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Zhong L, Dong Y, Liu S. KNTC1 knockdown inhibits the proliferation and migration of osteosarcoma cells by MCM2. Mol Carcinog 2024. [PMID: 38818892 DOI: 10.1002/mc.23748] [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: 10/25/2023] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 06/01/2024]
Abstract
Osteosarcoma (OS) is a common primary malignant bone tumor, and it is necessary to further investigate the molecular mechanism of OS progression. The expression of kinetochore associated protein 1 (KNTC1) and minichromosome maintenance 2 (MCM2) was detected by immunohistochemistry, quantitative PCR (qPCR) and Western blot. Gene knockdown or overexpression cell models were constructed and the proliferation, apoptosis, cell cycle and migration were detected in vitro, besides, xenograft models were established to explore the effects of KNTC1 downregulation in vivo. Public databased and bioinformatics analysis were performed to screen the downstream molecules and determine the expression of MCM2 in cancers. KNTC1 was overexpressed in OS tissues and positively correlated with overall survival of OS patients. KNTC1 knockdown inhibited the proliferation and migration, and arrested G2 phase, and induced apoptosis. Besides, KNTC1 downregulation restricted the xenograft tumor formation. MCM2, one of the coexpressed genes, was highly expressed in sarcoma and downregulated after KNTC1 knockdown. MCM2 overexpression heightened the proliferation and migration ability of OS cells, which was reversed the inhibiting effects of KNTC1 knockdown. KNTC1 was overexpressed in OS and promoted the progression of OS by upregulating MCM2.
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Affiliation(s)
- Lei Zhong
- Department of Orthopedics, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province, China
| | - Yuanwei Dong
- Department of Orthopedics, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province, China
| | - Shuqin Liu
- Department of Radiology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
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2
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Liu Z, Han S, Luo Y, Zhao Z, Ni L, Chai L, Tang H. PERP May Affect the Prognosis of Lung Adenocarcinoma by Inhibiting Apoptosis. Cancer Manag Res 2024; 16:199-214. [PMID: 38525370 PMCID: PMC10961073 DOI: 10.2147/cmar.s443490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/29/2024] [Indexed: 03/26/2024] Open
Abstract
Background PERP, a member of the peripheral myelin protein gene family, is a new therapeutic target in cancer. The relationships between PERP and immune cell infiltration in lung cancer have not been studied. Therefore, the role of PERP in the tumour microenvironment (TME) of lung cancer needs to be further explored. Methods In this study, we explored the association between PERP expression and clinical characteristics by analysing data from the TCGA database. Cox regression and Kaplan‒Meier methods were used to investigate the relationship between the expression of PERP and overall survival in patients with lung adenocarcinoma (LUAD). The relationship between PERP expression and the degree of infiltration of specific immune cell subsets in LUAD was evaluated using the TIMER database and GEPIA. We also performed GO enrichment analysis and KEGG enrichment analysis to reveal genes coexpressed with PERP using the Coexpedia database. Finally, we verified the expression and function of PERP in LUAD tissues and the A549 cell line by RT‒PCR, Western blot, CCK-8, IHC, and wound healing assays. The mouse model was used to study the in vivo effects of PERP. Results According to our results, PERP expression was significantly higher in LUAD tissues and associated with the clinical characteristics of the disease. Survival was independently associated with PERP in LUAD patients. We further verified that PERP might regulate B-cell infiltration in LUAD to affect the prognosis of LUAD. To identify PERP-related signalling pathways in LUAD, we performed a genome-aggregation analysis (GSEA) between low and high PERP expression datasets. LUAD cells express higher levels of PERP than paracarcinoma cells, and PERP inhibits the proliferation and metastasis of A549 cells through apoptosis. Conclusion PERP may affect the prognosis of lung adenocarcinoma by inhibiting apoptosis and is associated with immune cell infiltration.
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Affiliation(s)
- Zhongxiang Liu
- Department of Pulmonary and Critical Care Medicine, the Yancheng Clinical College of Xuzhou Medical University, The First People’s Hospital of Yancheng, the First Affiliated Hospital of Jiangsu Vocational College of Medicine, Yancheng, 224000, People’s Republic of China
| | - Shuhua Han
- Department of Respiratory and Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, People’s Republic of China
| | - Yuhong Luo
- College of Life Science and Technology, Guangxi University, Nanning, 530004, People’s Republic of China
| | - Zhangyan Zhao
- Department of Respiratory and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, People’s Republic of China
| | - Lingyu Ni
- China School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210046, People’s Republic of China
| | - Linlin Chai
- Department of Pathology, The Yancheng Clinical College of Xuzhou Medical University, The First People’s Hospital of Yancheng, The First Affiliated Hospital of Jiangsu Vocational College of Medicine, Yancheng, 224000, People’s Republic of China
| | - Haicheng Tang
- Department of Respiratory and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, People’s Republic of China
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3
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Deng Z, Dong Z, Wang Y, Dai Y, Liu J, Deng F. Identification of TACSTD2 as novel therapeutic targets for cisplatin-induced acute kidney injury by multi-omics data integration. Hum Genet 2024:10.1007/s00439-024-02641-w. [PMID: 38369676 DOI: 10.1007/s00439-024-02641-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 01/11/2024] [Indexed: 02/20/2024]
Abstract
Cisplatin-induced acute kidney injury (CP-AKI) is a common complication in cancer patients. Although ferroptosis is believed to contribute to the progression of CP-AKI, its mechanisms remain incompletely understood. In this study, after initially processed individual omics datasets, we integrated multi-omics data to construct a ferroptosis network in the kidney, resulting in the identification of the key driver TACSTD2. In vitro and in vivo results showed that TACSTD2 was notably upregulated in cisplatin-treated kidneys and BUMPT cells. Overexpression of TACSTD2 accelerated ferroptosis, while its gene disruption decelerated ferroptosis, likely mediated by its potential downstream targets HMGB1, IRF6, and LCN2. Drug prediction and molecular docking were further used to propose that drugs targeting TACSTD2 may have therapeutic potential in CP-AKI, such as parthenolide, progesterone, premarin, estradiol and rosiglitazone. Our findings suggest a significant association between ferroptosis and the development of CP-AKI, with TACSTD2 playing a crucial role in modulating ferroptosis, which provides novel perspectives on the pathogenesis and treatment of CP-AKI.
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Affiliation(s)
- Zebin Deng
- Department of Urology, The Second Xiangya Hospital at Central South University, 139 Middle Renmin Road, Changsha, 410011, Hunan, China
| | - Zheng Dong
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, USA
- Department of Nephrology, The Second Xiangya Hospital at Central South University, Changsha, Hunan, China
| | - Yinhuai Wang
- Department of Urology, The Second Xiangya Hospital at Central South University, 139 Middle Renmin Road, Changsha, 410011, Hunan, China
| | - Yingbo Dai
- Department of Urology, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, Guangdong, China
| | - Jiachen Liu
- Xiangya Hospital, Central South University, Changsha, Hunan, China.
- The Center of Systems Biology and Data Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, People's Republic of China.
| | - Fei Deng
- Department of Urology, The Second Xiangya Hospital at Central South University, 139 Middle Renmin Road, Changsha, 410011, Hunan, China.
- Department of Nephrology, The Second Xiangya Hospital at Central South University, Changsha, Hunan, China.
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4
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Liu YQ, Xu YC, Shuai ZW. Mir-142-3P regulates MAPK protein family by inhibiting 14-3-3η to enhance bone marrow mesenchymal stem cells osteogenesis. Sci Rep 2023; 13:22862. [PMID: 38129425 PMCID: PMC10739902 DOI: 10.1038/s41598-023-48950-4] [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: 04/13/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
Clinical studies have found 14-3-3η to be associated with osteoporosis through undefined mechanisms. We aimed to investigate the role of 14-3-3η in osteoporosis and its potential associations with miRNAs. The Gene Expression Omnibus(GEO) and Human Protein Atlas 1 databases were analyzed to examine both the mRNA and protein expression of 14-3-3η in OP. Gene enrichment analyses were performed to explore the underlying mechanism of 14-3-3η based on DAVID. miRWalk was used to predict the associated miRNAs. The statistics were analysed by R software and SPSS software. 14-3-3η was overexpressed and knock down expressed in BMSCs by lentiviral vector transfecting. And BMSCs were induced by hypoxia. qRT-PCR and Western-Blot verified the expression of mRNA and protein. Scratch assay detected the migration of osteocytes. Co-immunoprecipitation and luciferase assay studied the 14-3-3η targeted protein and miRNA. overexpression and knock down of miRNA to verify the relationship of 14-3-3η and target genes. The 14-3-3η mRNA expression level was low in patients with osteoporosis, as corroborated by immunohistochemical staining images. Functional analyses revealed enrichment of the MAPK-associated cascade. 14-3-3η was correlated with MAPK family proteins and five key miRNAs, including mir-142-3p. In addition, 14-3-3η knockdown in BMSCs increased the mRNA and protein expression levels of Hif-α, VEGF, BMP-2, OPN, OST, and Runx2, and enhanced the cells migration ability. Under hypoxic conditions, Hif-α and BMP-2 protein expression levels were upregulated, whereas those of 14-3-3η and MAPK3 were downregulated. Co-immunoprecipitation experiments showed decreased binding of 14-3-3η to MAPK3. 14-3-3η knockdown produced the same results as hypoxia induction. Adding caspase3 inhibitor and knocking down 14-3-3η again prevented MAPK3 cleavage by caspase3 and inhibited BMP-2 expression. Moreover, under hypoxic conditions, miR-142-3P expression was upregulated and luciferase assays revealed 14-3-3η as its target gene. miR-142-3P overexpression decreased mRNA and protein levels of 14-3-3η and MAPK3, while increasing BMP-2 expression. miR-142-3P knockdown reversed these results. BMSC osteogenesis was suppressed by 14-3-3η, whereas miRNA-142-3p promoted it through the inhibition of 14-3-3η.
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Affiliation(s)
- Ya-Qian Liu
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Anhui Medical University, No. 218, Ji-Xi Road, Hefei, 230022, Anhui, China
| | - Yue-Chen Xu
- Department of Radiotherapy, First Affiliated Hospital of Anhui Medical University, No. 218, Ji-Xi Road, Hefei, 230022, Anhui, China
| | - Zong-Wen Shuai
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Anhui Medical University, No. 218, Ji-Xi Road, Hefei, 230022, Anhui, China.
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5
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Tu T, Shi Y, Zhou B, Wang X, Zhang W, Zhou G, Mo X, Wang W, Wu J, Liu W. Type I collagen and fibromodulin enhance the tenogenic phenotype of hASCs and their potential for tendon regeneration. NPJ Regen Med 2023; 8:67. [PMID: 38092758 PMCID: PMC10719373 DOI: 10.1038/s41536-023-00341-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/09/2023] [Indexed: 12/17/2023] Open
Abstract
Our previous work demonstrated the tendon-derived extracellular matrix (ECM) extracts as vital niches to specifically direct mesenchymal stem cells towards tenogenic differentiation. This study aims to further define the effective ECM molecules capable of teno-lineage induction on human adipose-derived stem cells (hASCs) and test their function for tendon engineering. By detecting the teno-markers expression levels in hASCs exposed to various substrate coatings, collagen I (COL1) and fibromodulin (FMOD) were identified to be the key molecules as a combination and further employed to the modification of poly(L-lactide-co-ε-caprolactone) electrospun nanoyarns, which showed advantages in inducting seeded hASCs for teno-lineage specific differentiation. Under dynamic mechanical loading, modified scaffold seeded with hASCs formed neo-tendon in vitro at the histological level and formed better tendon tissue in vivo with mature histology and enhanced mechanical properties. Primary mechanistic investigation with RNA sequencing demonstrated that the inductive mechanism of these two molecules for hASCs tenogenic differentiation was directly correlated with positive regulation of peptidase activity, regulation of cell-substrate adhesion and regulation of cytoskeletal organization. These biological processes were potentially affected by LOC101929398/has-miR-197-3p/TENM4 ceRNA regulation axis. In summary, COL1 and FMOD in combination are the major bioactive molecules in tendon ECM for likely directing tenogenic phenotype of hASCs and certainly valuable for hASCs-based tendon engineering.
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Affiliation(s)
- Tian Tu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Plastic and Aesthetic Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, China
| | - Yuan Shi
- Department of Burn and Plastic Surgery, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215000, China
| | - Boya Zhou
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Xiaoyu Wang
- Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai, 201620, P. R. China
| | - Wenjie Zhang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- National Tissue Engineering Center of China, Shanghai, 200241, China
| | - Guangdong Zhou
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- National Tissue Engineering Center of China, Shanghai, 200241, China
| | - Xiumei Mo
- Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai, 201620, P. R. China
| | - Wenbo Wang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
| | - Jinglei Wu
- Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai, 201620, P. R. China.
| | - Wei Liu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
- National Tissue Engineering Center of China, Shanghai, 200241, China.
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6
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Zhang ML, Li WX, Wang XY, Zhang H, Wu YL, Yang LQ, Chen XF, Zhang SQ, Chen YL, Feng KR, Tang JF. A gene expression profile-based approach to screen the occurrence and predisposed host characteristics of drug-induced liver injury: a case study of Psoralea corylifolia Linn. Front Chem 2023; 11:1259569. [PMID: 37867998 PMCID: PMC10588485 DOI: 10.3389/fchem.2023.1259569] [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: 07/16/2023] [Accepted: 09/12/2023] [Indexed: 10/24/2023] Open
Abstract
Drug-induced liver injury (DILI) is one of the most common causes of a drug being withdrawn, and identifying the culprit drugs and the host factors at risk of causing DILI has become a current challenge. Recent studies have found that immune status plays a considerable role in the development of DILI. In this study, DILI-related differentially expressed genes mediated by immunoinflammatory cytokines were obtained from the Gene Expression Omnibus (GEO) database to predict the occurrence of DILI (named the DILI predictive gene set, DILI_PGS), and the predictability of the DILI_PGS was verified using the Connectivity Map (CMap) and LiverTox platforms. The results obtained DILI_PGS from the GEO database could predict 81.25% of liver injury drugs. In addition, the Coexpedia platform was used to predict the DILI_PGS-related characteristics of common host diseases and found that the DILI_PGS mainly involved immune-related diseases and tumor-related diseases. Then, animal models of immune stress (IS) and immunosuppressive (IP) were selected to simulate the immune status of the above diseases. Meanwhile, psoralen, a main component derived from Psoralea corylifolia Linn. with definite hepatotoxicity, was selected as an experimental drug with highly similar molecular fingerprints to three idiosyncratic hepatotoxic drugs (nefazodone, trovafloxacin, and nimesulide) from the same DILI_PGS dataset. The animal experiment results found a single administration of psoralen could significantly induce liver injury in IS mice, while there was no obvious liver function change in IP mice by repeatedly administering the same dose of psoralen, and the potential mechanism of psoralen-induced liver injury in IS mice may be related to regulating the expression of the TNF-related pathway. In conclusion, this study constructed the DILI_PGS with high accuracy to predict the occurrence of DILI and preliminarily identified the characteristics of host factors inducing DILI.
