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Weiner AC, Williams MJ, Shi H, Vázquez-García I, Salehi S, Rusk N, Aparicio S, Shah SP, McPherson A. Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data. Nat Commun 2024; 15:8512. [PMID: 39353885 PMCID: PMC11445576 DOI: 10.1038/s41467-024-52544-7] [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: 01/29/2024] [Accepted: 09/11/2024] [Indexed: 10/03/2024] Open
Abstract
Dysregulated DNA replication is a cause and a consequence of aneuploidy in cancer, yet the interplay between copy number alterations (CNAs), replication timing (RT) and cell cycle dynamics remain understudied in aneuploid tumors. We developed a probabilistic method, PERT, for simultaneous inference of cell-specific replication and copy number states from single-cell whole genome sequencing (scWGS) data. We used PERT to investigate clone-specific RT and proliferation dynamics in >50,000 cells obtained from aneuploid and clonally heterogeneous cell lines, xenografts and primary cancers. We observed bidirectional relationships between RT and CNAs, with CNAs affecting X-inactivation producing the largest RT shifts. Additionally, we found that clone-specific S-phase enrichment positively correlated with ground-truth proliferation rates in genomically stable but not unstable cells. Together, these results demonstrate robust computational identification of S-phase cells from scWGS data, and highlight the importance of RT and cell cycle properties in studying the genomic evolution of aneuploid tumors.
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Affiliation(s)
- Adam C Weiner
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Marc J Williams
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hongyu Shi
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ignacio Vázquez-García
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sohrab Salehi
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicole Rusk
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Andrew McPherson
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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2
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Shen C, Liu J, Xie F, Yu Y, Ma X, Hu D, Liu C, Wang Y. N6-Methyladenosine enhances the translation of ENO1 to promote the progression of bladder cancer by inhibiting PCNA ubiquitination. Cancer Lett 2024; 595:217002. [PMID: 38823761 DOI: 10.1016/j.canlet.2024.217002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/21/2024] [Accepted: 05/27/2024] [Indexed: 06/03/2024]
Abstract
The mechanism underlying N6-methyladenosine (m6A) modification in bladder cancer (BC) remains elusive. We identified that the RBM15/METTL3 complex enhances m6A modification and promotes the ENO1 protein translation efficiency through its 359A site by depending on YTHDF1 in BC cells. In the tumor microenvironment, TGF-β effectively stimulates RBM15/METTL3 expression to improve ENO1 mRNA m6A modification through the Smad2/3 pathway. Reduced ENO1 m6A levels hamper tumor proliferation both in vitro and in vivo. Mechanistically, ENO1 augments PCNA protein stability by reducing its K48-linked ubiquitination and thus prevents protein degradation through the endoplasmic reticulum-associated degradation pathway. According to the subsequent experiments, the ENO1 inhibitor significantly reduced tumor proliferation both in vitro and in vivo. Our study highlights the significance of RBM15/METTL3 complex-mediated ENO1 mRNA m6A modification in ENO1 expression. It also reveals a novel mechanism by which ENO1 promotes BC progression, thereby suggesting that ENO1 can be a therapeutic target for BC.
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Affiliation(s)
- Chengquan Shen
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Jing Liu
- Department of Research Management and International Cooperation, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Fei Xie
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Yongbo Yu
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Xiaocheng Ma
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Ding Hu
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Changxue Liu
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Yonghua Wang
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China; Qingdao Clinical Medical Research Center for Urinary System Diseases, Qingdao, Shandong, China; Shandong Province Medical and Health Key Laboratory of Urology, Qingdao, Shandong, China.
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3
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Ding Z, Zhang J, Li L, Wang C, Mei J. Prognostic biomarker HIF1α and its correlation with immune infiltration in gliomas. Oncol Lett 2024; 27:193. [PMID: 38495835 PMCID: PMC10941081 DOI: 10.3892/ol.2024.14326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/06/2023] [Indexed: 03/19/2024] Open
Abstract
Certain glioma subtypes, such as glioblastoma multiforme or low-grade glioma, are common malignant intracranial tumors with high rates of relapse and malignant progression even after standard therapy. The overall survival (OS) is poor in patients with gliomas; hence, effective prognostic prediction is crucial. Herein, the present study aimed to explore the potential role of hypoxia-inducible factor 1 subunit alpha (HIF1α) in gliomas and investigate the association between HIF1α and infiltrating immune cells in gliomas. Data from The Cancer Genome Atlas were evaluated via RNA sequencing, clinicopathological, immunological checkpoint, immune infiltration and functional enrichment analyses. Validation of protein abundance was performed using paraffin-embedded samples from patients with glioma. A nomogram model was created to forecast the OS rates at 1, 3 and 5 years after cancer diagnosis. The association between OS and HIF1α expression was estimated using Kaplan-Meier survival analysis and the log-rank test. Finally, HIF1α expression was validated using western blotting, reverse transcription-quantitative PCR, Cell Counting Kit-8 and Transwell assays. The results demonstrated that HIF1α expression was significantly upregulated in gliomas compared with normal human brain glial cells. Immunohistochemistry staining demonstrated differential expression of the HIF1α protein. Moreover, glioma cell viability and migration were inhibited via HIF1α downregulation. HIF1α impacted DNA replication, cell cycling, DNA repair and the immune microenvironment in glioma. HIF1α expression was also positively associated with several types of immune cells and immunological checkpoints and with neutrophils, plasmacytoid dendritic cells and CD56bright cells. The Kaplan-Meier survival analyses further demonstrated a strong association between high HIF1α expression and poor prognosis in patients with glioma. Analysis of the receiver operating characteristic curves demonstrated that HIF1α expression accurately differentiated paired normal brain cells from tumor tissues. Collectively, these findings suggested the potential for HIF1α to be used as a novel prognostic indicator for patients with glioma and that OS prediction models may help in the future to develop effective follow-up and treatment strategies for these patients.
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Affiliation(s)
- Zihan Ding
- Department of Neurosurgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Jiaming Zhang
- Department of Pathology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Lin Li
- Department of Neurosurgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Chunliang Wang
- Department of Neurosurgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Jinhong Mei
- Department of Pathology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
- Institute of Molecular Pathology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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4
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Zhao C, Guo Y, Chen Y, Shang G, Song D, Wang J, Yang J, Zhang H. Zinc finger Protein207 orchestrates glioma migration through regulation of epithelial-mesenchymal transition. ENVIRONMENTAL TOXICOLOGY 2024. [PMID: 38591780 DOI: 10.1002/tox.24271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/15/2024] [Accepted: 03/24/2024] [Indexed: 04/10/2024]
Abstract
BACKGROUND Glioma represents the predominant primary malignant brain tumor. For several years, molecular profiling has been instrumental in the management and therapeutic stratification of glioma, providing a deeper understanding of its biological complexity. Accumulating evidence unveils the putative involvement of zinc finger proteins (ZNFs) in cancer. This study aimed to elucidate the role and significance of ZNF207 in glioma. METHODS Utilizing online data such as The Cancer Genome Atlas (TCGA), the Chinese Glioma Genome Atlas (CGGA), the Genotype-Tissue Expression (GTEx) project, the Clinical Proteomic Tumor Analysis Consortium (CPTAC), and the Human Protein Atlas (HPA) databases, in conjunction with bioinformatics methodologies including GO, KEGG, GSEA, CIBERSORT immune cell infiltration estimation, and protein-protein interaction (PPI) analysis, enabled a comprehensive exploration of ZNF207's involvement in gliomagenesis. Immunohistochemistry and RT-PCR techniques were employed to validate the expression level of ZNF207 in glioma samples. Subsequently, the biological effects of ZNF207 on glioma cells were explored through in vitro assays. RESULTS Our results demonstrate elevated expression of ZNF207 in gliomas, correlating with unfavorable patient outcomes. Stratification analyses were used to delineate the prognostic efficacy of ZNF207 in glioma with different clinicopathological characteristics. Immunocorrelation analysis revealed a significant association between ZNF207 expression and the infiltration levels of T helper cells, macrophages, and natural killer (NK) cells. Utilizing ZNF207 expression and clinical features, we constructed an OS prediction model and displayed well discrimination with a C-index of 0.861. Moreover, the strategic silencing of ZNF207 attenuated glioma cell advancement, evidenced by diminished cellular proliferation, weakened cell tumorigenesis, augmented apoptotic activity, and curtailed migratory capacity alongside the inhibition of the epithelial-mesenchymal transition (EMT) pathway. CONCLUSIONS ZNF207 may identify as a prospective biomarker and therapeutic candidate for glioma prevention, providing valuable insights into understanding glioma pathogenesis and treatment strategies.
