analysis of ferroptosis-related genes reveals that ABHD12 is a novel prognostic biomarker and facilitates hepatocellular carcinoma tumorigenesis. Discov Oncol 2024; 15:330. [PMID: 39093379 PMCID: PMC11297018 DOI: 10.1007/s12672-024-01211-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 07/31/2024] [Indexed: 08/04/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a highly heterogeneous disease, making the prognostic prediction challenging. Ferroptosis, an iron-dependent form of cell death, is a key regulator in the initiation, progression, and metastasis of HCC. However, the expression and function of ferroptosis-related genes (FRGs) in HCC remained largely unclear. In this study, we analyzed TCGA datasets and identified 58 survival-related deferentially expressed FRGs (DE-FRGs). Then, based on the results of LASSO analysis, we developed a novel prognostic model based on 12 survival-related DE-FRGs. Survival assays indicated a strong prognostic ability of this new model in predicting clinical prognosis of HCC patients. In addition, we conducted an exploration of molecular subtypes related to HCC and delved into the associated immune characteristics and gene expression patterns. Among the 12 survival-related DE-FRGs, our attention focused on ABHD12 (abhydrolase domain containing 12) which was highly expressed in HCC and associated with advanced clinical stages. Multivariate assays confirmed that ABHD12 was a significant prognostic factor for HCC patients. Immune analysis revealed that ABHD12 may play an important role in tumor microenvironment. Finally, we performed RT-PCR and confirmed that ABHD12 was highly expressed in HCC cells. Functional experiments revealed that ABHD12 knockdown may suppress the proliferation and migration of HCC cells. These findings emphasized the significance of ABHD12 as a potential prognostic marker for HCC and its crucial role in the field of tumor biology. Additionally, the study introduces a novel survival model that holds promise for enhancing prognostic predictions in HCC patients. Overall, this research provided valuable insights for a deeper comprehension of the complexity of HCC and the development of personalized treatment strategies.
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Affiliation(s)
- Tiantao Mao
- Department of Oncology, Wuxi County People's Hospital, No. 100 Wantong Road, Baiyang Street, Chongqing, 405899, China
| | - Maosong Zhang
- Department of Oncology, Wuxi County People's Hospital, No. 100 Wantong Road, Baiyang Street, Chongqing, 405899, China
| | - Zupei Peng
- Department of Oncology, Wuxi County People's Hospital, No. 100 Wantong Road, Baiyang Street, Chongqing, 405899, China
| | - Min Tang
- Department of Oncology, Wuxi County People's Hospital, No. 100 Wantong Road, Baiyang Street, Chongqing, 405899, China.
| | - Tianyu Li
- Department of Oncology, Wuxi County People's Hospital, No. 100 Wantong Road, Baiyang Street, Chongqing, 405899, China.
| | - Chengshu Liang
- Department of Oncology, Wuxi County People's Hospital, No. 100 Wantong Road, Baiyang Street, Chongqing, 405899, China.
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Deng J, Lai G, Zhang C, Li K, Zhu W, Xie B, Zhong X. A robust primary liver cancer subtype related to prognosis and drug response based on a multiple combined classifying strategy. Heliyon 2024; 10:e25570. [PMID: 38352751 PMCID: PMC10861988 DOI: 10.1016/j.heliyon.2024.e25570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 01/13/2024] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
The recurrence or resistance to treatment of primary liver cancer (PLL) is significantly related to the heterogeneity present within the tumor. In this study, we integrated prognosis risk score, mRNAsi index, and immune characteristics clustering to classify patients. The four subtypes obtained from the combined classification are associated with PLC's prognosis and drug response. In these subtypes, we observed mRNAsiH_ICCA subtype, the intersection between high mRNAsi and immune characteristics clustering A, had the worst prognosis. Specifically, immune characteristics clustering B (ICC_B) had high drug sensitivity in most drugs regardless of the value of mRNAsi. On the other hand, patients with low mRNAsi responded better to ten drugs including KU-55933 and NU7441, while patients with high mRNAsi might benefit from drugs like Leflunomide. By matching the specific characteristics of each combined subtype with the drug-induced cell line expression profile, we identified a group of potential therapeutic drugs that might regulate the expression of disease signature genes. We developed a feasible multiple combined typing strategy, hoping to guide therapeutic selection and promote the development of precision medicine.