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Affiliation(s)
- Ming-Liang Zhang
- The Department of Pharmacy, First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Henan Province Engineering Research Center for Clinical Application, Evaluation and Transformation of Traditional Chinese Medicine, Zhengzhou, China
- Henan Provincial Key Laboratory for Clinical Pharmacy of Traditional Chinese Medicine, Zhengzhou, China
- Henan Province Engineering Research Center of Safety Evaluation and Risk Management of Traditional Chinese Medicine, Zhengzhou, China
| | - Wei-Xia Li
- The Department of Pharmacy, First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Henan Province Engineering Research Center for Clinical Application, Evaluation and Transformation of Traditional Chinese Medicine, Zhengzhou, China
- Henan Provincial Key Laboratory for Clinical Pharmacy of Traditional Chinese Medicine, Zhengzhou, China
- Henan Province Engineering Research Center of Safety Evaluation and Risk Management of Traditional Chinese Medicine, Zhengzhou, China
| | - Xiao-Yan Wang
- The Department of Pharmacy, First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Henan Province Engineering Research Center for Clinical Application, Evaluation and Transformation of Traditional Chinese Medicine, Zhengzhou, China
- Henan Provincial Key Laboratory for Clinical Pharmacy of Traditional Chinese Medicine, Zhengzhou, China
- Henan Province Engineering Research Center of Safety Evaluation and Risk Management of Traditional Chinese Medicine, Zhengzhou, China
| | - Hui Zhang
- The Department of Pharmacy, First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Henan Province Engineering Research Center for Clinical Application, Evaluation and Transformation of Traditional Chinese Medicine, Zhengzhou, China
- Henan Provincial Key Laboratory for Clinical Pharmacy of Traditional Chinese Medicine, Zhengzhou, China
- Henan Province Engineering Research Center of Safety Evaluation and Risk Management of Traditional Chinese Medicine, Zhengzhou, China
| | - Ya-Li Wu
- The Department of Pharmacy, First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Henan Province Engineering Research Center for Clinical Application, Evaluation and Transformation of Traditional Chinese Medicine, Zhengzhou, China
- Henan Provincial Key Laboratory for Clinical Pharmacy of Traditional Chinese Medicine, Zhengzhou, China
- Henan Province Engineering Research Center of Safety Evaluation and Risk Management of Traditional Chinese Medicine, Zhengzhou, China
| | - Liu-Qing Yang
- The Department of Pharmacy, First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Henan Province Engineering Research Center for Clinical Application, Evaluation and Transformation of Traditional Chinese Medicine, Zhengzhou, China
- Henan Provincial Key Laboratory for Clinical Pharmacy of Traditional Chinese Medicine, Zhengzhou, China
- Henan Province Engineering Research Center of Safety Evaluation and Risk Management of Traditional Chinese Medicine, Zhengzhou, China
| | - Xiao-Fei Chen
- The Department of Pharmacy, First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Henan Province Engineering Research Center for Clinical Application, Evaluation and Transformation of Traditional Chinese Medicine, Zhengzhou, China
- Henan Provincial Key Laboratory for Clinical Pharmacy of Traditional Chinese Medicine, Zhengzhou, China
- Henan Province Engineering Research Center of Safety Evaluation and Risk Management of Traditional Chinese Medicine, Zhengzhou, China
| | - Shu-Qi Zhang
- The Department of Pharmacy, First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Henan Province Engineering Research Center for Clinical Application, Evaluation and Transformation of Traditional Chinese Medicine, Zhengzhou, China
- Henan Provincial Key Laboratory for Clinical Pharmacy of Traditional Chinese Medicine, Zhengzhou, China
- Henan Province Engineering Research Center of Safety Evaluation and Risk Management of Traditional Chinese Medicine, Zhengzhou, China
| | - Yu-Long Chen
- Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Ke-Ran Feng
- The Department of Pharmacy, First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Henan Province Engineering Research Center for Clinical Application, Evaluation and Transformation of Traditional Chinese Medicine, Zhengzhou, China
- Henan Provincial Key Laboratory for Clinical Pharmacy of Traditional Chinese Medicine, Zhengzhou, China
- Henan Province Engineering Research Center of Safety Evaluation and Risk Management of Traditional Chinese Medicine, Zhengzhou, China
| | - Jin-Fa Tang
- The Department of Pharmacy, First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Henan Province Engineering Research Center for Clinical Application, Evaluation and Transformation of Traditional Chinese Medicine, Zhengzhou, China
- Henan Provincial Key Laboratory for Clinical Pharmacy of Traditional Chinese Medicine, Zhengzhou, China
- Henan Province Engineering Research Center of Safety Evaluation and Risk Management of Traditional Chinese Medicine, Zhengzhou, China
- Henan University of Traditional Chinese Medicine, Zhengzhou, China
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7
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Liang R, Xiang Y, Hu C, Tang X. Expression and clinical significance of RBBP4 gene in lower-grade glioma: An integrative analysis. Biochem Biophys Rep 2023; 35:101533. [PMID: 37664524 PMCID: PMC10469049 DOI: 10.1016/j.bbrep.2023.101533] [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: 06/19/2023] [Revised: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023] Open
Abstract
This study investigated the expression pattern of retinoblastoma binding protein 4 (RBBP4) gene in glioma and explored its associations with clinicopathologic characteristics and prognosis of patients. Data retrieved from the GEPIA, CGGA, HPA and TIMER databases were processed to analyze RBBP4 expression in glioma and investigate its relationship with clinicopathologic characteristics, tumor immune infiltration and prognosis in glioma patients. Immunohistochemistry was applied to determine the expression of RBBP4 protein in glioma tissue. Additionally, the Coexpedia database was visited to identify co-expressed genes for RBBP4 gene, while the Cytoscape software was run to visualize the enriched GO entries and KEGG pathways of these co-expressed genes. The expression levels of RBBP4 in lower-grade glioma (LGG) and glioblastoma (GBM) tissues were markedly elevated when compared to normal tissues (both p < 0.05). The up-regulation of RBBP4 expression was associated with an increase in WHO grade (II-IV), wild-type IDH, and 1p/19q non-codeletion (all p < 0.05). Multi-variate Cox regression analysis showed that both increased abundance of infiltrating macrophages and up-regulated RBBP4 expression independently predicted poor survival outcomes in LGG patients (both p < 0.05). Furthermore, RBBP4 expression exhibited significant positive correlations with the abundance of infiltrating B cell, CD8+ T cell, CD4+ T cell, macrophage, neutrophil, and dendritic cell in LGG (all p < 0.05). Functional enrichment analyses indicated that the co-expressed genes associated with RBBP4 were highly involved in pathways such as the p53 signaling pathway, cell cycle, DNA replication, glutathione metabolism, as well as biological processes including cell cycle process, DNA replication, and DNA repair. High levels of RBBP4 are predictive for the poor survival outcome of LGG patients. RBBP4 gene, therefore, is expected to be a potential biomarker for prognosis of LGG and a target for immunotherapy.
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Affiliation(s)
- Ruofei Liang
- Department of Neurosurgery, Affiliated Hospital of North Sichuan Medical College, China
| | - Yue Xiang
- Department of Pathology, Affiliated Hospital of North Sichuan Medical College, China
| | - Chao Hu
- Department of Neurosurgery, Affiliated Hospital of North Sichuan Medical College, China
| | - Xiaoping Tang
- Department of Neurosurgery, Affiliated Hospital of North Sichuan Medical College, China
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8
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Han M, Guo Y, Li Y, Zeng Q, Zhu W, Jiang J. SMURF2 facilitates ubiquitin-mediated degradation of ID2 to attenuate lung cancer cell proliferation. Int J Biol Sci 2023; 19:3324-3340. [PMID: 37497010 PMCID: PMC10367561 DOI: 10.7150/ijbs.80979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 06/10/2023] [Indexed: 07/28/2023] Open
Abstract
SMAD-specific E3 ubiquitin protein ligase 2 (SMURF2) functions as either a tumor promoter or tumor suppressor in several tumors. However, the detailed effect of SMURF2 on non-small cell lung cancer has not been fully understood. In this study, SMURF2 expression and its diagnostic value were analyzed. Co-Immunoprecipitation (Co-IP), proximity ligation assay (PLA), chromatin immunoprecipitation (ChIP) and nude mice tumor-bearing model were applied to further clarify the role of SMURF2 in lung cancer. SMURF2 expression was reduced in the tumor tissues of patients with NSCLC and high SMURF2 expression was significantly correlated with favorable outcomes. Furthermore, the overexpression of SMURF2 significantly inhibited lung cancer cell progression. Mechanistically, SMURF2 interacted with inhibitor of DNA binding 2 (ID2), subsequently promoting the poly-ubiquitination and degradation of ID2 through the ubiquitin-proteasome pathway. Downregulated ID2 in lung cells dissociates endogenous transcription factor E2A, a positive regulator of the cyclin-dependent kinase inhibitor p21, and finally induces G1/S arrest in lung cancer cells. This study revealed that the manipulation of ID2 via SMURF2 may control tumor progression and contribute to the development of novel targeted antitumor drugs.
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Affiliation(s)
| | | | | | | | | | - Jianli Jiang
- ✉ Corresponding author: Jianli Jiang, National Translational Science Center for Molecular Medicine and Department of Cell Biology, Fourth Military Medical University, Xi'an 710032, China.
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9
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Zhang C, Guo Q, Chen L, Wu Z, Yan XJ, Zou C, Zhang Q, Tan J, Fang T, Rao Q, Li Y, Shen S, Deng M, Wang L, Gao H, Yu J, Li H, Zhang C, Nowsheen S, Kloeber J, Zhao F, Yin P, Teng C, Lin Z, Song K, Yao S, Yao L, Wu L, Zhang Y, Cheng X, Gao Q, Yuan J, Lou Z, Zhang JS. A ribosomal gene panel predicting a novel synthetic lethality in non-BRCAness tumors. Signal Transduct Target Ther 2023; 8:183. [PMID: 37160887 PMCID: PMC10170152 DOI: 10.1038/s41392-023-01401-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 02/04/2023] [Accepted: 02/27/2023] [Indexed: 05/11/2023] Open
Abstract
Poly (ADP-ribose) polymerase (PARP) inhibitors are one of the most exciting classes of targeted therapy agents for cancers with homologous recombination (HR) deficiency. However, many patients without apparent HR defects also respond well to PARP inhibitors/cisplatin. The biomarker responsible for this mechanism remains unclear. Here, we identified a set of ribosomal genes that predict response to PARP inhibitors/cisplatin in HR-proficient patients. PARP inhibitor/cisplatin selectively eliminates cells with high expression of the eight genes in the identified panel via DNA damage (ATM) signaling-induced pro-apoptotic ribosomal stress, which along with ATM signaling-induced pro-survival HR repair constitutes a new model to balance the cell fate in response to DNA damage. Therefore, the combined examination of the gene panel along with HR status would allow for more precise predictions of clinical response to PARP inhibitor/cisplatin. The gene panel as an independent biomarker was validated by multiple published clinical datasets, as well as by an ovarian cancer organoids library we established. More importantly, its predictive value was further verified in a cohort of PARP inhibitor-treated ovarian cancer patients with both RNA-seq and WGS data. Furthermore, we identified several marketed drugs capable of upregulating the expression of the genes in the panel without causing HR deficiency in PARP inhibitor/cisplatin-resistant cell lines. These drugs enhance PARP inhibitor/cisplatin sensitivity in both intrinsically resistant organoids and cell lines with acquired resistance. Together, our study identifies a marker gene panel for HR-proficient patients and reveals a broader application of PARP inhibitor/cisplatin in cancer therapy.
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Affiliation(s)
- Chao Zhang
- Beijing Institute of Basic Medical Sciences, 100850, Beijing, China
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Qiang Guo
- School of Pharmaceutical Sciences, Wenzhou Medical University, 325035, Wenzhou, Zhejiang, China
| | - Lifeng Chen
- Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Zhejiang Provincial People's Hospital, 310014, Hangzhou, Zhejiang, China
- Department of Gynecology, Zhejiang Provincial People's Hospital, 310014, Hangzhou, Zhejiang, China
| | - Zheming Wu
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Xiao-Jian Yan
- Department of Gynecology, the First Affiliated Hospital of Wenzhou Medical University, 325000, Wenzhou, Zhejiang, China
| | - Chengyang Zou
- Department of Gynecology, the First Affiliated Hospital of Wenzhou Medical University, 325000, Wenzhou, Zhejiang, China
| | - Qiuxue Zhang
- Wuhan Kingwise Biotechnology Co., Ltd., 430206, Wuhan, Hubei, China
| | - Jiahong Tan
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China
| | - Tian Fang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China
| | - Qunxian Rao
- Department of Gynecological Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, Guangdong, China
| | - Yang Li
- Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, 310006, Hangzhou, Zhejiang, China
| | - Shizhen Shen
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, 310006, Hangzhou, Zhejiang, China
| | - Min Deng
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Huanyao Gao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jia Yu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Somaira Nowsheen
- Department of Dermatology, University of California San Diego, San Diego, CA, 92122, USA
| | - Jake Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Ping Yin
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Chunbo Teng
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, 150040, Harbin, China
| | - Zhongqiu Lin
- Department of Gynecological Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, Guangdong, China
| | - Kun Song
- Division of Gynecology Oncology, Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 250012, Jinan, Shandong, China
| | - Shuzhong Yao
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-Sen University, 510080, Guangzhou, Guangdong, China
| | - Liangqing Yao
- Department of Gynecologic Oncology, Obstetrics and Gynecology Hospital of Fudan University, 200090, Shanghai, China
| | - Lingying Wu
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Yong Zhang
- Department of Radiation Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China
| | - Xiaodong Cheng
- Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, 310006, Hangzhou, Zhejiang, China.
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, 310006, Hangzhou, Zhejiang, China.
| | - Qinglei Gao
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China.
| | - Jian Yuan
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, 200120, Shanghai, China.
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, 200120, Shanghai, China.
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Jin-San Zhang
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, 324000, Quzhou, Zhejiang, China.
- Medical Research Center, and Key Laboratory of Interventional Pulmonology of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, 325000, Wenzhou, Zhejiang, China.
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10
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Mazi FA, Cakiroglu E, Uysal M, Kalyoncu M, Demirci D, Sozeri PYG, Yilmaz GO, Ozhan SE, Senturk S. The paracaspase MALT1 is a downstream target of Smad3 and potentiates the crosstalk between TGF-β and NF-kB signaling pathways in cancer cells. Cell Signal 2023; 105:110611. [PMID: 36708753 DOI: 10.1016/j.cellsig.2023.110611] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 12/30/2022] [Accepted: 01/23/2023] [Indexed: 01/26/2023]
Abstract
TGF-β signaling mediates its biological effects by engaging canonical Smad proteins and crosstalking extensively with other signaling networks, including the NF-kB pathway. The paracaspase MALT1 is an intracellular signaling molecule essential for NF-kB activation downstream of several key cell surface receptors. Despite intensive research on TGF-β and NF-kB interactions, the significance of MALT1 in this context remains undecoded. Here we provide experimental evidence supporting that MALT1 functions to converge these pathways. Using A549 and Huh7 cancer cell line models, we report that TGF-β stimulation enhances MALT1 protein and transcript levels in a time- and dose-dependent manner. Systematic and selective perturbation of TGF-β signaling components identifies MALT1 as a downstream target of Smad3. Rescue experiments in SMAD3 knockout cells confirm that C-terminal phosphorylation of Smad3 is central to MALT1 induction. Corroborating these data, we document that the expression of SMAD3 and MALT1 genes are positively correlated in TCGA cohorts, and we trace the molecular basis of MALT1 elevation to promoter activation. Functional studies in parental as well as NF-kB p65 signaling reporter engineered cells conclusively reveal that MALT1 is paramount for TGF-β-stimulated nuclear translocation and transcriptional activation of NF-kB p65. Furthermore, we find that BCL10 is also implicated in TGF-β activation of NF-kB target genes, potentially coupling the TGF-β-MALT1-NF-kB signaling axis to the CARMA-BCL10-MALT1 (CBM) signalosome. The novel findings of this study indicate that MALT1 is a downstream target of the canonical TGF-β/Smad3 pathway and plays a critical role in modulating TGF-β and NF-kB crosstalk in cancer.
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Affiliation(s)
- Fatma Aybuke Mazi
- Izmir Biomedicine and Genome Center, Izmir, Turkey; Department of Genome Sciences and Molecular Biotechnology, Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Ece Cakiroglu
- Izmir Biomedicine and Genome Center, Izmir, Turkey; Department of Genome Sciences and Molecular Biotechnology, Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Merve Uysal
- Izmir Biomedicine and Genome Center, Izmir, Turkey; Department of Genome Sciences and Molecular Biotechnology, Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | | | | | - Perihan Yagmur Guneri Sozeri
- Izmir Biomedicine and Genome Center, Izmir, Turkey; Department of Genome Sciences and Molecular Biotechnology, Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | | | | | - Serif Senturk
- Izmir Biomedicine and Genome Center, Izmir, Turkey; Department of Genome Sciences and Molecular Biotechnology, Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey.
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11
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Wu Q, Hu Q, Hai Y, Li Y, Gao Y. METTL13 facilitates cell growth and metastasis in gastric cancer via an eEF1A/HN1L positive feedback circuit. J Cell Commun Signal 2023; 17:121-135. [PMID: 35925508 PMCID: PMC10030728 DOI: 10.1007/s12079-022-00687-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 07/03/2022] [Indexed: 10/16/2022] Open
Abstract
Although improved treatment could inhibit progression of gastric cancer (GC), the recurrence and metastasis remain challenging issues. Methyltransferase like 13 (METTL13) has been implicated in most human cancers, but its function and mechanism in GC remain elusive. In the present study, we evaluated its expression in GC samples and found it was aberrantly overexpressed in cancer tissues than that in normal stomach tissues. High expression of METTL13 was closely associated with age, tumor size and T classification. Biological experiments showed that silencing METTL13 suppressed gastric cancer cell proliferation and metastasis in vivo and vitro, whereas opposite effects were observed upon METTL13 overexpression. Further mechanistic explorations revealed that METTL13 regulated the expression of HN1L (Hematological and neurological expressed 1-like), which is reported to be an oncogene in various cancers. Knockdown of HN1L dampened gastric cancer cell growth induced by METTL13. Eukaryotic translation elongation factor-1A (eEF1A), the present sole methylation substrate of METTL13, was involved in the regulation of HN1L by METTL13 in a K55 methylation independent manner. In addition, we also found HN1L could facilitate METTL13 expression in GC cells consistent with a previous report in hepatocellular carcinoma. Thus, these findings demonstrate a METTL13/eEF1A/HN1L positive feedback circuit promoting gastric cancer development and metastasis. It will help develop promising diagnostic and therapeutic targets for this disease.
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Affiliation(s)
- Qiong Wu
- Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, 150 Ji-Mo Rd., Shanghai, 200120, China
| | - Qingqing Hu
- Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, 150 Ji-Mo Rd., Shanghai, 200120, China
| | - Yanan Hai
- Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, 150 Ji-Mo Rd., Shanghai, 200120, China
| | - Yandong Li
- Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, 150 Ji-Mo Rd., Shanghai, 200120, China.
- Research Center for Translational Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China.
| | - Yong Gao
- Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, 150 Ji-Mo Rd., Shanghai, 200120, China.
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12
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Mao J, Wang D, Xu P, Wang Y, Zhang H, Wang S, Xu F, Wang J, Zhang F. Structure-Based Drug Design and Synthesis of Novel N-Aryl-2,4-bithiazole-2-amine CYP1B1-Selective Inhibitors in Overcoming Taxol Resistance in A549 Cells. J Med Chem 2022; 65:16451-16480. [PMID: 36512763 DOI: 10.1021/acs.jmedchem.2c01306] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
As a promising therapeutic target for cancer, CYP1B1 is overexpressed in Taxol-resistant A549 cells; however, its role in drug resistance still remains unclear. Bioinformatic analysis data indicated that CYP1B1 was closely correlated with AKT/ERK1/2 and focal adhesion pathways, thereby playing an important role in Taxol resistance and cancer migration/invasion. Along similar lines, the AhR agonist 7,12-dimethylbenz[a]anthracene (DMBA) enhanced Taxol resistance and promoted migration/invasion of A549 and H460 cells likely stemming from CYP1B1 upregulation. Moreover, 83 novel N-aryl-2,4-bithiazole-2-amine CYP1B1-selective inhibitors were designed and synthesized to verify the role of CYP1B1 in Taxol-resistant A549 cells. Impressively, the most potent and selective one, namely, 77, remarkably inhibited AKT/ERK1/2 and FAK/SRC pathways and thereby reversed Taxol resistance as well as inhibited both migration and invasion of A549/Taxol cells. Collectively, this study not only displayed the role of CYP1B1 in Taxol resistance and cancer migration/invasion but also helped unlock the CYP1B1-oriented anticancer discovery.
