1
|
Meng M, Lan T, Tian D, Qin Z, Li Y, Li J, Cao H. Integrative Bioinformatics Analysis Demonstrates the Prognostic Value of Chromatin Accessibility Biomarkers in Clear Cell Renal Cell Carcinoma. Front Oncol 2022; 11:814396. [PMID: 34993155 PMCID: PMC8724435 DOI: 10.3389/fonc.2021.814396] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 11/24/2021] [Indexed: 01/22/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) accounts for 75%–85% of renal cell carcinoma (RCC) and has a poor 5-year survival rate. In recent years, medical advancement has promoted the understanding of the histopathological and molecular characterization of ccRCC; however, the carcinogenesis and molecular mechanisms of ccRCC remain unclear. Chromatin accessibility is an essential determinant of cellular phenotype. This study aimed to explore the potential role of chromatin accessibility in the development and progression of ccRCC. By the combination of open-access genome-wide chromatin accessibility profiles and gene expression profiles in ccRCC, we obtained a total of 13,474 crucial peaks, corresponding to 5,120 crucial genes and 9,185 differentially expressed genes. Moreover, two potential function modules (P2 and G4) that contained 129 upregulated genes were identified via the weighted gene co-expression network analysis (WGCNA). Furthermore, we obtained five independent predictors (FSCN1, SLC17A9, ANKRD13B, ADCY2, and MAPT), and a prognostic model was established based on these genes through the least absolute shrinkage and selection operator-proportional hazards model (LASSO-Cox) analysis. This model can stratify the ccRCC samples into a high-risk and a low-risk group, from which the patients have distinct prognosis. Further analysis demonstrated a completely different immune cell infiltration pattern between these two risk groups. This study also suggested that mast cell resting is associated with the prognosis of ccRCC and could be a target of immunotherapy. Overall, this study indicated that chromatin accessibility plays an essential role in ccRCC. The five prognostic chromatin accessibility biomarkers and the prognostic immune cells can provide a new direction for the treatment of ccRCC.
Collapse
Affiliation(s)
- Meng Meng
- Research Center of Medicine, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,National Supercomputer Center in Guangzhou, Sun Yat-sen University, Guangzhou, China
| | - Tianjun Lan
- Research Center of Medicine, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Oral & Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Duanqing Tian
- Research Center of Medicine, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zeman Qin
- Department of Stomatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yu Li
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, China
| | - Jinsong Li
- Research Center of Medicine, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Oral & Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Haotian Cao
- Research Center of Medicine, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Oral & Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
2
|
Gulfidan G, Beklen H, Sinha I, Kucukalp F, Caloglu B, Esen I, Turanli B, Ayyildiz D, Arga KY, Sinha R. Differential Protein Interactome in Esophageal Squamous Cell Carcinoma Offers Novel Systems Biomarker Candidates with High Diagnostic and Prognostic Performance. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:495-512. [PMID: 34297901 DOI: 10.1089/omi.2021.0085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is among the most dangerous cancers with high mortality and lack of robust diagnostics and personalized/precision therapeutics. To achieve a systems-level understanding of tumorigenesis, unraveling of variations in the protein interactome and determination of key proteins exhibiting significant alterations in their interaction patterns during tumorigenesis are crucial. To this end, we have described differential protein-protein interactions and differentially interacting proteins (DIPs) in ESCC by utilizing the human protein interactome and transcriptome. Furthermore, DIP-centered modules were analyzed according to their potential in elucidation of disease mechanisms and improvement of efficient diagnostic, prognostic, and treatment strategies. Seven modules were presented as potential diagnostic, and 16 modules were presented as potential prognostic biomarker candidates. Importantly, our findings also suggest that 30 out of the 53 repurposed drugs were noncancer drugs, which could be used in the treatment of ESCC. Interestingly, 25 of these, proposed as novel drug candidates here, have not been previously associated in a context of esophageal cancer. In this context, risperidone and clozapine were validated for their growth inhibitory potential in three ESCC lines. Our findings offer a high potential for the development of innovative diagnostic, prognostic, and therapeutic strategies for further experimental studies in line with predictive diagnostics, targeted prevention, and personalization of medical services in ESCC specifically, and personalized cancer care broadly.