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Affiliation(s)
- Jielian Deng
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
- Medical Department, Yidu Cloud (Beijing) Technology Co., Beijing, China
| | - Guichuan Lai
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Cong Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Kangjie Li
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Wenyan Zhu
- Chongqing Engineering Research Center of Pharmaceutical Sciences, Chongqing Medical and Pharmaceutical College, Chongqing, China
- College of Pharmacy, Chongqing Medical University, Chongqing, China
- Medical Department, Yidu Cloud (Beijing) Technology Co., Beijing, China
| | - Biao Xie
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Xiaoni Zhong
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
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Zheng L, Chen J, Ye W, Fan Q, Chen H, Yan H. An individualized stemness-related signature to predict prognosis and immunotherapy responses for gastric cancer using single-cell and bulk tissue transcriptomes. Cancer Med 2024; 13:e6908. [PMID: 38168907 PMCID: PMC10807574 DOI: 10.1002/cam4.6908] [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: 09/15/2023] [Revised: 12/01/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Currently, many stemness-related signatures have been developed for gastric cancer (GC) to predict prognosis and immunotherapy outcomes. However, due to batch effects, these signatures cannot accurately analyze patients one by one, rendering them impractical in real clinical scenarios. Therefore, we aimed to develop an individualized and clinically applicable signature based on GC stemness. METHODS Malignant epithelial cells from single-cell RNA-Seq data of GC were used to identify stemness-related signature genes based on the CytoTRACE score. Using two bulk tissue datasets as training data, the enrichment scores of the signature genes were applied to classify samples into two subtypes. Then, using the identified subtypes as criteria, we developed an individualized stemness-related signature based on the within-sample relative expression orderings of genes. RESULTS We identified 175 stemness-related signature genes, which exhibited significantly higher AUCell scores in poorly differentiated GCs compared to differentiated GCs. In training datasets, GC samples were classified into two subtypes with significantly different survival times and genomic characteristics. Utilizing the two subtypes, an individualized signature was constructed containing 47 gene pairs. In four independent testing datasets, GC samples classified as high risk exhibited significantly shorter survival times, higher infiltration of M2 macrophages, and lower immune responses compared to low-risk samples. Moreover, the potential therapeutic targets and corresponding drugs were identified for the high-risk group, such as CD248 targeted by ontuxizumab. CONCLUSIONS We developed an individualized stemness-related signature, which can accurately predict the prognosis and efficacy of immunotherapy for each GC sample.
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Affiliation(s)
- Linyong Zheng
- Fujian Key Laboratory of Medical Bioinformatics, Department of Bioinformatics, School of Medical Technology and EngineeringFujian Medical UniversityFuzhouChina
| | - Jingyan Chen
- Fujian Key Laboratory of Medical Bioinformatics, Department of Bioinformatics, School of Medical Technology and EngineeringFujian Medical UniversityFuzhouChina
| | - Wenhai Ye
- Fujian Key Laboratory of Medical Bioinformatics, Department of Bioinformatics, School of Medical Technology and EngineeringFujian Medical UniversityFuzhouChina
| | - Qi Fan
- Fujian Key Laboratory of Medical Bioinformatics, Department of Bioinformatics, School of Medical Technology and EngineeringFujian Medical UniversityFuzhouChina
| | - Haifeng Chen
- Department of Gastrointestinal SurgeryFuzhou Second HospitalFuzhouChina
| | - Haidan Yan
- Fujian Key Laboratory of Medical Bioinformatics, Department of Bioinformatics, School of Medical Technology and EngineeringFujian Medical UniversityFuzhouChina
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical SciencesFujian Medical UniversityFuzhouChina
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Wu JM, Qiu WR, Liu Z, Xu ZC, Zhang SH. Integrative approach for classifying male tumors based on DNA methylation 450K data. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:19133-19151. [PMID: 38052593 DOI: 10.3934/mbe.2023845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Malignancies such as bladder urothelial carcinoma, colon adenocarcinoma, liver hepatocellular carcinoma, lung adenocarcinoma and prostate adenocarcinoma significantly impact men's well-being. Accurate cancer classification is vital in determining treatment strategies and improving patient prognosis. This study introduced an innovative method that utilizes gene selection from high-dimensional datasets to enhance the performance of the male tumor classification algorithm. The method assesses the reliability of DNA methylation data to distinguish the five most prevalent types of male cancers from normal tissues by employing DNA methylation 450K data obtained from The Cancer Genome Atlas (TCGA) database. First, the chi-square test is used for dimensionality reduction and second, L1 penalized logistic regression is used for feature selection. Furthermore, the stacking ensemble learning technique was employed to integrate seven common multiclassification models. Experimental results demonstrated that the ensemble learning model utilizing multiple classification models outperformed any base classification model. The proposed ensemble model achieved an astonishing overall accuracy (ACC) of 99.2% in independent testing data. Moreover, it may present novel ideas and pathways for the early detection and treatment of future diseases.