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Affiliation(s)
- Jianping Mao
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang110016, Liaoning, P. R. China
| | - Dong Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang110016, Liaoning, P. R. China
| | - Ping Xu
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang110016, Liaoning, P. R. China
| | - Ying Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang110016, Liaoning, P. R. China
| | - Haoyu Zhang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang110016, Liaoning, P. R. China
| | - Shiyu Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang110016, Liaoning, P. R. China
| | - Feng Xu
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang110016, Liaoning, P. R. China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang110016, Liaoning, P. R. China
| | - Fengjiao Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang110016, Liaoning, P. R. China
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13
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Chai J, Lei Y, Xiang X, Ye J, Zhao H, Yi L. High expression of caspase‐8 as a predictive factor of poor prognosis in patients with esophageal cancer. Cancer Med 2022; 12:7651-7666. [PMID: 36533709 PMCID: PMC10067063 DOI: 10.1002/cam4.5496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 10/18/2022] [Accepted: 11/17/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Esophageal carcinoma (ESCA) is considered to be one of the most common gastrointestinal cancers. Caspase-8 (CASP8) is a key protein of cross-talk signaling in a variety of cancers. However, the role of CASP8 expression in the prognosis of patients with ESCA has remained unexplored. Hence, it is needed to explore the clinical significance of CASP8 expression in ESCA. METHODS The expression and prognosis of CASP8 were investigated in ESCA using the UALCAN, GEDS, TIMER, and OncoLnc databases. The CASP8 genetic variations in ESCA were assessed using the cBioPortal database. The correlation between CASP8 expression and tumor immune invasion and immune cell surface indicators was examined using the TIMER and TISIDTISIDB datasets. Meanwhile, the abundance of the immunological cells in the tumor and healthy tissues was assessed by the CIBERSORT method. Next, information on the co-expressed genes of the differentially expressed genes (DEGs) in ESCA-tumor and ESCA-healthy tissues was obtained using the cBioPortal, UALCAN, and Coexpedia databases. Subsequently, the PPI network was constructed and the GO and KEGG pathways were analyzed using the SIRING database. Finally, CASP8 mRNA and protein expression in the ESCA tissues and matched adjacent healthy tissues were analyzed using qRT-PCR, immune-blotting, and immunohistochemistry. Additionally, the relationship between clinicopathological features and CASP8 expression was assessed. RESULTS ESCA tissues had higher levels of CASP8 mRNA and protein expression compared to healthy tissues. patients with an elevated level of CASP8 expression had poor overall survival (OS). CASP8 expression was significantly correlated with the degree of differentiation (P = 0.004) and lymph node metastasis (P = 0.044). There were diverse patterns of association between immunological cell surface biomarkers and CASP8 expression. CONCLUSION ESCA showed significant levels of CASP8 expression which may serve as a prognostic biomarker correlated to immune infiltrates in ESCA.
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Affiliation(s)
- Jian Chai
- Joint Laboratory for Translational Medicine Research, Beijing Institute of Genomics Chinese Academy of Sciences & Liaocheng People's Hospital Liaocheng China
| | - Yongqiang Lei
- Joint Laboratory for Translational Medicine Research, Beijing Institute of Genomics Chinese Academy of Sciences & Liaocheng People's Hospital Liaocheng China
| | - Xindong Xiang
- The Key Laboratory of Molecular Pharmacology Liaocheng People's Hospital Liaocheng China
| | - Jing Ye
- Department of Pathology Liaocheng People's Hospital Liaocheng China
| | - Hang Zhao
- Department of Thoracic Surgery Liaocheng People's Hospital Liaocheng China
| | - Lili Yi
- Joint Laboratory for Translational Medicine Research, Beijing Institute of Genomics Chinese Academy of Sciences & Liaocheng People's Hospital Liaocheng China
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14
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Zeng TT, Deng TH, Liu Z, Zhan JR, Ma YZ, Yan YY, Sun X, Zhu YH, Li Y, Guan XY, Li L. HN1L/AP-2γ/PLK1 signaling drives tumor progression and chemotherapy resistance in esophageal squamous cell carcinoma. Cell Death Dis 2022; 13:1026. [PMID: 36476988 PMCID: PMC9729194 DOI: 10.1038/s41419-022-05478-1] [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: 05/17/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
Hematological and neurological expressed 1 like (HN1L) is a newly identified oncogene in lung cancer and hepatocellular carcinoma recently identified by our team, but its roles in the development and treatment of esophageal squamous cell carcinoma (ESCC) remain incompletely cataloged. Here, using ESCC tissue array and public database analysis, we demonstrated that HN1L was highly expressed in ESCC tissues, which was associated with tumor tissue invasion, poor clinical stage and short survival for ESCC patients. Loss- and gain-of-function studies in ESCC cells revealed that HN1L enhances ESCC cell metastasis and proliferation in vitro and in mice models. Moreover, high level of HN1L reduces the sensibility of ESCC cells to chemotherapeutic drugs, such as Docetaxel. Mechanism studies revealed that HN1L activated the transcription of polo-like kinase 1 (PLK1) by interacting with transcription factor AP-2γ, which increased the expression of malignancy related proteins Cyclin D1 and Slug in ESCC cells. Blocking PLK1 with inhibitor BI-2356 abrogated the oncogenic function of HN1L and significantly suppressed ESCC progression by combining with chemotherapy. Therefore, this study demonstrates the vital pro-tumor role of HN1L/AP-2γ/PLK1 signaling axis in ESCC, offering a potential therapeutic strategy for ESCC patients with high HN1L by blocking PLK1.
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Affiliation(s)
- Ting-Ting Zeng
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, 510060 Guangzhou, China
| | - Tian-Hao Deng
- grid.489633.3The Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, 410006 Changsha, China
| | - Zhen Liu
- grid.489633.3Hunan Academy of Traditional Chinese Medicine, 410006 Changsha, China
| | - Jia-Rong Zhan
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, 510060 Guangzhou, China
| | - Yuan-Zhen Ma
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, 510060 Guangzhou, China
| | - Yuan-Yuan Yan
- grid.412536.70000 0004 1791 7851Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120 Guangzhou, China ,grid.412536.70000 0004 1791 7851Nanhai Translational Innovation Center of Precision Immunology, Sun Yat-sen Memorial Hospital, 528200 Foshan, China
| | - Xiao Sun
- grid.412536.70000 0004 1791 7851Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120 Guangzhou, China ,grid.412536.70000 0004 1791 7851Nanhai Translational Innovation Center of Precision Immunology, Sun Yat-sen Memorial Hospital, 528200 Foshan, China
| | - Ying-Hui Zhu
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, 510060 Guangzhou, China
| | - Yan Li
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, 510060 Guangzhou, China
| | - Xin-Yuan Guan
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, 510060 Guangzhou, China ,grid.440671.00000 0004 5373 5131Department of Clinical Oncology, Shenzhen Key Laboratory for Metastasis and Personalized Therapy, The University of Hong Kong-Shenzhen Hospital, 518053 Shenzhen, China ,grid.194645.b0000000121742757Department of Clinical Oncology, The University of Hong Kong, Hong Kong, China
| | - Lei Li
- grid.412536.70000 0004 1791 7851Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120 Guangzhou, China ,grid.412536.70000 0004 1791 7851Nanhai Translational Innovation Center of Precision Immunology, Sun Yat-sen Memorial Hospital, 528200 Foshan, China ,grid.440671.00000 0004 5373 5131Department of Clinical Oncology, Shenzhen Key Laboratory for Metastasis and Personalized Therapy, The University of Hong Kong-Shenzhen Hospital, 518053 Shenzhen, China
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15
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Zhang L, Zhuo H, Hong Z, Hou J, Cheng J, Cai J. HSPA6, a novel prognostic and therapeutic biomarker, associated with Ming classification in gastric cancer. J Clin Lab Anal 2022; 37:e24763. [PMID: 36458368 PMCID: PMC9833989 DOI: 10.1002/jcla.24763] [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: 09/30/2022] [Revised: 10/26/2022] [Accepted: 10/29/2022] [Indexed: 12/04/2022] Open
Abstract
OBJECTIVE This study aimed to explore the clinical relevance of heat shock protein family A member 6 (HSPA6) in gastric cancer (GC) and its effect on GC cell proliferation. METHODS HSPA6 mRNA and protein levels were analyzed by bioinformatics, RT-qPCR, western blot and immunohistochemistry. HSPA6 was correlated with clinicopathological variables by the Chi-square test. Kaplan-Meier survival analysis and the univariate and multivariate Cox models were used to assess the prognostic value of HSPA6. Nomogram was used to predict overall survival in patients with GC. Knockdown or over-expression of HSPA6 in GC cell lines was constructed by lentiviral transduction. EdU and CCK-8 assay were used to detect cell proliferation. In vivo mouse tumor models were performed to evaluate the effects of HSPA6 on GC growth. RESULTS HSPA6 were significantly upregulated in the GC tissues compared to the normal stomach epithelium and were associated with Ming classification (p < 0.001) and tumor size (p = 0.002). Patients with high expression of HSPA6 showed worse survival compared to the low expression group. HSPA6 was identified to be an independent prognostic biomarker for GC. HSPA6 was functionally annotated with the cell cycle, G2M checkpoint and Hippo pathway. Knockdown of HSPA6 suppressed XGC-1 cell proliferation both in vitro and in vivo. Overexpression of HSPA6 in AGS cells increased proliferation rates, increased the levels of cyclinB1 and YAP and decreased that of phosphorylated YAP. HSPA6 knockdown in the NUGC2 cells had the opposite effect. CONCLUSIONS HSPA6 promotes GC proliferation by the Hippo pathway, as a novel prognostic biomarker and potential therapeutic target.
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Affiliation(s)
- Lihua Zhang
- Department of Gastrointestinal SurgeryZhongshan Hospital of Xiamen University, School of Medicine, Xiamen UniversityXiamenChina,Institute of Gastrointestinal Oncology, School of MedicineXiamen UniversityXiamenChina,Xiamen Municipal Key Laboratory of Gastrointestinal OncologyXiamenChina
| | - Hui‐qin Zhuo
- Department of Gastrointestinal SurgeryZhongshan Hospital of Xiamen University, School of Medicine, Xiamen UniversityXiamenChina,Institute of Gastrointestinal Oncology, School of MedicineXiamen UniversityXiamenChina,Xiamen Municipal Key Laboratory of Gastrointestinal OncologyXiamenChina
| | - Zhi‐jun Hong
- Department of Gastrointestinal SurgeryZhongshan Hospital of Xiamen University, School of Medicine, Xiamen UniversityXiamenChina,Institute of Gastrointestinal Oncology, School of MedicineXiamen UniversityXiamenChina,Xiamen Municipal Key Laboratory of Gastrointestinal OncologyXiamenChina
| | - Jing‐jing Hou
- Department of Gastrointestinal SurgeryZhongshan Hospital of Xiamen University, School of Medicine, Xiamen UniversityXiamenChina,Institute of Gastrointestinal Oncology, School of MedicineXiamen UniversityXiamenChina,Xiamen Municipal Key Laboratory of Gastrointestinal OncologyXiamenChina
| | - Jia Cheng
- Department of Gastrointestinal SurgeryZhongshan Hospital of Xiamen University, School of Medicine, Xiamen UniversityXiamenChina,Institute of Gastrointestinal Oncology, School of MedicineXiamen UniversityXiamenChina,Xiamen Municipal Key Laboratory of Gastrointestinal OncologyXiamenChina
| | - Jianchun Cai
- Department of Gastrointestinal SurgeryZhongshan Hospital of Xiamen University, School of Medicine, Xiamen UniversityXiamenChina,Institute of Gastrointestinal Oncology, School of MedicineXiamen UniversityXiamenChina,Xiamen Municipal Key Laboratory of Gastrointestinal OncologyXiamenChina
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16
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Li Y, Wang H, Wan J, Ma Q, Qi Y, Gu Z. The hnRNPK/A1/R/U Complex Regulates Gene Transcription and Translation and is a Favorable Prognostic Biomarker for Human Colorectal Adenocarcinoma. Front Oncol 2022; 12:845931. [PMID: 35875075 PMCID: PMC9301189 DOI: 10.3389/fonc.2022.845931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/17/2022] [Indexed: 12/24/2022] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) are emerging as a crucially important protein family in tumors. However, it is unclear which family members are essential for cancer progression, and their diverse expression patterns and prognostic values are rarely reported. In this work, we found that the expression levels of hnRNPs were all upregulated in colon adenocarcinoma (COAD) and rectal adenocarcinoma (READ) tissues. Immunohistochemical staining revealed that hnRNPA1, hnRNPA2B1, hnRNPC, hnRNPK, hnRNPR, and hnRNPU are overexpressed in colorectal adenocarcinoma. Additionally, the promoter methylation levels of hnRNPs were significantly elevated or decreased, and multiple genetic alterations of hnRNPs were found in colorectal adenocarcinoma patients. Correlation analysis showed that the expression levels of hnRNPs were positively correlated with each other. Furthermore, we demonstrated that high expressions of hnRNPA1, hnRNPK, hnRNPR, and hnRNPU were associated with better overall survival rates for colorectal adenocarcinoma patients. The co-expression network and functional prediction analysis indicated that hnRNPK/A1/R/U was involved in cellular gene transcription and translation. Moreover, hnRNPK/A1/R/U complex was identified and confirmed by mass spectrometry and co-immunoprecipitation. RNA sequencing analysis revealed that the transcription factor hnRNPK regulated transcription and translation of related genes. Finally, through establishment of stable cell lines in vitro, we verified that hnRNPK was a favorable factor in human colorectal adenocarcinoma which promoted immune cell infiltration and inhibited tumor growth. Our findings illustrate that the hnRNPK/A1/R/U complex is a favorable prognostic biomarker for human colorectal adenocarcinoma. Targeting hnRNPK during transcription and translation could be a promising therapeutic strategy for colorectal adenocarcinoma treatment.
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Affiliation(s)
- Yixin Li
- Department of Clinical Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Hui Wang
- Department of Clinical Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Jiajia Wan
- Post-Doctoral Station of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Qian Ma
- Post-Doctoral Station of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- *Correspondence: Qian Ma, ; Yu Qi, ; Zhuoyu Gu,
| | - Yu Qi
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- *Correspondence: Qian Ma, ; Yu Qi, ; Zhuoyu Gu,
| | - Zhuoyu Gu
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- *Correspondence: Qian Ma, ; Yu Qi, ; Zhuoyu Gu,
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Approaches in Gene Coexpression Analysis in Eukaryotes. BIOLOGY 2022; 11:biology11071019. [PMID: 36101400 PMCID: PMC9312353 DOI: 10.3390/biology11071019] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 11/22/2022]
Abstract
Simple Summary Genes whose expression levels rise and fall similarly in a large set of samples, may be considered coexpressed. Gene coexpression analysis refers to the en masse discovery of coexpressed genes from a large variety of transcriptomic experiments. The type of biological networks that studies gene coexpression, known as Gene Coexpression Networks, consist of an undirected graph depicting genes and their coexpression relationships. Coexpressed genes are clustered in smaller subnetworks, the predominant biological roles of which can be determined through enrichment analysis. By studying well-annotated gene partners, the attribution of new roles to genes of unknown function or assumption for participation in common metabolic pathways can be achieved, through a guilt-by-association approach. In this review, we present key issues in gene coexpression analysis, as well as the most popular tools that perform it. Abstract Gene coexpression analysis constitutes a widely used practice for gene partner identification and gene function prediction, consisting of many intricate procedures. The analysis begins with the collection of primary transcriptomic data and their preprocessing, continues with the calculation of the similarity between genes based on their expression values in the selected sample dataset and results in the construction and visualisation of a gene coexpression network (GCN) and its evaluation using biological term enrichment analysis. As gene coexpression analysis has been studied extensively, we present most parts of the methodology in a clear manner and the reasoning behind the selection of some of the techniques. In this review, we offer a comprehensive and comprehensible account of the steps required for performing a complete gene coexpression analysis in eukaryotic organisms. We comment on the use of RNA-Seq vs. microarrays, as well as the best practices for GCN construction. Furthermore, we recount the most popular webtools and standalone applications performing gene coexpression analysis, with details on their methods, features and outputs.
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A single-cell survey unveils cellular heterogeneity and sensitive responses in mouse cortices induced by oral exposure to triphenyl phosphate. Arch Toxicol 2022; 96:2545-2557. [PMID: 35752650 DOI: 10.1007/s00204-022-03301-6] [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: 02/17/2022] [Accepted: 04/07/2022] [Indexed: 11/02/2022]
Abstract
Triphenyl phosphate (TPhP) is a non-halogenated organophosphorus flame retardant, and there is a higher exposure risk in children. TPhP has been found to be neurotoxic upon developmental exposure, yet the specific mechanism remains unclear. To characterize the cellular responses underlying TPhP-induced developmental neurotoxicity, we administered TPhP (0.5, 5 or 50 mg/kg/day) to neonatal mice from postnatal day 10 (P10)-P70. A total of 17,229 cells and 26,338 genes were identified in cortical samples from control and low-dose (the internal doses of metabolite DPhP comparable to human exposure level) groups using single-cell RNA sequencing (scRNA-seq). TPhP exposure led to heterogeneous transcriptional alterations and intercellular crosstalk among neurons, neural stem/progenitor cells (NSPCs), endothelial cells, and immunocytes. Deprivation of NSPCs, loss of mature neurons, and concomitant neuroinflammation mediated by extrinsic and intrinsic immunocytes were found in TPhP-exposed cortices. In addition, we observed blood-brain barrier destruction prior to the anxiety/depression-like neurobehavioral changes. These results reveal the distinctive cellular processes in TPhP's neurodevelopmental toxicity and uncover that the impeded neurogenesis, disrupted vascular barrier, and concomitant neuroinflammation are the sensitive responses to TPhP exposure. Our study paves the way for the application of scRNA-seq in toxicity assessments for emerging neurotoxic pollutants.
