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He G, Liu X. Hypoxia-Inducible Factor-1α (HIF-1α) as a Factor to Predict the Prognosis of Spinal Chordoma. Spine (Phila Pa 1976) 2024; 49:661-669. [PMID: 38251727 DOI: 10.1097/brs.0000000000004925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024]
Abstract
STUDY DESIGN Retrospective study. OBJECTIVE In this study, the authors explore the potential relationship between hypoxia inducible factor-1α (HIF-1α) and the prognosis of patients with spinal chordoma. SUMMARY OF BACKGROUND DATA Currently, prognostic factors related to the clinical course in the setting of spinal chordoma are poorly understood. Although the close relationship between HIF-1α and tumor angiogenesis, metastasis, and recurrence have been widely reported, it has not been investigated in the context of spinal chordoma. MATERIALS AND METHODS In this study, 32 samples of chordoma patients were compared with 14 nucleus pulposus tissues as controls. The specific expression of HIF-1α was detected by immunohistochemistry. Continuous disease-free survival (CDFS) was defined as the interval from tumor resection to confirmation of the first local recurrence or distant metastasis. Overall survival (OS) was defined as the interval from the date of surgery to death related to any cause. The relationship between HIF-1α expression and the clinicopathologic characteristics of patients with chordoma was analyzed using the Pearson χ 2 test. Multivariate Cox analysis was used to evaluate whether HIF-1α expression was associated with the prognosis of patients after controlling for confounders. RESULTS HIF-1α was mainly expressed in the cytoplasm or nucleus in all of the chordoma samples, which showed significantly higher than that in the normal nucleus pulposus tissue ( P =0.004). Multivariate Cox regression analyses showed that high HIF-1α expression and location of HIF-1α expression were significantly associated with poor CDFS (hazard ratio (HR)=3.374; P =0.021) and OS (HR=4.511; P =0.012). In addition, we further found that high HIF-1α expression both in the cytoplasm and nucleus indicated a stronger prognostic factor for poor CDFS (HR=3.885; P =0.011) and OS (HR=4.014; P =0.011) in spinal chordoma patients. CONCLUSION High HIF-1α expression may become a potential new biological indicator to predict a poor prognosis in patients with spinal chordoma. HIF-1α may also represent a novel therapeutic target for the treatment of spinal chordoma.
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Affiliation(s)
- Guanping He
- Department of Orthopedics, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- Department of Orthopedics, Peking University Third Hospital, Beijing, China
| | - Xiaoguang Liu
- Department of Orthopedics, Peking University Third Hospital, Beijing, China
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2
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Peng C, Wang Y, Zhang H, Chen P. The platelet-related genes associated with the prognosis of HCC by regulating cycling T cell and prolif-TAMs. Heliyon 2024; 10:e26798. [PMID: 38486758 PMCID: PMC10938119 DOI: 10.1016/j.heliyon.2024.e26798] [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: 05/23/2023] [Revised: 01/15/2024] [Accepted: 02/20/2024] [Indexed: 03/17/2024] Open
Abstract
Accumulating evidence highlighted the important roles of platelets in the prognosis and progression of various tumors. Nevertheless, the role of platelet-related genes (PRGs) in HCC remains limited. In this work, 92 differentially expressed PRGs were described in HCC using TCGA and ICGC databases. Then, based on the different expressions of PRGs, we explored two subtypes and developed the PRGs prognostic signature in HCC. The PRGs signature was an independent prognosis factor associated with immune cell infiltration in HCC. Furthermore, two external validation sets verified the expression and prognosis of the PRGs signature gene in HCC. Finally, scRNA-seq analysis demonstrated that the signature genes (CENPE and KIF2C) were mainly expressed in cycling T cells and prolif-TAMs. Enrichment analysis showed that CENPE and KIF2C regulated the cell cycle and p53 pathways in these cells. In conclusion, this study builds the PRGs-related risk signature of HCC and reveals the potential mechanism by which these signature genes regulate the immune microenvironment in HCC.
