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Nithyasree V, Magdalene P, Praveen Kumar PK, Preethi J, Gromiha MM. Role of HSP90 in Type 2 Diabetes Mellitus and Its Association with Liver Diseases. Mol Biotechnol 2024:10.1007/s12033-024-01251-1. [PMID: 39162909 DOI: 10.1007/s12033-024-01251-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 07/31/2024] [Indexed: 08/21/2024]
Abstract
Non-alcoholic fatty acid liver disease (NAFLD), non-alcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC) are the fatal liver diseases which encompass a spectrum of disease severity associated with increased risk of type 2 diabetes mellitus (T2DM), a metabolic disorder. Heat shock proteins serve as markers in early prognosis and diagnosis of early stages of liver diseases associated with metabolic disorder. This review aims to comprehensively investigate the significance of HSP90 isoforms in T2DM and liver diseases. Additionally, we explore the collective knowledge on plant-based drug compounds that regulate HSP90 isoform targets, highlighting their potential in treating T2DM-associated liver diseases. Furthermore, this review focuses on the computational systems' biology and next-generation sequencing technology approaches that are used to unravel the potential medicine for the treatment of pleiotropy of these 2 diseases and to further elucidate the mechanism.
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Affiliation(s)
- V Nithyasree
- Department of Biotechnology, Sri Venkateswara College of Engineering, Sriperumbudur Tk, Pennalur, Tamil Nadu, 602117, India
| | - P Magdalene
- Department of Biotechnology, Sri Venkateswara College of Engineering, Sriperumbudur Tk, Pennalur, Tamil Nadu, 602117, India
| | - P K Praveen Kumar
- Department of Biotechnology, Sri Venkateswara College of Engineering, Sriperumbudur Tk, Pennalur, Tamil Nadu, 602117, India.
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, 600036, India.
| | - J Preethi
- Department of Biotechnology, Sri Venkateswara College of Engineering, Sriperumbudur Tk, Pennalur, Tamil Nadu, 602117, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, 600036, India
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Pan C, Gu Y, Ni Q. The Prognostic Value of Serum Albumin to Globulin Ratio in Patients with Breast Cancer: A Retrospective Study. BREAST CANCER (DOVE MEDICAL PRESS) 2024; 16:403-411. [PMID: 39081848 PMCID: PMC11287198 DOI: 10.2147/bctt.s471747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 07/24/2024] [Indexed: 08/02/2024]
Abstract
Objective This study examined the potential risk value of the serum albumin to globulin ratio (AGR) in patients with breast cancer (BC). Methods This study employed a retrospective design, enrolling 332 patients with BC and 38 patients without BC treated at Taizhou People's Hospital between September 2015 and May 2021. Multivariate Cox proportional hazard regression models were used to identify potential risk factors. A prognostic nomogram was developed based on the multivariate analyses. The receiver operating characteristic curve determined the optimal cutoff value for AGR. Results The results indicated a statistically significant decrease in AGR among patients with BC. Significant disparities were observed in globulin and AGR levels between the two cohorts. AGR was significantly associated with tumor size and stage, with a marked decline in advanced stages of BC. Additionally, AGR and aspartate transaminase/Alanine aminotransferase (AST/ALT) emerged as significant diagnostic indicators for invasive carcinoma and advanced stages (II-IV) of BC. Specifically, AGR exhibited an area under the curve of 0.645 (P < 0.003), highlighting the discriminatory capacity of serum globulin levels in distinguishing between BC and non-BC cohorts. Conclusions The AGR, routinely assessed due to its simplicity, objectivity, and cost-effectiveness, holds promise as a potential risk factor for BC and may have practical implications in clinical settings.
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Affiliation(s)
- Chi Pan
- Department of General Surgery, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, People’s Republic of China
| | - Yawen Gu
- Department of Oncology, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, People’s Republic of China
| | - Qingtao Ni
- Department of Oncology, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, People’s Republic of China
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Bian Y, Liu H, Huang J, Feng Z, Lin Y, Li J, Zhang L. eHSP90α in front-line therapy in EGFR exon 19 deletion and 21 Leu858Arg mutations in advanced lung adenocarcinoma. BMC Cancer 2024; 24:835. [PMID: 38997622 PMCID: PMC11245848 DOI: 10.1186/s12885-024-12573-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 06/27/2024] [Indexed: 07/14/2024] Open
Abstract
PURPOSE Extracellular heat shock protein 90 AA1(eHSP90α) is intricately linked to tumor progression and prognosis. This study aimed to investigate the difference in the value of eHSP90α in post-treatment response assessment and prognosis prediction between exon 19 deletion(19DEL) and exon 21 Leu858Arg(L858R) mutation types in lung adenocarcinoma(LUAD). METHODS We analyzed the relationship between the expression of eHSP90α and clinicopathological features in 89 patients with L858R mutation and 196 patients with 19DEL mutation in LUAD. The Kaplan-Meier survival curve was used to determine their respective cut-off values and analyze the relationship between eHSP90α expression and the survival time of the two mutation types. The area under the curve (AUC) was used to evaluate the diagnostic performance of biomarkers. Then, the prognostic model was developed using the univariate-Cox multivariate-Cox and LASSO-multivariate logistic methods. RESULTS In LUAD patients, eHSP90α was positively correlated with carcinoembryonic antigen(CEA), carbohydrate antigen 125(CA125), and carbohydrate antigen 153(CA153). The truncated values of eHSP90α in L858R and 19DEL patients were 44.5 ng/mL and 40.8 ng/mL, respectively. Among L858R patients, eHSP90α had the best diagnostic performance (AUC = 0.765), and higher eHSP90α and T helper cells(Th cells) expression were significantly related to shorter overall survival(OS) and worse treatment response. Also, high eHSP90a expression and short progression-free survival(PFS) were significantly correlated. Among 19DEL patients, CEA had the best diagnostic efficacy (AUC = 0.734), and CEA and Th cells were independent prognostic factors that predicted shorter OS. Furthermore, high CA125 was significantly associated with short PFS and poor curative effect. CONCLUSIONS eHSP90α has a better prognostic value in LUAD L858R patients than 19DEL, which provides a new idea for clinical diagnosis and treatment.
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Affiliation(s)
- Yingzhen Bian
- Department of Research, Guangxi Medical University Cancer Hospital, Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Haizhou Liu
- Department of Research, Guangxi Medical University Cancer Hospital, Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, 530021, China
- Guangxi Cancer Molecular Medicine Engineering Research Center, Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Jinglei Huang
- Department of Research, Guangxi Medical University Cancer Hospital, Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Zhaorong Feng
- Department of Research, Guangxi Medical University Cancer Hospital, Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Yanyan Lin
- Department of Research, Guangxi Medical University Cancer Hospital, Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Jilin Li
- Department of Research, Guangxi Medical University Cancer Hospital, Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, 530021, China.
- Guangxi Cancer Molecular Medicine Engineering Research Center, Guangxi Zhuang Autonomous Region, Nanning, 530021, China.
| | - Litu Zhang
- Department of Research, Guangxi Medical University Cancer Hospital, Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, 530021, China.
- Guangxi Cancer Molecular Medicine Engineering Research Center, Guangxi Zhuang Autonomous Region, Nanning, 530021, China.
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Zhang J, Shi X, Wang M, Zhai R, Wang M, Gong Z, Ni Z, Xu T, Zhu W, Liu L. Identification of immunogenic cell death-related damage-related molecular patterns (DAMPs) to predict outcomes in patients with head and neck squamous cell carcinoma. J Cancer Res Clin Oncol 2024; 150:240. [PMID: 38713284 PMCID: PMC11076381 DOI: 10.1007/s00432-024-05779-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 05/03/2024] [Indexed: 05/08/2024]
Abstract
PURPOSE Head and neck cancer is the sixth most common type of cancer worldwide, wherein the immune responses are closely associated with disease occurrence, development, and prognosis. Investigation of the role of immunogenic cell death-related genes (ICDGs) in adaptive immune response activation may provide cues into the mechanism underlying the outcome of HNSCC immunotherapy. METHODS ICDGs expression patterns in HNSCC were analyzed, after which consensus clustering in HNSCC cohort conducted. A 4-gene prognostic model was constructed through LASSO and Cox regression analyses to analyze the prognostic index using the TCGA dataset, followed by validation with two GEO datasets. The distribution of immune cells and the response to immunotherapy were compared between different risk subtypes through multiple algorithms. Moreover, immunohistochemical (IHC) analyses were conducted to validate the prognostic value of HSP90AA1 as a predictor of HNSCC patient prognosis. In vitro assays were performed to further detect the effect of HSP90AA1 in the development of HNSCC. RESULTS A novel prognostic index based on four ICDGs was constructed and proved to be useful as an independent factor of HNSCC prognosis. The risk score derived from this model grouped patients into high- and low-risk subtypes, wherein the high-risk subtype had worse survival outcomes and poorer immunotherapy response. IHC analysis validated the applicability of HSP90AA1 as a predictor of prognosis of HNSCC patients. HSP90AA1 expression in tumor cells promotes the progression of HNSCC. CONCLUSIONS Together, these results highlight a novel four-gene prognostic signature as a valuable tool to assess survival status and prognosis of HNSCC patients.
