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Wu J, Luo J, Cai H, Zhu H, Lei Z, Lu Y, Gao X, Ni L, Lu Z, Hu X. Expression characteristics of lipid metabolism-related genes and correlative immune infiltration landscape in acute myocardial infarction. Sci Rep 2024; 14:14095. [PMID: 38890389 PMCID: PMC11189450 DOI: 10.1038/s41598-024-65022-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 06/17/2024] [Indexed: 06/20/2024] Open
Abstract
Lipid metabolism is an important part of the heart's energy supply. The expression pattern and molecular mechanism of lipid metabolism-related genes (LMRGs) in acute myocardial infarction (AMI) are still unclear, and the link between lipid metabolism and immunity is far from being elucidated. In this study, 23 Common differentially expressed LMRGs were discovered in the AMI-related mRNA microarray datasets GSE61144 and GSE60993. These genes were mainly related to "leukotriene production involved in inflammatory response", "lipoxygenase pathway", "metabolic pathways", and "regulation of lipolysis in adipocytes" pathways. 12 LMRGs (ACSL1, ADCY4, ALOX5, ALOX5AP, CCL5, CEBPB, CEBPD, CREB5, GAB2, PISD, RARRES3, and ZNF467) were significantly differentially expressed in the validation dataset GSE62646 with their AUC > 0.7 except for ALOX5AP (AUC = 0.699). Immune infiltration analysis and Pearson correlation analysis explored the immune characteristics of AMI, as well as the relationship between these identified LMRGs and immune response. Lastly, the up-regulation of ACSL1, ALOX5AP, CEBPB, and GAB2 was confirmed in the mouse AMI model. Taken together, LMRGs ACSL1, ALOX5AP, CEBPB, and GAB2 are significantly upregulated in AMI patients' blood, peripheral blood of AMI mice, myocardial tissue of AMI mice, and therefore might be new potential biomarkers for AMI.
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Affiliation(s)
- Jiahe Wu
- Department of Cardiology, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuchang District, Wuhan, 430071, China
- Institute of Myocardial Injury and Repair, Wuhan University, Wuhan, China
| | - Jingyi Luo
- Department of Stomatology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Huanhuan Cai
- Department of Cardiology, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuchang District, Wuhan, 430071, China
- Institute of Myocardial Injury and Repair, Wuhan University, Wuhan, China
| | - Haoyan Zhu
- Department of Cardiology, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuchang District, Wuhan, 430071, China
- Institute of Myocardial Injury and Repair, Wuhan University, Wuhan, China
| | - Zhe Lei
- Department of Cardiology, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuchang District, Wuhan, 430071, China
- Institute of Myocardial Injury and Repair, Wuhan University, Wuhan, China
| | - Yi Lu
- Department of Cardiology, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuchang District, Wuhan, 430071, China
- Institute of Myocardial Injury and Repair, Wuhan University, Wuhan, China
| | - Xinchen Gao
- Department of Cardiology, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuchang District, Wuhan, 430071, China
- Institute of Myocardial Injury and Repair, Wuhan University, Wuhan, China
| | - Lihua Ni
- Department of Nephrology, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuchang District, Wuhan, 430071, China.
| | - Zhibing Lu
- Department of Cardiology, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuchang District, Wuhan, 430071, China.
- Institute of Myocardial Injury and Repair, Wuhan University, Wuhan, China.
| | - Xiaorong Hu
- Department of Cardiology, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuchang District, Wuhan, 430071, China.
- Institute of Myocardial Injury and Repair, Wuhan University, Wuhan, China.
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Zhu L, Lin Z, Wang K, Gu J, Chen X, Chen R, Wang L, Cheng X. A lactate metabolism-related signature predicting patient prognosis and immune microenvironment in ovarian cancer. Front Endocrinol (Lausanne) 2024; 15:1372413. [PMID: 38529390 PMCID: PMC10961354 DOI: 10.3389/fendo.2024.1372413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/15/2024] [Indexed: 03/27/2024] Open
Abstract
Introduction Ovarian cancer (OV) is a highly lethal gynecological malignancy with a poor prognosis. Lactate metabolism is crucial for tumor cell survival, proliferation, and immune evasion. Our study aims to investigate the role of lactate metabolism-related genes (LMRGs) in OV and their potential as biomarkers for prognosis, immune microenvironment, and immunotherapy response. Methods Ovarian samples were collected from the TCGA cohort. And 12 lactate-related pathways were identified from the MsigDB database. Differentially expressed genes within these pathways were designated as LMRGs, which undergo unsupervised clustering to identify distinct clusters based on LMRGs. Subsequently, we assessed survival outcomes, immune cell infiltration levels, Hallmaker pathway activation patterns, and chemotaxis among different subtypes. After conducting additional unsupervised clustering based on differentially expressed genes (DEGs), significant differences in the expression of LMRGs between the two clusters were observed. The differentially expressed genes were subjected to subsequent functional enrichment analysis. Furthermore, we construct a model incorporating LMRGs. Subsequently, the lactate score for each tumor sample was calculated based on this model, facilitating the classification of samples into high and low groups according to their respective lactate scores. Distinct groups examined disparities in survival prognosis, copy number variation (CNV), single nucleotide variation (SNV), and immune infiltration. The lactate score served as a quantitative measure of OV's lactate metabolism pattern and an independent prognostic factor. Results This study investigated the potential role of LMRGs in tumor microenvironment diversity and prognosis in OV, suggesting that LMRGs play a crucial role in OV progression and the tumor microenvironment, thus serving as novel indicators for prognosis, immune microenvironment status, and response to immunotherapy.
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Affiliation(s)
- Linhua Zhu
- Department of Obstetrics, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Zhuoqun Lin
- Department of Gynecologic Oncology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Kai Wang
- Department of Gynecologic Oncology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Department of Obstetrics and Gynecology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Jiaxin Gu
- Department of Gynecologic Oncology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaojing Chen
- Department of Gynecologic Oncology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ruizhe Chen
- Department of Gynecologic Oncology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lingfang Wang
- Department of Gynecologic Oncology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaodong Cheng
- Department of Gynecologic Oncology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Ma S, Wang J, Cui Z, Yang X, Cui X, Li X, Zhao L. HIF-2α-dependent TGFBI promotes ovarian cancer chemoresistance by activating PI3K/Akt pathway to inhibit apoptosis and facilitate DNA repair process. Sci Rep 2024; 14:3870. [PMID: 38365849 PMCID: PMC10873328 DOI: 10.1038/s41598-024-53854-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
Hypoxia-mediated chemoresistance plays a crucial role in the development of ovarian cancer (OC). However, the roles of hypoxia-related genes (HRGs) in chemoresistance and prognosis prediction and theirs underlying mechanisms remain to be further elucidated. We intended to identify and validate classifiers of hub HRGs for chemoresistance, diagnosis, prognosis as well as immune microenvironment of OC, and to explore the function of the most crucial HRG in the development of the malignant phenotypes. The RNA expression and clinical data of HRGs were systematically evaluated in OC training group. Univariate and multivariate Cox regression analysis were applied to construct hub HRGs classifiers for prognosis and diagnosis assessment. The relationship between classifiers and chemotherapy response and underlying pathways were detected by GSEA, CellMiner and CIBERSORT algorithm, respectively. OC cells were cultured under hypoxia or transfected with HIF-1α or HIF-2α plasmids, and the transcription levels of TGFBI were assessed by quantitative PCR. TGFBI was knocked down by siRNAs in OC cells, CCK8 and in vitro migration and invasion assays were performed to examine the changes in cell proliferation, motility and metastasis. The difference in TGFBI expression was examined between cisplatin-sensitive and -resistant cells, and the effects of TGFBI interference on cell apoptosis, DNA repair and key signaling molecules of cisplatin-resistant OC cells were explored. A total of 179 candidate HRGs were extracted and enrolled into univariate and multivariate Cox regression analysis. Six hub genes (TGFBI, CDKN1B, AKAP12, GPC1, TGM2 and ANGPTL4) were selected to create a HRGs prognosis classifier and four genes (TGFBI, AKAP12, GPC1 and TGM2) were selected to construct diagnosis classifiers. The HRGs prognosis classifier could precisely distinguish OC patients into high-risk and low-risk groups and estimate their clinical outcomes. Furthermore, the high-risk group had higher percentage of Macrophages M2 and exhibited higher expression of immunecheckpoints such as PD-L2. Additionally, the diagnosis classifiers could accurately distinguish OC from normal samples. TGFBI was further verified as a specific key target and demonstrated that its high expression was closely correlated with poor prognosis and chemoresistance of OC. Hypoxia upregulated the expression level of TGFBI. The hypoxia-induced factor HIF-2α but not HIF-1α could directly bind to the promoter region of TGFBI, and facilitate its transcription level. TGFBI was upregulated in cisplatin-sensitive and resistant ovarian cancer cells in a cisplatin time-dependent manner. TGFBI interference downregulated DNA repair-related markers (p-p95/NBS1, RAD51, p-DNA-PKcs, DNA Ligase IV and Artemis), apoptosis-related marker (BCL2) and PI3K/Akt pathway-related markers (PI3K-p110 and p-Akt) in cisplatin-resistant OC cells. In summary, the HRGs prognosis risk classifier could be served as a predictor for OC prognosis and efficacy evaluation. TGFBI, upregulated by HIF-2α as an HRG, promoted OC chemoresistance through activating PI3K/Akt pathway to reduce apoptosis and enhance DNA damage repair pathway.
