1
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Tian W, Zhao J, Zhang X, Li P, Li X, Hong Y, Li S. RUNX1 regulates MCM2/CDC20 to promote COAD progression modified by deubiquitination of USP31. Sci Rep 2024; 14:13906. [PMID: 38886545 PMCID: PMC11183096 DOI: 10.1038/s41598-024-64726-w] [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: 01/03/2024] [Accepted: 06/12/2024] [Indexed: 06/20/2024] Open
Abstract
Colon adenocarcinoma (COAD) is the second leading cause of cancer death, and there is still a lack of diagnostic biomarkers and therapeutic targets. In this study, bioinformatics analysis of the TCGA database was used to obtain RUNX1, a gene with prognostic value in COAD. RUNX1 plays an important role in many malignancies, and its molecular regulatory mechanisms in COAD remain to be fully understood. To explore the physiological role of RUNX1, we performed functional analyses, such as CCK-8, colony formation and migration assays. In addition, we investigated the underlying mechanisms using transcriptome sequencing and chromatin immunoprecipitation assays. RUNX1 is highly expressed in COAD patients and significantly correlates with survival. Silencing of RUNX1 significantly slowed down the proliferation and migratory capacity of COAD cells. Furthermore, we demonstrate that CDC20 and MCM2 may be target genes of RUNX1, and that RUNX1 may be physically linked to the deubiquitinating enzyme USP31, which mediates the upregulation of RUNX1 protein to promote transcriptional function. Our results may provide new insights into the mechanism of action of RUNX1 in COAD and reveal potential therapeutic targets for this disease.
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Affiliation(s)
- Wei Tian
- The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Dalian Medical University, Dalian, China
| | - Jingyuan Zhao
- Stem Cell Clinical Research Center, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xinyu Zhang
- The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Dalian Medical University, Dalian, China
| | - Pengfei Li
- The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Dalian Medical University, Dalian, China
| | - Xuening Li
- Dalian Medical University, Dalian, China
| | - Yuan Hong
- Clinical Laboratory Center, Dalian Municipal Central Hospital, Dalian, China.
| | - Shuai Li
- Department of Pharmacy, The First Affiliated Hospital of Dalian Medical University, Dalian, China.
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2
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Zhang Y, Li X, Liu F, Bai X, Liu X, Sun H, Gao C, Lin Y, Xing P, Zhu J, Liu R, Wang Z, Dai J, Shi D. Design of Selective PARP-1 Inhibitors and Antitumor Studies. J Med Chem 2024; 67:8877-8901. [PMID: 38776379 DOI: 10.1021/acs.jmedchem.3c02460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Designing selective PARP-1 inhibitors has become a new strategy for anticancer drug development. By sequence comparison of PARP-1 and PARP-2, we identified a possible selective site (S site) consisting of several different amino acid residues of α-5 helix and D-loop. Targeting this S site, 140 compounds were designed, synthesized, and characterized for their anticancer activities and mechanisms. Compound I16 showed the highest PARP-1 enzyme inhibitory activity (IC50 = 12.38 ± 1.33 nM) and optimal selectivity index over PARP-2 (SI = 155.74). Oral administration of I16 (25 mg/kg) showed high inhibition rates of Hela and SK-OV-3 tumor cell xenograft models, both of which were higher than those of the oral positive drug Olaparib (50 mg/kg). In addition, I16 has an excellent safety profile, without significant toxicity at high oral doses. These findings provide a novel design strategy and chemotype for the development of safe, efficient, and highly selective PARP-1 inhibitors.
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Affiliation(s)
- Yiting Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xiangqian Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Laboratory of Marine Drugs and Biological Products, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Fang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xiaoyi Bai
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xiaochun Liu
- Marine Biomedical Research Institute of Qingdao, Qingdao 266071, China
| | - Hao Sun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Chenxia Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yuxi Lin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Pan Xing
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Jiqiang Zhu
- Shandong Linghai Biotechnology Co.Ltd., Jinan 250299, Shandong, P. R. China
| | - Ruihua Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Zemin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Jiajia Dai
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, Shandong, China
| | - Dayong Shi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Laboratory of Marine Drugs and Biological Products, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Shandong Linghai Biotechnology Co.Ltd., Jinan 250299, Shandong, P. R. China
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3
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Yan R, Song Y, Liu D, Yu W, Sun Y, Tang C, Yang X, Ding W, Yu N, Zhang Z, Ling M, Li X, Zhao C, Xing Y. Multi-omics reveals the role of MCM2 and hnRNP K phosphorylation in mouse renal aging through genomic instability. Exp Cell Res 2024; 440:114115. [PMID: 38844260 DOI: 10.1016/j.yexcr.2024.114115] [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: 02/24/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024]
Abstract
The process of aging is characterized by structural degeneration and functional decline, as well as diminished adaptability and resistance. The aging kidney exhibits a variety of structural and functional impairments. In aging mice, thinning and graying of fur were observed, along with a significant increase in kidney indices compared to young mice. Biochemical indicators revealed elevated levels of creatinine, urea nitrogen and serum uric acid, suggesting impaired kidney function. Histological analysis unveiled glomerular enlargement and sclerosis, severe hyaline degeneration, capillary occlusion, lymphocyte infiltration, tubular and glomerular fibrosis, and increased collagen deposition. Observations under electron microscopy showed thickened basement membranes, altered foot processes, and increased mesangium and mesangial matrix. Molecular marker analysis indicated upregulation of aging-related β-galactosidase, p16-INK4A, and the DNA damage marker γH2AX in the kidneys of aged mice. In metabolomics, a total of 62 significantly different metabolites were identified, and 10 pathways were enriched. We propose that citrulline, dopamine, and indoxyl sulfate have the potential to serve as markers of kidney damage related to aging in the future. Phosphoproteomics analysis identified 6656 phosphosites across 1555 proteins, annotated to 62 pathways, and indicated increased phosphorylation at the Ser27 site of Minichromosome maintenance complex component 2 (Mcm2) and decreased at the Ser284 site of heterogeneous nuclear ribonucleoprotein K (hnRNP K), with these modifications being confirmed by western blotting. The phosphorylation changes in these molecules may contribute to aging by affecting genome stability. Eleven common pathways were detected in both omics, including arginine biosynthesis, purine metabolism and biosynthesis of unsaturated fatty acids, etc., which are closely associated with aging and renal insufficiency.
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Affiliation(s)
- Rong Yan
- Department of Geriatrics, Qilu Hospital, Shandong University, Jinan, China
| | - Yiping Song
- Department of Geriatrics, Qilu Hospital, Shandong University, Jinan, China
| | - Di Liu
- Department of Geriatrics, Qilu Hospital, Shandong University, Jinan, China
| | - Wenzhuo Yu
- Department of Geriatrics, Qilu Hospital, Shandong University, Jinan, China
| | - Yan Sun
- Department of Geriatrics, Qilu Hospital, Shandong University, Jinan, China
| | - Congmin Tang
- Department of Geriatrics, Qilu Hospital, Shandong University, Jinan, China
| | - Xuechun Yang
- Department of Geriatrics, Qilu Hospital, Shandong University, Jinan, China
| | - Wenjing Ding
- Department of Geriatrics, Qilu Hospital, Shandong University, Jinan, China
| | - Na Yu
- Shandong Precision Medicine Engineering Laboratory of Bacterial Anti-tumor Drugs, Jinan, China
| | - Zhen Zhang
- Department of Geriatrics, Qilu Hospital, Shandong University, Jinan, China
| | - Mingying Ling
- Department of Geriatrics, Qilu Hospital, Shandong University, Jinan, China
| | - Xuehui Li
- Department of Geriatrics, Qilu Hospital, Shandong University, Jinan, China
| | - Chuanli Zhao
- Department of Hematology, Qilu Hospital, Shandong University, Jinan, China
| | - Yanqiu Xing
- Department of Geriatrics, Qilu Hospital, Shandong University, Jinan, China.
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4
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Radhakrishnan A, Gangopadhyay R, Sharma C, Kapardar RK, Sharma NK, Srivastav R. Unwinding Helicase MCM Functionality for Diagnosis and Therapeutics of Replication Abnormalities Associated with Cancer: A Review. Mol Diagn Ther 2024; 28:249-264. [PMID: 38530633 DOI: 10.1007/s40291-024-00701-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2024] [Indexed: 03/28/2024]
Abstract
The minichromosome maintenance (MCM) protein is a component of an active helicase that is essential for the initiation of DNA replication. Dysregulation of MCM functions contribute to abnormal cell proliferation and genomic instability. The interactions of MCM with cellular factors, including Cdc45 and GINS, determine the formation of active helicase and functioning of helicase. The functioning of MCM determines the fate of DNA replication and, thus, genomic integrity. This complex is upregulated in precancerous cells and can act as an important tool for diagnostic applications. The MCM protein complex can be an important broad-spectrum therapeutic target in various cancers. Investigations have supported the potential and applications of MCM in cancer diagnosis and its therapeutics. In this article, we discuss the physiological roles of MCM and its associated factors in DNA replication and cancer pathogenesis.
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Affiliation(s)
| | - Ritwik Gangopadhyay
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | | | | | - Nilesh Kumar Sharma
- Cancer and Translational Research Lab, Dr. DY Patil Biotechnology and Bioinformatics Institute, Dr. DY Patil Vidyapeeth, Pune, Maharashtra, India
| | - Rajpal Srivastav
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India.
- Department of Science and Technology, Ministry of Science and Technology, New Delhi, India.
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5
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Shi Q, Xu G, Jiang Y, Yang J, Han X, Wang Q, Li Y, Zhang Z, Wang K, Peng H, Chen F, Ma Y, Zhao L, Chen Y, Liu Z, Yang L, Jia X, Wen T, Tong Z, Cui X, Li F. Phospholipase PLCE1 Promotes Transcription and Phosphorylation of MCM7 to Drive Tumor Progression in Esophageal Cancer. Cancer Res 2024; 84:560-576. [PMID: 38117512 DOI: 10.1158/0008-5472.can-23-1633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 10/03/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023]
Abstract
Phospholipase C epsilon 1 (PLCE1) is a well-established susceptibility gene for esophageal squamous cell carcinoma (ESCC). Identification of the underlying mechanism(s) regulated by PLCE1 could lead to a better understanding of ESCC tumorigenesis. In this study, we found that PLCE1 enhances tumor progression by regulating the replicative helicase MCM7 via two pathways. PLCE1 activated PKCα-mediated phosphorylation of E2F1, which led to the transcriptional activation of MCM7 and miR-106b-5p. The increased expression of miR-106b-5p, located in intron 13 of MCM7, suppressed autophagy and apoptosis by targeting Beclin-1 and RBL2, respectively. Moreover, MCM7 cooperated with the miR-106b-25 cluster to promote PLCE1-dependent cell-cycle progression both in vivo and in vitro. In addition, PLCE1 potentiated the phosphorylation of MCM7 at six threonine residues by the atypical kinase RIOK2, which promoted MCM complex assembly, chromatin loading, and cell-cycle progression. Inhibition of PLCE1 or RIOK2 hampered MCM7-mediated DNA replication, resulting in G1-S arrest. Furthermore, MCM7 overexpression in ESCC correlated with poor patient survival. Overall, these findings provide insights into the role of PLCE1 as an oncogenic regulator, a promising prognostic biomarker, and a potential therapeutic target in ESCC. SIGNIFICANCE PLCE1 promotes tumor progression in ESCC by activating PKCα-mediated phosphorylation of E2F1 to upregulate MCM7 and miR-106b-5p expression and by potentiating MCM7 phosphorylation by RIOK2.
