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Wei C, Ma Y, Wang M, Wang S, Yu W, Dong S, Deng W, Bie L, Zhang C, Shen W, Xia Q, Luo S, Li N. Tumor-associated macrophage clusters linked to immunotherapy in a pan-cancer census. NPJ Precis Oncol 2024; 8:176. [PMID: 39117688 PMCID: PMC11310399 DOI: 10.1038/s41698-024-00660-4] [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: 11/24/2023] [Accepted: 07/17/2024] [Indexed: 08/10/2024] Open
Abstract
Transcriptional heterogeneity of tumor-associated macrophages (TAMs) has been investigated in individual cancers, but the extent to which these states transcend tumor types and represent a general feature of cancer remains unclear. We performed pan-cancer single-cell RNA sequencing analysis across nine cancer types and identified distinct monocyte/TAM composition patterns. Using spatial analysis from clinical study tissues, we assessed TAM functions in shaping the tumor microenvironment (TME) and influencing immunotherapy. Two specific TAM clusters (pro-inflammatory and pro-tumor) and four TME subtypes showed distinct immunological features, genomic profiles, immunotherapy responses, and cancer prognosis. Pro-inflammatory TAMs resided in immune-enriched niches with exhausted CD8+ T cells, while pro-tumor TAMs were restricted to niches associated with a T-cell-excluded phenotype and hypoxia. We developed a machine learning model to predict immune checkpoint blockade response by integrating TAMs and clinical data. Our study comprehensively characterizes the common features of TAMs and highlights their interaction with the TME.
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Affiliation(s)
- Chen Wei
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Yijie Ma
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Mengyu Wang
- Department of Radiation Oncology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Siyi Wang
- Department of Surgical Oncology and General Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Wenyue Yu
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Shuailei Dong
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Wenying Deng
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Liangyu Bie
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Chi Zhang
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Wei Shen
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Qingxin Xia
- Department of Pathology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China.
| | - Suxia Luo
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China.
| | - Ning Li
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China.
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Li Y, Wu X, Fang D, Luo Y. Informing immunotherapy with multi-omics driven machine learning. NPJ Digit Med 2024; 7:67. [PMID: 38486092 PMCID: PMC10940614 DOI: 10.1038/s41746-024-01043-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 02/14/2024] [Indexed: 03/18/2024] Open
Abstract
Progress in sequencing technologies and clinical experiments has revolutionized immunotherapy on solid and hematologic malignancies. However, the benefits of immunotherapy are limited to specific patient subsets, posing challenges for broader application. To improve its effectiveness, identifying biomarkers that can predict patient response is crucial. Machine learning (ML) play a pivotal role in harnessing multi-omic cancer datasets and unlocking new insights into immunotherapy. This review provides an overview of cutting-edge ML models applied in omics data for immunotherapy analysis, including immunotherapy response prediction and immunotherapy-relevant tumor microenvironment identification. We elucidate how ML leverages diverse data types to identify significant biomarkers, enhance our understanding of immunotherapy mechanisms, and optimize decision-making process. Additionally, we discuss current limitations and challenges of ML in this rapidly evolving field. Finally, we outline future directions aimed at overcoming these barriers and improving the efficiency of ML in immunotherapy research.
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Affiliation(s)
- Yawei Li
- Department of Preventive Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Collaborative AI in Healthcare, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Xin Wu
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Deyu Fang
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Yuan Luo
- Department of Preventive Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Center for Collaborative AI in Healthcare, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA.
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3
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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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4
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Marcu LG, Dell’Oro M, Bezak E. Opportunities in Cancer Therapies: Deciphering the Role of Cancer Stem Cells in Tumour Repopulation. Int J Mol Sci 2023; 24:17258. [PMID: 38139085 PMCID: PMC10744048 DOI: 10.3390/ijms242417258] [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: 11/18/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Tumour repopulation during treatment is a well acknowledged yet still challenging aspect of cancer management. The latest research results show clear evidence towards the existence of cancer stem cells (CSCs) that are responsible for tumour repopulation, dissemination, and distant metastases in most solid cancers. Cancer stem cell quiescence and the loss of asymmetrical division are two powerful mechanisms behind repopulation. Another important aspect in the context of cancer stem cells is cell plasticity, which was shown to be triggered during fractionated radiotherapy, leading to cell dedifferentiation and thus reactivation of stem-like properties. Repopulation during treatment is not limited to radiotherapy, as there is clinical proof for repopulation mechanisms to be activated through other conventional treatment techniques, such as chemotherapy. The dynamic nature of stem-like cancer cells often elicits resistance to treatment by escaping drug-induced cell death. The aims of this scoping review are (1) to describe the main mechanisms used by cancer stem cells to initiate tumour repopulation during therapy; (2) to present clinical evidence for tumour repopulation during radio- and chemotherapy; (3) to illustrate current trends in the identification of CSCs using specific imaging techniques; and (4) to highlight novel technologies that show potential in the eradication of CSCs.
