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Fan Q, Wang Y, Cheng J, Pan B, Zang X, Liu R, Deng Y. Single-cell RNA-seq reveals T cell exhaustion and immune response landscape in osteosarcoma. Front Immunol 2024; 15:1362970. [PMID: 38629071 PMCID: PMC11018946 DOI: 10.3389/fimmu.2024.1362970] [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: 12/29/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
Background T cell exhaustion in the tumor microenvironment has been demonstrated as a substantial contributor to tumor immunosuppression and progression. However, the correlation between T cell exhaustion and osteosarcoma (OS) remains unclear. Methods In our present study, single-cell RNA-seq data for OS from the GEO database was analysed to identify CD8+ T cells and discern CD8+ T cell subsets objectively. Subgroup differentiation trajectory was then used to pinpoint genes altered in response to T cell exhaustion. Subsequently, six machine learning algorithms were applied to develop a prognostic model linked with T cell exhaustion. This model was subsequently validated in the TARGETs and Meta cohorts. Finally, we examined disparities in immune cell infiltration, immune checkpoints, immune-related pathways, and the efficacy of immunotherapy between high and low TEX score groups. Results The findings unveiled differential exhaustion in CD8+ T cells within the OS microenvironment. Three genes related to T cell exhaustion (RAD23A, SAC3D1, PSIP1) were identified and employed to formulate a T cell exhaustion model. This model exhibited robust predictive capabilities for OS prognosis, with patients in the low TEX score group demonstrating a more favorable prognosis, increased immune cell infiltration, and heightened responsiveness to treatment compared to those in the high TEX score group. Conclusion In summary, our research elucidates the role of T cell exhaustion in the immunotherapy and progression of OS, the prognostic model constructed based on T cell exhaustion-related genes holds promise as a potential method for prognostication in the management and treatment of OS patients.
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Affiliation(s)
- Qizhi Fan
- Department of Spine Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - Yiyan Wang
- Department of Spine Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - Jun Cheng
- Department of Spine Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - Boyu Pan
- Department of Orthopedics, Third Hospital of Changsha, Changsha, China
| | - Xiaofang Zang
- Department of Spine Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - Renfeng Liu
- Department of Spine Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - Youwen Deng
- Department of Spine Surgery, Third Xiangya Hospital, Central South University, Changsha, China
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Xie K, Chen Z, Feng J, Pan L, Wang N, Luo J, Yao Y, Ma H, Feng Y, Jiang W. Identification and validation of prognostic and immunotherapeutic responses in esophageal squamous carcinoma based on hypoxia phenotype-related genes. Front Pharmacol 2024; 15:1344317. [PMID: 38515846 PMCID: PMC10955338 DOI: 10.3389/fphar.2024.1344317] [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: 11/25/2023] [Accepted: 02/21/2024] [Indexed: 03/23/2024] Open
Abstract
The study aimed to investigate the clinical significance of the interaction between hypoxia and the immune system in esophageal squamous cell carcinoma (ESCC) microenvironment. A comprehensive evaluation of 13 hypoxia phenotype-related genes (HPRs) was conducted using data from TCGA-ESCC and two GEO cohorts. Three distinct HPRclusters were identified, and the HPRscore was established as an independent prognostic factor (p = 0.001), with higher scores indicating poorer prognosis. The HPRscore was validated in various immunotherapy cohorts, demonstrating its efficacy in evaluating immunotherapy and chemotherapy outcomes. Additionally, phenome-wide association study (PheWAS) analysis showed that PKP1 had no significant correlation with other traits at the gene level. PKP1 was identified as a potential prognostic marker for ESCC, with upregulated expression observed in ESCC patients. In vitro experiments showed that the knockdown of PKP1 inhibited ESCC cell proliferation and migration. These findings suggest that the novel HPRscore and PKP1 may serve as prognostic tools and therapeutic targets for ESCC patients.