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Affiliation(s)
- Chao Zhao
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Yuduo Guo
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Yujia Chen
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Guanjie Shang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Dixiang Song
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Jun Wang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Jingjing Yang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Hongwei Zhang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
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Zheng CS, Huang WM, Xia HM, Mi JL, Li YQ, Liang HQ, Zhou L, Lu ZX, Wu F. Oncogenic and immunological roles of RACGAP1 in pan-cancer and its potential value in nasopharyngeal carcinoma. Apoptosis 2024; 29:243-266. [PMID: 37670104 DOI: 10.1007/s10495-023-01884-8] [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] [Accepted: 08/17/2023] [Indexed: 09/07/2023]
Abstract
A particular GTPase-activating protein called RACGAP1 is involved in apoptosis, proliferation, invasion, metastasis, and drug resistance in a variety of malignancies. Nevertheless, the role of RACGAP1 in pan-cancer was less studied, and its value of the expression and prognostic of nasopharyngeal carcinoma (NPC) has not been explored. Hence, the goal of this study was to investigate the oncogenic and immunological roles of RACGAP1 in various cancers and its potential value in NPC. We comprehensively analyzed RACGAP1 expression, prognostic value, function, methylation levels, relationship with immune cells, immune infiltration, and immunotherapy response in pan-cancer utilizing multiple databases. The results discovered that RACGAP1 expression was elevated in most cancers and suggested poor prognosis, which could be related to the involvement of RACGAP1 in various cancer-related pathways such as the cell cycle and correlated with RACGAP1 methylation levels, immune cell infiltration and reaction to immunotherapy, and chemoresistance. RACGAP1 could inhibit anti-tumor immunity and immunotherapy responses by fostering immune cell infiltration and cytotoxic T lymphocyte dysfunction. Significantly, we validated that RACGAP1 mRNA and protein were highly expressed in NPC. The Gene Expression Omnibus database revealed that elevated RACGAP1 expression was associated with shorter PFS in patients with NPC, and RACGAP1 potentially influenced cell cycle progression, DNA replication, metabolism, and immune-related pathways, resulting in the recurrence and metastasis of NPC. This study indicated that RACGAP1 could be a potential biomarker in pan-cancer and NPC.
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Affiliation(s)
- Cheng-Shan Zheng
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, 530021, Guangxi, China
| | - Wei-Mei Huang
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Hong-Mei Xia
- Department of Gynecology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, 350014, China
| | - Jing-Lin Mi
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, 530021, Guangxi, China
| | - Yuan-Qing Li
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, 530021, Guangxi, China
| | - Hui-Qing Liang
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, 530021, Guangxi, China
| | - Li Zhou
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, 530021, Guangxi, China
| | - Zhou-Xue Lu
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, 530021, Guangxi, China
| | - Fang Wu
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, 530021, Guangxi, China.
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Chen J, Wu S, Wang J, Han C, Zhao L, He K, Jia Y, Cui M. MCM10: An effective treatment target and a prognostic biomarker in patients with uterine corpus endometrial carcinoma. J Cell Mol Med 2023; 27:1708-1724. [PMID: 37246638 PMCID: PMC10273062 DOI: 10.1111/jcmm.17772] [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: 01/31/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/30/2023] Open
Abstract
Molecular profiling has been applied for uterine corpus endometrial carcinoma (UCEC) management for many years. The aim of this study was to explore the role of MCM10 in UCEC and construct its overall survival (OS) prediction models. Data from TCGA, GEO, cbioPotal and COSMIC databases and the methods, such as GO, KEGG, GSEA, ssGSEA and PPI, were employed to bioinformatically detect the effects of MCM10 on UCEC. RT-PCR, Western blot and immunohistochemistry were used to validate the effects of MCM10 on UCEC. Based on Cox regression analysis using the data from TCGA and our clinical data, two OS prediction models for UCEC were established. Finally, the effects of MCM10 on UCEC were detected in vitro. Our study revealed that MCM10 was variated and overexpressed in UCEC tissue and involved in DNA replication, cell cycle, DNA repair and immune microenvironment in UCEC. Moreover, silencing MCM10 significantly inhibited the proliferation of UCEC cells in vitro. Importantly, based on MCM10 expression and clinical features, the OS prediction models were constructed with good accuracy. MCM10 could be an effective treatment target and a prognostic biomarker for UCEC patients. The OS prediction models might help establish the strategies of follow-up and treatment for UCEC patients.
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Affiliation(s)
- Junyu Chen
- Department of Gynecology and ObstetricsThe Second Hospital of Jilin UniversityChangchunChina
| | - Shan Wu
- Department of Gynecology and ObstetricsThe Second Hospital of Jilin UniversityChangchunChina
- Department of Reproductive Endocrinology, Key Laboratory of Reproductive Genetics (Ministry of Education)Women's Hospital, Zhejiang University, School of MedicineHangzhouChina
| | - Junwei Wang
- Department of Obstetrics and GynecologyThe First Hospital of Jilin UniversityChangchunChina
| | - Chunying Han
- Third Department of Gynecological OncologyJilin Cancer HospitalChangchunChina
| | - Lijing Zhao
- Department of Rehabilitation, School of NursingJilin UniversityChangchunChina
| | - Kang He
- Department of Rehabilitation, School of NursingJilin UniversityChangchunChina
| | - Yan Jia
- Department of Gynecology and ObstetricsThe Second Hospital of Jilin UniversityChangchunChina
| | - Manhua Cui
- Department of Gynecology and ObstetricsThe Second Hospital of Jilin UniversityChangchunChina
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Hatoyama Y, Kanemaki MT. The assembly of the MCM2-7 hetero-hexamer and its significance in DNA replication. Biochem Soc Trans 2023:233028. [PMID: 37145026 DOI: 10.1042/bst20221465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/06/2023]
Abstract
The mini-chromosome maintenance proteins 2-7 (MCM2-7) hexamer is a protein complex that is key for eukaryotic DNA replication, which occurs only once per cell cycle. To achieve DNA replication, eukaryotic cells developed multiple mechanisms that control the timing of the loading of the hexamer onto chromatin and its activation as the replicative helicase. MCM2-7 is highly abundant in proliferating cells, which confers resistance to replication stress. Thus, the presence of an excess of MCM2-7 is important for maintaining genome integrity. However, the mechanism via which high MCM2-7 levels are achieved, other than the transcriptional upregulation of the MCM genes in the G1 phase, remained unknown. Recently, we and others reported that the MCM-binding protein (MCMBP) plays a role in the maintenance of high MCM2-7 levels and hypothesized that MCMBP functions as a chaperone in the assembly of the MCM2-7 hexamer. In this review, we discuss the roles of MCMBP in the control of MCM proteins and propose a model of the assembly of the MCM2-7 hexamer. Furthermore, we discuss a potential mechanism of the licensing checkpoint, which arrests the cells in the G1 phase when the levels of chromatin-bound MCM2-7 are reduced, and the possibility of targeting MCMBP as a chemotherapy for cancer.