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Liu X, Liu Y. Comprehensive Analysis of the Expression and Prognostic Significance of the CENP Family in Breast Cancer. Int J Gen Med 2022; 15:3471-3482. [PMID: 35378917 PMCID: PMC8976518 DOI: 10.2147/ijgm.s354200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/23/2022] [Indexed: 12/13/2022] Open
Abstract
Background Centromere proteins (CENPs) are a set of protein-coding genes involved in the transient assembly of the kinetochore which occurs during mitosis. This study intended to clarify the expression patterns, prognosis and potential mechanisms of CENPs in breast cancer (BC). Methods Coexpedia was used to screen GEO datasets and PubMed articles related to CENPs and BC. CENPs expressions, prognosis and alteration were analyzed by Oncomine, Ualcan and Kaplan Meier plotter and cBioPortal. The correlation and interaction of CENPs was performed by Breast Cancer Gene-Expression Miner, GeneMANIA and STRING portal. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were conducted to clarify the functional roles of CENPs. CENPF, E, U, A, N, I, K, W, M, L were selected for further analysis. Results All CENPs were highly expressed in BC compared to normal tissue. High expression of CENPF, E, U, A, N, I, W, M, L and CENPF, E, U, A, N, I, M correlated with worse relapse free survival (RFS) and worse overall survival (OS), respectively. All of 10 CENPs indicated positive correlations and complex interactions between each other at mRNA expression and protein level. CENPs were enriched GO terms mainly in centromere complex assembly and KEGG terms in progesterone-mediated oocyte maturation, cell cycle and oocyte meiosis. Conclusion The 10 CENPs could be diagnostic biomarkers and all of them except CENPK can be used as prognosis biomarkers in BC. CENPs play an oncogenic role and may be the potential therapy targets of treatment for BC patients.
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Affiliation(s)
- Xueliang Liu
- Breast Cancer Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People’s Republic of China
| | - Yunjiang Liu
- Breast Cancer Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People’s Republic of China
- Correspondence: Yunjiang Liu, Tel +86-13703297890, Email
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20
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Clarelli F, Barizzone N, Mangano E, Zuccalà M, Basagni C, Anand S, Sorosina M, Mascia E, Santoro S, Guerini FR, Virgilio E, Gallo A, Pizzino A, Comi C, Martinelli V, Comi G, De Bellis G, Leone M, Filippi M, Esposito F, Bordoni R, Martinelli Boneschi F, D'Alfonso S. Contribution of Rare and Low-Frequency Variants to Multiple Sclerosis Susceptibility in the Italian Continental Population. Front Genet 2022; 12:800262. [PMID: 35047017 PMCID: PMC8762330 DOI: 10.3389/fgene.2021.800262] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022] Open
Abstract
Genome-wide association studies identified over 200 risk loci for multiple sclerosis (MS) focusing on common variants, which account for about 50% of disease heritability. The goal of this study was to investigate whether low-frequency and rare functional variants, located in MS-established associated loci, may contribute to disease risk in a relatively homogeneous population, testing their cumulative effect (burden) with gene-wise tests. We sequenced 98 genes in 588 Italian patients with MS and 408 matched healthy controls (HCs). Variants were selected using different filtering criteria based on allelic frequency and in silico functional impacts. Genes showing a significant burden (n = 17) were sequenced in an independent cohort of 504 MS and 504 HC. The highest signal in both cohorts was observed for the disruptive variants (stop-gain, stop-loss, or splicing variants) located in EFCAB13, a gene coding for a protein of an unknown function (p < 10-4). Among these variants, the minor allele of a stop-gain variant showed a significantly higher frequency in MS versus HC in both sequenced cohorts (p = 0.0093 and p = 0.025), confirmed by a meta-analysis on a third independent cohort of 1298 MS and 1430 HC (p = 0.001) assayed with an SNP array. Real-time PCR on 14 heterozygous individuals for this variant did not evidence the presence of the stop-gain allele, suggesting a transcript degradation by non-sense mediated decay, supported by the evidence that the carriers of the stop-gain variant had a lower expression of this gene (p = 0.0184). In conclusion, we identified a novel low-frequency functional variant associated with MS susceptibility, suggesting the possible role of rare/low-frequency variants in MS as reported for other complex diseases.
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Affiliation(s)
- Ferdinando Clarelli
- Laboratory of Human Genetics of Neurological Disorders, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Nadia Barizzone
- Department of Health Sciences, UPO, University of Eastern Piedmont, and CAAD (Center for Translational Research on Autoimmune and Allergic Disease), Novara, Italy
| | - Eleonora Mangano
- Institute for Biomedical Technologies, National Research Council of Italy, Segrate, Italy
| | - Miriam Zuccalà
- Department of Health Sciences, UPO, University of Eastern Piedmont, and CAAD (Center for Translational Research on Autoimmune and Allergic Disease), Novara, Italy
| | - Chiara Basagni
- Department of Health Sciences, UPO, University of Eastern Piedmont, and CAAD (Center for Translational Research on Autoimmune and Allergic Disease), Novara, Italy
| | - Santosh Anand
- Department of Informatics, Systems and Communications (DISCo), University of Milano-Bicocca, Milan, Italy
| | - Melissa Sorosina
- Laboratory of Human Genetics of Neurological Disorders, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elisabetta Mascia
- Laboratory of Human Genetics of Neurological Disorders, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Santoro
- Laboratory of Human Genetics of Neurological Disorders, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | | | | | - Eleonora Virgilio
- Department of Translational Medicine, Section of Neurology and IRCAD, UNIUPO, Novara, Italy
| | - Antonio Gallo
- MS Center, I Division of Neurology, Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Alessandro Pizzino
- Department of Health Sciences, UPO, University of Eastern Piedmont, and CAAD (Center for Translational Research on Autoimmune and Allergic Disease), Novara, Italy
| | - Cristoforo Comi
- Department of Translational Medicine, Section of Neurology and IRCAD, UNIUPO, Novara, Italy
| | - Vittorio Martinelli
- Neurology Unit and Neurorehabilitation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Gianluca De Bellis
- Institute for Biomedical Technologies, National Research Council of Italy, Segrate, Italy
| | - Maurizio Leone
- Neurology Unit, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo, Italy
| | - Massimo Filippi
- Neurology Unit and Neurorehabilitation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Vita-Salute San Raffaele University, Milan, Italy.,Neuroimaging Research Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Neurophysiology Service, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federica Esposito
- Laboratory of Human Genetics of Neurological Disorders, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Neurology Unit and Neurorehabilitation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Roberta Bordoni
- Institute for Biomedical Technologies, National Research Council of Italy, Segrate, Italy
| | - Filippo Martinelli Boneschi
- Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, Neuroscience Section, University of Milan, Milan, Italy.,Neurology Unit, MS Centre, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Sandra D'Alfonso
- Department of Health Sciences, UPO, University of Eastern Piedmont, and CAAD (Center for Translational Research on Autoimmune and Allergic Disease), Novara, Italy
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21
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Tian Y, Huang B, Li J, Tian X, Zeng X. Identification of the Association Between Toll-Like Receptors and T-Cell Activation in Takayasu’s Arteritis. Front Immunol 2022; 12:792901. [PMID: 35126357 PMCID: PMC8812403 DOI: 10.3389/fimmu.2021.792901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/22/2021] [Indexed: 12/26/2022] Open
Abstract
To explore the relationships between Toll-like receptors (TLRs) and the activation and differentiation of T-cells in Takayasu’s arteritis (TAK), using real-time fluorescence quantitative polymerase chain reaction, mRNA abundance of 29 target genes in peripheral blood mononuclear cells (PBMCs) were detected from 27 TAK patients and 10 healthy controls. Compared with the healthy control group, the untreated TAK group and the treated TAK group had an increased mRNA level of TLR2 and TLR4. A sample-to-sample matrix revealed that 80% of healthy controls could be separated from the TAK patients. Correlation analysis showed that the inactive-treated TAK group exhibited a unique pattern of inverse correlations between the TLRs gene clusters (including TLR1/2/4/6/8, BCL6, TIGIT, NR4A1, etc) and the gene cluster associated with T-cell activation and differentiation (including TCR, CD28, T-bet, GATA3, FOXP3, CCL5, etc). The dynamic gene co-expression network indicated the TAK groups had more active communication between TLRs and T-cell activation than healthy controls. BCL6, CCL5, FOXP3, GATA3, CD28, T-bet, TIGIT, IκBα, and NR4A1 were likely to have a close functional relation with TLRs at the inactive stage. The co-expression of TLR4 and TLR6 could serve as a biomarker of disease activity in treated TAK (the area under curve/sensitivity/specificity, 0.919/100%/90.9%). The largest gene co-expression cluster of the inactive-treated TAK group was associated with TLR signaling pathways, while the largest gene co-expression cluster of the active-treated TAK group was associated with the activation and differentiation of T-cells. The miRNA sequencing of the plasma exosomes combining miRDB, DIANA-TarBase, and miRTarBase databases suggested that the miR-548 family miR-584, miR-3613, and miR-335 might play an important role in the cross-talk between TLRs and T-cells at the inactive stage. This study found a novel relation between TLRs and T-cell in the pathogenesis of autoimmune diseases, proposed a new concept of TLR-co-expression signature which might distinguish different disease activity of TAK, and highlighted the miRNA of exosomes in TLR signaling pathway in TAK.
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Affiliation(s)
- Yixiao Tian
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, Peking Union Medical College Hospital (PUMCH), Beijing, China
- National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH), Beijing, China
- Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Biqing Huang
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, Peking Union Medical College Hospital (PUMCH), Beijing, China
- National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH), Beijing, China
- Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Jing Li
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, Peking Union Medical College Hospital (PUMCH), Beijing, China
- National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH), Beijing, China
- Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
- *Correspondence: Jing Li, ; Xiaofeng Zeng,
| | - Xinping Tian
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, Peking Union Medical College Hospital (PUMCH), Beijing, China
- National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH), Beijing, China
- Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Xiaofeng Zeng
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, Peking Union Medical College Hospital (PUMCH), Beijing, China
- National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH), Beijing, China
- Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
- *Correspondence: Jing Li, ; Xiaofeng Zeng,
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22
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Subramanian A, Zakeri P, Mousa M, Alnaqbi H, Alshamsi FY, Bettoni L, Damiani E, Alsafar H, Saeys Y, Carmeliet P. Angiogenesis goes computational – The future way forward to discover new angiogenic targets? Comput Struct Biotechnol J 2022; 20:5235-5255. [PMID: 36187917 PMCID: PMC9508490 DOI: 10.1016/j.csbj.2022.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 11/26/2022] Open
Abstract
Multi-omics technologies are being increasingly utilized in angiogenesis research. Yet, computational methods have not been widely used for angiogenic target discovery and prioritization in this field, partly because (wet-lab) vascular biologists are insufficiently familiar with computational biology tools and the opportunities they may offer. With this review, written for vascular biologists who lack expertise in computational methods, we aspire to break boundaries between both fields and to illustrate the potential of these tools for future angiogenic target discovery. We provide a comprehensive survey of currently available computational approaches that may be useful in prioritizing candidate genes, predicting associated mechanisms, and identifying their specificity to endothelial cell subtypes. We specifically highlight tools that use flexible, machine learning frameworks for large-scale data integration and gene prioritization. For each purpose-oriented category of tools, we describe underlying conceptual principles, highlight interesting applications and discuss limitations. Finally, we will discuss challenges and recommend some guidelines which can help to optimize the process of accurate target discovery.
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23
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Kan J, Hu Y, Ge Y, Zhang W, Lu S, Zhao C, Zhang R, Liu Y. Declined expressions of vast mitochondria-related genes represented by CYCS and transcription factor ESRRA in skeletal muscle aging. Bioengineered 2021; 12:3485-3502. [PMID: 34229541 PMCID: PMC8806411 DOI: 10.1080/21655979.2021.1948951] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 11/23/2022] Open
Abstract
Age-related skeletal muscle deterioration (sarcopenia) has a significant effect on the elderly's health and quality of life, but the molecular and gene regulatory mechanisms remain largely unknown. It is necessary to identify the candidate genes related to skeletal muscle aging and prospective therapeutic targets for effective treatments. The age-line-related genes (ALRGs) and age-line-related transcripts (ALRTs) were investigated using the gene expression profiles of GSE47881 and GSE118825 from the Gene Expression Omnibus (GEO) database. The protein-protein interaction (PPI) networks were performed to identify the key molecules with Cytoscape, and Gene Set Enrichment Analysis (GSEA) was used to clarify the potential molecular functions. Two hub molecules were finally obtained and verified with quantitative real-time PCR (qRT-PCR). The results showed that the expression of mitochondria genes involved in mitochondrial electron transport, complex assembly of the respiratory chain, tricarboxylic acid cycle, oxidative phosphorylation, and ATP synthesis were down-regulated in skeletal muscle with aging. We further identified a primary hub gene of CYCS (Cytochrome C) and a key transcription factor of ESRRA (Estrogen-related Receptor Alpha) to be associated closely with skeletal muscle aging. PCR analysis confirmed the expressions of CYCS and ESRRA in gastrocnemius muscles of mice of different ages were significantly different, and decreased gradually with age. In conclusion, the main cause of skeletal muscle aging may be the systematically reduced expression of mitochondrial functional genes. The CYCS and ESRRA may play significant roles in the progression of skeletal muscle aging and serve as potential biomarkers for future diagnosis and treatment.
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Affiliation(s)
- Jingbao Kan
- Department of Geriatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yifang Hu
- Department of Geriatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yaoqi Ge
- Department of Geriatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - WenSong Zhang
- Department of Geriatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shan Lu
- Department of Geriatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Cuiping Zhao
- Department of Geriatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Rihua Zhang
- Department of Geriatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yun Liu
- Department of Geriatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Medical Informatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
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24
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Hossain MS, Tonmoy MIQ, Fariha A, Islam MS, Roy AS, Islam MN, Kar K, Alam MR, Rahaman MM. Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. Bioinform Biol Insights 2021; 15:11779322211054684. [PMID: 34720581 PMCID: PMC8554545 DOI: 10.1177/11779322211054684] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/02/2021] [Indexed: 12/15/2022] Open
Abstract
A new strain of the beta coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is solely responsible for the ongoing coronavirus disease 2019 (COVID-19) pandemic. Although several studies suggest that the spike protein of this virus interacts with the cell surface receptor, angiotensin-converting enzyme 2 (ACE2), and is subsequently cleaved by TMPRSS2 and FURIN to enter into the host cell, conclusive insight about the interaction pattern of the variants of these proteins is still lacking. Thus, in this study, we analyzed the functional conjugation among the spike protein, ACE2, TMPRSS2, and FURIN in viral pathogenesis as well as the effects of the mutations of the proteins through the implementation of several bioinformatics approaches. Analysis of the intermolecular interactions revealed that T27A (ACE2), G476S (receptor-binding domain [RBD] of the spike protein), C297T (TMPRSS2), and P812S (cleavage site for TMPRSS2) coding variants may render resistance in viral infection, whereas Q493L (RBD), S477I (RBD), P681R (cleavage site for FURIN), and P683W (cleavage site for FURIN) may lead to increase viral infection. Genotype-specific expression analysis predicted several genetic variants of ACE2 (rs2158082, rs2106806, rs4830971, and rs4830972), TMPRSS2 (rs458213, rs468444, rs4290734, and rs6517666), and FURIN (rs78164913 and rs79742014) that significantly alter their normal expression which might affect the viral spread. Furthermore, we also found that ACE2, TMPRSS2, and FURIN proteins are functionally co-related with each other, and several genes are highly co-expressed with them, which might be involved in viral pathogenesis. This study will thus help in future genomics and proteomics studies of SARS-CoV-2 and will provide an opportunity to understand the underlying molecular mechanism during SARS-CoV-2 pathogenesis.
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Affiliation(s)
- Md. Shahadat Hossain
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | | | - Atqiya Fariha
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md. Sajedul Islam
- Department of Biochemistry & Biotechnology, University of Barishal, Barishal, Bangladesh
| | - Arpita Singha Roy
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md. Nur Islam
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Kumkum Kar
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Mohammad Rahanur Alam
- Department of Food Technology & Nutrition Science, Noakhali Science and Technology University, Noakhali, Bangladesh
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Zeng Z, Jiang X, Pan Z, Zhou R, Lin Z, Tang Y, Cui Y, Zhang E, Cao Z. Highly expressed centromere protein L indicates adverse survival and associates with immune infiltration in hepatocellular carcinoma. Aging (Albany NY) 2021; 13:22802-22829. [PMID: 34607313 PMCID: PMC8544325 DOI: 10.18632/aging.203574] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/11/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is characterized by rapid progression, high recurrence rate and poor prognosis. Early prediction for the prognosis and immunotherapy efficacy is of great significance to improve the survival of HCC patients. However, there is still no reliable predictor at present. This study is aimed to explore the role of centromere protein L (CENPL) in predicting prognosis and its association with immune infiltration in HCC. METHODS The expression of CENPL was identified through analyzing the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) data. The association between CENPL expression and clinicopathological features was investigated by the Wilcoxon signed-rank test or Kruskal Wallis test and logistic regression. The role of CENPL in prognosis was examined via Kaplan-Meier method and Log-rank test as well as univariate and multivariate Cox regression analysis. Besides, in TIMER and GEPIA database, we investigated the correlation between CENPL level and immunocyte and immunocyte markers, and the prognostic-related methylation sites in CENPL were identified by MethSurv. RESULTS CENPL had a high expression in HCC samples. Increased CENPL was prominently associated with unfavorable survival, and maybe an independent prognostic factor of worse overall survival (OS), disease-specific survival (DSS), disease-free interval (DFI), progression-free interval (PFI). Additionally, CENPL expression was significantly correlated with immune cell infiltration and some markers. CENPL also contained a methylation site that was notably related to poor prognosis. CONCLUSIONS Elevated CENPL may be a promising prognostic marker and associate with immune infiltration in HCC.
