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Miao M, Song Y, Jin M, Du Y, Xin P, Jiang Y, Zhang H. Single-cell RNA combined with bulk RNA analysis to explore oxidative stress and energy metabolism factors and found a new prostate cancer oncogene MXRA8. Aging (Albany NY) 2024; 16:4469-4502. [PMID: 38441550 DOI: 10.18632/aging.205599] [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: 10/09/2023] [Accepted: 01/29/2024] [Indexed: 03/14/2024]
Abstract
BACKGROUND Prostate cancer is the most common malignancy among men worldwide, and its diagnosis and treatment are challenging due to its heterogeneity. METHODS Integrating single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data, we identified two molecular subtypes of prostate cancer based on dysregulated genes involved in oxidative stress and energy metabolism. We constructed a risk score model (OMR) using common differentially expressed genes, which effectively evaluated prostate cancer prognosis. RESULTS Our analysis demonstrated a significant correlation between the risk score model and various factors, including tumor immune microenvironment, genomic variations, chemotherapy resistance, and immune response. Notably, patients with low-risk scores exhibited increased sensitivity to chemotherapy and immunotherapy compared to those with high-risk scores, indicating the model's potential to predict patient response to treatment. Additionally, our investigation of MXRA8 in prostate cancer showed significant upregulation of this gene in the disease as confirmed by PCR and immunohistochemistry. Functional assays including CCK-8, transwell, plate cloning, and ROS generation assay demonstrated that depletion of MXRA8 reduced the proliferative, invasive, migratory capabilities of PC-3 cells, as well as their ROS generation capacity. CONCLUSIONS Our study highlights the potential of oxidative stress and energy metabolism-related genes as prognostic markers and therapeutic targets in prostate cancer. The integration of scRNA-seq and bulk RNA-seq data enables a better understanding of prostate cancer heterogeneity and promotes personalized treatment development. Additionally, we identified a novel oncogene MXRA8 in prostate cancer.
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Affiliation(s)
- Miao Miao
- Department of Urology, The First Hospital of China Medical University, Shenyang 110001, China
| | - Yan Song
- Operating Room, The First Hospital of China Medical University, Shenyang 110001, China
| | - Mingyue Jin
- Department of Endocrinology, Shenzhen University General Hospital, Shenzhen, Guangdong, China
| | - Yang Du
- Department of Urology, The First Hospital of China Medical University, Shenyang 110001, China
| | - Peng Xin
- Department of Urology, The First Hospital of China Medical University, Shenyang 110001, China
| | - Yuanjun Jiang
- Department of Urology, The First Hospital of China Medical University, Shenyang 110001, China
| | - Hao Zhang
- Department of Urology, The First Hospital of China Medical University, Shenyang 110001, China
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Li L, Shen L, Wu H, Li M, Chen L, Zhou Q, Ma J, Huai C, Zhou W, Wei M, Zhao M, Zhao X, Du H, Jiang B, Sun Y, Zhang N, Qin S, Xing T. An integrated analysis identifies six molecular subtypes of pancreatic ductal adenocarcinoma revealing cellular and molecular landscape. Carcinogenesis 2023; 44:726-740. [PMID: 37747815 DOI: 10.1093/carcin/bgad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 09/05/2023] [Accepted: 09/22/2023] [Indexed: 09/27/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDA) has been found to have a high mortality rate. Despite continuous efforts, current histopathological classification is insufficient to guide individualized therapies of PDA. We first define the molecular subtypes of PDA (MSOP) based on a meta-cohort of 845 samples from 11 PDA datasets. We then performed functional analyses involving immunity, fibrosis and metabolism. We recognized six molecular subtypes with different survival statistics and molecular composition. The squamous basal-like (SBL) subtype had a poor prognosis and high infiltration of ENO1+ (Enolase 1)/ADM+ (Adrenomedullin) cancer-associated fibroblasts (CAFs). The immune mesenchymal-like (IML) subtype and the normal mesenchymal-like (NML) subtype were characterized by genes associated with extracellular matrix (ECM) activities and immune responses, having favorable prognoses. IML was featured by elevated exhausted immune signaling and inflammatory CAFs infiltration, whereas NML was featured with myofibroblastic CAFs infiltration. The exocrine-like (EL) subtype was high in exocrine signals, while the pure classical-like (PCL) subtype lacked immunocytes infiltration. The quiescent-like (QL) subtype had diminished metabolic signaling and high infiltration of NK cells. SBL, IML and NML were enriched in innate anti-PD-1 resistance signatures. In sum, this MSOP depicts a vivid cell-to-molecular atlas of the tumor microenvironment of PDA and might facilitate to design a precise combination of therapies that target immunity, metabolism and stroma.