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Affiliation(s)
- Sijia Ma
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, People's Republic of China
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, People's Republic of China
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Jia Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Zhiwei Cui
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Xiling Yang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, People's Republic of China
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, People's Republic of China
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Xi Cui
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, People's Republic of China
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, People's Republic of China
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Xu Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, People's Republic of China
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, People's Republic of China
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Le Zhao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, People's Republic of China.
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, People's Republic of China.
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, People's Republic of China.
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
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Zhang W, Zhou D, Song S, Hong X, Xu Y, Wu Y, Li S, Zeng S, Huang Y, Chen X, Liang Y, Guo S, Pan H, Li H. Prediction and verification of the prognostic biomarker SLC2A2 and its association with immune infiltration in gastric cancer. Oncol Lett 2024; 27:70. [PMID: 38192676 PMCID: PMC10773219 DOI: 10.3892/ol.2023.14203] [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: 07/01/2023] [Accepted: 11/15/2023] [Indexed: 01/10/2024] Open
Abstract
Gastric cancer (GC) is the fifth most common cause of cancer-associated deaths; however, its treatment options are limited. Despite clinical improvements, chemotherapy resistance and metastasis are major challenges in improving the prognosis and quality of life of patients with GC. Therefore, effective prognostic biomarkers and targets associated with immunological interventions need to be identified. Solute carrier family 2 member 2 (SLC2A2) may serve a role in tumor development and invasion. The present study aimed to evaluate SLC2A2 as a prospective prognostic marker and chemotherapeutic target for GC. SLC2A2 expression in several types of cancer and GC was analyzed using online databases, and the effects of SLC2A2 expression on survival prognosis in GC were investigated. Clinicopathological parameters were examined to explore the association between SLC2A2 expression and overall survival (OS). Associations between SLC2A2 expression and immune infiltration, immune checkpoints and IC50 were estimated using quantification of the tumor immune contexture from human RNA-seq data, the Tumor Immune Estimation Resource 2.0 database and the Genomics of Drug Sensitivity in Cancer database. Differential SLC2A2 expression and the predictive value were validated using the Human Protein Atlas, Gene Expression Omnibus, immunohistochemistry and reverse transcription-quantitative PCR. SLC2A2 expression was downregulated in most types of tumor but upregulated in GC. Functional enrichment analysis revealed an association between SLC2A2 expression and lipid metabolism and the tumor immune microenvironment. According to Gene Ontology term functional enrichment analysis, SLC2A2-related differentially expressed genes were enriched predominantly in 'chylomicron assembly', 'plasma lipoprotein particle assembly', 'high-density lipoprotein particle', 'chylomicron', 'triglyceride-rich plasma lipoprotein particle', 'very-low-density lipoprotein particle'. 'intermembrane lipid transfer activity', 'lipoprotein particle receptor binding', 'cholesterol transporter activity' and 'intermembrane cholesterol transfer activity'. In addition, 'cholesterol metabolism', and 'fat digestion and absorption' were significantly enriched in the Kyoto Encyclopedia of Genes and Genomes pathway analysis. Patients with GC with high SLC2A2 expression had higher levels of neutrophil and M2 macrophage infiltration and a significant inverse correlation was observed between SLC2A2 expression and MYC targets, tumor mutation burden, microsatellite instability and immune checkpoints. Furthermore, patients with high SLC2A2 expression had worse prognosis, including OS, disease-specific survival and progression-free interval. Multivariate regression analysis demonstrated that SLC2A2 could independently prognosticate GC and the nomogram model showed favorable performance for survival prediction. SLC2A2 may be a prospective prognostic marker for GC. The prediction model may improve the prognosis of patients with GC in clinical practice, and SLC2A2 may serve as a novel therapeutic target to provide immunotherapy plans for GC.
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Affiliation(s)
- Weijian Zhang
- The Fourth Clinical Medical College, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, P.R. China
| | - Dishu Zhou
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, P.R. China
| | - Shuya Song
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, P.R. China
| | - Xinxin Hong
- Department of Gastroenterology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Yifei Xu
- Department of Gastroenterology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Yuqi Wu
- The Fourth Clinical Medical College, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Shiting Li
- The Fourth Clinical Medical College, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Sihui Zeng
- The Fourth Clinical Medical College, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Yanzi Huang
- Department of Gastroenterology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Xinbo Chen
- Department of Gastroenterology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Yizhong Liang
- Department of Gastroenterology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Shaoju Guo
- Department of Gastroenterology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Huafeng Pan
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, P.R. China
| | - Haiwen Li
- Department of Gastroenterology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
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Wu J, Cai H, Hu X, Wu W. Transcriptomic analysis reveals the lipid metabolism-related gene regulatory characteristics and potential therapeutic agents for myocardial ischemia-reperfusion injury. Front Cardiovasc Med 2024; 11:1281429. [PMID: 38347951 PMCID: PMC10859419 DOI: 10.3389/fcvm.2024.1281429] [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: 08/22/2023] [Accepted: 01/18/2024] [Indexed: 02/15/2024] Open
Abstract
Background Impaired energy balance caused by lipid metabolism dysregulation is an essential mechanism of myocardial ischemia-reperfusion injury (MI/RI). This study aims to explore the lipid metabolism-related gene (LMRG) expression patterns in MI/RI and to find potential therapeutic agents. Methods Differential expression analysis was performed to screen the differentially expressed genes (DEGs) and LMRGs in the MI/RI-related dataset GSE61592. Enrichment and protein-protein interaction (PPI) analyses were performed to identify the key signaling pathways and genes. The expression trends of key LMRGs were validated by external datasets GSE160516 and GSE4105. The corresponding online databases predicted miRNAs, transcription factors (TFs), and potential therapeutic agents targeting key LMRGs. Finally, the identified LMRGs were confirmed in the H9C2 cell hypoxia-reoxygenation (H/R) model and the mouse MI/RI model. Results Enrichment analysis suggested that the "lipid metabolic process" was one of the critical pathways in MI/RI. Further differential expression analysis and PPI analysis identified 120 differentially expressed LMRGs and 15 key LMRGs. 126 miRNAs, 55 TFs, and 51 therapeutic agents were identified targeting these key LMRGs. Lastly, the expression trends of Acadm, Acadvl, and Suclg1 were confirmed by the external datasets, the H/R model and the MI/RI model. Conclusion Acadm, Acadvl, and Suclg1 may be the key genes involved in the MI/RI-related lipid metabolism dysregulation; and acting upon these factors may serve as a potential therapeutic strategy.
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Affiliation(s)
- Jiahe Wu
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Institute of Myocardial Injury and Repair, Wuhan University, Wuhan, China
| | - Huanhuan Cai
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Institute of Myocardial Injury and Repair, Wuhan University, Wuhan, China
| | - Xiaorong Hu
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Institute of Myocardial Injury and Repair, Wuhan University, Wuhan, China
| | - Wei Wu
- Department of Clinical Laboratory, Institute of Translational Medicine, Renmin Hospital of Wuhan University, Wuhan, China
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Wilczyński J, Paradowska E, Wilczyński M. Personalization of Therapy in High-Grade Serous Tubo-Ovarian Cancer-The Possibility or the Necessity? J Pers Med 2023; 14:49. [PMID: 38248751 PMCID: PMC10817599 DOI: 10.3390/jpm14010049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/17/2023] [Accepted: 12/25/2023] [Indexed: 01/23/2024] Open
Abstract
High-grade serous tubo-ovarian cancer (HGSTOC) is the most lethal tumor of the female genital tract. The foregoing therapy consists of cytoreduction followed by standard platinum/taxane chemotherapy; alternatively, for primary unresectable tumors, neo-adjuvant platinum/taxane chemotherapy followed by delayed interval cytoreduction. In patients with suboptimal surgery or advanced disease, different forms of targeted therapy have been accepted or tested in clinical trials. Studies on HGSTOC discovered its genetic and proteomic heterogeneity, epigenetic regulation, and the role of the tumor microenvironment. These findings turned attention to the fact that there are several distinct primary tumor subtypes of HGSTOC and the unique biology of primary, metastatic, and recurrent tumors may result in a differential drug response. This results in both chemo-refractoriness of some primary tumors and, what is significantly more frequent and destructive, secondary chemo-resistance of metastatic and recurrent HGSTOC tumors. Treatment possibilities for platinum-resistant disease include several chemotherapeutics with moderate activity and different targeted drugs with difficult tolerable effects. Therefore, the question appears as to why different subtypes of ovarian cancer are predominantly treated based on the same therapeutic schemes and not in an individualized way, adjusted to the biology of a specific tumor subtype and temporal moment of the disease. The paper reviews the genomic, mutational, and epigenetic signatures of HGSTOC subtypes and the tumor microenvironment. The clinical trials on personalized therapy and the overall results of a new, comprehensive approach to personalized therapy for ovarian cancer have been presented and discussed.