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Affiliation(s)
- Yuki Hatoyama
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Yata 1111, Mishima, Shizuoka 411-8540, Japan
- Department of Biological Science, The University of Tokyo, Tokyo 113-0033, Japan
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8
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Song H, Shen R, Mahasin H, Guo Y, Wang D. 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] [Grants] [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 SciencesLanzhou UniversityLanzhouGansuChina
| | - Rong Shen
- School of Basic Medical SciencesLanzhou UniversityLanzhouGansuChina
| | - Hamid Mahasin
- School of Basic Medical SciencesLanzhou UniversityLanzhouGansuChina
| | - Ya‐Nan Guo
- School of Basic Medical SciencesLanzhou UniversityLanzhouGansuChina
| | - De‐Gui Wang
- School of Basic Medical SciencesLanzhou UniversityLanzhouGansuChina
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Zahir R, Khan ZA, Aleem B, Ahmad S, Ali A, Issrani R, Alruwaili MK, Iqbal S, Alghumaiz SF, Alanazi SH, Umer MF, Ullah I, Sumera, Ganji KK. Association of High Immunohistochemical Expression of Minichromosome Maintenance 3 with Human Oral Squamous Cell Carcinoma-A Preliminary Study. Diagnostics (Basel) 2022; 13:61. [PMID: 36611359 PMCID: PMC9818330 DOI: 10.3390/diagnostics13010061] [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: 08/26/2022] [Revised: 11/06/2022] [Accepted: 11/10/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Oral squamous cell carcinoma (OSCC) may arise from premalignant oral lesions (PMOL) in most cases. Minichromosome maintenance 3 (MCM3) is a proliferative marker that has been investigated as a potential diagnostic biomarker in the diagnosis of oral cancer. OBJECTIVES To evaluate the association of MCM3 expression, its clinicopathologic parameters and to identify snuff (also called naswar) as a potential risk factor for changes in MCM3 expression in PMOL and OSCC. METHODOLOGY Immunohistochemistry (IHC) of MCM3 was performed on 32 PMOL, 32 OSCC and 16 normal controls after optimization of IHC methodology. Histoscore (0-300) was used as a scoring system and seven different cut-offs were identified for analyses. Data were analyzed using various statistical tests. RESULTS Among the seven cutoffs, 40% strong positive cells were found to be a better cut-off as they were associated with many pathological variables (Broder's grade, Aneroth's grade, and mitotic activity). The differential MCM3 expression in oral lesions (PMOL and OSCC) was statistically significant (p = 0.03). Moreover, MCM3 expression is raised with increased duration and frequency of snuff use. CONCLUSION High MCM3 expression is associated with disease progression and is a potential indicator of malignant transformations from PMOL to OSCC. Moreover, the use of snuff is associated with MCM3 over-expression.
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Affiliation(s)
- Rabia Zahir
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar 25100, Pakistan
| | - Zafar Ali Khan
- Department of Oral & Maxillofacial Surgery and Diagnostic Sciences, College of Dentistry, Jouf University, Sakaka 72388, Saudi Arabia
| | - Benish Aleem
- Institute of Pathology & Diagnostic Medicine, Khyber Medical University, Peshawar 25100, Pakistan
| | - Shahzad Ahmad
- Department of Oral Medicine & Diagnostic Sciences, Vision College, Riyadh 0096611, Saudi Arabia
| | - Asif Ali
- Institute of Pathology & Diagnostic Medicine, Khyber Medical University, Peshawar 25100, Pakistan
- Institute of Cancer Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Rakhi Issrani
- Department of Preventive Dentistry, College of Dentistry, Jouf University, Sakaka 72388, Saudi Arabia
| | - Mohammed Katib Alruwaili
- Department of Preventive Dentistry, College of Dentistry, Jouf University, Sakaka 72388, Saudi Arabia
- Department of Periodontology and Endodontology, Faculty of Dental Medicine, Hokkaido University, N13W7, Kita-ku, Sapporo, Hokkaido 060-8586, Japan
| | - Shazia Iqbal
- Department of Obstetrics & Gynecology, Vision College, Riyadh 0096611, Saudi Arabia
| | | | | | | | - Ihsan Ullah
- Institute of Pathology & Diagnostic Medicine, Khyber Medical University, Peshawar 25100, Pakistan
| | - Sumera
- Institute of Pathology & Diagnostic Medicine, Khyber Medical University, Peshawar 25100, Pakistan
| | - Kiran Kumar Ganji
- Department of Preventive Dentistry, College of Dentistry, Jouf University, Sakaka 72388, Saudi Arabia
- Department of Periodontology and Implantology, Sharad Pawar Dental College & Hospital, Datta Meghe Institute of Medical Sciences, Nagpur 442001, India
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10
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Zhong ME, Duan X, Ni-jia-ti MYDL, Qi H, Xu D, Cai D, Li C, Huang Z, Zhu Q, Gao F, Wu X. CT-based radiogenomic analysis dissects intratumor heterogeneity and predicts prognosis of colorectal cancer: a multi-institutional retrospective study. J Transl Med 2022; 20:574. [PMID: 36482390 PMCID: PMC9730572 DOI: 10.1186/s12967-022-03788-8] [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: 10/18/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND This study aimed to develop a radiogenomic prognostic prediction model for colorectal cancer (CRC) by investigating the biological and clinical relevance of intratumoural heterogeneity. METHODS This retrospective multi-cohort study was conducted in three steps. First, we identified genomic subclones using unsupervised deconvolution analysis. Second, we established radiogenomic signatures to link radiomic features with prognostic subclone compositions in an independent radiogenomic dataset containing matched imaging and gene expression data. Finally, the prognostic value of the identified radiogenomic signatures was validated using two testing datasets containing imaging and survival information collected from separate medical centres. RESULTS This multi-institutional retrospective study included 1601 patients (714 females and 887 males; mean age, 65 years ± 14 [standard deviation]) with CRC from 5 datasets. Molecular heterogeneity was identified using unsupervised deconvolution analysis of gene expression data. The relative prevalence of the two subclones associated with cell cycle and extracellular matrix pathways identified patients with significantly different survival outcomes. A radiogenomic signature-based predictive model significantly stratified patients into high- and low-risk groups with disparate disease-free survival (HR = 1.74, P = 0.003). Radiogenomic signatures were revealed as an independent predictive factor for CRC by multivariable analysis (HR = 1.59, 95% CI:1.03-2.45, P = 0.034). Functional analysis demonstrated that the 11 radiogenomic signatures were predominantly associated with extracellular matrix and immune-related pathways. CONCLUSIONS The identified radiogenomic signatures might be a surrogate for genomic signatures and could complement the current prognostic strategies.