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Affiliation(s)
- Kai Xie
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhe Chen
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of Soochow University, Suzhou, China
| | - Jian Feng
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Liangbin Pan
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Nan Wang
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of Soochow University, Suzhou, China
| | - Jing Luo
- Department of Cardiothoracic Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yu Yao
- Department of Respiratory Medicine, Nanjing Second Hospital, Nanjing, China
| | - Haitao Ma
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of Soochow University, Suzhou, China
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yu Feng
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Wei Jiang
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of Soochow University, Suzhou, China
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Guo F, Ling G, Zhai Z, Lei Y, Mo L, Piao H. Identification and validation of prognostic genes and immune landscape signatures based on a fatty acid oxidation‑related risk score model in glioma. Oncol Lett 2024; 27:88. [PMID: 38249808 PMCID: PMC10797317 DOI: 10.3892/ol.2024.14222] [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: 09/13/2023] [Accepted: 12/04/2023] [Indexed: 01/23/2024] Open
Abstract
Fatty acid oxidation (FAO) plays a crucial role in glioma metabolism and its interaction with the immune microenvironment. The aim of the present study was to investigate the relationship between FAO-related genes and glioma by constructing gene clusters using a glioma cohort. A total of 287 differentially expressed genes related to FAO were identified and the top 50 genes were selected based on their P-values. Subsequently, patients were classified into two distinct gene subtypes (A and B) based on these genes. Scores for each patient were calculated using the 50 genes and the patients were divided into the high and low-score groups accordingly. Patients in subtype B exhibited higher tumor grades and poor prognostic factors such as older age and worse survival rates. The high-score subgroup had unfavorable indicators, including isocitrate dehydrogenase 1 wild-type, high tumor grade and 1p19q non-codeleted, while immune checkpoint expression was generally higher in the high-score subgroup. The constructed scoring model was validated using an external dataset, and the tissue inhibitor of metalloproteinase 1 gene was identified through protein interaction analysis, suggesting its potential involvement in glioma malignancy and promotion of glioblastoma proliferation. In conclusion, FAO-related genes may contribute to tumor development through immune mechanisms and the present study may provide novel insights for potential therapeutic strategies in glioma treatment.
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Affiliation(s)
- Fangzhou Guo
- Graduate School, The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning 116000, P.R. China
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Guoyuan Ling
- Graduate School, The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning 116000, P.R. China
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Zhenzhu Zhai
- Department of Neurosurgery, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110801, P.R. China
- The First Clinical College, Liaoning University of Traditional Chinese Medicine, Shenyang, Liaoning 110801, P.R. China
| | - Yi Lei
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Ligen Mo
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Haozhe Piao
- Department of Neurosurgery, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110801, P.R. China
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Zhang C, Cao K, Yang M, Wang Y, He M, Lu J, Huang Y, Zhang G, Liu H. C5aR1 blockade reshapes immunosuppressive tumor microenvironment and synergizes with immune checkpoint blockade therapy in high-grade serous ovarian cancer. Oncoimmunology 2023; 12:2261242. [PMID: 37791232 PMCID: PMC10543342 DOI: 10.1080/2162402x.2023.2261242] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/15/2023] [Indexed: 10/05/2023] Open
Abstract
High-grade serous ovarian cancer (HGSC), with a modest response to immune checkpoint blockade (ICB) targeting PD-1/PD-L1 monotherapy, is densely infiltrated by M2-polarized tumor-associated macrophages (TAMs) and regulatory T (Treg) cells. The complement C5a/C5aR1 axis contributes to the programming of the immunosuppressive phenotype of TAMs in solid tumors and represents a promising immunomodulatory target for treating HGSCs. Here, we aimed to identify the relevance of C5aR1 in prognosis, immune microenvironment, and immunotherapy response in HGSCs. The expression and relationship of C5aR1 with tumor-infiltrating immune cells were assessed by immunohistochemistry and flow cytometry in the training cohort (n = 120) and fresh HGSC tissues (n = 36). Transcriptomic analyses of the xenografts delineated the mechanisms driving the immunomodulatory activity of PMX53, an orally bioavailable C5aR1 inhibitor. Therapeutic relevance was confirmed in ex vivo tumor cultures and The Cancer Genome Atlas (TCGA) datasets. C5aR1 expression independently predicted dismal prognosis and was linked to the immunoevasive subtype of HGSC, characterized by increased infiltration of pro-tumor cells (Treg cells, M2-polarized macrophages, and neutrophils) and impaired CD8+T functions. PMX53 antagonized subcutaneous tumor growth, modulated immunosuppressive mechanisms and synergized with aPD-1 in several tumor types. Single-cell RNA-seq analysis revealed predominant C5aR1 expression in TAMs, with an immunosuppressive-related expression signature in C5aR1+TAMs. Furthermore, the combination of C5aR1 and PD-L1 was associated with specific molecular characteristics and matched clinical response annotations. Therefore, the abundance of C5aR1 could predict an inferior prognosis in HGSCs, and incorporating PD-L1 may serve as a novel predictive biomarker to guide therapeutic options.