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Affiliation(s)
- Jiayi Zhang
- Department of Basic Science of Stomatology, The Affiliated Stomatological Hospital of Nanjing Medical University, Jiangsu, China
- State Key Laboratory Cultivation Base of Research, Prevention and Treatment for Oral Diseases, Nanjing Medical University, Jiangsu, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Jiangsu, China
| | - Xinzhan Shi
- Department of Basic Science of Stomatology, The Affiliated Stomatological Hospital of Nanjing Medical University, Jiangsu, China
- State Key Laboratory Cultivation Base of Research, Prevention and Treatment for Oral Diseases, Nanjing Medical University, Jiangsu, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Jiangsu, China
| | - Mengqi Wang
- Department of Basic Science of Stomatology, The Affiliated Stomatological Hospital of Nanjing Medical University, Jiangsu, China
- State Key Laboratory Cultivation Base of Research, Prevention and Treatment for Oral Diseases, Nanjing Medical University, Jiangsu, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Jiangsu, China
| | - Rundong Zhai
- Department of Basic Science of Stomatology, The Affiliated Stomatological Hospital of Nanjing Medical University, Jiangsu, China
- State Key Laboratory Cultivation Base of Research, Prevention and Treatment for Oral Diseases, Nanjing Medical University, Jiangsu, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Jiangsu, China
| | - Mengyao Wang
- Department of Basic Science of Stomatology, The Affiliated Stomatological Hospital of Nanjing Medical University, Jiangsu, China
- State Key Laboratory Cultivation Base of Research, Prevention and Treatment for Oral Diseases, Nanjing Medical University, Jiangsu, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Jiangsu, China
| | - Zizhen Gong
- Department of Basic Science of Stomatology, The Affiliated Stomatological Hospital of Nanjing Medical University, Jiangsu, China
- State Key Laboratory Cultivation Base of Research, Prevention and Treatment for Oral Diseases, Nanjing Medical University, Jiangsu, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Jiangsu, China
| | - Zihui Ni
- Department of Basic Science of Stomatology, The Affiliated Stomatological Hospital of Nanjing Medical University, Jiangsu, China
- State Key Laboratory Cultivation Base of Research, Prevention and Treatment for Oral Diseases, Nanjing Medical University, Jiangsu, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Jiangsu, China
| | - Teng Xu
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital of Nanjing Medical University, Jiangsu, China
- State Key Laboratory Cultivation Base of Research, Prevention and Treatment for Oral Diseases, Nanjing Medical University, Jiangsu, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Jiangsu, China
| | - Weiwen Zhu
- Department of Basic Science of Stomatology, The Affiliated Stomatological Hospital of Nanjing Medical University, Jiangsu, China
- State Key Laboratory Cultivation Base of Research, Prevention and Treatment for Oral Diseases, Nanjing Medical University, Jiangsu, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Jiangsu, China
| | - Laikui Liu
- Department of Basic Science of Stomatology, The Affiliated Stomatological Hospital of Nanjing Medical University, Jiangsu, China.
- State Key Laboratory Cultivation Base of Research, Prevention and Treatment for Oral Diseases, Nanjing Medical University, Jiangsu, China.
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Jiangsu, China.
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Liu XW, Wang P, Zhang L, Zhu Y, Zhai JY, Wang CN, Li J, Xiao J. Single-cell RNA sequencing and ATAC sequencing identify novel biomarkers for bicuspid aortic valve-associated thoracic aortic aneurysm. Front Cardiovasc Med 2024; 11:1265378. [PMID: 38685981 PMCID: PMC11057375 DOI: 10.3389/fcvm.2024.1265378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 02/26/2024] [Indexed: 05/02/2024] Open
Abstract
Introduction Bicuspid aortic valve (BAV) is the most prevalent congenital cardiovascular defect and known to cause thoracic aortic aneurysms (TAAs). To improve our understanding of BAV pathogenesis, we characterized the cellular composition of BAV tissues and identified molecular changes in each cell population. Methods Tissue samples from two patients with BAV and two heart transplant donors were analyzed using single-cell RNA sequencing, assay for transposase-accessible chromatin using sequencing, and weighted gene coexpression network analysis for differential gene analysis. TAA-related changes were evaluated by comparing the proportion of each cell type and gene expression profiles between TAA and control tissues. Further, by combining our single-cell RNA sequencing data with publicly available data from genome-wide association studies, we determined critical genes for BAV. Results We found 20 cell subpopulations in TAA tissues, including multiple subtypes of smooth muscle cells, fibroblasts, macrophages, and T lymphocytes. This result suggested that these cells play multiple functional roles in BAV development. Several differentially expressed genes, including CD9, FHL1y, HSP90AA1, GAS6, PALLD, and ACTA2, were identified. Discussion We believe that this comprehensive assessment of the cellular composition of TAA tissues and the insights into altered gene expression patterns can facilitate identification of novel diagnostic biomarkers and therapeutic targets for BAV-associated TAA.
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Affiliation(s)
- Xu-Wen Liu
- School of Medicine, Guangxi University, Nanning, China
| | - Pei Wang
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Li Zhang
- School of Medicine, Guangxi University, Nanning, China
| | - Yu Zhu
- School of Health Sciences and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Jun-Yu Zhai
- Department of Cardiac Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chang-Nan Wang
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Jun Li
- Department of Cardiac Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jian Xiao
- School of Medicine, Guangxi University, Nanning, China
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China
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Wang HF, Chen Y, Cao B, Pei J. Potential Value of HSP90α in Prognosis of Triple-Negative Breast Cancer. Med Sci Monit 2024; 30:e943049. [PMID: 38553816 PMCID: PMC10989195 DOI: 10.12659/msm.943049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/08/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is a distinct subtype of breast cancer, accounting for 12-18% of all breast cancer cases. It exhibits high heterogeneity and aggressiveness, resulting in a poorer prognosis with a high risk of early recurrence and metastasis. Due to the lack of expression of estrogen receptors (ER), progesterone receptors (PR), and human epidermal growth factor receptor 2 (HER2), as well as insensitivity to endocrine therapy, determining a standard treatment for TNBC is challenging. The identification of potential prognostic biomarkers is crucial for developing personalized treatment strategies for patients. MATERIAL AND METHODS Our study investigated the potential value of HSP90a in TNBC prognosis. A retrospective analysis was conducted on 127 TNBC patients and 127 Healthy controls from March 1, 2019 to July 31, 2022. Venous blood was collected and tested for HSP90alpha, CEA, CA199, and CA125, and we recorded the clinical characteristics of the patients, including age, BMI, alcohol consumption status, surgical history, CEA level, CA199 level, CA125 level, HSP90alpha level, tumor size, distant metastases, lymph node metastasis, and TNM stage. Univariate and multivariate methods were used to screen independent risk factors for progression-free survival (PFS) and overall survival (OS). RESULTS HSP90alpha is not only upregulated in TNBC but is also highly correlated with lymph node metastasis and TNM stage. The results of multivariate analysis showed that distant metastasis, TNM stage and HSP90a level were independent factors associated with PFS. BMI, tumor size, TNM stage, surgical history, and HSP90a level were independent factors influencing OS. CONCLUSIONS Our research findings demonstrate a significant association between high HSP90alpha expression and adverse clinical features, suggesting a poorer prognosis for TNBC patients.
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Affiliation(s)
- Han Fei Wang
- Department of Breast Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Ying Chen
- Department of Breast Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Bang Cao
- Department of Breast Surgery, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Jing Pei
- Department of Breast Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
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Paromov V, Uversky VN, Cooley A, Liburd LE, Mukherjee S, Na I, Dayhoff GW, Pratap S. The Proteomic Analysis of Cancer-Related Alterations in the Human Unfoldome. Int J Mol Sci 2024; 25:1552. [PMID: 38338831 PMCID: PMC10855131 DOI: 10.3390/ijms25031552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 02/12/2024] Open
Abstract
Many proteins lack stable 3D structures. These intrinsically disordered proteins (IDPs) or hybrid proteins containing ordered domains with intrinsically disordered protein regions (IDPRs) often carry out regulatory functions related to molecular recognition and signal transduction. IDPs/IDPRs constitute a substantial portion of the human proteome and are termed "the unfoldome". Herein, we probe the human breast cancer unfoldome and investigate relations between IDPs and key disease genes and pathways. We utilized bottom-up proteomics, MudPIT (Multidimensional Protein Identification Technology), to profile differentially expressed IDPs in human normal (MCF-10A) and breast cancer (BT-549) cell lines. Overall, we identified 2271 protein groups in the unfoldome of normal and cancer proteomes, with 148 IDPs found to be significantly differentially expressed in cancer cells. Further analysis produced annotations of 140 IDPs, which were then classified to GO (Gene Ontology) categories and pathways. In total, 65% (91 of 140) IDPs were related to various diseases, and 20% (28 of 140) mapped to cancer terms. A substantial portion of the differentially expressed IDPs contained disordered regions, confirmed by in silico characterization. Overall, our analyses suggest high levels of interactivity in the human cancer unfoldome and a prevalence of moderately and highly disordered proteins in the network.
