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Rakina M, Larionova I, Kzhyshkowska J. Macrophage diversity in human cancers: New insight provided by single-cell resolution and spatial context. Heliyon 2024; 10:e28332. [PMID: 38571605 PMCID: PMC10988020 DOI: 10.1016/j.heliyon.2024.e28332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 04/05/2024] Open
Abstract
M1/M2 paradigm of macrophage plasticity has existed for decades. Now it becomes clear that this dichotomy doesn't adequately reflect the diversity of macrophage phenotypes in tumor microenvironment (TME). Tumor-associated macrophages (TAMs) are a major population of innate immune cells in the TME that promotes tumor cell proliferation, angiogenesis and lymphangiogenesis, invasion and metastatic niche formation, as well as response to anti-tumor therapy. However, the fundamental restriction in therapeutic TAM targeting is the limited knowledge about the specific TAM states in distinct human cancer types. Here we summarized the results of the most recent studies that use advanced technologies (e.g. single-cell RNA sequencing and spatial transcriptomics) allowing to decipher novel functional subsets of TAMs in numerous human cancers. The transcriptomic profiles of these TAM subsets and their clinical significance were described. We emphasized the characteristics of specific TAM subpopulations - TREM2+, SPP1+, MARCO+, FOLR2+, SIGLEC1+, APOC1+, C1QC+, and others, which have been most extensively characterized in several cancers, and are associated with cancer prognosis. Spatial transcriptomics technologies defined specific spatial interactions between TAMs and other cell types, especially fibroblasts, in tumors. Spatial transcriptomics methods were also applied to identify markers of immunotherapy response, which are expressed by macrophages or in the macrophage-abundant regions. We highlighted the perspectives for novel techniques that utilize spatial and single cell resolution in investigating new ligand-receptor interactions for effective immunotherapy based on TAM-targeting.
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Affiliation(s)
- Militsa Rakina
- Laboratory of Translational Cellular and Molecular Biomedicine, National Research Tomsk State University, Tomsk, 634050, Russia
- Laboratory of Molecular Therapy of Cancer, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia
| | - Irina Larionova
- Laboratory of Translational Cellular and Molecular Biomedicine, National Research Tomsk State University, Tomsk, 634050, Russia
- Laboratory of Molecular Therapy of Cancer, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia
| | - Julia Kzhyshkowska
- Laboratory of Translational Cellular and Molecular Biomedicine, National Research Tomsk State University, Tomsk, 634050, Russia
- Institute of Transfusion Medicine and Immunology, Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, University of Heidelberg, Mannheim, 68167, Germany
- German Red Cross Blood Service Baden-Württemberg – Hessen, Mannheim, 68167, Germany
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Bose A, Datta S, Mandal R, Ray U, Dhar R. Increased heterogeneity in expression of genes associated with cancer progression and drug resistance. Transl Oncol 2024; 41:101879. [PMID: 38262110 PMCID: PMC10832509 DOI: 10.1016/j.tranon.2024.101879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/16/2023] [Accepted: 12/29/2023] [Indexed: 01/25/2024] Open
Abstract
Fluctuations in the number of regulatory molecules and differences in timings of molecular events can generate variation in gene expression among genetically identical cells in the same environmental condition. This variation, termed as expression noise, can create differences in metabolic state and cellular functions, leading to phenotypic heterogeneity. Expression noise and phenotypic heterogeneity have been recognized as important contributors to intra-tumor heterogeneity, and have been associated with cancer growth, progression, and therapy resistance. However, how expression noise changes with cancer progression in actual cancer patients has remained poorly explored. Such an analysis, through identification of genes with increasing expression noise, can provide valuable insights into generation of intra-tumor heterogeneity, and could have important implications for understanding immune-suppression, drug tolerance and therapy resistance. In this work, we performed a genome-wide identification of changes in gene expression noise with cancer progression using single-cell RNA-seq data of lung adenocarcinoma patients at different stages of cancer. We identified 37 genes in epithelial cells that showed an increasing noise trend with cancer progression, many of which were also associated with cancer growth, EMT and therapy resistance. We found that expression of several of these genes was positively associated with expression of mitochondrial genes, suggesting an important role of mitochondria in generation of heterogeneity. In addition, we uncovered substantial differences in sample-specific noise profiles which could have implications for personalized prognosis and treatment.
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Affiliation(s)
- Anwesha Bose
- Department of Bioscience and Biotechnology, Indian Institute of Technology (IIT) Kharagpur, India
| | - Subhasis Datta
- Department of Bioscience and Biotechnology, Indian Institute of Technology (IIT) Kharagpur, India
| | - Rakesh Mandal
- Department of Bioscience and Biotechnology, Indian Institute of Technology (IIT) Kharagpur, India
| | - Upasana Ray
- Department of Bioscience and Biotechnology, Indian Institute of Technology (IIT) Kharagpur, India
| | - Riddhiman Dhar
- Department of Bioscience and Biotechnology, Indian Institute of Technology (IIT) Kharagpur, India.
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Kang Z, Zhao YX, Qiu RSQ, Chen DN, Zheng QS, Xue XY, Xu N, Wei Y. Identification macrophage signatures in prostate cancer by single-cell sequencing and machine learning. Cancer Immunol Immunother 2024; 73:41. [PMID: 38349474 PMCID: PMC10864475 DOI: 10.1007/s00262-024-03633-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 01/12/2024] [Indexed: 02/15/2024]
Abstract
BACKGROUND The tumor microenvironment (TME) encompasses a variety of cells that influence immune responses and tumor growth, with tumor-associated macrophages (TAM) being a crucial component of the TME. TAM can guide prostate cancer in different directions in response to various external stimuli. METHODS First, we downloaded prostate cancer single-cell sequencing data and second-generation sequencing data from multiple public databases. From these data, we identified characteristic genes associated with TAM clusters. We then employed machine learning techniques to select the most accurate TAM gene set and developed a TAM-related risk label for prostate cancer. We analyzed the tumor-relatedness of the TAM-related risk label and different risk groups within the population. Finally, we validated the accuracy of the prognostic label using single-cell sequencing data, qPCR, and WB assays, among other methods. RESULTS In this study, the TAM_2 cell cluster has been identified as promoting the progression of prostate cancer, possibly representing M2 macrophages. The 9 TAM feature genes selected through ten machine learning methods and demonstrated their effectiveness in predicting the progression of prostate cancer patients. Additionally, we have linked these TAM feature genes to clinical pathological characteristics, allowing us to construct a nomogram. This nomogram provides clinical practitioners with a quantitative tool for assessing the prognosis of prostate cancer patients. CONCLUSION This study has analyzed the potential relationship between TAM and PCa and established a TAM-related prognostic model. It holds promise as a valuable tool for the management and treatment of PCa patients.
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Affiliation(s)
- Zhen Kang
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
- Department of Urology, National Region Medical Centre, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Yu-Xuan Zhao
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
- Department of Urology, National Region Medical Centre, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Ren Shun Qian Qiu
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
- Department of Urology, National Region Medical Centre, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Dong-Ning Chen
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
- Department of Urology, National Region Medical Centre, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Qing-Shui Zheng
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
- Department of Urology, National Region Medical Centre, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Xue-Yi Xue
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
- Department of Urology, National Region Medical Centre, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
- Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Ning Xu
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
- Department of Urology, National Region Medical Centre, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
- Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
| | - Yong Wei
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
- Department of Urology, National Region Medical Centre, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
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He L, Shi M, Ren S, Zhang J, Tian Y, Yang X, Liu H. Jun-APOE-LRP1 axis promotes tumor metastasis in colorectal cancer. Biomol Biomed 2023; 23:1026-1037. [PMID: 37310025 PMCID: PMC10655886 DOI: 10.17305/bb.2023.9248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/03/2023] [Accepted: 06/03/2023] [Indexed: 06/14/2023]
Abstract
Apolipoprotein E (apoE) has previously been reported to play vital roles in tumor progression. However, the impact of apoE on colorectal cancer (CRC) metastasis remains largely unexplored. This study aimed to investigate the role of apoE in CRC metastasis and to identify the transcription factor and receptor of apoE involved in regulation of CRC metastasis. Bioinformatic analyses were conducted to examine the expression pattern and prognosis of apolipoproteins. APOE-overexpressing cell lines were utilized to explore the effects of apoE on proliferation, migration and invasion of CRC cells. Additionally, the transcription factor and receptor of apoE were screened via bioinformatics, and further validated through knockdown experiments. We discovered that the mRNA levels of APOC1, APOC2, APOD and APOE were higher in lymphatic invasion group, and a higher apoE level indicated poorer overall survival and progression-free interval. In vitro studies demonstrated that APOE-overexpression did not affect proliferation but promoted the migration and invasion of CRC cells. We also reported that APOE-expression was modulated by the transcription factor Jun by activating the proximal promoter region of APOE, and APOE-overexpression reversed the metastasis suppression of JUN knockdown. Furthermore, bioinformatics analysis suggested an interaction between apoE and low-density lipoprotein receptor-related protein 1 (LRP1). LRP1 was highly expressed in both the lymphatic invasion group and the APOEHigh group. Additionally, we found that APOE-overexpression upregulated LRP1 protein levels, and LRP1 knockdown attenuated the metastasis-promoting function of APOE. Overall, our study suggests that the Jun-APOE-LRP1 axis contributes to tumor metastasis in CRC.
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Affiliation(s)
- Lingyuan He
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Mengchen Shi
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shuwei Ren
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jingdan Zhang
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yu Tian
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiangling Yang
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Huanliang Liu
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
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Myers BL, Brayer KJ, Paez-Beltran LE, Keith MS, Suzuki H, Newville J, Anderson RH, Lo Y, Mertz CM, Kollipara R, Borromeo MD, Bachoo RM, Johnson JE, Vue TY. Glioblastoma initiation, migration, and cell types are regulated by core bHLH transcription factors ASCL1 and OLIG2. bioRxiv 2023:2023.09.30.560206. [PMID: 37873200 PMCID: PMC10592871 DOI: 10.1101/2023.09.30.560206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Glioblastomas (GBMs) are highly aggressive, infiltrative, and heterogeneous brain tumors driven by complex driver mutations and glioma stem cells (GSCs). The neurodevelopmental transcription factors ASCL1 and OLIG2 are co-expressed in GBMs, but their role in regulating the heterogeneity and hierarchy of GBM tumor cells is unclear. Here, we show that oncogenic driver mutations lead to dysregulation of ASCL1 and OLIG2, which function redundantly to initiate brain tumor formation in a mouse model of GBM. Subsequently, the dynamic levels and reciprocal binding of ASCL1 and OLIG2 to each other and to downstream target genes then determine the cell types and degree of migration of tumor cells. Single-cell RNA sequencing (scRNA-seq) reveals that a high level of ASCL1 is key in defining GSCs by upregulating a collection of ribosomal protein, mitochondrial, neural stem cell (NSC), and cancer metastasis genes - all essential for sustaining the high proliferation, migration, and therapeutic resistance of GSCs.