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Affiliation(s)
- Chen Zhang
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Kankan Cao
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Moran Yang
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Yiying Wang
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Mengdi He
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Jiaqi Lu
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Yan Huang
- Department of Gynecologic Oncology, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Guodong Zhang
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Haiou Liu
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
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Xu J, Yang Z, Xie W, Wan R, Li C, Fei K, Sun B, Yang X, Chen P, Meng F, Wang G, Zhao J, Han Y, Cai S, Wang J, Wang Z. A prognostic and immunotherapeutic predictive model based on the cell-originated characterization of tumor microenvironment in lung adenocarcinoma. iScience 2023; 26:106616. [PMID: 37168563 PMCID: PMC10165414 DOI: 10.1016/j.isci.2023.106616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/24/2023] [Accepted: 04/04/2023] [Indexed: 05/13/2023] Open
Abstract
Tumor microenvironment (TME) plays a crucial role in predicting prognosis and response to therapy in lung cancer. Our study established a prognostic and immunotherapeutic predictive model, the tumor immune cell score (TICS), by differentiating cell origins in lung adenocarcinoma (LUAD) based on the transcriptomic data of 2,510 patients in 14 independent cohorts, including 12 public datasets and two in-house cohorts. The high TICS was associated with prolonged overall survival (OS), especially in the early-stage LUAD. For the advanced-stage LUAD, high TICS predicted a superior OS in patients who were treated with immunotherapy instead of chemotherapy or TKI. The result suggested that TICS could serve as an indicator for the prognostic stratification management of patients in the early-stage LUAD, and as a potential guide for therapeutic decision-marking in the advanced-stage LUAD. Our findings provided an insight into prognosis stratification and potential guidance for treatment strategy selection.
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Affiliation(s)
- Jiachen Xu
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
- Guangdong Provincial People’s Hospital/Guangdong Provincial Academy of Medical Sciences, Guangdong Provincial Key Lab of Translational Medicine in Lung Cancer, Guangdong 510317, P.R. China
| | - Zhenlin Yang
- Department of Thoracic Surgery, National Cancer Center/ National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
| | - Wenchuan Xie
- Burning Rock Biotech, Guangdong 510300, P.R. China
| | - Rui Wan
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
| | | | - Kailun Fei
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
| | - Boyang Sun
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
| | - Xu Yang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
| | - Ping Chen
- Department of Oncology, Yancheng First Hospital, Affiliated Hospital of Nanjing University Medical School, The First People’s Hospital of Yancheng; Jiangsu 224001, P.R. China
| | - Fanqi Meng
- Burning Rock Biotech, Guangdong 510300, P.R. China
| | | | - Jing Zhao
- Burning Rock Biotech, Guangdong 510300, P.R. China
| | - Yusheng Han
- Burning Rock Biotech, Guangdong 510300, P.R. China
| | - Shangli Cai
- Burning Rock Biotech, Guangdong 510300, P.R. China
| | - Jie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
| | - Zhijie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
- Corresponding author
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Ji SM, Choi JS, Lee JY, Kim S, Bae WY, Jang YW, Kim JE, Lee SH, Nam S, Jeong JW. Mild exposure to fine particulate matter promotes angiogenesis in non-small cell lung carcinoma. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 329:121715. [PMID: 37120000 DOI: 10.1016/j.envpol.2023.121715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 05/06/2023]
Abstract
Fine particulate matter (PM2.5) is associated with public health problems worldwide. Especially, PM2.5 induces epigenetic and microenvironmental changes in lung cancer. Angiogenesis is important for the development and growth of cancer and is mediated by angiogenic factors, including vascular endothelial growth factor. However, the effects of mild PM2.5 exposure on angiogenesis in lung cancer remain unclear. In this study, we examined angiogenic effects using relatively lower concentrations of PM2.5 than in other studies and found that PM2.5 increased angiogenic activities in both endothelial cells and non-small cell lung carcinoma cells. PM2.5 also promoted the growth and angiogenesis of lung cancer via the induction of hypoxia-inducible factor-1α (HIF-1α) in a xenograft mouse tumor model. Angiogenic factors, including vascular endothelial growth factor (VEGF), were highly expressed in lung cancer patients in countries with high PM2.5 levels in the atmosphere, and high expression of VEGF in lung cancer patients lowered the survival rate. Collectively, these results provide new insight into the mechanisms by which mild exposure to PM2.5 is involved in HIF-1α-mediated angiogenesis in lung cancer patients.