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Affiliation(s)
- Ji-Ming Wu
- Computer Department, Jing-De-Zhen Ceramic University, Jingdezhen 333403, China
| | - Wang-Ren Qiu
- Computer Department, Jing-De-Zhen Ceramic University, Jingdezhen 333403, China
| | - Zi Liu
- Computer Department, Jing-De-Zhen Ceramic University, Jingdezhen 333403, China
| | - Zhao-Chun Xu
- Computer Department, Jing-De-Zhen Ceramic University, Jingdezhen 333403, China
| | - Shou-Hua Zhang
- Department of General Surgery, Jiangxi Provincial Children's Hospital, Nanchang 330006, China
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Huang Y, Zhang Z, Sui M, Li Y, Hu Y, Zhang H, Zhang F. A novel stemness classification in acute myeloid leukemia by the stemness index and the identification of cancer stem cell-related biomarkers. Front Immunol 2023; 14:1202825. [PMID: 37409118 PMCID: PMC10318110 DOI: 10.3389/fimmu.2023.1202825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 05/19/2023] [Indexed: 07/07/2023] Open
Abstract
Background Stem cells play an important role in acute myeloid leukemia (AML). However, their precise effect on AML tumorigenesis and progression remains unclear. Methods The present study aimed to characterize stem cell-related gene expression and identify stemness biomarker genes in AML. We calculated the stemness index (mRNAsi) based on transcription data using the one-class logistic regression (OCLR) algorithm for patients in the training set. According to the mRNAsi score, we performed consensus clustering and identified two stemness subgroups. Eight stemness-related genes were identified as stemness biomarkers through gene selection by three machine learning methods. Results We found that patients in stemness subgroup I had a poor prognosis and benefited from nilotinib, MK-2206 and axitinib treatment. In addition, the mutation profiles of these two stemness subgroups were different, which suggested that patients in different subgroups had different biological processes. There was a strong significant negative correlation between mRNAsi and the immune score (r= -0.43, p<0.001). Furthermore, we identified eight stemness-related genes that have potential to be biomarkers, including SLC43A2, CYBB, CFP, GRN, CST3, TIMP1, CFD and IGLL1. These genes, except IGLL1, had a negative correlation with mRNAsi. SLC43A2 is expected to be a potential stemness-related biomarker in AML. Conclusion Overall, we established a novel stemness classification using the mRNAsi score and eight stemness-related genes that may be biomarkers. Clinical decision-making should be guided by this new signature in prospective studies.
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Affiliation(s)
- Yue Huang
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Zhuo Zhang
- National Health Commission (NHC) Key Laboratory of Cell Transplantation, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Department of Hematology, Southern University of Science and Technology Hospital, Shenzhen, China
| | - Meijuan Sui
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yang Li
- Medical Insurance Office, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yi Hu
- Center for Bioinformatics, Faculty of Computing, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Haiyu Zhang
- Key Laboratory of Cardiovascular Disease Acousto-Optic Electromagnetic Diagnosis and Treatment in Heilongjiang Province, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Fan Zhang
- National Health Commission (NHC) Key Laboratory of Cell Transplantation, The First Affiliated Hospital of Harbin Medical University, Harbin, China
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Lai J, Lin X, Zheng H, Xie B, Fu D. Characterization of stemness features and construction of a stemness subtype classifier to predict survival and treatment responses in lung squamous cell carcinoma. BMC Cancer 2023; 23:525. [PMID: 37291533 DOI: 10.1186/s12885-023-10918-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/04/2023] [Indexed: 06/10/2023] Open
Abstract
BACKGROUND Cancer stemness has been proven to affect tumorigenesis, metastasis, and drug resistance in various cancers, including lung squamous cell carcinoma (LUSC). We intended to develop a clinically applicable stemness subtype classifier that could assist physicians in predicting patient prognosis and treatment response. METHODS This study collected RNA-seq data from TCGA and GEO databases to calculate transcriptional stemness indices (mRNAsi) using the one-class logistic regression machine learning algorithm. Unsupervised consensus clustering was conducted to identify a stemness-based classification. Immune infiltration analysis (ESTIMATE and ssGSEA algorithms) methods were used to investigate the immune infiltration status of different subtypes. Tumor Immune Dysfunction and Exclusion (TIDE) and Immunophenotype Score (IPS) were used to evaluate the immunotherapy response. The pRRophetic algorithm was used to estimate the efficiency of chemotherapeutic and targeted agents. Two machine learning algorithms (LASSO and RF) and multivariate logistic regression analysis were performed to construct a novel stemness-related classifier. RESULTS We observed that patients in the high-mRNAsi group had a better prognosis than those in the low-mRNAsi group. Next, we identified 190 stemness-related differentially expressed genes (DEGs) that could categorize LUSC patients into two stemness subtypes. Patients in the stemness subtype B group with higher mRNAsi scores exhibited better overall survival (OS) than those in the stemness subtype A group. Immunotherapy prediction demonstrated that stemness subtype A has a better response to immune checkpoint inhibitors (ICIs). Furthermore, the drug response prediction indicated that stemness subtype A had a better response to chemotherapy but was more resistant to epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs). Finally, we constructed a nine-gene-based classifier to predict patients' stemness subtype and validated it in independent GEO validation sets. The expression levels of these genes were also validated in clinical tumor specimens. CONCLUSION The stemness-related classifier could serve as a potential prognostic and treatment predictor and assist physicians in selecting effective treatment strategies for patients with LUSC in clinical practice.