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Affiliation(s)
- Qi Shi
- Medical Research Center and Department of Pathology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, P.R. China
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, P.R. China
| | - Guixuan Xu
- Medical Research Center and Department of Pathology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, P.R. China
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, P.R. China
| | - Yuliang Jiang
- Department of Oncology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, P.R. China
| | - Ju Yang
- The Comprehensive Cancer Centre of Drum Tower Hospital, Medical School of Nanjing University and Clinical Cancer Institute of Nanjing University, Nanjing, P.R. China
| | - Xueping Han
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, P.R. China
| | - Qian Wang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, P.R. China
| | - Ya Li
- Medical Research Center and Department of Pathology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, P.R. China
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, P.R. China
| | - Zhiyu Zhang
- Medical Research Center and Department of Pathology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, P.R. China
| | - Kaige Wang
- Medical Research Center and Department of Pathology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, P.R. China
| | - Hao Peng
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, P.R. China
| | - Fangfang Chen
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, P.R. China
| | - Yandi Ma
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, P.R. China
| | - Linyue Zhao
- Department of Pathology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, P.R. China
| | - Yunzhao Chen
- Department of Pathology, The people's Hospital of Suzhou National Hi-Tech District, Suzhou, P.R. China
| | - Zheng Liu
- Medical Research Center and Department of Pathology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, P.R. China
| | - Lan Yang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, P.R. China
| | - Xingyuan Jia
- Medical Research Center and Department of Pathology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, P.R. China
| | - Tao Wen
- Medical Research Center and Department of Pathology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, P.R. China
| | - Zhaohui Tong
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, P.R. China
| | - Xiaobin Cui
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, P.R. China
- Department of Pathology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, P.R. China
| | - Feng Li
- Medical Research Center and Department of Pathology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, P.R. China
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, P.R. China
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6
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Tanigawa K, Tomioka Y, Misono S, Asai S, Kikkawa N, Hagihara Y, Suetsugu T, Inoue H, Mizuno K, Seki N. Minichromosome maintenance proteins in lung adenocarcinoma: Clinical significance and therapeutic targets. FEBS Open Bio 2023; 13:1737-1755. [PMID: 37517032 PMCID: PMC10476565 DOI: 10.1002/2211-5463.13681] [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: 04/01/2023] [Revised: 06/29/2023] [Accepted: 07/27/2023] [Indexed: 08/01/2023] Open
Abstract
Lung cancer is the most common cause of cancer-related death worldwide, accounting for 1.8 million deaths annually. Analysis of The Cancer Genome Atlas data showed that all members of the minichromosome maintenance (MCM) family (hexamers involved in DNA replication: MCM2-MCM7) were upregulated in lung adenocarcinoma (LUAD) tissues. High expression of MCM4 (P = 0.0032), MCM5 (P = 0.0032), and MCM7 (P = 0.0110) significantly predicted 5-year survival rates in patients with LUAD. Simurosertib (TAK-931) significantly suppressed the proliferation of LUAD cells by inhibiting cell division cycle 7-mediated MCM2 phosphorylation. This finding suggested that MCM2 might be a therapeutic target for LUAD. Moreover, analysis of the epigenetic regulation of MCM2 showed that miR-139-3p, miR-378a-5p, and miR-2110 modulated MCM2 expression in LUAD cells. In patients with LUAD, understanding the role of these miRNAs may improve prognoses.
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Affiliation(s)
- Kengo Tanigawa
- Department of Pulmonary Medicine, Graduate School of Medical and Dental SciencesKagoshima UniversityJapan
| | - Yuya Tomioka
- Department of Pulmonary Medicine, Graduate School of Medical and Dental SciencesKagoshima UniversityJapan
| | - Shunsuke Misono
- Department of Pulmonary Medicine, Graduate School of Medical and Dental SciencesKagoshima UniversityJapan
| | - Shunichi Asai
- Department of Functional GenomicsChiba University Graduate School of MedicineJapan
| | - Naoko Kikkawa
- Department of Functional GenomicsChiba University Graduate School of MedicineJapan
| | - Yoko Hagihara
- Department of Pulmonary Medicine, Graduate School of Medical and Dental SciencesKagoshima UniversityJapan
| | - Takayuki Suetsugu
- Department of Pulmonary Medicine, Graduate School of Medical and Dental SciencesKagoshima UniversityJapan
| | - Hiromasa Inoue
- Department of Pulmonary Medicine, Graduate School of Medical and Dental SciencesKagoshima UniversityJapan
| | - Keiko Mizuno
- Department of Pulmonary Medicine, Graduate School of Medical and Dental SciencesKagoshima UniversityJapan
| | - Naohiko Seki
- Department of Functional GenomicsChiba University Graduate School of MedicineJapan
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7
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Kim SJ, Maric C, Briu LM, Fauchereau F, Baldacci G, Debatisse M, Koundrioukoff S, Cadoret JC. Firing of Replication Origins Is Disturbed by a CDK4/6 Inhibitor in a pRb-Independent Manner. Int J Mol Sci 2023; 24:10629. [PMID: 37445805 DOI: 10.3390/ijms241310629] [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: 06/01/2023] [Revised: 06/21/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Over the last decade, CDK4/6 inhibitors (palbociclib, ribociclib and abemaciclib) have emerged as promising anticancer drugs. Numerous studies have demonstrated that CDK4/6 inhibitors efficiently block the pRb-E2F pathway and induce cell cycle arrest in pRb-proficient cells. Based on these studies, the inhibitors have been approved by the FDA for treatment of advanced hormonal receptor (HR) positive breast cancers in combination with hormonal therapy. However, some evidence has recently shown unexpected effects of the inhibitors, underlining a need to characterize the effects of CDK4/6 inhibitors beyond pRb. Our study demonstrates how palbociclib impairs origin firing in the DNA replication process in pRb-deficient cell lines. Strikingly, despite the absence of pRb, cells treated with palbociclib synthesize less DNA while showing no cell cycle arrest. Furthermore, this CDK4/6 inhibitor treatment disturbs the temporal program of DNA replication and reduces the density of replication forks. Cells treated with palbociclib show a defect in the loading of the Pre-initiation complex (Pre-IC) proteins on chromatin, indicating a reduced initiation of DNA replication. Our findings highlight hidden effects of palbociclib on the dynamics of DNA replication and of its cytotoxic consequences on cell viability in the absence of pRb. This study provides a potential therapeutic application of palbociclib in combination with other drugs to target genomic instability in pRB-deficient cancers.
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Affiliation(s)
- Su-Jung Kim
- CNRS, Institut Jacques Monod, Université Paris Cité, F-75013 Paris, France
- CNRS UMR9019, Institut Gustave Roussy, 94805 Villejuif, France
| | - Chrystelle Maric
- CNRS, Institut Jacques Monod, Université Paris Cité, F-75013 Paris, France
| | - Lina-Marie Briu
- CNRS, Institut Jacques Monod, Université Paris Cité, F-75013 Paris, France
| | - Fabien Fauchereau
- CNRS, Institut Jacques Monod, Université Paris Cité, F-75013 Paris, France
| | - Giuseppe Baldacci
- CNRS, Institut Jacques Monod, Université Paris Cité, F-75013 Paris, France
| | - Michelle Debatisse
- CNRS UMR9019, Institut Gustave Roussy, 94805 Villejuif, France
- Sorbonne Université, 75005 Paris, France
| | - Stéphane Koundrioukoff
- CNRS UMR9019, Institut Gustave Roussy, 94805 Villejuif, France
- Sorbonne Université, 75005 Paris, France
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8
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Gao C, Li J, Zeng F, Wang L, Chen K, Chen D, Hong J, Qu C. MCM6 promotes intrahepatic cholangiocarcinoma progression by upregulating E2F1 and enhancing epithelial-mesenchymal transition. Carcinogenesis 2023; 44:279-290. [PMID: 37185675 DOI: 10.1093/carcin/bgad023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/22/2022] [Accepted: 04/21/2023] [Indexed: 05/17/2023] Open
Abstract
Minichromosome maintenance complex component 6 (MCM6), a member of the MCM family, plays a pivotal role in DNA replication initiation and genome duplication of proliferating cells. MCM6 is upregulated in multiple malignancies and is considered a novel diagnostic biomarker. However, the functional contributions and prognostic value of MCM6 in intrahepatic cholangiocarcinoma (ICC) remain unexplored. In this study, we investigated the molecular function of MCM6 in ICC. Data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO, GSE107943) indicated an upregulation of MCM6 in tumor tissues. Immunohistochemical analysis performed on 115 cases of ICC samples confirmed the upregulation of MCM6 and further suggested that a high level of MCM6 expression predicted shorter overall and disease-free survival in ICC patients. Functional studies suggested that MCM6 knockdown significantly suppressed cell viability, blocked cell cycle progression and inhibited metastasis, while the enhancement of MCM6 expression promoted the proliferation and migration of ICC cells both in vitro and in vivo. Mechanistically, Gene Set Enrichment Analysis (GSEA) suggested that the epithelial-mesenchymal transition (EMT) and E2F1-correlated genes were enriched in ICC tissues with high MCM6 expression. Further verification indicated that MCM6 promoted the EMT of ICC cells via upregulating E2F1. In addition, E2F1 knockdown partially blocked the pro-malignant effects of MCM6 overexpression. In summary, MCM6 was found to be a novel prognostic and predictive marker for ICC. MCM6 promoted ICC progression via activation of E2F1-mediated EMT.
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Affiliation(s)
- Chongqing Gao
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510630, China
| | - Jing Li
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510630, China
| | - Fuling Zeng
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510630, China
| | - Lijuan Wang
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510630, China
| | - Kaiyun Chen
- Department of General Surgery, Guangzhou Hospital of Integrated Traditional and West Medicine, Guangzhou, Guangdong 510632, China
| | - Dong Chen
- Department of Pancreato-Biliary Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510632, China
| | - Jian Hong
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510630, China
- Department of General Surgery, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317, China
| | - Chen Qu
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510630, China
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9
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Andalib KMS, Rahman MH, Habib A. Bioinformatics and cheminformatics approaches to identify pathways, molecular mechanisms and drug substances related to genetic basis of cervical cancer. J Biomol Struct Dyn 2023; 41:14232-14247. [PMID: 36852684 DOI: 10.1080/07391102.2023.2179542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 02/07/2023] [Indexed: 03/01/2023]
Abstract
Cervical cancer (CC) is a global threat to women and our knowledge is frighteningly little about its underlying genomic contributors. Our research aimed to understand the underlying molecular and genetic mechanisms of CC by integrating bioinformatics and network-based study. Transcriptomic analyses of three microarray datasets identified 218 common differentially expressed genes (DEGs) within control samples and CC specimens. KEGG pathway analysis revealed pathways in cell cycle, drug metabolism, DNA replication and the significant GO terms were cornification, proteolysis, cell division and DNA replication. Protein-protein interaction (PPI) network analysis identified 20 hub genes and survival analyses validated CDC45, MCM2, PCNA and TOP2A as CC biomarkers. Subsequently, 10 transcriptional factors (TFs) and 10 post-transcriptional regulators were detected through TFs-DEGs and miRNAs-DEGs regulatory network assessment. Finally, the CC biomarkers were subjected to a drug-gene relationship analysis to find the best target inhibitors. Standard cheminformatics method including in silico ADMET and molecular docking study substantiated PD0325901 and Selumetinib as the most potent candidate-drug for CC treatment. Overall, this meticulous study holds promises for further in vitro and in vivo research on CC diagnosis, prognosis and therapies. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- K M Salim Andalib
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia, Bangladesh
- Center for Advanced Bioinformatics and Artificial Intelligent Research, Islamic University, Kushtia, Bangladesh
| | - Ahsan Habib
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
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10
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Song HY, Shen R, Mahasin H, Guo YN, Wang DG. DNA replication: Mechanisms and therapeutic interventions for diseases. MedComm (Beijing) 2023; 4:e210. [PMID: 36776764 PMCID: PMC9899494 DOI: 10.1002/mco2.210] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 02/09/2023] Open
Abstract
Accurate and integral cellular DNA replication is modulated by multiple replication-associated proteins, which is fundamental to preserve genome stability. Furthermore, replication proteins cooperate with multiple DNA damage factors to deal with replication stress through mechanisms beyond their role in replication. Cancer cells with chronic replication stress exhibit aberrant DNA replication and DNA damage response, providing an exploitable therapeutic target in tumors. Numerous evidence has indicated that posttranslational modifications (PTMs) of replication proteins present distinct functions in DNA replication and respond to replication stress. In addition, abundant replication proteins are involved in tumorigenesis and development, which act as diagnostic and prognostic biomarkers in some tumors, implying these proteins act as therapeutic targets in clinical. Replication-target cancer therapy emerges as the times require. In this context, we outline the current investigation of the DNA replication mechanism, and simultaneously enumerate the aberrant expression of replication proteins as hallmark for various diseases, revealing their therapeutic potential for target therapy. Meanwhile, we also discuss current observations that the novel PTM of replication proteins in response to replication stress, which seems to be a promising strategy to eliminate diseases.
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Affiliation(s)
- Hao-Yun Song
- School of Basic Medical Sciences Lanzhou University Lanzhou Gansu China
| | - Rong Shen
- School of Basic Medical Sciences Lanzhou University Lanzhou Gansu China
| | - Hamid Mahasin
- School of Basic Medical Sciences Lanzhou University Lanzhou Gansu China
| | - Ya-Nan Guo
- School of Basic Medical Sciences Lanzhou University Lanzhou Gansu China
| | - De-Gui Wang
- School of Basic Medical Sciences Lanzhou University Lanzhou Gansu China
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11
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Identification of the Interaction between Minichromosome Maintenance Proteins and the Core Protein of Hepatitis B Virus. Curr Issues Mol Biol 2023; 45:752-764. [PMID: 36661536 PMCID: PMC9857746 DOI: 10.3390/cimb45010050] [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: 12/26/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Chronic HBV infection is a major cause of cirrhosis and hepatocellular carcinoma. Finding host factors involved in the viral life cycle and elucidating their mechanisms is essential for developing innovative strategies for treating HBV. The HBV core protein has pleiotropic roles in HBV replication; thus, finding the interactions between the core protein and host factors is important in clarifying the mechanism of viral infection and proliferation. Recent studies have revealed that core proteins are involved in cccDNA formation, transcriptional regulation, and RNA metabolism, in addition to their primary functions of capsid formation and pgRNA packaging. Here, we report the interaction of the core protein with MCMs, which have an essential role in host DNA replication. The knockdown of MCM2 led to increased viral replication during infection, suggesting that MCM2 serves as a restriction factor for HBV proliferation. This study opens the possibility of elucidating the relationship between core proteins and host factors and their function in viral proliferation.