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Affiliation(s)
- Victor Paromov
- Meharry Proteomics Core, RCMI Research Capacity Core, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
| | - Vladimir N. Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33613, USA; (V.N.U.); (I.N.)
| | - Ayorinde Cooley
- Meharry Bioinformatics Core, Department of Microbiology, Immunology and Physiology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
| | - Lincoln E. Liburd
- Department of Biochemistry, Cancer Biology, Neuroscience & Pharmacology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA (S.M.)
| | - Shyamali Mukherjee
- Department of Biochemistry, Cancer Biology, Neuroscience & Pharmacology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA (S.M.)
| | - Insung Na
- Department of Molecular Medicine, USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33613, USA; (V.N.U.); (I.N.)
| | - Guy W. Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, FL 33613, USA;
| | - Siddharth Pratap
- Meharry Proteomics Core, RCMI Research Capacity Core, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
- Meharry Bioinformatics Core, Department of Microbiology, Immunology and Physiology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
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Zhu L, Wu Y, Zhao H, Guo Z, Bo B, Zheng L. Immunogenic cell death-related classification reveals prognosis and effectiveness of immunotherapy in breast cancer. Sci Rep 2024; 14:2025. [PMID: 38263419 PMCID: PMC10805874 DOI: 10.1038/s41598-024-52353-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/17/2024] [Indexed: 01/25/2024] Open
Abstract
Lack of specific biomarkers and effective drug targets constrains therapeutic research in breast cancer (BC). In this regard, therapeutic modulation of damage-associated molecular patterns (DAMPs)-induced immunogenic cell death (ICD) may help improve the effect of immunotherapy in individuals with BC. The aim of this investigation was to develop biomarkers for ICD and to construct ICD-related risk estimation models to predict prognosis and immunotherapy outcomes of BC. RNA-seq transcriptome information and medical data from individuals with BC (n = 943) were obtained from TCGA. Expression data from a separate BC cohort (GEO: GSE20685) were used for validation. We identified subtypes of high and low ICD gene expression by consensus clustering and assessed the connection between ICD subtypes and tumor microenvironment (TME). In addition, different algorithms were used to construct ICD-based prognostic models of BC. BC samples were categorized into subtypes of high and low ICD expression depending on the expression of genes correlated with ICD. The subtype of ICD high-expression subtypes are correlated with poor prognosis in breast cancer, while ICD low-expression subtypes may predict better clinical outcomes. We also created and verified a predictive signature model depending on four ICD-related genes (ATG5, CD8A, CD8B, and HSP90AA1), which correlates with TME status and predicts clinical outcomes of BC patients. We highlight the connection of ICD subtypes with the dynamic evolution of TME in BC and present a novel ICD-based prognostic model of BC. In clinical practice, distinction of ICD subtype and assessment of ICD-related biomarkers should help guide treatment planning and improve the effectiveness of tumor immunotherapy.
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Affiliation(s)
- Lei Zhu
- Department of General Surgery, Panjin Liao-Oil Field Gem Flower Hospital, Panjin, 124000, China
| | - Yanmei Wu
- Department of Rheumatology and Immunology, Panjin Liao-Oil Field Gem Flower Hospital, Panjin, 124000, China
| | - Haichun Zhao
- Department of General Surgery, Panjin Liao-Oil Field Gem Flower Hospital, Panjin, 124000, China
| | - Zicheng Guo
- Department of General Surgery, Panjin Liao-Oil Field Gem Flower Hospital, Panjin, 124000, China
| | - Biao Bo
- Department of General Surgery, Panjin Liao-Oil Field Gem Flower Hospital, Panjin, 124000, China
| | - Li Zheng
- Department of General Surgery, Panjin Liao-Oil Field Gem Flower Hospital, Panjin, 124000, China.
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Lee JXT, Tan WR, Low ZS, Lee JQ, Chua D, Yeo WDC, See B, Vos MIG, Yasuda T, Nomura S, Cheng HS, Tan NS. YWHAG Deficiency Disrupts the EMT-Associated Network to Induce Oxidative Cell Death and Prevent Metastasis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301714. [PMID: 37759388 PMCID: PMC10625110 DOI: 10.1002/advs.202301714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 08/28/2023] [Indexed: 09/29/2023]
Abstract
Metastasis involves epithelial-to-mesenchymal transition (EMT), a process that is regulated by complex gene networks, where their deliberate disruption may yield a promising outcome. However, little is known about mechanisms that coordinate these metastasis-associated networks. To address this gap, hub genes with broad engagement across various human cancers by analyzing the transcriptomes of different cancer cell types undergoing EMT are identified. The oncogenic signaling adaptor protein tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein gamma (YWHAG) is ranked top for its clinical relevance and impact. The cellular kinome and transcriptome data are surveyed to construct the regulome of YWHAG, revealing stress responses and metabolic processes during cancer EMT. It is demonstrated that a YWHAG-dependent cytoprotective mechanism in the regulome is embedded in EMT-associated networks to protect cancer cells from oxidative catastrophe through enhanced autophagy during EMT. YWHAG deficiency results in a rapid accumulation of reactive oxygen species (ROS), delayed EMT, and cell death. Tumor allografts show that metastasis potential and overall survival time are correlated with the YWHAG expression level of cancer cell lines. Metastasized tumors have higher expression of YWHAG and autophagy-related genes than primary tumors. Silencing YWHAG diminishes primary tumor volumes, prevents metastasis, and prolongs the median survival period of the mice.
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Affiliation(s)
- Jeannie Xue Ting Lee
- Lee Kong Chian School of MedicineClinical Sciences BuildingNanyang Technological University Singapore11 Mandalay RoadSingapore308232Singapore
| | - Wei Ren Tan
- Lee Kong Chian School of MedicineClinical Sciences BuildingNanyang Technological University Singapore11 Mandalay RoadSingapore308232Singapore
| | - Zun Siong Low
- Lee Kong Chian School of MedicineClinical Sciences BuildingNanyang Technological University Singapore11 Mandalay RoadSingapore308232Singapore
| | - Jia Qi Lee
- School of Biological SciencesNanyang Technological University Singapore60 Nanyang DriveSingapore637551Singapore
| | - Damien Chua
- Lee Kong Chian School of MedicineClinical Sciences BuildingNanyang Technological University Singapore11 Mandalay RoadSingapore308232Singapore
| | - Wisely Duan Chi Yeo
- School of Biological SciencesNanyang Technological University Singapore60 Nanyang DriveSingapore637551Singapore
| | - Benedict See
- School of Biological SciencesNanyang Technological University Singapore60 Nanyang DriveSingapore637551Singapore
| | - Marcus Ivan Gerard Vos
- Lee Kong Chian School of MedicineClinical Sciences BuildingNanyang Technological University Singapore11 Mandalay RoadSingapore308232Singapore
| | - Tomohiko Yasuda
- Department of Gastrointestinal SurgeryGraduate School of MedicineThe University of TokyoTokyo113‐8654Japan
- Department of Gastrointestinal SurgeryNippon Medical School Chiba Hokusoh HospitalChiba270‐1694Japan
| | - Sachiyo Nomura
- Department of Gastrointestinal SurgeryGraduate School of MedicineThe University of TokyoTokyo113‐8654Japan
| | - Hong Sheng Cheng
- Lee Kong Chian School of MedicineClinical Sciences BuildingNanyang Technological University Singapore11 Mandalay RoadSingapore308232Singapore
| | - Nguan Soon Tan
- Lee Kong Chian School of MedicineClinical Sciences BuildingNanyang Technological University Singapore11 Mandalay RoadSingapore308232Singapore
- School of Biological SciencesNanyang Technological University Singapore60 Nanyang DriveSingapore637551Singapore
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10
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Tapak L, Hamidi O, Amini P, Afshar S, Salimy S, Dinu I. Identification of Prognostic Biomarkers for Breast Cancer Metastasis
Using Penalized Additive Hazards Regression Model. Cancer Inform 2023; 22:11769351231157942. [PMID: 36968522 PMCID: PMC10034277 DOI: 10.1177/11769351231157942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/30/2023] [Indexed: 03/24/2023] Open
Abstract
Background: Breast cancer (BC) has been reported as one of the most common cancers
diagnosed in females throughout the world. Survival rate of BC patients is
affected by metastasis. So, exploring its underlying mechanisms and
identifying related biomarkers to monitor BC relapse/recurrence using new
statistical methods is essential. This study investigated the
high-dimensional gene-expression profiles of BC patients using penalized
additive hazards regression models. Methods: A publicly available dataset related to the time to metastasis in BC patients
(GSE2034) was used. There was information of 22 283 genes expression
profiles related to 286 BC patients. Penalized additive hazards regression
models with different penalties, including LASSO, SCAD, SICA, MCP and
Elastic net were used to identify metastasis related genes. Results: Five regression models with penalties were applied in the additive hazards
model and jointly found 9 genes including SNU13,
CLINT1, MAPK9, ABCC5,
NKX3-1, NCOR2,
COL2A1, and ZNF219. According the median
of the prognostic index calculated using the regression coefficients of the
penalized additive hazards model, the patients were labeled as high/low risk
groups. A significant difference was detected in the survival curves of the
identified groups. The selected genes were examined using validation data
and were significantly associated with the hazard of metastasis. Conclusion: This study showed that MAPK9, NKX3-1,
NCOR1, ABCC5, and
CD44 are the potential recurrence and metastatic
predictors in breast cancer and can be taken into account as candidates for
further research in tumorigenesis, invasion, metastasis, and
epithelial-mesenchymal transition of breast cancer.