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Affiliation(s)
- Zhili Zeng
- The First School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, PR China
| | - Xiao Jiang
- The First School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, PR China
| | - Zhibin Pan
- Foshan Hospital of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Foshan 528000, Guangdong, PR China
| | - Ruisheng Zhou
- The First School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, PR China
| | - Zhuangteng Lin
- Department of Medical Technologic, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 518000, PR China
| | - Ying Tang
- Department of Oncology, Lingnan Medical Research Center of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, PR China.,Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 518000, PR China
| | - Ying Cui
- Department of Psychiatry, The Third Affiliated Hospital of Guangzhou Medical University, Guangdong 510150, PR China
| | - Enxin Zhang
- Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 518000, PR China.,Department of Oncology, Shenzhen Hospital of Guangzhou University of Chinese Medicine, Shenzhen 518000, Guangdong, PR China
| | - Zebiao Cao
- The First School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, PR China
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Zhang X, Bustos MA, Gross R, Ramos RI, Takeshima T, Mills GB, Yu Q, Hoon DSB. Interleukin enhancer-binding factor 2 promotes cell proliferation and DNA damage response in metastatic melanoma. Clin Transl Med 2021; 11:e608. [PMID: 34709752 PMCID: PMC8516365 DOI: 10.1002/ctm2.608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND 1q21.3 amplification, which is frequently observed in metastatic melanoma, is associated with cancer progression. Interleukin enhancer-binding factor 2 (ILF2) is located in the 1q21.3 amplified region, but its functional role or contribution to tumour aggressiveness in cutaneous melanoma is unknown. METHODS In silico analyses were performed using the TCGA SKCM dataset with clinical annotations and three melanoma microarray cohorts from the GEO datasets. RNA in situ hybridisation and immunohistochemistry were utilised to validate the gene expression in melanoma tissues. Four stable melanoma cell lines were established for in vitro ILF2 functional characterisation. RESULTS Our results showed that the ILF2 copy number variation (CNV) is positively correlated with ILF2 mRNA expression (r = 0.68, p < .0001). Additionally, ILF2 expression is significantly increased with melanoma progression (p < .0001), and significantly associated with poor overall survival for metastatic melanoma patients (p = .026). The overexpression of ILF2 (ILF2-OV) promotes proliferation in metastatic melanoma cells, whereas ILF2 knockdown decreases proliferation by blocking the cell cycle. Mechanistically, we demonstrated the interaction between ILF2 and the splicing factor U2AF2, whose knockdown reverses the proliferation effects mediated by ILF2-OV. Stage IIIB-C melanoma patients with high ILF2-U2AF2 expression showed significantly shorter overall survival (p = .024). Enhanced ILF2/U2AF2 expression promotes a more efficient DNA-damage repair by increasing RAD50 and ATM mRNA expression. Paradoxically, metastatic melanoma cells with ILF2-OV were more sensitive to ATM inhibitors. CONCLUSION Our study uncovered that ILF2 amplification of the 1q21.3 chromosome is associated with melanoma progression and triggers a functional downstream pathway in metastatic melanoma promoting drug resistance.
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Affiliation(s)
- Xiaoqing Zhang
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
| | - Matias A. Bustos
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
| | - Rebecca Gross
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
| | - Romela Irene Ramos
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
| | - Teh‐Ling Takeshima
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
| | - Gordon B. Mills
- Department of Cell Development and Cancer BiologyKnight Cancer InstituteOregon Health and Science UniversityPortlandOregon
| | - Qiang Yu
- Agency for Science Technology and Research (A*STAR)Genome Institute of SingaporeBiopolisSingapore
| | - Dave S. B. Hoon
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
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Lin Y, Zhou X, Peng W, Wu J, Wu X, Chen Y, Cui Z. Expression and clinical implications of basic leucine zipper ATF-like transcription factor 2 in breast cancer. BMC Cancer 2021; 21:1062. [PMID: 34565331 PMCID: PMC8474811 DOI: 10.1186/s12885-021-08785-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 09/15/2021] [Indexed: 12/28/2022] Open
Abstract
Background Basic leucine zipper ATF-like transcription factor 2 (BATF2) has been reported to participate in the occurrence and development of some malignancies. Herein, we aimed to explore the expression pattern and clinical implications of BATF2 in breast cancer (BC). Methods We assessed the differences in BATF2 mRNA expression between cancerous and noncancerous tissues in BC using GEPIA and UALCAN data and in BATF2 protein expression pattern using Human Protein Atlas (HPA) data. BATF2 co-expression networks were analyzed in Coexpedia. The association between the differentially expressed BATF2 mRNA and BC prognosis was assessed using UALCAN, OSbrca, and GEPIA databases. In external validations, BATF2 protein expression in BC tissues was quantitated using a tissue microarray and immunohistochemistry (IHC) analysis, and BATF2 mRNA expression in serum and serum-derived exosomes of BC patients using real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). Results No difference in the BATF2 mRNA expression level was found between cancerous and noncancerous tissues in BC based on databases. There were low-to-moderate levels of increases in BATF2 protein expressions in BC cases from the HPA cohort. BATF2 mRNA expression was negatively correlated with androgen receptor (AR) and positively correlated with BRCA2 DNA repair associated (BRCA2), marker of proliferation Ki-67 (Mki67), and tumor protein p53 (TP53) expressions. Generally, BATF2 mRNA exhibited a non-significant association with BC prognosis; yet the subgroup analyses showed that triple-negative breast cancer (TNBC) patients with high BATF2 mRNA expressions had a longer overall survival (OS). Our IHC analysis revealed a positive rate of BATF2 protein expression of 46.90%, mainly located in the nucleus of cancer cells in BC, and the OS of BC patients with high BATF2 protein expressions was prolonged. The positive rates of BATF2 mRNA expressions in the serum and exosomes were 45.00 and 41.67%, respectively. Besides, the AUCs of serum and exosomal BATF2 mRNA for BC diagnosis were 0.8929 and 0.8869, respectively. Conclusions BC patients exhibit low-to-moderate expressions in BATF2 mRNA expression levels in cancerous tissues. The high BATF2 protein expression can be a potential indicator of a better BC prognosis. Serum and exosomal BATF2 mRNA levels also serve as promising noninvasive biomarkers for BC diagnosis. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08785-6.
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Affiliation(s)
- Yingying Lin
- Laboratory of Biochemistry and Molecular Biology Research, Department of Clinical Laboratory, Fujian Medical University Cancer Hospital, No. 420 Fuma Road, Jin'an District, Fuzhou, 350014, Fujian Province, China
| | - Xusheng Zhou
- Laboratory of Biochemistry and Molecular Biology Research, Department of Clinical Laboratory, Fujian Medical University Cancer Hospital, No. 420 Fuma Road, Jin'an District, Fuzhou, 350014, Fujian Province, China
| | - Wei Peng
- Laboratory of Biochemistry and Molecular Biology Research, Department of Clinical Laboratory, Fujian Medical University Cancer Hospital, No. 420 Fuma Road, Jin'an District, Fuzhou, 350014, Fujian Province, China
| | - Jing Wu
- Laboratory of Biochemistry and Molecular Biology Research, Department of Clinical Laboratory, Fujian Medical University Cancer Hospital, No. 420 Fuma Road, Jin'an District, Fuzhou, 350014, Fujian Province, China
| | - Xiufeng Wu
- Department of Breast Surgical Oncology, Fujian Medical University Cancer Hospital, Fuzhou, Fujian, China.
| | - Yan Chen
- Laboratory of Biochemistry and Molecular Biology Research, Department of Clinical Laboratory, Fujian Medical University Cancer Hospital, No. 420 Fuma Road, Jin'an District, Fuzhou, 350014, Fujian Province, China.
| | - Zhaolei Cui
- Laboratory of Biochemistry and Molecular Biology Research, Department of Clinical Laboratory, Fujian Medical University Cancer Hospital, No. 420 Fuma Road, Jin'an District, Fuzhou, 350014, Fujian Province, China.
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Zhang X, Pang X, Zhang Z, Liu Q, Zhang H, Xiang Q, Cui Y. Co-expression and prognosis analyses of GLUT1-4 and RB1 in breast cancer. BMC Cancer 2021; 21:1026. [PMID: 34525987 PMCID: PMC8442321 DOI: 10.1186/s12885-021-08763-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/31/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Current treatment methods for patients with triple-negative breast cancer (TNBC) are very limited, and the prognosis of TNBC is relatively poor. It has been reported that glucose transporter 1 (GLUT1) is overexpressed in breast cancer cells; however, its association with the prognosis is mostly unclear. Moreover, retinoblastoma gene 1 (RB1) might be used as a biomarker for the sensitivity of breast cancer cells to GLUT1 inhibitors, which brought us to the hypothesis that there might be a close correlation between the expression of GLUT1-4 and the expression of RB1. METHODS In this study, we systematically analyzed the co-expression of GLUT1-4 and the influence of GLUT1-4 gene expression on the prognosis of breast cancer using data mining methods. We also explored possible relationships between GLUT1-4 and RB1 expression in breast cancer tissues. We used public databases such as ONCOMINE, GEPIA, LinkedOmics, and COEXPEDIA. RESULTS According to the results, the mRNA expression of SLC2A1 was significantly higher in breast cancer, while the expression levels of SLC2A2-4 were downregulated. The results also indicate that GLUT1 expression does not have significant influence on the overall survival of patients with breast cancer. The mRNA expression of SLC2A1 and RB1 is significantly correlated, which means that tissues with high RB1 mRNA expression might have relatively higher mRNA expression of SLC2A1; however, further study analyzing their roles in the expression regulation pathways with human samples is needed to verify the hypothesis. CONCLUSIONS The mRNA expression of SLC2A1 was significantly higher in breast cancer. The overall survival of breast cancer patients wasn't significantly correlated with GLUT1-4 expression. The mRNA expression of SLC2A1 and RB1 is significantly correlated according to the analysis conducted in LinkedOmics. It provides reference for future possible individualized treatment of TNBC using GLUT1 inhibitors, especially in patients with higher mRNA expression of RB1. Further study analyzing the roles of these two genes in the regulation pathways is needed.
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Affiliation(s)
- Xiaodan Zhang
- Department of Pharmacy, Base for Clinical Trial, Peking University First Hospital, No. 8, Xishku Street, Beijing, 100034, P. R. China
| | - Xiaocong Pang
- Department of Pharmacy, Base for Clinical Trial, Peking University First Hospital, No. 8, Xishku Street, Beijing, 100034, P. R. China
| | - Zhuo Zhang
- Department of Pharmacy, Base for Clinical Trial, Peking University First Hospital, No. 8, Xishku Street, Beijing, 100034, P. R. China
| | - Qianxin Liu
- Department of Pharmacy, Base for Clinical Trial, Peking University First Hospital, No. 8, Xishku Street, Beijing, 100034, P. R. China
| | - Hanxu Zhang
- Department of Pharmacy, Base for Clinical Trial, Peking University First Hospital, No. 8, Xishku Street, Beijing, 100034, P. R. China
- Department of Pharmacy Administration and Clinical Pharmacy, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing, 100191, P. R. China
| | - Qian Xiang
- Department of Pharmacy, Base for Clinical Trial, Peking University First Hospital, No. 8, Xishku Street, Beijing, 100034, P. R. China.
| | - Yimin Cui
- Department of Pharmacy, Base for Clinical Trial, Peking University First Hospital, No. 8, Xishku Street, Beijing, 100034, P. R. China.
- Institute of Clinical Pharmacology, Peking University, No.38, Xue Yuan Street, Haidian District, Beijing, 100191, China.
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Qu J, Li J, Zhang Y, He R, Liu X, Gong K, Duan L, Luo W, Hu Z, Wang G, Xia C, Luo D. AKR1B10 promotes breast cancer cell proliferation and migration via the PI3K/AKT/NF-κB signaling pathway. Cell Biosci 2021; 11:163. [PMID: 34419144 PMCID: PMC8379827 DOI: 10.1186/s13578-021-00677-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 08/09/2021] [Indexed: 01/14/2023] Open
Abstract
Background Aberrant expression of Aldo-Keto reductase family 1 member B10 (AKR1B10) was associated with tumor size and metastasis of breast cancer in our published preliminary studies. However, little is known about the detailed function and underlying molecular mechanism of AKR1B10 in the pathological process of breast cancer. Methods The relationship between elevated AKR1B10 expression and the overall survival and disease-free survival of breast cancer patients was analyzed by Kaplan–Meier Plotter database. Breast cancer cell lines overexpressing AKR1B10 (MCF-7/AKR1B10) and breast cancer cell lines with knockdown of AKR1B10 (BT-20/shAKR1B10) were constructed to analyze the impact of AKR1B10 expression on cell proliferation and migration of breast cancer. The expression levels of AKR1B10 were detected and compared in the breast cancer cell lines and tissues by RT-qPCR, western blot and immunohistochemistry. The proliferation of breast cancer cells was monitored by CCK8 cell proliferation assay, and the migration and invasion of breast cancer cells was observed by cell scratch test and transwell assay. The proliferation- and EMT-related proteins including cyclinD1, c-myc, Survivin, Twist, SNAI1, SLUG, ZEB1, E-cadherin, PI3K, p-PI3K, AKT, p-AKT, IKBα, p-IKBα, NF-κB p65, p-NF-κB p65 were detected by western blot in breast cancer cells. MCF-7/AKR1B10 cells were treated with LY294002, a PI3K inhibitor, to consider the impact of AKR1B10 overexpression on the PI3K/AKT/NF-κB signal cascade and the presence of NF-κB p65 in nuclear. In vivo tumor xenograft experiments were used to observe the role of AKR1B10 in breast cancer growth in mice. Results AKR1B10 expression was significantly greater in breast cancer tissue compared to paired non-cancerous tissue. The expression of AKR1B10 positively correlated with lymph node metastasis, tumor size, Ki67 expression, and p53 expression, but inversely correlated with overall and disease-free survival rates. Gene Ontology analysis showed that AKR1B10 activity contributes to cell proliferation. Overexpression of AKR1B10 facilitated the proliferation of MCF-7 cells, and induced the migration and invasion of MCF-7 cells in vitro in association with induction of epithelial-mesenchymal transition (EMT). Conversely, knockdown of AKR1B10 inhibited these effects in BT-20 cells. Mechanistically, AKR1B10 activated PI3K, AKT, and NF-κB p65, and induced nuclear translocation of NF-κB p65, and expression of proliferation-related proteins including c-myc, cyclinD1, Survivin, and EMT-related proteins including ZEB1, SLUG, Twist, but downregulated E-cadherin expression in MCF-7 cells. AKR1B10 silencing reduced the phosphorylation of PI3K, AKT, and NF-κB p65, the nuclear translocation of NF-κB p65, and the expression of proliferation- and migration-related proteins in BT-20 cells. LY294002, a PI3K inhibitor, attenuated the phosphorylation of PI3K, AKT, and NF-κB p65, and the nuclear translocation of NF-κB p65. In vivo tumor xenograft experiments confirmed that AKR1B10 promoted breast cancer growth in mice. Conclusions AKR1B10 promotes the proliferation, migration and invasion of breast cancer cells via the PI3K/AKT/NF-κB signaling pathway and represents a novel prognostic indicator as well as a potential therapeutic target in breast cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-021-00677-3.
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Affiliation(s)
- Jiayao Qu
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Nanshan Avenue, Shenzhou, 518000, Guangdong, People's Republic of China.,Center for Laboratory and Pathology, National & Local Joint Engineering Laboratory for High-through Molecular Diagnosis Technology, The First People's Hospital of Chenzhou, Southern Medical University, Changsha, 423000, Hunan, People's Republic of China
| | - Jia Li
- Translational Medicine Institute, The First People's Hospital of Chenzhou, University of South China, Hengyang, 423000, Hunan, People's Republic of China
| | - Yaming Zhang
- Translational Medicine Institute, The First People's Hospital of Chenzhou, University of South China, Hengyang, 423000, Hunan, People's Republic of China
| | - Rongzhang He
- Translational Medicine Institute, The First People's Hospital of Chenzhou, University of South China, Hengyang, 423000, Hunan, People's Republic of China
| | - Xiangting Liu
- Translational Medicine Institute, The First People's Hospital of Chenzhou, University of South China, Hengyang, 423000, Hunan, People's Republic of China
| | - Ke Gong
- Translational Medicine Institute, The First People's Hospital of Chenzhou, University of South China, Hengyang, 423000, Hunan, People's Republic of China
| | - Lili Duan
- Translational Medicine Institute, The First People's Hospital of Chenzhou, University of South China, Hengyang, 423000, Hunan, People's Republic of China
| | - Weihao Luo
- Translational Medicine Institute, The First People's Hospital of Chenzhou, University of South China, Hengyang, 423000, Hunan, People's Republic of China
| | - Zheng Hu
- Translational Medicine Institute, The First People's Hospital of Chenzhou, University of South China, Hengyang, 423000, Hunan, People's Republic of China
| | - Gengsheng Wang
- Center for Laboratory and Pathology, National & Local Joint Engineering Laboratory for High-through Molecular Diagnosis Technology, The First People's Hospital of Chenzhou, Southern Medical University, Changsha, 423000, Hunan, People's Republic of China.,Department of Emergency, The Second Affiliation Hospital, Hunan Normal University, Changsha, Hunan, People's Republic of China
| | - Chenglai Xia
- South Medical University Affiliated Maternal & Child Health Hospital of Foshan, Foshan, 528000, Guangdong, People's Republic of China. .,School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 520150, Guangdong, People's Republic of China.
| | - Dixian Luo
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Nanshan Avenue, Shenzhou, 518000, Guangdong, People's Republic of China. .,Center for Laboratory and Pathology, National & Local Joint Engineering Laboratory for High-through Molecular Diagnosis Technology, The First People's Hospital of Chenzhou, Southern Medical University, Changsha, 423000, Hunan, People's Republic of China.