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Ersoz NS, Bakir-Gungor B, Yousef M. GeNetOntology: identifying affected gene ontology terms via grouping, scoring, and modeling of gene expression data utilizing biological knowledge-based machine learning. Front Genet 2023; 14:1139082. [PMID: 37671046 PMCID: PMC10476493 DOI: 10.3389/fgene.2023.1139082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 07/05/2023] [Indexed: 09/07/2023] Open
Abstract
Introduction: Identifying significant sets of genes that are up/downregulated under specific conditions is vital to understand disease development mechanisms at the molecular level. Along this line, in order to analyze transcriptomic data, several computational feature selection (i.e., gene selection) methods have been proposed. On the other hand, uncovering the core functions of the selected genes provides a deep understanding of diseases. In order to address this problem, biological domain knowledge-based feature selection methods have been proposed. Unlike computational gene selection approaches, these domain knowledge-based methods take the underlying biology into account and integrate knowledge from external biological resources. Gene Ontology (GO) is one such biological resource that provides ontology terms for defining the molecular function, cellular component, and biological process of the gene product. Methods: In this study, we developed a tool named GeNetOntology which performs GO-based feature selection for gene expression data analysis. In the proposed approach, the process of Grouping, Scoring, and Modeling (G-S-M) is used to identify significant GO terms. GO information has been used as the grouping information, which has been embedded into a machine learning (ML) algorithm to select informative ontology terms. The genes annotated with the selected ontology terms have been used in the training part to carry out the classification task of the ML model. The output is an important set of ontologies for the two-class classification task applied to gene expression data for a given phenotype. Results: Our approach has been tested on 11 different gene expression datasets, and the results showed that GeNetOntology successfully identified important disease-related ontology terms to be used in the classification model. Discussion: GeNetOntology will assist geneticists and scientists to identify a range of disease-related genes and ontologies in transcriptomic data analysis, and it will also help doctors design diagnosis platforms and improve patient treatment plans.
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Affiliation(s)
- Nur Sebnem Ersoz
- Department of Bioengineering, Graduate School of Engineering and Science, Abdullah Gul University, Kayseri, Türkiye
| | - Burcu Bakir-Gungor
- Department of Computer Engineering, Faculty of Engineering, Abdullah Gul University, Kayseri, Türkiye
- Department of Bioengineering, Faculty of Life and Natural Sciences, Abdullah Gul University, Kayseri, Türkiye
| | - Malik Yousef
- Department of Information Systems, Zefat Academic College, Zefat, Israel
- Galilee Digital Health Research Center (GDH), Zefat Academic College, Zefat, Israel
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Dietsch B, Weller C, Sticht C, de la Torre C, Kramer M, Goerdt S, Géraud C, Wohlfeil SA. Hepatic passaging of NRAS-mutant melanoma influences adhesive properties and metastatic pattern. BMC Cancer 2023; 23:436. [PMID: 37179302 PMCID: PMC10182637 DOI: 10.1186/s12885-023-10912-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Liver metastasis is a poor prognostic factor for treatment of advanced cutaneous melanoma with either immunotherapy or targeted therapies. In this study we focused on NRAS mutated melanoma, a cohort with high unmet clinical need. METHODS WT31 melanoma was repeatedly passaged over the liver after intravenous injections five times generating the subline WT31_P5IV. The colonization of target organs, morphology, vascularization and the gene expression profiles of metastases were analyzed. RESULTS After intravenous injection lung metastasis was significantly decreased and a trend towards increased liver metastasis was detected for WT31_P5IV as compared to parental WT31. Besides, the ratio of lung to liver metastases was significantly smaller. Histology of lung metastases revealed reduced proliferation of WT31_P5IV in relation to WT31 while both size and necrotic areas were unaltered. Liver metastases of both sublines showed no differences in vascularization, proliferation or necrosis. To identify tumor-intrinsic factors that altered the metastatic pattern of WT31_P5IV RNA sequencing was performed and revealed a differential regulation of pathways involved in cell adhesion. Ex vivo fluorescence imaging confirmed that initial tumor cell retention in the lungs was significantly reduced in WT31_P5IV in comparison to WT31. CONCLUSION This study demonstrates that tumor-intrinsic properties influencing the metastatic pattern of NRAS mutated melanoma are strongly affected by hepatic passaging and the hematogenous route tumor cells take. It has implications for the clinical setting as such effects might also occur during metastatic spread or disease progression in melanoma patients.
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Affiliation(s)
- Bianca Dietsch
- Department of Dermatology, Venereology, and Allergology, University Medical Center and Medical Faculty Mannheim, Heidelberg University, and Center of Excellence in Dermatology, Mannheim, Germany
- Section of Clinical and Molecular Dermatology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Céline Weller
- Department of Dermatology, Venereology, and Allergology, University Medical Center and Medical Faculty Mannheim, Heidelberg University, and Center of Excellence in Dermatology, Mannheim, Germany
- Section of Clinical and Molecular Dermatology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Carsten Sticht
- NGS Core Facility, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Carolina de la Torre
- NGS Core Facility, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Martin Kramer
- Department of Veterinary Clinical Sciences, Small Animal Clinic, Justus-Liebig-University Giessen, Giessen, Germany
| | - Sergij Goerdt
- Department of Dermatology, Venereology, and Allergology, University Medical Center and Medical Faculty Mannheim, Heidelberg University, and Center of Excellence in Dermatology, Mannheim, Germany
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Cyrill Géraud
- Department of Dermatology, Venereology, and Allergology, University Medical Center and Medical Faculty Mannheim, Heidelberg University, and Center of Excellence in Dermatology, Mannheim, Germany
- Section of Clinical and Molecular Dermatology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Sebastian A Wohlfeil
- Department of Dermatology, Venereology, and Allergology, University Medical Center and Medical Faculty Mannheim, Heidelberg University, and Center of Excellence in Dermatology, Mannheim, Germany.
- Section of Clinical and Molecular Dermatology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Ferri-Borgogno S, Zhu Y, Sheng J, Burks JK, Gomez JA, Wong KK, Wong ST, Mok SC. Spatial Transcriptomics Depict Ligand-Receptor Cross-talk Heterogeneity at the Tumor-Stroma Interface in Long-Term Ovarian Cancer Survivors. Cancer Res 2023; 83:1503-1516. [PMID: 36787106 PMCID: PMC10159916 DOI: 10.1158/0008-5472.can-22-1821] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 12/06/2022] [Accepted: 02/10/2023] [Indexed: 02/15/2023]
Abstract
Advanced high-grade serous ovarian cancer (HGSC) is an aggressive disease that accounts for 70% of all ovarian cancer deaths. Nevertheless, 15% of patients diagnosed with advanced HGSC survive more than 10 years. The elucidation of predictive markers of these long-term survivors (LTS) could help identify therapeutic targets for the disease, and thus improve patient survival rates. To investigate the stromal heterogeneity of the tumor microenvironment (TME) in ovarian cancer, we used spatial transcriptomics to generate spatially resolved transcript profiles in treatment-naïve advanced HGSC from LTS and short-term survivors (STS) and determined the association between cancer-associated fibroblasts (CAF) heterogeneity and survival in patients with advanced HGSC. Spatial transcriptomics and single-cell RNA-sequencing data were integrated to distinguish tumor and stroma regions, and a computational method was developed to investigate spatially resolved ligand-receptor interactions between various tumor and CAF subtypes in the TME. A specific subtype of CAFs and its spatial location relative to a particular ovarian cancer cell subtype in the TME correlated with long-term survival in patients with advanced HGSC. Also, increased APOE-LRP5 cross-talk occurred at the stroma-tumor interface in tumor tissues from STS compared with LTS. These findings were validated using multiplex IHC. Overall, this spatial transcriptomics analysis revealed spatially resolved CAF-tumor cross-talk signaling networks in the ovarian TME that are associated with long-term survival of patients with HGSC. Further studies to confirm whether such cross-talk plays a role in modulating the malignant phenotype of HGSC and could serve as a predictive biomarker of patient survival are warranted. SIGNIFICANCE Generation of spatially resolved gene expression patterns in tumors from patients with ovarian cancer surviving more than 10 years allows the identification of novel predictive biomarkers and therapeutic targets for better patient management. See related commentary by Kelliher and Lengyel, p. 1383.
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Affiliation(s)
- Sammy Ferri-Borgogno
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ying Zhu
- Systems Medicine and Bioengineering Department, Houston Methodist Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA
- Departments of Pathology and Laboratory Medicine and Radiology, Houston Methodist Hospital, Weill Cornell Medicine, Houston, TX 77030, USA
| | - Jianting Sheng
- Systems Medicine and Bioengineering Department, Houston Methodist Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA
- Departments of Pathology and Laboratory Medicine and Radiology, Houston Methodist Hospital, Weill Cornell Medicine, Houston, TX 77030, USA
| | - Jared K. Burks
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Javier A. Gomez
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kwong Kwok Wong
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Stephen T.C. Wong
- Systems Medicine and Bioengineering Department, Houston Methodist Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA
- Departments of Pathology and Laboratory Medicine and Radiology, Houston Methodist Hospital, Weill Cornell Medicine, Houston, TX 77030, USA
| | - Samuel C. Mok
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Dai W, Guo C, Wang Y, Li Y, Xie R, Wu J, Yao B, Xie D, He L, Li Y, Huang H, Wang Y, Liu S. Identification of hub genes and pathways in lung metastatic colorectal cancer. BMC Cancer 2023; 23:323. [PMID: 37024866 PMCID: PMC10080892 DOI: 10.1186/s12885-023-10792-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 03/30/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most prevalent types of malignant tumours. Metastasis is the leading cause of cancer-related mortality, with lung metastases accounting for 32.9% of all metastatic CRCs. However, since the biological mechanism of lung metastatic CRC is poorly understood, limited therapeutic targets are available. In the present study, we aimed to identify the key genes and molecular processes involved in CRC lung metastasis. METHODS The differentially expressed genes (DEGs) between primary and lung metastatic CRC patients were obtained from the Gene Expression Omnibus (GEO) database via the GEO2R tool. The enriched biological processes and pathways modulated by the DEGs were determined with Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Reactome Gene Sets analyses. The search tool Retrieval of Interacting Genes (STRING) and Cytoscape were used to construct a protein-protein interaction (PPI) network among DEGs. RESULTS The DEGs were enriched in surfactant metabolism, cell-cell communication and chemokine signaling pathways. The defined hub genes were included CLU, SFTPD, CCL18, SPP1, APOE, BGN and MMP3. Among them, CLU, SFTPD and CCL18 might be associated with the specific lung tropism metastasis in CRC. In addition, the expression and prognostic values of the hub genes in CRC patients were verified in database of The Cancer Genome Atlas (TCGA) and GEO. Moreover, the protein levels of the hub genes were detected in primary and lung metastatic CRC cells, serum or tissues. Furthermore, SFTPD was confirmed to facilitate cellular proliferation and lung metastasis in CRC. CONCLUSION This bioinformatics study may provide a better understanding of the candidate therapeutic targets and molecular mechanisms for CRC lung metastasis.
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Affiliation(s)
- Wei Dai
- School of Pharmacy, Gannan Medical University, Ganzhou, 341000, China
| | - Caiyao Guo
- School of Rehabilitation Medicine, Gannan Medical University, Ganzhou, 341000, China
| | - Yu Wang
- School of Rehabilitation Medicine, Gannan Medical University, Ganzhou, 341000, China
| | - Yumei Li
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, 341000, China
| | - Renjian Xie
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, 341000, China
| | - Junhong Wu
- School of Pharmacy, Gannan Medical University, Ganzhou, 341000, China
| | - Baole Yao
- School of Rehabilitation Medicine, Gannan Medical University, Ganzhou, 341000, China
| | - Dong Xie
- School of Rehabilitation Medicine, Gannan Medical University, Ganzhou, 341000, China
| | - Ling He
- School of Rehabilitation Medicine, Gannan Medical University, Ganzhou, 341000, China
| | - Yingying Li
- School of Pharmacy, Gannan Medical University, Ganzhou, 341000, China
| | - Hao Huang
- School of Pharmacy, Gannan Medical University, Ganzhou, 341000, China
| | - Yun Wang
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China.
| | - Shenglan Liu
- School of Pharmacy, Gannan Medical University, Ganzhou, 341000, China.