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Affiliation(s)
- Loredana G. Marcu
- UniSA Allied Health & Human Performance, University of South Australia, Adelaide, SA 5001, Australia;
- Faculty of Informatics and Science, University of Oradea, 410087 Oradea, Romania
| | - Mikaela Dell’Oro
- Australian Centre for Quantitative Imaging, School of Medicine, The University of Western Australia, Perth, WA 6009, Australia;
| | - Eva Bezak
- UniSA Allied Health & Human Performance, University of South Australia, Adelaide, SA 5001, Australia;
- Faculty of Chemistry & Physics, University of Adelaide, Adelaide, SA 5000, Australia
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Deng C, Ye C, Liao X, Zhou F, Shi Y, Zhong H, Huang J. KMT2A maintains stemness of gastric cancer cells through regulating Wnt/β-catenin signaling-activated transcriptional factor KLF11. Open Med (Wars) 2023; 18:20230764. [PMID: 38025523 PMCID: PMC10655684 DOI: 10.1515/med-2023-0764] [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: 12/22/2022] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 12/01/2023] Open
Abstract
The molecular mechanisms of epigenetic regulation in gastric cancer development are not yet well established. In this study, we demonstrated that KMT2A was highly expressed in gastric cancer and associated with poor outcomes of patients and revealed that KMT2A was significantly associated with stemness and increased nuclear β-catenin in gastric cancer. Mechanistically, KMT2A activated the translocation of β-catenin into the nucleus of gastric cancer cells, and then, β-catenin served as a coactivator of KLF11, which promoted the expression of specific gastric cancer stemness-related molecules, including SOX2 and FOXM1. Together, KMT2A is an important epigenetic regulator of gastric cancer stemness, which provides a novel insight to the potential application of targeting against KMT2A in treating gastric cancer.
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Affiliation(s)
- Chongwen Deng
- Department of General Surgery, Loudi Central Hospital, No. 51, Changqing Middle Street, Loudi, 417000, People’s Republic of China
| | - Chunhua Ye
- Department of General Surgery, Loudi Central Hospital, Loudi, 417000, People’s Republic of China
| | - Xiwang Liao
- Department of General Surgery, Loudi Central Hospital, Loudi, 417000, People’s Republic of China
| | - Fuyin Zhou
- Department of General Surgery, Loudi Central Hospital, Loudi, 417000, People’s Republic of China
| | - Youxiong Shi
- Department of General Surgery, Loudi Central Hospital, Loudi, 417000, People’s Republic of China
| | - Hong Zhong
- Department of General Surgery, Loudi Central Hospital, Loudi, 417000, People’s Republic of China
| | - Junbiao Huang
- Department of General Surgery, Loudi Central Hospital, Loudi, 417000, People’s Republic of China
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Wang Z, Liu Y, Niu X. Application of artificial intelligence for improving early detection and prediction of therapeutic outcomes for gastric cancer in the era of precision oncology. Semin Cancer Biol 2023; 93:83-96. [PMID: 37116818 DOI: 10.1016/j.semcancer.2023.04.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/12/2023] [Accepted: 04/24/2023] [Indexed: 04/30/2023]
Abstract
Gastric cancer is a leading contributor to cancer incidence and mortality globally. Recently, artificial intelligence approaches, particularly machine learning and deep learning, are rapidly reshaping the full spectrum of clinical management for gastric cancer. Machine learning is formed from computers running repeated iterative models for progressively improving performance on a particular task. Deep learning is a subtype of machine learning on the basis of multilayered neural networks inspired by the human brain. This review summarizes the application of artificial intelligence algorithms to multi-dimensional data including clinical and follow-up information, conventional images (endoscope, histopathology, and computed tomography (CT)), molecular biomarkers, etc. to improve the risk surveillance of gastric cancer with established risk factors; the accuracy of diagnosis, and survival prediction among established gastric cancer patients; and the prediction of treatment outcomes for assisting clinical decision making. Therefore, artificial intelligence makes a profound impact on almost all aspects of gastric cancer from improving diagnosis to precision medicine. Despite this, most established artificial intelligence-based models are in a research-based format and often have limited value in real-world clinical practice. With the increasing adoption of artificial intelligence in clinical use, we anticipate the arrival of artificial intelligence-powered gastric cancer care.