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Baltoumas FA, Zafeiropoulou S, Karatzas E, Koutrouli M, Thanati F, Voutsadaki K, Gkonta M, Hotova J, Kasionis I, Hatzis P, Pavlopoulos GA. Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. Biomolecules 2021; 11:1245. [PMID: 34439912 PMCID: PMC8391349 DOI: 10.3390/biom11081245] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 02/06/2023] Open
Abstract
Technological advances in high-throughput techniques have resulted in tremendous growth of complex biological datasets providing evidence regarding various biomolecular interactions. To cope with this data flood, computational approaches, web services, and databases have been implemented to deal with issues such as data integration, visualization, exploration, organization, scalability, and complexity. Nevertheless, as the number of such sets increases, it is becoming more and more difficult for an end user to know what the scope and focus of each repository is and how redundant the information between them is. Several repositories have a more general scope, while others focus on specialized aspects, such as specific organisms or biological systems. Unfortunately, many of these databases are self-contained or poorly documented and maintained. For a clearer view, in this article we provide a comprehensive categorization, comparison and evaluation of such repositories for different bioentity interaction types. We discuss most of the publicly available services based on their content, sources of information, data representation methods, user-friendliness, scope and interconnectivity, and we comment on their strengths and weaknesses. We aim for this review to reach a broad readership varying from biomedical beginners to experts and serve as a reference article in the field of Network Biology.
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Affiliation(s)
- Fotis A. Baltoumas
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; (S.Z.); (E.K.); (M.K.); (F.T.); (K.V.); (M.G.); (J.H.); (I.K.); (P.H.)
| | - Sofia Zafeiropoulou
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; (S.Z.); (E.K.); (M.K.); (F.T.); (K.V.); (M.G.); (J.H.); (I.K.); (P.H.)
| | - Evangelos Karatzas
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; (S.Z.); (E.K.); (M.K.); (F.T.); (K.V.); (M.G.); (J.H.); (I.K.); (P.H.)
| | - Mikaela Koutrouli
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; (S.Z.); (E.K.); (M.K.); (F.T.); (K.V.); (M.G.); (J.H.); (I.K.); (P.H.)
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Foteini Thanati
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; (S.Z.); (E.K.); (M.K.); (F.T.); (K.V.); (M.G.); (J.H.); (I.K.); (P.H.)
| | - Kleanthi Voutsadaki
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; (S.Z.); (E.K.); (M.K.); (F.T.); (K.V.); (M.G.); (J.H.); (I.K.); (P.H.)
| | - Maria Gkonta
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; (S.Z.); (E.K.); (M.K.); (F.T.); (K.V.); (M.G.); (J.H.); (I.K.); (P.H.)
| | - Joana Hotova
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; (S.Z.); (E.K.); (M.K.); (F.T.); (K.V.); (M.G.); (J.H.); (I.K.); (P.H.)
| | - Ioannis Kasionis
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; (S.Z.); (E.K.); (M.K.); (F.T.); (K.V.); (M.G.); (J.H.); (I.K.); (P.H.)
| | - Pantelis Hatzis
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; (S.Z.); (E.K.); (M.K.); (F.T.); (K.V.); (M.G.); (J.H.); (I.K.); (P.H.)
- Center for New Biotechnologies and Precision Medicine, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Georgios A. Pavlopoulos
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; (S.Z.); (E.K.); (M.K.); (F.T.); (K.V.); (M.G.); (J.H.); (I.K.); (P.H.)
- Center for New Biotechnologies and Precision Medicine, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
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Sun R, He L, Lee H, Glinka A, Andresen C, Hübschmann D, Jeremias I, Müller-Decker K, Pabst C, Niehrs C. RSPO2 inhibits BMP signaling to promote self-renewal in acute myeloid leukemia. Cell Rep 2021; 36:109559. [PMID: 34407399 DOI: 10.1016/j.celrep.2021.109559] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/18/2021] [Accepted: 07/28/2021] [Indexed: 12/21/2022] Open
Abstract
Acute myeloid leukemia (AML) is a rapidly progressing cancer, for which chemotherapy remains standard treatment and additional therapeutic targets are requisite. Here, we show that AML cells secrete the stem cell growth factor R-spondin 2 (RSPO2) to promote their self-renewal and prevent cell differentiation. Although RSPO2 is a well-known WNT agonist, we reveal that it maintains AML self-renewal WNT independently, by inhibiting BMP receptor signaling. Autocrine RSPO2 signaling is also required to prevent differentiation and to promote self-renewal in normal hematopoietic stem cells as well as primary AML cells. Comprehensive datamining reveals that RSPO2 expression is elevated in patients with AML of poor prognosis. Consistently, inhibiting RSPO2 prolongs survival in AML mouse xenograft models. Our study indicates that in AML, RSPO2 acts as an autocrine BMP antagonist to promote cancer cell renewal and may serve as a marker for poor prognosis.
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Affiliation(s)
- Rui Sun
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
| | - Lixiazi He
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, 69120 Heidelberg, Germany; Molecular Medicine Partnership Unit, European Molecular Biology Laboratory-Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Hyeyoon Lee
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
| | - Andrey Glinka
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
| | - Carolin Andresen
- Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), 69120 Heidelberg, Germany
| | - Daniel Hübschmann
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), 69120 Heidelberg, Germany; Computational Oncology, Molecular Diagnostics Program, National Center for Tumor Diseases (NCT) Heidelberg and DKFZ, 69120 Heidelberg, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany; German Cancer Consortium (DKTK), partner site Munich, Germany
| | - Karin Müller-Decker
- Core Facility Tumor Models, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
| | - Caroline Pabst
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, 69120 Heidelberg, Germany; Molecular Medicine Partnership Unit, European Molecular Biology Laboratory-Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Christof Niehrs
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany; Institute of Molecular Biology (IMB), 55128 Mainz, Germany.
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Varisli L, Javed A, Ozturk BE, Akyuz GK, Takir G, Roumelioti FM, Gagos S, Yorukoglu K, Korkmaz KS. HN1 interacts with γ-tubulin to regulate centrosomes in advanced prostate cancer cells. Cell Cycle 2021; 20:1723-1744. [PMID: 34382911 DOI: 10.1080/15384101.2021.1962624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Prostate cancer is one of the most common cancer for men worldwide with advanced forms showing supernumerary or clustered centrosomes. Hematological and neurological expressed 1 (HN1) also known as Jupiter Microtubule Associated Homolog 1 (JPT1) belongs to a small poorly understood family of genes that are evolutionarily conserved across vertebrate species. The co-expression network of HN1 from the TCGA PRAD dataset indicates the putative role of HN1 in centrosome-related processes in the context of prostate cancer. HN1 expression is low in normal RWPE-1 cells as compared to cancerous androgen-responsive LNCaP and androgen insensitive PC-3 cells. HN1 overexpression resulted in differential response for cell proliferation and cell cycle changes in RWPE-1, LNCaP, and PC-3 cells. Since HN1 overexpression increased the proliferation rate in PC-3 cells, these cells were used for functional characterization of HN1 in advanced prostate carcinogenesis. Furthermore, alterations in HN expression led to an increase in abnormal to normal nuclei ratio and increased chromosomal aberrations in PC-3 cells. We observed the co-localization of HN1 with γ-tubulin foci in prostate cancer cells, further validated by immunoprecipitation. HN1 was observed as physically associated with γ-tubulin and its depletion led to increased γ-tubulin foci and disruption in microtubule spindle assembly. Higher HN1 expression was correlated with prostate cancer as compared to normal tissues. The restoration of HN1 expression after silencing suggested that it has a role in centrosome clustering, implicating a potential role of HN1 in cell division as well as in prostate carcinogenesis warranting further studies.
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Affiliation(s)
- Lokman Varisli
- Faculty of Engineering, Department of Bioengineering, Cancer Biology Laboratory, Ege University, Izmir, Turkey
| | - Aadil Javed
- Faculty of Engineering, Department of Bioengineering, Cancer Biology Laboratory, Ege University, Izmir, Turkey
| | - Bilge Esin Ozturk
- Faculty of Engineering, Department of Bioengineering, Cancer Biology Laboratory, Ege University, Izmir, Turkey
| | - Gencer Kaan Akyuz
- Faculty of Engineering, Department of Bioengineering, Cancer Biology Laboratory, Ege University, Izmir, Turkey
| | - Gulevin Takir
- Faculty of Engineering, Department of Bioengineering, Cancer Biology Laboratory, Ege University, Izmir, Turkey
| | - Fani-Marlen Roumelioti
- Biomedical Research Foundation of the Academy of Athens, Basic Research II, Laboratory of Genetics, Greece (BRFAA), Izmir, Turkey
| | - Sarantis Gagos
- Biomedical Research Foundation of the Academy of Athens, Basic Research II, Laboratory of Genetics, Greece (BRFAA), Izmir, Turkey
| | - Kutsal Yorukoglu
- Faculty of Medicine, Department of Pathology, Dokuz Eylul University, Izmir, Turkey
| | - Kemal Sami Korkmaz
- Faculty of Engineering, Department of Bioengineering, Cancer Biology Laboratory, Ege University, Izmir, Turkey
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33
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Zhang Z, Jia H, Wang Y, Du B, Zhong J. Association of MACC1 expression with lymphatic metastasis in colorectal cancer: A nested case-control study. PLoS One 2021; 16:e0255489. [PMID: 34343214 PMCID: PMC8330891 DOI: 10.1371/journal.pone.0255489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 07/16/2021] [Indexed: 12/24/2022] Open
Abstract
MACC1 gene is a newly discovered gene and plays an important role in the metastasis of colorectal cancer (CRC). The objective of this study was to investigate whether MACC1 is an independent factor associated with lymphatic metastasis in CRC patients. We analyzed the association between MACC1 expression and lymphatic metastasis in a nested case-control study including 99 cases and 198 matched controls in CRC patients, assessed from August 2001 to March 2015. Cases were defined as lymphatic metastasis and non-lymphatic metastasis according to AJCC TNM stages; for each case, two age-matched control without lymphatic and distant metastasis was randomly selected from the study participants. Demographic, variables about metastasis and MACC1 expression were collected. In multivariate analysis, the OR (95% CI) of MACC1 expression was 1.5 (1.1 to 2.0) in patients with lymphatic metastasis versus non-lymphatic metastasis after adjusting all variables. After adjustment for all variables and age stratification, MACC1 expression was found to be an independent risk factor for lymph node metastasis in the middle-aged group (OR 2.1, 95%CI 1.1–4.0). A nonlinear relationship between MACC1 expression and 64–75 age group was observed. The probability of metastasis slightly increased with the MACC1 level lower than turning point 1.4. At the same time, the probability of lymphatic metastasis was obviously increased even after adjusting all variables when MACC1 level higher than 1.4 (OR 11.2, 95% CI 1.5–81.5; p = 0.017) in the middle age group. The expression of MACC1 was not associated with lymphatic metastasis in populations younger than 64 or older than 75. The results demonstrates that increased MACC1 level in 64–75 age group might be associated with lymphatic metastasis in CRC patients.
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Affiliation(s)
- Zheying Zhang
- Department of Pathology, Xinxiang Medical University, Xinxiang, 453003, P.R. China
| | - Huijie Jia
- Department of Pathology, Xinxiang Medical University, Xinxiang, 453003, P.R. China
| | - Yuhang Wang
- Department of Pathology, Xinxiang Medical University, Xinxiang, 453003, P.R. China
| | - Baoshun Du
- Second Department of Neurosurgery, Xinxiang Central Hospital, Xinxiang, 453003, P.R. China
| | - Jiateng Zhong
- Department of Pathology, Xinxiang Medical University, Xinxiang, 453003, P.R. China
- * E-mail:
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34
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Yang K, Pei L, Wen K, Zhou S, Tao L. Investigating Research Hotspots and Publication Trends of Spinal Stenosis: A Bibliometric Analysis During 2000-2018. Front Med (Lausanne) 2021; 8:556022. [PMID: 34354999 PMCID: PMC8330839 DOI: 10.3389/fmed.2021.556022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/18/2021] [Indexed: 11/19/2022] Open
Abstract
Spinal stenosis is a common disease affecting the elderly that is present in a various forms. Its high incidence forces researchers to pay more attention and offer countermeasures. We used the Web of Science Core collection and PubMed database to obtain 5,606 scientific studies concerning spinal stenosis, and the number of publications maintained a roughly increasing trend from 108 in 2000 to 512 in 2018, only declining in 2011. Bibliometric analysis was conducted using the online analysis software CiteSpace and Bibliographic Item Co-Occurrence Matrix Builder (BICOMB). The United States maintains academic leadership in this field. The journal SPINE was the most authoritative, with 695 articles and an average of 12.73 citations. The exported major MeSH terms were further biclustered with gCLUTO according to co-word analysis to reveal research hotspots, including etiology, pathogenesis, clinical manifestation, conservative treatment, operative indication, internal implantation, and postoperative complications. After combination, the main topics focused on pathogenesis and surgical treatment. Narrowing causes flavum ligamentum hypertrophy, and posterior longitudinal ligament ossification is widely accepted. Additionally, minimally invasive surgery and internal implantation fixation are more valid in the clinic. Refining pathological classification and optimizing surgical methods and instrument properties will be important future research directions for spinal stenosis.
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Affiliation(s)
- Keda Yang
- Department of Orthopaedics, First Hospital of China Medical University, Shenyang, China
| | - Lei Pei
- Department of Orthopaedics, First Hospital of China Medical University, Shenyang, China
| | - Kaicheng Wen
- Department of Orthopaedics, First Hospital of China Medical University, Shenyang, China
| | - Siming Zhou
- Department of Orthopaedics, First Hospital of China Medical University, Shenyang, China
| | - Lin Tao
- Department of Orthopaedics, First Hospital of China Medical University, Shenyang, China
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35
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Dai X, Chen X, Chen W, Chen Y, Zhao J, Zhang Q, Lu J. A Pan-cancer Analysis Reveals the Abnormal Expression and Drug Sensitivity of CSF1. Anticancer Agents Med Chem 2021; 22:1296-1312. [PMID: 34102987 DOI: 10.2174/1871520621666210608105357] [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: 12/19/2020] [Revised: 03/17/2021] [Accepted: 04/12/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Colony-stimulating factor-1 (CSF1) is a cytokine that is closely related to normal organ growth and development as well as tumor progression. OBJECTIVE We aimed to summarize and clarify the reasons for the abnormal expression of CSF1 in tumors and explore the role of CSF1 in tumor progression. Furthermore, drug response analysis may provide a reference for clinical medication. METHODS The expression of CSF1 was analyzed by TCGA and CCLE. Besides, cBioPortal and MethSurv databases were used to conduct mutation and DNA methylation analyses. Further, correlations between CSF1 expression and tumor stage, survival, immune infiltration, drug sensitivity and enrichment analyses were validated via UALCAN, Kaplan-Meier plotter, TIMER, CTRP and Coexperia databases. RESULTS CSF1 is expressed in a variety of tissues, meaningfully, it can be detected in blood. Compared with normal tissues, CSF1 expression was significantly decreased in most tumors. The missense mutation and DNA methylation of CSF1 may cause the downregulated expression. Moreover, decreased CSF1 expression was related with higher tumor stage and worse survival. Further, the promoter DNA methylation level of CSF1 was prognostically significant in most tumors. Besides, CSF1 was closely related to immune infiltration, especially macrophages. Importantly, CSF1 expression was associated with a good response to VEGFRs inhibitors, which may be due to the possible involvement of CSF1 in tumor angiogenesis and metastasis processes. CONCLUSION The abnormal expression of CSF1 could serve as a promising biomarker of tumor progression and prognosis in pan-cancer. Significantly, angiogenesis and metastasis inhibitors may show a good response to CSF1-related tumors.
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Affiliation(s)
- Xiaoshuo Dai
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China
| | - Xinhuan Chen
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China
| | - Wei Chen
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China
| | - Yihuan Chen
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China
| | - Jun Zhao
- Department of Oncology, Changzhi People's Hospital, Changzhi 046000, Shanxi, China
| | - Qiushuang Zhang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China
| | - Jing Lu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China
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36
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Hossain MS, Quadery Tonmoy MI, Islam MN, Islam MS, Afif IK, Singha Roy A, Fariha A, Al Reza H, Bahadur NM, Rahaman MM. MicroRNAs expression analysis shows key affirmation of Synaptopodin-2 as a novel prognostic and therapeutic biomarker for colorectal and cervical cancers. Heliyon 2021; 7:e07347. [PMID: 34195444 PMCID: PMC8239731 DOI: 10.1016/j.heliyon.2021.e07347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/30/2021] [Accepted: 06/15/2021] [Indexed: 12/26/2022] Open
Abstract
MicroRNAs play a crucial role in tumorigenesis, tumor progression, and metastasis, and thus they contribute in development of different malignancies including cervical cancer (CC) and colorectal cancer (CRC). Through integrated strategies of computational biology, this study aims to identify prognostic biomarkers responsible for CRC and CC prognosis, and potential therapeutic agents to halt the progression of these cancers. Expression analysis of miRNA datasets of CRC and CC identified 17 differentially expressed miRNAs (DEMs). SYNPO2, NEGR1, FGF7, LIFR, RUNX1T1, CFL2, BNC2, EPHB2, PMAIP1, and CDC25A differentially expressed genes (DEGs) regulated by these DEMs were classified as candidate genes responsible for CRC and CC. Down-regulation of Synaptopodin-2 (SYNPO2) is involved in emergence and progression of these cancers by activating ER, PI3K/AKT, and EMT pathways as well as by suppressing DNA damage response, and cell cycle pathways. Higher methylation rate in promoter region of SYNPO2 could be a possible reason for lowering the expression of SYNPO2 in tumor stages. Hence, the lower expression of SYNPO2 is associated with poor prognosis of CRC and CC and could function as prognostic biomarker and therapeutic target. Fourteen transcription factors were recognized which can activate/inhibit the transcription of SYNPO2 and may be a potential target to regulate expression of SYNPO2 in CRC and CC. Retinoic acid and Estradiol were identified as putative therapeutic drugs for CRC and CC patients. This study will thus help in understanding the underlying molecular events in CRC and CC that may improve the detection of malignant lesions in primary screening and will broaden the clinical applications.