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10
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Xu K, Zheng S, Li B, Shao Y, Yin X. Molecular characterization of colorectal mucinous adenocarcinoma and adenocarcinoma, not otherwise specified, identified by multiomic data analysis. Front Mol Biosci 2023; 10:1150362. [PMID: 37091868 PMCID: PMC10114614 DOI: 10.3389/fmolb.2023.1150362] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 02/27/2023] [Indexed: 04/08/2023] Open
Abstract
Adenocarcinoma not otherwise specified (AC) and mucinous adenocarcinoma (MC) have different biological behaviors and clinical features. We utilized our previous proteomic data and public transcriptome, single-cell transcriptome, and spatial transcriptome databases to profile the molecular atlas of the tumor microenvironments of MC, AC, and normal colon tissues. By exploring the general and specific molecular features of AC and MC, we found that AC was immune-active but exposed to a hypoxic microenvironment. MC cells could protect against DNA damage, and the microenvironment was unfavorable to leukocyte transendothelial migration. We identified several potential molecular and cellular targets of AC and MC for future research. We also highlighted that the major difference between AC and MC was not the variety of cell types and functions but possibly cell interactions. Stromal and epithelial cell interactions play important roles in both MC and AC, but different regulatory pathways were involved.
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Affiliation(s)
- Kailun Xu
- Department of Breast Surgery and Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Cancer, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
| | - Shu Zheng
- Department of Breast Surgery and Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Cancer, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
| | - Baosheng Li
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Yingkuan Shao
- Department of Breast Surgery and Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Cancer, Cancer Center of Zhejiang University, Hangzhou, Zhejiang, China
- *Correspondence: Yingkuan Shao, ; Xiaoyang Yin,
| | - Xiaoyang Yin
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- *Correspondence: Yingkuan Shao, ; Xiaoyang Yin,
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11
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Baichan P, Naicker P, Augustine TN, Smith M, Candy G, Devar J, Nweke EE. Proteomic analysis identifies dysregulated proteins and associated molecular pathways in a cohort of gallbladder cancer patients of African ancestry. Clin Proteomics 2023; 20:8. [PMID: 36855072 PMCID: PMC9976386 DOI: 10.1186/s12014-023-09399-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Gallbladder cancer (GBC) is a lethal cancer with a poor prognosis. The lack of specific and sensitive biomarkers results in delayed diagnosis with most patients presenting at late stages of the disease. Furthermore, there is little known about the molecular mechanisms associated with GBC, especially in patients of African ancestry. This study aimed to determine dysregulated proteins in South African GBC patients to identify potential mechanisms of the disease progression and plausible biomarkers. METHODS Tissues (27 GBC, 13 Gallstone disease, and 5 normal tissues) and blood plasma (54 GBC and 73 Benign biliary pathology) were obtained from consenting patients. Protein extraction was performed on all tissues and liquid chromatography-mass spectrometry was used for proteomic profiling. A project-specific spectral library was built using the Pulsar search algorithm. Principal component and Spearman's rank correlation analyses were performed using PAST (V4.07b). Pathway and Network analyses were conducted using REACTOME (v3.7) and stringAPP (v1.7.0), respectively. RESULTS In the tissue sample group, there were 62 and 194 dysregulated proteins in GBC compared to normal and gallstone groups, respectively. In the plasma group, there were 33 altered proteins in GBC compared to the benign biliary pathology group. We found 9 proteins (APOA1, APOA2, RET4, TTR, HEMO, HBB, HBA, PIGR, and APOE) to be commonly dysregulated in both tissue and plasma. Furthermore, a subset analysis demonstrated that 2 proteins, S100A8 and S100A9, were downregulated in GBC patients with GD history compared to those without. Pathway analysis showed that the dysregulated proteins in GBC patients were enriched in pathways involved in smooth muscle contraction, metabolism, ECM organization, and integrin cell surface interactions. CONCLUSION The identified dysregulated proteins help in understanding GBC molecular mechanisms in our patient group. Furthermore, the alteration of specific proteins in both tissue and plasma samples suggests their potential utility as biomarkers of GBC in this sample cohort.
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Affiliation(s)
- Pavan Baichan
- grid.11951.3d0000 0004 1937 1135Department of Surgery, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road Parktown, Johannesburg, 2193 South Africa
| | - Previn Naicker
- grid.7327.10000 0004 0607 1766Council for Scientific and Industrial Research, Pretoria, 0001 South Africa
| | - Tanya Nadine Augustine
- grid.11951.3d0000 0004 1937 1135School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193 South Africa
| | - Martin Smith
- grid.11951.3d0000 0004 1937 1135Department of Surgery, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road Parktown, Johannesburg, 2193 South Africa ,grid.414240.70000 0004 0367 6954Hepatopancreatobiliary Unit, Department of Surgery, Chris Hani-Baragwanath Academic Hospital, Soweto, Johannesburg, South Africa
| | - Geoffrey Candy
- grid.11951.3d0000 0004 1937 1135Department of Surgery, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road Parktown, Johannesburg, 2193 South Africa
| | - John Devar
- grid.11951.3d0000 0004 1937 1135Department of Surgery, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road Parktown, Johannesburg, 2193 South Africa ,grid.414240.70000 0004 0367 6954Hepatopancreatobiliary Unit, Department of Surgery, Chris Hani-Baragwanath Academic Hospital, Soweto, Johannesburg, South Africa
| | - Ekene Emmanuel Nweke
- Department of Surgery, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road Parktown, Johannesburg, 2193, South Africa.
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12
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Miao G, Zhuo D, Han X, Yao W, Liu C, Liu H, Cao H, Sun Y, Chen Z, Feng T. From degenerative disease to malignant tumors: Insight to the function of ApoE. Biomed Pharmacother 2023; 158:114127. [PMID: 36516696 DOI: 10.1016/j.biopha.2022.114127] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/03/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Apolipoprotein E (ApoE) is a multifunctional protein involved in lipid transport and lipoprotein metabolism, mediating lipid distribution/redistribution in tissues and cells. It can also regulate inflammation and immune function, maintain cytoskeleton stability, and improve neural tissue Function. Due to genetic polymorphisms of ApoE (ε2, ε3, and ε4), its three common structural isoforms (ApoE2, ApoE3, ApoE4) are also associated with the risk of many diseases, especially degenerative diseases, such as vascular degenerative diseases including atherosclerosis (AS), coronary heart disease (CHD), and neurodegenerative disease like Alzheimer's disease (AD). The frequency of the ε4 allele and APOE variants were significantly higher than that of the ε2 and ε3 alleles in the patients with CHD or AD. In recent years, ApoE has frequently appeared in tumor research and become a tumor biomarker gradually. It has been found that ApoE is highly expressed in most solid tumor tissues, such as glioblastoma, gastric cancer, pancreatic ductal cell carcinoma, etc. Studies illustrated that ApoE could regulate the polarization changes of macrophages, participate in the construction of tumor immune microenvironment, regulate tumor inflammation and immune response and play a role in tumor progression, invasion, and metastasis. Of course, many functions of ApoE and its relationship with diseases are still under research. By reviewing the structure and function of ApoE from degeneration diseases to tumor neoplasms, we hope to better understand such a biomarker and further explore the value of ApoE in later studies.
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Affiliation(s)
- Ganggang Miao
- Department of General Surgery, The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Danyang, Jiangsu, China; Department of General Surgery, The Affiliated Nanjing Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Danping Zhuo
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xue Han
- Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao, Shangdong, China
| | - Wentao Yao
- Department of Urology, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, Jiangsu, China
| | - Chuan Liu
- Hepatobiliary/Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Living Donor Transplantation, Chinese Academy of Medical Sciences, Nanjing, China
| | - Hanyuan Liu
- Department of General Surgery, The Affiliated Nanjing Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hongyong Cao
- Department of General Surgery, The Affiliated Nanjing Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Yangbai Sun
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Zhiqiang Chen
- Department of Nuclear Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China.
| | - Tingting Feng
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Soochow University, Suzhou, China.
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13
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Sommella E, Capaci V, Aloisio M, Salviati E, Campiglia P, Molinario G, Licastro D, Di Lorenzo G, Romano F, Ricci G, Monasta L, Ura B. A Label-Free Proteomic Approach for the Identification of Biomarkers in the Exosome of Endometrial Cancer Serum. Cancers (Basel) 2022; 14. [PMID: 36551747 DOI: 10.3390/cancers14246262] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/14/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Endometrial cancers (ECs) are mostly adenocarcinomas arising from the inner part of the uterus. The identification of serum biomarkers, either soluble or carried in the exosome, may be useful in making an early diagnosis. We used label-free quantification mass spectrometry (LFQ-MS)-based proteomics to investigate the proteome of exosomes in the albumin-depleted serum from 12 patients with EC, as compared to 12 healthy controls. After quantification and statistical analysis, we found significant changes in the abundance (p < 0.05) of 33 proteins in EC vs. control samples, with a fold change of ≥1.5 or ≤0.6. Validation using Western blotting analysis in 36 patients with EC as compared to 36 healthy individuals confirmed the upregulation of APOA1, HBB, CA1, HBD, LPA, SAA4, PF4V1, and APOE. A multivariate logistic regression model based on the abundance of these proteins was able to separate the controls from the EC patients with excellent sensitivity levels, particularly for stage 1 ECs. The results show that using LFQ-MS to explore the specific proteome of serum exosomes allows for the identification of biomarkers in EC. These observations suggest that PF4V1, CA1, HBD, and APOE represent biomarkers that are able to reach the clinical stage, after a validation phase.
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14
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Abstract
Apolipoproteins (APOs), the primary protein moiety of lipoproteins, are known for their crucial role in lipid traffic and metabolism. Despite extensive exploration of APOs in cardiovascular diseases, their roles in cancers did not attract enough attention. Recently, research focusing on the roles of APOs in cancers has flourished. Multiple studies demonstrate the interaction of APOs with classical pathways of tumorigenesis. Besides, the dysregulation of APOs may indicate cancer occurrence and progression, thus serving as potential biomarkers for cancer patients. Herein, we summarize the mechanisms of APOs involved in the development of various cancers, their applications as cancer biomarkers and their genetic polymorphism associated with cancer risk. Additionally, we also discuss the potential anti-cancer therapies by virtue of APOs. The comprehensive review of APOs in cancers may advance the understanding of the roles of APOs in cancers and their potential mechanisms. We hope that it will provide novel clues and new therapeutic strategies for cancers.