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Affiliation(s)
- Zhe Wang
- Department of Digestive Diseases 1, Cancer Hospital of China Medical University, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, Shenyang 110042, Liaoning, China
| | - Yang Liu
- Department of Gastric Surgery, Cancer Hospital of China Medical University, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, Shenyang 110042, Liaoning, China.
| | - Xing Niu
- China Medical University, Shenyang 110122, Liaoning, China.
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7
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Zhou H, Chen B, Zhang L, Li C. Machine learning-based identification of lower grade glioma stemness subtypes discriminates patient prognosis and drug response. Comput Struct Biotechnol J 2023; 21:3827-3840. [PMID: 37560125 PMCID: PMC10407594 DOI: 10.1016/j.csbj.2023.07.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/06/2023] [Accepted: 07/19/2023] [Indexed: 08/11/2023] Open
Abstract
Glioma stem cells (GSCs) remodel their tumor microenvironment to sustain a supportive niche. Identification and stratification of stemness related characteristics in patients with glioma might aid in the diagnosis and treatment of the disease. In this study, we calculated the mRNA stemness index in bulk and single-cell RNA-sequencing datasets using machine learning methods and investigated the correlation between stemness and clinicopathological characteristics. A glioma stemness-associated score (GSScore) was constructed using multivariate Cox regression analysis. We also generated a GSC cell line derived from a patient diagnosed with glioma and used glioma cell lines to validate the performance of the GSScore in predicting chemotherapeutic responses. Differentially expressed genes (DEGs) between GSCs with high and low GSScores were used to cluster lower-grade glioma (LGG) samples into three stemness subtypes. Differences in clinicopathological characteristics, including survival, copy number variations, mutations, tumor microenvironment, and immune and chemotherapeutic responses, among the three LGG stemness-associated subtypes were identified. Using machine learning methods, we further identified genes as subtype predictors and validated their performance using the CGGA datasets. In the current study, we identified a GSScore that correlated with LGG chemotherapeutic response. Through the score, we also identified a novel classification of the LGG subtype and associated subtype predictors, which might facilitate the development of precision therapy.
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Affiliation(s)
- Hongshu Zhou
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- Hypothalamic-pituitary Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Bo Chen
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- Hypothalamic-pituitary Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- Department of Surgery, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
| | - Liyang Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- Hypothalamic-pituitary Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- Clinical Diagnosis and Therapy Center for Glioma, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Chuntao Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- Hypothalamic-pituitary Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- Clinical Diagnosis and Therapy Center for Glioma, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
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Wang Y, Zhou J, Zhang N, Zhu Y, Zhong Y, Wang Z, Jin H, Wang X. A Novel Defined PANoptosis-Related miRNA Signature for Predicting the Prognosis and Immune Characteristics in Clear Cell Renal Cell Carcinoma: A miRNA Signature for the Prognosis of ccRCC. Int J Mol Sci 2023; 24:ijms24119392. [PMID: 37298343 DOI: 10.3390/ijms24119392] [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: 04/11/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is one of the most prevalent cancers, and PANoptosis is a distinct, inflammatory-programmed cell death regulated by the PANoptosome. The essential regulators of cancer occurrence and progression are microRNAs (miRNAs). However, the potential function of PANoptosis-related microRNAs (PRMs) in ccRCC remains obscure. This study retrieved ccRCC samples from The Cancer Genome Atlas database and three Gene Expression Omnibus datasets. PRMs were recognized based on previous reports in the scientific literature. Regression analyses were used to identify the prognosis PRMs and construct a PANoptosis-related miRNA prognostic signature based on the risk score. We discovered that high-risk patients had poorer survival prognoses and were significantly linked to high-grade and advanced-stage tumors, using a variety of R software packages and web analysis tools. Furthermore, we demonstrated that the low-risk group had significant changes in their metabolic pathways. In contrast, the high-risk group was characterized by high immune cell infiltration, immune checkpoint expression, and low half-maximum inhibition concentration (IC50) values of chemotherapeutic agents. This suggests that high-risk patients may benefit more from immunotherapy and chemotherapy. In conclusion, we constructed a PANoptosis-related microRNA signature and revealed its potential significance in clinicopathological features and tumor immunity, thereby providing new precise treatment strategies.