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12
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Yang X, Wang C, Nie H, Zhou J, He X, Ou C. Minichromosome maintenance gene family: potential therapeutic targets and prognostic biomarkers for lung squamous cell carcinoma. Aging (Albany NY) 2022; 14:9167-9185. [PMID: 36445337 PMCID: PMC9740372 DOI: 10.18632/aging.204399] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/16/2022] [Indexed: 11/29/2022]
Abstract
The minichromosome maintenance (MCM) gene family comprises of ten members with key roles in eukaryotic DNA replication and are associated with the occurrence and progression of many tumors. However, whether the MCM family contributes to lung squamous cell carcinoma (LUSC) is unclear. In this study, we performed bioinformatic analysis to identify the roles of MCM genes in patients with LUSC. We also evaluated their differential gene expression, prognostic correlation, DNA methylation, functional enrichment of genetic alterations, and immunomodulation. According to the Tumor Immune Estimation Resource database, the expression of MCM2-10 mRNA was elevated in LUSC tissues. According to the Gene Expression Profiling Interactive Analysis database, MCM2-8 and MCM10 were considerably upregulated in LUSC tissues, and protein levels of all MCMs were increased in LUSC tissues. In addition, among the MCM family members, the expression of MCM3 and MCM7 showed the strongest correlation with the prognoses of patients with LUSC. To clarify the role and mechanisms of the MCM family, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology enrichment studies were performed. We detected a significant correlation between the expression patterns of MCM family members and infiltrating immune cells. In conclusion, our results improve the understanding of the aberrant expression of MCM family members in LUSC. These findings demonstrate the potential of the MCM family as therapeutic targets and biomarkers for the diagnosis and prognosis of LUSC.
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Affiliation(s)
- Xuejie Yang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Chunrong Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Hui Nie
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Jianhua Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xiaoyun He
- Departments of Ultrasound Imaging, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
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13
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Welch N, Singh SS, Musich R, Mansuri MS, Bellar A, Mishra S, Chelluboyina AK, Sekar J, Attaway AH, Li L, Willard B, Hornberger TA, Dasarathy S. Shared and unique phosphoproteomics responses in skeletal muscle from exercise models and in hyperammonemic myotubes. iScience 2022; 25:105325. [PMID: 36345342 PMCID: PMC9636548 DOI: 10.1016/j.isci.2022.105325] [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: 04/18/2022] [Revised: 08/22/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Skeletal muscle generation of ammonia, an endogenous cytotoxin, is increased during exercise. Perturbations in ammonia metabolism consistently occur in chronic diseases, and may blunt beneficial skeletal muscle molecular responses and protein homeostasis with exercise. Phosphorylation of skeletal muscle proteins mediates cellular signaling responses to hyperammonemia and exercise. Comparative bioinformatics and machine learning-based analyses of published and experimentally derived phosphoproteomics data identified differentially expressed phosphoproteins that were unique and shared between hyperammonemic murine myotubes and skeletal muscle from exercise models. Enriched processes identified in both hyperammonemic myotubes and muscle from exercise models with selected experimental validation included protein kinase A (PKA), calcium signaling, mitogen-activated protein kinase (MAPK) signaling, and protein homeostasis. Our approach of feature extraction from comparative untargeted "omics" data allows for selection of preclinical models that recapitulate specific human exercise responses and potentially optimize functional capacity and skeletal muscle protein homeostasis with exercise in chronic diseases.
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Affiliation(s)
- Nicole Welch
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Shashi Shekhar Singh
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Ryan Musich
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | - M. Shahid Mansuri
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Annette Bellar
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Saurabh Mishra
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | | | - Jinendiran Sekar
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Amy H. Attaway
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Ling Li
- Proteomics Core, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Belinda Willard
- Proteomics Core, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Troy A. Hornberger
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Srinivasan Dasarathy
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, OH 44195, USA
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14
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MCM2 in human cancer: functions, mechanisms, and clinical significance. Mol Med 2022; 28:128. [PMID: 36303105 PMCID: PMC9615236 DOI: 10.1186/s10020-022-00555-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/10/2022] [Indexed: 11/18/2022] Open
Abstract
Background Aberrant DNA replication is the main source of genomic instability that leads to tumorigenesis and progression. MCM2, a core subunit of eukaryotic helicase, plays a vital role in DNA replication. The dysfunction of MCM2 results in the occurrence and progression of multiple cancers through impairing DNA replication and cell proliferation. Conclusions MCM2 is a vital regulator in DNA replication. The overexpression of MCM2 was detected in multiple types of cancers, and the dysfunction of MCM2 was correlated with the progression and poor prognoses of malignant tumors. According to the altered expression of MCM2 and its correlation with clinicopathological features of cancer patients, MCM2 was thought to be a sensitive biomarker for cancer diagnosis, prognosis, and chemotherapy response. The anti-tumor effect induced by MCM2 inhibition implies the potential of MCM2 to be a novel therapeutic target for cancer treatment. Since DNA replication stress, which may stimulate anti-tumor immunity, frequently occurs in MCM2 deficient cells, it also proposes the possibility that MCM2 targeting improves the effect of tumor immunotherapy.
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15
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Ashrafian S, Zarrineh M, Jensen P, Nawrocki A, Rezadoost H, Ansari AM, Farahmand L, Ghassempour A, Larsen MR. Quantitative Phosphoproteomics and Acetylomics of Safranal Anticancer Effects in Triple-Negative Breast Cancer Cells. J Proteome Res 2022; 21:2566-2585. [PMID: 36173113 DOI: 10.1021/acs.jproteome.2c00168] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Safranal, as an aroma in saffron, is one of the cytotoxic compounds in saffron that causes cell death in triple-negative breast cancer cells. Our recent research reported the anti-cancer effects of safranal, which further demonstrated its impact on protein translation, mitochondrial dysfunction, and DNA fragmentation. To better understand the underlying mechanisms, we identified acetylated and phosphorylated peptides in safranal-treated cancer cells. We conducted a comprehensive phosphoproteomics and acetylomics analysis of safranal-treated MDA-MB-231 cells by using a combination of TMT labeling and enrichment methods including titanium dioxide and immunoprecipitation. We provide a wide range of phosphoproteome regulation in different signaling pathways that are disrupted by safranal treatment. Safranal influences the phosphorylation level on proteins involved in DNA replication and repair, translation, and EGFR activation/accumulation, which can lead the cells into apoptosis. Safranal causes DNA damage which is followed by the activation of cell cycle checkpoints for DNA repair. Over time, checkpoints and DNA repair are inhibited and cells are under a mitotic catastrophe. Moreover, safranal prevents repair by the hypo-acetylation of H4 and facilitates the transcription of proapoptotic genes by hyper-acetylation of H3, which push the cells to the brink of death.
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Affiliation(s)
- Shahrbanou Ashrafian
- Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran 1983963113, Iran
| | - Mahshid Zarrineh
- Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran 1983963113, Iran.,Department of Oncology and Pathology, Science for Life Laboratory, Karolinska Institutet, Solna SE17165, Sweden
| | - Pia Jensen
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Arkadiusz Nawrocki
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Hassan Rezadoost
- Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran 1983963113, Iran
| | - Alireza Madjid Ansari
- Integrative Oncology Department, Breast Cancer Research Center, Moatamed Cancer Institute, ACECR, Tehran 1517964311, Iran
| | - Leila Farahmand
- Integrative Oncology Department, Breast Cancer Research Center, Moatamed Cancer Institute, ACECR, Tehran 1517964311, Iran
| | - Alireza Ghassempour
- Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran 1983963113, Iran
| | - Martin R Larsen
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
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16
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Yang N, Lu X, Jiang Y, Zhao L, Wang D, Wei Y, Yu Y, Kim MO, Laster KV, Li X, Yuan B, Dong Z, Liu K. Arbidol inhibits human esophageal squamous cell carcinoma growth in vitro and in vivo through suppressing ataxia telangiectasia and Rad3-related protein kinase. eLife 2022; 11:73953. [PMID: 36082941 PMCID: PMC9512399 DOI: 10.7554/elife.73953] [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: 09/16/2021] [Accepted: 09/08/2022] [Indexed: 12/24/2022] Open
Abstract
Human esophageal cancer has a global impact on human health due to its high incidence and mortality. Therefore, there is an urgent need to develop new drugs to treat or prevent the prominent pathological subtype of esophageal cancer, esophageal squamous cell carcinoma (ESCC). Based upon the screening of drugs approved by the Food and Drug Administration, we discovered that Arbidol could effectively inhibit the proliferation of human ESCC in vitro. Next, we conducted a series of cell-based assays and found that Arbidol treatment inhibited the proliferation and colony formation ability of ESCC cells and promoted G1-phase cell cycle arrest. Phosphoproteomics experiments, in vitro kinase assays and pull-down assays were subsequently performed in order to identify the underlying growth inhibitory mechanism. We verified that Arbidol is a potential ataxia telangiectasia and Rad3-related (ATR) inhibitor via binding to ATR kinase to reduce the phosphorylation and activation of minichromosome maintenance protein 2 at Ser108. Finally, we demonstrated Arbidol had the inhibitory effect of ESCC in vivo by a patient-derived xenograft model. All together, Arbidol inhibits the proliferation of ESCC in vitro and in vivo through the DNA replication pathway and is associated with the cell cycle.
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Affiliation(s)
- Ning Yang
- Department of Pathophysiology, Zhengzhou University
| | - Xuebo Lu
- Department of Pathophysiology, Zhengzhou University
| | - Yanan Jiang
- Department of Pathophysiology, Zhengzhou University
| | - Lili Zhao
- Department of Pathophysiology, Zhengzhou University
| | - Donghao Wang
- Department of Pathophysiology, Zhengzhou University
| | - Yaxing Wei
- Department of Pathophysiology, Zhengzhou University
| | - Yin Yu
- Department of Pathophysiology, Zhengzhou University
| | - Myoung Ok Kim
- Department of Animal Science and Biotechnology, Kyungpook National University
| | | | - Xin Li
- Department of Pathophysiology, Zhengzhou University
| | - Baoyin Yuan
- Department of Pathophysiology, Zhengzhou University
| | - Zigang Dong
- Department of Pathophysiology, Zhengzhou University
| | - Kangdong Liu
- Department of Pathophysiology, Zhengzhou University
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17
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Chen JM, Chen SK, Jin PP, Sun SC. Identification of the ataxin-1 interaction network and its impact on spinocerebellar ataxia type 1. Hum Genomics 2022; 16:29. [PMID: 35906672 PMCID: PMC9335979 DOI: 10.1186/s40246-022-00404-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 07/22/2022] [Indexed: 12/03/2022] Open
Abstract
Background Spinocerebellar ataxia type 1 (SCA1) is a neurodegenerative disease caused by a polyglutamine expansion in the ataxin-1 protein. The pathogenic mechanism resulting in SCA1 is still unclear. Protein–protein interactions affect the function and stability of ataxin-1. Methods Wild-type and mutant ataxin-1 were expressed in HEK-293T cells. The levels of expression were assessed using real-time polymerase chain reaction (PCR) and Western blots. Co-immunoprecipitation was done in HEK-293T cells expressing exogenous wild-type and mutant ataxin-1 using anti-Flag antibody following by tandem affinity purification in order to study protein–protein interactions. The candidate interacting proteins were validated by immunoprecipitation. Chromatin immunoprecipitation and high-throughput sequencing and RNA immunoprecipitation and high-throughput sequencing were performed using HEK-293T cells expressing wild-type or mutant ataxin-1. Results In this study using HEK-293T cells, we found that wild-type ataxin-1 interacted with MCM2, GNAS, and TMEM206, while mutant ataxin-1 lost its interaction with MCM2, GNAS, and TMEM206. Two ataxin-1 binding targets containing the core GGAG or AAAT were identified in HEK-293T cells using ChIP-seq. Gene Ontology analysis of the top ataxin-1 binding genes identified SLC6A15, NTF3, KCNC3, and DNAJC6 as functional genes in neurons in vitro. Ataxin-1 also was identified as an RNA-binding protein in HEK-293T cells using RIP-seq, but the polyglutamine expansion in the ataxin-1 had no direct effects on the RNA-binding activity of ataxin-1. Conclusions An expanded polyglutamine tract in ataxin-1 might interfere with protein–protein or protein–DNA interactions but had little effect on protein–RNA interactions. This study suggested that the dysfunction of protein–protein or protein–DNA interactions is involved in the pathogenesis of SCA1.
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Affiliation(s)
- Jiu-Ming Chen
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201801, China
| | - Shi-Kai Chen
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201801, China
| | - Pei-Pei Jin
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201801, China
| | - Shun-Chang Sun
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201801, China.