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Affiliation(s)
- Jinzhi Lai
- Department of Oncology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian, China
| | - Xinyi Lin
- Department of Oncology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian, China
| | - Huangna Zheng
- Department of Hematology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian, China
| | - Bilan Xie
- Department of Oncology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian, China.
| | - Deqiang Fu
- Department of Oncology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian, China.
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Wang H, Wang Y, Luo W, Zhang X, Cao R, Yang Z, Duan J, Wang K. Integrative stemness characteristics associated with prognosis and the immune microenvironment in lung adenocarcinoma. BMC Pulm Med 2022; 22:463. [PMID: 36471379 PMCID: PMC9724367 DOI: 10.1186/s12890-022-02184-8] [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: 04/22/2022] [Revised: 09/08/2022] [Accepted: 10/04/2022] [Indexed: 12/09/2022] Open
Abstract
BACKGROUND To comprehensively analyze the stemness characteristics related to prognosis and the immune microenvironment in lung adenocarcinoma (LUAD). METHODS The OCLR machine learning method was used to calculate the stemness index (mRNAsi) of the LUAD samples. DEGs common between the low mRNAsi, normal, and high mRNAsi groups were screened and the immune-stemness genes were obtained. Then the PPI network was created and enrichment analyses were performed. Moreover, different subtypes based on immune-stemness genes associated with prognosis were identified, and the relationships between LUAD stemness and TIME variables were systematically analyzed, followed by TMB analysis. RESULTS Patients in the high mRNAsi groups with poor prognosis were screened along with 144 immune-stemness genes. IL-6, FPR2, and RLN3 showed a higher degree in the PPI network. A total of 26 immune-stemness genes associated with prognosis were screened. Two clusters were obtained (cluster 1 and cluster 2). Survival analysis revealed that patients in cluster 2 had a poor prognosis. A total of 12 immune cell subpopulations exhibited significant differences between cluster 1 and cluster 2 (P < 0.05). A total of 10 immune checkpoint genes exhibited significantly higher expression in cluster 1 (P < 0.05) than in cluster 2. Further, the TMB value in cluster 2 was higher than that in cluster 1 (P < 0.05). CONCLUSION Immune-stemness genes, including L-6, FPR2, and RLN3, might play significant roles in LUAD development via cytokine-cytokine receptor interaction, neuroactive ligand‒receptor interaction, and the JAK‒STAT pathway. Immune-stemness genes were related to tumor-infiltrating immune cells, TMB, and expression of immune checkpoint gene.
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Affiliation(s)
- Han Wang
- grid.414918.1Department of Thoracic Surgery, The First People’s Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, 650031 Kunming, Yunnan China
| | - Ying Wang
- grid.452826.fDepartment of Thoracic Surgery, Yan’an Hospital of Kunming, 650000 Kunming, Yunnan China
| | - Wei Luo
- grid.218292.20000 0000 8571 108XDepartment of Thoracic Surgery, The Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming Fourth People’s Hospital, No. 2 Ganghe Road, Wanghu Neighborhood Committee, Jinfang Street, 650302 Anning, Yunnan China
| | - Xugang Zhang
- grid.218292.20000 0000 8571 108XDepartment of Thoracic Surgery, The Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming Fourth People’s Hospital, No. 2 Ganghe Road, Wanghu Neighborhood Committee, Jinfang Street, 650302 Anning, Yunnan China
| | - Ran Cao
- grid.218292.20000 0000 8571 108XDepartment of Thoracic Surgery, The Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming Fourth People’s Hospital, No. 2 Ganghe Road, Wanghu Neighborhood Committee, Jinfang Street, 650302 Anning, Yunnan China
| | - Zhi Yang
- The IVD Medical Marketing Department, 3D Medicines Inc, 201114 Shanghai, China
| | - Jin Duan
- grid.414902.a0000 0004 1771 3912Department of Thoracic Surgery, the First Affiliated Hospital of Kunming Medical University, 650031 Kunming, Yunman China
| | - Kun Wang
- grid.218292.20000 0000 8571 108XDepartment of Thoracic Surgery, The Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming Fourth People’s Hospital, No. 2 Ganghe Road, Wanghu Neighborhood Committee, Jinfang Street, 650302 Anning, Yunnan China
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