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Affiliation(s)
- Leili Tapak
- Department of Biostatistics, School of
Public Health and Modeling of Noncommunicable Diseases Research Center, Hamadan
University of Medical Sciences, Hamadan, Iran
| | - Omid Hamidi
- Department of Science, Hamedan
University of Technology, Hamedan, Iran
- Omid Hamidi, Department of Science, Hamedan
University of Technology, Pajouhesh Square, Hamedan 6516717432, Iran.
| | - Payam Amini
- Department of Biostatistics, School of
Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Saeid Afshar
- Research Center for Molecular Medicine,
Hamadan University of Medical Sciences, Hamadan, Iran
| | - Siamak Salimy
- Laboratory of System Biology and
Bioinformatics (LBB), Department of Bioinformatics, University of Tehran, Kish,
Iran
| | - Irina Dinu
- School of Public Health, University of
Alberta, Edmonton, AB, Canada
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11
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Pan Z, Bao Y, Hu M, Zhu Y, Tan C, Fan L, Yu H, Wang A, Cui J, Sun G. Role of NAT10-mediated ac4C-modified HSP90AA1 RNA acetylation in ER stress-mediated metastasis and lenvatinib resistance in hepatocellular carcinoma. Cell Death Discov 2023; 9:56. [PMID: 36765042 PMCID: PMC9918514 DOI: 10.1038/s41420-023-01355-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/25/2023] [Accepted: 01/31/2023] [Indexed: 02/12/2023] Open
Abstract
Emerging evidence showed that epigenetic regulation plays important role in the pathogenesis of HCC. N4-acetocytidine (ac4C) was an acetylation chemical modification of mRNA, and NAT10 is reported to regulate ac4C modification and enhance endoplasmic reticulum stress (ERS) in tumor metastasis. Here, we report a novel mechanism by which NAT10-mediated mRNA ac4C-modified HSP90AA1 regulates metastasis and tumor resistance in ERS of HCC. Immunohistochemical, bioinformatics analyses, and in vitro and in vivo experiments, e.g., acRIP-Seq, RNA-Seq, and double luciferase reporter experiment, were employed to investigate the effect of NAT10 on metastasis and drug resistance in HCC. The increased expression of NAT10 was associated with HCC risk and poor prognosis. Cell and animal experiments showed that NAT10 enhanced the metastasis ability and apoptosis resistance of HCC cells in ERS and ERS state. NAT10 could upregulate the modification level of HSP90AA1 mRNA ac4C, maintain the stability of HSP90AA1, and upregulate the expression of HSP90AA1, which further promotes the metastasis of ERS hepatoma cells and the resistance to apoptosis of Lenvatinib. This study proposes a novel mechanism by which NAT10-mediated mRNA ac4C modification regulates tumor metastasis. In addition, we demonstrated the regulatory effect of NAT10-HSP90AA1 on metastasis and drug resistance of ERS in HCC cells.
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Affiliation(s)
- Zhipeng Pan
- grid.412679.f0000 0004 1771 3402Department of Medical Oncology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022 China
| | - Yawei Bao
- grid.59053.3a0000000121679639Department of Radiation Oncology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Mengyao Hu
- grid.412679.f0000 0004 1771 3402Department of Medical Oncology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022 China ,grid.412679.f0000 0004 1771 3402Department of Integrated Traditional Chinese and Western Medicine, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022 China
| | - Yue Zhu
- grid.412679.f0000 0004 1771 3402Department of Medical Oncology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022 China
| | - Chaisheng Tan
- grid.412679.f0000 0004 1771 3402Department of Medical Oncology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022 China
| | - Lulu Fan
- grid.412679.f0000 0004 1771 3402Department of Medical Oncology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022 China
| | - Hanqing Yu
- grid.412679.f0000 0004 1771 3402Department of Medical Oncology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022 China
| | - Anqi Wang
- grid.412679.f0000 0004 1771 3402Department of Medical Oncology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022 China
| | - Jie Cui
- grid.412679.f0000 0004 1771 3402Department of Medical Oncology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022 China
| | - Guoping Sun
- Department of Medical Oncology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, China.
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12
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Ling J, Zhang L, Wang Y, Chang A, Huang Y, Zhao H, Zhuo X. Fisetin, a dietary flavonoid, increases the sensitivity of chemoresistant head and neck carcinoma cells to cisplatin possibly through HSP90AA1/IL-17 pathway. Phytother Res 2023; 37:1997-2011. [PMID: 36631292 DOI: 10.1002/ptr.7723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/05/2022] [Accepted: 12/18/2022] [Indexed: 01/13/2023]
Abstract
Cisplatin (DDP) resistance is a bottleneck in the treatment of head and neck cancer (HNC), leading to poor prognosis. Fisetin, a dietary flavonoid, has low toxicity and high antitumor activity with unclear mechanisms. We intended to predict the targets of fisetin for reversing DDP-resistance and further verify their expressions and roles. A network pharmacology approach was applied to explore the target genes. The hub genes were screened out and subjected to molecular docking and experimental verification (in vivo and in vitro). Thirty-two genes common to fisetin and DDP-resistance were screened, including three hub genes, namely HSP90AA1, PPIA, and PTPRS. Molecular docking suggested that fisetin and the candidate proteins could bind tightly. HSP90AA1 was identified as the key gene. Administration of fisetin increased the sensitivity of chemoresistant cells (Cal27/DDP and FaDu/DDP) to DDP, accompanied by the downregulation of HSP90AA1 and IL-17. HSP90AA1 silencing increases the sensitivity of DDP-resistant cells to DDP, which was mediated by IL-17. In summary, fisetin might inhibit the chemoresistance of HNC cells to DDP by targeting the HSP90AA1/IL-17 pathway. Several hub genes might be the targets of fisetin for reversing DDP-resistance in HNC cells and might also serve as prognostic factors and therapeutic targets for HNC.
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Affiliation(s)
- Junjun Ling
- Department of Otorhinolaryngology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Liang Zhang
- Department of Otorhinolaryngology, Affiliated Hospital of Guizhou Medical University, Guiyang, China.,Department of Respiratory Medicine, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Yan Wang
- Department of Internal Medicine, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Aoshuang Chang
- Department of Otorhinolaryngology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Yi Huang
- Department of Respiratory Medicine, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Houyu Zhao
- Department of Otorhinolaryngology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Xianlu Zhuo
- Department of Otorhinolaryngology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
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13
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Alagundagi DB, Ghate SD, Rajendra VKJ, Gollapalli P, Shetty VV, D’Souza C, Shetty P, Patil P. Exploring breast cancer exosomes for novel biomarkers of potential diagnostic and prognostic importance. 3 Biotech 2023; 13:7. [PMID: 36532861 PMCID: PMC9751250 DOI: 10.1007/s13205-022-03422-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
The comprehensive bioinformatics analysis of breast cancer exosomes revealed that HSP90AA1, CCT2, and ENO1 were novel hub genes in the giant protein-protein interaction network of 110 exosomal proteins. Exosomes and their cargo such as discrete proteins, nucleic acids, and lipids are having potential role in the pathophysiology of breast cancer (BC). This study showed that the identified hub genes were particularly abundant in GO and KEGG pathways relevant to the positive regulation of telomerase. In addition, these hub genes were found to be considerably overexpressed in breast adenocarcinoma patients compared to healthy controls, and further, this overexpression is linked to the poor prognosis in BC patients. Furthermore, the ROC analysis revealed that CCT2 gene has strong diagnostic and prognostic value for BC. Additionally, this in silico analysis found that the anticancer agents and HSP90 inhibitors such as ganetespib, retaspimycin, and tanespimycin would have considerable potential in the treatment of BC. Overall, this study findings imply that HSP90AA1, a molecular chaperon and CCT2, a chaperonin would serve as diagnostic and prognostic biomarkers, respectively, for BC. However, these findings need to be further confirmed by laboratory and clinical studies for validating their potential applications. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03422-w.