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Affiliation(s)
- Jacek Wilczyński
- Department of Gynecological Surgery and Gynecological Oncology, Medical University of Lodz, 4 Kosciuszki Street, 90-419 Lodz, Poland
| | - Edyta Paradowska
- Laboratory of Virology, Institute of Medical Biology of the Polish Academy of Sciences, 106 Lodowa Street, 93-232 Lodz, Poland;
| | - Miłosz Wilczyński
- Department of Gynecological, Endoscopic and Oncological Surgery, Polish Mother’s Health Center—Research Institute, 281/289 Rzgowska Street, 93-338 Lodz, Poland;
- Department of Surgical and Endoscopic Gynecology, Medical University of Lodz, 4 Kosciuszki Street, 90-419 Lodz, Poland
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Xu Q, Yao M, Tang C. RGS2 and female common diseases: a guard of women's health. J Transl Med 2023; 21:583. [PMID: 37649067 PMCID: PMC10469436 DOI: 10.1186/s12967-023-04462-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023] Open
Abstract
Currently, women around the world are still suffering from various female common diseases with the high incidence, such as ovarian cancer, uterine fibroids and preeclampsia (PE), and some diseases are even with the high mortality rate. As a negative feedback regulator in G Protein-Coupled Receptor signaling (GPCR), the Regulator of G-protein Signaling (RGS) protein family participates in regulating kinds of cell biological functions by destabilizing the enzyme-substrate complex through the transformation of hydrolysis of G Guanosine Triphosphate (GTP). Recent work has indicated that, the Regulator of G-protein Signaling 2 (RGS2), a member belonging to the RGS protein family, is closely associated with the occurrence and development of certain female diseases, providing with the evidence that RGS2 functions in sustaining women's health. In this review paper, we summarize the current knowledge of RGS2 in female common diseases, and also tap and discuss its therapeutic potential by targeting multiple mechanisms.
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Affiliation(s)
- Qiang Xu
- National Clinical Research Center for Child Health of the Children's Hospital, Zhejiang University School of Medicine, No. 3333, Binsheng Rd, Hangzhou, 310052, People's Republic of China
| | - Mukun Yao
- Department of Gynecology, Tongde Hospital of Zhejiang Province, Hangzhou, 310012, China
| | - Chao Tang
- National Clinical Research Center for Child Health of the Children's Hospital, Zhejiang University School of Medicine, No. 3333, Binsheng Rd, Hangzhou, 310052, People's Republic of China.
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Tang Z, Feng H, Shu L, Guo M, Qi B, Pu L, Shi H, Ren J, Li C. Identification of two novel lipid metabolism-related long non-coding RNAs (SNHG17 and LINC00837) as potential signatures for osteosarcoma prognosis and precise treatment. BMC Med Genomics 2023; 16:115. [PMID: 37231440 DOI: 10.1186/s12920-023-01553-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023] Open
Abstract
OBJECTIVE Dysregulated lipid metabolism enhances the development and advancement of many cancers, including osteosarcoma (OS); however, the underlying mechanisms are still largely unknown. Therefore, this investigation aimed to elucidate novel potential lipid metabolism-related long non-coding RNAs (lncRNAs) that regulate OS development and provide novel signatures for its prognosis and precise treatment. MATERIALS AND METHODS The GEO datasets (GSE12865 and GSE16091) were downloaded and analyzed using R software packages. Immunohistochemistry (IHC) was used to evaluate protein levels in OS tissues while real-time qPCR was used to measure lncRNA levels, and MTT assays were used to assess OS cell viability. RESULTS Two lipid metabolism-associated lncRNAs (LM-lncRNAs), small nucleolar RNA host gene 17 (SNHG17) and LINC00837, were identified as efficient and independent prognostic indicators for OS. In addition, further experiments confirmed that SNHG17 and LINC00837 were significantly elevated in OS tissues and cells than para-cancerous counterparts. Knockdown of SNHG17 and LINC00837 synergistically suppressed the viability of OS cells, whereas overexpression of the two lncRNAs promoted OS cell proliferation. Moreover, bioinformatics analysis was conducted to construct six novel SNHG17-microRNA-mRNA competing endogenous RNA (ceRNA) networks, and three lipid metabolism-associated genes (MIF, VDAC2, and CSNK2A2) were found to be abnormally upregulated in OS tissues, suggesting that they were potential effector genes of SNHG17. CONCLUSION In summary, SNHG17 and LINC00837 were found to promote OS cell malignancy, suggesting their use as ideal biomarkers for OS prognosis and treatment.
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Affiliation(s)
- Zhifang Tang
- Clinical Medical College of Dali University, Dali, Yunnan, 671000, China
| | - Hanzhen Feng
- Clinical Medical College of Dali University, Dali, Yunnan, 671000, China
| | - Longjun Shu
- Department of Orthopedics, The First People's Hospital of Dali City, Yunnan, 671000, Dali, China
| | - Minzheng Guo
- Department of Orthopedics, Kunming Medical University, Kunming, Yunnan, China
| | - Baochuang Qi
- Department of Orthopedics, Kunming Medical University, Kunming, Yunnan, China
| | - Luqiao Pu
- Department of Orthopedics, The 920th Hospital of Joint Logistics Support Force of Chinese People's Liberation Army, Kunming, Yunnan, China
| | - Hongxin Shi
- Clinical Medical College of Dali University, Dali, Yunnan, 671000, China
| | - Junxiao Ren
- Department of Orthopedics, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Chuan Li
- Department of Orthopedics, The 920th Hospital of Joint Logistics Support Force of Chinese People's Liberation Army, Kunming, Yunnan, China.
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Pirrotta S, Masatti L, Corrà A, Pedrini F, Esposito G, Martini P, Risso D, Romualdi C, Calura E. signifinder enables the identification of tumor cell states and cancer expression signatures in bulk, single-cell and spatial transcriptomic data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.530940. [PMID: 36945491 PMCID: PMC10028855 DOI: 10.1101/2023.03.07.530940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Over the last decade, many studies and some clinical trials have proposed gene expression signatures as a valuable tool for understanding cancer mechanisms, defining subtypes, monitoring patient prognosis, and therapy efficacy. However, technical and biological concerns about reproducibility have been raised. Technical reproducibility is a major concern: we currently lack a computational implementation of the proposed signatures, which would provide detailed signature definition and assure reproducibility, dissemination, and usability of the classifier. Another concern regards intratumor heterogeneity, which has never been addressed when studying these types of biomarkers using bulk transcriptomics. With the aim of providing a tool able to improve the reproducibility and usability of gene expression signatures, we propose signifinder, an R package that provides the infrastructure to collect, implement, and compare expression-based signatures from cancer literature. The included signatures cover a wide range of biological processes from metabolism and programmed cell death, to morphological changes, such as quantification of epithelial or mesenchymal-like status. Collected signatures can score tumor cell characteristics, such as the predicted response to therapy or the survival association, and can quantify microenvironmental information, including hypoxia and immune response activity. signifinder has been used to characterize tumor samples and to investigate intra-tumor heterogeneity, extending its application to single-cell and spatial transcriptomic data. Through these higher-resolution technologies, it has become increasingly apparent that the single-sample score assessment obtained by transcriptional signatures is conditioned by the phenotypic and genetic intratumor heterogeneity of tumor masses. Since the characteristics of the most abundant cell type or clone might not necessarily predict the properties of mixed populations, signature prediction efficacy is lowered, thus impeding effective clinical diagnostics. Through signifinder, we offer general principles for interpreting and comparing transcriptional signatures, as well as suggestions for additional signatures that would allow for more complete and robust data inferences. We consider signifinder a useful tool to pave the way for reproducibility and comparison of transcriptional signatures in oncology.