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Affiliation(s)
- Min-Er Zhong
- grid.488525.6Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655 China ,grid.413405.70000 0004 1808 0686Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China ,grid.488525.6Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xin Duan
- grid.12981.330000 0001 2360 039XSchool of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Ma-yi-di-li Ni-jia-ti
- Department of Radiology, The First People’s Hospital of Kashi Prefecture, Kashi, Xinjiang China
| | - Haoning Qi
- grid.488525.6Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655 China ,grid.488525.6Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Dongwei Xu
- grid.488525.6Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655 China ,grid.488525.6Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Du Cai
- grid.488525.6Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655 China ,grid.488525.6Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Chenghang Li
- grid.488525.6Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655 China ,grid.488525.6Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Zeping Huang
- grid.488525.6Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655 China ,grid.488525.6Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Qiqi Zhu
- grid.488525.6Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655 China ,grid.507012.10000 0004 1798 304XDepartment of Colorectal Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China
| | - Feng Gao
- grid.488525.6Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655 China ,grid.488525.6Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China ,Shanghai Artificial Intelligence Laboratory, Shanghai, China
| | - Xiaojian Wu
- grid.488525.6Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655 China ,grid.488525.6Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
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11
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Identification and Functional Analysis of Individual-Specific Subpathways in Lung Adenocarcinoma. Genes (Basel) 2022; 13:genes13071122. [PMID: 35885905 PMCID: PMC9315518 DOI: 10.3390/genes13071122] [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: 05/16/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 11/26/2022] Open
Abstract
Small molecular networks within complex pathways are defined as subpathways. The identification of patient-specific subpathways can reveal the etiology of cancer and guide the development of personalized therapeutic strategies. The dysfunction of subpathways has been associated with the occurrence and development of cancer. Here, we propose a strategy to identify aberrant subpathways at the individual level by calculating the edge score and using the Gene Set Enrichment Analysis (GSEA) method. This provides a novel approach to subpathway analysis. We applied this method to the expression data of a lung adenocarcinoma (LUAD) dataset from The Cancer Genome Atlas (TCGA) database. We validated the effectiveness of this method in identifying LUAD-relevant subpathways and demonstrated its reliability using an independent Gene Expression Omnibus dataset (GEO). Additionally, survival analysis was applied to illustrate the clinical application value of the genes and edges in subpathways that were associated with the prognosis of patients and cancer immunity, which could be potential biomarkers. With these analyses, we show that our method could help uncover subpathways underlying lung adenocarcinoma.
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12
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Wu Z, Wang Y, Li J, Wang H, Tuo X, Zheng J. MCM10 is a Prognostic Biomarker and Correlated With Immune Checkpoints in Ovarian Cancer. Front Genet 2022; 13:864578. [PMID: 35664337 PMCID: PMC9161093 DOI: 10.3389/fgene.2022.864578] [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: 01/28/2022] [Accepted: 05/02/2022] [Indexed: 11/25/2022] Open
Abstract
Background: Microchromosome maintenance protein 10 (MCM10) is required for DNA replication in all eukaryotes, and it plays a key role in the development of many types of malignancies. However, we currently still do not know the relationship between MCM10 and ovarian cancer (OV) prognosis and immune checkpoints. Methods: The Gene Expression Profiling Interactive Analysis and Tumor Immunology Estimation Resource (TIMER) databases were used to investigate MCM10 expression in Fan cancer. The Kaplan-Meier Plotter and PrognoScan were used to assess the relationship between MCM10 and OV prognosis. The LinkedOmics database was used to analyze the MCM10 co-expression network and explore GO term annotation and the KEGG pathway. The relationship between MCM10 expression and immune infiltration in OV was investigated using the Tumor Immunology Estimation Resource database. cBioPortal database was used to explore the relationship between MCM10 expression and 25 immune checkpoints. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) was performed to detect MCM10 expression. The prognosis was also analyzed by distinguishing between high and low expression groups based on median expression values. Results: The results of the three data sets (220,651_s_at, 222,962_s_at and 223,570_at) in KM Plotter all indicated that the overall survivalof the high MCM10 expression group was lower than that of the low expression group OV, and the results of GSE9891 also reached the same conclusion. The expression level of MCM10 was negatively correlated with B cells and CD8+T cells, and positively correlated with CD4+T Cells and Macrophages. GO term annotation and KEGG pathway analysis showed that the co-expressed genes of MCM10 were mainly enriched in cell cycle and DNA replication. The alterations in MCM10 coexisted statistically with the immune checkpoints CTLA4, TNFSF4, TNFSF18, CD80, ICOSLG, LILRB1 and CD200. PCR results displayed that MCM10 was highly expressed in OV tissues, and the increased expression of MCM10 was significantly associated with poor overall survival. Conclusion: These results demonstrated that high expression of MCM10 was associated with poor prognosis in OV and correlated with immune checkpoints.
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Affiliation(s)
- Zhenzhen Wu
- Department of Gynecology, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Yueyuan Wang
- Department of Pathology, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Juan Li
- Department of Gynecology, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Huiling Wang
- Department of Gynecological Oncology, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Xunyuan Tuo
- Department of Gynecological Oncology, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Jing Zheng
- Department of Gynecology, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
- *Correspondence: Jing Zheng,
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13
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Saito Y, Santosa V, Ishiguro KI, Kanemaki MT. MCMBP promotes the assembly of the MCM2-7 hetero-hexamer to ensure robust DNA replication in human cells. eLife 2022; 11:77393. [PMID: 35438632 PMCID: PMC9018068 DOI: 10.7554/elife.77393] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/08/2022] [Indexed: 12/26/2022] Open
Abstract
The MCM2–7 hetero-hexamer is the replicative DNA helicase that plays a central role in eukaryotic DNA replication. In proliferating cells, the expression level of the MCM2–7 hexamer is kept high, which safeguards the integrity of the genome. However, how the MCM2–7 hexamer is assembled in living cells remains unknown. Here, we revealed that the MCM-binding protein (MCMBP) plays a critical role in the assembly of this hexamer in human cells. MCMBP associates with MCM3 which is essential for maintaining the level of the MCM2–7 hexamer. Acute depletion of MCMBP demonstrated that it contributes to MCM2–7 assembly using nascent MCM3. Cells depleted of MCMBP gradually ceased to proliferate because of reduced replication licensing. Under this condition, p53-positive cells exhibited arrest in the G1 phase, whereas p53-null cells entered the S phase and lost their viability because of the accumulation of DNA damage, suggesting that MCMBP is a potential target for killing p53-deficient cancers.