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Affiliation(s)
- Chenjia Peng
- School of Mathematics and Computational Science, Hunan First Normal University, Changsha, 410205, PR China
- The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, 410081, PR China
| | - Ying Wang
- The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, 410081, PR China
| | - Hengbo Zhang
- Physical Education Department, First Hunan Normal University, Changsha, 410081, PR China
| | - Ping Chen
- The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, 410081, PR China
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Luo Z, Yang F, Liu K, Ding Z. ZC3H12A inhibits tumor growth and metastasis of breast cancer under hypoxic condition via the inactivation of IL-17 signaling pathway. Cell Cycle 2024; 23:188-204. [PMID: 38357935 PMCID: PMC11037279 DOI: 10.1080/15384101.2024.2314441] [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: 06/12/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Hypoxia is a major contributor to tumor microenvironment (TME) and metastasis in most solid tumors. We seek to screen hypoxia-related genes affecting metastasis in breast cancer and to reveal relative potential regulatory pathway. Based on gene expression profiling of GSE17188 dataset, differential expressed genes (DEGs) were identified between highly metastatic breast cancer cells under hypoxia and samples under normoxia. The protein-protein interaction (PPI) network was utilized to determine hub genes. The gene expression profiling interactive analysis database (GEPIA2) and quantitative reverse-transcription polymerase chain reaction (qRT-PCR) were employed to quantify hub genes. Moreover, overexpression of zinc finger CCCH-type containing 12A (ZC3H12A) was performed both in breast cancer cells and xenograft mouse model to determine the role of ZC3H12A. We identified 134 DEGs between hypoxic and normoxic samples. Based on PPI analysis, 5 hub genes interleukin (IL)-6, GALN (GAL), CD22 molecule (CD22), ZC3H12A and TNF receptor associated factor 1 (TRAF1) were determined; the expression levels of TRAF1, IL-6, ZC3H12A and GAL were remarkably downregulated while CD22 was upregulated in breast cancer cells. Besides, patients with higher expression of ZC3H12A had favorable prognosis. Overexpression of ZC3H12A could inhibit metastasis and tumor growth of breast cancer; overexpression of ZC3H12A downregulated the expression of IL-17 signaling pathway-related proteins such as IL-17 receptor A (IL-17RA), IL-17A and nuclear factor κB activator 1 (Act1). This study reveals ZC3H12A and IL-17 signaling pathway as potential therapeutic targets for hypoxic breast cancer.
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Affiliation(s)
- Zhongbing Luo
- Department of Breast Surgery, Ganzhou People’s Hospital, Ganzhou City, Jiangxi Province, China
| | - Fulan Yang
- Department of Breast Surgery, Ganzhou People’s Hospital, Ganzhou City, Jiangxi Province, China
| | - Kang Liu
- Department of Breast Surgery, Ganzhou People’s Hospital, Ganzhou City, Jiangxi Province, China
| | - Zhenluo Ding
- Department of Breast Surgery, Ganzhou People’s Hospital, Ganzhou City, Jiangxi Province, China
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Zhang J, Zhang M, Tian Q, Yang J. A novel model associated with tumor microenvironment on predicting prognosis and immunotherapy in triple negative breast cancer. Clin Exp Med 2023; 23:3867-3881. [PMID: 37219794 PMCID: PMC10618350 DOI: 10.1007/s10238-023-01090-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/11/2023] [Indexed: 05/24/2023]
Abstract
Triple negative breast cancer (TNBC) is the most aggressive and malignant subtype in breast cancer. Immunotherapy is a currently promising and effective treatment for TNBC, while not all patients are responsive. Therefore, it is necessary to explore novel biomarkers to screen sensitive populations for immunotherapy. All mRNA expression profiles of TNBC from The Cancer Genome Atlas (TCGA) database were clustered into two subgroups by analyzing tumor immune microenvironment (TIME) with single sample gene set enrichment analysis (ssGSEA). A risk score model was constructed based on differently expressed genes (DEGs) identified from two subgroups using Cox and Least Absolute Shrinkage and Selector Operation (LASSO) regression model. And it was validated by Kaplan-Meier analysis and Receiver Operating Characteristic (ROC) analysis in Gene Expression Omnibus (GEO) and the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) databases. Multiplex immunofluorescence (mIF) and Immunohistochemical (IHC) staining were performed on clinical TNBC tissue samples. The relationship between risk score and immune checkpoint blockades (ICB) related signatures was further investigated, as well as the biological processes were performed by gene set enrichment analysis (GSEA). We obtained three DEGs positively related to prognosis and infiltrating immune cells in TNBC. Our risk score model could be an independent prognostic factor and the low risk group exhibited a prolonged overall survival (OS). Patients in low risk group were more likely to present a higher immune infiltration and stronger response to immunotherapy. GSEA revealed the model was associated with immune-related pathways. We constructed and validated a novel model based on three prognostic genes related to TIME in TNBC. The model contributed a robust signature that could predict the prognosis in TNBC, especially for the efficacy of immunotherapy.
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Affiliation(s)
- Juan Zhang
- Cancer Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta Western Road, Xi'an, 710061, Shaanxi, China
| | - Mi Zhang
- Cancer Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta Western Road, Xi'an, 710061, Shaanxi, China
| | - Qi Tian
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta Western Road, Xi'an, 710061, Shaanxi, China
| | - Jin Yang
- Cancer Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta Western Road, Xi'an, 710061, Shaanxi, China.