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Affiliation(s)
| | - Laura Masatti
- Department of Biology, University of Padua, Padua, Italy
| | - Anna Corrà
- Department of Biology, University of Padua, Padua, Italy
| | | | - Giovanni Esposito
- Immunology and Molecular Oncology Diagnostic Unit of The Veneto Institute of Oncology IOV – IRCCS, Padua, Italy
| | - Paolo Martini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Davide Risso
- Department of Statistical Sciences, University of Padua, Italy
| | | | - Enrica Calura
- Department of Biology, University of Padua, Padua, Italy
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10
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Mou L, Pu Z, Luo Y, Quan R, So Y, Jiang H. Construction of a lipid metabolism-related risk model for hepatocellular carcinoma by single cell and machine learning analysis. Front Immunol 2023; 14:1036562. [PMID: 36936948 PMCID: PMC10014552 DOI: 10.3389/fimmu.2023.1036562] [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: 09/04/2022] [Accepted: 02/15/2023] [Indexed: 03/05/2023] Open
Abstract
One of the most common cancers is hepatocellular carcinoma (HCC). Numerous studies have shown the relationship between abnormal lipid metabolism-related genes (LMRGs) and malignancies. In most studies, the single LMRG was studied and has limited clinical application value. This study aims to develop a novel LMRG prognostic model for HCC patients and to study its utility for predictive, preventive, and personalized medicine. We used the single-cell RNA sequencing (scRNA-seq) dataset and TCGA dataset of HCC samples and discovered differentially expressed LMRGs between primary and metastatic HCC patients. By using the least absolute selection and shrinkage operator (LASSO) regression machine learning algorithm, we constructed a risk prognosis model with six LMRGs (AKR1C1, CYP27A1, CYP2C9, GLB1, HMGCS2, and PLPP1). The risk prognosis model was further validated in an external cohort of ICGC. We also constructed a nomogram that could accurately predict overall survival in HCC patients based on cancer status and LMRGs. Further investigation of the association between the LMRG model and somatic tumor mutational burden (TMB), tumor immune infiltration, and biological function was performed. We found that the most frequent somatic mutations in the LMRG high-risk group were CTNNB1, TTN, TP53, ALB, MUC16, and PCLO. Moreover, naïve CD8+ T cells, common myeloid progenitors, endothelial cells, granulocyte-monocyte progenitors, hematopoietic stem cells, M2 macrophages, and plasmacytoid dendritic cells were significantly correlated with the LMRG high-risk group. Finally, gene set enrichment analysis showed that RNA degradation, spliceosome, and lysosome pathways were associated with the LMRG high-risk group. For the first time, we used scRNA-seq and bulk RNA-seq to construct an LMRG-related risk score model, which may provide insights into more effective treatment strategies for predictive, preventive, and personalized medicine of HCC patients.
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Affiliation(s)
- Lisha Mou
- Imaging Department, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
- MetaLife Center, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Zuhui Pu
- Imaging Department, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Yongxiang Luo
- Department of General Surgery, The First People's Hospital of Qinzhou/The Tenth Affiliated Hospital of Guangxi Medical University, Qinzhou, Guangxi, China
| | - Ryan Quan
- MetaLife Center, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Yunhu So
- MetaLife Center, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Hui Jiang
- Department of General Surgery, The First People's Hospital of Qinzhou/The Tenth Affiliated Hospital of Guangxi Medical University, Qinzhou, Guangxi, China
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Identification of an Individualized Prognostic Biomarker for Serous Ovarian Cancer: A Qualitative Model. Diagnostics (Basel) 2022; 12:diagnostics12123128. [PMID: 36553135 PMCID: PMC9777083 DOI: 10.3390/diagnostics12123128] [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: 11/03/2022] [Revised: 12/03/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Serous ovarian cancer is the most common type of ovarian epithelial cancer and usually has a poor prognosis. The objective of this study was to construct an individualized prognostic model for predicting overall survival in serous ovarian cancer. Based on the relative expression orderings (Ea > Eb/Ea ≤ Eb) of gene pairs closely associated with serous ovarian prognosis, we tried constructing a potential individualized qualitative biomarker by the greedy algorithm and evaluated the performance in independent validation datasets. We constructed a prognostic biomarker consisting of 20 gene pairs (SOV-P20). The overall survival between high- and low-risk groups stratified by SOV-P20 was statistically significantly different in the training and independent validation datasets from other platforms (p < 0.05, Wilcoxon test). The average area under the curve (AUC) values of the training and three validation datasets were 0.756, 0.590, 0.630, and 0.680, respectively. The distribution of most immune cells between high- and low-risk groups was quite different (p < 0.001, Wilcoxon test). The low-risk patients tended to show significantly better tumor response to chemotherapy than the high-risk patients (p < 0.05, Fisher’s exact test). SOV-P20 achieved the highest mean index of concordance (C-index) (0.624) compared with the other seven existing prognostic signatures (ranging from 0.511 to 0.619). SOV-P20 is a promising prognostic biomarker for serous ovarian cancer, which will be applicable for clinical predictive risk assessment.
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12
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Lutgendorf SK, Thaker PH, Goodheart MJ, Arevalo JM, Chowdhury MA, Noble AE, Dahmoush L, Slavich GM, Penedo FJ, Sood AK, Cole SW. Biobehavioral factors predict an exosome biomarker of ovarian carcinoma disease progression. Cancer 2022; 128:4157-4165. [PMID: 36251340 PMCID: PMC9744596 DOI: 10.1002/cncr.34496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 01/12/2023]
Abstract
BACKGROUND Biobehavioral factors such as social isolation and depression have been associated with disease progression in ovarian and other cancers. Here, the authors developed a noninvasive, exosomal RNA profile for predicting ovarian cancer disease progression and subsequently tested whether it increased in association with biobehavioral risk factors. METHODS Exosomes were isolated from plasma samples from 100 women taken before primary surgical resection or neoadjuvant (NACT) treatment of ovarian carcinoma and 6 and 12 months later. Biobehavioral measures were sampled at all time points. Plasma from 76 patients was allocated to discovery analyses in which morning presurgical/NACT exosomal RNA profiles were analyzed by elastic net machine learning to identify a biomarker predicting rapid (≤6 months) versus more extended disease-free intervals following initial treatment. Samples from a second subgroup of 24 patients were analyzed by mixed-effects linear models to determine whether the progression-predictive biomarker varied longitudinally as a function of biobehavioral risk factors (social isolation and depressive symptoms). RESULTS An RNA-based molecular signature was identified that discriminated between individuals who had disease progression in ≤6 months versus >6 months, independent of clinical variables (age, disease stage, and grade). In a second group of patients analyzed longitudinally, social isolation and depressive symptoms were associated with upregulated expression of the disease progression propensity biomarker, adjusting for covariates. CONCLUSION These data identified a novel exosome-derived biomarker indicating propensity of ovarian cancer progression that is sensitive to biobehavioral variables. This derived biomarker may be potentially useful for risk assessment, intervention targeting, and treatment monitoring.
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Affiliation(s)
- Susan K. Lutgendorf
- Department of Psychological & Brain Sciences, University of Iowa, Iowa City, IA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Iowa, Iowa City, IA
| | - Premal H. Thaker
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO
| | - Michael J. Goodheart
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Iowa, Iowa City, IA
| | - Jesusa M.G. Arevalo
- Division of Hematology/Oncology, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Mamur A. Chowdhury
- Departments of Gynecologic Oncology, Cancer Biology and Center for RNA Interference and Noncoding RNA, University of Texas M.D. Anderson Cancer Center, Houston TX
| | - Alyssa E. Noble
- Department of Psychological & Brain Sciences, University of Iowa, Iowa City, IA
| | - Laila Dahmoush
- Department of Pathology, University of Iowa, Iowa City, IA
| | - George M. Slavich
- Cousins Center for Psychoneuroimmunology, University of California, Los Angeles, CA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA
| | - Frank J. Penedo
- Department of Psychology and Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Anil K. Sood
- Departments of Gynecologic Oncology, Cancer Biology and Center for RNA Interference and Noncoding RNA, University of Texas M.D. Anderson Cancer Center, Houston TX
| | - Steven W. Cole
- Division of Hematology/Oncology, David Geffen School of Medicine, University of California, Los Angeles, CA
- Cousins Center for Psychoneuroimmunology, University of California, Los Angeles, CA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA
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GDPD5 Related to Lipid Metabolism Is a Potential Prognostic Biomarker in Neuroblastoma. Int J Mol Sci 2022; 23:ijms232213740. [PMID: 36430219 PMCID: PMC9695425 DOI: 10.3390/ijms232213740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022] Open
Abstract
Neuroblastoma (NB) is an extracranial solid tumor in children with poor prognosis in high-risk patients and its pathogenesis and prognostic markers urgently need to be explored. This study aimed to explore potential biomarkers related to NB from the aspect of lipid metabolism. Fifty-eight lipid metabolism-related differentially expressed genes between high-risk NB and non-high-risk NB in the GSE49710 dataset were analyzed using bioinformatics, including 45 down-regulated genes and 13 up-regulated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified steroid hormone biosynthesis as an abnormal metabolic pathway in high-risk NB. Survival analysis established a three-gene prognostic model, including ACHE, GDPD5 and PIK3R1. In the test data, the AUCs of the established prognostic models used to predict patient survival at 1, 3 and 5 years were 0.84, 0.90 and 0.91, respectively. Finally, in the SH-SY5Y cell line, it was verified that overexpression of GDPD5 can inhibit cell proliferation and migration, as well as affect the lipid metabolism of SH-SY5Y, but not the sugar metabolism. hsa-miR-592 was predicted to be a potential target miRNA of GDPD5 by bioinformatics. In conclusion, this study develops a lipid-metabolism-related gene-based prognostic model for NB and demonstrates that GDPD5 inhibits SH-SY5Y proliferation and migration and may be targeted by hsa-miR-592 and inhibit SH-SY5Y fat synthesis.