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Affiliation(s)
- Dhananjay B. Alagundagi
- Central Research Laboratory, K S Hegde Medical Academy, NITTE (Deemed to be University), Deralakatte, Mangaluru, Karnataka 575018 India
| | - Sudeep D. Ghate
- Center for Bioinformatics and Biostatistics, K S Hegde Medical Academy, NITTE (Deemed to be University), Mangaluru, Karnataka 575018 India
| | - Vinay Kumar J. Rajendra
- Department of Oncology, Justice K S Hegde Charitable Hospital, K S Hegde Medical Academy, NITTE (Deemed to be University), Mangaluru, Karnataka 575018 India
| | - Pavan Gollapalli
- Center for Bioinformatics and Biostatistics, K S Hegde Medical Academy, NITTE (Deemed to be University), Mangaluru, Karnataka 575018 India
| | - Vijith V. Shetty
- Department of Oncology, Justice K S Hegde Charitable Hospital, K S Hegde Medical Academy, NITTE (Deemed to be University), Mangaluru, Karnataka 575018 India
| | - Caren D’Souza
- Department of General Surgery, Justice K S Hegde Charitable Hospital, K S Hegde Medical Academy, NITTE (Deemed to be University), Mangaluru, Karnataka 575018 India
| | - Praveenkumar Shetty
- Central Research Laboratory, Department of Biochemistry, K S Hegde Medical Academy, NITTE (Deemed to be University), Mangaluru, Karnataka 575018 India
| | - Prakash Patil
- Central Research Laboratory, K S Hegde Medical Academy, NITTE (Deemed to be University), Deralakatte, Mangaluru, Karnataka 575018 India
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14
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Jayathirtha M, Whitham D, Alwine S, Donnelly M, Neagu AN, Darie CC. Investigating the Function of Human Jumping Translocation Breakpoint Protein (hJTB) and Its Interacting Partners through In-Solution Proteomics of MCF7 Cells. Molecules 2022; 27:8301. [PMID: 36500393 PMCID: PMC9740069 DOI: 10.3390/molecules27238301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/30/2022] Open
Abstract
Human jumping translocation breakpoint (hJTB) gene is located on chromosome 1q21 and is involved in unbalanced translocation in many types of cancer. JTB protein is ubiquitously present in normal cells but it is found to be overexpressed or downregulated in various types of cancer cells, where this protein and its isoforms promote mitochondrial dysfunction, resistance to apoptosis, genomic instability, proliferation, invasion and metastasis. Hence, JTB could be a tumor biomarker for different types of cancer, such as breast cancer (BC), and could be used as a drug target for therapy. However, the functions of the protein or the pathways through which it increases cell proliferation and invasiveness of cancer cells are not well-known. Therefore, we aim to investigate the functions of JTB by using in-solution digestion-based cellular proteomics of control and upregulated and downregulated JTB protein in MCF7 breast cancer cell line, taking account that in-solution digestion-based proteomics experiments are complementary to the initial in-gel based ones. Proteomics analysis allows investigation of protein dysregulation patterns that indicate the function of the protein and its interacting partners, as well as the pathways and biological processes through which it functions. We concluded that JTB dysregulation increases the epithelial-mesenchymal transition (EMT) potential and cell proliferation, harnessing cytoskeleton organization, apical junctional complex, metabolic reprogramming, and cellular proteostasis. Deregulated JTB expression was found to be associated with several proteins involved in mitochondrial organization and function, oxidative stress (OS), apoptosis, and interferon alpha and gamma signaling. Consistent and complementary to our previous results emerged by using in-gel based proteomics of transfected MCF7 cells, JTB-related proteins that are overexpressed in this experiment suggest the development of a more aggressive phenotype and behavior for this luminal type A non-invasive/poor-invasive human BC cell line that does not usually migrate or invade compared with the highly metastatic MDA-MB-231 cells. This more aggressive phenotype of MCF7 cells related to JTB dysregulation and detected by both in-gel and in-solution proteomics could be promoted by synergistic upregulation of EMT, Mitotic spindle and Fatty acid metabolism pathways. However, in both JTB dysregulated conditions, several downregulated JTB-interacting proteins predominantly sustain antitumor activities, attenuating some of the aggressive phenotypical and behavioral traits promoted by the overexpressed JTB-related partners.
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Affiliation(s)
- Madhuri Jayathirtha
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Shelby Alwine
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Mary Donnelly
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, “AlexandruIoanCuza” University of Iasi, Carol I bvd. No. 20A, 700505 Iasi, Romania
| | - Costel C. Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
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15
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Du QC, Wang XY, Hu CK, Zhou L, Fu Z, Liu S, Wang J, Ma YY, Liu MY, Yu H. Integrative analysis of platelet-related genes for the prognosis of esophageal cancer. World J Clin Cases 2022; 10:12077-12088. [PMID: 36483802 PMCID: PMC9724514 DOI: 10.12998/wjcc.v10.i33.12077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 08/15/2022] [Accepted: 10/11/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Every year, esophageal cancer is responsible for 509000 deaths and around 572000 new cases worldwide. Although esophageal cancer treatment options have advanced, patients still have a dismal 5-year survival rate.
AIM To investigate the relationship between genes associated to platelets and the prognosis of esophageal cancer.
METHODS We searched differentially expressed genes for changes between 151 tumor tissues and 653 normal, healthy tissues using the “limma” package. To develop a prediction model of platelet-related genes, a univariate Cox regression analysis and least absolute shrinkage and selection operator Cox regression analysis were carried out. Based on a median risk score, patients were divided into high-risk and low-risk categories. A nomogram was created to predict the 1-, 2-, and 3-year overall survival (OS) of esophageal cancer patients using four platelet-related gene signatures, TNM stages, and pathological type. Additionally, the concordance index, receiver operating characteristic curve, and calibration curve were used to validate the nomogram.
RESULTS The prognosis of esophageal cancer was associated to APOOL, EP300, PLA2G6, and VAMP7 according to univariate Cox regression analysis and least absolute shrinkage and selection operator regression analysis. Patients with esophageal cancer at high risk had substantially shorter OS than those with cancer at low risk, according to a Kaplan-Meier analysis (P < 0.05). TNM stage (hazard ratio: 2.187, 95% confidence interval: 1.242-3.852, P = 0.007) in both univariate and multivariate Cox regression and risk score were independently correlated with OS (hazard ratio: 2.451, 95% confidence interval: 1.599-3.756, P < 0.001).
CONCLUSION A survival risk score model and independent prognostic variables for esophageal cancer have been developed using APOOL, EP300, PLA2G6, and VAMP7. OS for esophageal cancer might be predicted using the nomogram based on TNM stage, pathological type, and risk score. The nomogram demonstrated strong predictive ability, as shown by the concordance index, receiver operating characteristic curve, and calibration curve.
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Affiliation(s)
- Qian-Cheng Du
- Department of Thoracic Surgery, Shanghai Xuhui Central Hospital, Shanghai 200031, China
| | - Xin-Yu Wang
- Department of General Surgery, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, Shanghai 200434, China
| | - Cheng-Kai Hu
- Department of Thoracic Surgery, Shanghai Xuhui Central Hospital, Shanghai 200031, China
| | - Ling Zhou
- Department of General Surgery, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, Shanghai 200434, China
| | - Zheng Fu
- Department of Thoracic Surgery, Shanghai Xuhui Central Hospital, Shanghai 200031, China
| | - Shun Liu
- Department of Thoracic Surgery, Shanghai Xuhui Central Hospital, Shanghai 200031, China
| | - Jian Wang
- Department of Thoracic Surgery, Shanghai Xuhui Central Hospital, Shanghai 200031, China
| | - Ying-Ying Ma
- Department of Thoracic Surgery, Shanghai Xuhui Central Hospital, Shanghai 200031, China
| | - Meng-Yao Liu
- Department of Thoracic Surgery, Shanghai Xuhui Central Hospital, Shanghai 200031, China
| | - Hua Yu
- Department of General Surgery, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, Shanghai 200434, China
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16
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Wang X, Huang H, Liu X, Li J, Wang L, Li L, Li Y, Han T. Immunogenic cell death-related classifications in breast cancer identify precise immunotherapy biomarkers and enable prognostic stratification. Front Genet 2022; 13:1052720. [PMID: 36437951 PMCID: PMC9685311 DOI: 10.3389/fgene.2022.1052720] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 10/27/2022] [Indexed: 12/01/2023] Open
Abstract
Background: Immunogenic cell death (ICD) remodels the tumor immune microenvironment, plays an inherent role in tumor cell apoptosis, and promotes durable protective antitumor immunity. Currently, appropriate biomarker-based ICD immunotherapy for breast cancer (BC) is under active exploration. Methods: To determine the potential link between ICD genes and the clinical risk of BC, TCGA-BC was used as the training set and GSE58812 was used as the validation set. Gene expression, consistent clustering, enrichment analysis, and mutation omics analyses were performed to analyze the potential biological pathways of ICD genes involved in BC. Furthermore, a risk and prognosis model of ICD was constructed to evaluate the correlation between risk grade and immune infiltration, clinical stage, and survival prognosis. Results: We identified two ICD-related subtypes by consistent clustering and found that the C2 subtype was associated with good survival prognosis, abundant immune cell infiltration, and high activity of immune biological processes. Based on this, we constructed and validated an ICD risk and prognosis model of BC, including ATG5, HSP90AA1, PIK3CA, EIF2AK3, MYD88, IL1R1, and CD8A. This model can effectively predict the survival rate of patients with BC and is negatively correlated with the immune microenvironment and clinical stage. Conclusion: This study provides new insights into the role of ICD in BC. The novel classification risk model based on ICD in BC established in this study can aid in estimating the potential prognosis of patients with BC and the clinical outcomes of immunotherapy and postulates targets that are more useful in comprehensive treatment strategies.