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Hui H, Li D, Lin Y, Miao H, Zhang Y, Li H, Qiu F, Jiang B. Construction of subtype classifiers and validation of a prognostic risk model based on hypoxia-associated lncRNAs for lung adenocarcinoma. J Thorac Dis 2023; 15:3919-3933. [PMID: 37559652 PMCID: PMC10407533 DOI: 10.21037/jtd-23-952] [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: 06/16/2023] [Accepted: 07/18/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Studies have shown that long non-coding RNAs (lncRNAs) are found to be hypoxia-regulated lncRNAs in cancer. Lung adenocarcinoma (LUAD) is the leading cause of cancer death worldwide, and despite early surgical removal, has a poor prognosis and a high recurrence rate. Thus, we aimed to identify subtype classifiers and construct a prognostic risk model using hypoxia-associated long noncoding RNAs (hypolncRNAs) for LUAD. METHODS Clinical data of LUAD samples with prognosis information obtained from the Gene Expression Omnibus (GEO), acted as validation dataset, and The Cancer Genome Atlas (TCGA) databases, served as training dataset, were used to screen hypolncRNAs in each dataset by univariate Cox regression analysis; the intersection set was used for subsequent analyses. Unsupervised clustering analysis was performed based on the expression of hypolncRNAs using the 'ConsensuClusterPlus' package. The tumor microenvironment (TME) was compared between LUAD subgroups by analyzing the expression of immune cell infiltration, immune components, stromal components, immune checkpoints, and chemokine secretion. To identify robust prognostically associated hypolncRNAs and construct a risk score model, multivariate Cox regression analysis was performed. RESULTS A total of 14 hypolncRNAs were identified. Based on the expression of these hypolncRNAs, patients with LUAD were classified into three hypolncRNA-regulated subtypes. The three subtypes differed significantly in immune cell infiltration, stromal score, specific immune checkpoints, and secretion of chemokines and their receptors. The Tumor Immune Dysfunction and Exclusion (TIDE) scores and myeloid-derived suppressor cell (MDSC) scores were also found to differ significantly among the three hypolncRNA-regulated subtypes. Four of the 14 hypolncRNAs were used to construct a signature to distinguish the overall survival (OS) in TCGA dataset (P<0.0001) and GEO dataset (P=0.0032) and sensitivity to targeted drugs in patients at different risks of LUAD. CONCLUSIONS We characterized three regulatory subtypes of hypolncRNAs with different TMEs. We developed a signature based on hypolncRNAs, contributing to the development of personalized therapy and representing a new potential therapeutic target for LUAD.
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Affiliation(s)
- Hongliang Hui
- Department of Thoracic Surgery, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Dan Li
- Community Health Center, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Yangui Lin
- Department of Thoracic Surgery, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Haoran Miao
- Department of Thoracic Surgery, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Yiqian Zhang
- Department of Thoracic Surgery, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Huaming Li
- Department of Thoracic Surgery, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Fan Qiu
- Department of Thoracic Surgery, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Bo Jiang
- Department of Thoracic Surgery, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
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Srivastava N, Usmani SS, Subbarayan R, Saini R, Pandey PK. Hypoxia: syndicating triple negative breast cancer against various therapeutic regimens. Front Oncol 2023; 13:1199105. [PMID: 37492478 PMCID: PMC10363988 DOI: 10.3389/fonc.2023.1199105] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 06/05/2023] [Indexed: 07/27/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is one of the deadliest subtypes of breast cancer (BC) for its high aggressiveness, heterogeneity, and hypoxic nature. Based on biological and clinical observations the TNBC related mortality is very high worldwide. Emerging studies have clearly demonstrated that hypoxia regulates the critical metabolic, developmental, and survival pathways in TNBC, which include glycolysis and angiogenesis. Alterations to these pathways accelerate the cancer stem cells (CSCs) enrichment and immune escape, which further lead to tumor invasion, migration, and metastasis. Beside this, hypoxia also manipulates the epigenetic plasticity and DNA damage response (DDR) to syndicate TNBC survival and its progression. Hypoxia fundamentally creates the low oxygen condition responsible for the alteration in Hypoxia-Inducible Factor-1alpha (HIF-1α) signaling within the tumor microenvironment, allowing tumors to survive and making them resistant to various therapies. Therefore, there is an urgent need for society to establish target-based therapies that overcome the resistance and limitations of the current treatment plan for TNBC. In this review article, we have thoroughly discussed the plausible significance of HIF-1α as a target in various therapeutic regimens such as chemotherapy, radiotherapy, immunotherapy, anti-angiogenic therapy, adjuvant therapy photodynamic therapy, adoptive cell therapy, combination therapies, antibody drug conjugates and cancer vaccines. Further, we also reviewed here the intrinsic mechanism and existing issues in targeting HIF-1α while improvising the current therapeutic strategies. This review highlights and discusses the future perspectives and the major alternatives to overcome TNBC resistance by targeting hypoxia-induced signaling.