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Affiliation(s)
- Yuichiro Saito
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Japan
| | - Venny Santosa
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Japan
| | - Kei-Ichiro Ishiguro
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Japan.,Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
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14
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Etemad-Moghadam S, Ghaseminejad-Bandpey A, Mahmoodzadeh H, Alaeddini M. Clinicopathologic significance of DNA replication licensing factors in head and neck diffuse large B-cell lymphoma. Oral Surg Oral Med Oral Pathol Oral Radiol 2022; 133:462-469. [PMID: 35153182 DOI: 10.1016/j.oooo.2021.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/13/2021] [Accepted: 10/22/2021] [Indexed: 10/19/2022]
Abstract
OBJECTIVE Diffuse large B-cell lymphoma (DLBCL) harbors defects in the proliferation pathway. We performed multiparameter analysis of proteins expressed during different cell cycle phases and correlated them with clinical parameters of head and neck DLBCLs. STUDY DESIGN Thirty-nine DLBCLs were staged and immunohistochemically stained with MCM2, Ki67, and geminin. The receiver operating characteristic curve and its area under the curve were calculated, and sensitivity vs specificity curve analysis was performed. RESULTS The highest labeling index was in MCM2, followed by Ki67 and geminin (P < .001). All pairs showed significant differences (P < .001). The best cutoff points to differentiate limited from advanced disease were 68% and 45% for MCM2 and Ki67, respectively. There was no acceptable cutoff for geminin (area under the curve = 0.667, P = .134). MCM2/Ki67 (P = .293) and geminin/Ki67 (P = .233) ratios did not differ between the stages. The median (interquartile range) of the geminin/Ki67 ratio was 0.57 (0.68), translating to a reduced G1. CONCLUSIONS We suggest a role for cell cycle-related proteins in the biology and behavior of DLBCLs. MCM2 and Ki67 cutoffs can be a potential option to differentiate limited from advanced disease, where imaging and laboratory techniques are unavailable. The G1 decrease and the significantly higher MCM2 expression compared to Ki67 indicate replication disturbances, making factors involved in the G1 phase targets for treatment.
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Affiliation(s)
| | | | - Habibollah Mahmoodzadeh
- Division of Surgical Oncology, Department of Surgery, Cancer Institute, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mojgan Alaeddini
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences.
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15
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Almadori G, Coli A, De Corso E, Mele DA, Settimi S, Di Cintio G, Brigato F, Scannone D, Carey TE, Paludetti G, Lauriola L, Ranelletti FO. Nuclear HER3 expression improves the prognostic stratification of patients with HER1 positive advanced laryngeal squamous cell carcinoma. J Transl Med 2021; 19:408. [PMID: 34579737 PMCID: PMC8477517 DOI: 10.1186/s12967-021-03081-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/14/2021] [Indexed: 11/24/2022] Open
Abstract
Background Compared to the other members of human epidermal growth factor family receptors (HER), the role of HER3 has not been well defined in laryngeal cancer. The predictive and prognostic role of HER3 has been the focus of clinical attention but the research findings are contradictory, especially in laryngeal squamous cell carcinoma (LSCC). The variable localization of HER3 within cancer cells and the role of HER3 in primary and acquired resistance to HER1-targeted therapies remain unclear. Methods We performed a retrospective analysis of two cohorts of 66 homogeneous consecutive untreated primary advanced LSCC patients, in which co-expression of HER1, HER2 and HER3 receptors was investigated by semi-quantitative immunohistochemistry. The association of their pattern of expression with survival was evaluated by Kaplan–Meier and Cox’s proportional hazard analyses. Multivariable Cox proportional hazards models were developed to predict median 2- and 3-year RFS and 2.5- and 5-year OS. The Akaike information criterion technique and backwards stepwise procedure were used for model selections. The performance of the final Cox models was assessed with respect to calibration and discrimination. Results Immunohistochemical labeling for HER1 and HER2 was localized both in the cell membrane and in the cytoplasm, while HER3 labeling was observed both in the cell cytoplasm and in the nucleus. HER3 expression was inversely correlated with HER1 positivity. The expression patterns of HERs were associated with tumor differentiation. In both cohorts of patients, HER1 expression was associated with reduced relapse-free (RFS) and overall survival (OS). In HER1 positive tumors, the co-expression with nuclear HER3 was associated with better RFS and OS, compared with HER3 negative tumors or tumors expressing HER3 at cytoplasmic level. HER3 expressing tumors had a higher Geminin/MCM7 ratio than HER3 negative ones, regardless of HER1 co-expression. Multivariable analyses identified age at diagnosis, tumor site, HER1, HER3 and age at diagnosis, tumor stage, HER1, HER3, as covariates significantly associated with RFS and OS, respectively. Bootstrapping verified the good fitness of these models for predicting survivals and the optimism-corrected C-indices were 0.76 and 0.77 for RFS and OS, respectively. Conclusions Nuclear HER3 expression was strongly associated with favourable prognosis and allows to improve the prognostic stratification of patients with HER1 positive advanced LSCC carcinoma. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-03081-0.
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Affiliation(s)
- Giovanni Almadori
- Unit of Head and Neck Oncology, "A. Gemelli" University Hospital Foundation IRCCS-Catholic University of the Sacred Heart, Largo A. Gemelli 8, 00168, Rome, Italy. .,Unit of Otorhinolaryngology, "A. Gemelli" University Hospital Foundation IRCCS, Roma, Italy. .,Università Cattolica del Sacro Cuore, Roma, Italy.
| | - Antonella Coli
- Università Cattolica del Sacro Cuore, Roma, Italy.,Unit of Anatomic Pathology, "A. Gemelli" University Hospital Foundation IRCCS, Roma, Italy
| | - Eugenio De Corso
- Unit of Otorhinolaryngology, "A. Gemelli" University Hospital Foundation IRCCS, Roma, Italy
| | - Dario Antonio Mele
- Unit of Otorhinolaryngology, "A. Gemelli" University Hospital Foundation IRCCS, Roma, Italy
| | - Stefano Settimi
- Unit of Otorhinolaryngology, "A. Gemelli" University Hospital Foundation IRCCS, Roma, Italy
| | - Giovanni Di Cintio
- Unit of Otorhinolaryngology, "A. Gemelli" University Hospital Foundation IRCCS, Roma, Italy
| | - Francesca Brigato
- Unit of Otorhinolaryngology, "A. Gemelli" University Hospital Foundation IRCCS, Roma, Italy
| | - Domenico Scannone
- Unit of Anatomic Pathology, "A. Gemelli" University Hospital Foundation IRCCS, Roma, Italy
| | - Thomas E Carey
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Gaetano Paludetti
- Unit of Otorhinolaryngology, "A. Gemelli" University Hospital Foundation IRCCS, Roma, Italy.,Università Cattolica del Sacro Cuore, Roma, Italy
| | - Libero Lauriola
- Università Cattolica del Sacro Cuore, Roma, Italy.,Unit of Anatomic Pathology, "A. Gemelli" University Hospital Foundation IRCCS, Roma, Italy
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16
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Vergès-Castillo A, González-Vargas IA, Muñoz-Cueto JA, Martín-Robles ÁJ, Pendon C. Establishment and characterisation of single cell-derived embryonic stem cell lines from the gilthead seabream, Sparus aurata. Comp Biochem Physiol B Biochem Mol Biol 2021; 256:110626. [PMID: 34044158 DOI: 10.1016/j.cbpb.2021.110626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 04/16/2021] [Accepted: 05/21/2021] [Indexed: 12/27/2022]
Abstract
An important bottleneck in fish aquaculture research is the supply and maintenance of embryos, larvae, juvenile and adult specimens. In this context, cell lines represent alternative experimental models for in vitro studies that complement in vivo assays. This allows us to perform easier experimental design and sampling and avoid the sacrifice of animals. Embryonic stem (ES) cell lines have attracted increasing attention because they have the capability to proliferate indefinitely and could be differentiated into any cell type of the organism. To minimise cell heterogeneity and increase uniformity of in vitro studies results, in this manuscript we report the development and characterisation of two single cell-derived ES cell lines (monoclonal) from the morula stage embryos of the gilthead seabream, Sparus aurata, named as SAEC-A3 and SAEC-H7. Both cell lines have been passaged for over 100 times, indicating the establishment of long-term, immortalised ES cell cultures. Sequence analyses confirmed the seabream origin of the cell lines, and growth analyses evidenced their high viability and proliferating activity, particularly in culture medium supplemented with 10-15% fetal bovine serum and 22 °C. Both cell lines showed the ability to generate embryoid bodies and show different sensitivity and response to all-trans retinoic acid. The analysis of epithelial (col1α1) and neuronal (sox3) markers in differentiated cultures revealed that SAEC-A3 tended to differentiate towards epithelial-like cells whereas SAEC-H7 tended to differentiate towards neuronal-like cells. Both cell lines were efficiently transfected with pDsRed2-ER and/or pEGFP-N1 plasmids, indicating that they could represent useful biotechnological tools. Daily expression of pcna showed significant expression rhythms, with maximum levels of cell proliferation during the day-night transition. Currently, these cell lines are being successfully used as experimental models for the study of cellular metabolism, physiology and rhythms as well as for toxicological, pharmacological and gene expression analyses.