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Affiliation(s)
- Xue Wang
- Pharmacology of Traditional Chinese Medical Formulae, College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Hailiang Huang
- College of Rehabilitation Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xijian Liu
- Pharmacology of Traditional Chinese Medical Formulae, College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jiuwei Li
- College of Medical, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Lu Wang
- Office of Academic Research, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Ling Li
- Pharmacology of Traditional Chinese Medical Formulae, College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yaxing Li
- Pharmacology of Traditional Chinese Medical Formulae, College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Tao Han
- Pharmacology of Traditional Chinese Medical Formulae, College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
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17
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Transcription profiling of feline mammary carcinomas and derived cell lines reveals biomarkers and drug targets associated with metabolic and cell cycle pathways. Sci Rep 2022; 12:17025. [PMID: 36220861 PMCID: PMC9553959 DOI: 10.1038/s41598-022-20874-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/20/2022] [Indexed: 12/29/2022] Open
Abstract
The molecular heterogeneity of feline mammary carcinomas (FMCs) represents a prognostic and therapeutic challenge. RNA-Seq-based comparative transcriptomic profiling serves to identify recurrent and exclusive differentially expressed genes (DEGs) across sample types and molecular subtypes. Using mass-parallel RNA-Seq, we identified DEGs and performed comparative function-based analysis across 15 tumours (four basal-like triple-negative [TN], eight normal-like TN, and three luminal B fHER2 negative [LB fHER2-]), two cell lines (CL, TiHo-0906, and TiHo-1403) isolated from the primary tumours (LB fHER2-) of two cats included in this study, and 13 healthy mammary tissue controls. DEGs in tumours were predominantly upregulated; dysregulation of CLs transcriptome was more extensive, including mostly downregulated genes. Cell-cycle and metabolic-related DEGs were upregulated in both tumours and CLs, including therapeutically-targetable cell cycle regulators (e.g. CCNB1, CCNB2, CDK1, CDK4, GTSE1, MCM4, and MCM5), metabolic-related genes (e.g. FADS2 and SLC16A3), heat-shock proteins (e.g. HSPH1, HSP90B1, and HSPA5), genes controlling centrosome disjunction (e.g. RACGAP1 and NEK2), and collagen molecules (e.g. COL2A1). DEGs specifically upregulated in basal-like TN tumours were involved in antigen processing and presentation, in normal-like TN tumours encoded G protein-coupled receptors (GPCRs), and in LB fHER2- tumours were associated with lysosomes, phagosomes, and endosomes formation. Downregulated DEGs in CLs were associated with structural and signalling cell surface components. Hence, our results suggest that upregulation of genes enhancing proliferation and metabolism is a common feature among FMCs and derived CLs. In contrast, the dissimilarities observed in dysregulation of membrane components highlight CLs' disconnection with the tumour microenvironment. Furthermore, recurrent and exclusive DEGs associated with dysregulated pathways might be useful for the development of prognostically and therapeutically-relevant targeted panels.
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18
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El Bezawy R, Percio S, Ciniselli CM, De Cesare M, Colella G, Dugo M, Veneroni S, Doldi V, Martini S, Baratti D, Kusamura S, Verderio P, Deraco M, Gandellini P, Zaffaroni N, Zuco V. miR-550a-3p is a prognostic biomarker and exerts tumor-suppressive functions by targeting HSP90AA1 in diffuse malignant peritoneal mesothelioma. Cancer Gene Ther 2022; 29:1394-1404. [PMID: 35352023 PMCID: PMC9576593 DOI: 10.1038/s41417-022-00460-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/10/2022] [Indexed: 11/08/2022]
Abstract
Diffuse malignant peritoneal mesothelioma (DMPM) is a rare and rapidly lethal tumor, poorly responsive to conventional treatments. In this regards, the identification of molecular alterations underlying DMPM onset and progression might be exploited to develop novel therapeutic strategies. Here, we focused on miR-550a-3p, which we found downregulated in 45 DMPM clinical samples compared to normal tissues and whose expression levels were associated with patient outcome. Through a gain-of-function approach using miRNA mimics in 3 DMPM cell lines, we demonstrated the tumor-suppressive role of miR-550a-3p. Specifically, miRNA ectopic expression impaired cell proliferation and invasiveness, enhanced the apoptotic response, and reduced the growth of DMPM xenografts in mice. Antiproliferative and proapoptotic effects were also observed in prostate and ovarian cancer cell lines following miR-550a-3p ectopic expression. miR-550a-3p effects were mediated, at least in part, by the direct inhibition of HSP90AA1 and the consequent downregulation of its target proteins, the levels of which were rescued upon disruption of miRNA-HSP90AA1 mRNA pairing, partially abrogating miR-550a-3p-induced cellular effects. Our results show that miR-550a-3p reconstitution affects several tumor traits, thus suggesting this approach as a potential novel therapeutic strategy for DMPM.
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Affiliation(s)
- Rihan El Bezawy
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, 20133, Milan, Italy
| | - Stefano Percio
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, 20133, Milan, Italy
| | - Chiara Maura Ciniselli
- Bioinformatics and Biostatistics Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, 20133, Milan, Italy
| | - Michelandrea De Cesare
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, 20133, Milan, Italy
| | - Gennaro Colella
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, 20133, Milan, Italy
| | - Matteo Dugo
- Department of Medical Oncology, IRCCS Ospedale San Raffaele, 20132, Milan, Italy
| | - Silvia Veneroni
- Biomarkers Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, 20133, Milan, Italy
| | - Valentina Doldi
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, 20133, Milan, Italy
| | - Silvia Martini
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, 20133, Milan, Italy
| | - Dario Baratti
- Peritoneal Surface Malignancies Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, 20133, Milan, Italy
| | - Shigeki Kusamura
- Peritoneal Surface Malignancies Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, 20133, Milan, Italy
| | - Paolo Verderio
- Bioinformatics and Biostatistics Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, 20133, Milan, Italy
| | - Marcello Deraco
- Peritoneal Surface Malignancies Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, 20133, Milan, Italy
| | - Paolo Gandellini
- Department of Biosciences, University of Milan, 20133, Milan, Italy
| | - Nadia Zaffaroni
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, 20133, Milan, Italy.
| | - Valentina Zuco
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, 20133, Milan, Italy
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Hu X, Zhao S, Cai Y, Swain SS, Yao L, Liu W, Yan T. Network Pharmacology-Integrated Molecular Docking Reveals the Expected Anticancer Mechanism of Picrorhizae Rhizoma Extract. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3268773. [PMID: 36158891 PMCID: PMC9507705 DOI: 10.1155/2022/3268773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/17/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022]
Abstract
This study sought to explore the anticancer mechanism of Picrorhizae Rhizoma (PR) extract based on network pharmacology and molecular docking. The potential chemicals of PR were screened through the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database and relevant literatures. Corresponding targets of active ingredients were found with the help of the UniProtKB database, and therapeutic targets for cancer action were screened with the help of the GeneCards database. We used Cytoscape software to construct the compound-target-pathway network of PR extract. We utilized the STRING database to obtain the protein-protein interaction (PPI) network. We used DAVID database combining Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Finally, molecular docking was employed for initial efficacy checking. We have identified 16 potential active components of PR through screening, involving 112 disease action targets. Utilizing the GeneCards database, 112 intersecting targets between PR extract and cancer were found, which mainly exerts anticancer effects by regulating tumor necrosis factor (TNF), recombinant caspase 3 (CASP3), c-Jun NH2-terminal kinase (JNK)/JUN, epidermal growth factor receptor (EGFR), and estrogen receptor-1 (ESR1) with some other target genes and pathways associated with cancer. The major anticancer species are prostate cancer, colorectal cancer, small cell lung cancer, etc. In the molecular docking study, herbactin had a strong affinity for TNF. Based on network pharmacology and molecular docking studies, PR and their compounds have demonstrated potential anticancer activities against several key targets. Our preliminary findings provide a strong foundation for further experiments with PR constituents.
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Affiliation(s)
- Xiaomeng Hu
- University and College Key Lab of Natural Product Chemistry and Application in Xinjiang, School of Chemistry and Environmental Science, Yili Normal University, Yining 835000, China
| | - Shengchao Zhao
- University and College Key Lab of Natural Product Chemistry and Application in Xinjiang, School of Chemistry and Environmental Science, Yili Normal University, Yining 835000, China
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Yi Cai
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China
| | - Shasank S. Swain
- Division of Microbiology and NCDs, ICMR-Regional Medical Research Centre, Bhubaneswar, 751023 Odisha, India
| | - Liangliang Yao
- Affiliated Hospital of Jiangxi University of Chinese Medicine, Nanchang 330006, China
| | - Wei Liu
- University and College Key Lab of Natural Product Chemistry and Application in Xinjiang, School of Chemistry and Environmental Science, Yili Normal University, Yining 835000, China
| | - Tingdong Yan
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai 200444, China
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Tian Y, Gao M, Huang L, Zhou H, Wang J. ATP6AP1 is a potential prognostic biomarker and is associated with iron metabolism in breast cancer. Front Genet 2022; 13:958290. [PMID: 36147483 PMCID: PMC9486317 DOI: 10.3389/fgene.2022.958290] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/10/2022] [Indexed: 11/24/2022] Open
Abstract
Cancer occurrence and progression may be facilitated by aberrant expression of ATPase H+ transporting accessory protein 1 (ATP6AP1). However, the clinical relevance of ATP6AP1 in breast cancer remains unclear. In this study, we investigated the association between ATP6AP1 and breast cancer. Data collected from patients with breast cancer from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) were used in this study. To determine the relationship between ATP6AP1 and breast cancer survival rates, Kaplan-Meier analysis was used. To determine the prognostic value of ATP6AP1, a receiver operating characteristic (ROC) curve was constructed. To identify the major pathways involving ATP6AP1, we performed functional enrichment analysis using gene set enrichment analysis (GSEA). We analyzed the association between ATP6AP1 expression and tumor immunity using the ESTIMATE algorithm and single-sample GSEA (ssGSEA). A nomogram based on a Cox regression analysis was constructed to predict the impact of ATP6AP1 on prognosis. ATP6AP1 expression was significantly upregulated in breast cancer tissues. Moreover, patients with elevated ATP6AP1 expression had shorter total survival rates than those with lower expression levels (p = 0.032). The area under the receiver operating characteristic curve for ATP6AP1 was 0.939. Gene set enrichment analysis revealed that reaction iron uptake and transport, proteasome degradation, glutathione metabolism, and pyruvate metabolism were enriched in the ATP6AP1 high expression phenotype. The relationship between immune infiltration cells and ATP6AP1 expression, including macrophages, B cells, dendritic cells, cytotoxic cells, NK cells, and T cells, was found to be negative, suggesting that ATP6AP1 overexpression results in immunosuppression. Based on the Cox regression analyses, the calibration plot of the nomogram demonstrated effective performance in predicting breast cancer patients. ATP6AP1 may facilitate breast cancer progression by inhibiting antitumor immunity and promoting iron metabolism and may be a biomarker for breast cancer prognosis.