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Affiliation(s)
- Lixing Li
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Lu Shen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Hao Wu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Mo Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Luan Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Qiang Zhou
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Jingsong Ma
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China
- School of Engineering, Westlake University, Hangzhou 310024, Zhejiang Province, China
| | - Cong Huai
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Wei Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Muyun Wei
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Mingzhe Zhao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Xianglong Zhao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Huihui Du
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Bixuan Jiang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Yidan Sun
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Na Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Shengying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Tonghai Xing
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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Hu H, Liang L, Zheng X, Jiang X, Fu Z, Liu C, Long J. Fibulin-1: a novel biomarker for predicting disease activity of the thyroid-associated ophthalmopathy. Eye (Lond) 2023; 37:2216-2219. [PMID: 36418908 PMCID: PMC10366185 DOI: 10.1038/s41433-022-02318-6] [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: 03/17/2022] [Revised: 10/04/2022] [Accepted: 11/14/2022] [Indexed: 11/25/2022] Open
Abstract
PURPOSE This study was designed to investigate the association between fibulin-1(FBLN1) and thyroid-associated ophthalmopathy (TAO). METHOD The plasma FBLN1 levels were measured in 80 participants, including 30 active TAO patients, 25 inactive TAO patients, and 25 Graves disease (GD) patients without TAO using enzyme-linked immunosorbent assay (ELISA). RESULTS TAO patients had significantly higher TRAb level than GD patients (p < 0.05). The active TAO patients consumed more tobacco and had higher CAS than inactive TAO patients (all p < 0.05). No significant differences were found in age, sex, and the level of FT3, FT4, and TSH between TAO and GD patients, and between the active and inactive TAO patients (all p > 0.05). The plasma FBLN1 level in TAO patients was higher than that in GD patients, and that in active patients was higher than that in inactive patients (all p < 0.05). Furthermore, the plasma FBLN1 level showed strong association with clinical activity score (CAS) of TAO (r = 0.67, p < 0.01). By receiver operator characteristic (ROC) curve analysis, FBLN1 demonstrated good efficiency for predicting disease activity at the cut-off value > 625.33 pg/ml with a sensitivity of 93.3% and a specificity of 88.0% (AUC:0.92, p < 0.01). CONCLUSION The plasma FBLN1 levels correlated with TAO activity and a value >625.33 pg/ml was associated with active disease. Our results suggest that the plasma FBLN1 level could be a novel biomarker for predicting disease activity of TAO.
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Affiliation(s)
- Hong Hu
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Liang Liang
- Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaoya Zheng
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xin Jiang
- Department of Endocrinology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Zhizhen Fu
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chun Liu
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jian Long
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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Xi Y, Song L, Wang S, Zhou H, Ren J, Zhang R, Fu F, Yang Q, Duan G, Wang J. Identification of basement membrane-related prognostic signature for predicting prognosis, immune response and potential drug prediction in papillary renal cell carcinoma. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:10694-10724. [PMID: 37322956 DOI: 10.3934/mbe.2023474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Papillary renal cell carcinoma (PRCC) is a malignant neoplasm of the kidney and is highly interesting due to its increasing incidence. Many studies have shown that the basement membrane (BM) plays an important role in the development of cancer, and structural and functional changes in the BM can be observed in most renal lesions. However, the role of BM in the malignant progression of PRCC and its impact on prognosis has not been fully studied. Therefore, this study aimed to explore the functional and prognostic value of basement membrane-associated genes (BMs) in PRCC patients. We identified differentially expressed BMs between PRCC tumor samples and normal tissue and systematically explored the relevance of BMs to immune infiltration. Moreover, we constructed a risk signature based on these differentially expressed genes (DEGs) using Lasso regression analysis and demonstrated their independence using Cox regression analysis. Finally, we predicted 9 small molecule drugs with the potential to treat PRCC and compared the differences in sensitivity to commonly used chemotherapeutic agents between high and low-risk groups to better target patients for more precise treatment planning. Taken together, our study suggested that BMs might play a crucial role in the development of PRCC, and these results might provide new insights into the treatment of PRCC.