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Affiliation(s)
- A Vergès-Castillo
- Department of Biology, Faculty of Marine and Environmental Sciences, University of Cádiz, Puerto Real, Cádiz, Spain.
| | - I A González-Vargas
- Bioquímica y Biología Molecular, Departamento de Biomedicina, Biotecnología y Salud Pública, Universidad de Cádiz, Puerto Real, Cádiz, Spain; Departamento de Ciencias Naturales, Exactas y Estadística, Facultad de Ciencias, Universidad de Santiago de Cali, Cali, Colombia
| | - J A Muñoz-Cueto
- Department of Biology, Faculty of Marine and Environmental Sciences, University of Cádiz, Puerto Real, Cádiz, Spain; INMAR Research Institute, Marine Campus of International Excellence (CEIMAR), Agrifood Campus of International Excellence (ceiA3), The European University of the Seas (SEA-EU), University of Cádiz, Puerto Real, Cádiz, Spain.
| | - Á J Martín-Robles
- Bioquímica y Biología Molecular, Departamento de Biomedicina, Biotecnología y Salud Pública, Universidad de Cádiz, Puerto Real, Cádiz, Spain; INMAR Research Institute, Marine Campus of International Excellence (CEIMAR), Agrifood Campus of International Excellence (ceiA3), The European University of the Seas (SEA-EU), University of Cádiz, Puerto Real, Cádiz, Spain.
| | - C Pendon
- Bioquímica y Biología Molecular, Departamento de Biomedicina, Biotecnología y Salud Pública, Universidad de Cádiz, Puerto Real, Cádiz, Spain; INBIO, Facultad de Ciencias, Universidad de Cádiz, Puerto Real, Cádiz, Spain.
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17
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Prospect of reprogramming replication licensing for cancer drug development. Biomed Pharmacother 2021; 136:111190. [PMID: 33497909 DOI: 10.1016/j.biopha.2020.111190] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/15/2020] [Accepted: 12/26/2020] [Indexed: 12/15/2022] Open
Abstract
Eukaryotic chromosomal DNA replication is preceded by replication licensing which involves the identification of the origin of replication by origin recognition complex (ORC). The ORC loads pre-replication complexes (pre-RCs) through a series of tightly regulated mechanisms where the ORC interacts with Cdc6 to recruit cdt1-MCM2-7 complexes to the origin of replication. In eukaryotes, adherence to regulatory mechanisms of the replication program is required to ensure that all daughter cells carry the exact copy of genetic material as the parent cell. Failure of which leads to the development of genome instability syndromes like cancer, diabetes, etc. In an event of such occurrence, preventing cells from carrying the defaulted genetic material and passing it to other cells hinges on the regulation of chromosomal DNA replication. Thus, understanding the mechanisms underpinning chromosomal DNA replication and particularly replication licensing can expose druggable enzymes, effector molecules, and secondary messengers that can be targeted for diagnosis and therapeutic purposes. Effectively drugging these molecular markers to reprogram pre-replication events can be used to control the fate of chromosomal DNA replication for the treatment of genome instability disorders and in this case, cancer. This review discusses available knowledge of replication licensing in the contest of molecular drug discovery for the treatment of cancer.
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18
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Chang HR, Jung E, Cho S, Jeon YJ, Kim Y. Targeting Non-Oncogene Addiction for Cancer Therapy. Biomolecules 2021; 11:129. [PMID: 33498235 PMCID: PMC7909239 DOI: 10.3390/biom11020129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 12/12/2022] Open
Abstract
While Next-Generation Sequencing (NGS) and technological advances have been useful in identifying genetic profiles of tumorigenesis, novel target proteins and various clinical biomarkers, cancer continues to be a major global health threat. DNA replication, DNA damage response (DDR) and repair, and cell cycle regulation continue to be essential systems in targeted cancer therapies. Although many genes involved in DDR are known to be tumor suppressor genes, cancer cells are often dependent and addicted to these genes, making them excellent therapeutic targets. In this review, genes implicated in DNA replication, DDR, DNA repair, cell cycle regulation are discussed with reference to peptide or small molecule inhibitors which may prove therapeutic in cancer patients. Additionally, the potential of utilizing novel synthetic lethal genes in these pathways is examined, providing possible new targets for future therapeutics. Specifically, we evaluate the potential of TONSL as a novel gene for targeted therapy. Although it is a scaffold protein with no known enzymatic activity, the strategy used for developing PCNA inhibitors can also be utilized to target TONSL. This review summarizes current knowledge on non-oncogene addiction, and the utilization of synthetic lethality for developing novel inhibitors targeting non-oncogenic addiction for cancer therapy.
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Affiliation(s)
- Hae Ryung Chang
- Department of Biological Sciences and Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Korea; (E.J.); (S.C.)
| | - Eunyoung Jung
- Department of Biological Sciences and Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Korea; (E.J.); (S.C.)
| | - Soobin Cho
- Department of Biological Sciences and Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Korea; (E.J.); (S.C.)
| | - Young-Jun Jeon
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea;
| | - Yonghwan Kim
- Department of Biological Sciences and Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Korea; (E.J.); (S.C.)