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Shao F, Mao H, Luo T, Li Q, Xu L, Xie Y. HPGDS is a novel prognostic marker associated with lipid metabolism and aggressiveness in lung adenocarcinoma. Front Oncol 2022; 12:894485. [PMID: 36324576 PMCID: PMC9618883 DOI: 10.3389/fonc.2022.894485] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 10/03/2022] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is the most common respiratory globallywith a poor prognosis. Lipid metabolism is extremely important for the occurrence and development of cancer. However, the role of genes involved in lipid metabolism in LUAD development is unclear. We aimed to identify the abnormal lipid metabolism pathway of LUAD, construct a novel prognostic model of LUAD, and discover novel biomarkers involved in lipid metabolism in LUAD. METHODS Based on differentially expressed genes involved in lipid metabolism in LUAD samples from The Cancer Genome Atlas (TCGA), abnormal lipid metabolism pathways in LUAD were analyzed. The lasso penalized regression analysis was performed on the TCGA cohort (training set) to construct a risk score formula. The predictive ability of the risk score was validated in the Gene Expression Omnibus (GEO) dataset (validation set) using Kaplan-Meier analysis and ROC curves. Finally, based on CRISPR gene editing technology, hematopoietic prostaglandin D synthase (HPGDS) was knocked out in A549 cell lines, the changes in lipid metabolism-related markers were detected by western blotting, and the changes in cell migration were detected by transwell assay. RESULTS Based on the differential genes between lung cancer tissue and normal tissue, we found that the arachidonic acid metabolism pathway is an abnormal lipid metabolism pathway in both lung adenocarcinoma and lung squamous cell carcinoma. Based on the sample information of TCGA and abnormally expressed lipid metabolism-related genes, a 9-gene prognostic risk score was successfully constructed and validated in the GEO dataset. Finally, we found that knockdown of HPGDS in A549 cell lines promoted lipid synthesis and is more invasive than in control cells. Rescue assays showed that ACSL1 knockdown reversed the pro-migration effects of HPGDS knockdown. The knockdown of HPGDS promoted migration response by upregulating the expression of the lipid metabolism key enzymes ACSL1 and ACC. CONCLUSION The genes involved in lipid metabolism are associated with the occurrence and development of LUAD. HPGDS can be a therapeutic target of a potential lipid metabolism pathway in LUAD, and the therapeutic target of lipid metabolism genes in LUAD should be studied further.
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Affiliation(s)
- Fengling Shao
- The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Huajie Mao
- Department of Laboratory Medicine, The First Hospital of Xi’an, Xi’an, China
| | - Tengling Luo
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China
| | - Qijun Li
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China
| | - Lei Xu
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China
| | - Yajun Xie
- The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, China
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15
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Wu H, Xu H, Huang S, Tang Y, Tang J, Zhou H, Xie L, Qiao G. m 6A-binding protein IGF2BP1 promotes the malignant phenotypes of lung adenocarcinoma. Front Oncol 2022; 12:989817. [PMID: 36249006 PMCID: PMC9554348 DOI: 10.3389/fonc.2022.989817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/06/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD), the most common type of lung cancer, poses a significant threat to the life of patients. N6-methyladenosine modification is the most abundant epigenetic modification and may play an important role in the lung carcinogenesis. IGF2BP1 is a newly discovered m6A-binding protein, but little is known about its role in LUAD. METHODS Data from TCGA, GEO, Kaplan-Meier Plotter, and GEPIA databases were systematically analyzed to access the expression and prognostic value of IGF2BP1 on LUAD. Real-time polymerase chain reaction, Western blot, and immunohistochemistry were performed to detect the mRNA and protein level of IGF2BP1 in LUAD tissues and para-carcinoma tissues. Functional cell experiments, including Cell Counting Kit-8 assay, Transwell invasion assay, wound healing assay, Annexin V-FITC/PI double-staining assay, and TUNEL assay, were used to investigate the functions of IGF2BP1 on LUAD cell proliferation, invasion, migration, and apoptosis, respectively. The top 50 genes that were positively or negatively related to the expression of IGF2BP1 were identified, and pathway enrichment analysis was performed. m6A modification sites within IGF2BP1-related genes were predicted by SRAMP. RESULT 16 m6A regulators were significantly differentially expressed in LUAD tissues. IGF2BP1 was upregulated in LUAD tissues compared with para-carcinoma tissues. High expression of IGF2PB1 was significantly associated with higher clinical stages and poor prognosis of LUAD patients. Furthermore, our functional experiments indicated that IGF2BP1 facilitated cell proliferation, invasion, and migration and suppressed apoptosis in LUAD. Functional enrichment analysis of IGF2BP1-related genes indicated enrichment in several pathways related to oncogenesis. Additionally, m6A modification sites were detected within IGF2BP1-related genes. CONCLUSIONS Our findings demonstrate that IGF2BP1 plays a contributory role in the development and progression of LUAD. IGF2BP1 has the potential to become a prognostic predictor and therapeutic target for LUAD.
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Affiliation(s)
- Hansheng Wu
- Department of Thoracic Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Haijie Xu
- Department of Thoracic Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Shantou University Medical College, Shantou, China
| | - Shujie Huang
- Shantou University Medical College, Shantou, China
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yong Tang
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jiming Tang
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Haiyu Zhou
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Liang Xie
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Guibin Qiao
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
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Integration of Transcriptome and Epigenome to Identify and Develop Prognostic Markers for Ovarian Cancer. JOURNAL OF ONCOLOGY 2022; 2022:3744466. [PMID: 36081667 PMCID: PMC9448543 DOI: 10.1155/2022/3744466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/04/2022] [Accepted: 06/29/2022] [Indexed: 11/21/2022]
Abstract
DNA methylation is a widely researched epigenetic modification. It is associated with the occurrence and development of cancer and has helped evaluate patients' prognoses. However, most existing DNA methylation prognosis models have not simultaneously considered the changes of the downstream transcriptome. Methods. The RNA-Sequencing data and DNA methylation omics data of ovarian cancer patients were downloaded from The Cancer Genome Atlas (TCGA) database. The Consensus Cluster Plus algorithm was used to construct the methylated molecular subtypes of the ovary. Lasso regression was employed to build a multi-gene signature. An independent data set was applied to verify the prognostic value of the signature. The Gene Set Variation Analysis (GSVA) was used to carry out the enrichment analysis of the pathways linked to the gene signature. The IMvigor 210 cohort was used to explore the predictive efficacy of the gene signature for immunotherapy response. Results. We distinguished ovarian cancer samples into two subtypes with different prognosis, based on the omics data of DNA methylation. Differentially expressed genes and enrichment analysis among subtypes indicated that DNA methylation was related to fatty acid metabolism and the extracellular matrix (ECM)-receptor. Furthermore, we constructed an 8-gene signature, which proved to be efficient and stable in predicting prognostics in ovarian cancer patients with different data sets and distinctive pathological characteristics. Finally, the 8-gene signature could predict patients' responses to immunotherapy. The polymerase chain reaction experiment was further used to verify the expression of 8 genes. Conclusion. We analyzed the prognostic value of the related genes of methylation in ovarian cancer. The 8-gene signature predicted the prognosis and immunotherapy response of ovarian cancer patients well and is expected to be valuable in clinical application.