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Affiliation(s)
- Nityanand Srivastava
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Salman Sadullah Usmani
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Rajasekaran Subbarayan
- Department of Radiation Oncology, Albert Einstein College of Medicine, Bronx, NY, United States
- Research, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Educations, Chennai, India
| | - Rashmi Saini
- Department of Zoology, Gargi College, University of Delhi, New Delhi, India
| | - Pranav Kumar Pandey
- Dr. R.P. Centre for Opthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
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Zhao K, Zheng Y, Lu W, Chen B. Identification of ubiquitination-related gene classification and a novel ubiquitination-related gene signature for patients with triple-negative breast cancer. Front Genet 2023; 13:932027. [PMID: 36685836 PMCID: PMC9853012 DOI: 10.3389/fgene.2022.932027] [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: 04/29/2022] [Accepted: 12/08/2022] [Indexed: 01/07/2023] Open
Abstract
Background: Ubiquitination-related genes (URGs) are important biomarkers and therapeutic targets in cancer. However, URG prognostic prediction models have not been established in triple-negative breast cancer (TNBC) before. Our study aimed to explore the roles of URGs in TNBC. Methods: The Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) and the Gene Expression Omnibus (GEO) databases were used to identify URG expression patterns in TNBC. Non-negative matrix factorization (NMF) analysis was used to cluster TNBC patients. The least absolute shrinkage and selection operator (LASSO) analysis was used to construct the multi-URG signature in the training set (METABRIC). Next, we evaluated and validated the signature in the test set (GSE58812). Finally, we evaluated the immune-related characteristics to explore the mechanism. Results: We identified four clusters with significantly different immune signatures in TNBC based on URGs. Then, we developed an 11-URG signature with good performance for patients with TNBC. According to the 11-URG signature, TNBC patients can be classified into a high-risk group and a low-risk group with significantly different overall survival. The predictive ability of this 11-URG signature was favorable in the test set. Moreover, we constructed a nomogram comprising the risk score and clinicopathological characteristics with favorable predictive ability. All of the immune cells and immune-related pathways were higher in the low-risk group than in the high-risk group. Conclusion: Our study indicated URGs might interact with the immune phenotype to influence the development of TNBC, which contributes to a further understanding of molecular mechanisms and the development of novel therapeutic targets for TNBC.
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Napier TS, Lynch SE, Lu Y, Song PN, Burns AC, Sorace AG. Molecular Imaging of Oxygenation Changes during Immunotherapy in Combination with Paclitaxel in Triple Negative Breast Cancer. Biomedicines 2023; 11:125. [PMID: 36672633 PMCID: PMC9856084 DOI: 10.3390/biomedicines11010125] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/16/2022] [Accepted: 12/27/2022] [Indexed: 01/06/2023] Open
Abstract
Hypoxia is a common feature of the tumor microenvironment, including that of triple-negative breast cancer (TNBC), an aggressive breast cancer subtype with a high five-year mortality rate. Using [18F]-fluoromisonidazole (FMISO) positron emission tomography (PET) imaging, we aimed to monitor changes in response to immunotherapy (IMT) with chemotherapy in TNBC. TNBC-tumor-bearing mice received paclitaxel (PTX) ± immune checkpoint inhibitors anti-programmed death 1 and anti-cytotoxic T-lymphocyte 4. FMISO-PET imaging was performed on treatment days 0, 6, and 12. Max and mean standard uptake values (SUVmax and SUVmean, respectively), histological analyses, and flow cytometry results were compared. FMISO-PET imaging revealed differences in tumor biology between treatment groups prior to tumor volume changes. 4T1 responders showed SUVmean 1.6-fold lower (p = 0.02) and 1.8-fold lower (p = 0.02) than non-responders on days 6 and 12, respectively. E0771 responders showed SUVmean 3.6-fold lower (p = 0.001) and 2.7-fold lower (p = 0.03) than non-responders on days 6 and 12, respectively. Immunohistochemical analyses revealed IMT plus PTX decreased hypoxia and proliferation and increased vascularity compared to control. Combination IMT/PTX recovered the loss of CD4+ T-cells observed with single-agent therapies. PET imaging can provide timely, longitudinal data on the TNBC tumor microenvironment, specifically intratumoral hypoxia, predicting therapeutic response to IMT plus chemotherapy.