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18
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Yang J, Chen Z, Gong Z, Li Q, Ding H, Cui Y, Tang L, Li S, Wan L, Li Y, Ju S, Ding C, Zhao J. Immune Landscape and Classification in Lung Adenocarcinoma Based on a Novel Cell Cycle Checkpoints Related Signature for Predicting Prognosis and Therapeutic Response. Front Genet 2022; 13:908104. [PMID: 35646074 PMCID: PMC9130860 DOI: 10.3389/fgene.2022.908104] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/26/2022] [Indexed: 12/24/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is one of the most common malignancies with the highest mortality globally, and it has a poor prognosis. Cell cycle checkpoints play a central role in the entire system of monitoring cell cycle processes, by regulating the signalling pathway of the cell cycle. Cell cycle checkpoints related genes (CCCRGs) have potential utility in predicting survival, and response to immunotherapies and chemotherapies. To examine this, based on CCCRGs, we identified two lung adenocarcinoma subtypes, called cluster1 and cluster2, by consensus clustering. Enrichment analysis revealed significant discrepancies between the two subtypes in gene sets associated with cell cycle activation and tumor progression. In addition, based on Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression, we have developed and validated a cell cycle checkpoints-related risk signature to predict prognosis, tumour immune microenvironment: (TIME), immunotherapy and chemotherapy responses for lung adenocarcinoma patients. Results from calibration plot, decision curve analysis (DCA), and time-dependent receiver operating characteristic curve (ROC) revealed that combining age, gender, pathological stages, and risk score in lung adenocarcinoma patients allowed for a more accurate and predictive nomogram. The area under curve for lung adenocarcinoma patients with 1-, 3-, 5-, and 10-year overall survival was: 0.74, 0.73, 0.75, and 0.81, respectively. Taken together, our proposed 4-CCCRG signature can serve as a clinically useful indicator to help predict patients outcomes, and could provide important guidance for immunotherapies and chemotherapies decision for lung adenocarcinoma patients.
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Affiliation(s)
- Jian Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhike Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zetian Gong
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qifan Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hao Ding
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yuan Cui
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Lijuan Tang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Shiqin Li
- Department of Urinary Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Li Wan
- Soochow University Laboratory of Cancer Molecular Genetics, Medical College of Soochow University, Suzhou, China
| | - Yu Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Sheng Ju
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Cheng Ding
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jun Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
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19
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Schaefer‐Ramadan S, Aleksic J, Al‐Thani NM, Malek JA. Novel protein contact points among TP53 and minichromosome maintenance complex proteins 2, 3, and 5. Cancer Med 2022; 11:4989-5000. [PMID: 35567389 PMCID: PMC9761056 DOI: 10.1002/cam4.4805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 04/11/2022] [Accepted: 04/26/2022] [Indexed: 02/03/2023] Open
Abstract
OBJECTIVE Identify protein contact points between TP53 and minichromosome maintenance (MCM) complex proteins 2, 3, and 5 with high resolution allowing for potential novel Cancer drug design. METHODS A next-generation sequencing-based protein-protein interaction method developed in our laboratory called AVA-Seq was applied to a gold-standard human protein interaction set. Proteins including TP53, MCM2, MCM3, MCM5, HSP90AA1, PCNA, NOD1, and others were sheared and ligated into the AVA-Seq system. Protein-protein interactions were then identified in both mild and stringent selective conditions. RESULTS Known interactions among MCM2, MCM3, and MCM5 were identified with the AVA-Seq system. The interacting regions detected between these three proteins overlap with the structural data of the MCM complex, and novel domains were identified with high resolution determined by multiple overlapping fragments. Fragments of wild type TP53 were shown to interact with MCM2, MCM3, and MCM5, and details on the location of the interactions were provided. Finally, a mini-network of known and novel cancer protein interactions was provided, which could have implications for fundamental changes in multiple cancers. CONCLUSION We provide a high-resolution mini-interactome that could direct novel drug targets and implicate possible effects of specific cancer mutations.
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Affiliation(s)
| | - Jovana Aleksic
- Department of Genetic MedicineWeill Cornell Medicine in QatarDohaQatar
| | - Nayra M. Al‐Thani
- Department of Genetic MedicineWeill Cornell Medicine in QatarDohaQatar
| | - Joel A. Malek
- Department of Genetic MedicineWeill Cornell Medicine in QatarDohaQatar
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20
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Long-term exposure to genistein inhibits the proliferation of gallbladder cancer by downregulating the MCM complex. Sci Bull (Beijing) 2022; 67:813-824. [PMID: 36546234 DOI: 10.1016/j.scib.2022.01.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/10/2021] [Accepted: 12/31/2021] [Indexed: 02/08/2023]
Abstract
Soy isoflavones are natural tyrosine kinase inhibitors closely associated with decreased morbidity and mortality of various tumors. The activation of tyrosine kinases such as ERBB2 is the mechanism by which cholecystitis transforms into gallbladder cancer (GBC), therefore, it is important to investigate the relationship between long-term exposure to soy isoflavones and the occurrence and progression of GBC. This case-control study (n = 85 pairs) found that the high level of plasma soy isoflavone-genistein (GEN) was associated with a lower risk of gallbladder cancer (≥326.00 ng/mL compared to ≤19.30 ng/mL, crude odds ratio 0.15, 95% CI 0.04-0.59; P for trend = 0.016), and that the level of GEN exposure negatively correlated with Ki67 expression in GBC tissue (n = 85). Consistent with these results, the proliferation of GBC cells was inhibited in the long-term exposure models of GEN in vitro and in vivo. The long-term exposure to GEN reduced the tyrosine kinase activity of ERBB2 and impaired the function of the PTK6-AKT-GSK3β axis, leading to downregulation of the MCM complex in GBC cells. In summary, long-term exposure to GEN associated with soy products intake might play a certain role in preventing GBC and even inhibiting the proliferation of GBC cells.
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21
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Hartono AB, Kang HJ, Shi L, Phipps W, Ungerleider N, Giardina A, Chen W, Spraggon L, Somwar R, Moroz K, Drewry DH, Burow ME, Flemington E, Ladanyi M, Lee SB. Salt-Inducible Kinase 1 is a potential therapeutic target in Desmoplastic Small Round Cell Tumor. Oncogenesis 2022; 11:18. [PMID: 35443736 PMCID: PMC9021191 DOI: 10.1038/s41389-022-00395-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/28/2022] [Accepted: 04/01/2022] [Indexed: 11/10/2022] Open
Abstract
Desmoplastic Small Round Cell Tumor (DSRCT) is a rare and aggressive malignant cancer caused by a chromosomal translocation t(11;22)(p13;q12) that produces an oncogenic transcription factor, EWSR1-WT1. EWSR1-WT1 is essential for the initiation and progression of DSRCT. However, the precise mechanism by which EWSR1-WT1 drives DSRCT oncogenesis remains unresolved. Through our integrative gene expression analysis, we identified Salt Inducible Kinase 1 (SIK1) as a direct target of EWSR1-WT1. SIK1 as a member of the AMPK related kinase is involved in many biological processes. We showed that depletion of SIK1 causes inhibition of tumor cell growth, similar to the growth inhibition observed when EWSR1-WT1 is depleted. We further showed that silencing SIK1 leads to cessation of DNA replication in DSRCT cells and inhibition of tumor growth in vivo. Lastly, combined inhibition of SIK1 and CHEK1with small molecule inhibitors, YKL-05-099 and prexasertib, respectively, showed enhanced cytotoxicity in DSRCT cells compared to inhibition of either kinases alone. This work identified SIK1 as a new potential therapeutic target in DSRCT and the efficacy of SIK1 inhibition may be improved when combined with other intervention strategies.
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Affiliation(s)
- Alifiani Bonita Hartono
- Tulane University School of Medicine, Department of Pathology and Laboratory Medicine, New Orleans, LA, USA
| | - Hong-Jun Kang
- Tulane University School of Medicine, Department of Pathology and Laboratory Medicine, New Orleans, LA, USA
| | - Lawrence Shi
- Tulane University School of Medicine, Department of Pathology and Laboratory Medicine, New Orleans, LA, USA
| | - Whitney Phipps
- Tulane University School of Medicine, Department of Pathology and Laboratory Medicine, New Orleans, LA, USA
| | - Nathan Ungerleider
- Tulane University School of Medicine, Department of Pathology and Laboratory Medicine, New Orleans, LA, USA
| | - Alexandra Giardina
- Tulane University School of Medicine, Department of Pathology and Laboratory Medicine, New Orleans, LA, USA
| | - WeiPing Chen
- Genomics Core, National Institute of Diabetes and Digestive and Kidney Diseases, Maryland, USA
| | - Lee Spraggon
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Romel Somwar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Krzysztof Moroz
- Tulane University School of Medicine, Department of Pathology and Laboratory Medicine, New Orleans, LA, USA
| | - David H Drewry
- University of North Carolina, Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | | | - Erik Flemington
- Tulane University School of Medicine, Department of Pathology and Laboratory Medicine, New Orleans, LA, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sean Bong Lee
- Tulane University School of Medicine, Department of Pathology and Laboratory Medicine, New Orleans, LA, USA.
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22
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Ahmadi S, Shamloo N, Taghavi N, Shalpoush S. Immunohistochemical analysis of proliferating cell nuclear antigen and minichromosome maintenance complex component 7 in benign and malignant salivary gland tumors. Dent Res J (Isfahan) 2022; 19:17. [PMID: 35308440 PMCID: PMC8927963 DOI: 10.4103/1735-3327.338780] [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: 06/28/2020] [Revised: 03/12/2021] [Accepted: 08/07/2021] [Indexed: 11/17/2022] Open
Abstract
Background: Proliferation markers have been used to determine the behavior and prognosis of benign and malignant tumors; this study was aimed to compare the immunohistochemical (IHC) expression of proliferating cell nuclear antigen (PCNA) and novel marker minichromosome maintenance complex component 7 (MCM7) in common salivary gland tumors including pleomorphic adenoma (PA), mucoepidermoid carcinoma (MEC), and adenoid cystic carcinoma (AdCC), to find a possible significant correlation between benign and malignant tumors. Materials and Methods: In this cross-sectional study, a total of 90 cases, including 30 PAs, 30 MECs, and 30 AdCCs, were collected. The IHC expressions of PCNA and MCM7 were evaluated. Their expressions were compared with each other and between benign and malignant tumors. Statistical analysis was performed by Chi-square and Tukey's test. P value was considered 0.05. Results: Out of 30 cases of PA, 28 cases (93.3%) were PCNA positive and 28 cases (93.3%) were MCM7 positive. In the AdCC cases, 29 cases (96.6%) were PCNA positive and 29 cases (96.6%) were MCM7 positive. In the MEC cases, all cases (100%) were PCNA positive and 23 cases (76.6%) were MCM7 positive. The labeling index (LI) of MCM7 and PCNA was evaluated, and this index was lower in MCM7 LI than PCNA in all tumors. The MCM7 and PCNA expression showed a significant difference in PA and MEC (P < 0.001). Conclusion: PCNA expression was higher than MCM7 expression in salivary gland tumors. However, more studies are needed to evaluate the malignant activity of these tumors with group of markers such as MCM family members.
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23
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Nistorescu S, Udrea AM, Badea MA, Lungu I, Boni M, Tozar T, Dumitrache F, Maraloiu VA, Popescu RG, Fleaca C, Andronescu E, Dinischiotu A, Staicu A, Balas M. Low Blue Dose Photodynamic Therapy with Porphyrin-Iron Oxide Nanoparticles Complexes: In Vitro Study on Human Melanoma Cells. Pharmaceutics 2021; 13:pharmaceutics13122130. [PMID: 34959411 PMCID: PMC8705854 DOI: 10.3390/pharmaceutics13122130] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 01/10/2023] Open
Abstract
The purpose of this study was to investigate the effectiveness in photodynamic therapy of iron oxide nanoparticles (γ-Fe2O3 NPs), synthesized by laser pyrolysis technique, functionalized with 5,10,15,20-(Tetra-4-sulfonatophenyl) porphyrin tetraammonium (TPPS) on human cutaneous melanoma cells, after only 1 min blue light exposure. The efficiency of porphyrin loading on the iron oxide nanocarriers was estimated by using absorption and FTIR spectroscopy. The singlet oxygen yield was determined via transient characteristics of singlet oxygen phosphorescence at 1270 nm both for porphyrin functionalized nanoparticles and rose bengal used as standard. The irradiation was performed with a LED (405 nm, 1 mW/cm2) for 1 min after melanoma cells were treated with TPPS functionalized iron oxide nanoparticles (γ-Fe2O3 NPs_TPPS) and incubated for 24 h. Biological tests revealed a high anticancer effect of γ-Fe2O3 NPs_TPPS complexes indi-cated by the inhibition of tumor cell proliferation, reduction of cell adhesion, and induction of cell death through ROS generated by TPPS under light exposure. The biological assays were combined with the pharmacokinetic prediction of the porphyrin.