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Zhu Y, Lin X, Zhou X, Prochownik EV, Wang F, Li Y. Posttranslational control of lipogenesis in the tumor microenvironment. J Hematol Oncol 2022; 15:120. [PMID: 36038892 PMCID: PMC9422141 DOI: 10.1186/s13045-022-01340-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/11/2022] [Indexed: 11/30/2022] Open
Abstract
Metabolic reprogramming of cancer cells within the tumor microenvironment typically occurs in response to increased nutritional, translation and proliferative demands. Altered lipid metabolism is a marker of tumor progression that is frequently observed in aggressive tumors with poor prognosis. Underlying these abnormal metabolic behaviors are posttranslational modifications (PTMs) of lipid metabolism-related enzymes and other factors that can impact their activity and/or subcellular localization. This review focuses on the roles of these PTMs and specifically on how they permit the re-wiring of cancer lipid metabolism, particularly within the context of the tumor microenvironment.
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Affiliation(s)
- Yahui Zhu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China.,Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China.,School of Medicine, Chongqing University, Chongqing, 400030, China
| | - Xingrong Lin
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China.,Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China
| | - Xiaojun Zhou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China.,Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China
| | - Edward V Prochownik
- Division of Hematology/Oncology, Children's Hospital of Pittsburgh of UPMC, The Department of Microbiology and Molecular Genetics, The Pittsburgh Liver Research Center and The Hillman Cancer Center of UPMC, The University of Pittsburgh Medical Center, Pittsburgh, PA, 15224, USA
| | - Fubing Wang
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430072, China.
| | - Youjun Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China. .,Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China.
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Identification of an Amino Acid Metabolism Signature Participating in Immunosuppression in Ovarian Cancer. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:4525540. [PMID: 35783506 PMCID: PMC9242802 DOI: 10.1155/2022/4525540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/28/2022] [Indexed: 12/24/2022]
Abstract
Ovarian cancer is one of the most fatal gynecologic cancer types, and its heterogeneity in the microenvironment limited the efficacy of the current treatment. In this study, we aimed at building a risk score to predict patient survival based on the amino acid metabolic genes and TCGA RNA-seq dataset (n = 376). We first used univariate analysis and PCA to select and test the survival-related genes, and the LASSO regression was applied to build the risk score signature with prediction accuracy estimation by survival analysis and ROC. We then conducted GSEA and GSVA to investigate the biological roles of the signature and run ESTIMATE and 4 different immunocyte infiltration algorithms to investigate the immunological diversity between the risk groups. Furthermore, the immune checkpoint expression was compared. We finally explored the cMap and PRISM database to screen out sensitive drugs for high-risk patients and analyzed the oncogenic role of TPH1 by clone formation and transwell migration assays. As a result, the risk score predicted patients' survival and stage with high accuracy. We found that the signature mainly affected the extracellular activities and cancer immunity by functional enrichment. We further discovered that the high-risk OV harbored a high level of stromal cell infiltration and was associated with highly infiltrated fibroblasts and decreased CD8+ T cells. The immune checkpoint analyses showed that TGFB1 and CD276 were upregulated. Finally, we screened out 4 PRISM drugs with lower IC50 in the high-risk group and validated the oncogenic role of TPH1 in OV cancers. We believe this research offered a novel understanding of the interplay between amino acid metabolism and immunity in OV and will benefit patients with better prognostic management and therapeutic strategy development.
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Targeting lipid metabolism in the treatment of ovarian cancer. Oncotarget 2022; 13:768-783. [PMID: 35634242 PMCID: PMC9132258 DOI: 10.18632/oncotarget.28241] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 05/07/2022] [Indexed: 11/25/2022] Open
Abstract
Cancer cells undergo alterations in lipid metabolism to support their high energy needs, tumorigenesis and evade an anti-tumor immune response. Alterations in fatty acid production are controlled by multiple enzymes, chiefly Acetyl CoA Carboxylase, ATP-Citrate Lyase, Fatty Acid Synthase, and Stearoyl CoA Desaturase 1. Ovarian cancer (OC) is a common gynecological malignancy with a high rate of aggressive carcinoma progression and drug resistance. The accumulation of unsaturated fatty acids in ovarian cancer supports cell growth, increased cancer cell migration, and worse patient outcomes. Ovarian cancer cells also expand their lipid stores via increased uptake of lipids using fatty acid translocases, fatty acid-binding proteins, and low-density lipoprotein receptors. Furthermore, increased lipogenesis and lipid uptake promote chemotherapy resistance and dampen the adaptive immune response needed to eliminate tumors. In this review, we discuss the role of lipid synthesis and metabolism in driving tumorigenesis and drug resistance in ovarian cancer conferring poor prognosis and outcomes in patients. We also cover some aspects of how lipids fuel ovarian cancer stem cells, and how these metabolic alterations in intracellular lipid content could potentially serve as biomarkers of ovarian cancer.
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Xu M, Guo YY, Li D, Cen XF, Qiu HL, Ma YL, Huang SH, Tang QZ. Screening of Lipid Metabolism-Related Gene Diagnostic Signature for Patients With Dilated Cardiomyopathy. Front Cardiovasc Med 2022; 9:853468. [PMID: 35433888 PMCID: PMC9010535 DOI: 10.3389/fcvm.2022.853468] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/16/2022] [Indexed: 11/24/2022] Open
Abstract
Background Dilated cardiomyopathy (DCM) is characterized by enlarged ventricular dimensions and systolic dysfunction and poor prognosis. Myocardial lipid metabolism appears abnormal in DCM. However, the mechanism of lipid metabolism disorders in DCM remains unclear. Methods A gene set variation analysis (GSVA) were performed to estimate pathway activity related to DCM progression. Three datasets and clinical data downloaded from the Gene Expression Omnibus (GEO), including dilated cardiomyopathy and donor hearts, were integrated to obtain gene expression profiles and identify differentially expressed genes related to lipid metabolism. GO enrichment analyses of differentially expressed lipid metabolism-related genes (DELs) were performed. The clinical information used in this study were obtained from GSE21610 dataset. Data from the EGAS00001003263 were used for external validation and our hospital samples were also tested the expression levels of these genes through RT-PCR. Subsequently, logistic regression model with the LASSO method for DCM prediction was established basing on the 7 DELs. Results GSVA analysis showed that the fatty acid metabolism was closely related to DCM progression. The integrated dataset identified 19 DELs, including 8 up-regulated and 11 down-regulated genes. A total of 7 DELs were identified by further external validation of the data from the EGAS00001003263 and verified by RT-PCR. By using the LASSO model, 6 genes, including CYP2J2, FGF1, ETNPPL, PLIN2, LPCAT3, and DGKG, were identified to construct a logistic regression model. The area under curve (AUC) values over 0.8 suggested the good performance of the model. Conclusion Integrated bioinformatic analysis of gene expression in DCM and the effective logistic regression model construct in our study may contribute to the early diagnosis and prevention of DCM in people with high risk of the disease.
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Affiliation(s)
- Man Xu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, China
| | - Ying-ying Guo
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, China
| | - Dan Li
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, China
| | - Xian-feng Cen
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, China
| | - Hong-liang Qiu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, China
| | - Yu-lan Ma
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, China
| | - Si-hui Huang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, China
| | - Qi-zhu Tang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, China
- *Correspondence: Qi-zhu Tang,
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21
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CXCL9 inhibits tumour growth and drives anti-PD-L1 therapy in ovarian cancer. Br J Cancer 2022; 126:1470-1480. [PMID: 35314795 PMCID: PMC9090786 DOI: 10.1038/s41416-022-01763-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/09/2022] [Accepted: 02/15/2022] [Indexed: 12/19/2022] Open
Abstract
Background Response to immune checkpoint blockade (ICB) in ovarian cancer remains disappointing. Several studies have identified the chemokine CXCL9 as a robust prognosticator of improved survival in ovarian cancer and a characteristic of the immunoreactive subtype, which predicts ICB response. However, the function of CXCL9 in ovarian cancer has been poorly studied. Methods Impact of Cxcl9 overexpression in the murine ID8-Trp53−/− and ID8-Trp53−/–Brca2−/− ovarian cancer models on survival, cellular immune composition, PD-L1 expression and anti-PD-L1 therapy. CXCL9 expression analysis in ovarian cancer subtypes and correlation to reported ICB response. Results CXCL9 overexpression resulted in T-cell accumulation, delayed ascites formation and improved survival, which was dependent on adaptive immune function. In the ICB-resistant mouse model, the chemokine was sufficient to enable a successful anti-PD-L1 therapy. In contrast, these effects were abrogated in Brca2-deficient tumours, most likely due to an already high intrinsic chemokine expression. Finally, in ovarian cancer patients, the clear-cell subtype, known to respond best to ICB, displayed a significantly higher proportion of CXCL9high tumours than the other subtypes. Conclusions CXCL9 is a driver of successful ICB in preclinical ovarian cancer. Besides being a feasible predictive biomarker, CXCL9-inducing agents thus represent attractive combination partners to improve ICB in this cancer entity.