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Affiliation(s)
- Tiara S. Napier
- Graduate Biomedical Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Shannon E. Lynch
- Graduate Biomedical Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yun Lu
- Graduate Biomedical Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Patrick N. Song
- Graduate Biomedical Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Andrew C. Burns
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Anna G. Sorace
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Capobianco E. Overview of triple negative breast cancer prognostic signatures in the context of data science-driven clinico-genomics research. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1300. [PMID: 36660729 PMCID: PMC9843365 DOI: 10.21037/atm-22-5477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/15/2022] [Indexed: 01/01/2023]
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Li J, Qiao H, Wu F, Sun S, Feng C, Li C, Yan W, Lv W, Wu H, Liu M, Chen X, Liu X, Wang W, Cai Y, Zhang Y, Zhou Z, Zhang Y, Zhang S. A novel hypoxia- and lactate metabolism-related signature to predict prognosis and immunotherapy responses for breast cancer by integrating machine learning and bioinformatic analyses. Front Immunol 2022; 13:998140. [PMID: 36275774 PMCID: PMC9585224 DOI: 10.3389/fimmu.2022.998140] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/23/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundBreast cancer is the most common cancer worldwide. Hypoxia and lactate metabolism are hallmarks of cancer. This study aimed to construct a novel hypoxia- and lactate metabolism-related gene signature to predict the survival, immune microenvironment, and treatment response of breast cancer patients.MethodsRNA-seq and clinical data of breast cancer from The Cancer Genome Atlas database and Gene Expression Omnibus were downloaded. Hypoxia- and lactate metabolism-related genes were collected from publicly available data sources. The differentially expressed genes were identified using the “edgeR” R package. Univariate Cox regression, random survival forest (RSF), and stepwise multivariate Cox regression analyses were performed to construct the hypoxia-lactate metabolism-related prognostic model (HLMRPM). Further analyses, including functional enrichment, ESTIMATE, CIBERSORTx, Immune Cell Abundance Identifier (ImmuCellAI), TIDE, immunophenoscore (IPS), pRRophetic, and CellMiner, were performed to analyze immune status and treatment responses.ResultsWe identified 181 differentially expressed hypoxia-lactate metabolism-related genes (HLMRGs), 24 of which were valuable prognostic genes. Using RSF and stepwise multivariate Cox regression analysis, five HLMRGs were included to establish the HLMRPM. According to the medium-risk score, patients were divided into high- and low-risk groups. Patients in the high-risk group had a worse prognosis than those in the low-risk group (P < 0.05). A nomogram was further built to predict overall survival (OS). Functional enrichment analyses showed that the low-risk group was enriched with immune-related pathways, such as antigen processing and presentation and cytokine-cytokine receptor interaction, whereas the high-risk group was enriched in mTOR and Wnt signaling pathways. CIBERSORTx and ImmuCellAI showed that the low-risk group had abundant anti-tumor immune cells, whereas in the high-risk group, immunosuppressive cells were dominant. Independent immunotherapy datasets (IMvigor210 and GSE78220), TIDE, IPS and pRRophetic analyses revealed that the low-risk group responded better to common immunotherapy and chemotherapy drugs.ConclusionsWe constructed a novel prognostic signature combining lactate metabolism and hypoxia to predict OS, immune status, and treatment response of patients with breast cancer, providing a viewpoint for individualized treatment.
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Affiliation(s)
- Jia Li
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Hao Qiao
- Department of Orthopedics, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Fei Wu
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Shiyu Sun
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Cong Feng
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Chaofan Li
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Wanjun Yan
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Wei Lv
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Huizi Wu
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Mengjie Liu
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Xi Chen
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Xuan Liu
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Weiwei Wang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yifan Cai
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yu Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Zhangjian Zhou
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Shuqun Zhang, ; Yinbin Zhang, ; Zhangjian Zhou,
| | - Yinbin Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Shuqun Zhang, ; Yinbin Zhang, ; Zhangjian Zhou,
| | - Shuqun Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Shuqun Zhang, ; Yinbin Zhang, ; Zhangjian Zhou,
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Bartoszewska S, Collawn JF, Bartoszewski R. The Role of the Hypoxia-Related Unfolded Protein Response (UPR) in the Tumor Microenvironment. Cancers (Basel) 2022; 14:4870. [PMID: 36230792 PMCID: PMC9562011 DOI: 10.3390/cancers14194870] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/29/2022] [Accepted: 10/03/2022] [Indexed: 11/19/2022] Open
Abstract
Despite our understanding of the unfolded protein response (UPR) pathways, the crosstalk between the UPR and the complex signaling networks that different cancers utilize for cell survival remains to be, in most cases, a difficult research barrier. A major problem is the constant variability of different cancer types and the different stages of cancer as well as the complexity of the tumor microenvironments (TME). This complexity often leads to apparently contradictory results. Furthermore, the majority of the studies that have been conducted have utilized two-dimensional in vitro cultures of cancer cells that were exposed to continuous hypoxia, and this approach may not mimic the dynamic and cyclic conditions that are found in solid tumors. Here, we discuss the role of intermittent hypoxia, one of inducers of the UPR in the cellular component of TME, and the way in which intermittent hypoxia induces high levels of reactive oxygen species, the activation of the UPR, and the way in which cancer cells modulate the UPR to aid in their survival. Although the past decade has resulted in defining the complex, novel non-coding RNA-based regulatory networks that modulate the means by which hypoxia influences the UPR, we are now just to beginning to understand some of the connections between hypoxia, the UPR, and the TME.