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Affiliation(s)
- Yujia Xi
- Department of Urology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Liying Song
- Second School of Clinical Medicine, Shanxi Medical University, Taiyuan, China
| | - Shuang Wang
- Second School of Clinical Medicine, Shanxi Medical University, Taiyuan, China
| | - Haonan Zhou
- First School of Clinical Medicine, Shanxi Medical University, Taiyuan, China
| | - Jieying Ren
- School of Basic Medicine, Shanxi Medical University, Taiyuan, China
| | - Ran Zhang
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Feifan Fu
- School of Basic Medicine, Shanxi Medical University, Taiyuan, China
| | - Qian Yang
- School of Basic Medicine, Shanxi Medical University, Taiyuan, China
| | - Guosheng Duan
- Second School of Clinical Medicine, Shanxi Medical University, Taiyuan, China
| | - Jingqi Wang
- Department of Urology, The Second Hospital of Shanxi Medical University, Taiyuan, China
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Gao H, Cai B, Lu Z, Wang G, Gao Y, Miao Y, Jiang K, Zhang K. Cancer‐testis gene
STK31
is regulated by methylation and promotes the development of pancreatic cancer. Cancer Med 2022; 12:7273-7282. [PMID: 36424885 PMCID: PMC10067059 DOI: 10.1002/cam4.5472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/22/2022] [Accepted: 11/13/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUD Pancreatic cancer (PC) is a highly invasive malignancy with extremely poor prognosis. STK31 has been identified as a cancer-testis (CT) gene, but its function in PC has not been elucidated well. METHODS The effect of STK31 on cell proliferation, migration and invasion was investigated by in vitro and in vivo experiments and total RNA sequencing and targeted bisulfite sequencing was applied to explore the potential regulatory mechanisms of STK31 in PC. RESULTS By analysis of tissue samples and the clinicopathologic features, we found that STK31 was reactivated in PC and associated with poor prognosis. In addition, the vitro and vivo studies indicated that STK31 could promote PC progression by facilitating cell proliferation, migration and invasion, and the indication. Targeted Bisulfite Sequencing showed that STK31 was regulated by methylation. Furthermore, the results of total RNA sequencing suggested that STK31 was closely related to signal transduction, metabolism, and the immune system. CONCLUSIONS This study demonstrates that STK31, as a CT gene, can promote the development of PC and is regulated by methylation. STK31 could be considered as a potential therapeutic target for PC.
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Affiliation(s)
- Hao Gao
- Pancreas Center the First Affiliated Hospital of Nanjing Medical University Nanjing China
- Pancreas Institution of Nanjing Medical University Nanjing China
| | - Baobao Cai
- Pancreas Center the First Affiliated Hospital of Nanjing Medical University Nanjing China
- Pancreas Institution of Nanjing Medical University Nanjing China
| | - Zipeng Lu
- Pancreas Center the First Affiliated Hospital of Nanjing Medical University Nanjing China
- Pancreas Institution of Nanjing Medical University Nanjing China
| | - Guangfu Wang
- Pancreas Center the First Affiliated Hospital of Nanjing Medical University Nanjing China
- Pancreas Institution of Nanjing Medical University Nanjing China
| | - Yong Gao
- Pancreas Center the First Affiliated Hospital of Nanjing Medical University Nanjing China
- Pancreas Institution of Nanjing Medical University Nanjing China
| | - Yi Miao
- Pancreas Center the First Affiliated Hospital of Nanjing Medical University Nanjing China
- Pancreas Institution of Nanjing Medical University Nanjing China
| | - Kuirong Jiang
- Pancreas Center the First Affiliated Hospital of Nanjing Medical University Nanjing China
- Pancreas Institution of Nanjing Medical University Nanjing China
| | - Kai Zhang
- Pancreas Center the First Affiliated Hospital of Nanjing Medical University Nanjing China
- Pancreas Institution of Nanjing Medical University Nanjing China
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6
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Multi-Omics Approaches in Colorectal Cancer Screening and Diagnosis, Recent Updates and Future Perspectives. Cancers (Basel) 2022; 14:cancers14225545. [PMID: 36428637 PMCID: PMC9688479 DOI: 10.3390/cancers14225545] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/15/2022] Open
Abstract
Colorectal cancer (CRC) is common Cancer as well as the third leading cause of mortality around the world; its exact molecular mechanism remains elusive. Although CRC risk is significantly correlated with genetic factors, the pathophysiology of CRC is also influenced by external and internal exposures and their interactions with genetic factors. The field of CRC research has recently benefited from significant advances through Omics technologies for screening biomarkers, including genes, transcripts, proteins, metabolites, microbiome, and lipidome unbiasedly. A promising application of omics technologies could enable new biomarkers to be found for the screening and diagnosis of CRC. Single-omics technologies cannot fully understand the molecular mechanisms of CRC. Therefore, this review article aims to summarize the multi-omics studies of Colorectal cancer, including genomics, transcriptomics, proteomics, microbiomics, metabolomics, and lipidomics that may shed new light on the discovery of novel biomarkers. It can contribute to identifying and validating new CRC biomarkers and better understanding colorectal carcinogenesis. Discovering biomarkers through multi-omics technologies could be difficult but valuable for disease genotyping and phenotyping. That can provide a better knowledge of CRC prognosis, diagnosis, and treatments.