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22
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Belotti Y, Lim EH, Lim CT. The Role of the Extracellular Matrix and Tumor-Infiltrating Immune Cells in the Prognostication of High-Grade Serous Ovarian Cancer. Cancers (Basel) 2022; 14:404. [PMID: 35053566 PMCID: PMC8773831 DOI: 10.3390/cancers14020404] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/05/2022] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
Ovarian cancer is the eighth global leading cause of cancer-related death among women. The most common form is the high-grade serous ovarian carcinoma (HGSOC). No further improvements in the 5-year overall survival have been seen over the last 40 years since the adoption of platinum- and taxane-based chemotherapy. Hence, a better understanding of the mechanisms governing this aggressive phenotype would help identify better therapeutic strategies. Recent research linked onset, progression, and response to treatment with dysregulated components of the tumor microenvironment (TME) in many types of cancer. In this study, using bioinformatic approaches, we identified a 19-gene TME-related HGSOC prognostic genetic panel (19 prognostic genes (PLXNB2, HMCN2, NDNF, NTN1, TGFBI, CHAD, CLEC5A, PLXNA1, CST9, LOXL4, MMP17, PI3, PRSS1, SERPINA10, TLL1, CBLN2, IL26, NRG4, and WNT9A) by assessing the RNA sequencing data of 342 tumors available in the TCGA database. Using machine learning, we found that specific patterns of infiltrating immune cells characterized each risk group. Furthermore, we demonstrated the predictive potential of our risk score across different platforms and its improved prognostic performance compared with other gene panels.
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Affiliation(s)
- Yuri Belotti
- Institute for Health Innovation and Technology, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore;
| | - Elaine Hsuen Lim
- Division of Medical Oncology, National Cancer Center Singapore, 11 Hospital Drive, Singapore 169610, Singapore;
| | - Chwee Teck Lim
- Institute for Health Innovation and Technology, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore;
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore
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23
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Nomogram for predicting postoperative cancer-specific early death in patients with epithelial ovarian cancer based on the SEER database: a large cohort study. Arch Gynecol Obstet 2021; 305:1535-1549. [PMID: 34841445 PMCID: PMC9166879 DOI: 10.1007/s00404-021-06342-x] [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: 06/18/2021] [Accepted: 11/18/2021] [Indexed: 11/12/2022]
Abstract
Purpose Ovarian cancer is a common gynecological malignant tumor. Poor prognosis is strongly associated with early death, but there is no effective tool to predict this. This study aimed to construct a nomogram for predicting cancer-specific early death in patients with ovarian cancer.
Methods We used data from the Surveillance, Epidemiology, and End Results database of patients with ovarian cancer registered from 1988 to 2016. Important independent prognostic factors were determined by univariate and multivariate logistic regression and LASSO Cox regression. Several risk factors were considered in constructing the nomogram. Nomogram discrimination and calibration were evaluated using C-index, internal validation, and receiver operating characteristic (ROC) curves. Results A total of 4769 patients were included. Patients were assigned to the training set (n = 3340; 70%) and validation set (n = 1429; 30%). Based on the training set, eight variables were shown to be significant factors for early death and were incorporated in the nomogram: American Joint Committee on Cancer (AJCC) stage, residual lesion size, chemotherapy, serum CA125 level, tumor size, number of lymph nodes examined, surgery of primary site, and age. The concordance indices and ROC curves showed that the nomogram had better predictive ability than the AJCC staging system and good clinical practicability. Internal validation based on validation set showed good consistency between predicted and observed values for early death. Conclusion Compared with predictions made based on AJCC stage or residual lesion size, the nomogram could provide more robust predictions for early death in patients with ovarian cancer.
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24
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Liang ZQ, Gao L, Chen JH, Dai WB, Su YS, Chen G. Downregulation of the Coiled-Coil Domain Containing 80 and Its Perspective Mechanisms in Ovarian Carcinoma: A Comprehensive Study. Int J Genomics 2021; 2021:3752871. [PMID: 34820451 PMCID: PMC8608537 DOI: 10.1155/2021/3752871] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 09/21/2021] [Accepted: 10/23/2021] [Indexed: 12/24/2022] Open
Abstract
INTRODUCTION We aimed to explore the downregulation of the coiled-coil domain containing 80 (CCDC80) and its underlying molecular mechanisms in ovarian carcinoma (OVCA). Materials/Methods. Immunohistochemical staining was performed to confirm the expression status of CCDC80 protein. Combining the data from in-house tissue microarrays and high-throughput datasets, we identified the expression level of CCDC80 in OVCA. We utilized cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) algorithm and single-sample gene set enrichment analysis (ssGSEA) to explore the relationship between CCDC80 and the tumor microenvironment (TME) landscape in OVCA. Pathway enrichment, function annotation, and transcription factor (TFs) exploration were conducted to study the latent molecular mechanisms. Moreover, the cell line data in the Genomics of Drug Sensitivity in Cancer (GDSC) database was used to discover the relationship between CCDC80 and drug sensitivity. RESULTS An integrated standard mean difference (SMD) of -0.919 (95% CI: -1.515-0.324, P = 0.002) identified the downregulation of CCDC80 in OVCA based on 1048 samples, and the sROC (AUC = 0.76) showed a moderate discriminatory ability of CCDC80 in OVCA. The fraction of infiltrating naive B cells showed significant differences between the high- and low-CCDC80 expression groups. Also, CCDC80-related genes are enriched in the Ras signaling pathway and metabolic of lipid. Nuclear receptor subfamily three group C member 1 (NR3C1) may be an upstream TF of CCDC80, and CCDC80 may be related to the sensitivity of mitocycin C and nilotinib. CONCLUSION CCDC80 was downregulated in OVCA and may play a role as a tumor suppressor in OVCA.
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Affiliation(s)
- Zi-Qian Liang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No. 6. Shuangyong Rd, Nanning, Guangxi Zhuang Autonomous Region 530021, China
| | - Li Gao
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No. 6. Shuangyong Rd, Nanning, Guangxi Zhuang Autonomous Region 530021, China
| | - Jun-Hong Chen
- Department of Pathology, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, No. 59. Xiangzhu Rd, Nanning, Guangxi Zhuang Autonomous Region 530003, China
| | - Wen-Bin Dai
- Department of Pathology, Liuzhou People's Hospital, NO.8, Wenchang Road, Chengzhong District, Liuzhou, Guangxi Zhuang Autonomous Region 545006, China
| | - Ya-Si Su
- Department of Pathology, Liuzhou People's Hospital, NO.8, Wenchang Road, Chengzhong District, Liuzhou, Guangxi Zhuang Autonomous Region 545006, China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No. 6. Shuangyong Rd, Nanning, Guangxi Zhuang Autonomous Region 530021, China
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25
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Zhang D, Li Y, Yang S, Wang M, Yao J, Zheng Y, Deng Y, Li N, Wei B, Wu Y, Zhai Z, Dai Z, Kang H. Identification of a glycolysis-related gene signature for survival prediction of ovarian cancer patients. Cancer Med 2021; 10:8222-8237. [PMID: 34609082 PMCID: PMC8607265 DOI: 10.1002/cam4.4317] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 08/22/2021] [Accepted: 08/31/2021] [Indexed: 12/17/2022] Open
Abstract
Background Ovarian cancer (OV) is deemed the most lethal gynecological cancer in women. The aim of this study was to construct an effective gene prognostic model for predicting overall survival (OS) in patients with OV. Methods The expression profiles of glycolysis‐related genes (GRGs) and clinical data of patients with OV were extracted from The Cancer Genome Atlas (TCGA) database. Univariate, multivariate, and least absolute shrinkage and selection operator Cox regression analyses were conducted, and a prognostic signature based on GRGs was constructed. The predictive ability of the signature was analyzed using training and test sets. Results A gene risk signature based on nine GRGs (ISG20, CITED2, PYGB, IRS2, ANGPTL4, TGFBI, LHX9, PC, and DDIT4) was identified to predict the survival outcome of patients with OV. The signature showed a good prognostic ability for OV, particularly high‐grade OV, in the TCGA dataset, with areas under the curve (AUC) of 0.709 and 0.762 for 3‐ and 5‐year survival, respectively. Similar results were found in the test sets, and the AUCs of 3‐, 5‐year OS were 0.714 and 0.772 in the combined test set. And our signature was an independent prognostic factor. Moreover, a nomogram combining the prediction model and clinical factors was developed. Conclusion Our study established a nine‐GRG risk model and nomogram to better predict OS in patients with OV. The risk model represents a promising and independent prognostic predictor for patients with OV. Moreover, our study on GRGs could offer guidance for the elucidation of underlying mechanisms in future studies.