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Affiliation(s)
- Sylwia Bartoszewska
- Department of Inorganic Chemistry, Medical University of Gdansk, 80-416 Gdansk, Poland
| | - James F. Collawn
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Rafal Bartoszewski
- Department of Biophysics, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14a Street, 50-383 Wroclaw, Poland
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12
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Lu X, Gou Z, Yu L, Bu H. A novel risk model based on immune response predicts clinical outcomes and characterizes immunophenotypes in triple-negative breast cancer. Am J Cancer Res 2022; 12:3913-3931. [PMID: 36119814 PMCID: PMC9442003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is highly heterogeneous in prognosis. The current TNM staging system shows its limitation in accurate risk evaluation. Immune response and immune cell abundances in the tumor immune microenvironment (TIME) are critical for cancer progression, clinical outcome and therapeutic response in TNBC. However, there is a lack of an effective risk model based on the overall transcriptional alterations relevant to different immune responses. In this study, multiple bioinformatics and statistical approaches were used to develop an immune-related risk (IRR) signature based on the differentially expressed genes between the immune-active and immune-inactive samples. The IRR model showed great performance in risk stratification, immune landscape evaluation and immunotherapy response prediction. Compared with the low-IRR group, the high-IRR group exhibited a poorer prognosis, less cytotoxic cell infiltration, higher M2/M1 ratio and upregulated glycolytic activity. Moreover, the high-IRR group showed more resistance to immunotherapy than the low-IRR group. Our study reveals that the IRR model may be a promising tool to help clinicians assess risk and optimize treatment for TNBC patients.
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Affiliation(s)
- Xunxi Lu
- Department of Pathology, West China Hospital, Sichuan UniversityChengdu 610041, China
- Institute of Clinical Pathology, West China Hospital, Sichuan UniversityChengdu 610041, China
| | - Zongchao Gou
- Department of Breast Surgery, West China Hospital, Sichuan UniversityChengdu 610041, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan UniversityChengdu 610041, China
| | - Luoting Yu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan UniversityChengdu 610041, China
| | - Hong Bu
- Department of Pathology, West China Hospital, Sichuan UniversityChengdu 610041, China
- Institute of Clinical Pathology, West China Hospital, Sichuan UniversityChengdu 610041, China
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13
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Jinna N, Rida P, Smart M, LaBarge M, Jovanovic-Talisman T, Natarajan R, Seewaldt V. Adaptation to Hypoxia May Promote Therapeutic Resistance to Androgen Receptor Inhibition in Triple-Negative Breast Cancer. Int J Mol Sci 2022; 23:ijms23168844. [PMID: 36012111 PMCID: PMC9408190 DOI: 10.3390/ijms23168844] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/03/2022] [Accepted: 08/06/2022] [Indexed: 12/27/2022] Open
Abstract
Triple-negative breast cancer (TNBC) surpasses other BC subtypes as the most challenging to treat due to its lack of traditional BC biomarkers. Nearly 30% of TNBC patients express the androgen receptor (AR), and the blockade of androgen production and AR signaling have been the cornerstones of therapies for AR-positive TNBC. However, the majority of women are resistant to AR-targeted therapy, which is a major impediment to improving outcomes for the AR-positive TNBC subpopulation. The hypoxia signaling cascade is frequently activated in the tumor microenvironment in response to low oxygen levels; activation of the hypoxia signaling cascade allows tumors to survive despite hypoxia-mediated interference with cellular metabolism. The activation of hypoxia signaling networks in TNBC promotes resistance to most anticancer drugs including AR inhibitors. The activation of hypoxia network signaling occurs more frequently in TNBC compared to other BC subtypes. Herein, we examine the (1) interplay between hypoxia signaling networks and AR and (2) whether hypoxia and hypoxic stress adaptive pathways promote the emergence of resistance to therapies that target AR. We also pose the well-supported question, “Can the efficacy of androgen-/AR-targeted treatments be enhanced by co-targeting hypoxia?” By critically examining the evidence and the complex entwinement of these two oncogenic pathways, we argue that the simultaneous targeting of androgen biosynthesis/AR signaling and hypoxia may enhance the sensitivity of AR-positive TNBCs to AR-targeted treatments, derail the emergence of therapy resistance, and improve patient outcomes.
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Affiliation(s)
- Nikita Jinna
- Department of Population Science, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | | | - Max Smart
- Rowland Hall, Salt Lake City, UT 84102, USA
| | - Mark LaBarge
- Department of Population Science, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | | | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Victoria Seewaldt
- Department of Population Science, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
- Correspondence:
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14
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Jiang R, Hu J, Zhou H, Wei H, He S, Xiao J. A Novel Defined Hypoxia-Related Gene Signature for Prognostic Prediction of Patients With Ewing Sarcoma. Front Genet 2022; 13:908113. [PMID: 35719404 PMCID: PMC9201760 DOI: 10.3389/fgene.2022.908113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/18/2022] [Indexed: 11/25/2022] Open
Abstract
The therapeutic strategy of Ewing sarcoma (EWS) remains largely unchanged over the past few decades. Hypoxia is reported to have an impact on tumor cell progression and is regarded as a novel potential therapeutic target in tumor treatment. This study aimed at developing a prognostic gene signature based on hypoxia-related genes (HRGs). EWS patients from GSE17674 in the GEO database were analyzed as a training cohort, and differently expressed HRGs between tumor and normal samples were identified. The univariate Cox regression, Least Absolute Shrinkage and Selection Operator (LASSO) and multivariate Cox regression analyses were used in this study. A total of 57 EWS patients from the International Cancer Genome Consortium (ICGC) database were set as the validation cohort. A total of 506 differently expressed HRGs between tumor and normal tissues were identified, among which 52 were associated with the prognoses of EWS patients. Based on 52 HRGs, EWS patients were divided into two molecular subgroups with different survival statuses. In addition, a prognostic signature based on 4 HRGs (WSB1, RXYLT1, GLCE and RORA) was constructed, dividing EWS patients into low- and high-risk groups. The 2-, 3- and 5-years area under the receiver operator characteristic curve of this signature was 0.913, 0.97 and 0.985, respectively. It was found that the survival rates of patients in the high-risk group were significantly lower than those in the low-risk group (p < 0.001). The risk level based on the risk score could serve as an independent clinical factor for predicting the survival probabilities of EWS patients. Additionally, antigen-presenting cell (APC) related pathways and T cell co-inhibition were differently activated in two risk groups, which may result in different prognoses. CTLA4 may be an effective immune checkpoint inhibitor to treat EWS patients. All results were verified in the validation cohort. This study constructed 4-HRGs as a novel prognostic marker for predicting survival in EWS patients.