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Samad A, Haque F, Nain Z, Alam R, Al Noman MA, Rahman Molla MH, Hossen MS, Islam MR, Khan MI, Ahammad F. Computational assessment of MCM2 transcriptional expression and identification of the prognostic biomarker for human breast cancer. Heliyon 2020; 6:e05087. [PMID: 33024849 PMCID: PMC7530310 DOI: 10.1016/j.heliyon.2020.e05087] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/09/2020] [Accepted: 09/24/2020] [Indexed: 12/24/2022] Open
Abstract
Minichromosome maintenance protein 2 (MCM2) is a highly conserved protein from the MCM protein family that plays an important role in eukaryotic DNA replication as well as in cell cycle progression. In addition, it maintains the ploidy level consistency in eukaryotic cells, hence, mutations or alteration of this protein could result in the disintegration of the fine-tuned molecular machinery that can lead to uncontrolled cell proliferation. Moreover, MCM2 has been found to be an important marker for progression and prognosis in different cancers. Therefore, we aimed to analyze the MCM2 expression and the associated outcome in breast cancer (BC) patients based on the publicly available online databases. In this study, server-based gene expression analyses indicate the upregulation of MCM2 (p < 10-6; fold change>2.0) in various BC subtypes as compared to the respective normal tissues. Besides, the evaluation of histological sections from healthy and cancer tissues showed strong staining signals indicating higher expression of MCM2 protein. The overexpression of MCM2 was significantly correlated to promoter methylation and was related to patients' clinical features. Further, mutation analysis suggested missense as the predominant type of mutation (71.4%) with 18 copy-number alterations and 0.2% mutation frequency in the MCM2 gene. This study revealed a significant correlation (Cox p ≤ 0.05) between the higher MCM2 expression and lower patient survival. Finally, we identified the co-expressed genes with gene ontological features and signaling pathways associated in BC development. We believe that this study will provide a basis for MCM2 to be a significant biomarker for human BC prognosis.
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Affiliation(s)
- Abdus Samad
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Farhana Haque
- Department of Biotechnology and Genetic Engineering, Khulna University, Khulna, 9208, Bangladesh
| | - Zulkar Nain
- Department of Genetic Engineering and Biotechnology, Faculty of Sciences and Engineering, East West University, Dhaka, 1212, Bangladesh.,Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, 7003, Bangladesh
| | - Rahat Alam
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.,Molecular and Cellular Biology Laboratory, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Abdullah Al Noman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.,Molecular and Cellular Biology Laboratory, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Mohammad Habibur Rahman Molla
- Institute of Marine Sciences and Fisheries, University of Chittagong, Chittagong, 4331, Bangladesh.,Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Md Saddam Hossen
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Raquibul Islam
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Iqbal Khan
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.,Department of Biotechnology and Genetic Engineering, Khulna University, Khulna, 9208, Bangladesh
| | - Foysal Ahammad
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.,Molecular and Cellular Biology Laboratory, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.,Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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Radiogenomic signatures reveal multiscale intratumour heterogeneity associated with biological functions and survival in breast cancer. Nat Commun 2020; 11:4861. [PMID: 32978398 PMCID: PMC7519071 DOI: 10.1038/s41467-020-18703-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 09/08/2020] [Indexed: 12/24/2022] Open
Abstract
Advanced tumours are often heterogeneous, consisting of subclones with various genetic alterations and functional roles. The precise molecular features that characterize the contributions of multiscale intratumour heterogeneity to malignant progression, metastasis, and poor survival are largely unknown. Here, we address these challenges in breast cancer by defining the landscape of heterogeneous tumour subclones and their biological functions using radiogenomic signatures. Molecular heterogeneity is identified by a fully unsupervised deconvolution of gene expression data. Relative prevalence of two subclones associated with cell cycle and primary immunodeficiency pathways identifies patients with significantly different survival outcomes. Radiogenomic signatures of imaging scale heterogeneity are extracted and used to classify patients into groups with distinct subclone compositions. Prognostic value is confirmed by survival analysis accounting for clinical variables. These findings provide insight into how a radiogenomic analysis can identify the biological activities of specific subclones that predict prognosis in a noninvasive and clinically relevant manner. Tumours are made up of heterogeneous subclones. Here, the authors show using breast cancer imaging and gene expression datasets that these subclones can be inferred by the deconvolution of gene expression data, mapped to MRI derived radiogenomic signatures and used to estimate prognosis.
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21
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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: 44] [Impact Index Per Article: 11.0] [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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22
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Maros ME, Schnaidt S, Balla P, Kelemen Z, Sapi Z, Szendroi M, Laszlo T, Forsyth R, Picci P, Krenacs T. In situ cell cycle analysis in giant cell tumor of bone reveals patients with elevated risk of reduced progression-free survival. Bone 2019; 127:188-198. [PMID: 31233932 DOI: 10.1016/j.bone.2019.06.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 05/23/2019] [Accepted: 06/21/2019] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Giant cell tumor of bone (GCTB) is a frequently recurring locally aggressive osteolytic lesion, where pathological osteoclastogenesis and bone destruction are driven by neoplastic stromal cells. Here, we studied if cell cycle fractions within the mononuclear cell compartment of GCTB can predict its progression-free survival (PFS). METHODS 154 cases (100 primaries and 54 recurrent) from 139 patients of 40 progression events, was studied using tissue microarrays. Ploidy and in situ cell cycle progression related proteins including Ki67 and those linked with replication licensing (mcm2), G1-phase (cyclin D1, Cdk4), and S-G2-M-phase (cyclin A; Cdk2) fractions; cell cycle control (p21waf1) and repression (geminin), were tested. The Prentice-Williams-Peterson (PWP) gap-time models with the Akaike information criterion (AIC) were used for PFS analysis. RESULTS Cluster analysis showed good correlation between functionally related marker positive cell fractions indicating no major cell cycle arrested cell populations in GCTB. Increasing hazard of progression was statistically associated with the elevated post-G1/S-phase cell fractions. Univariate analysis revealed significant negative association of poly-/aneuploidy (p < 0.0001), and elevated cyclin A (p < 0.001), geminin (p = 0.015), mcm2 (p = 0.016), cyclin D1 (p = 0.022) and Ki67 (B56: p = 0.0543; and Mib1: p = 0.0564 -strong trend) positive cell fractions with PFS. The highest-ranked multivariate interaction model (AIC = 269.5) also included ploidy (HR 5.68, 95%CI: 2.62-12.31, p < 0.0001), mcm2 (p = 0.609), cyclin D1 (HR 1.89, 95%CI: 0.88-4.09, p = 0.105) and cyclin A (p < 0.0001). The first and second best prognostic models without interaction (AIC = 271.6) and the sensitivity analysis (AIC = 265.7) further confirmed the prognostic relevance of combining these markers. CONCLUSION Ploidy and elevated replication licensing (mcm2), G1-phase (cyclin D1) and post-G1 phase (cyclin A) marker positive cell fractions, indicating enhanced cell cycle progression, can assist in identifying GCTB patients with increased risk for a reduced PFS.
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Affiliation(s)
- Mate E Maros
- 1(st) Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary; Department of Neuroradiology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Sven Schnaidt
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Peter Balla
- 1(st) Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Zoltan Kelemen
- 1(st) Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Zoltan Sapi
- 1(st) Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Miklos Szendroi
- Department of Orthopedics, Semmelweis University, Budapest, Hungary
| | - Tamas Laszlo
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Semmelweis University, Budapest, Hungary
| | - Ramses Forsyth
- Department of Anatomic Pathology, University of Brussels, Belgium
| | - Piero Picci
- Laboratory of Experimental Oncology, Institute of Orthopedics Rizzoli, Bologna, Italy
| | - Tibor Krenacs
- 1(st) Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary.