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Naryzhny S, Ronzhina N, Zorina E, Kabachenko F, Klopov N, Zgoda V. Construction of 2DE Patterns of Plasma Proteins: Aspect of Potential Tumor Markers. Int J Mol Sci 2022; 23:ijms231911113. [PMID: 36232415 PMCID: PMC9569744 DOI: 10.3390/ijms231911113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/16/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
The use of tumor markers aids in the early detection of cancer recurrence and prognosis. There is a hope that they might also be useful in screening tests for the early detection of cancer. Here, the question of finding ideal tumor markers, which should be sensitive, specific, and reliable, is an acute issue. Human plasma is one of the most popular samples as it is commonly collected in the clinic and provides noninvasive, rapid analysis for any type of disease including cancer. Many efforts have been applied in searching for “ideal” tumor markers, digging very deep into plasma proteomes. The situation in this area can be improved in two ways—by attempting to find an ideal single tumor marker or by generating panels of different markers. In both cases, proteomics certainly plays a major role. There is a line of evidence that the most abundant, so-called “classical plasma proteins”, may be used to generate a tumor biomarker profile. To be comprehensive these profiles should have information not only about protein levels but also proteoform distribution for each protein. Initially, the profile of these proteins in norm should be generated. In our work, we collected bibliographic information about the connection of cancers with levels of “classical plasma proteins”. Additionally, we presented the proteoform profiles (2DE patterns) of these proteins in norm generated by two-dimensional electrophoresis with mass spectrometry and immunodetection. As a next step, similar profiles representing protein perturbations in plasma produced in the case of different cancers will be generated. Additionally, based on this information, different test systems can be developed.
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Affiliation(s)
- Stanislav Naryzhny
- Institute of Biomedical Chemistry, Pogodinskaya, 10, 119121 Moscow, Russia
- Petersburg Institute of Nuclear Physics (PNPI) of National Research Center “Kurchatov Institute”, 188300 Gatchina, Russia
- Correspondence: ; Tel.: +7-911-176-4453
| | - Natalia Ronzhina
- Petersburg Institute of Nuclear Physics (PNPI) of National Research Center “Kurchatov Institute”, 188300 Gatchina, Russia
| | - Elena Zorina
- Institute of Biomedical Chemistry, Pogodinskaya, 10, 119121 Moscow, Russia
| | - Fedor Kabachenko
- Institute of Biomedical Systems and Biotechnology, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Nikolay Klopov
- Petersburg Institute of Nuclear Physics (PNPI) of National Research Center “Kurchatov Institute”, 188300 Gatchina, Russia
| | - Victor Zgoda
- Institute of Biomedical Chemistry, Pogodinskaya, 10, 119121 Moscow, Russia
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Upregulated Fibulin-1 Increased Endometrial Stromal Cell Viability and Migration by Repressing EFEMP1-Dependent Ferroptosis in Endometriosis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4809415. [PMID: 35127942 PMCID: PMC8816540 DOI: 10.1155/2022/4809415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 12/16/2021] [Accepted: 12/28/2021] [Indexed: 11/17/2022]
Abstract
Endometriosis (EMS) is a prevalent disease in women characterized by the presence of endometrial stroma and glands outside the uterus. Recent studies have showed that EMS is correlated with the resistance of endometrial stromal cells (ESCs) to ferroptosis, an iron-dependent nonapoptotic cell death. Fibulin-1 (FBLN1) is a newly identified target regulated by progesterone in the process of ESC decidualization. However, the role of FBLN1 in regulating ESC ferroptosis and EMS remains unclear. In the present study, the gene expression profiles of GSE58178, GSE23339, and GSE25628 were downloaded from the Gene Expression Omnibus (GEO) database, and the commonly differential genes were identified using Venn diagram analysis. The role of FBLN1 in ESC viability and migration was evaluated using Cell Counting Kit-8, transwell, and western blot analysis. We found that the FBLN1 expression was increased significantly in eutopic and ectopic endometrial tissues of patients with EMS compared with normal endometrium. FBLN1 overexpression in normal ESCs (NESCs) promoted cell viability and migration, whereas FBLN1 inhibition in ectopic ESCs (EESCs) decreased cell viability and migration. Furthermore, FBLN1 inhibition facilitated EESC death by triggering ferroptosis, as evidenced by increased Fe2+, lipid ROS, and malondialdehyde (MDA) level and decreased glutathione peroxidase 4 (GPX4) expression and glutathione (GSH) level. Mechanistically, FBLN1 interacted with EGF-containing fibulin-like extracellular matrix protein 1 (EFEMP1) and increased the protein stability of EFEMP1. More importantly, EFEMP1 silencing repressed the effect of FBLN1 on regulating EESC ferroptosis, death, and migration. Taken together, these results verify the role of the FBLN1/EFEMP1/ferroptosis pathway in the pathogenesis of EMS, and silencing of FBLN1/EFEMP1 might be an effective approach to treat EMS.