Collapse
Affiliation(s)
- Gizem Gulfidan
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Hande Beklen
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Indu Sinha
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Fulya Kucukalp
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Buse Caloglu
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Ipek Esen
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Beste Turanli
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Dilara Ayyildiz
- Department of Bioengineering, Marmara University, Istanbul, Turkey.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Raghu Sinha
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| |
Collapse
|
3
|
Integrated analysis of ceRNA network and tumor-infiltrating immune cells in esophageal cancer. Biosci Rep 2021; 41:228599. [PMID: 33960364 PMCID: PMC8164107 DOI: 10.1042/bsr20203804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 04/03/2021] [Accepted: 04/23/2021] [Indexed: 12/24/2022] Open
Abstract
Background: Esophageal cancer (ESCA) is one of the most commonly diagnosed cancers in the world. Tumor immune microenvironment is closely related to tumor prognosis. The present study aimed at analyzing the competing endogenous RNA (ceRNA) network and tumor-infiltrating immune cells in ESCA. Methods: The expression profiles of mRNAs, lncRNAs, and miRNAs were downloaded from the Cancer Genome Atlas database. A ceRNA network was established based on the differentially expressed RNAs by Cytoscape. CIBERSORT was applied to estimate the proportion of immune cells in ESCA. Prognosis-associated genes and immune cells were applied to establish prognostic models basing on Lasso and multivariate Cox analyses. The survival curves were constructed with Kaplan–Meier method. The predictive efficacy of the prognostic models was evaluated by the receiver operating characteristic (ROC) curves. Results: The differentially expressed mRNAs, lncRNAs, and miRNAs were identified. We constructed the ceRNA network including 23 lncRNAs, 19 miRNAs, and 147 mRNAs. Five key molecules (HMGB3, HOXC8, HSPA1B, KLHL15, and RUNX3) were identified from the ceRNA network and five significant immune cells (plasma cells, T cells follicular helper, monocytes, dendritic cells activated, and neutrophils) were selected via CIBERSORT. The ROC curves based on key genes and significant immune cells all showed good sensitivity (AUC of 3-year survival: 0.739, AUC of 5-year survival: 0.899, AUC of 3-year survival: 0.824, AUC of 5-year survival: 0.876). There was certain correlation between five immune cells and five key molecules. Conclusion: The present study provides an effective bioinformatics basis for exploring the potential biomarkers of ESCA and predicting its prognosis.
Collapse
|
4
|
Zhou MH, Wang XK. Microenvironment-related prognostic genes in esophageal cancer. Transl Cancer Res 2020; 9:7531-7539. [PMID: 35117353 PMCID: PMC8797339 DOI: 10.21037/tcr-20-2288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/26/2020] [Indexed: 11/09/2022]
Abstract
Background Esophageal cancer is one of the most common malignant tumors. The role of tumor microenvironment in esophageal cancer is unclear. Methods The gene expression profiles and clinical data of 158 patients with esophageal cancer were extracted from The Cancer Genome Atlas database. Immune scores and stromal scores were calculated based on ESTIMATE algorithm. According to different immune/stromal scores, differentially expressed genes (DEGs) were identified. The function enrichment, protein interactions of shared DEGs and their associations with overall survival were analyzed. Results In regard to the association of the immune/stromal scores and disease stage, pathological type and overall survival, only the stromal scores among the different stages were significantly different (P=0.015). In the high immune and stromal score groups, 603 shared up-regulated genes were found. The related function and pathways included regulation of lymphocyte activation, cytokine binding and chemokine signaling pathway. Protein-protein interaction analysis showed that ITGAM had the most connections, followed by CXCL10 and CCR2. High expression of 11 genes, including MS4A7, TMIGD3, MS4A4A, EVI2A, MS4A6A, FCER1G, AIF1, GNGT2, LCP2, DNAJC5B and RNASE6, were found to be associated with shorter overall survival. Conclusions Microenvironment-associated functions and pathways were analyzed in esophageal cancer, and 11 microenvironment-associated genes were correlated to poor prognoses. Further studies on these genes may be helpful to understand the tumor microenvironment and provide new therapies for esophageal cancer.
Collapse
Affiliation(s)
- Min-Hang Zhou
- Department of Geriatric Oncology, the Fourth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xin-Kun Wang
- Department of Radiology, the Fourth Medical Center, Chinese PLA General Hospital, Beijing, China
| |
Collapse
|
5
|
Gundersen CB. Cysteine string proteins. Prog Neurobiol 2020; 188:101758. [DOI: 10.1016/j.pneurobio.2020.101758] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 01/06/2020] [Accepted: 01/13/2020] [Indexed: 12/17/2022]
|
6
|
Caruso Bavisotto C, Cipolla C, Graceffa G, Barone R, Bucchieri F, Bulone D, Cabibi D, Campanella C, Marino Gammazza A, Pitruzzella A, Porcasi R, San Biagio PL, Tomasello G, Conway de Macario E, Macario AJL, Cappello F, Rappa F. Immunomorphological Pattern of Molecular Chaperones in Normal and Pathological Thyroid Tissues and Circulating Exosomes: Potential Use in Clinics. Int J Mol Sci 2019; 20:ijms20184496. [PMID: 31514388 PMCID: PMC6770414 DOI: 10.3390/ijms20184496] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 08/31/2019] [Accepted: 09/08/2019] [Indexed: 02/07/2023] Open
Abstract
The thyroid is a major component of the endocrine system and its pathology can cause serious diseases, e.g., papillary carcinoma (PC). However, the carcinogenic mechanisms are poorly understood and clinical useful biomarkers are scarce. Therefore, we determined if there are quantitative patterns of molecular chaperones in the tumor tissue and circulating exosomes that may be useful in diagnosis and provide clues on their participation in carcinogenesis. Hsp27, Hsp60, Hsp70, and Hsp90 were quantified by immunohistochemistry in PC, benign goiter (BG), and normal peritumoral tissue (PT). The same chaperones were assessed in plasma exosomes from PC and BG patients before and after ablative surgery, using Western blotting. Hsp27, Hsp60, and Hsp90 were increased in PC in comparison with PT and BG but no differences were found for Hsp70. Similarly, exosomal levels of Hsp27, Hsp60, and Hsp90 were higher in PC than in BG, and those in PC were higher before ablative surgery than after it. Hsp27, Hsp60, and Hsp90 show distinctive quantitative patterns in thyroid tissue and circulating exosomes in PC as compared with BG, suggesting some implication in the carcinogenesis of these chaperones and indicating their potential as biomarkers for clinical applications.