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Affiliation(s)
- Su Min Ji
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Jae-Sun Choi
- Department of Anatomy and Neurobiology, College of Medicine, Kyung Hee University, Seoul, 02447, Republic of Korea; Clinical Research Institute, Kyung Hee University Medical Center, Seoul, 02447, Republic of Korea
| | - Ji Young Lee
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Sungyeon Kim
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon, 21565, Republic of Korea
| | - Woom-Yee Bae
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, 02447, Republic of Korea; Department of Anatomy and Neurobiology, College of Medicine, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Ye Won Jang
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Ja-Eun Kim
- Department of Anatomy and Neurobiology, College of Medicine, Kyung Hee University, Seoul, 02447, Republic of Korea; Department of Pharmacology, College of Medicine, Kyung Hee Univeristy, Seoul, 02447, Republic of Korea
| | - Seung Hyeun Lee
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Seungyoon Nam
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon, 21565, Republic of Korea
| | - Joo-Won Jeong
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, 02447, Republic of Korea; Department of Anatomy and Neurobiology, College of Medicine, Kyung Hee University, Seoul, 02447, Republic of Korea.
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Dai Z, Zhang N, Zhou R, Zhang H, Zhang L, Wang Z, Zeng W, Luo P, Zhang J, Liu Z, Cheng Q. Identification of a single cell-based signature for predicting prognosis risk and immunotherapy response in patients with glioblastoma. Clin Immunol 2023; 251:109345. [PMID: 37100336 DOI: 10.1016/j.clim.2023.109345] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/20/2022] [Accepted: 04/14/2023] [Indexed: 04/28/2023]
Abstract
This study constructed a novel gene pair signature based on bulk and single-cell sequencing samples in relative expression order within the samples. The subsequent analysis included glioma samples from Xiangya Hospital. Gene pair signatures possessed a solid ability to predict the prognosis of glioblastoma and pan-cancer. Samples having different malignant biological hallmarks were distinguished by the algorithm, with the high gene pair score group featuring classic copy number variations, oncogenic mutations, and extensive hypomethylation, mediating poor prognosis. The increased gene pair score group with a poorer prognosis demonstrated significant enrichment in tumor and immune-related signaling pathways while presenting immunological diversity. The remarkable infiltration of M2 macrophages in the high gene pair score group was validated by multiplex immunofluorescence, suggesting that combination therapies targeting adaptive and innate immunity may serve as a therapeutic option. Overall, a gene pair signature applicable to predict prognosis hopefully provides a reference to guide clinical practice.
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Affiliation(s)
- Ziyu Dai
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China
| | - Nan Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410078, China; One-Third Lab, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150088, China
| | - Ran Zhou
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China; Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Hao Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China
| | - Liyang Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China; Department of Medicine, The University of Oklahoma Health Sciences Center, OK 73104, USA; Clinical Diagnosis and Therapeutic Center of Glioma, Xiangya Hospital, Central South University, Changsha 410078, China
| | - Zeyu Wang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China
| | - Wenjing Zeng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410078, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Zhixiong Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410078, China.
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410078, China; Clinical Diagnosis and Therapeutic Center of Glioma, Xiangya Hospital, Central South University, Changsha 410078, China.