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Gan L, Shi H, Zhang Y, Sun J, Chen H. Proteomic Screening and Verification of Biomarkers in Different Stages of Mycosis Fungoides: A pilot Study. Front Cell Dev Biol 2021; 9:747017. [PMID: 34966737 PMCID: PMC8711087 DOI: 10.3389/fcell.2021.747017] [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: 07/31/2021] [Accepted: 11/04/2021] [Indexed: 11/18/2022] Open
Abstract
Mycosis fungoides (MF) is the most common cutaneous T-cell lymphoma; in advanced stages, it can involve multiple organs and has a poor prognosis. Early detection of the disease is still urgent, but there is no optimal therapy for advanced MF. In the present study, quantitative proteomic analyses (label-free quantitation, LFQ) were applied to tissue samples of different stages of MF and tissue samples from controls (eczema patients and healthy donors) to conduct preliminary molecular analysis to clarify the pathogenesis of the disease. Differential protein expression analysis demonstrated that 113 and 305 proteins were associated with the early and advanced stages of MF, respectively. Gene ontology (GO) enrichment analysis was conducted to determine the potential functions of the proteins, which could be classified into three categories: biological process, cellular component, and molecular function. The results revealed that a series of biological processes, including “initiation of DNA replication” and “nucleosome assembly,” were involved in the disease. Moreover, cellular components, including the “desmosome” and “integrin complex,” may affect the invasion and metastasis of MF via molecular functions, including “integrin binding” and “cadherin binding”. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis demonstrated that “focal adhesion DNA replication,” “Toll-like receptor signalling pathway” and other pathways were also involved. A parallel reaction monitoring (PRM) assay was applied to validate the identified differentially expressed proteins. In conclusion, the above proteomic findings may have great diagnostic and prognostic value in diverse malignancies, especially MF. Nevertheless, further studies are still needed to explore the precise mechanisms of MF.
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Affiliation(s)
- Lu Gan
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Haoze Shi
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Ying Zhang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Jianfang Sun
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Hao Chen
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
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10
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Nie X, Song L, Li X, Wang Y, Qu B. Prognostic signature of ovarian cancer based on 14 tumor microenvironment-related genes. Medicine (Baltimore) 2021; 100:e26574. [PMID: 34260536 PMCID: PMC8284754 DOI: 10.1097/md.0000000000026574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/09/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Ovarian cancer is one of the lethal gynecological diseases in women. However, using tumor microenvironment related genes to identify prognostic signature of ovarian cancer has not been discussed in detail. METHODS The mRNA profiles of 386 ovarian cancer patients were retrieved from The Cancer Genome Atlas. Univariate Cox regression and LASSO Cox regression analyses were performed and 14 optimized prognostic genes related to tumor microenvironment were identified. RESULTS The multivariate Cox hazards regression showed risk score was an independent prognostic signature for ovarian cancer. Nomogram model could reliably predict the patients' survival. Furthermore, M1 macrophages, M2 macrophages, and follicular helper T cells, differentially expressed between the high- and low-risk groups, were found to be associated with the risk score. CONCLUSION CTL-associated antigen 4 (CTLA4) and indoleamine 2,3-Dioxygenase 1 (IDO1), which were previously shown to be important immune checkpoints, probably contribute to the immunosuppressive microenvironment aberration. This study may shed light on the prognosis of ovarian cancer.