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Affiliation(s)
- Runyi Jiang
- Spinal Tumor Center, Department of Orthopaedic Oncology, No.905 Hospital of PLA Navy, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Jinbo Hu
- Spinal Tumor Center, Department of Orthopaedic Oncology, No.905 Hospital of PLA Navy, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Hongfei Zhou
- Spinal Tumor Center, Department of Orthopaedic Oncology, No.905 Hospital of PLA Navy, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
- The Third Convalescent Department, Hangzhou Sanatorium, Hangzhou, China
| | - Haifeng Wei
- Spinal Tumor Center, Department of Orthopaedic Oncology, No.905 Hospital of PLA Navy, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
- *Correspondence: Jianru Xiao, ; Shaohui He, ; Haifeng Wei,
| | - Shaohui He
- Spinal Tumor Center, Department of Orthopaedic Oncology, No.905 Hospital of PLA Navy, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
- *Correspondence: Jianru Xiao, ; Shaohui He, ; Haifeng Wei,
| | - Jianru Xiao
- Spinal Tumor Center, Department of Orthopaedic Oncology, No.905 Hospital of PLA Navy, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
- *Correspondence: Jianru Xiao, ; Shaohui He, ; Haifeng Wei,
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15
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Feng S, Xia T, Ge Y, Zhang K, Ji X, Luo S, Shen Y. Computed Tomography Imaging-Based Radiogenomics Analysis Reveals Hypoxia Patterns and Immunological Characteristics in Ovarian Cancer. Front Immunol 2022; 13:868067. [PMID: 35418998 PMCID: PMC8995567 DOI: 10.3389/fimmu.2022.868067] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 02/28/2022] [Indexed: 12/15/2022] Open
Abstract
Purpose The hypoxic microenvironment is involved in the tumorigenesis of ovarian cancer (OC). Therefore, we aim to develop a non-invasive radiogenomics approach to identify a hypoxia pattern with potential application in patient prognostication. Methods Specific hypoxia-related genes (sHRGs) were identified based on RNA-seq of OC cell lines cultured with different oxygen conditions. Meanwhile, multiple hypoxia-related subtypes were identified by unsupervised consensus analysis and LASSO–Cox regression analysis. Subsequently, diversified bioinformatics algorithms were used to explore the immune microenvironment, prognosis, biological pathway alteration, and drug sensitivity among different subtypes. Finally, optimal radiogenomics biomarkers for predicting the risk status of patients were developed by machine learning algorithms. Results One hundred forty sHRGs and three types of hypoxia-related subtypes were identified. Among them, hypoxia-cluster-B, gene-cluster-B, and high-risk subtypes had poor survival outcomes. The subtypes were closely related to each other, and hypoxia-cluster-B and gene-cluster-B had higher hypoxia risk scores. Notably, the low-risk subtype had an active immune microenvironment and may benefit from immunotherapy. Finally, a four-feature radiogenomics model was constructed to reveal hypoxia risk status, and the model achieved area under the curve (AUC) values of 0.900 and 0.703 for the training and testing cohorts, respectively. Conclusion As a non-invasive approach, computed tomography-based radiogenomics biomarkers may enable the pretreatment prediction of the hypoxia pattern, prognosis, therapeutic effect, and immune microenvironment in patients with OC.