Collapse
Affiliation(s)
- Celeste Caruso Bavisotto
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), Institute of Human Anatomy and Histology, University of Palermo, 90127 Palermo, Italy.
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90100 Palermo, Italy.
- Institute of Biophysics, National Research Council, 90100 Palermo, Italy.
| | - Calogero Cipolla
- Department of Surgical Oncology and Oral Sciences, University of Palermo, 90127 Palermo, Italy.
| | - Giuseppa Graceffa
- Department of Surgical Oncology and Oral Sciences, University of Palermo, 90127 Palermo, Italy.
| | - Rosario Barone
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), Institute of Human Anatomy and Histology, University of Palermo, 90127 Palermo, Italy.
| | - Fabio Bucchieri
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), Institute of Human Anatomy and Histology, University of Palermo, 90127 Palermo, Italy.
- Institute of Biomedicine and Molecular Immunology, National Research Council, 90100 Palermo, Italy.
| | - Donatella Bulone
- Institute of Biophysics, National Research Council, 90100 Palermo, Italy.
| | - Daniela Cabibi
- Department "G. D'Alessandro", Pathology Institute, University of Palermo, 90127 Palermo, Italy.
| | - Claudia Campanella
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), Institute of Human Anatomy and Histology, University of Palermo, 90127 Palermo, Italy.
| | - Antonella Marino Gammazza
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), Institute of Human Anatomy and Histology, University of Palermo, 90127 Palermo, Italy.
| | - Alessandro Pitruzzella
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), Institute of Human Anatomy and Histology, University of Palermo, 90127 Palermo, Italy.
| | - Rossana Porcasi
- Department "G. D'Alessandro", Pathology Institute, University of Palermo, 90127 Palermo, Italy.
| | | | - Giovanni Tomasello
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), Institute of Human Anatomy and Histology, University of Palermo, 90127 Palermo, Italy.
| | - Everly Conway de Macario
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90100 Palermo, Italy.
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore-Institute of Marine and Environmental Technology (IMET), Baltimore, MD 21202, USA.
| | - Alberto J L Macario
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90100 Palermo, Italy.
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore-Institute of Marine and Environmental Technology (IMET), Baltimore, MD 21202, USA.
| | - Francesco Cappello
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), Institute of Human Anatomy and Histology, University of Palermo, 90127 Palermo, Italy.
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90100 Palermo, Italy.
| | - Francesca Rappa
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), Institute of Human Anatomy and Histology, University of Palermo, 90127 Palermo, Italy.
| |
Collapse
|
7
|
Genetic Analyses Confirm SNPs in HSPA8 and ERBB2 are Associated with Milk Protein Concentration in Chinese Holstein Cattle. Genes (Basel) 2019; 10:genes10020104. [PMID: 30704154 PMCID: PMC6409942 DOI: 10.3390/genes10020104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 11/17/2022] Open
Abstract
Heat shock 70 kDa protein 8 (HSPA8) and erb-b2 receptor tyrosine kinase 2 (ERBB2) were the promising candidates for milk protein concentration in dairy cattle revealed through previous RNA sequencing (RNA-Seq) study. The objective of this post-RNA-Seq study was to confirm genetic effects of HSPA8 and ERBB2 on milk protein concentration in a large Chinese Holstein population and to evaluate the genetic effects of both genes on other milk production traits. There were 2 single-nucleotide polymorphisms (SNPs) identified for HSPA8 and 11 SNPs for ERBB2 by sequencing 17 unrelated Chinese Holstein sires. The SNP-rs136632043 in HSPA8 had significant associations with all five milk production traits (p = 0.0086 to p < 0.0001), whereas SNP-rs132976221 was remarkably associated with three yield traits (p < 0.0001). Nine (ss1996900615, rs109017161, rs109122971, ss1996900614, rs110133654, rs109941438, rs110552983, rs133031530, and rs109763505) of 11 SNPs in ERBB2 were significantly associated with milk protein percentage (p = 0.0177 to p < 0.0001). A 12 Kb haplotype block was formed in ERBB2 and haplotype associations revealed similar effects on milk protein traits. Our findings confirmed the significant genetic effects of HSPA8 and ERBB2 on milk protein concentration and other milk production traits and SNP phenotypic variances above 1% may serve as genetic markers in dairy cattle breeding programs.
Collapse
|