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Affiliation(s)
- Xiazi Nie
- Department of Obstetrics and Gynaecology, Gansu Provincial Hospital, Lanzhou City, Gansu Province, China
| | - Lina Song
- Department of Obstetrics and Gynaecology, Gannan Tibetan Autonomous Prefecture State People's Hospital, Hezuo City, Gansu Province, China
| | - Xiaohua Li
- Department of Gynecology and Obstertrics, People's Hospital of Gangu County, Tianshui City, Gansu Province, China
| | - Yirong Wang
- Department of Pediatric Intensive Care Unit (PICU), Gansu Maternal and Child Health Care Hospital, Lanzhou City, Gansu Province, China
| | - Bo Qu
- Department of Obstetrics and Gynaecology, Gansu Provincial Hospital, Lanzhou City, Gansu Province, China
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11
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Large contribution of copy number alterations in early stage of Papillary Thyroid Carcinoma. Comput Biol Med 2021; 135:104584. [PMID: 34171638 DOI: 10.1016/j.compbiomed.2021.104584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/10/2021] [Accepted: 06/13/2021] [Indexed: 11/23/2022]
Abstract
Papillary Thyroid Carcinoma (PTC) accounts for approximately 85% of patients with thyroid cancer. Despite its indolent nature, progression to higher stages is expected in a subgroup of patients. Hence, genomic characterization of the early stages of PTC may help to identify this subgroup, leading to better clinical management. Here, we conducted a comprehensive mutational and somatic copy number alteration (SCNA) investigation on 277 stage one PTC from TCGA. SCNA analysis revealed amplification and deletion of several cancer related genes. We found amplification of 60 oncogenes (Oncs), from which 15 were recurrently observed. Deletion of 58 tumor suppressors (TSs) was also detected. MAPK, PI3K-Akt, Rap1 and Ras were the signaling pathways with large numbers of amplified Oncs. On the other hand, deleted TSs belonged mostly to cell cycle, PI3K-Akt, mTOR and cellular senescence pathways. This suggests that despite heterogeneity in SCNA events, the final results would be the activation/deactivation of a few cancer signaling pathways. Of note, despite large amounts of heterogeneity in stage one PTC, recurrent broad deletion on Chr22 was detected in 21 individuals, leading to deletion of several tumor suppressors. In parallel, the oncogenic/pathogenic mutations in the RTK-RAS and PI3k-Akt pathways were detected. However, no pathogenic mutation was identified in known tumor suppressor genes. In order to identify a potential subgroup of BRAF (V600E) positive patients, who might progress to higher stages, low frequency mutations accompanying BRAF (V600E) were also identified. In conclusion, our findings imply that SCNA have a substantial contribution to early stages of PTC. Experimental validation of the observed genomic alterations could help to stratify patients at the time of diagnosis, and to move toward precision medicine in PTC.
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Proteomic Analyses of Fibroblast- and Serum-Derived Exosomes Identify QSOX1 as a Marker for Non-invasive Detection of Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13061351. [PMID: 33802764 PMCID: PMC8002505 DOI: 10.3390/cancers13061351] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 01/05/2023] Open
Abstract
Simple Summary Early diagnosis of colorectal cancer (CRC) is crucial to improve patient outcomes. The tumour microenvironment immediately adapts to malignant transformations, including the activation of fibroblasts in the connective tissue nearby. In this study, we investigated fibroblast activity-related protein secretion via extracellular vesicles (EVs). QSOX1, a protein identified to be significantly reduced in activated fibroblasts and derived EVs, was also found to be significantly reduced in circulating blood plasma EVs of CRC patients as compared to control patients. Hence, blood plasma EV-associated QSOX1 represents a promising platform for diagnostic CRC screening. Abstract The treatment of colorectal cancer (CRC) has improved during the last decades, but methods for crucial early diagnosis are yet to be developed. The influence of the tumour microenvironment on liquid biopsies for early cancer diagnostics are gaining growing interest, especially with emphasis on exosomes (EXO), a subgroup of extracellular vesicles (EVs). In this study, we established paired cancer-associated (CAFs) and normal fibroblasts (NF) from 13 CRC patients and investigated activation status-related protein abundance in derived EXOs. Immunohistochemical staining of matched patient tissue was performed and an independent test cohort of CRC patient plasma-derived EXOs was assessed by ELISA. A total of 11 differentially abundant EV proteins were identified between NFs and CAFs. In plasma EXOs, the CAF-EXO enriched protein EDIL3 was elevated, while the NF-EXO enriched protein QSOX1 was diminished compared to whole plasma. Both markers were significantly reduced in patient-matched CRC tissue compared to healthy colon tissue. In an independent test cohort, a significantly reduced protein abundance of QSOX1 was observed in plasma EXOs from CRC patients compared to controls and diagnostic ROC curve analysis revealed an AUC of 0.904. In conclusion, EXO-associated QSOX1 is a promising novel marker for early diagnosis and non-invasive risk stratification in CRC.