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Affiliation(s)
- Simona Nistorescu
- National Institute of Laser, Plasma and Radiation Physics, 409 Atomistilor Str., 077125 Magurele, Romania; (S.N.); (A.-M.U.); (I.L.); (M.B.); (T.T.); (F.D.); (C.F.)
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independentei, 050095 Bucharest, Romania; (M.A.B.); (R.G.P.); (A.D.)
| | - Ana-Maria Udrea
- National Institute of Laser, Plasma and Radiation Physics, 409 Atomistilor Str., 077125 Magurele, Romania; (S.N.); (A.-M.U.); (I.L.); (M.B.); (T.T.); (F.D.); (C.F.)
- Research Institute of the University of Bucharest, Earth, Environmental and Life Sciences, Section-ICUB, 050663 Bucharest, Romania
| | - Madalina Andreea Badea
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independentei, 050095 Bucharest, Romania; (M.A.B.); (R.G.P.); (A.D.)
| | - Iulia Lungu
- National Institute of Laser, Plasma and Radiation Physics, 409 Atomistilor Str., 077125 Magurele, Romania; (S.N.); (A.-M.U.); (I.L.); (M.B.); (T.T.); (F.D.); (C.F.)
- Faculty of Applied Chemistry and Materials Science, University Politehnica of Bucharest, 1-7 Gh. Polizu Str., 011061 Bucharest, Romania;
| | - Mihai Boni
- National Institute of Laser, Plasma and Radiation Physics, 409 Atomistilor Str., 077125 Magurele, Romania; (S.N.); (A.-M.U.); (I.L.); (M.B.); (T.T.); (F.D.); (C.F.)
| | - Tatiana Tozar
- National Institute of Laser, Plasma and Radiation Physics, 409 Atomistilor Str., 077125 Magurele, Romania; (S.N.); (A.-M.U.); (I.L.); (M.B.); (T.T.); (F.D.); (C.F.)
| | - Florian Dumitrache
- National Institute of Laser, Plasma and Radiation Physics, 409 Atomistilor Str., 077125 Magurele, Romania; (S.N.); (A.-M.U.); (I.L.); (M.B.); (T.T.); (F.D.); (C.F.)
| | | | - Roua Gabriela Popescu
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independentei, 050095 Bucharest, Romania; (M.A.B.); (R.G.P.); (A.D.)
| | - Claudiu Fleaca
- National Institute of Laser, Plasma and Radiation Physics, 409 Atomistilor Str., 077125 Magurele, Romania; (S.N.); (A.-M.U.); (I.L.); (M.B.); (T.T.); (F.D.); (C.F.)
| | - Ecaterina Andronescu
- Faculty of Applied Chemistry and Materials Science, University Politehnica of Bucharest, 1-7 Gh. Polizu Str., 011061 Bucharest, Romania;
| | - Anca Dinischiotu
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independentei, 050095 Bucharest, Romania; (M.A.B.); (R.G.P.); (A.D.)
| | - Angela Staicu
- National Institute of Laser, Plasma and Radiation Physics, 409 Atomistilor Str., 077125 Magurele, Romania; (S.N.); (A.-M.U.); (I.L.); (M.B.); (T.T.); (F.D.); (C.F.)
- Correspondence: (A.S.); (M.B.)
| | - Mihaela Balas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independentei, 050095 Bucharest, Romania; (M.A.B.); (R.G.P.); (A.D.)
- Correspondence: (A.S.); (M.B.)
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24
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Schaefer-Ramadan S, Aleksic J, Al-Thani NM, Mohamoud YA, Hill DE, Malek JA. Scaling-up a fragment-based protein-protein interaction method using a human reference interaction set. Proteins 2021; 90:959-972. [PMID: 34850971 PMCID: PMC9299658 DOI: 10.1002/prot.26288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/09/2021] [Accepted: 11/26/2021] [Indexed: 12/13/2022]
Abstract
Protein–protein interactions (PPIs) are essential in understanding numerous aspects of protein function. Here, we significantly scaled and modified analyses of the recently developed all‐vs‐all sequencing (AVA‐Seq) approach using a gold‐standard human protein interaction set (hsPRS‐v2) containing 98 proteins. Binary interaction analyses recovered 20 of 47 (43%) binary PPIs from this positive reference set (PRS), comparing favorably with other methods. However, the increase of 20× in the interaction search space for AVA‐Seq analysis in this manuscript resulted in numerous changes to the method required for future use in genome‐wide interaction studies. We show that standard sequencing analysis methods must be modified to consider the possible recovery of thousands of positives among millions of tested interactions in a single sequencing run. The PRS data were used to optimize data scaling, auto‐activator removal, rank interaction features (such as orientation and unique fragment pairs), and statistical cutoffs. Using these modifications to the method, AVA‐Seq recovered >500 known and novel PPIs, including interactions between wild‐type fragments of tumor protein p53 and minichromosome maintenance complex proteins 2 and 5 (MCM2 and MCM5) that could be of interest in human disease.
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Affiliation(s)
| | - Jovana Aleksic
- Department of Genetic Medicine, Weill Cornell Medicine in Qatar, Doha, Qatar
| | - Nayra M Al-Thani
- Department of Genetic Medicine, Weill Cornell Medicine in Qatar, Doha, Qatar
| | - Yasmin A Mohamoud
- Department of Genetic Medicine, Weill Cornell Medicine in Qatar, Doha, Qatar
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Joel A Malek
- Department of Genetic Medicine, Weill Cornell Medicine in Qatar, Doha, Qatar
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25
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Taglialatela A, Leuzzi G, Sannino V, Cuella-Martin R, Huang JW, Wu-Baer F, Baer R, Costanzo V, Ciccia A. REV1-Polζ maintains the viability of homologous recombination-deficient cancer cells through mutagenic repair of PRIMPOL-dependent ssDNA gaps. Mol Cell 2021; 81:4008-4025.e7. [PMID: 34508659 PMCID: PMC8500949 DOI: 10.1016/j.molcel.2021.08.016] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 05/29/2021] [Accepted: 08/11/2021] [Indexed: 12/11/2022]
Abstract
BRCA1/2 mutant tumor cells display an elevated mutation burden, the etiology of which remains unclear. Here, we report that these cells accumulate ssDNA gaps and spontaneous mutations during unperturbed DNA replication due to repriming by the DNA primase-polymerase PRIMPOL. Gap accumulation requires the DNA glycosylase SMUG1 and is exacerbated by depletion of the translesion synthesis (TLS) factor RAD18 or inhibition of the error-prone TLS polymerase complex REV1-Polζ by the small molecule JH-RE-06. JH-RE-06 treatment of BRCA1/2-deficient cells results in reduced mutation rates and PRIMPOL- and SMUG1-dependent loss of viability. Through cellular and animal studies, we demonstrate that JH-RE-06 is preferentially toxic toward HR-deficient cancer cells. Furthermore, JH-RE-06 remains effective toward PARP inhibitor (PARPi)-resistant BRCA1 mutant cells and displays additive toxicity with crosslinking agents or PARPi. Collectively, these studies identify a protective and mutagenic role for REV1-Polζ in BRCA1/2 mutant cells and provide the rationale for using REV1-Polζ inhibitors to treat BRCA1/2 mutant tumors.
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Affiliation(s)
- Angelo Taglialatela
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Giuseppe Leuzzi
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Vincenzo Sannino
- DNA Metabolism Laboratory, IFOM, FIRC Institute for Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Raquel Cuella-Martin
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Jen-Wei Huang
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Foon Wu-Baer
- Institute for Cancer Genetics, Department of Pathology & Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Richard Baer
- Institute for Cancer Genetics, Department of Pathology & Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Vincenzo Costanzo
- DNA Metabolism Laboratory, IFOM, FIRC Institute for Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
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26
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Güzel C, van Sten-Van't Hoff J, de Kok IMCM, Govorukhina NI, Boychenko A, Luider TM, Bischoff R. Molecular markers for cervical cancer screening. Expert Rev Proteomics 2021; 18:675-691. [PMID: 34551656 DOI: 10.1080/14789450.2021.1980387] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Cervical cancer remains a significant healthcare problem, notably in low- to middle-income countries. While a negative test for hrHPV has a predictive value of more than 99.5%, its positive predictive value is less than 10% for CIN2+ stages. This makes the use of a so-called triage test indispensable for population-based screening to avoid referring women, that are ultimately at low risk of developing cervical cancer, to a gynecologist. This review will give an overview of tests that are based on epigenetic marker panels and protein markers. AREAS COVERED There is a medical need for molecular markers with a better predictive value to discriminate hrHPV-positive women that are at risk of developing cervical cancer from those that are not. Areas covered are epigenetic and protein markers as well as health economic considerations in view of the fact that most cases of cervical cancer arise in low-to-middle-income countries. EXPERT OPINION While there are biomarker assays based on changes at the nucleic acid (DNA methylation patterns, miRNAs) and at the protein level, they are not widely used in population screening. Combining nucleic acid-based and protein-based tests could improve the overall specificity for discriminating CIN2+ lesions that carry a low risk of progressing to cervical cancer within the screening interval from those that carry an elevated risk. The challenge is to reduce unnecessary referrals without an undesired increase in false-negative diagnoses resulting in cases of cervical cancer that could have been prevented. A further challenge is to develop tests for low-and middle-income countries, which is critical to reduce the worldwide burden of cervical cancer.
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Affiliation(s)
- Coşkun Güzel
- Erasmus MC, Department of Neurology, University of Groningen, Rotterdam, The Netherlands
| | | | | | - Natalia I Govorukhina
- Department of Analytical Biochemistry, University of Groningen, Groningen, The Netherlands
| | | | - Theo M Luider
- Erasmus MC, Department of Neurology, University of Groningen, Rotterdam, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, University of Groningen, Groningen, The Netherlands
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27
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Yang LG, Wang Y, Wang Y, Fang WH, Feng GP, Ying N, Zhou JY, Li XC. Transcriptome analysis of pacific white shrimp (Penaeus vannamei) intestines and hepatopancreas in response to Enterocytozoon hepatopenaei (EHP) infection. J Invertebr Pathol 2021; 186:107665. [PMID: 34520799 DOI: 10.1016/j.jip.2021.107665] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 08/19/2021] [Accepted: 09/06/2021] [Indexed: 10/20/2022]
Abstract
Penaeus vannamei is the most economically important species of shrimp cultured worldwide. Enterocytozoon hepatopenaei (EHP) is an emerging pathogen that severely affects the growth and development of shrimps. In this study, the transcriptome differences between EHP-infected and uninfected shrimp were investigated through next-generation sequencing. The unigenes were assembled with the reads from all the four libraries. The differentially expressed genes (DEGs) of intestines and hepatopancreas were analyzed. There were 2,884 DEGs in the intestines and 2,096 DEGs in the hepatopancreas. The GO and KEGG enrichment analysis indicated that DEGs were significantly enriched in signaling pathways associated with nutritional energy metabolism and mobilizing autoimmunity. Moreover, the results suggested the downregulation of key genes in energy synthesis pathways contributed greatly to shrimp growth retardation; the upregulation of immune-related genes enhanced the resistance of shrimp against EHP infection. This study provided identified genes and pathways associated with EHP infection revealing the molecular mechanisms of growth retardation.
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Affiliation(s)
- Li-Guo Yang
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China
| | - Yuan Wang
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China
| | - Yue Wang
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China; Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Wen-Hong Fang
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China
| | - Guang-Peng Feng
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China
| | - Na Ying
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China
| | - Jin-Yang Zhou
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China
| | - Xin-Cang Li
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China.
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28
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Najar MA, Aravind A, Dagamajalu S, Sidransky D, Ashktorab H, Smoot DT, Gowda H, Prasad TSK, Modi PK, Chatterjee A. Hyperactivation of MEK/ERK pathway by Ca 2+ /calmodulin-dependent protein kinase kinase 2 promotes cellular proliferation by activating cyclin-dependent kinases and minichromosome maintenance protein in gastric cancer cells. Mol Carcinog 2021; 60:769-783. [PMID: 34437731 DOI: 10.1002/mc.23343] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 01/04/2023]
Abstract
Although CAMKK2 is overexpressed in several cancers, its role and relevant downstream signaling pathways in gastric cancer (GC) are poorly understood. Treatment of AGS GC cells with a CAMKK2 inhibitor, STO-609, resulted in decreased cell proliferation, cell migration, invasion, colony-forming ability, and G1/S-phase arrest. Quantitative phosphoproteomics in AGS cells with the CAMKK2 inhibitor led to the identification of 9603 unique phosphosites mapping to 3120 proteins. We observed decreased phosphorylation of 1101 phosphopeptides (1.5-fold) corresponding to 752 proteins upon CAMKK2 inhibition. Bioinformatics analysis of hypo-phosphorylated proteins revealed enrichment of MAPK1/MAPK3 signaling. Kinase enrichment analysis of hypo-phosphorylated proteins using the X2K Web tool identified ERK1, cyclin-dependant kinase 1 (CDK1), and CDK2 as downstream substrates of CAMKK2. Moreover, inhibition of CAMKK2 and MEK1 resulted in decreased phosphorylation of ERK1, CDK1, MCM2, and MCM3. Immunofluorescence results were in concordance with our mass spectroscopy data and Western blot analysis results. Taken together, our data reveal the essential role of CAMKK2 in the pathobiology of GC through the activation of the MEK/ERK1 signaling cascade.