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Affiliation(s)
- Yingcheng He
- Department of Histology and Embryology, Medical College of Nanchang University, Nanchang, Jiangxi, China,Medical Department, Queen Mary School, Nanchang University, Nanchang, Jiangxi, China
| | - Jianrui Chen
- Department of Histology and Embryology, Medical College of Nanchang University, Nanchang, Jiangxi, China,Medical Department, Queen Mary School, Nanchang University, Nanchang, Jiangxi, China
| | - Yanbing Ma
- Department of Histology and Embryology, Medical College of Nanchang University, Nanchang, Jiangxi, China,Medical Department, Queen Mary School, Nanchang University, Nanchang, Jiangxi, China
| | - Hongping Chen
- Department of Histology and Embryology, Medical College of Nanchang University, Nanchang, Jiangxi, China,Jiangxi Key Laboratory of Experimental Animals, Nanchang University, Nanchang, Jiangxi, China,*Correspondence: Hongping Chen,
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15
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Wu X, Srinivasan P, Basu M, Zhang P, Saruwatari M, Thommandru B, Jacobi A, Behlke M, Sandler A. Tumor Apolipoprotein E is a key checkpoint blocking anti-tumor immunity in mouse melanoma. Front Immunol 2022; 13:991790. [PMID: 36341364 PMCID: PMC9626815 DOI: 10.3389/fimmu.2022.991790] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/28/2022] [Indexed: 11/29/2022] Open
Abstract
Immunotherapy is a key modality in the treatment of cancer, but many tumors remain immune resistant. The classic mouse model of B16-F10 melanoma is immune resistant even in the face of checkpoint inhibition. Apolipoprotein E (apoE), a known immune suppressant is strikingly elevated in many human tumors, but its role in cancer immunology is not defined. We investigated the role of apoE in the immune micro-environment using a mouse melanoma model. We demonstrate that ApoE is -highly expressed in wild-type B16-F10 melanoma and serum levels progressively increase as tumors grow. The conditioned media from wild type ApoE secreting melanoma cells suppress T-cell activation in vitro while this suppressive effect is absent in conditioned media from ApoE knock out tumor cells. Mechanistically, apoE induces IL-10 secreting dendritic cells and stimulates T-cell apoptosis and arrest partially via the lrp8 receptor. Ablating ApoE in mice inoculated with tumor cells enabled tumor cell rejection and was associated with induction of immune pathway activation and immune cell infiltration. Tumor secreted apoE appears to be a potent immune cell checkpoint and targeting apoE is associated with enhanced tumor immunity in the mouse melanoma model.
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Affiliation(s)
- Xiaofang Wu
- The Joseph E. Robert Jr. Center for Surgical Care and The Sheikh Zayed Institute for Pediatric Surgical Innovation, Children’s National Hospital, George Washington University, Washington, DC, United States
| | - Priya Srinivasan
- The Joseph E. Robert Jr. Center for Surgical Care and The Sheikh Zayed Institute for Pediatric Surgical Innovation, Children’s National Hospital, George Washington University, Washington, DC, United States
| | - Mousumi Basu
- The Joseph E. Robert Jr. Center for Surgical Care and The Sheikh Zayed Institute for Pediatric Surgical Innovation, Children’s National Hospital, George Washington University, Washington, DC, United States
| | - Peng Zhang
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Michele Saruwatari
- The Joseph E. Robert Jr. Center for Surgical Care and The Sheikh Zayed Institute for Pediatric Surgical Innovation, Children’s National Hospital, George Washington University, Washington, DC, United States
| | | | - Ashley Jacobi
- Integrated DNA Technologies, Inc., Coralville, IA, United States
| | - Mark Behlke
- Integrated DNA Technologies, Inc., Coralville, IA, United States
| | - Anthony Sandler
- The Joseph E. Robert Jr. Center for Surgical Care and The Sheikh Zayed Institute for Pediatric Surgical Innovation, Children’s National Hospital, George Washington University, Washington, DC, United States
- *Correspondence: Anthony Sandler,
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16
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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Wu C, Li T, Cheng W. The correlation between APOE expression and the clinical characteristics and prognosis of patients with endometrial cancer. Medicine (Baltimore) 2022; 101:e30536. [PMID: 36123916 PMCID: PMC9478276 DOI: 10.1097/md.0000000000030536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
To analyze the expression of apolipoprotein E (APOE) in endometrial cancer and its influence on the long-term prognostic survival of endometrial cancer patients. The specimens of tumor tissues and adjacent normal tissues from 96 endometrial cancer patients from January 2013 to December 2015 were included in this study. Immunohistochemistry was used to measure the expression of APOE in tumor tissues and adjacent normal tissues. Statistical analysis was used to examine the correlation between APOE expression and the clinicopathological characteristics and survival of patients. Kaplan-Meier survival curve was drawn to study the effects of APOE on the prognosis of patients. The positive rate of APOE in endometrial cancer tissue was higher than that in adjacent normal tissues. The expression level of APOE in endometrial cancer was correlated with histological grade, lymph node metastasis, and FIGO stage (P < .05). Lymph node metastasis and APOE were independent risk factors affecting the prognosis and survival of patients (P < .05). The results of Kaplan-Meier survival analysis showed that the survival time of APOE high expression group was shorter than that of low APOE expression. APOE is overexpressed in endometrial cancer tissues, and its expression level can provide important information for clinical diagnosis and treatment.
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Affiliation(s)
- Chaoying Wu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Gynecology, Changzhou Maternal and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, Jiangsu, China
| | - Ting Li
- Department of Pathology, Changzhou Maternal and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, Jiangsu, China
| | - Wenjun Cheng
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- * Correspondence: Wenjun Cheng, Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China (e-mail: )
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18
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Liutkeviciene R, Auzelyte J, Liutkevicius V, Vilkeviciute A, Gedvilaite G, Vaiciulis P, Uloza V. The Role of ApoE Serum Levels and ApoE Gene Polymorphisms in Patients with Laryngeal Squamous Cell Carcinoma. Biomolecules 2022; 12:1013. [PMID: 35892323 PMCID: PMC9331506 DOI: 10.3390/biom12081013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/13/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
Abstract
Recent studies have revealed that the inflammatory ApoE effect may play a significant role in various cancer development. However, this effect has still not been analyzed in patients with laryngeal squamous cell carcinoma (LSCC). In the present study, we evaluated two single nucleotide polymorphisms (SNPs) of ApoE (rs7412 and rs429358) and determined their associations with LSCC development and the LSCC patients’ five-year survival rate. Additionally, we analyzed serum ApoE levels using an enzyme-linked immunosorbent assay. A total of 602 subjects (291 histologically verified LSCC patients and 311 healthy controls) were involved in this study. The genotyping was carried out using the real-time PCR. We revealed that ApoE ε3/ε3 was associated with a 1.7-fold higher probability of developing LSCC (p = 0.001), with 1.7-fold increased odds of developing LSCC without metastasis to the lymph nodes (p = 0.002) and with a 2.0-fold increased odds of developing well-differentiated LSCC (p = 0.008), as well as 1.6-fold increased odds of developing poorly differentiated LSCC development (p = 0.012). The ApoE ε2/ε4 and ε3/ε4 genotypes were associated with a 2.9-fold and 1.5-fold decrease in the likelihood of developing LSCC (p = 0.042; p = 0.037, respectively). ApoE ε3/ε4 was found associated with a 2.4-fold decreased likelihood of developing well-differentiated LSCC (p = 0.013). Conclusion: ApoE ε2/ε4 and ε3/ε4 were found to play a protective role in LSCC development, while ApoE ε3/ε3 may have a risk position in LSCC development.
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Abstract
Nanoparticles (NPs) have demonstrated great promise as immunotherapies for applications ranging from cancer, autoimmunity, and infectious disease. Upon encountering biological fluids, NPs rapidly adsorb biomolecules, forming the "biomolecular corona" (BC), and the altered character of NPs due to their newly acquired biological identity can impact their in vivo fate. Recently, it has been shown that the NP-BC is person-specific, and even minute differences in the biomolecule composition can give rise to altered immune recognition, cellular interactions, pharmacokinetics, and biodistribution. Given the current rise in the development of NP-based therapeutics, it is of utmost importance to better understand how pre-existing conditions, that result in the formation of a personalized BC, can be leveraged to aid in the prediction of the therapeutic outcomes of NPs. In this minireview, we will discuss the formation of the BC, implications of the BC for NP-biological interactions, and its clinical importance in the context of immunomodulation and cancer therapeutics.
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Affiliation(s)
- Jacob Shaw
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 685 W. Baltimore Street, Baltimore, MD 21201, USA.
| | - Ryan M Pearson
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 685 W. Baltimore Street, Baltimore, MD 21201, USA.
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine Street, Baltimore, MD 21201, USA
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, 22 S. Greene Street, Baltimore, MD 21201, USA
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20
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Da W, Yinhang W, Jing Z, Jiamin X, Xinyi G, Yongmao S, Yuefen P. Immune-Related Biomarkers Associated with Lung Metastasis from the Colorectal Cancer Microenvironment. J Interferon Cytokine Res 2022; 42:220-234. [PMID: 35576491 PMCID: PMC9142768 DOI: 10.1089/jir.2021.0214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Immune-associated biomarkers can predict lung metastases from colorectal cancer. Differentially expressed genes (DEGs) were screened from sample data extracted from gene expression omnibus (GEO) database. The DEGs were screened from the lung metastasis (LM) and primary cancer (PC) groups of the Moffitt Cancer Center cohort dataset. Then, the tumor immune microenvironment and abundance of immune cell infiltration analyses were performed, and the immune-related DEGs were retrieved. In addition, the transcription factor (TF)-miRNA-mRNA network was constructed and enrichment analyses of the immune-related DEGs and upregulated and downregulated DEGs were carried out. Then, the protein-protein interaction (PPI) network was conducted and the drug-gene interaction was predicted. A total of 268 DEGs were screened. The Immune_Score of samples in the LM group was significantly higher compared with the PC group. The infiltration ratio of M0 macrophages and M2 macrophages of samples was higher than others. A total of 54 immune-related DEGs in M0 macrophages were screened. Moreover, the TF-miRNA-mRNA network was constructed among 8 miRNA-mRNA and 50 TF-mRNA, and the secreted phosphoprotein 1 was regulated by 12 TFs, and the oxidized low-density lipoprotein receptor 1 was regulated by 3 miRNAs and 3 TFs. The TF SAM pointed domain containing ETS TF was also a downregulated DEG. The Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the DEGs in the TF-miRNA-mRNA network were mainly involved in the interleukin-7 signaling pathway and cell adhesion molecules. In total, 23 protein interactions in this PPI network of M0 macrophage cells were involved in 27 mRNAs. There were 38 drug-gene interactions of immune-related DEGs of M0 macrophage cells predicted to contain 34 small molecule drugs and 8 mRNAs. Finally, the CON cohort dataset verified that the infiltration ratio of M0 and M2 macrophages of the samples was higher.
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Affiliation(s)
- Wang Da
- Department of Colorectal Surgery, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education (Key Laboratory of Molecular Biology in Medical Sciences); The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education (Key Laboratory of Molecular Biology in Medical Sciences); The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wu Yinhang
- Graduate School of Second Clinical Medicine Faculty, Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhuang Jing
- Department of Oncology, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Xu Jiamin
- Department of Nursing, Shaoxing People's Hospital (Shaoxing Hospital, Zhejiang University School of Medicine), Shaoxing, China
| | - Gao Xinyi
- Department of Nephrology, Zhejiang Provincial People's Hospital and Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Hangzhou, China
| | - Song Yongmao
- Department of Colorectal Surgery, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education (Key Laboratory of Molecular Biology in Medical Sciences); The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education (Key Laboratory of Molecular Biology in Medical Sciences); The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Pan Yuefen
- Department of Oncology, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, China
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21
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Zhou H, Liu Z, Wang Y, Wen X, Amador EH, Yuan L, Ran X, Xiong L, Ran Y, Chen W, Wen Y. Colorectal liver metastasis: molecular mechanism and interventional therapy. Signal Transduct Target Ther 2022; 7:70. [PMID: 35246503 PMCID: PMC8897452 DOI: 10.1038/s41392-022-00922-2] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/25/2022] [Accepted: 02/09/2022] [Indexed: 02/08/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most frequently occurring malignancy tumors with a high morbidity additionally, CRC patients may develop liver metastasis, which is the major cause of death. Despite significant advances in diagnostic and therapeutic techniques, the survival rate of colorectal liver metastasis (CRLM) patients remains very low. CRLM, as a complex cascade reaction process involving multiple factors and procedures, has complex and diverse molecular mechanisms. In this review, we summarize the mechanisms/pathophysiology, diagnosis, treatment of CRLM. We also focus on an overview of the recent advances in understanding the molecular basis of CRLM with a special emphasis on tumor microenvironment and promise of newer targeted therapies for CRLM, further improving the prognosis of CRLM patients.