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Ganig N, Baenke F, Thepkaysone ML, Lin K, Rao VS, Wong FC, Polster H, Schneider M, Helm D, Pecqueux M, Seifert AM, Seifert L, Weitz J, Rahbari NN, Kahlert C. Proteomic Analyses of Fibroblast- and Serum-Derived Exosomes Identify QSOX1 as a Marker for Non-invasive Detection of Colorectal Cancer. Cancers (Basel) 2021. [PMID: 33802764 DOI: 10.3390/cancers130613510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
The treatment of colorectal cancer (CRC) has improved during the last decades, but methods for crucial early diagnosis are yet to be developed. The influence of the tumour microenvironment on liquid biopsies for early cancer diagnostics are gaining growing interest, especially with emphasis on exosomes (EXO), a subgroup of extracellular vesicles (EVs). In this study, we established paired cancer-associated (CAFs) and normal fibroblasts (NF) from 13 CRC patients and investigated activation status-related protein abundance in derived EXOs. Immunohistochemical staining of matched patient tissue was performed and an independent test cohort of CRC patient plasma-derived EXOs was assessed by ELISA. A total of 11 differentially abundant EV proteins were identified between NFs and CAFs. In plasma EXOs, the CAF-EXO enriched protein EDIL3 was elevated, while the NF-EXO enriched protein QSOX1 was diminished compared to whole plasma. Both markers were significantly reduced in patient-matched CRC tissue compared to healthy colon tissue. In an independent test cohort, a significantly reduced protein abundance of QSOX1 was observed in plasma EXOs from CRC patients compared to controls and diagnostic ROC curve analysis revealed an AUC of 0.904. In conclusion, EXO-associated QSOX1 is a promising novel marker for early diagnosis and non-invasive risk stratification in CRC.
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Affiliation(s)
- Nicole Ganig
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Franziska Baenke
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
| | - May-Linn Thepkaysone
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Kuailu Lin
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Venkatesh S Rao
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Fang Cheng Wong
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Heike Polster
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Martin Schneider
- MS-based Protein Analysis Unit, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Dominic Helm
- MS-based Protein Analysis Unit, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Mathieu Pecqueux
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Adrian M Seifert
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, D-69120 Heidelberg, Germany
| | - Lena Seifert
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, D-69120 Heidelberg, Germany
| | - Jürgen Weitz
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Nuh N Rahbari
- Department of Surgery, University Medicine Mannheim, Medical Faculty Mannheim, University of Heidelberg, Mannheim, D-68167 Mannheim, Germany
| | - Christoph Kahlert
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, D-69120 Heidelberg, Germany
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Low level of plasma fibulin-1 in patients with thyroid lesions: a case-control study and literature review. Mol Biol Rep 2020; 47:8859-8866. [PMID: 33106982 DOI: 10.1007/s11033-020-05938-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/20/2020] [Indexed: 12/13/2022]
Abstract
Investigating novel biomarkers discriminating thyroid nodules is a matter of great importance for differential diagnosis. The current study was planned to investigate the diagnostic value of fibulin-1 in plasma specimens of patients with thyroid nodules. A literature review was also performed to gain an understanding of the existing research relevant to the main role of fibulin-1 in carcinogenesis. In this case-control study, the levels of plasma fibulin-1 were compared in 82 subjects including papillary thyroid cancer (PTC; n = 30), multinodular goiter (MNG; n = 30), and healthy subjects (n = 22) using enzyme-linked immunosorbent assay (ELISA). Fibulin-1 levels of patients with PTC and MNG were documented to be significantly lower than those of healthy subjects (PTC vs. Healthy; P = 0.000, MNG vs. Healthy; P = 0.000). No statistically significant differences were found between PTC and MNG groups when fibulin-1 levels were compared (P > 0.05). Low level of plasma fibulin-1 was associated with an increased risk of PTC tumorigenesis (odds ratio = 0.810; 95% CI: 0.704-0.933; P = 0.003). Further, fibulin-1 had an appropriate diagnostic value for detecting PTC patients with a sensitivity of 73.33%, and specificity of 100% at the cutoff value > 4.9 (ng/ml). According to the results of the present research which are tied well with previous studies, the abnormal downregulation of fibulin-1 may play a role in the PTC and MNG tumorigenesis. In addition, fibulin-1 probably promotes the development and progression of other human cancer; however, further studies are needed to improve current understandings.