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Affiliation(s)
- Songwei Feng
- Department of Obstetrics and Gynaecology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Tianyi Xia
- Department of Radiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Yu Ge
- Department of Obstetrics and Gynaecology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Ke Zhang
- Department of Obstetrics and Gynaecology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Xuan Ji
- Department of Obstetrics and Gynaecology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Shanhui Luo
- Department of Gynaecology, The Second Affiliated Hospital of Soochow University, Soochow University, Suzhou, China
| | - Yang Shen
- Department of Obstetrics and Gynaecology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
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16
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Shi Y, Huang X, Du Z, Tan J. Analysis of single-cell RNA-sequencing data identifies a hypoxic tumor subpopulation associated with poor prognosis in triple-negative breast cancer. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:5793-5812. [PMID: 35603379 DOI: 10.3934/mbe.2022271] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype of mammary carcinoma characterized by low expression levels of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). Along with the rapid development of the single-cell RNA-sequencing (scRNA-seq) technology, the heterogeneity within the tumor microenvironment (TME) could be studied at a higher resolution level, facilitating an exploration of the mechanisms leading to poor prognosis during tumor progression. In previous studies, hypoxia was considered as an intrinsic characteristic of TME in solid tumors, which would activate downstream signaling pathways associated with angiogenesis and metastasis. Moreover, hypoxia-related genes (HRGs) based risk score models demonstrated nice performance in predicting the prognosis of TNBC patients. However, it is essential to further investigate the heterogeneity within hypoxic TME, such as intercellular communications. In the present study, utilizing single-sample Gene Set Enrichment Analysis (ssGSEA) and cell-cell communication analysis on the scRNA-seq data retrieved from Gene Expression Omnibus (GEO) database with accession number GSM4476488, we identified four tumor subpopulations with diverse functions, particularly a hypoxia-related one. Furthermore, results of cell-cell communication analysis revealed the dominant role of the hypoxic tumor subpopulation in angiogenesis- and metastasis-related signaling pathways as a signal sender. Consequently, regard the TNBC cohorts acquired from The Cancer Genome Atlas (TCGA) and GEO as train set and test set respectively, we constructed a risk score model with reliable capacity for the prediction of overall survival (OS), where ARTN and L1CAM were identified as risk factors promoting angiogenesis and metastasis of tumors. The expression of ARTN and L1CAM were further analyzed through tumor immune estimation resource (TIMER) platform. In conclusion, these two marker genes of the hypoxic tumor subpopulation played vital roles in tumor development, indicating poor prognosis in TNBC patients.
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Affiliation(s)
- Yi Shi
- Department of Biomedical Engineering, Faculty of Environment and Life, Beijing University of Technology, Beijing International Science and Technology Cooperation Base for Intelligent Physiological Measurement and Clinical Transformation, Beijing 100124, China
| | - Xiaoqian Huang
- Department of Biomedical Engineering, Faculty of Environment and Life, Beijing University of Technology, Beijing International Science and Technology Cooperation Base for Intelligent Physiological Measurement and Clinical Transformation, Beijing 100124, China
| | - Zhaolan Du
- Department of Biomedical Engineering, Faculty of Environment and Life, Beijing University of Technology, Beijing International Science and Technology Cooperation Base for Intelligent Physiological Measurement and Clinical Transformation, Beijing 100124, China
| | - Jianjun Tan
- Department of Biomedical Engineering, Faculty of Environment and Life, Beijing University of Technology, Beijing International Science and Technology Cooperation Base for Intelligent Physiological Measurement and Clinical Transformation, Beijing 100124, China
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17
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Chen X, Zhang Y, Wang F, Zhou X, Fu Q, Yang X, Lin J, Jin X. A Novel Assessment Model Based on Molecular Subtypes of Hypoxia-Related LncRNAs for Prognosis of Bladder Cancer. Front Cell Dev Biol 2021; 9:718991. [PMID: 34869309 PMCID: PMC8634255 DOI: 10.3389/fcell.2021.718991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/11/2021] [Indexed: 12/19/2022] Open
Abstract
Hypoxia is a common feature in various tumors that regulates aggressiveness. Previous studies have demonstrated that some dysregulated long non-coding RNAs (lncRNAs) are correlated with tumor progression, including bladder cancer (BCa). However, the prognostic effect of hypoxia-related lncRNAs (HRLs) and their clinical relevance, as well as their regulatory effect on the tumor immune microenvironment, are largely unknown in BCa. A co-expression analysis between hypoxia genes and lncRNA expression, which was downloaded from the TCGA database, was performed to identify HRLs. Univariate Cox regression analysis was performed to select the most desirable lncRNAs for molecular subtype, and further LASSO analysis was performed to develop a prognostic model. This molecular subtype based on four HRLs (AC104653, AL136084, AL139393, and LINC00892) showed good performance in the tumor microenvironment and tumor mutation burden. The prognostic risk model suggested better performance in predicting BCa patients' prognosis and obtained a close correlation with clinicopathologic features. Furthermore, four of five first-line clinical chemotherapies showed different sensitivities to this model, and nine immune checkpoints showed different expression in the molecular subtypes or the risk model. In conclusion, this study indicates that this molecular subtype and risk model based on HRLs may be useful in improving the prognostic prediction of BCa patients with different clinical situations and may help to find a useful target for tumor therapy.
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Affiliation(s)
- Xianwu Chen
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Zhang
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Feifan Wang
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xuejian Zhou
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qinghe Fu
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xintao Yang
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Juntao Lin
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaodong Jin
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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