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Affiliation(s)
- Mohd A Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Anjana Aravind
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hassan Ashktorab
- Department of Medicine, Howard University, Washington, District of Columbia, USA
| | - Duane T Smoot
- Department of Medicine, Meharry Medical Center, Nashville, Tennessee, USA
| | - Harsha Gowda
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India.,Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Prashant K Modi
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Aditi Chatterjee
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India.,Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
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29
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Zhou J, Wang M, Zhou Z, Wang W, Duan J, Wu G. Expression and Prognostic Value of MCM Family Genes in Osteosarcoma. Front Mol Biosci 2021; 8:668402. [PMID: 34239894 PMCID: PMC8257954 DOI: 10.3389/fmolb.2021.668402] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/10/2021] [Indexed: 11/16/2022] Open
Abstract
We performed a detailed cancer VS normal analysis to explore the expression and prognostic value of minichromosome maintenance (MCM) proteinsin human sarcoma. The mRNA expression levels of the MCM family genes in sarcoma were analyzed using data from ONCOMINE, GEPIA and CCLE databases. KEGG database was used to analyze the function of MCM2–7 complex in DNA replication and cell cycle. QRT-PCR and western blot were used to confirm the differential expression of key MCMs in osteosarcoma cell lines. Cell Counting Kit-8 and flow cytometry method were used to detect the cell proliferation and apoptosis of hFOB1.19 cells. The results showed that MCM1–7 and MCM10 were all upregulated in sarcoma in ONCOMINE database. MCM2, and MCM4–7 were highly expressed in sarcoma in GEPIA database. Moreover, all these ten factors were highly expressed in sarcoma cell lines. Furthermore, we analyzed the prognostic value of MCMs for sarcoma in GEPIA and found that MCM2, MCM3, MCM4, and MCM10 are prognostic biomarkers for human sarcoma. Analysis results using KEGG datasets showed that MCM4 and MCM6–7 constituted a core structure of MCM2-7 hexamers. We found that AzadC treatment and overexpression of MCM4 significantly promoted hFOB1.19 cell proliferation and inhibited apoptosis. The present study implied that MCM2–4 and 10 are potential biomarkers for the prognosis of sarcoma. The prognostic role of MCM4 may be attributable to the change in its DNA methylation patterns.
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Affiliation(s)
- Jian Zhou
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Mingyong Wang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China.,Institute of Osteoporosis Diagnosis and Treatments of Soochow University, Suzhou, China
| | - Zhen Zhou
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Wanchun Wang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Juan Duan
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Gen Wu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
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Chang Y, Rager JE, Tilton SC. Linking Coregulated Gene Modules with Polycyclic Aromatic Hydrocarbon-Related Cancer Risk in the 3D Human Bronchial Epithelium. Chem Res Toxicol 2021; 34:1445-1455. [PMID: 34048650 PMCID: PMC8560124 DOI: 10.1021/acs.chemrestox.0c00333] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Exposure to polycyclic aromatic hydrocarbons (PAHs) often occurs as complex chemical mixtures, which are linked to numerous adverse health outcomes in humans, with cancer as the greatest concern. The cancer risk associated with PAH exposures is commonly evaluated using the relative potency factor (RPF) approach, which estimates PAH mixture carcinogenic potential based on the sum of relative potency estimates of individual PAHs, compared to benzo[a]pyrene (BAP), a reference carcinogen. The present study evaluates molecular mechanisms related to PAH cancer risk through integration of transcriptomic and bioinformatic approaches in a 3D human bronchial epithelial cell model. Genes with significant differential expression from human bronchial epithelium exposed to PAHs were analyzed using a weighted gene coexpression network analysis (WGCNA) two-tiered approach: first to identify gene sets comodulated to RPF and second to link genes to a more comprehensive list of regulatory values, including inhalation-specific risk values. Over 3000 genes associated with processes of cell cycle regulation, inflammation, DNA damage, and cell adhesion processes were found to be comodulated with increasing RPF with pathways for cell cycle S phase and cytoskeleton actin identified as the most significantly enriched biological networks correlated to RPF. In addition, comodulated genes were linked to additional cancer-relevant risk values, including inhalation unit risks, oral cancer slope factors, and cancer hazard classifications from the World Health Organization's International Agency for Research on Cancer (IARC). These gene sets represent potential biomarkers that could be used to evaluate cancer risk associated with PAH mixtures. Among the values tested, RPF values and IARC categorizations shared the most similar responses in positively and negatively correlated gene modules. Together, we demonstrated a novel manner of integrating gene sets with chemical toxicity equivalence estimates through WGCNA to understand potential mechanisms.
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Affiliation(s)
- Yvonne Chang
- Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, United States
| | - Julia E. Rager
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina, Chapel Hill, NC, United States
- Institute for Environmental Health Solutions, and Curriculum in Toxicology, The University of North Carolina, Chapel Hill, NC, United States
| | - Susan C. Tilton
- Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, United States
- Superfund Research Program, Oregon State University, Corvallis, OR, United States
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Pan Y, Zhan L, Chen L, Chen L, Sun C. miR-660 promotes liver cancer cell proliferation by targeting PPP2R2A. Exp Ther Med 2021; 22:683. [PMID: 33986848 DOI: 10.3892/etm.2021.10115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 11/25/2019] [Indexed: 12/31/2022] Open
Abstract
Liver cancer (LC) is the leading cause for tumor-related death worldwide, and microRNAs (miRs) have been demonstrated to regulate the progression of LC. In the current study, the function of miR-660 in LC cells was investigated, and the results indicated that miR-660 was highly expressed in LC tissues and cells. This increased expression promoted LC cell proliferation and increased the percentage of S phase cells, while miR-660 knockdown inhibited cell proliferation and increased the percentage of G0/G1 phase cells. A Ser/Thr phosphatase protein phosphatase 2 regulatory subunit βα (PPP2R2A) was indicated as the target of miR-660, and miR-660 could inhibit PPP2R2A levels. The luciferase reporter assay suggested that miR-660 directly bound to the 3'-untranslated region of PPP2R2A. Additionally, it was revealed that miR-660 inhibited p21 expression and promoted cyclin D1 expression, confirming that miR-660 regulated LC cell proliferation by regulating cell cycle progression. The double knockdown of miR-660 and PPP2R2A promoted LC cell proliferation, suggesting that miR-660 promoted LC proliferation by targeting PPP2R2A.
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Affiliation(s)
- Yaozhen Pan
- Department of Biliary-Hepatic Surgery, The Affiliated Tumor Hospital of Guizhou Medical University, Guiyang, Guizhou 550000, P.R China.,Department of Biliary-Hepatic Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550025, P.R China
| | - Lei Zhan
- Department of Biliary-Hepatic Surgery, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550000, P.R China
| | - Ling Chen
- Department of Biliary-Hepatic Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550025, P.R China
| | - Liwen Chen
- Department of Biliary-Hepatic Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550025, P.R China
| | - Chengyi Sun
- Department of Biliary-Hepatic Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550025, P.R China
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32
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Huang C, Lei C, Pan B, Fang S, Chen Y, Cao W, Liu L. Potential Prospective Biomarkers for Non-small Cell Lung Cancer: Mini-Chromosome Maintenance Proteins. Front Genet 2021; 12:587017. [PMID: 33936158 PMCID: PMC8079985 DOI: 10.3389/fgene.2021.587017] [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: 07/24/2020] [Accepted: 03/18/2021] [Indexed: 11/13/2022] Open
Abstract
Minichromosome maintenance proteins (MCMs) are considered to be essential factors coupling DNA replication to both cell cycle progression and checkpoint regulation. Previous studies have shown that dysregulation of MCMs are implicated in tumorigenesis of lung cancer. However, the distinct expression/mutation patterns and prognostic values of MCMs in lung cancer have yet to be systematically elucidated. In the present study, we analyzed the transcriptional levels, mutations, and prognostic value of MCM1-10 in non-small cell lung cancer (NSCLC) patients using multiple bioinformatics tools, including ONCOMINE, GEPIA, Kaplan-Meier Plotter, cBioPortal, and GESA. The analysis results from GEPIA dataset showed that MCM2/4/10 was significantly high expressed in both lung adenocarcinoma (LUAD) and squamous cell lung carcinomas (LUSCs). Meanwhile, the expression levels of MCM2/4/6/7/8 were associated with advanced tumor stages. Subsequent survival analysis using the Kaplan-Meier Plotter indicated that high expression levels of MCM1/2/3/4/5/6/7/8/10 were associated with worse overall survival (OS), while high expression level of MCM9 predicted better OS in these patients. Furthermore, we experimentally validated overexpression of MCM2 and MCM4 in NSCLC, thus the results from this study support a view that they may serve as potential prospective biomarkers to identify high-risk subgroups of NSCLC patients.
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Affiliation(s)
- Chen Huang
- Department of Gastrointestinal Cancer Biology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy-Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Chuqi Lei
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
| | - Boyu Pan
- Department of Gastrointestinal Cancer Biology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy-Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Senbiao Fang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
| | - Yubao Chen
- Department of Computational Biology, Beijing Computing Center, Beijing, China
| | - Wenfeng Cao
- Department of Pathology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy-Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Liren Liu
- Department of Gastrointestinal Cancer Biology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy-Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin, China
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33
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Ren Z, Li J, Zhao S, Qiao Q, Li R. Knockdown of MCM8 functions as a strategy to inhibit the development and progression of osteosarcoma through regulating CTGF. Cell Death Dis 2021; 12:376. [PMID: 33828075 PMCID: PMC8027380 DOI: 10.1038/s41419-021-03621-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 12/19/2022]
Abstract
Osteosarcoma is the most common primary malignant tumor of bone derived from osteoblasts, which is a noteworthy threat to the health of children and adolescents. In this study, we found that MCM8 has significantly higher expression level in osteosarcoma tissues in comparison with normal tissues, which was also correlated with more advanced tumor grade and pathological stage. In agreement with the role of MCM proteins as indicators of cell proliferation, knockdown/overexpression of MCM8 inhibited/promoted osteosarcoma cell proliferation in vitro and tumor growth in vivo. Also, MCM8 knockdown/overexpression was also significantly associated with the promotion/inhibition of cell apoptosis and suppression/promotion of cell migration. More importantly, mechanistic study identified CTGF as a potential downstream target of MCM8, silencing of which could enhance the regulatory effects of MCM8 knockdown and alleviate the effects of MCM8 overexpression on osteosarcoma development. In summary, MCM8/CTGF axis was revealed as critical participant in the development and progression of osteosarcoma and MCM8 may be a promising therapeutic target for osteosarcoma treatment.
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Affiliation(s)
- Zhinan Ren
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Jun Li
- Department of Orthopedics, The Second Affiliated Hospital of Anhui Medical University, 678 Furong, Hefei, 230601, China
| | - Shanwen Zhao
- Department of Foot and Ankle Surgery, Center for Orthopaedic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510610, China.,Orthopaedic Hospital of Guangdong Province, Guangzhou, 510630, China.,Academy of Orthopaedics, Guangdong Province, Guangzhou, 510630, China.,Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Guangzhou, 510515, China
| | - Qi Qiao
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Runguang Li
- Department of Foot and Ankle Surgery, Center for Orthopaedic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510610, China. .,Orthopaedic Hospital of Guangdong Province, Guangzhou, 510630, China. .,Academy of Orthopaedics, Guangdong Province, Guangzhou, 510630, China. .,Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Guangzhou, 510515, China. .,Department of Orthopedics, Linzhi People's Hospital, Linzhi, 860000, China.