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Affiliation(s)
- Ye Tian
- Department of Thyroid and Breast Surgery, Wuhan No, 1 Hospital, Wuhan, China
| | - Ming Gao
- Department of Blood Transfusion, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liang Huang
- Department of Blood Transfusion, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hu Zhou
- Department of Blood Transfusion, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Juan Wang
- Department of Blood Transfusion, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Juan Wang,
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21
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Sager RA, Khan F, Toneatto L, Votra SD, Backe SJ, Woodford MR, Mollapour M, Bourboulia D. Targeting extracellular Hsp90: A unique frontier against cancer. Front Mol Biosci 2022; 9:982593. [PMID: 36060252 PMCID: PMC9428293 DOI: 10.3389/fmolb.2022.982593] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
The molecular chaperone Heat Shock Protein-90 (Hsp90) is known to interact with over 300 client proteins as well as regulatory factors (eg. nucleotide and proteins) that facilitate execution of its role as a chaperone and, ultimately, client protein activation. Hsp90 associates transiently with these molecular modulators during an eventful chaperone cycle, resulting in acquisition of flexible structural conformations, perfectly customized to the needs of each one of its client proteins. Due to the plethora and diverse nature of proteins it supports, the Hsp90 chaperone machinery is critical for normal cellular function particularly in response to stress. In diseases such as cancer, the Hsp90 chaperone machinery is hijacked for processes which encompass many of the hallmarks of cancer, including cell growth, survival, immune response evasion, migration, invasion, and angiogenesis. Elevated levels of extracellular Hsp90 (eHsp90) enhance tumorigenesis and the potential for metastasis. eHsp90 has been considered one of the new targets in the development of anti-cancer drugs as there are various stages of cancer progression where eHsp90 function could be targeted. Our limited understanding of the regulation of the eHsp90 chaperone machinery is a major drawback for designing successful Hsp90-targeted therapies, and more research is still warranted.
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Affiliation(s)
- Rebecca A. Sager
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, United States
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Farzana Khan
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, United States
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Lorenzo Toneatto
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, United States
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, United States
- Department of Medicine and Surgery, Vita-Salute San Raffaele University, Milan, Italy
| | - SarahBeth D. Votra
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Sarah J. Backe
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, United States
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, United States
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Mark R. Woodford
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, United States
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, United States
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Mehdi Mollapour
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, United States
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, United States
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Dimitra Bourboulia
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, United States
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, United States
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
- *Correspondence: Dimitra Bourboulia,
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Xiao J, Liu T, Liu Z, Xiao C, Du J, Zuo S, Li H, Gu H. A Differentiation-Related Gene Prognostic Index Contributes to Prognosis and Immunotherapy Evaluation in Patients with Hepatocellular Carcinoma. Cells 2022; 11:cells11152302. [PMID: 35892599 PMCID: PMC9367442 DOI: 10.3390/cells11152302] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/14/2022] [Accepted: 07/21/2022] [Indexed: 12/04/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common gastrointestinal tumor with a poor prognosis, which is associated with poor differentiation of tumor cells. However, the potential value of cell differentiation-related molecules in predicting the benefit and prognosis of immune checkpoint inhibitors (ICI) therapy remains unknown. Herein, to investigate the differentiation trajectory of HCC cells and their clinical significance, a differentiation-related gene prognostic index (DRGPI) based on HCC differentiation-related genes (HDRGs) was constructed to elucidate the immune characteristics and therapeutic benefits of ICI in the HCC subgroup defined by DRGPI. Single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data from four HCC samples were integrated for bioinformatics analysis. Then, PON1, ADH4, SQSTM1, HSP90AA1, and STMN1 were screened out to construct a DRGPI. More intriguingly, RT-qPCR validation of the expression of these genes yielded consistent results with the TCGA database. Next, the risk scoring (RS) constructed based on DRGPI suggested that the overall survival (OS) of the DRGPI-high patients was significantly worse than that of the DRGPI-low patients. A nomogram was constructed based on DRGPI-RS and clinical characteristics, which showed strong predictive performance and high accuracy. The comprehensive results indicated that a low DRGPI score was associated with low TP53 mutation rates, high CD8 T cell infiltration, and more benefit from ICI therapy. Homoplastically, the high DRGPI score reflected the opposite results. Taken together, our study highlights the significance of HCC cell differentiation in predicting prognosis, indicating immune characteristics, and understanding the therapeutic benefits of ICI, and suggests that DRGPI is a valuable prognostic biomarker for HCC.
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Affiliation(s)
- Jingjing Xiao
- School of Clinical Medicine, Guizhou Medical University, Guiyang 550000, China; (J.X.); (T.L.); (C.X.); (J.D.); (S.Z.); (H.L.)
- Department of Hepatobiliary Surgery, Guizhou Provincial People’s Hospital, Guiyang 550002, China;
- Department of Pediatric Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang 550000, China
| | - Tao Liu
- School of Clinical Medicine, Guizhou Medical University, Guiyang 550000, China; (J.X.); (T.L.); (C.X.); (J.D.); (S.Z.); (H.L.)
- Department of Hepatobiliary Surgery, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi 445000, China
| | - Zhenhua Liu
- Department of Hepatobiliary Surgery, Guizhou Provincial People’s Hospital, Guiyang 550002, China;
| | - Chuan Xiao
- School of Clinical Medicine, Guizhou Medical University, Guiyang 550000, China; (J.X.); (T.L.); (C.X.); (J.D.); (S.Z.); (H.L.)
| | - Jun Du
- School of Clinical Medicine, Guizhou Medical University, Guiyang 550000, China; (J.X.); (T.L.); (C.X.); (J.D.); (S.Z.); (H.L.)
- Department of Pediatric Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang 550000, China
| | - Shi Zuo
- School of Clinical Medicine, Guizhou Medical University, Guiyang 550000, China; (J.X.); (T.L.); (C.X.); (J.D.); (S.Z.); (H.L.)
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang 550000, China
| | - Haiyang Li
- School of Clinical Medicine, Guizhou Medical University, Guiyang 550000, China; (J.X.); (T.L.); (C.X.); (J.D.); (S.Z.); (H.L.)
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang 550000, China
| | - Huajian Gu
- School of Clinical Medicine, Guizhou Medical University, Guiyang 550000, China; (J.X.); (T.L.); (C.X.); (J.D.); (S.Z.); (H.L.)
- Department of Pediatric Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang 550000, China
- Correspondence: ; Tel.: +86-851-8677-2723
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23
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Comprehensive Computational Analysis of Honokiol Targets for Cell Cycle Inhibition and Immunotherapy in Metastatic Breast Cancer Stem Cells. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:4172531. [PMID: 35845599 PMCID: PMC9286982 DOI: 10.1155/2022/4172531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/12/2022] [Indexed: 11/18/2022]
Abstract
Breast cancer stem cells (BCSCs) play a critical role in chemoresistance, metastasis, and poor prognosis of breast cancer. BCSCs are mostly dormant, and therefore, activating them and modulating the cell cycle are important for successful therapy against BCSCs. The tumor microenvironment (TME) promotes BCSC survival and cancer progression, and targeting the TME can aid in successful immunotherapy. Honokiol (HNK), a bioactive polyphenol isolated from the bark and seed pods of Magnolia spp., is known to exert anticancer effects, such as inducing cell cycle arrest, inhibiting metastasis, and overcoming immunotherapy resistance in breast cancer cells. However, the molecular mechanisms of action of HNK in BCSCs, as well as its effects on the cell cycle, remain unclear. This study aimed to explore the potential targets and molecular mechanisms of HNK on metastatic BCSC (mBCSC)-cell cycle arrest and the impact of the TME. Using bioinformatics analyses, we predicted HNK protein targets from several databases and retrieved the genes differentially expressed in mBCSCs from the GEO database. The intersection between the differentially expressed genes (DEGs) and the HNK-targets was determined using a Venn diagram, and the results were analyzed using a protein-protein interaction network, hub gene selection, gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses, genetic alteration analysis, survival rate, and immune cell infiltration levels. Finally, the interaction between HNK and two HNK-targets regulating the cell cycle was analyzed using molecular docking analysis. The identified potential therapeutic targets of HNK (PTTH) included CCND1, SIRT2, AURKB, VEGFA, HDAC1, CASP9, HSP90AA1, and HSP90AB1, which can potentially inhibit the cell cycle of mBCSCs. Moreover, our results showed that PTTH could modulate the PI3K/Akt/mTOR and HIF1/NFkB/pathways. Overall, these findings highlight the potential of HNK as an immunotherapeutic agent for mBCSCs by modulating the tumor immune environment.