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Dong H, Sun M, Li H, Yue Y. CXCR3 predicts the prognosis of endometrial adenocarcinoma. BMC Med Genomics 2023; 16:20. [PMID: 36750966 PMCID: PMC9903462 DOI: 10.1186/s12920-023-01451-9] [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: 05/13/2022] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
OBJECTIVES Currently, endometrial adenocarcinoma lacks an effective prognostic indicator. This study was to develop and validate a gene biomarker and a nomogram to predict the survival of endometrial adenocarcinoma, explore potential mechanisms and select sensitive drugs. METHODS 425 endometrial adenocarcinoma cases with RNA sequencing data from TCGA were used to identify the most immune-related module by WGCNA. As an external test set, 103 cases from GSE17025 were used. Immune-related genes were downloaded from Innate DB. The three sets of data were used to identify the prognostic genes. Based on 397 cases with complete clinical data from TCGA, randomly divided into the training set (n = 199) and test set (n = 198), we identified CXCR3 as the prognostic gene biomarker. Age, grade, FIGO stage, and risk were used to develop and validate a predictive nomogram. AUC, C-index, calibration curve and K-M estimate evaluated the model's predictive performance. KEGG enrichment analysis, immune functions, TMB, the effectiveness of immunotherapy, and drug sensitivity between the high-risk and low-risk groups. RESULTS CXCR3 was identified as a prognostic biomarker. We calculated the risk score and divided the cases into the high-risk and low-risk groups by the median value of the risk score. The OS of the high-risk group was better than the low-risk group. The risk was the prognostic indicator independent of age, grade, and FIGO stage. We constructed the nomogram including age, grade, FIGO stage, and risk to predict the prognosis of endometrial adenocarcinoma. The top five KEGG pathways enriched by the DEGs between the high- and low-risk groups were viral protein interaction with cytokine and cytokine receptors, cytokine-cytokine receptor interaction, chemokine signaling pathway, natural killer cell-mediated cytotoxicity, and cell adhesion molecules. We analyzed the difference in immune cells and found that CD8+ T cells, activated CD4+ T cells, T helper cells, monocytes, and M1 macrophages were infiltrated more in the low-risk group. However, M0 macrophages and activated dendritic cells were more in the high-risk group. The immune function including APC coinhibition, APC costimulation, CCR, checkpoint, cytolytic activity, HLA, inflammation-promoting, MHC-I, parainflammation, T cell coinhibition, T cell costimulation, type I-IFN-response, and type II-IFN-response were better in the low-risk group. TMB and TIDE scores were both better in the low-risk group. By 'the pRRophetic' package, we found 56 sensitive drugs for different risk groups. CONCLUSION We identified CXCR3 as the prognostic biomarker. We also developed and validated a predictive nomogram model combining CXCR3, age, histological grade, and FIGO stage for endometrial adenocarcinoma, which could help explore the precise treatment.
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Affiliation(s)
- He Dong
- grid.430605.40000 0004 1758 4110Department of Gynecologic Oncology, The First Hospital of Jilin University, Changchun, China
| | - Mengzi Sun
- grid.64924.3d0000 0004 1760 5735Department of Epidemiology and Statistics, School of Public Health, Jilin University, Changchun, China
| | - Hua Li
- grid.430605.40000 0004 1758 4110Department of Abdominal Ultrasound, The First Hospital of Jilin University, Changchun, China
| | - Ying Yue
- Department of Gynecologic Oncology, The First Hospital of Jilin University, Changchun, China.
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Zhao Q, Hu W, Xu J, Zeng S, Xi X, Chen J, Wu X, Hu S, Zhong T. Comprehensive Pan-Cancer Analysis of Senescence With Cancer Prognosis and Immunotherapy. Front Mol Biosci 2022; 9:919274. [PMID: 35911954 PMCID: PMC9334796 DOI: 10.3389/fmolb.2022.919274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/31/2022] [Indexed: 12/03/2022] Open
Abstract
Senescence is a double-edged sword in tumorigenesis and affects the immunotherapy response through the modulation of the host’s immune system. However, there is currently a lack of comprehensive analysis of the senescence-related genes (SRGs) in human cancers, and the predictive role of senescence in cancer immunotherapy response has not been explored. The multi-omics approaches were performed in this article to conduct a systematic pan-cancer genomic analysis of SRGs in cancer. In addition, we calculated the generic senescence score (SS) to quantify the senescence levels in cancers and explored the correlations of SS with cancer prognosis, biological processes, and tumor microenvironment (TME). The gene signatures were deregulated in multiple cancers and indicated a context-dependent correlation with prognosis, tumor-immune evasion, and response to therapy across various tumor types. Further analysis disclosed that SS was positively associated with the infiltration levels of immune suppressive cells, including induced Tregs (iTregs), central memory Ts (Tcms), and natural Tregs (nTregs), and negatively associated with immune killer cells, including natural killers (NKs) and mucosal-associated invariant Ts (MAITs). Moreover, the SS was significantly correlated with tumor-associated macrophages (TAMs), cancer-associated fibroblasts (CAFs), immune-related genes, and immune checkpoints and had a predictive value of immunotherapy response. Thus, the expression of SRGs was involved in resistance to several anticancer drugs. Our work illustrates the characterization of senescence across various malignancies and highlights the potential of senescence as a biomarker of the response to immunotherapy.