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Affiliation(s)
- Hui Zhou
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan Province, China
| | - Zhongtao Liu
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan Province, China
| | - Yongxiang Wang
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan Province, China
| | - Xiaoyong Wen
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan Province, China
| | - Eric H Amador
- Department of Physics, The University of Texas, Arlington, TX, 76019, USA
| | - Liqin Yuan
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan Province, China
| | - Xin Ran
- Department of Dermatovenereology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Li Xiong
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan Province, China.
| | - Yuping Ran
- Department of Dermatovenereology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Wei Chen
- Department of Physics, The University of Texas, Arlington, TX, 76019, USA. .,Medical Technology Research Centre, Chelmsford Campus, Anglia Ruskin University, Chelmsford, CM1 1SQ, UK.
| | - Yu Wen
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan Province, China.
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22
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Xiao Z, Zhao H. Ferroptosis-Related APOE, BCL3 and ALOX5AP Gene Polymorphisms are Associated with the Risk of Thyroid Cancer. Pharmgenomics Pers Med 2022; 15:157-165. [PMID: 35241926 PMCID: PMC8887669 DOI: 10.2147/pgpm.s352225] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/17/2022] [Indexed: 01/25/2023] Open
Abstract
Purpose This study aimed to evaluate the association between polymorphisms in the ferroptosis-related genes apolipoprotein E (APOE), BCL3 transcription coactivator (BCL3) and arachidonate 5-lipoxygenase activating protein (ALOX5AP) and the risk of thyroid cancer. Methods Six single nucleotide polymorphisms (SNPs) of APOE (rs429358 and rs7412), BCL3 (rs34698726 and rs8100239) and ALOX5AP (rs4076128 and rs4073259) were genotyped in 520 papillary thyroid carcinoma cases and 520 healthy controls using the MassARRAY platform. Results The rs429358-TC, rs34698726-TA/TT, and rs8100239-AT/AA genotypes exhibited an elevated risk of thyroid cancer (prs429358 = 0.002, prs34698726 = 0.007, prs8100239 = 0.002), while rs7412-CT/TT and rs4076128-GA/GG were found to be protective genotypes against the risk of disease (prs7412 = 0.0003, prs4076128 = 0.0001). Genetic model analysis showed that APOE-rs429358 was correlated with an increased risk of disease under dominant and log-additive models (pdominant = 0.0004, plog-additive = 0.0006). BCL3-s34698726 and rs8100239 were associated with an elevated risk of disease under all three genetic models (p < 0.05). In contrast, APOE-rs7412 was related to a decreased risk of thyroid cancer under dominant and log-additive models (pdominant = 0.0001, plog-additive = 0.0001). Moreover, ALOX5AP-rs4076128 was also correlated with a reduced risk of disease under all three genetic models (p < 0.05). Conclusion The results help us better understand how genetic polymorphisms in ferroptosis-related genes are relevant to thyroid cancer susceptibility.
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Affiliation(s)
- Zhifu Xiao
- Department of Thyroid Surgery, Shanxi Provincial People’s Hospital, Taiyuan, Shanxi, 030012, People’s Republic of China
- Correspondence: Zhifu Xiao, Department of Thyroid Surgery, Shanxi Provincial People’s Hospital, 29 Shuangtasi Road, Taiyuan, Shanxi, 030012, People’s Republic of China, Tel/Fax +86 0351-4960327, Email
| | - Haixia Zhao
- Central Lab, General Hospital of Taiyuan Iron and Steel Group, Taiyuan, Shanxi, 030003, People’s Republic of China
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23
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Brasó‐Maristany F, Paré L, Chic N, Martínez‐Sáez O, Pascual T, Mallafré‐Larrosa M, Schettini F, González‐Farré B, Sanfeliu E, Martínez D, Galván P, Barnadas E, Salinas B, Tolosa P, Ciruelos E, Carcelero E, Guillén C, Adamo B, Moreno R, Vidal M, Muñoz M, Prat A. Gene expression profiles of breast cancer metastasis according to organ site. Mol Oncol 2022; 16:69-87. [PMID: 34051058 PMCID: PMC8732356 DOI: 10.1002/1878-0261.13021] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/30/2021] [Accepted: 05/26/2021] [Indexed: 12/22/2022] Open
Abstract
In advanced breast cancer, biomarker identification and patient selection using a metastatic tumor biopsy is becoming more necessary. However, the biology of metastasis according to the organ site is largely unknown. Here, we evaluated the expression of 771 genes in 184 metastatic samples across 11 organs, including liver, lung, brain, and bone, and made the following observations. First, all PAM50 molecular intrinsic subtypes were represented across organs and within immunohistochemistry-based groups. Second, HER2-low disease was identified across all organ sites, including bone, and HER2 expression significantly correlated with ERBB2 expression. Third, the majority of expression variation was explained by intrinsic subtype and not organ of metastasis. Fourth, subtypes and individual subtype-related genes/signatures were significantly associated with overall survival. Fifth, we identified 74 genes whose expression was organ-specific and subtype-independent. Finally, immune profiles were found more expressed in lung compared to brain or liver metastasis. Our results suggest that relevant tumor biology can be captured in metastatic tissues across a variety of organ sites; however, unique biological features according to organ site were also identified and future studies should explore their implications in diagnostic and therapeutic interventions.
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Affiliation(s)
- Fara Brasó‐Maristany
- Translational Genomics and Targeted Therapies in Solid TumorsAugust Pi i Sunyer Biomedical Research Institute (IDIBAPS)BarcelonaSpain
- Department of Medical OncologyHospital Clínic of BarcelonaSpain
| | - Laia Paré
- SOLTI Cooperative GroupBarcelonaSpain
| | - Nuria Chic
- Translational Genomics and Targeted Therapies in Solid TumorsAugust Pi i Sunyer Biomedical Research Institute (IDIBAPS)BarcelonaSpain
- Department of Medical OncologyHospital Clínic of BarcelonaSpain
| | - Olga Martínez‐Sáez
- Translational Genomics and Targeted Therapies in Solid TumorsAugust Pi i Sunyer Biomedical Research Institute (IDIBAPS)BarcelonaSpain
- Department of Medical OncologyHospital Clínic of BarcelonaSpain
| | | | - Meritxell Mallafré‐Larrosa
- Translational Genomics and Targeted Therapies in Solid TumorsAugust Pi i Sunyer Biomedical Research Institute (IDIBAPS)BarcelonaSpain
| | - Francesco Schettini
- Translational Genomics and Targeted Therapies in Solid TumorsAugust Pi i Sunyer Biomedical Research Institute (IDIBAPS)BarcelonaSpain
- Department of Medical OncologyHospital Clínic of BarcelonaSpain
| | - Blanca González‐Farré
- Translational Genomics and Targeted Therapies in Solid TumorsAugust Pi i Sunyer Biomedical Research Institute (IDIBAPS)BarcelonaSpain
- Department of PathologyHospital Clínic de BarcelonaSpain
| | - Esther Sanfeliu
- Translational Genomics and Targeted Therapies in Solid TumorsAugust Pi i Sunyer Biomedical Research Institute (IDIBAPS)BarcelonaSpain
- Department of PathologyHospital Clínic de BarcelonaSpain
| | - Débora Martínez
- Translational Genomics and Targeted Therapies in Solid TumorsAugust Pi i Sunyer Biomedical Research Institute (IDIBAPS)BarcelonaSpain
- Department of Medical OncologyHospital Clínic of BarcelonaSpain
| | - Patricia Galván
- Translational Genomics and Targeted Therapies in Solid TumorsAugust Pi i Sunyer Biomedical Research Institute (IDIBAPS)BarcelonaSpain
- Department of Medical OncologyHospital Clínic of BarcelonaSpain
| | - Esther Barnadas
- Translational Genomics and Targeted Therapies in Solid TumorsAugust Pi i Sunyer Biomedical Research Institute (IDIBAPS)BarcelonaSpain
- Department of Medical OncologyHospital Clínic of BarcelonaSpain
| | | | - Pablo Tolosa
- Department of Clinical OncologyUniversity Hospital 12 de OctubreMadridSpain
| | - Eva Ciruelos
- SOLTI Cooperative GroupBarcelonaSpain
- Department of Clinical OncologyUniversity Hospital 12 de OctubreMadridSpain
| | | | - Cecilia Guillén
- Translational Genomics and Targeted Therapies in Solid TumorsAugust Pi i Sunyer Biomedical Research Institute (IDIBAPS)BarcelonaSpain
- Department of Medical OncologyHospital Clínic of BarcelonaSpain
| | - Barbara Adamo
- Translational Genomics and Targeted Therapies in Solid TumorsAugust Pi i Sunyer Biomedical Research Institute (IDIBAPS)BarcelonaSpain
- Department of Medical OncologyHospital Clínic of BarcelonaSpain
| | - Reinaldo Moreno
- Translational Genomics and Targeted Therapies in Solid TumorsAugust Pi i Sunyer Biomedical Research Institute (IDIBAPS)BarcelonaSpain
- Department of Medical OncologyHospital Clínic of BarcelonaSpain
| | - Maria Vidal
- Translational Genomics and Targeted Therapies in Solid TumorsAugust Pi i Sunyer Biomedical Research Institute (IDIBAPS)BarcelonaSpain
- Department of Medical OncologyHospital Clínic of BarcelonaSpain
- Department of OncologyIOB Institute of OncologyQuironsalud GroupBarcelonaSpain
| | - Montserrat Muñoz
- Translational Genomics and Targeted Therapies in Solid TumorsAugust Pi i Sunyer Biomedical Research Institute (IDIBAPS)BarcelonaSpain
- Department of Medical OncologyHospital Clínic of BarcelonaSpain
| | - Aleix Prat
- Translational Genomics and Targeted Therapies in Solid TumorsAugust Pi i Sunyer Biomedical Research Institute (IDIBAPS)BarcelonaSpain
- Department of Medical OncologyHospital Clínic of BarcelonaSpain
- SOLTI Cooperative GroupBarcelonaSpain
- Department of OncologyIOB Institute of OncologyQuironsalud GroupBarcelonaSpain
- Department of MedicineUniversity of BarcelonaSpain
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24
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Kotula-Balak M, Duliban M, Gurgul A, Krakowska I, Grzmil P, Bilinska B, Wolski JK. Transcriptome analysis of human Leydig cell tumours reveals potential mechanisms underlying its development. Andrologia 2021; 53:e14222. [PMID: 34494678 DOI: 10.1111/and.14222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/01/2021] [Accepted: 08/10/2021] [Indexed: 11/27/2022] Open
Abstract
Leydig cell tumours are the most common sex cord-stromal tumours. In the last years, apparent increased incidence is noted while aetiology of the tumour is still unknown. Therefore, here, we focused on the genetics of Leydig cell tumours using the next-generation sequencing. Leydig cell micronodules were revealed in patients with azoospermia who were qualified for testicular biopsy. Complete gene set of Leydig cell tumours was compared with transcriptome of healthy Leydig cells obtained from donors. Bioinformatic analysis of the obtained sequencing data revealed alterations in expression of 219 transcripts. We showed, for the first time, that a significant proportion of differentially expressed genes is directly involved in regulation of apoptotic process, which downregulation might be important to Leydig cell tumour development. Additionally, we found a significant upregulation of heat shock protein genes that might be a unique feature of Leydig cell tumours when compared to other tumour types. Our study offers fundamental transcriptomic data for future studies on human Leydig cell tumour that are crucial to determine its causes. Moreover, presented here the in-depth analysis and discussion of alterations observed in tumour transcriptome may be important for the diagnosis and therapy of this pathology.