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Affiliation(s)
- Yanmei Wang
- School of Medicine, Zhejiang University, Hangzhou 310030, China
| | - Jia Zhou
- School of Medicine, Zhejiang University, Hangzhou 310030, China
| | - Nan Zhang
- School of Medicine, Zhejiang University, Hangzhou 310030, China
| | - Yiran Zhu
- School of Medicine, Zhejiang University, Hangzhou 310030, China
| | - Yiming Zhong
- School of Medicine, Zhejiang University, Hangzhou 310030, China
| | - Zhuo Wang
- School of Medicine, Zhejiang University, Hangzhou 310030, China
| | - Hongchuan Jin
- Laboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, School of Medicine, Zhejiang University, Hangzhou 310016, China
| | - Xian Wang
- School of Medicine, Zhejiang University, Hangzhou 310030, China
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9
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Development and Experimental Validation of a Novel Prognostic Signature for Gastric Cancer. Cancers (Basel) 2023; 15:cancers15051610. [PMID: 36900401 PMCID: PMC10000504 DOI: 10.3390/cancers15051610] [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: 11/11/2022] [Revised: 01/18/2023] [Accepted: 02/16/2023] [Indexed: 03/08/2023] Open
Abstract
BACKGROUND Gastric cancer is a malignant tumor with high morbidity and mortality. Therefore, the accurate recognition of prognostic molecular markers is the key to improving treatment efficacy and prognosis. METHODS In this study, we developed a stable and robust signature through a series of processes using machine-learning approaches. This PRGS was further experimentally validated in clinical samples and a gastric cancer cell line. RESULTS The PRGS is an independent risk factor for overall survival that performs reliably and has a robust utility. Notably, PRGS proteins promote cancer cell proliferation by regulating the cell cycle. Besides, the high-risk group displayed a lower tumor purity, higher immune cell infiltration, and lower oncogenic mutation than the low-PRGS group. CONCLUSIONS This PRGS could be a powerful and robust tool to improve clinical outcomes for individual gastric cancer patients.
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10
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Kong W, Wang Z, Wang B. Unveiling DNA damage repair-based molecular subtypes, tumor microenvironment and pharmacogenomic landscape in gastric cancer. Front Genet 2023; 14:1118889. [PMID: 37124627 PMCID: PMC10140566 DOI: 10.3389/fgene.2023.1118889] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/28/2023] [Indexed: 05/02/2023] Open
Abstract
Objective: The current molecular classification system for gastric cancer covers genomic, molecular, and morphological characteristics. Non-etheless, classification of gastric cancer based upon DNA damage repair is still lacking. Here, we defined DNA damage repair-based subtypes across gastric cancer and identified clinicopathological, tumor microenvironment and pharmacogenomic features. Methods: Unsupervised clustering analysis was executed in the TCGA-STAD cohort based upon the transcriptional expression profiling of DNA damage repair genes. LASSO computational approach was adopted for generating a DNA damage repair-relevant gene signature. The identified subtypes or signature were externally verified in the GSE84426 or GSE84433 cohort. The transcriptional levels of immunomodulators, abundance of immune cells and somatic mutations were measured, respectively. Immunotherapeutic response, and drug sensitivity were investigated. The DNA damage repair-relevant genes were further experimentally verified. Results: Two DNA damage repair-based subtypes were identified, with the notable heterogeneity in prognostic stratification, tumor microenvironment and somatic mutations. The gene signature was generated for risk stratification and prognostic prediction, which was in relation to immunomodulators and immune cells. High-risk cases were more likely to respond to immunotherapy, with distinct pharmacogenomic landscapes between low- and high-risk groups. Higher levels of PAPPA2, MPO, MAGEA11, DEPP1, CPZ, and COLEC12 and lower level of CYTL1 were proven in gastric cancer cells versus controls. Silencing CYTL1 facilitated intracellular ROS accumulation and suppressed migration in gastric cancer cells. Conclusion: Collectively, the DNA damage repair-based classification is a suitable complement to existing molecular classification system, and the quantitative gene signature provides a robust tool in selecting specific therapeutic options.