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Affiliation(s)
- Md. Shahadat Hossain
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | | | - Md. Nur Islam
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md. Sajedul Islam
- Department of Biochemistry & Biotechnology, University of Barishal, Barishal, Bangladesh
| | - Ibrahim Khalil Afif
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Arpita Singha Roy
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Atqiya Fariha
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Hasan Al Reza
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Newaz Mohammed Bahadur
- Department of Applied Chemistry and Chemical Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
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Darbani B. Genome Evolutionary Dynamics Meets Functional Genomics: A Case Story on the Identification of SLC25A44. Int J Mol Sci 2021; 22:ijms22115669. [PMID: 34073512 PMCID: PMC8199184 DOI: 10.3390/ijms22115669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/09/2021] [Accepted: 05/23/2021] [Indexed: 12/14/2022] Open
Abstract
Gene clusters are becoming promising tools for gene identification. The study reveals the purposive genomic distribution of genes toward higher inheritance rates of intact metabolic pathways/phenotypes and, thereby, higher fitness. The co-localization of co-expressed, co-interacting, and functionally related genes was found as genome-wide trends in humans, mouse, golden eagle, rice fish, Drosophila, peanut, and Arabidopsis. As anticipated, the analyses verified the co-segregation of co-localized events. A negative correlation was notable between the likelihood of co-localization events and the inter-loci distances. The evolution of genomic blocks was also found convergent and uniform along the chromosomal arms. Calling a genomic block responsible for adjacent metabolic reactions is therefore recommended for identification of candidate genes and interpretation of cellular functions. As a case story, a function in the metabolism of energy and secondary metabolites was proposed for Slc25A44, based on its genomic local information. Slc25A44 was further characterized as an essential housekeeping gene which has been under evolutionary purifying pressure and belongs to the phylogenetic ETC-clade of SLC25s. Pathway enrichment mapped the Slc25A44s to the energy metabolism. The expression of peanut and human Slc25A44s in oocytes and Saccharomyces cerevisiae strains confirmed the transport of common precursors for secondary metabolites and ubiquinone. These results suggest that SLC25A44 is a mitochondrion-ER-nucleus zone transporter with biotechnological applications. Finally, a conserved three-amino acid signature on the cytosolic face of transport cavity was found important for rational engineering of SLC25s.
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Affiliation(s)
- Behrooz Darbani
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; or ; Tel.: +45-(53)-578055
- Research Center Flakkebjerg, Department of Agroecology, Aarhus University, 4200 Slagelse, Denmark
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38
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Wang S, Wang D, Cai X, Wu Q, Han Y. Identification of the ZEB2 gene as a potential target for epilepsy therapy and the association between rs10496964 and ZEB2 expression. J Int Med Res 2021; 48:300060520980527. [PMID: 33870748 PMCID: PMC8061191 DOI: 10.1177/0300060520980527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Objective An association between the rs10496964 polymorphism and the
ZEB2 gene has not yet been reported, and the role of
ZEB2 in epilepsy therapy is also unclear. The aims of
this research were to evaluate the role of ZEB2 in the
therapy of epilepsy and to explore the association between rs10496964 and
ZEB2 expression. Methods We used the expression quantitative trait loci (eQTL) dataset resource from
the Brain eQTL Almanac to evaluate the association between rs10496964 and
ZEB2 expression in human brain tissue. Pathway and
process enrichment analysis, protein–protein interaction analysis, and
PhosphoSitePlus® analysis were then performed to further evaluate the role
of ZEB2 in the therapy of epilepsy. Results The rs10496964 polymorphism was found to regulate the expression of
ZEB2 in human brain tissue. The ZEB2 protein interacts
with the targets of approved antiepileptic drugs, and a post-translational
acetylation modification of ZEB2 was associated with an epilepsy drug
therapy. Conclusion Our findings suggest that ZEB2 may be involved in the
therapy of epilepsy, and rs10496964 regulates ZEB2
expression in human brain tissue.
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Affiliation(s)
- Shitao Wang
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Dan Wang
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xuemei Cai
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Qian Wu
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yanbing Han
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China
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CLCA4 and MS4A12 as the significant gene biomarkers of primary colorectal cancer. Biosci Rep 2021; 40:226087. [PMID: 32797167 PMCID: PMC7441370 DOI: 10.1042/bsr20200963] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023] Open
Abstract
Background: Primary colorectal cancer (PCRC) is a common digestive tract cancer in the elderly. However, the treatment effect of PCRC is still limited, and the long-term survival rate is low. Therefore, further exploring the pathogenesis of PCRC, and searching for specific molecular targets for diagnosis are the development trends of precise medical treatment, which have important clinical significance. Methods: The public data were downloaded from Gene Expression Omnibus (GEO) database. Verification for repeatability of intra-group data was performed by Pearson’s correlation test and principal component analysis. Differentially expressed genes (DEGs) between normal and PCRC were identified, and the protein–protein interaction (PPI) network was constructed. Significant module and hub genes were found in the PPI network. A total of 192 PCRC patients were recruited between 2010 and 2019 from the Fourth Hospital of Hebei Medical University. RT-PCR was used to measure the relative expression of CLCA4 and MS4A12. Furthermore, the study explored the effect of expression of CLCA4 and MS4A12 for overall survival. Results: A total of 53 DEGs were identified between PCRC and normal colorectal tissues. Ten hub genes concerned to PCRC were screened, namely CLCA4, GUCA2A, GCG, SST, MS4A12, PLP1, CHGA, PYY, VIP, and GUCA2B. The PCRC patients with low expression of CLCA4 and MS4A12 has a worse overall survival than high expression of CLCA4 and MS4A12 (P<0.05). Conclusion: The research of DEGs in PCRC (53 DEGs, 10 hub genes, especially CLCA4 and MS4A12) and related signaling pathways is conducive to the differential analysis of the molecular mechanism of PCRC.
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40
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Xiang Y, Liang B, Jiang Y, Sun F, Zhao Y, Wu Q, Hu X, Liu Y, Huang Q, Liao W, Yao Z, Li S, Shi M. MET transcriptional regulator/serine peptidase inhibitor kunitz type 1 panel operating through HGF/c-MET axis as a prognostic signature in pan-cancer. Cancer Med 2021; 10:2442-2460. [PMID: 33751856 PMCID: PMC7982633 DOI: 10.1002/cam4.3834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 01/24/2021] [Accepted: 02/10/2021] [Indexed: 12/17/2022] Open
Abstract
Dysregulations in transcription factors (TFs) and their genetic products play important roles in tumorigenesis, tumor progression and metastasis. However, prognostic value of the transcriptional regulatory networks in different cancers has not been investigated in depth. The purpose of our study was to identify and validate a potential predictive signature that combines TFs and their regulatory products in eight solid tumors. We used bioinformatics analysis to identify MET Transcriptional Regulator (MACC1) and Serine Peptidase Inhibitor Kunitz Type 1 (SPINT1) as candidate TFs with the respective downstream regulatory proteins for patient prognosis in pan‐cancer. Subsequent molecular analysis of clinical gastric cancer tissue samples further verified the negative correlation between MACC1 and SPINT1. Further, we showed that mechanistically, MACC1/SPINT1 mediated the pro‐HGF proteolysis and c‐Met phosphorylation in HGF/c‐MET signaling pathway. Kaplan‐Meier plots and receiver operating characteristics analysis revealed that the two‐gene signature combining MACC1 with SPINT1 was effective in predicting survival in all eight cancer cohorts tested. In conclusion, our study clarified the regulatory relationship between MACC1 and SPINT1 in the context of the HGF/c‐MET signaling pathway and determined MACC1/SPINT1 panel as a valuable signature for the prediction of prognosis in patients for multiple solid cancer types.
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Affiliation(s)
- Yi Xiang
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Bishan Liang
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yu Jiang
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Fei Sun
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yang Zhao
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qijing Wu
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xingbin Hu
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yajing Liu
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qiong Huang
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wangjun Liao
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhiqi Yao
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shaowei Li
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Min Shi
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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41
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von Scheidt M, Zhao Y, de Aguiar Vallim TQ, Che N, Wierer M, Seldin MM, Franzén O, Kurt Z, Pang S, Bongiovanni D, Yamamoto M, Edwards PA, Ruusalepp A, Kovacic JC, Mann M, Björkegren JLM, Lusis AJ, Yang X, Schunkert H. Transcription Factor MAFF (MAF Basic Leucine Zipper Transcription Factor F) Regulates an Atherosclerosis Relevant Network Connecting Inflammation and Cholesterol Metabolism. Circulation 2021; 143:1809-1823. [PMID: 33626882 DOI: 10.1161/circulationaha.120.050186] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Coronary artery disease (CAD) is a multifactorial condition with both genetic and exogenous causes. The contribution of tissue-specific functional networks to the development of atherosclerosis remains largely unclear. The aim of this study was to identify and characterize central regulators and networks leading to atherosclerosis. METHODS Based on several hundred genes known to affect atherosclerosis risk in mouse (as demonstrated in knockout models) and human (as shown by genome-wide association studies), liver gene regulatory networks were modeled. The hierarchical order and regulatory directions of genes within the network were based on Bayesian prediction models, as well as experimental studies including chromatin immunoprecipitation DNA-sequencing, chromatin immunoprecipitation mass spectrometry, overexpression, small interfering RNA knockdown in mouse and human liver cells, and knockout mouse experiments. Bioinformatics and correlation analyses were used to clarify associations between central genes and CAD phenotypes in both human and mouse. RESULTS The transcription factor MAFF (MAF basic leucine zipper transcription factor F) interacted as a key driver of a liver network with 3 human genes at CAD genome-wide association studies loci and 11 atherosclerotic murine genes. Most importantly, expression levels of the low-density lipoprotein receptor (LDLR) gene correlated with MAFF in 600 CAD patients undergoing bypass surgery (STARNET [Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task]) and a hybrid mouse diversity panel involving 105 different inbred mouse strains. Molecular mechanisms of MAFF were tested in noninflammatory conditions and showed positive correlation between MAFF and LDLR in vitro and in vivo. Interestingly, after lipopolysaccharide stimulation (inflammatory conditions), an inverse correlation between MAFF and LDLR in vitro and in vivo was observed. Chromatin immunoprecipitation mass spectrometry revealed that the human CAD genome-wide association studies candidate BACH1 (BTB domain and CNC homolog 1) assists MAFF in the presence of lipopolysaccharide stimulation with respective heterodimers binding at the MAF recognition element of the LDLR promoter to transcriptionally downregulate LDLR expression. CONCLUSIONS The transcription factor MAFF was identified as a novel central regulator of an atherosclerosis/CAD-relevant liver network. MAFF triggered context-specific expression of LDLR and other genes known to affect CAD risk. Our results suggest that MAFF is a missing link between inflammation, lipid and lipoprotein metabolism, and a possible treatment target.
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Affiliation(s)
- Moritz von Scheidt
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany (M.v.S., S.P., H.S.).,Deutsches Zentrum für Herz- und Kreislauferkrankungen, Partner Site Munich Heart Alliance, Germany (M.v.S., D.B., H.S.)
| | | | - Thomas Q de Aguiar Vallim
- Departments of Medicine (T.Q.d.A.V., N.C., P.A.E., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles.,Biological Chemistry (T.Q.d.A.V., P.A.E.), David Geffen School of Medicine, University of California, Los Angeles
| | - Nam Che
- Departments of Medicine (T.Q.d.A.V., N.C., P.A.E., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles.,Microbiology, Immunology and Molecular Genetics (N.C., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles.,Human Genetics (N.C., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany (M.W., M.M.)
| | - Marcus M Seldin
- Department of Biological Chemistry and Center for Epigenetics and Metabolism, University of California, Irvine (M.M.S.)
| | - Oscar Franzén
- Integrated Cardio Metabolic Centre, Karolinska Institutet, Novum, Huddinge, Sweden (O.F., J.L.M.B.)
| | - Zeyneb Kurt
- Department of Computer and Information Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom (Z.K.)
| | - Shichao Pang
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany (M.v.S., S.P., H.S.)
| | - Dario Bongiovanni
- Deutsches Zentrum für Herz- und Kreislauferkrankungen, Partner Site Munich Heart Alliance, Germany (M.v.S., D.B., H.S.).,Department of Internal Medicine, School of Medicine, University Hospital Rechts der Isar, Technical University of Munich, Germany (D.B.)
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan (M.Y.)
| | - Peter A Edwards
- Departments of Medicine (T.Q.d.A.V., N.C., P.A.E., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles.,Biological Chemistry (T.Q.d.A.V., P.A.E.), David Geffen School of Medicine, University of California, Los Angeles
| | - Arno Ruusalepp
- Department of Cardiac Surgery, Tartu University Hospital, Estonia (A.R.).,Clinical Gene Networks AB, Stockholm, Sweden (A.R., J.L.M.B.)
| | - Jason C Kovacic
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York (J.C.K., J.L.M.B.)
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany (M.W., M.M.)
| | - Johan L M Björkegren
- Integrated Cardio Metabolic Centre, Karolinska Institutet, Novum, Huddinge, Sweden (O.F., J.L.M.B.).,Clinical Gene Networks AB, Stockholm, Sweden (A.R., J.L.M.B.).,Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York (J.C.K., J.L.M.B.)
| | - Aldons J Lusis
- Departments of Medicine (T.Q.d.A.V., N.C., P.A.E., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles.,Microbiology, Immunology and Molecular Genetics (N.C., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles.,Human Genetics (N.C., A.J.L.), David Geffen School of Medicine, University of California, Los Angeles
| | - Xia Yang
- Department of Integrative Biology and Physiology, Institute for Quantitative and Computational Biosciences (Y.Z., X.Y.), David Geffen School of Medicine, University of California, Los Angeles
| | - Heribert Schunkert
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany (M.v.S., S.P., H.S.).,Deutsches Zentrum für Herz- und Kreislauferkrankungen, Partner Site Munich Heart Alliance, Germany (M.v.S., D.B., H.S.)
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Transcriptome analysis of the procession from chronic pancreatitis to pancreatic cancer and metastatic pancreatic cancer. Sci Rep 2021; 11:3409. [PMID: 33564087 PMCID: PMC7873308 DOI: 10.1038/s41598-021-83015-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 01/28/2021] [Indexed: 02/08/2023] Open
Abstract
Exploring the underlying mechanisms of cancer development is useful for cancer treatment. In this paper, we analyzed the transcriptome profiles from the human normal pancreas, pancreatitis, pancreatic cancer and metastatic pancreatic cancer to study the intricate associations among pancreatic cancer progression. We clustered the transcriptome data, and analyzed the differential expressed genes. WGCNA was applied to construct co-expression networks and detect important modules. Importantly we selected the module in a different way. As the pancreatic disease deteriorates, the number of differentially expressed genes increases. The gene networks of T cells and interferon are upregulated in stages. In conclusion, the network-based study provides gradually activated gene networks in the disease progression of pancreatitis, pancreatic cancer, and metastatic pancreatic cancer. It may contribute to the rational design of anti-cancer drugs.
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Yu S, Li L, Cai H, He B, Gao Y, Li Y. Overexpression of NELFE contributes to gastric cancer progression via Wnt/β-catenin signaling-mediated activation of CSNK2B expression. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:54. [PMID: 33526068 PMCID: PMC7851912 DOI: 10.1186/s13046-021-01848-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/17/2021] [Indexed: 02/08/2023]
Abstract
Background Accumulating evidence has highlighted the importance of negative elongation factor complex member E (NELFE) in tumorigenesis. However, the relationship between NELFE and gastric cancer (GC) remains unclear. This study aimed to explore the expression pattern and specific function of NELFE in GC. Methods NELFE expression was evaluated by immunohistochemistry and qRT-PCR in GC tissues, respectively. Cell proliferation, migration and invasion were measured by CCK-8, colony formation, transwell assays, and nude mice model. Bioinformatics analysis was performed to search potential target genes of NELFE, and a Cignal Finder 10-Pathway Reporter Array was used to explore potential signaling pathways regulated by NELFE. Dual-luciferase reporter assays, qRT-PCR and western blotting were conducted to verify their regulatory relationship. The expression correlations among NELFE, β-catenin and CSNK2B were further explored by immunohistochemistry on consecutive resections. Results NELFE was significantly overexpressed in GC tissues both in protein and mRNA level and negatively correlated with the prognosis of GC patients. Gain- and loss-of-function experiments showed that NELFE potentiated GC cell proliferation and metastasis in vitro and in vivo. CSNK2B was identified as a downstream effector of NELFE. Wnt/β-catenin signaling may mediate the regulation of CSNK2B by NELFE. In addition, NELFE, β-catenin and CSNK2B were all remarkably upregulated in tumor tissues compared with adjacent normal tissues, and their expression levels in GC were positively correlated with each other. Conclusion Our findings reveal a new NELFE-Wnt/β-catenin-CSNK2B axis to promote GC progression and provide new candidate targets against this disease. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-01848-3.
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Affiliation(s)
- Shijun Yu
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Li Li
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Hui Cai
- Department of Geriatrics, The Second Affiliated Hospital of Zhejiang University, Hangzhou, 310009, China
| | - Bin He
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Yong Gao
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China.
| | - Yandong Li
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China.