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Affiliation(s)
- Malgorzata Kotula-Balak
- University Centre of Veterinary Medicine JU-UA, University of Agriculture in Krakow, Krakow, Poland
| | - Michal Duliban
- Department of Endocrinology, Institute of Zoology and Biomedical Research, Jagiellonian University in Krakow, Krakow, Poland
| | - Artur Gurgul
- University Centre of Veterinary Medicine JU-UA, University of Agriculture in Krakow, Krakow, Poland
| | - Izabela Krakowska
- University Centre of Veterinary Medicine JU-UA, University of Agriculture in Krakow, Krakow, Poland
| | - Pawel Grzmil
- Department of Genetics and Evolutionism, Institute of Zoology and Biomedical Research, Jagiellonian University in Krakow, Krakow, Poland
| | - Barbara Bilinska
- Department of Endocrinology, Institute of Zoology and Biomedical Research, Jagiellonian University in Krakow, Krakow, Poland
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25
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Lin R, Fogarty CE, Ma B, Li H, Ni G, Liu X, Yuan J, Wang T. Identification of ferroptosis genes in immune infiltration and prognosis in thyroid papillary carcinoma using network analysis. BMC Genomics 2021; 22:576. [PMID: 34315405 PMCID: PMC8314640 DOI: 10.1186/s12864-021-07895-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/13/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Papillary thyroid carcinoma (PTC) is the most common thyroid cancer. While many patients survive, a portion of PTC cases display high aggressiveness and even develop into refractory differentiated thyroid carcinoma. This may be alleviated by developing a novel model to predict the risk of recurrence. Ferroptosis is an iron-dependent form of regulated cell death (RCD) driven by lethal accumulation of lipid peroxides, is regulated by a set of genes and shows a variety of metabolic changes. To elucidate whether ferroptosis occurs in PTC, we analyse the gene expression profiles of the disease and established a new model for the correlation. METHODS The thyroid carcinoma (THCA) datasets were downloaded from The Cancer Genome Atlas (TCGA), UCSC Xena and MisgDB, and included 502 tumour samples and 56 normal samples. A total of 60 ferroptosis related genes were summarised from MisgDB database. Gene set enrichment analysis (GSEA) and Gene set variation analysis (GSVA) were used to analyse pathways potentially involving PTC subtypes. Single sample GSEA (ssGSEA) algorithm was used to analyse the proportion of 28 types of immune cells in the tumour immune infiltration microenvironment in THCA and the hclust algorithm was used to conduct immune typing according to the proportion of immune cells. Spearman correlation analysis was performed on the ferroptosis gene expression and the correlation between immune infiltrating cells proportion. We established the WGCNA to identify genes modules that are highly correlated with the microenvironment of immune invasion. DEseq2 algorithm was further used for differential analysis of sequencing data to analyse the functions and pathways potentially involving hub genes. GO and KEGG enrichment analysis was performed using Clusterprofiler to explore the clinical efficacy of hub genes. Univariate Cox analysis was performed for hub genes combined with clinical prognostic data, and the results was included for lasso regression and constructed the risk regression model. ROC curve and survival curve were used for evaluating the model. Univariate Cox analysis and multivariate Cox analysis were performed in combination with the clinical data of THCA and the risk score value, the clinical efficacy of the model was further evaluated. RESULTS We identify two subtypes in PTC based on the expression of ferroptosis related genes, with the proportion of cluster 1 significantly higher than cluster 2 in ferroptosis signature genes that are positively associated. The mutations of Braf and Nras are detected as the major mutations of cluster 1 and 2, respectively. Subsequent analyses of TME immune cells infiltration indicated cluster 1 is remarkably richer than cluster 2. The risk score of THCA is in good performance evaluated by ROC curve and survival curve, in conjunction with univariate Cox analysis and multivariate Cox analysis results based on the clinical data shows that the risk score of the proposed model could be used as an independent prognostic indicator to predict the prognosis of patients with papillary thyroid cancer. CONCLUSIONS Our study finds seven crucial genes, including Ac008063.2, Apoe, Bcl3, Acap3, Alox5ap, Atxn2l and B2m, and regulation of apoptosis by parathyroid hormone-related proteins significantly associated with ferroptosis and immune cells in PTC, and we construct the risk score model which can be used as an independent prognostic index to predict the prognosis of patients with PTC.
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Affiliation(s)
- Ruoting Lin
- Department of Nuclear Medicine, The First Affiliated Hospital/Clinical Medical School, Guangdong Pharmaceutical University, Guangzhou, 510080, Guangdong, China
| | - Conor E Fogarty
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
| | - Bowei Ma
- Department of TCM Resident Training, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510405, Guangdong, China
| | - Hejie Li
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
| | - Guoying Ni
- Department of Nuclear Medicine, The First Affiliated Hospital/Clinical Medical School, Guangdong Pharmaceutical University, Guangzhou, 510080, Guangdong, China.,Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.,Cancer Research Institute, First People's Hospital of Foshan, Foshan, 528000, Guangdong, China
| | - Xiaosong Liu
- Department of Nuclear Medicine, The First Affiliated Hospital/Clinical Medical School, Guangdong Pharmaceutical University, Guangzhou, 510080, Guangdong, China.,Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.,Cancer Research Institute, First People's Hospital of Foshan, Foshan, 528000, Guangdong, China
| | - Jianwei Yuan
- Department of Nuclear Medicine, The First Affiliated Hospital/Clinical Medical School, Guangdong Pharmaceutical University, Guangzhou, 510080, Guangdong, China.
| | - Tianfang Wang
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.
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26
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Yuan Z, Zhao Z, Hu H, Zhu Y, Zhang W, Tang Q, Huang R, Gao F, Zou C, Wang G, Wang X. IgG Fc Binding Protein ( FCGBP) is Down-Regulated in Metastatic Lesions and Predicts Survival in Metastatic Colorectal Cancer Patients. Onco Targets Ther 2021; 14:967-977. [PMID: 33603401 PMCID: PMC7886382 DOI: 10.2147/ott.s285171] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 01/18/2021] [Indexed: 12/17/2022] Open
Abstract
Background The liver is the most frequent site for metastatic spread in colorectal cancer (CRC) patients, and these patients have much poorer prognosis than those without metastasis. Previous studies have shown that IgG Fc binding protein (FCGBP) plays important roles in tumorigenesis, progression, and prognosis, but its role in CRC metastasis remains unclear. Purpose In this study, we are aimed to explore the significance of FCGBP in liver metastatic CRC (LMCRC) patients. Methods We analyzed the expression of FCGBP RNA between CRC primary samples and liver metastatic samples in the Gene Expression Omnibus (GEO) database and The Cancer Genome Atlas (TCGA). Next, we assessed the expression of FCGBP protein in 135 paired primary CRC (PC) samples and LMCRC samples. Finally, we explored the relationship between the expression features and clinicopathological characteristics. Results The expression data of FCGBP were obtained from the GEO and TCGA databases. FCGBP RNA expression was evaluated between primary lesions (PC) and liver metastatic lesions (LM). FCGBP RNA was down-regulated in PC and LM, and especially lower in LM (p<0.001). Next, the expression of FCGBP protein was evaluated by an immunohistochemistry array in 135 paired primary tumor tissues and metastatic tissues. We found that FCGBP protein was down-regulated in primary lesions and metastatic lesions, especially in metastatic lesions. According to the immunohistochemistry score (SI), each cohort was divided into FCGBP-positive (SI=4–12) and FCGBP-negative (SI=0–3) groups. In both groups, the levels of CEA (PC group, 3.880 vs 77.049, p<0.001; LM group, 3.890 vs 14.239, p=0.008) and CA19-9 (PC group, 8.610 vs 111.700, p<0.001; LM group, 7.660 vs 19.380, p=0.037) were lower than those in the FCGBP-negative group. FCGBP positivity in the LM cohort was an independent risk factor in both overall survival (HR 1.573, 95% Cl [1.017–2.433], p=0.042) and disease-free survival (HR 1.869, 95% Cl [1.256–2.781], p=0.002). Conclusion This study found a relationship between FCGBP expression and clinical information of LMCRC patients, and found that FCGBP expression decreased with disease development. The expression of FCGBP in liver metastasis is associated with both the overall and progression-free survival. Our results show that FCGBP could be a promising prognostic factor for LMCRC.
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Affiliation(s)
- Ziming Yuan
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, People's Republic of China
| | - Zhixun Zhao
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Hanqing Hu
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, People's Republic of China
| | - Yihao Zhu
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, People's Republic of China
| | - Weiyuan Zhang
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, People's Republic of China
| | - Qingchao Tang
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, People's Republic of China
| | - Rui Huang
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, People's Republic of China
| | - Feng Gao
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, People's Republic of China
| | - Chaoxia Zou
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang, People's Republic of China
| | - Guiyu Wang
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, People's Republic of China
| | - Xishan Wang
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, People's Republic of China.,Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
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27
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Rahman MM, Takashima S, Kamatari YO, Badr Y, Kitamura Y, Shimizu K, Okada A, Inoshima Y. Proteomic profiling of milk small extracellular vesicles from bovine leukemia virus-infected cattle. Sci Rep 2021; 11:2951. [PMID: 33536533 DOI: 10.1038/s41598-021-82598-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/22/2021] [Indexed: 12/15/2022] Open
Abstract
Milk small extracellular vesicles (sEV) contain proteins that provide potential information of host physiology and immunology. Bovine leukemia virus (BLV) is an oncogenic virus that causes progressive B-cell lymphosarcoma in cattle. In this study, we aimed to explore the proteomic profile of milk sEV from BLV-infected cattle compared with those from uninfected cattle. Milk sEV were isolated from three BLV-infected and three uninfected cattle. Proteomic analysis was performed by using a comprehensive nanoLC-MS/MS method. Furthermore, gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were used to evaluate the candidates for uniquely or differentially expressed proteins in milk sEV from BLV-infected cattle. Proteomic analysis revealed a total of 1330 common proteins in milk sEV among BLV-infected cattle, whereas 118 proteins were uniquely expressed compared with those from uninfected cattle. Twenty-six proteins in milk sEV were differentially expressed proteins more than two-fold significant difference (p < 0.05) in BLV-infected cattle. GO and KEGG analyses indicated that the candidates for uniquely or differentially expressed proteins in milk sEV had been involved in diverse biological activities including metabolic processes, cellular processes, respond to stimulus, binding, catalytic activities, cancer pathways, focal adhesion, and so on. Taken together, the present findings provided a novel insight into the proteomes of milk sEV from BLV-infected cattle.