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11
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Wei C, Wang M, Gao Q, Yuan S, Deng W, Bie L, Ma Y, Zhang C, Li S, Luo S, Li N. Dynamic peripheral blood immune cell markers for predicting the response of patients with metastatic cancer to immune checkpoint inhibitors. Cancer Immunol Immunother 2023; 72:23-37. [PMID: 35661905 PMCID: PMC9813029 DOI: 10.1007/s00262-022-03221-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 05/01/2022] [Indexed: 01/09/2023]
Abstract
PURPOSE Immune checkpoint inhibitors (ICIs) have shown durable responses in various malignancies. However, the response to ICI therapy is unpredictable, and investigation of predictive biomarkers needs to be improved. EXPERIMENTAL DESIGN In total, 120 patients receiving ICI therapy and 40 patients receiving non-ICI therapy were enrolled. Peripheral blood immune cell markers (PBIMs), as liquid biopsy biomarkers, were analyzed by flow cytometry before ICI therapy, and before the first evaluation. In the ICI cohort, patients were randomly divided into training (n = 91) and validation (n = 29) cohorts. Machine learning algorithms were applied to construct the prognostic and predictive immune-related models. RESULTS Using the training cohort, a peripheral blood immune cell-based signature (BICS) based on four hub PBIMs was developed. In both the training and the validation cohorts, and the whole cohort, the BICS achieved a high accuracy for predicting overall survival (OS) benefit. The high-BICS group had significantly shorter progression-free survival and OS than the low-BICS group. The BICS demonstrated the predictive ability of patients to achieve durable clinical outcomes. By integrating these PBIMs, we further constructed and validated the support vector machine-recursive and feature elimination classifier model, which robustly predicts patients who will achieve optimal clinical benefit. CONCLUSIONS Dynamic PBIM-based monitoring as a noninvasive, cost-effective, highly specific and sensitive biomarker has broad potential for prognostic and predictive utility in patients receiving ICI therapy.
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Affiliation(s)
- Chen Wei
- grid.414008.90000 0004 1799 4638Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, 127 Dongming Road, Zhengzhou, 450008 Henan China
| | - Mengyu Wang
- grid.414008.90000 0004 1799 4638Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, 127 Dongming Road, Zhengzhou, 450008 Henan China
| | - Quanli Gao
- grid.414008.90000 0004 1799 4638Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, 127 Dongming Road, Zhengzhou, 450008 Henan China ,grid.414008.90000 0004 1799 4638Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, 127 Dongming Road, Zhengzhou, 450008 Henan China
| | - Shasha Yuan
- grid.414008.90000 0004 1799 4638Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, 127 Dongming Road, Zhengzhou, 450008 Henan China
| | - Wenying Deng
- grid.414008.90000 0004 1799 4638Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, 127 Dongming Road, Zhengzhou, 450008 Henan China
| | - Liangyu Bie
- grid.414008.90000 0004 1799 4638Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, 127 Dongming Road, Zhengzhou, 450008 Henan China
| | - Yijie Ma
- grid.414008.90000 0004 1799 4638Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, 127 Dongming Road, Zhengzhou, 450008 Henan China
| | - Chi Zhang
- grid.414008.90000 0004 1799 4638Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, 127 Dongming Road, Zhengzhou, 450008 Henan China
| | - Shuyi Li
- grid.414008.90000 0004 1799 4638Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, 127 Dongming Road, Zhengzhou, 450008 Henan China
| | - Suxia Luo
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, 127 Dongming Road, Zhengzhou, 450008, Henan, China.
| | - Ning Li
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, 127 Dongming Road, Zhengzhou, 450008, Henan, China.
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12
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ERR-activated GPR35 promotes immune infiltration level of macrophages in gastric cancer tissues. Cell Death Dis 2022; 8:444. [DOI: 10.1038/s41420-022-01238-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
AbstractEnhancer release and retargeting (ERR) events could activate disease-causing gene promoters for increasing the expression level of oncogenes. Meanwhile, class A orphan GPCRs (oGPCRs) are known as potential biomarkers or drug targets for various cancers, such as gastric cancer (GC). Hence, systemic investigation of ERR events for class A oGPCRs in GC could help to explore biomarkers for GC. In this study, ENCODE and GTEx eQTL data were utilized to define ERR events in GC. Only GPR35 was then detected that could be activated by ERR in GC based on these data and ChIP-seq. Then, activated GPR35 functional in GC cells were explored by flow cytometry, cell-based wound healing assay, Transwell migration assay, and M2 polarization of macrophages assay. Meanwhile, according to TCGA and GEO database, overall survival, immune-related gene expression, and immune cell infiltration level in different GPR35 expressions were calculated. Here, we found ERR event activate GPR35 results in GC cells proliferation and migration, and partly immune cells significance exhaustion (CD8 + T-cells and CD4 + memory T-cells) and/or infiltration (T-cells and macrophage). Meanwhile, high GRP35 level leads to a poor prognosis in GC patients, probably partly due to it promoting the immune infiltration level of macrophages and then inducing polarization of M2 macrophages. Notably, GPR35’s high expression in CTSB+ and CD68 + macrophage could be a genetic indicator for early warning of primary GC. Hence, our findings provide a novel activation approach for oGPCRs, and GPR35 could be determined as a new drugable receptor and early genetic indicator for GC.
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