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Li L, Wei JR, Song Y, Fang S, Du Y, Li Z, Zeng TT, Zhu YH, Li Y, Guan XY. TROAP switches DYRK1 activity to drive hepatocellular carcinoma progression. Cell Death Dis 2021; 12:125. [PMID: 33500384 PMCID: PMC7838256 DOI: 10.1038/s41419-021-03422-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the common malignancy and lacks effective therapeutic targets. Here, we demonstrated that ectopic expression of trophinin-associated protein (TROAP) dramatically drove HCC cell growth assessed by foci formation in monolayer culture, colony formation in soft agar and orthotopic liver transplantation in nude mice. Inversely, silencing TROAP expression with short-hairpin RNA attenuated the malignant proliferation of HCC cells in vitro and in vivo. Next, mechanistic investigation revealed that TROAP directly bound to dual specificity tyrosine phosphorylation regulated kinase 1A/B (DYRK1A/B), resulting in the cytoplasmic retention of proteins DYRK1A/B and promoting cell cycle process via activation of Akt/GSK-3β signaling. Combination of cisplatin with an inhibitor of DYRK1 AZ191 effectively inhibited tumor growth in mouse model for HCC cells with high level of TROAP. Clinically, TROAP was significantly upregulated by miR-142-5p in HCC tissues, which predicted the poor survival of patients with HCC. Therefore, TROAP/DYRK1/Akt axis may be a promising therapeutic target and prognostic indicator for patients with HCC.
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Affiliation(s)
- Lei Li
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 510060, Guangzhou, China.
- Department of Clinical Oncology, State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, China.
- Department of Clinical Oncology Center, The University of Hongkong-Shenzhen Hospital, 518053, Shenzhen, China.
| | - Jia-Ru Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Ye Song
- Affiliated Cancer Hospital & Institutes of Guangzhou Medical University, Guangzhou Key Medical Discipline Construction Project, 510095, Guangzhou, China
| | - Shuo Fang
- The Seventh Affiliated Hospital, Sun Yat-sen University, 518100, Shenzhen, China
| | - Yanyu Du
- The Seventh Affiliated Hospital, Sun Yat-sen University, 518100, Shenzhen, China
| | - Zhuo Li
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 510060, Guangzhou, China
| | - Ting-Ting Zeng
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 510060, Guangzhou, China
| | - Ying-Hui Zhu
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 510060, Guangzhou, China
| | - Yan Li
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 510060, Guangzhou, China
| | - Xin-Yuan Guan
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 510060, Guangzhou, China.
- Department of Clinical Oncology, State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, China.
- Department of Clinical Oncology Center, The University of Hongkong-Shenzhen Hospital, 518053, Shenzhen, China.
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Yu B, Zhang J, Sun Z, Cao P, Zheng X, Gao Z, Cao H, Zhang F, Wang W. Interferon-inducible protein 16 may be a biomarker and prognostic factor in renal cell carcinoma by bioinformatics analysis. Medicine (Baltimore) 2021; 100:e24257. [PMID: 33429832 PMCID: PMC7793379 DOI: 10.1097/md.0000000000024257] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/15/2020] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Renal cell carcinoma (RCC) accounts for 2% to 3% of all human malignancies and is the 9th most common malignancy in Western countries. Due to the development of surgical procedures and the use of novel drugs, survival has been significantly prolonged. However, current challenges include how to diagnose RCC earlier and how to overcome drug resistance. Methods: We explored the relationship between the transcription level of IFI16 and clinical data in RCC through various online databases, including ONCOMINE, GEPIA, HPA, Timer and COEXPEDIA. RESULTS In comparison with corresponding normal tissues, IFI16 mRNA expression levels were higher in kidney renal clear cell carcinoma (KIRC) and kidney renal papillary cell carcinoma (KIRP) tissues. In KIRC, the higher expression of IFI16 was associated with lower overall survival (P = .037). In KIRP, the higher expression IFI16 was associated with lower disease-free survival and overall survival (P = .037 and P = .011). In contrast, the IFI16 expression was negatively correlated with tumor purity in kidney chromophobe, KIRC and KIRP (all P < .05). In KIRC and KIRP, the expression of IFI16 was positively correlated with tumor-infiltrating immune cells (TIICs) (all P < .05), except macrophages in KIRP. In KIRC, the main TIICs were B cells, CD4+T cells, neutrophils, and dendritic cells, while the main TIICs in the high amplification state were macrophage (all P < .0001). Functional enrichment analysis by gene ontology and Kyoto Encyclopedia of Genes and Genomes highlighted enrichment of neutrophil degranulation, phagocytosis and vesicle-mediated transport regulation, and pathways including tuberculosis, toxoplasmosis, phagosome, leishmaniasis, and Fc gamma R-mediated. CONCLUSIONS IFI16 is overexpressed in RCC and may be an important oncogene in the progression of kidney. In addition, IFI16 may a marker for RCC diagnosis and prognosis, which may be related to immune infiltration.
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Affiliation(s)
- Baozhong Yu
- Department of Urology, Affiliated Beijing Chaoyang Hospital of Capital Medical University
| | - Jiandong Zhang
- Department of Urology, Affiliated Beijing Chaoyang Hospital of Capital Medical University
| | - Zejia Sun
- Department of Urology, Affiliated Beijing Chaoyang Hospital of Capital Medical University
| | - Peng Cao
- Capital Medical University, Beijing, China
| | | | - Zihao Gao
- Capital Medical University, Beijing, China
| | | | | | - Wei Wang
- Department of Urology, Affiliated Beijing Chaoyang Hospital of Capital Medical University
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Zhan YT, Li L, Zeng TT, Zhou NN, Guan XY, Li Y. SNRPB-mediated RNA splicing drives tumor cell proliferation and stemness in hepatocellular carcinoma. Aging (Albany NY) 2020; 13:537-554. [PMID: 33289700 PMCID: PMC7834993 DOI: 10.18632/aging.202164] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/28/2020] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the leading malignant diseases worldwide, but therapeutic targets for HCC are lacking. Here, we characterized a significant upregulation of Small Nuclear Ribonucleoprotein Polypeptides B and B1 (SNRPB) in HCC via qRT-PCR, western blotting, tissue microarray and public database analyses. Increased SNRPB expression was positively associated with adjacent organ invasion, tumor size, serum AFP level and poor HCC patient survival. Next, we transfected SNRPB into HCC cells to construct SNRPB-overexpressing cell lines, and short hairpin RNA targeting SNRPB was used to silence SNRPB in HCC cells. Functional studies showed that SNRPB overexpression could promote HCC cell malignant proliferation and stemness maintenance. Inversely, SNRPB knockdown in HCC cells caused inverse effects. Importantly, analysis of alternative splicing by RNA sequencing revealed that SNRPB promoted the formation of AKT3-204 and LDHA-220 splice variants, which activated the Akt pathway and aerobic glycolysis in HCC cells. In conclusion, SNRPB could serve as a prognostic predictor for patients with HCC, and it promotes HCC progression by inducing metabolic reprogramming.
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Affiliation(s)
- Yu-Ting Zhan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
| | - Lei Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China.,Department of Clinical Oncology, The University of Hong Kong, Hong Kong 852, P. R. China
| | - Ting-Ting Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
| | - Ning-Ning Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
| | - Xin-Yuan Guan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China.,Department of Clinical Oncology, The University of Hong Kong, Hong Kong 852, P. R. China
| | - Yan Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
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Mongre RK, Mishra CB, Jung S, Lee BS, Quynh NTN, Anh NH, Myagmarjav D, Jo T, Lee MS. Exploring the Role of TRIP-Brs in Human Breast Cancer: An Investigation of Expression, Clinicopathological Significance, and Prognosis. MOLECULAR THERAPY-ONCOLYTICS 2020; 19:105-126. [PMID: 33102693 PMCID: PMC7554327 DOI: 10.1016/j.omto.2020.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/10/2020] [Indexed: 02/06/2023]
Abstract
TRIP-Brs, a group of transcription factors (TFs) that modulate several mechanisms in higher organisms. However, the novel paradigm to target TRIP-Brs in specific cancer remains to be deciphered. In particular, comprehensive analysis of TRIP-Brs in clinicopathological and patients’ prognosis, especially in breast cancer (BRCA), is being greatly ignored. Therefore, we explored the key roles of TRIP-Br expression, modulatory effects, mutations, immune infiltration, and prognosis in BRCA using multidimensional approaches. We found elevated levels of TRIP-Brs in numerous cancer tissues than normal. Higher expression of TRIP-Br-2/4/5 was shown to be positively associated with lower survival, tumor grade, and malignancy of patients with BRCA. Additionally, higher TRIP-Br-3/4 were also significantly linked with worse/short survival of BRCA patients. TRIP-Br-1/4/5 were significantly overexpressed and enhanced tumorigenesis in large-scale BRCA datasets. The mRNA levels of TRIP-Brs have been also correlated with tumor immune infiltrate in BRCA patients. In addition, TRIP-Brs synergistically play a pivotal role in central carbon metabolism, cancer-associated pathways, cell cycle, and thyroid hormone signaling, which evoke that TRIP-Brs may be a potential target for the therapy of BRCA. Thus, this investigation may lay a foundation for further research on TRIP-Br-mediated management of BRCA.
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Affiliation(s)
- Raj Kumar Mongre
- Molecular Cancer Biology Laboratory, Cellular Heterogeneity Research Center, Department of Biosystem, Sookmyung Women's University, Hyochangwon gil-52, Yongsan-Gu, Seoul 140-742, Republic of Korea
| | - Chandra Bhushan Mishra
- College of Pharmacy, Sookmyung Women's University, Hyochangwon gil-52, Yongsan-Gu, Seoul 140-742, Republic of Korea
| | - Samil Jung
- Molecular Cancer Biology Laboratory, Cellular Heterogeneity Research Center, Department of Biosystem, Sookmyung Women's University, Hyochangwon gil-52, Yongsan-Gu, Seoul 140-742, Republic of Korea
| | - Beom Suk Lee
- Molecular Cancer Biology Laboratory, Cellular Heterogeneity Research Center, Department of Biosystem, Sookmyung Women's University, Hyochangwon gil-52, Yongsan-Gu, Seoul 140-742, Republic of Korea
| | - Nguyen Thi Ngoc Quynh
- Molecular Cancer Biology Laboratory, Cellular Heterogeneity Research Center, Department of Biosystem, Sookmyung Women's University, Hyochangwon gil-52, Yongsan-Gu, Seoul 140-742, Republic of Korea
| | - Nguyen Hai Anh
- Molecular Cancer Biology Laboratory, Cellular Heterogeneity Research Center, Department of Biosystem, Sookmyung Women's University, Hyochangwon gil-52, Yongsan-Gu, Seoul 140-742, Republic of Korea
| | - Davaajragal Myagmarjav
- Molecular Cancer Biology Laboratory, Cellular Heterogeneity Research Center, Department of Biosystem, Sookmyung Women's University, Hyochangwon gil-52, Yongsan-Gu, Seoul 140-742, Republic of Korea
| | - Taeyeon Jo
- Molecular Cancer Biology Laboratory, Cellular Heterogeneity Research Center, Department of Biosystem, Sookmyung Women's University, Hyochangwon gil-52, Yongsan-Gu, Seoul 140-742, Republic of Korea
| | - Myeong-Sok Lee
- Molecular Cancer Biology Laboratory, Cellular Heterogeneity Research Center, Department of Biosystem, Sookmyung Women's University, Hyochangwon gil-52, Yongsan-Gu, Seoul 140-742, Republic of Korea
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Li Z, Liu J, Wang W, Zhao Y, Yang D, Geng X. Investigation of hub genes involved in diabetic nephropathy using biological informatics methods. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1087. [PMID: 33145306 PMCID: PMC7575993 DOI: 10.21037/atm-20-5647] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background The aim of this study was to find genes with significantly aberrant expression in diabetic nephropathy (DN) and determine their underlying mechanisms. Methods GSE30528 and GSE1009 were obtained by querying the Gene Expression Omnibus (GEO) database. The difference in target gene expression between normal renal tissues and kidney tissues in patients with DN was screened by using the GEO2R tool. Using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) database, differentially expressed genes (DEGs) were analysed by Gene Ontology (GO) annotation and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Then, the protein-protein interactions (PPIs) of DEGs were analyzed by Cytoscape with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, and the hub genes in this PPI network were recognized by centrality analysis. Results There were 110 genes with significant expression differences between normal and DN tissues. The differences in gene expression involved many functions and expression pathways, such as the formation of the extracellular matrix and the construction of the extracellular domain. The correlation analysis and subgroup analysis of 14 hub genes and the clinical characteristics of DN showed that CTGF, ALB, PDPN, FLT1, IGF1, WT1, GJA1, IGFBP2, FGF9, BMP2, FGF1, BMP7, VEGFA, and TGFBR3 may be involved in the progression of DN. Conclusions We confirmed the differentially expressed hub genes and other genes which may be the novel biomarker and target candidates in DN.
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Affiliation(s)
- Zhanting Li
- Department of Nephrology, Xi'an International Medical Center Hospital, Xi'an, China
| | - Jianxin Liu
- Physical Examination Section, Qinhuangdao Jungong Hospital, Qinhuangdao, China
| | - Weiwei Wang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Dengfeng Yang
- Department of Laboratory Medicine, Mianxian Hospital, Mianxian, China
| | - Xiaodong Geng
- Medical School of Chinese PLA, Chinese PLA General Hospital, Beijing, China.,Kidney Diagnostic and Therapeutic Center of the Chinese PLA, Beidaihe Rehabilitation and Recuperation Center of the Chinese PLA, Qinhuangdao, China
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Prognostic Values for the mRNA Expression of the ADAMTS Family of Genes in Gastric Cancer. JOURNAL OF ONCOLOGY 2020; 2020:9431560. [PMID: 32884571 PMCID: PMC7455834 DOI: 10.1155/2020/9431560] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/28/2020] [Indexed: 12/24/2022]
Abstract
The “A Disintegrin and Metalloproteinase with Thrombospondin Motif” (ADAMTS) family of genes is involved in the occurrence and development of different cancers. However, the prognostic value of these genes in gastric cancer (GC) has not been revealed. The present study was thus conducted to determine the prognostic value for the ADAMTS family of genes in GC. First, we evaluated the mRNA expression levels of the ADAMTS family in GC patients using a GEPIA dataset. Thereafter, we determined the prognostic value of these genes by analyzing their mRNA level using the Kaplan–Meier Plotter database. The mRNA expression level of ADAMTS12 was randomly validated by qRT-PCR and meta-analysis while its coexpression genes were derived using Coexpedia. Finally, we performed Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses using the OmicShare Tools. Compared to normal tissues, expression of ADAMTS2 and 12 was significantly higher while that of ADAMTS1, 13, and 15 was significantly lower in GC tissues. According to the RNA-seq and gene chip data, the ADAMTS family (6, 7, 12, 15, and 18) of genes was closely related to the prognosis of GC, and their high expression levels were associated with poor prognosis and survival time. In addition, ADAMTS12 was highly expressed in 20 pairs of GC tissues based on RT-PCR (P=0.016) and meta-analysis (SMD: 0.73, 95% CI: 0.32–1.14, P < 0.001). GO and KEGG pathway analyses indicated that the ADAMTS12 coexpressed genes were enriched in the pathways of extracellular matrix organization, extracellular matrix structural constituent, extracellular matrix, and protein digestion and absorption. Herein, we discovered the prognostic values and biological roles of the ADAMTS genes in GC.
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Xiong Q, Fan S, Duan L, Liu B, Jiang X, Chen X, Xiong C, Tao Q, Wang J, Zhang H, Chen C, Duan Y. NCAPH is negatively associated with Mcl‑1 in non‑small cell lung cancer. Mol Med Rep 2020; 22:2916-2924. [PMID: 32945371 PMCID: PMC7453632 DOI: 10.3892/mmr.2020.11359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/25/2020] [Indexed: 01/09/2023] Open
Abstract
Lung cancer has a high mortality rate worldwide. Non‑SMC condensin I complex subunit H (NCAPH) has been identified to be one of the regulatory subunits of the condensin I complex, which is essential for the correct packaging and segregation of chromosomes in eukaryotes. NCAPH is abnormally overexpressed in various types of cancer. A pro‑survival member of the Bcl‑2 family, myeloid cell leukemia sequence 1 (Mcl‑1) is also frequently overexpressed in multiple cancers and is associated with poorer clinical outcomes for patients. The association of NCAPH and Mcl‑1 proteins with the clinical and pathological features of non‑small cell lung cancer (NSCLC) remains to be elucidated. In the current study, the positive percentage of NCAPH in the non‑cancerous lung tissues was revealed to be higher compared with that in NSCLC. However, the positive percentage of Mcl‑1 in the non‑cancerous lung tissues was lower compared with NSCLC. In addition, NCAPH high‑expression patients had a higher overall survival rate compared with patients exhibiting low expression, whereas the Mcl‑1 high‑expression group had a lower survival rate. Pairwise association in 260 cases of NSCLC revealed that overexpression of the NCAPH protein was negatively associated with Mcl‑1 expression and vice versa. The results of multivariate Cox proportional hazard regression analysis also indicated that NCAPH and Mcl‑1 demonstrated potential as distinct prognostic factors that may be used in NSCLC. The expression of NCAPH and Mcl‑1 may be associated with, and act as distinct molecular marks for the prediction of a poor prognosis in patients with NSCLC.
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Affiliation(s)
- Qiuxia Xiong
- Department of Clinical Laboratory, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Songqing Fan
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410000, P.R. China
| | - Lincan Duan
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, P.R. China
| | - Baiyang Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, P.R. China
| | - Xiulin Jiang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, P.R. China
| | - Xiaobo Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Chunyan Xiong
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Zhaotong, Zhaotong, Yunnan 657000, P.R. China
| | - Qingyuan Tao
- Department of Nuclear Medicine, The Fourth Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650021, P.R. China
| | - Juan Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Hui Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Chuanjiang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Yong Duan
- Department of Clinical Laboratory, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
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