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Ahluwalia P, Kolhe R, Gahlay GK. The clinical relevance of gene expression based prognostic signatures in colorectal cancer. Biochim Biophys Acta Rev Cancer 2021; 1875:188513. [PMID: 33493614 DOI: 10.1016/j.bbcan.2021.188513] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 01/14/2021] [Accepted: 01/14/2021] [Indexed: 12/24/2022]
Abstract
Colorectal cancer (CRC) is one of the most prevalent cancers, with more than one million new cases every year. In the last few decades, several advancements in therapeutic and preventative levels have reduced the mortality rate, but new biomarkers are required for improved prognosis. The alterations at the genetic and epigenetic level have been recognized as major players in tumorigenesis. The products of gene expression in the form of mRNA, microRNA, and long-noncoding RNA, have started to emerge as important regulatory molecules, playing an important role in cancer. Gene-expression based prognostic risk scores, which quantify and compare their expression, have emerged as promising biomarkers with enormous clinical value. These composite multi-gene models in which more than one gene is used to predict prognosis have been shown to be significantly effective in identifying patients with multiple clinico-pathological risks like overall mortality, response to chemotherapy, risk of metastasis, etc. The advent of microarray and advanced sequencing technologies have led to the generation of large datasets like TCGA (The Cancer Genome Atlas) and GEO (Gene Expression Omnibus), which have fueled the search for new biomarkers. Continuous evaluation of these candidate biomarkers in clinical settings is promising to improve the management of CRC. These composite gene signatures provide potential in identifying high-risk patients, which might help clinicians to better manage these patients and design appropriate personalized therapeutic interventions. In this review, we emphasize on composite prognostic scores from diverse resources with clinical utility in CRC.
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Affiliation(s)
- Pankaj Ahluwalia
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, India; Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Gagandeep K Gahlay
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, India.
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Kamperidis N, Kamperidis V, Zegkos T, Kostourou I, Nikolaidou O, Arebi N, Karvounis H. Atherosclerosis and Inflammatory Bowel Disease-Shared Pathogenesis and Implications for Treatment. Angiology 2020; 72:303-314. [PMID: 33601945 DOI: 10.1177/0003319720974552] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Atherosclerosis and inflammatory bowel disease (IBD) are often regarded as 2 distinct entities. The commonest manifestation of atherosclerosis is ischemic heart disease (IHD), and an association between IHD and IBD has been reported. Atherosclerosis and IBD share common pathophysiological mechanisms in terms of their genetics, immunology, and contributing environmental factors. Factors associated with atherosclerosis are implicated in the development of IBD and vice versa. Therefore, treatments targeting the common pathophysiology pathways may be effective in both conditions. The current review considers the pathophysiological pathways that are shared between the 2 conditions and discusses the implications for treatment and research.
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Affiliation(s)
- Nikolaos Kamperidis
- 3749St Mark's Hospital, Harrow, London, United Kingdom.,* Nikolaos Kamperidis and Vasileios Kamperidis are sharing first authorship
| | - Vasileios Kamperidis
- 1st Cardiology Department, 37788AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece.,* Nikolaos Kamperidis and Vasileios Kamperidis are sharing first authorship
| | - Thomas Zegkos
- 1st Cardiology Department, 37788AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Olga Nikolaidou
- Radiology Department, Pananikolaou General Hospital, Thessaloniki, Greece
| | - Naila Arebi
- 3749St Mark's Hospital, Harrow, London, United Kingdom
| | - Haralambos Karvounis
- 1st Cardiology Department, 37788AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Chong X, Peng R, Sun Y, Zhang L, Zhang Z. Identification of Key Genes in Gastric Cancer by Bioinformatics Analysis. Biomed Res Int 2020; 2020:7658230. [PMID: 33015179 DOI: 10.1155/2020/7658230] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/12/2020] [Accepted: 09/01/2020] [Indexed: 12/22/2022]
Abstract
Gastric cancer (GC) is one of the most common malignancies of the digestive system with few genetic markers for its early detection and prevention. In this study, differentially expressed genes (DEGs) were analyzed using GEO2R from GSE54129 and GSE13911 of the Gene Expression Omnibus (GEO). Then, gene enrichment analysis, protein-protein interaction (PPI) network construction, and topological analysis were performed on the DEGs by the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, STRING, and Cytoscape. Finally, we performed survival analysis of key genes through the Kaplan-Meier plotter. A total of 1034 DEGs were identified in GC. GO and KEGG results showed that DEGs mainly enriched in plasma membrane, cell adhesion, and PI3K-Akt signaling pathway. Subsequently, the PPI network with 44 nodes and 333 edges was constructed, and 18 candidate genes in the network were focused on by centrality analysis and module analysis. Furthermore, data showed that high expressions of fibronectin 1(FN1), the tissue inhibitor of metalloproteinases 1 (TIMP1), secreted phosphoprotein 1 (SPP1), apolipoprotein E (APOE), and versican (VCAN) were related to poor overall survivals in GC patients. In summary, this study suggests that FN1, TIMP1, SPP1, APOE, and VCAN may act as the key genes in GC.
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Perepitchka M, Galat Y, Beletsky IP, Iannaccone PM, Galat V. Down syndrome iPSC model: endothelial perspective on tumor development. Oncotarget 2020; 11:3387-404. [PMID: 32934781 DOI: 10.18632/oncotarget.27712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 08/01/2020] [Indexed: 12/12/2022] Open
Abstract
Trisomy 21 (T21), known as Down syndrome (DS), is a widely studied chromosomal abnormality. Previous studies have shown that DS individuals have a unique cancer profile. While exhibiting low solid tumor prevalence, DS patients are at risk for hematologic cancers, such as acute megakaryocytic leukemia and acute lymphoblastic leukemia. We speculated that endothelial cells are active players in this clinical background. To this end, we hypothesized that impaired DS endothelial development and functionality, impacted by genome-wide T21 alterations, potentially results in a suboptimal endothelial microenvironment with the capability to prevent solid tumor growth. To test this hypothesis, we assessed molecular and phenotypic differences of endothelial cells differentiated from Down syndrome and euploid iPS cells. Microarray, RNA-Seq, and bioinformatic analyses revealed that most significantly expressed genes belong to angiogenic, cytoskeletal rearrangement, extracellular matrix remodeling, and inflammatory pathways. Interestingly, the majority of these genes are not located on Chromosome 21. To substantiate these findings, we carried out functional assays. The obtained phenotypic results correlated with the molecular data and showed that Down syndrome endothelial cells exhibit decreased proliferation, reduced migration, and a weak TNF-α inflammatory response. Based on this data, we provide a set of genes potentially associated with Down syndrome’s elevated leukemic incidence and its unfavorable solid tumor microenvironment—highlighting the potential use of these genes as therapeutic targets in translational cancer research.
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Li C, Quan J, Wei R, Zhao Z, Guan X, Liu Z, Zou S, Wang X, Jiang Z. Leptin Overexpression as a Poor Prognostic Factor for Colorectal Cancer. Biomed Res Int. 2020;2020:7532514. [PMID: 32596369 DOI: 10.1155/2020/7532514.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Leptin acts as an adipocytokine functions via the leptin receptor, which stimulates growth, migration, and invasion of cancer cells. This study is aimed at identifying leptin as a prognostic factor in colorectal cancer (CRC). The differentially expressed genes with prognostic value in CRC tissues either with or without liver metastasis were assessed based on The Cancer Genomic Atlas (TCGA). Leptin was considered a candidate gene for further analysis. Its expression features of 206 CRC patients without liver metastasis and 201 patients with metastasis on tissue microarrays were assessed by immunochemical staining, and the effect of leptin on survival was assessed by Kaplan-Meier analyses. Overexpressed leptin indicated a poorer prognosis for CRC patients in overall survival (p < 0.05, log-rank test) based on the TCGA database. The leptin expression significantly correlated with metastasis stage (p < .010) and lymph node involvement (p < .010). Multivariate analysis also indicated that strong leptin expression was an independent adverse prognosticator in CRC (p = .017). Leptin may be valued as a prognostic marker could contribute to predicting a clinical outcome for patients with CRC.
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Li C, Quan J, Wei R, Zhao Z, Guan X, Liu Z, Zou S, Wang X, Jiang Z. Leptin Overexpression as a Poor Prognostic Factor for Colorectal Cancer. Biomed Res Int 2020; 2020:7532514. [PMID: 32596369 DOI: 10.1155/2020/7532514] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 04/03/2020] [Indexed: 12/19/2022]
Abstract
Leptin acts as an adipocytokine functions via the leptin receptor, which stimulates growth, migration, and invasion of cancer cells. This study is aimed at identifying leptin as a prognostic factor in colorectal cancer (CRC). The differentially expressed genes with prognostic value in CRC tissues either with or without liver metastasis were assessed based on The Cancer Genomic Atlas (TCGA). Leptin was considered a candidate gene for further analysis. Its expression features of 206 CRC patients without liver metastasis and 201 patients with metastasis on tissue microarrays were assessed by immunochemical staining, and the effect of leptin on survival was assessed by Kaplan-Meier analyses. Overexpressed leptin indicated a poorer prognosis for CRC patients in overall survival (p < 0.05, log-rank test) based on the TCGA database. The leptin expression significantly correlated with metastasis stage (p < .010) and lymph node involvement (p < .010). Multivariate analysis also indicated that strong leptin expression was an independent adverse prognosticator in CRC (p = .017). Leptin may be valued as a prognostic marker could contribute to predicting a clinical outcome for patients with CRC.
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Abstract
Digestive tract cancer, which is characterized by high morbidity and mortality, seriously affects the quality of life of patients worldwide. The digestive tract has abundant blood supply and nutriment, providing a suitable environment for tumor cells. Under chemical, physical, and biological stimuli, the activated cancer-related genes promote tumorigenesis. The synthesis of apolipoprotein occurs in the liver, intestine, and other digestive organs. However, the functions of apolipoproteins are not limited to lipid metabolism. An increasing number of studies have revealed that apolipoproteins take part in the regulation of tumor behavior. Apolipoprotein A (apoA) has recently been acknowledged as a beneficial indicator of several cancers, including colon, hepatocellular, and pancreatic cancer. Apolipoprotein E (apoE) can affect tumor susceptibility on account of genetic polymorphism. Levels of apolipoprotein C (apoC), B (apoB), and D (apoD) also impact tumor progression and the prognosis of patients. However, because of individual, racial, and genetic differences, a consensus has not yet been reached. Based on clinical data and analysis, apolipoproteins could be a novel target and marker in tumor therapy and prevention.
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Affiliation(s)
- Yibo Zhang
- Comprehensive Laboratory, the Third Affiliated Hospital of Soochow University, Changzhou 213003, China
| | - Lu Zheng
- Comprehensive Laboratory, the Third Affiliated Hospital of Soochow University, Changzhou 213003, China
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Son KH, Ahn CB, Kim HJ, Kim JS. Quantitative proteomic analysis of bile in extrahepatic cholangiocarcinoma patients. J Cancer 2020; 11:4073-4080. [PMID: 32368289 PMCID: PMC7196276 DOI: 10.7150/jca.40964] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 03/29/2020] [Indexed: 12/17/2022] Open
Abstract
Background and Aims: Extrahepatic cholangiocarcinoma (CCA) without liver-fluke is increasing. Multifactorial carcinogenesis makes it hard to find biomarkers related to CCA. Although there are a few studies of bile proteomics, these showed different protein profiles because of having heterogeneous groups of patients and different sampling methods. Our aim was to identify the specific bile proteins of extrahepatic CCA patients. Methods: We collected bile from 23 patients undergoing endoscopic nasobiliary drainage in Korea University Guro Hospital from May 2018 to January 2019. The CCA group included 18 patients diagnosed with extrahepatic CCA, and the control group included 5 patients with benign biliary conditions. We analyzed bile proteome using liquid chromatography mass spectrometry. We compared the relative abundance of various proteins in the CCA and control groups. Results: In all, we identified a total of 245 proteins in the bile of CCA and control patients. Increased top 14 proteins in CCA patients were immunoglobulin kappa light chain, apolipoprotein B, inter-alpha-trypsin inhibitor heavy chain H4, apolipoprotein E, Mucin 5B, inter-alpha-trypsin inhibitor heavy chain H1, apolipoprotein A-IV, intercellular adhesion molecule 1, complement C7, complement C5, apolipoprotein C-III, albumin, antithrombin-III, and apolipoprotein A-II. However, the significantly increased proteins in bile of CCA patients comparing with control patients were immunoglobulin kappa light chain, apolipoprotein E, albumin, apolipoprotein A-I, antithrombin-III, α1-antitrypsin, serotransferrin, immunoglobulin heavy constant mu, immunoglobulin J chain, complement C4-A, and complement C3 (p<0.05). Conclusions: In this study, we identified several proteins that were significantly increased in the bile of extrahepatic CCA. Further study is needed to validate them as potential tumor-associated proteins that may be potential biomarkers for CCA.