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Affiliation(s)
- Qinfei Zhao
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Weiquan Hu
- Department of Joint Surgery, Ganzhou People’s Hospital, Ganzhou, China
| | - Jing Xu
- Department of Orthopaedic Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Shaoying Zeng
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Xuxiang Xi
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Jing Chen
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Xiangsheng Wu
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Suping Hu
- Department of Emergency, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Tianyu Zhong
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- *Correspondence: Tianyu Zhong,
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10
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Cristiano L. The pseudogenes of eukaryotic translation elongation factors (EEFs): Role in cancer and other human diseases. Genes Dis 2022; 9:941-958. [PMID: 35685457 PMCID: PMC9170609 DOI: 10.1016/j.gendis.2021.03.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/29/2021] [Indexed: 02/06/2023] Open
Abstract
The eukaryotic translation elongation factors (EEFs), i.e. EEF1A1, EEF1A2, EEF1B2, EEF1D, EEF1G, EEF1E1 and EEF2, are coding-genes that play a central role in the elongation step of translation but are often altered in cancer. Less investigated are their pseudogenes. Recently, it was demonstrated that pseudogenes have a key regulatory role in the cell, especially via non-coding RNAs, and that the aberrant expression of ncRNAs has an important role in cancer development and progression. The present review paper, for the first time, collects all that published about the EEFs pseudogenes to create a base for future investigations. For most of them, the studies are in their infancy, while for others the studies suggest their involvement in normal cell physiology but also in various human diseases. However, more investigations are needed to understand their functions in both normal and cancer cells and to define which can be useful biomarkers or therapeutic targets.
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11
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Bagchee-Clark AJ, Mucaki EJ, Whitehead T, Rogan PK. Pathway-extended gene expression signatures integrate novel biomarkers that improve predictions of patient responses to kinase inhibitors. MedComm (Beijing) 2021; 1:311-327. [PMID: 34766125 PMCID: PMC8491218 DOI: 10.1002/mco2.46] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/11/2020] [Accepted: 11/15/2020] [Indexed: 12/11/2022] Open
Abstract
Cancer chemotherapy responses have been related to multiple pharmacogenetic biomarkers, often for the same drug. This study utilizes machine learning to derive multi‐gene expression signatures that predict individual patient responses to specific tyrosine kinase inhibitors, including erlotinib, gefitinib, sorafenib, sunitinib, lapatinib and imatinib. Support vector machine (SVM) learning was used to train mathematical models that distinguished sensitivity from resistance to these drugs using a novel systems biology‐based approach. This began with expression of genes previously implicated in specific drug responses, then expanded to evaluate genes whose products were related through biochemical pathways and interactions. Optimal pathway‐extended SVMs predicted responses in patients at accuracies of 70% (imatinib), 71% (lapatinib), 83% (sunitinib), 83% (erlotinib), 88% (sorafenib) and 91% (gefitinib). These best performing pathway‐extended models demonstrated improved balance predicting both sensitive and resistant patient categories, with many of these genes having a known role in cancer aetiology. Ensemble machine learning‐based averaging of multiple pathway‐extended models derived for an individual drug increased accuracy to >70% for erlotinib, gefitinib, lapatinib and sorafenib. Through incorporation of novel cancer biomarkers, machine learning‐based pathway‐extended signatures display strong efficacy predicting both sensitive and resistant patient responses to chemotherapy.
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Affiliation(s)
- Ashis J Bagchee-Clark
- Department of Biochemistry, Schulich School of Medicine and Dentistry University of Western Ontario, London, Canada N6A 2C8 Canada
| | - Eliseos J Mucaki
- Department of Biochemistry, Schulich School of Medicine and Dentistry University of Western Ontario, London, Canada N6A 2C8 Canada
| | - Tyson Whitehead
- SHARCNET University of Western Ontario London Ontario N6A 5B7 Canada
| | - Peter K Rogan
- Department of Biochemistry, Schulich School of Medicine and Dentistry University of Western Ontario, London, Canada N6A 2C8 Canada.,Cytognomix Inc., 60 North Centre Road, Box 27052, London, Canada N5X 3X5 Canada
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