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Dalal N, Jalandra R, Sharma M, Prakash H, Makharia GK, Solanki PR, Singh R, Kumar A. Omics technologies for improved diagnosis and treatment of colorectal cancer: Technical advancement and major perspectives. Biomed Pharmacother 2020; 131:110648. [PMID: 33152902 DOI: 10.1016/j.biopha.2020.110648] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/09/2020] [Accepted: 08/16/2020] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer (CRC) ranks third among the most commonly occurring cancers worldwide, and it causes half a million deaths annually. Alongside mechanistic study for CRC detection and treatment by conventional techniques, new technologies have been developed to study CRC. These technologies include genomics, transcriptomics, proteomics, and metabolomics which elucidate DNA markers, RNA transcripts, protein and, metabolites produced inside the colon and rectum part of the gut. All these approaches form the omics arena, which presents a remarkable opportunity for the discovery of novel prognostic, diagnostic and therapeutic biomarkers and also delineate the underlying mechanism of CRC causation, which may further help in devising treatment strategies. This review also mentions the latest developments in metagenomics and culturomics as emerging evidence suggests that metagenomics of gut microbiota has profound implications in the causation, prognosis, and treatment of CRC. A majority of bacteria cannot be studied as they remain unculturable, so culturomics has also been strengthened to develop culture conditions suitable for the growth of unculturable bacteria and identify unknown bacteria. The overall purpose of this review is to succinctly evaluate the application of omics technologies in colorectal cancer research for improving the diagnosis and treatment strategies.
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Affiliation(s)
- Nishu Dalal
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi 110067, India; Department of Environmental Science, Satyawati College, Delhi University, Delhi 110052, India
| | - Rekha Jalandra
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi 110067, India; Department of Zoology, Maharshi Dayanand University, Rohtak 124001, India
| | - Minakshi Sharma
- Department of Zoology, Maharshi Dayanand University, Rohtak 124001, India
| | - Hridayesh Prakash
- Amity Institute of Virology and Immunology, Amity University, Sector 125, Noida 201313, Uttar Pradesh, India
| | - Govind K Makharia
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Pratima R Solanki
- Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rajeev Singh
- Department of Environmental Science, Satyawati College, Delhi University, Delhi 110052, India.
| | - Anil Kumar
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi 110067, India.
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STK31 regulates the proliferation and cell cycle of lung cancer cells via the Wnt/β‑catenin pathway and feedback regulation by c‑myc. Oncol Rep 2020; 43:395-404. [PMID: 31894338 PMCID: PMC6967196 DOI: 10.3892/or.2019.7441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 01/25/2019] [Indexed: 12/29/2022] Open
Abstract
Lung cancer, which is a leading cause of cancer‑related deaths, is diagnosed at a male to female ratio of 2.1:1. Serine‑threonine kinase 31 (STK31) is a novel cancer/testis (CT)‑related gene that is highly expressed in several types of cancers, such as lung and colorectal cancer, and plays crucial roles in cancer. In the present study, increased expression of STK31 and β‑catenin was observed in lung cancer tissues and cell lines. Downregulation of STK31 expression in lung cancer cells significantly inhibited their proliferation by arresting the cell cycle in the G1 phase concurrent with decreased β‑catenin, c‑myc and cyclin D1 protein levels, while upregulation of STK31 had the opposite effects. In addition, STK31‑induced lung cancer cell viability, proliferation, cell cycle progression, and expression of related genes were completely attenuated by a Wnt/β‑catenin inhibitor (XAV939). Similar to XAV939, a c‑myc inhibitor (10058‑F4) also significantly attenuated STK31‑induced proliferation and cell cycle progression in lung cancer cells. Inhibiting c‑myc and TRRAP significantly decreased the expression of STK31, and a chromatin immunoprecipitation (ChIP) assay confirmed that c‑myc directly bound to the STK31 promoter. These results indicated that STK31 may act as an oncogene in lung cancer and that c‑myc may be the transcription factor that promotes STK31 expression. Moreover, the results suggested that c‑myc can also regulate STK31 expression in a positive feedback loop, and the downregulation of STK31 in lung cancer cells had an inhibitory effect on cell viability, cell proliferation and cell cycle progression, likely by inactivating the Wnt/β‑catenin pathway and positive feedback regulation by c‑myc.
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