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Comprehensive Genomic Characterization of Fifteen Early-Onset Lynch-Like Syndrome Colorectal Cancers. Cancers (Basel) 2021; 13:cancers13061259. [PMID: 33809179 PMCID: PMC7999079 DOI: 10.3390/cancers13061259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/04/2021] [Accepted: 03/09/2021] [Indexed: 12/30/2022] Open
Abstract
Simple Summary The most prevalent type of hereditary colorectal cancer is called Lynch syndrome and it is characterized by a tumor phenotype called microsatellite instability (MSI). This disease is a consequence of germline (inheritable) variants in any of the four mismatch repair (MMR) DNA genes, being their identification essential to ensure their appropriate diagnosis and implementation of preventive measurements. Nevertheless, only 50% of patients with MSI and suspected Lynch syndrome actually carry a germline pathogenic variant in an MMR gene that explains the clinical entity. The remaining 50% are termed Lynch-like syndrome, and their causes remain unknown. In this work, we tried to elucidate the molecular mechanisms that underlie this rare entity in a group of early-onset Lynch-like syndrome colorectal cancer, through whole-exome sequencing of germline and tumor samples. We observed that one-third of these patients have somatic alterations in genes associated with the MMR system and that these could be the mechanism causing their unexplained MSI. Furthermore, we found that patients who showed biallelic somatic alterations also carried germline variants in new candidate genes associated with DNA repair functions and that this could be, partly, the cause of the early onset in this cohort. Abstract Lynch-like syndrome (LLS) is an increasingly common clinical challenge with an underlying molecular basis mostly unknown. To shed light onto it, we focused on a very young LLS early-onset colorectal cancer (CRC) cohort (diagnosis ≤ 40 y.o.), performing germline and tumor whole-exome sequencing (WES) of 15 patients, and additionally analyzing their corresponding tumor mutational burden (TMB) and mutational signatures. We identified four cases (27%) with double somatic putative variants in mismatch repair (MMR) core genes, as well as three additional cases (20%) with double MSH3 somatic alterations in tumors with unexplained MSH2/MSH6 loss of expression, and two cases (13%) with POLD1 potential biallelic alterations. Average TMB was significantly higher for LLS cases with double somatic alterations. Lastly, nine predicted deleterious variants in genes involved in the DNA repair functions and/or previously associated with CRC were found in nine probands, four of which also showed MMR biallelic somatic inactivation. In conclusion, we contribute new insights into LLS CRC, postulating MSH3 and POLD1 double somatic alterations as an underlying cause of a microsatellite instability (MSI) phenotype, proposing intrinsic biological differences between LLS with and without somatic alterations, and suggesting new predisposing candidate genes in this scenario.
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Molecular Signature of Small Cell Lung Cancer after Treatment Failure: The MCM Complex as Therapeutic Target. Cancers (Basel) 2021; 13:cancers13061187. [PMID: 33801812 PMCID: PMC7998124 DOI: 10.3390/cancers13061187] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 12/12/2022] Open
Abstract
Small cell lung cancer (SCLC) is a highly aggressive cancer, and patients who become refractory to first-line treatment have a poor prognosis. The development of effective treatment regimens is urgently needed. In this study, we identified a gene expression signature of SCLC after treatment failure using SCLC clinical specimens (GEO accession number: GSE162102). A total of 1,136 genes were significantly upregulated in SCLC tissues. These upregulated genes were subjected to KEGG pathway analysis, and "cell cycle", "Fanconi anemia", "alcoholism", "systemic lupus erythematosus", "oocyte meiosis", "homologous recombination", "DNA replication", and "p53 signaling" were identified as the enriched pathways among the genes. We focused on the cell cycle pathway and investigated the clinical significance of four genes associated with this pathway: minichromosome maintenance (MCM) 2, MCM4, MCM6, and MCM7. The overexpression of these MCM genes was confirmed in SCLC clinical specimens. Knockdown assays using siRNAs targeting each of these four MCM genes showed significant attenuation of cancer cell proliferation. Moreover, siRNA-mediated knockdown of each MCM gene enhanced the cisplatin sensitivity of SCLC cells. Our SCLC molecular signature based on SCLC clinical specimens after treatment failure will provide useful information to identify novel molecular targets for this disease.
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36
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Xue H, Sun Z, Wu W, Du D, Liao S. Identification of Hub Genes as Potential Prognostic Biomarkers in Cervical Cancer Using Comprehensive Bioinformatics Analysis and Validation Studies. Cancer Manag Res 2021; 13:117-131. [PMID: 33447084 PMCID: PMC7802793 DOI: 10.2147/cmar.s282989] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/24/2020] [Indexed: 12/20/2022] Open
Abstract
Background Cervical cancer belongs to one of the most common female cancers; yet, the exact underlying mechanisms are still elusive. Recently, microarray and sequencing technologies have been widely used for screening biomarkers and molecular mechanism discovery in cancer studies. In this study, we aimed to analyse the microarray datasets using comprehensive bioinformatics tools and identified novel biomarkers associated with the prognosis of patients with cervical cancer. Methods The differentially expressed genes (DEGs) from Gene Expression Omnibus (GEO) datasets including GSE138080, GSE113942 and GSE63514 were analysed using GEO2R tool. The functional enrichment analysis was performed using g:Profiler tool. The protein-protein interaction (PPI) network construction and hub genes identification were performed using the STRING database and Cytoscape software, respectively. The hub genes were subjected to expression and survival analysis in the cervical cancer. The EdU incorporation and Cell Counting Kit-8 assays were performed to evaluate the effects of hub gene knockdown on the proliferation of cervical cancer cells. Results A total of 89 overlapping DEGs (63 up-regulated and 26 down-regulated genes) were identified in the microarray datasets. The functional enrichment analysis indicated that the overlapping DEGs were mainly associated with "DNA replication" and "cell cycle". Furthermore, the PPI network analysis revealed that the network contains 87 nodes and 309 edges. Sub-module analysis using the Molecular Complex Detection tool identified 21 hub genes from the PPI network. The expression levels of the 21 hub genes were all up-regulated in the cervical cancer tissues when compared to normal cervical tissues as analysed by GEPIA tool. The survival analysis showed that the low expression of cell division cycle 45 (CDC45), GINS complex subunit 2 (GINS2), minichromosome maintenance complex component 2 (MCM2) and proliferating cell nuclear antigen (PCNA) was significantly correlated with the shorter overall survival of patients with cervical cancer. Moreover, the protein expression levels of GINS2, MCM2 and PCNA, but not CDC45, were significantly up-regulated in the cervical cancer tissues when compared to normal cervical tissues. Finally, knockdown of MCM2 significantly suppressed the proliferation of HeLa and SiHa cells. Conclusion In conclusion, we screened a total of 89 overlapping DEGs from the GEO datasets, and further analysis identified four hub genes (CDC45, GINS2, MCM2 and PCNA) that were likely associated with the prognosis of patients with cervical cancer. MCM2 knockdown repressed the cervical cancer cell proliferation. The current findings may provide novel insights into understanding the pathophysiology of cervical cancer and develop therapeutic targets for patients with cervical cancer.
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Affiliation(s)
- Han Xue
- Department of Health Management, Shenzhen People's Hospital, Shenzhen City, Guangdong Province, People's Republic of China
| | - Zhaojun Sun
- Department of Dermatology, Shenzhen People's Hospital, Shenzhen City, GuangdongProvince, People's Republic of China
| | - Weiqing Wu
- Department of Health Management, Shenzhen People's Hospital, Shenzhen City, Guangdong Province, People's Republic of China
| | - Dong Du
- Department of Health Management, Shenzhen People's Hospital, Shenzhen City, Guangdong Province, People's Republic of China
| | - Shuping Liao
- Department of Health Management, Shenzhen People's Hospital, Shenzhen City, Guangdong Province, People's Republic of China
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37
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Petralia F, Tignor N, Reva B, Koptyra M, Chowdhury S, Rykunov D, Krek A, Ma W, Zhu Y, Ji J, Calinawan A, Whiteaker JR, Colaprico A, Stathias V, Omelchenko T, Song X, Raman P, Guo Y, Brown MA, Ivey RG, Szpyt J, Guha Thakurta S, Gritsenko MA, Weitz KK, Lopez G, Kalayci S, Gümüş ZH, Yoo S, da Veiga Leprevost F, Chang HY, Krug K, Katsnelson L, Wang Y, Kennedy JJ, Voytovich UJ, Zhao L, Gaonkar KS, Ennis BM, Zhang B, Baubet V, Tauhid L, Lilly JV, Mason JL, Farrow B, Young N, Leary S, Moon J, Petyuk VA, Nazarian J, Adappa ND, Palmer JN, Lober RM, Rivero-Hinojosa S, Wang LB, Wang JM, Broberg M, Chu RK, Moore RJ, Monroe ME, Zhao R, Smith RD, Zhu J, Robles AI, Mesri M, Boja E, Hiltke T, Rodriguez H, Zhang B, Schadt EE, Mani DR, Ding L, Iavarone A, Wiznerowicz M, Schürer S, Chen XS, Heath AP, Rokita JL, Nesvizhskii AI, Fenyö D, Rodland KD, Liu T, Gygi SP, Paulovich AG, Resnick AC, Storm PB, Rood BR, Wang P. Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer. Cell 2020; 183:1962-1985.e31. [PMID: 33242424 PMCID: PMC8143193 DOI: 10.1016/j.cell.2020.10.044] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 06/19/2020] [Accepted: 10/26/2020] [Indexed: 02/06/2023]
Abstract
We report a comprehensive proteogenomics analysis, including whole-genome sequencing, RNA sequencing, and proteomics and phosphoproteomics profiling, of 218 tumors across 7 histological types of childhood brain cancer: low-grade glioma (n = 93), ependymoma (32), high-grade glioma (25), medulloblastoma (22), ganglioglioma (18), craniopharyngioma (16), and atypical teratoid rhabdoid tumor (12). Proteomics data identify common biological themes that span histological boundaries, suggesting that treatments used for one histological type may be applied effectively to other tumors sharing similar proteomics features. Immune landscape characterization reveals diverse tumor microenvironments across and within diagnoses. Proteomics data further reveal functional effects of somatic mutations and copy number variations (CNVs) not evident in transcriptomics data. Kinase-substrate association and co-expression network analysis identify important biological mechanisms of tumorigenesis. This is the first large-scale proteogenomics analysis across traditional histological boundaries to uncover foundational pediatric brain tumor biology and inform rational treatment selection.
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Affiliation(s)
- Francesca Petralia
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicole Tignor
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mateusz Koptyra
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shrabanti Chowdhury
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dmitry Rykunov
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yuankun Zhu
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jiayi Ji
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Calinawan
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Antonio Colaprico
- Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Vasileios Stathias
- Department of Pharmacology, Institute for Data Science and Computing, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33146, USA
| | - Tatiana Omelchenko
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiaoyu Song
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pichai Raman
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yiran Guo
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Miguel A Brown
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Richard G Ivey
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - John Szpyt
- Thermo Fisher Scientific Center for Multiplexed Proteomics, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sanjukta Guha Thakurta
- Thermo Fisher Scientific Center for Multiplexed Proteomics, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Karl K Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Gonzalo Lopez
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Selim Kalayci
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Seungyeul Yoo
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Hui-Yin Chang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02412, USA
| | - Lizabeth Katsnelson
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Ying Wang
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jacob J Kennedy
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Lei Zhao
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Krutika S Gaonkar
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Brian M Ennis
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Bo Zhang
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Valerie Baubet
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lamiya Tauhid
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jena V Lilly
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jennifer L Mason
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Bailey Farrow
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nathan Young
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sarah Leary
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Cancer and Blood Disorders Center, Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Jamie Moon
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Javad Nazarian
- Children's National Research Institute, George Washington University School of Medicine, Washington, DC 20010, USA; Department of Oncology, Children's Research Center, University Children's Hospital Zürich, Zürich 8032, Switzerland
| | - Nithin D Adappa
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James N Palmer
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert M Lober
- Department of Neurosurgery, Dayton Children's Hospital, Dayton, OH 45404, USA
| | - Samuel Rivero-Hinojosa
- Children's National Research Institute, George Washington University School of Medicine, Washington, DC 20010, USA
| | - Liang-Bo Wang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Joshua M Wang
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Matilda Broberg
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Rosalie K Chu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emily Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02412, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Department of Neurology, Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Maciej Wiznerowicz
- Poznan University of Medical Sciences, 61-701 Poznań, Poland; International Institute for Molecular Oncology, 61-203 Poznań, Poland
| | - Stephan Schürer
- Department of Pharmacology, Institute for Data Science and Computing, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33146, USA
| | - Xi S Chen
- Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Allison P Heath
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jo Lynne Rokita
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - David Fenyö
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Steven P Gygi
- Thermo Fisher Scientific Center for Multiplexed Proteomics, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Adam C Resnick
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Phillip B Storm
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Brian R Rood
- Children's National Research Institute, George Washington University School of Medicine, Washington, DC 20010, USA.
| | - Pei Wang
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Niu Y, Shan L, Gao H, Zhang C, Qian Z, Wang Z, Xu X, Zhang X, Wang J, Ma L, Chen L, Yu Y. Huaier Suppresses the Hepatocellular Carcinoma Cell Cycle by Regulating Minichromosome Maintenance Proteins. Onco Targets Ther 2020; 13:12015-12025. [PMID: 33244243 PMCID: PMC7685376 DOI: 10.2147/ott.s279723] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/07/2020] [Indexed: 12/24/2022] Open
Abstract
Purpose Hepatocellular carcinoma (HCC) is a common malignant tumor with limited treatment. Our previous studies demonstrated that Huaier enhanced chemotherapy sensitivity and restrained HCC proliferation. This study aimed to identify differentially expressed proteins with Huaier treatment in HCC cells, providing molecular targets for future targeted therapy of HCC. Materials and Methods The effects of Huaier on the cell cycle were determined by flow cytometry and Western blot (WB). Xenograft models were used to verify the effects of Huaier on tumor growth. Then, proteomics was performed to identify the potential proteins regulated by Huaier. The enrichment analysis of GO and KEGG was performed for the differentially expressed proteins. Western blot (WB) and immunohistochemistry (IHC) were used to detect the levels of proteins after Huaier treatment. After that the correlation of differentially expressed proteins with pathological stages was analyzed via the GEPIA database. We also analyzed candidate expression after Huaier treatment in HCC cells by WB and qRT-PCR. Furthermore, siRNA was performed to verify the targeted regulation of Huaier on candidate proteins. Results First, the proteomics data showed that a total of 160 proteins were identified as differentially expressed proteins, among which six minichromosome maintenance (MCM) family members were enriched in the tumor-associated pathways after Huaier treatment. Moreover, MCM proteins were highly expressed in HCC and closely correlated with the survival of HCC patients. Finally, we confirmed that MCM proteins were targets of Huaier treatment in HCC cells. Conclusion Huaier treatment was closely associated with the activation and inhibition of cancer-related pathways, and the MCM family was identified as a potential target in the antitumor process of Huaier. This study is helpful in understanding the molecular alterations and clinical relevance of HCC after Huaier treatment, which is beneficial for finding new targets and designing effective chemotherapy regimens for the future treatment of HCC.