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Affiliation(s)
- Kuk Hui Son
- Department of Thoracic and Cardiovascular Surgery, Gachon University Gil Medical Center, Gachon University, Incheon, 21565, Republic of Korea
| | - Chi Bum Ahn
- Center for information security technologies, Korea University
| | - Hyo Jung Kim
- Department of Internal Medicine, Korea University Guro Hospital
| | - Jae Seon Kim
- Department of Internal Medicine, Korea University Guro Hospital
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Kopylov AT, Stepanov AA, Malsagova KA, Soni D, Kushlinsky NE, Enikeev DV, Potoldykova NV, Lisitsa AV, Kaysheva AL. Revelation of Proteomic Indicators for Colorectal Cancer in Initial Stages of Development. Molecules 2020; 25:E619. [PMID: 32023884 DOI: 10.3390/molecules25030619] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 02/07/2023] Open
Abstract
Background: Colorectal cancer (CRC) at a current clinical level is still hardly diagnosed, especially with regard to nascent tumors, which are typically asymptotic. Searching for reliable biomarkers of early diagnosis is an extremely essential task. Identification of specific post-translational modifications (PTM) may also significantly improve net benefits and tailor the process of CRC recognition. We examined depleted plasma samples obtained from 41 healthy volunteers and 28 patients with CRC at different stages to conduct comparative proteome-scaled analysis. The main goal of the study was to establish a constellation of protein markers in combination with their PTMs and semi-quantitative ratios that may support and realize the distinction of CRC until the disease has a poor clinical manifestation. Results: Proteomic analysis revealed 119 and 166 proteins for patients in stages I–II and III–IV, correspondingly. Plenty of proteins (44 proteins) reflected conditions of the immune response, lipid metabolism, and response to stress, but only a small portion of them were significant (p < 0.01) for distinguishing stages I–II of CRC. Among them, some cytokines (Clusterin (CLU), C4b-binding protein (C4BP), and CD59 glycoprotein (CD59), etc.) were the most prominent and the lectin pathway was specifically enhanced in patients with CRC. Significant alterations in Inter-alpha-trypsin inhibitor heavy chains (ITIH1, ITIH2, ITIH3, and ITIH4) levels were also observed due to their implication in tumor growth and the malignancy process. Other markers (Alpha-1-acid glycoprotein 2 (ORM2), Alpha-1B-glycoprotein (A1BG), Haptoglobin (HP), and Leucine-rich alpha-2-glycoprotein (LRG1), etc.) were found to create an ambiguous core involved in cancer development but also to exactly promote tumor progression in the early stages. Additionally, we identified post-translational modifications, which according to the literature are associated with the development of colorectal cancer, including kininogen 1 protein (T327-p), alpha-2-HS-glycoprotein (S138-p) and newly identified PTMs, i.e., vitamin D-binding protein (K75-ac and K370-ac) and plasma protease C1 inhibitor (Y294-p), which may also contribute and negatively impact on CRC progression. Conclusions: The contribution of cytokines and proteins of the extracellular matrix is the most significant factor in CRC development in the early stages. This can be concluded since tumor growth is tightly associated with chronic aseptic inflammation and concatenated malignancy related to loss of extracellular matrix stability. Due attention should be paid to Apolipoprotein E (APOE), Apolipoprotein C1 (APOC1), and Apolipoprotein B-100 (APOB) because of their impact on the malfunction of DNA repair and their capability to regulate mTOR and PI3K pathways. The contribution of the observed PTMs is still equivocal, but a significant decrease in the likelihood between modified and native proteins was not detected confidently.
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Jiang Q, Feng W, Xiong C, Lv Y. Integrated bioinformatics analysis of the association between apolipoprotein E expression and patient prognosis in papillary thyroid carcinoma. Oncol Lett 2020; 19:2295-2305. [PMID: 32194729 PMCID: PMC7039105 DOI: 10.3892/ol.2020.11316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 10/16/2019] [Indexed: 01/06/2023] Open
Abstract
The prognosis of most patients with papillary thyroid carcinoma (PTC) is excellent despite some cases of tumor progression or relapse. The present study was designed to reveal possible prognostic risk indicators for PTC. Differentially expressed genes (DEGs) extracted from 4 Gene Expression Omnibus (GEO) cohorts were subjected to functional enrichment analyses by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis. A dataset from The Cancer Genome Atlas (TCGA) was obtained to filter and validate significant genes using cytoHubba, followed by analysis of their association with clinicopathological characteristics and prognosis. In total, 240 DEGs were identified after data preprocessing. These DEGs were enriched in ‘intracellular redox equilibrium’, ‘release of exosome’, ‘cell adhesion’, ‘regulation of extracellular matrix’, ‘collagen binding’ and ‘energy metabolism’ based on GO analysis which including cellular component, molecular function and biological process. KEGG pathway analysis revealed that the DEGs were enriched in thyroid hormone synthesis, pathways in cancer, focal adhesion, metabolic pathways, apoptosis, PPAR signaling pathway and PI3K/AKT signaling pathway. Using cytoHubba, the following hub genes were identified: Apolipoprotein E (APOE); hemoglobin subunit α1 (HBA1); angiotensin II receptor 1 (AGTR1); collagen I α1 (COL1A1); galectin 3 (LGALS3) and TIMP metallopeptidase inhibitor 1 (TIMP1). The expression of these genes was found to be consistent in TCGA datasets. Kaplan-Meier analysis revealed that APOE was significantly associated with overall survival (P=0.00067) and disease free survival (P=0.00220). Additionally, low expression of APOE was significantly associated with older age (P<0.001) and higher TNM stage (P<0.001) compared with the high expression group. Therefore, APOE may function as a predictive risk indicator for progression as well as prognosis of PTC.
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Affiliation(s)
- Qunguang Jiang
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Wenqian Feng
- Department of Operating Room, Nanchang University Second Affiliated Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Chengfeng Xiong
- Department of Thyroid Surgery, Nanchang University Second Affiliated Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Yunxia Lv
- Department of Thyroid Surgery, Nanchang University Second Affiliated Hospital, Nanchang, Jiangxi 330006, P.R. China
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An HJ, Koh HM, Song DH. Apolipoprotein E is a predictive marker for assessing non-small cell lung cancer patients with lymph node metastasis. Pathol Res Pract 2019; 215:152607. [PMID: 31472996 DOI: 10.1016/j.prp.2019.152607] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/06/2019] [Accepted: 08/18/2019] [Indexed: 11/19/2022]
Abstract
BACKGROUND Apolipoprotein E (APOE) modulates lipid homeostasis in the systemic circulation and induces inflammatory immune responses in the tumor microenvironment. We evaluated APOE expression in order to assess tumor progression in non-small cell lung cancer (NSCLC). METHODS Immunohistochemical staining for APOE was performed on tissue microarray blocks from 148 patients who had undergone surgery for NSCLC. The staining intensity and the proportion of APOE-positive tumor cells (based on distinct membranous and cytoplasmic staining) were scored. The relationships between APOE expression and clinical (age, sex, and smoking history) and pathological (TNM stage and histological type) factors were evaluated. RESULTS Positive APOE staining was observed in 93 (64.6%) patients. APOE expression patterns differed among NSCLC histological types (p-value = 0.016). Negative APOE expression was significantly associated with lymph node metastasis in NSCLC (p-value = 0.040). Both cases of N2 (stage IIIA) disease showed negative APOE expression. CONCLUSIONS APOE is a useful marker for assessing NSCLC patients with lymph node metastasis.
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Affiliation(s)
- Hyo Jung An
- Department of Pathology, Gyeongsang National University Changwon Hospital, Changwon, South Korea
| | - Hyun Min Koh
- Department of Pathology, Gyeongsang National University Changwon Hospital, Changwon, South Korea
| | - Dae Hyun Song
- Department of Pathology, Gyeongsang National University Changwon Hospital, Changwon, South Korea; Gyeongsang National University School of Medicine, Jinju, South Korea; Gyeongsang Institute of Health Science, Jinju, South Korea.
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Ahluwalia P, Mondal AK, Bloomer C, Fulzele S, Jones K, Ananth S, Gahlay GK, Heneidi S, Rojiani AM, Kota V, Kolhe R. Identification and Clinical Validation of a Novel 4 Gene-Signature with Prognostic Utility in Colorectal Cancer. Int J Mol Sci 2019; 20:ijms20153818. [PMID: 31387239 PMCID: PMC6696416 DOI: 10.3390/ijms20153818] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 12/22/2022] Open
Abstract
Colorectal cancer (CRC) is a high burden disease with several genes involved in tumor progression. The aim of the present study was to identify, generate and clinically validate a novel gene signature to improve prediction of overall survival (OS) to effectively manage colorectal cancer. We explored The Cancer Genome Atlas (TCGA), COAD and READ datasets (597 samples) from The Protein Atlas (TPA) database to extract a total of 595 candidate genes. In parallel, we identified 29 genes with perturbations in > 6 cancers which are also affected in CRC. These genes were entered in cBioportal to generate a 17 gene panel with highest perturbations. For clinical validation, this gene panel was tested on the FFPE tissues of colorectal cancer patients (88 patients) using Nanostring analysis. Using multivariate analysis, a high prognostic score (composite 4 gene signature-DPP7/2, YWHAB, MCM4 and FBXO46) was found to be a significant predictor of poor prognosis in CRC patients (HR: 3.42, 95% CI: 1.71-7.94, p < 0.001 *) along with stage (HR: 4.56, 95% CI: 1.35-19.15, p = 0.01 *). The Kaplan-Meier analysis also segregated patients on the basis of prognostic score (log-rank test, p = 0.001 *). The external validation using GEO dataset (GSE38832, 122 patients) corroborated the prognostic score (HR: 2.7, 95% CI: 1.99-3.73, p < 0.001 *). Additionally, higher score was able to differentiate stage II and III patients (130 patients) on the basis of OS (HR: 2.5, 95% CI: 1.78-3.63, p < 0.001 *). Overall, our results identify a novel 4 gene prognostic signature that has clinical utility in colorectal cancer.
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Affiliation(s)
- Pankaj Ahluwalia
- Department of Pathology, Anatomic Pathology Section, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar 143005, India
| | - Ashis K Mondal
- Department of Pathology, Anatomic Pathology Section, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA
| | - Chance Bloomer
- Department of Pathology, Anatomic Pathology Section, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA
| | - Sadanand Fulzele
- Department of Orthopedics, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA
| | - Kimya Jones
- Department of Pathology, Anatomic Pathology Section, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA
| | - Sudha Ananth
- Department of Pathology, Anatomic Pathology Section, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA
| | - Gagandeep K Gahlay
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar 143005, India
| | - Saleh Heneidi
- Department of Pathology, Anatomic Pathology Section, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA
| | - Amyn M Rojiani
- Department of Pathology, Anatomic Pathology Section, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA
| | - Vamsi Kota
- Department of Medicine, Hematology Oncology Section, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA.
| | - Ravindra Kolhe
- Department of Pathology, Anatomic Pathology Section, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA.
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