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A Risk Model Based on Sorafenib-Response Target Genes Predicts the Prognosis of Patients with HCC. JOURNAL OF ONCOLOGY 2022; 2022:7257738. [PMID: 35799605 PMCID: PMC9256406 DOI: 10.1155/2022/7257738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/23/2022] [Accepted: 05/19/2022] [Indexed: 12/14/2022]
Abstract
Sorafenib is used to treat digestive system tumors in patients who do not respond to or cannot tolerate surgery. However, the roles and inhibitory mechanisms of sorafenib against hepatocellular carcinoma (HCC) are unclear. Differentially expressed genes in tissues from responders and nonresponders to sorafenib were investigated using the HCC GSE109211 data set. Biological functions and mechanisms were studied using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases. The expression levels of differential expressed target genes were identified in HCC tissues, using The Cancer Genome Atlas database, and their prognostic and diagnostic values were explored using survival and receiver operating characteristic curve analysis. A nomogram and risk model of sorafenib-response target genes enabled the evaluation of the prognosis of patients with HCC. The relationship between risk scores and levels of infiltrating immune cells was visualized via correlation analysis. We identified 1620 sorafenib-response target genes involved in the PPAR signaling pathway, antigen processing and presentation, and ferroptosis. SLC41A3, SEC61A1, LRP4, PPM1G, and HSP90AA1 were independent risk factors for a poor prognosis for patients with HCC and had diagnostic value. A risk model based on SLC41A3, SEC61A1, LRP4, PPM1G, and HSP90AA1 expression showed that patients with HCC in the high-risk group had a worse prognosis. Consensus-clustering analysis (performed with K set to 2) distinguished two clusters (the cluster 1 and cluster 2 groups). Patients in cluster 1 survived significantly longer than those in cluster 2. The risk score correlated with the levels of T cells, cytotoxic lymphocytes, CD8+ T cells, macrophages, memory B cells, follicular helper T cells, and other immune cells. The high risk based on the sorafenib-response targets SLC41A3, SEC61A1, LRP4, PPM1G, and HSP90AA1 represented the poor prognosis for patients with HCC and significantly correlated with the levels of immune infiltrating cells in HCC.
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25
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Jayathirtha M, Neagu AN, Whitham D, Alwine S, Darie CC. Investigation of the effects of overexpression of jumping translocation breakpoint (JTB) protein in MCF7 cells for potential use as a biomarker in breast cancer. Am J Cancer Res 2022; 12:1784-1823. [PMID: 35530281 PMCID: PMC9077082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023] Open
Abstract
Jumping translocation breakpoint (JTB) gene acts as a tumor suppressor or an oncogene in different malignancies, including breast cancer (BC), where it was reported as overexpressed. However, the molecular functions, biological processes and underlying mechanisms through which JTB protein causes increased cell growth, proliferation and invasion is still not fully deciphered. Our goal is to identify the functions of JTB protein by cellular proteomics approaches. MCF7 breast cancer cells were transfected with sense orientation of hJTB cDNA in HA, His and FLAG tagged CMV expression vector to overexpress hJTB and the expression levels were confirmed by Western blotting (WB). Proteins extracted from transfected cells were separated by SDS-PAGE and the in-gel digested peptides were analyzed by nano-liquid chromatography tandem mass spectrometry (nanoLC-MS/MS). By comparing the proteome of cells with upregulated conditions of JTB vs control and identifying the protein dysregulation patterns, we aim to understand the function of this protein and its contribution to tumorigenesis. Gene Set Enrichment Analysis (GSEA) algorithm was performed to investigate the biological processes and pathways that are associated with the JTB protein upregulation. The results demonstrated four significantly enriched gene sets from the following significantly upregulated pathways: mitotic spindle assembly, estrogen response late, epithelial-to-mesenchymal transition (EMT) and estrogen response early. JTB protein itself is involved in mitotic spindle pathway by its role in cell division/cytokinesis, and within estrogen response early and late pathways, contributing to discrimination between luminal and mesenchymal breast cancer. Thus, the overexpressed JTB condition was significantly associated with an increased expression of ACTNs, FLNA, FLNB, EZR, MYOF, COL3A1, COL11A1, HSPA1A, HSP90A, WDR, EPPK1, FASN and FOXA1 proteins related to deregulation of cytoskeletal organization and biogenesis, mitotic spindle organization, ECM remodeling, cellular response to estrogen, proliferation, migration, metastasis, increased lipid biogenesis, endocrine therapy resistance, antiapoptosis and discrimination between different breast cancer subtypes. Other upregulated proteins for overexpressed JTB condition are involved in multiple cellular functions and pathways that become dysregulated, such as tumor microenvironment (TME) acidification, the transmembrane transport pathways, glycolytic flux, iron metabolism and oxidative stress, metabolic reprogramming, nucleocytosolic mRNA transport, transcriptional activation, chromatin remodeling, modulation of cell death pathways, stress responsive pathways, and cancer drug resistance. The downregulated proteins for overexpressed JTB condition are involved in adaptive communication between external and internal environment of cells and maintenance between pro-apoptotic and anti-apoptotic signaling pathways, vesicle trafficking and secretion, DNA lesions repair and suppression of genes involved in tumor progression, proteostasis, redox state regulation, biosynthesis of macromolecules, lipolytic pathway, carbohydrate metabolism, dysregulation of ubiquitin-mediated degradation system, cancer cell immune escape, cell-to-cell and cell-to-ECM interactions, and cytoskeletal behaviour. There were no significantly enriched downregulated pathways.
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Affiliation(s)
- Madhuri Jayathirtha
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, “Alexandru Ioan Cuza” University of IasiCarol I Bvd. No. 22, Iasi 700505, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
| | - Shelby Alwine
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
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Chen S, Yu Q, Zhou S. Plasmatic Levels of HSP90α at Diagnosis: A Novel Prognostic Indicator of Clinical Outcome in Advanced Lung Cancer Patients Treated With PD-1/PD-L1 Inhibitors Plus Chemotherapy. Front Oncol 2021; 11:765115. [PMID: 34926266 PMCID: PMC8678125 DOI: 10.3389/fonc.2021.765115] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/03/2021] [Indexed: 12/27/2022] Open
Abstract
Background The purpose of this study was set to investigate the prognostic role of plasmatic levels of heat shock protein 90 alpha (HSP90α) at diagnosis in advanced lung cancer patients treated with Programmed cell death protein 1 (PD-1)/Programmed cell death-Ligand protein 1 (PD-L1) inhibitors plus chemotherapy. Methods A total of 137 advanced lung cancer patients treated with PD-1/PD-L1 inhibitors plus chemotherapy admitted to the Guangxi Medical University Cancer Hospital were enrolled in this study. Smooth curve fitting was conducted to address the nonlinearity of HSP90α and progression-free survival (PFS) and overall survival (OS). We calculated the inflection point using a recursive algorithm. Kaplan–Meier survival analysis and Cox proportional hazards regression model were used to assess the prognostic value of HSP90α for PFS and OS. Subgroup analysis was performed to evaluate the relationship between high HSP90α and disease progression and death risk. Results The average age of patients was 58.6 ± 9.8 years, and 73.7% of them were men. We divided patients according to their plasmatic levels of HSP90α into low (HSP90α <52.7 ng/ml) group and high (HSP90α ≥52.7 ng/ml) group. Kaplan–Meier analysis showed a shorter PFS and OS for the high group with log-rank P < 0.05. Univariate and multivariate analyses indicated that high HSP90α was associated with an increased risk of disease progression and death after fully adjusting potential confounders with hazard ratio (HR) 1.8 (95% CI = 1.0–3.2) and HR 2.4 (95% CI = 1.1–5.1), respectively (P < 0.05). After stratification by subgroup analysis, the relationship between high HSP90α and the risk of disease progression and death was consistent across all patient subgroups. Conclusion Plasmatic levels of HSP90α at diagnosis can be considered a potential independent prognostic marker of advanced lung cancer patients treated with PD-1/PD-L1 inhibitors plus chemotherapy. A further large-scale prospective validation study is needed to determine whether these results are widely applicable.
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Affiliation(s)
- Shubin Chen
- Medical Oncology of Respiratory, Guangxi Cancer Hospital and Guangxi Medical University Affiliated Cancer Hospital, Nanning, China
| | - Qitao Yu
- Medical Oncology of Respiratory, Guangxi Cancer Hospital and Guangxi Medical University Affiliated Cancer Hospital, Nanning, China
| | - Shaozhang Zhou
- Medical Oncology of Respiratory, Guangxi Cancer Hospital and Guangxi Medical University Affiliated Cancer Hospital, Nanning, China
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Poggio P, Sorge M, Seclì L, Brancaccio M. Extracellular HSP90 Machineries Build Tumor Microenvironment and Boost Cancer Progression. Front Cell Dev Biol 2021; 9:735529. [PMID: 34722515 PMCID: PMC8551675 DOI: 10.3389/fcell.2021.735529] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/20/2021] [Indexed: 12/21/2022] Open
Abstract
HSP90 is released by cancer cells in the tumor microenvironment where it associates with different co-chaperones generating complexes with specific functions, ranging from folding and activation of extracellular clients to the stimulation of cell surface receptors. Emerging data indicate that these functions are essential for tumor growth and progression. The understanding of the exact composition of extracellular HSP90 complexes and the molecular mechanisms at the basis of their functions in the tumor microenvironment may represent the first step to design innovative diagnostic tools and new effective therapies. Here we review the impact of extracellular HSP90 complexes on cancer cell signaling and behavior.
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Affiliation(s)
- Pietro Poggio
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Matteo Sorge
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Laura Seclì
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Mara Brancaccio
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
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