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Affiliation(s)
- Yongjie Niu
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, People's Republic of China
| | - Liang Shan
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, People's Republic of China
| | - Han Gao
- Encephalopathy Department, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, People's Republic of China
| | - Congcong Zhang
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, People's Republic of China
| | - Zijun Qian
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, People's Republic of China
| | - Zhixian Wang
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, People's Republic of China
| | - Xin Xu
- Institute for Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Xiao Zhang
- Institute for Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Jiayi Wang
- Institute for Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Lifang Ma
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, People's Republic of China.,Institute for Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Liyun Chen
- Institute of Science, Technology and Humanities of Shanghai University of Traditional Chinese Medicine, Shanghai 200071, People's Republic of China
| | - Yongchun Yu
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, People's Republic of China.,Institute for Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
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39
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Pan L, Wang X, Yang L, Zhao L, Zhai L, Xu J, Yang Y, Mao Y, Cheng S, Xiao T, Tan M. Proteomic and Phosphoproteomic Maps of Lung Squamous Cell Carcinoma From Chinese Patients. Front Oncol 2020; 10:963. [PMID: 32612956 PMCID: PMC7308564 DOI: 10.3389/fonc.2020.00963] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/15/2020] [Indexed: 12/29/2022] Open
Abstract
Lung squamous cell carcinoma (LUSC) is one of the leading causes of tumor-driven deaths in the world. To date, studies on the tumor heterogeneity of LUSC at genomic level have only revealed limited therapeutic benefits. Therefore, system-wide research of LUSC at proteomic level may further improve precision medicine strategies on individual demands. To this end, we performed proteomic and phosphoproteomic study for LUSC samples of 25 Chinese patients. From our results, two subgroups (Cluster I and II) based on proteomic data were identified, which were associated with distinct molecular characteristics and clinicopathologic features. Combined with phosphoproteomic data, our result showed that spliceosome pathway was enriched in Cluster I, while focal adhesion pathway, immune-related pathways and Ras signaling pathway were enriched in Cluster II. In addition, we found that lymph node metastasis (LNM) was associated with our proteomic subgroups and cell cycle pathway was enriched in patients with LNM. Further analysis showed that MCM2, a DNA replication licensing factor involved in cell cycle pathway, was highly expressed in patients with poor prognosis, which was further proved by immunohistochemistry (IHC) analysis. In summary, our study provided a resource of the proteomic and phosphoproteomic features of LUSC in Chinese patients.
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Affiliation(s)
- Lulu Pan
- Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Xijun Wang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Longhai Yang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Cardiothoracic Surgery, Shenzhen University General Hospital/Shenzhen University Clinical Medical Academy, Shenzhen, China
| | - Lei Zhao
- Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Linhui Zhai
- Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Junyu Xu
- Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yikun Yang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yousheng Mao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shujun Cheng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting Xiao
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Minjia Tan
- Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
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40
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Yamada Y, Nohata N, Uchida A, Kato M, Arai T, Moriya S, Mizuno K, Kojima S, Yamazaki K, Naya Y, Ichikawa T, Seki N. Replisome genes regulation by antitumor miR-101-5p in clear cell renal cell carcinoma. Cancer Sci 2020; 111:1392-1406. [PMID: 31975570 PMCID: PMC7156888 DOI: 10.1111/cas.14327] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 01/07/2020] [Accepted: 01/12/2020] [Indexed: 12/25/2022] Open
Abstract
Analysis of microRNA (miRNA) regulatory networks is useful for exploring novel biomarkers and therapeutic targets in cancer cells. The Cancer Genome Atlas dataset shows that low expression of both strands of pre‐miR‐101 (miR‐101‐5p and miR‐101‐3p) significantly predicted poor prognosis in clear cell renal cell carcinoma (ccRCC). The functional significance of miR‐101‐5p in cancer cells is poorly understood. Here, we focused on miR‐101‐5p to investigate the antitumor function and its regulatory networks in ccRCC cells. Ectopic expression of mature miRNAs or siRNAs was investigated in cancer cell lines to characterize cell function, ie, proliferation, apoptosis, migration, and invasion. Genome‐wide gene expression and in silico database analyses were undertaken to predict miRNA regulatory networks. Expression of miR‐101‐5p caused cell cycle arrest and apoptosis in ccRCC cells. Downstream neighbor of son (DONSON) was directly regulated by miR‐101‐5p, and its aberrant expression was significantly associated with shorter survival in propensity score‐matched analysis (P = .0001). Knockdown of DONSON attenuated ccRCC cell aggressiveness. Several replisome genes controlled by DONSON and their expression were closely associated with ccRCC pathogenesis. The antitumor miR‐101‐5p/DONSON axis and its modulated replisome genes might be a novel diagnostic and therapeutic target for ccRCC.
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Affiliation(s)
- Yasutaka Yamada
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba, Japan.,Department of Urology, Chiba University Graduate School of Medicine, Chiba, Japan
| | | | - Akifumi Uchida
- Department of Pulmonary Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Mayuko Kato
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba, Japan.,Department of Urology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Takayuki Arai
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba, Japan.,Department of Urology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Shogo Moriya
- Department of Biochemistry and Genetics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Keiko Mizuno
- Department of Pulmonary Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Satoko Kojima
- Department of Urology, Teikyo University Chiba Medical Center, Ichihara, Japan
| | - Kazuto Yamazaki
- Department of Pathology, Teikyo University Chiba Medical Center, Ichihara, Japan
| | - Yukio Naya
- Department of Urology, Teikyo University Chiba Medical Center, Ichihara, Japan
| | - Tomohiko Ichikawa
- Department of Urology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Naohiko Seki
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba, Japan
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MCMs in Cancer: Prognostic Potential and Mechanisms. Anal Cell Pathol (Amst) 2020; 2020:3750294. [PMID: 32089988 PMCID: PMC7023756 DOI: 10.1155/2020/3750294] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/25/2020] [Indexed: 12/17/2022] Open
Abstract
Enabling replicative immortality and uncontrolled cell cycle are hallmarks of cancer cells. Minichromosome maintenance proteins (MCMs) exhibit helicase activity in replication initiation and play vital roles in controlling replication times within a cell cycle. Overexpressed MCMs are detected in various cancerous tissues and cancer cell lines. Previous studies have proposed MCMs as promising proliferation markers in cancers, while the prognostic values remain controversial and the underlying mechanisms remain unascertained. This review provides an overview of the significant findings regarding the cellular and tumorigenic functions of the MCM family. Besides, current evidence of the prognostic roles of MCMs is retrospectively reviewed. This work also offers insight into the mechanisms of MCMs prompting carcinogenesis and adverse prognosis, providing information for future research. Finally, MCMs in liver cancer are specifically discussed, and future perspectives are provided.
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42
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Phosphoproteomic analysis sheds light on intracellular signaling cascades triggered by Formyl-Peptide Receptor 2. Sci Rep 2019; 9:17894. [PMID: 31784636 PMCID: PMC6884478 DOI: 10.1038/s41598-019-54502-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 11/14/2019] [Indexed: 12/12/2022] Open
Abstract
Formyl peptide receptors (FPRs) belong to the family of seven transmembrane Gi-protein coupled receptors (GPCR). FPR2 is considered the most promiscuous member of this family since it recognizes a wide variety of ligands. It plays a crucial role in several physio-pathological processes and different studies highlighted the correlation between its expression and the higher propensity to invasion and metastasis of some cancers. FPR2 stimulation by its synthetic agonist WKYMVm triggers multiple phosphorylations of intracellular signaling molecules, such as ERKs, PKC, PKB, p38MAPK, PI3K, PLC, and of non-signaling proteins, such as p47phox and p67phox which are involved in NADPH oxidase-dependent ROS generation. Biological effects of FPR2 stimulation include intracellular Ca2+ mobilization, cellular proliferation and migration, and wound healing. A systematic analysis of the phosphoproteome in FPR2-stimulated cells has not been yet reported. Herein, we describe a large-scale phosphoproteomic study in WKYMVm-stimulated CaLu-6 cells. By using high resolution MS/MS we identified 290 differentially phosphorylated proteins and 53 unique phosphopeptides mapping on 40 proteins. Phosphorylations on five selected phospho-proteins were further validated by western blotting, confirming their dependence on FPR2 stimulation. Interconnection between some of the signalling readout identified was also evaluated. Furthermore, we show that FPR2 stimulation with two anti-inflammatory agonists induces the phosphorylation of selected differentially phosphorylated proteins, suggesting their role in the resolution of inflammation. These data provide a promising resource for further studies on new signaling networks triggered by FPR2 and on novel molecular drug targets for human diseases.
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43
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Joshi P, Katsushima K, Zhou R, Meoded A, Stapleton S, Jallo G, Raabe E, Eberhart CG, Perera RJ. The therapeutic and diagnostic potential of regulatory noncoding RNAs in medulloblastoma. Neurooncol Adv 2019; 1:vdz023. [PMID: 31763623 PMCID: PMC6859950 DOI: 10.1093/noajnl/vdz023] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Medulloblastoma, a central nervous system tumor that predominantly affects children, always requires aggressive therapy. Nevertheless, it frequently recurs as resistant disease and is associated with high morbidity and mortality. While recent efforts to subclassify medulloblastoma based on molecular features have advanced our basic understanding of medulloblastoma pathogenesis, optimal targets to increase therapeutic efficacy and reduce side effects remain largely undefined. Noncoding RNAs (ncRNAs) with known regulatory roles, particularly long noncoding RNAs (lncRNAs) and microRNAs (miRNAs), are now known to participate in medulloblastoma biology, although their functional significance remains obscure in many cases. Here we review the literature on regulatory ncRNAs in medulloblastoma. In providing a comprehensive overview of ncRNA studies, we highlight how different lncRNAs and miRNAs have oncogenic or tumor suppressive roles in medulloblastoma. These ncRNAs possess subgroup specificity that can be exploited to personalize therapy by acting as theranostic targets. Several of the already identified ncRNAs appear specific to medulloblastoma stem cells, the most difficult-to-treat component of the tumor that drives metastasis and acquired resistance, thereby providing opportunities for therapy in relapsing, disseminating, and therapy-resistant disease. Delivering ncRNAs to tumors remains challenging, but this limitation is gradually being overcome through the use of advanced technologies such as nanotechnology and rational biomaterial design.
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Affiliation(s)
- Piyush Joshi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland.,Cancer and Blood Disorders Institute, Johns Hopkins All Children's Hospital, St. Petersburg, Florida
| | - Keisuke Katsushima
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland.,Cancer and Blood Disorders Institute, Johns Hopkins All Children's Hospital, St. Petersburg, Florida
| | - Rui Zhou
- Cancer and Blood Disorders Institute, Johns Hopkins All Children's Hospital, St. Petersburg, Florida
| | - Avner Meoded
- Pediatric Neuroradiology, Johns Hopkins All Children's Hospital, St. Petersburg, Florida
| | - Stacie Stapleton
- Cancer and Blood Disorders Institute, Johns Hopkins All Children's Hospital, St. Petersburg, Florida
| | - George Jallo
- Institute Brain Protection Sciences, Johns Hopkins All Children's Hospital, St. Petersburg, Florida
| | - Eric Raabe
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Charles G Eberhart
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ranjan J Perera
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland.,Cancer and Blood Disorders Institute, Johns Hopkins All Children's Hospital, St. Petersburg, Florida.,Sanford Burnham Prebys Medical Discovery Institute, NCI-Designated Cancer Center, La Jolla, California
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44
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Yamamoto K, Makino N, Nagai M, Honma Y, Araki H, Ushimaru T. TORC1 signaling regulates DNA replication via DNA replication protein levels. Biochem Biophys Res Commun 2018; 505:1128-1133. [DOI: 10.1016/j.bbrc.2018.10.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 10/04/2018] [Indexed: 02/07/2023]
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