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Affiliation(s)
- Dai Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Department of Thyroid, Breast and Vascular Surgery, Xijing Hospital, The Air Force Medical University, Xi'an, China
| | - Yiche Li
- Department of Tumor Surgery, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Si Yang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Meng Wang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jia Yao
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yi Zheng
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yujiao Deng
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Na Li
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Bajin Wei
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ying Wu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Zhen Zhai
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhijun Dai
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Huafeng Kang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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26
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Identification of a Novel Tumor Microenvironment Prognostic Signature for Advanced-Stage Serous Ovarian Cancer. Cancers (Basel) 2021; 13:cancers13133343. [PMID: 34283076 PMCID: PMC8268985 DOI: 10.3390/cancers13133343] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/22/2021] [Accepted: 06/29/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary The expression of tumor microenvironment-related genes is known to be correlated with ovarian cancer patients’ prognosis. Immunotherapeutic targets are in part located in this complex cluster of cells and soluble factors. In our study, we constructed a prognostic 11-gene signature for advanced serous ovarian cancer from tumor microenvironment-related genes through lasso regression. The established risk score can quantify the prognosis of ovarian cancer patients more accurately and is able to predict the putative biological response of cancer samples to a programmed death ligand 1 blocking immunotherapy. This might empower the role of immunotherapy in ovarian cancer through its usage in future study protocols. Abstract (1) Background: The tumor microenvironment is involved in the growth and proliferation of malignant tumors and in the process of resistance towards systemic and targeted therapies. A correlation between the gene expression profile of the tumor microenvironment and the prognosis of ovarian cancer patients is already known. (2) Methods: Based on data from The Cancer Genome Atlas (379 RNA sequencing samples), we constructed a prognostic 11-gene signature (SNRPA1, CCL19, CXCL11, CDC5L, APCDD1, LPAR2, PI3, PLEKHF1, CCDC80, CPXM1 and CTAG2) for Fédération Internationale de Gynécologie et d’Obstétrique stage III and IV serous ovarian cancer through lasso regression. (3) Results: The established risk score was able to predict the 1-, 3- and 5-year prognoses more accurately than previously known models. (4) Conclusions: We were able to confirm the predictive power of this model when we applied it to cervical and urothelial cancer, supporting its pan-cancer usability. We found that immune checkpoint genes correlate negatively with a higher risk score. Based on this information, we used our risk score to predict the biological response of cancer samples to an anti-programmed death ligand 1 immunotherapy, which could be useful for future clinical studies on immunotherapy in ovarian cancer.
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Ye Z, Zou S, Niu Z, Xu Z, Hu Y. A Novel Risk Model Based on Lipid Metabolism-Associated Genes Predicts Prognosis and Indicates Immune Microenvironment in Breast Cancer. Front Cell Dev Biol 2021; 9:691676. [PMID: 34195202 PMCID: PMC8236894 DOI: 10.3389/fcell.2021.691676] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/07/2021] [Indexed: 02/05/2023] Open
Abstract
Background Breast cancer (BRCA) is the most common tumor in women, and lipid metabolism involvement has been demonstrated in its tumorigenesis and development. However, the role of lipid metabolism-associated genes (LMAGs) in the immune microenvironment and prognosis of BRCA remains unclear. Methods A total of 1076 patients with BRCA were extracted from The Cancer Genome Atlas database and randomly assigned to the training cohort (n = 760) or validation cohort (n = 316). Kaplan–Meier analysis was used to assess differences in survival. Consensus clustering was performed to categorize the patients with BRCA into subtypes. Using multivariate Cox regression analysis, an LMAG-based prognostic risk model was constructed from the training cohort and validated using the validation cohort. The immune microenvironment was evaluated using the ESTIMATE and tumor immune estimation resource algorithms, CIBERSORT, and single sample gene set enrichment analyses. Results Consensus clustering classified the patients with BRCA into two subgroups with significantly different overall survival rates and immune microenvironments. Better prognosis was associated with high immune infiltration. The prognostic risk model, based on four LMAGs (MED10, PLA2G2D, CYP4F11, and GPS2), successfully stratified the patients into high- and low-risk groups in both the training and validation sets. High risk scores predicted poor prognosis and indicated low immune status. Subgroup analysis suggested that the risk model was an independent predictor of prognosis in BRCA. Conclusion This study demonstrated, for the first time, that LMAG expression plays a crucial role in BRCA. The LMAG-based risk model successfully predicted the prognosis and indicated the immune microenvironment of patients with BRCA. Our study may provide inspiration for further research on BRCA pathomechanisms.
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Affiliation(s)
- Zhimin Ye
- Department of Pathology, School of Basic Medical Sciences, Central South University, Changsha, China.,Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Shengmei Zou
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhiyuan Niu
- Department of Pathology, School of Basic Medical Sciences, Central South University, Changsha, China.,Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Yongbin Hu
- Department of Pathology, School of Basic Medical Sciences, Central South University, Changsha, China.,Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
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28
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Qian H, Lei T, Hu Y, Lei P. Expression of Lipid-Metabolism Genes Is Correlated With Immune Microenvironment and Predicts Prognosis in Osteosarcoma. Front Cell Dev Biol 2021; 9:673827. [PMID: 33937273 PMCID: PMC8085431 DOI: 10.3389/fcell.2021.673827] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/30/2021] [Indexed: 12/29/2022] Open
Abstract
Objectives Osteosarcoma was the most popular primary malignant tumor in children and adolescent, and the 5-year survival of osteosarcoma patients gained no substantial improvement over the past 35 years. This study aims to explore the role of lipid metabolism in the development and diagnosis of osteosarcoma. Methods Clinical information and corresponding RNA data of osteosarcoma patients were downloaded from TRGET and GEO databases. Consensus clustering was performed to identify new molecular subgroups. ESTIMATE, TIMER and ssGSEA analyses were applied to determinate the tumor immune microenvironment (TIME) and immune status of the identified subgroups. Functional analyses including GO, KEGG, GSVA and GSEA analyses were conducted to elucidate the underlying mechanisms. Prognostic risk model was constructed using LASSO algorithm and multivariate Cox regression analysis. Results Two molecular subgroups with significantly different survival were identified. Better prognosis was associated with high immune score, low tumor purity, high abundance of immune infiltrating cells and relatively high immune status. GO and KEGG analyses revealed that the DEGs between the two subgroups were mainly enriched in immune- and bone remodeling-associated pathways. GSVA and GSEA analyses indicated that, lipid catabolism downregulation and lipid hydroxylation upregulation may impede the bone remodeling and development of immune system. Risk model based on lipid metabolism related genes (LMRGs) showed potent potential for survival prediction in osteosarcoma. Nomogram integrating risk model and clinical characteristics could predict the prognosis of osteosarcoma patients accurately. Conclusion Expression of lipid-metabolism genes is correlated with immune microenvironment of osteosarcoma patients and could be applied to predict the prognosis of in osteosarcoma accurately.
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Affiliation(s)
- Hu Qian
- Department of Orthopeadic Surgery, Xiangya Hospital Central South University, Changsha, China
| | - Ting Lei
- Department of Orthopeadic Surgery, Xiangya Hospital Central South University, Changsha, China
| | - Yihe Hu
- Department of Orthopeadic Surgery, Xiangya Hospital Central South University, Changsha, China.,Hunan Engineering Research Center of Biomedical Metal and Ceramic Implants, Changsha, China.,Department of Sports Medicine, Xiangya Hospital Central South University, Changsha, China
| | - Pengfei Lei
- Department of Orthopeadic Surgery, Xiangya Hospital Central South University, Changsha, China.,Hunan Engineering Research Center of Biomedical Metal and Ceramic Implants, Changsha, China
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29
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Kobayashi Y, Banno K, Aoki D. Current status and future directions of ovarian cancer prognostic models. J Gynecol Oncol 2021; 32:e34. [PMID: 33559415 PMCID: PMC7930438 DOI: 10.3802/jgo.2021.32.e34] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 01/13/2021] [Indexed: 11/30/2022] Open
Affiliation(s)
- Yusuke Kobayashi
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan.
| | - Kouji Banno
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Daisuke Aoki
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
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