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23
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Li S, Jiang Z, Li Y, Xu Y. Prognostic significance of minichromosome maintenance mRNA expression in human lung adenocarcinoma. Oncol Rep 2019; 42:2279-2292. [PMID: 31545501 PMCID: PMC6826304 DOI: 10.3892/or.2019.7330] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 08/09/2019] [Indexed: 12/21/2022] Open
Abstract
The minichromosome maintenance (MCM) gene family plays an essential role in DNA replication and cell cycle progression. However, MCM gene expression has not been well-studied in lung adenocarcinoma (LUAD). In the present study, the expression, prognostic value and functions of MCMs in LUAD were investigated using several databases and bioinformatic tools, including Oncomine, GEPIA, cBioPortal, CancerSEA and Kaplan-Meier plotter. It was demonstrated that the mRNA expression of MCM2, MCM4 and MCM10 were significantly increased in patients with LUAD. High mRNA expression of MCM2-5, MCM8 and MCM10 were associated with poor overall survival and progression-free survival. High MCM4 expression was associated with adverse post-progression survival. In addition, the Human Protein Atlas database showed that MCM protein expression was consistent with the mRNA expression. These results demonstrate that MCM2, MCM4 and MCM10 are potential prognostic markers and therapeutic targets for LUAD.
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Affiliation(s)
- Shu Li
- Department of Hematology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Zhou Jiang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Yirun Li
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, P.R. China
| | - Yang Xu
- Department of Hematology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
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24
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Malvia S, Bagadi SAR, Pradhan D, Chintamani C, Bhatnagar A, Arora D, Sarin R, Saxena S. Study of Gene Expression Profiles of Breast Cancers in Indian Women. Sci Rep 2019; 9:10018. [PMID: 31292488 PMCID: PMC6620270 DOI: 10.1038/s41598-019-46261-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 06/25/2019] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is the most common cancer among women globally. In India, the incidence of breast cancer has increased significantly during the last two decades with a higher proportion of the disease at a young age compared to the west. To understand the molecular processes underlying breast cancer in Indian women, we analysed gene expression profiles of 29 tumours and 9 controls using microarray. In the present study, we obtained 2413 differentially expressed genes, consisting of overexpressed genes such as COL10A1, COL11A1, MMP1, MMP13, MMP11, GJB2, and CST1 and underexpressed genes such as PLIN1, FABP4, LIPE, AQP7, LEP, ADH1A, ADH1B, and CIDEC. The deregulated pathways include cell cycle, focal adhesion and metastasis, DNA replication, PPAR signaling, and lipid metabolism. Using PAM50 classifier, we demonstrated the existence of molecular subtypes in Indian women. In addition, qPCR validation of expression of metalloproteinase genes, MMP1, MMP3, MMP11, MMP13, MMP14, ADAMTS1, and ADAMTS5 showed concordance with that of the microarray data; wherein we found a significant association of ADAMTS5 down-regulation with older age (≥55 years) of patients. Together, this study reports gene expression profiles of breast tumours from the Indian subcontinent, throwing light on the pathways and genes associated with the breast tumourigenesis in Indian women.
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Affiliation(s)
- Shreshtha Malvia
- Tumour Biology Division, ICMR-National Institute of Pathology, New Delhi, 110029, India
| | | | - Dibyabhaba Pradhan
- Bioinformatics Cell, ICMR-National Institute of Pathology, New Delhi, 110029, India
| | | | - Amar Bhatnagar
- Department of Cancer Surgery, Safdarjung Hospital, New Delhi, 110029, India
| | - Deepshikha Arora
- Department of Pathology, Indraprastha Apollo Hospital, New Delhi, 110076, India
| | - Ramesh Sarin
- Department of Surgery, Indraprastha Apollo Hospital, New Delhi, 110076, India
| | - Sunita Saxena
- Tumour Biology Division, ICMR-National Institute of Pathology, New Delhi, 110029, India.
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25
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Yu Q, Pu SY, Wu H, Chen XQ, Jiang JJ, Gu KS, He YH, Kong QP. TICRR Contributes to Tumorigenesis Through Accelerating DNA Replication in Cancers. Front Oncol 2019; 9:516. [PMID: 31275851 PMCID: PMC6591320 DOI: 10.3389/fonc.2019.00516] [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] [Received: 11/03/2018] [Accepted: 05/29/2019] [Indexed: 12/31/2022] Open
Abstract
DNA replication is precisely regulated in cells and its dysregulation can trigger tumorigenesis. Here we identified that the TOPBP1 interacting checkpoint and replication regulator (TICRR) mRNA level was universally and highly expressed in 15 solid cancer types. Depletion of TICRR significantly inhibited tumor cell growth, colony formation and migration in vitro, and strikingly inhibited tumor growth in the xenograft model. We reveal that knockdown of TICRR inhibited not only the initiation but also the fork progression of DNA replication. Suppression of DNA synthesis by TICRR silencing caused DNA damage accumulation, subsequently activated the ATM/CHK2 dependent p53 signaling, and finally induced cell cycle arrest and apoptosis at least in p53-wild cancer cells. Further, we show that a higher TICRR level was associated with poorer overall survival (OS) and disease free survival (DFS) in multiple cancer types. In conclusion, our study shows that TICRR is involved in tumorigenesis by regulating DNA replication, acting as a common biomarker for cancer prognosis and could be a promising target for drug-development and cancer treatment.
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Affiliation(s)
- Qin Yu
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Shao-Yan Pu
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
| | - Huan Wu
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
| | - Xiao-Qiong Chen
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
| | - Jian-Jun Jiang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
| | - Kang-Shuyun Gu
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yong-Han He
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
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26
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Xia WX, Yu Q, Li GH, Liu YW, Xiao FH, Yang LQ, Rahman ZU, Wang HT, Kong QP. Identification of four hub genes associated with adrenocortical carcinoma progression by WGCNA. PeerJ 2019; 7:e6555. [PMID: 30886771 PMCID: PMC6421058 DOI: 10.7717/peerj.6555] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 02/02/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Adrenocortical carcinoma (ACC) is a rare and aggressive malignant cancer in the adrenal cortex with poor prognosis. Though previous research has attempted to elucidate the progression of ACC, its molecular mechanism remains poorly understood. METHODS Gene transcripts per million (TPM) data were downloaded from the UCSC Xena database, which included ACC (The Cancer Genome Atlas, n = 77) and normal samples (Genotype Tissue Expression, n = 128). We used weighted gene co-expression network analysis to identify gene connections. Overall survival (OS) was determined using the univariate Cox model. A protein-protein interaction (PPI) network was constructed by the search tool for the retrieval of interacting genes. RESULTS To determine the critical genes involved in ACC progression, we obtained 2,953 significantly differentially expressed genes and nine modules. Among them, the blue module demonstrated significant correlation with the "Stage" of ACC. Enrichment analysis revealed that genes in the blue module were mainly enriched in cell division, cell cycle, and DNA replication. Combined with the PPI and co-expression networks, we identified four hub genes (i.e., TOP2A, TTK, CHEK1, and CENPA) that were highly expressed in ACC and negatively correlated with OS. Thus, these identified genes may play important roles in the progression of ACC and serve as potential biomarkers for future diagnosis.
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Affiliation(s)
- Wang-Xiao Xia
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Qin Yu
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Gong-Hua Li
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
| | - Yao-Wen Liu
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
| | - Fu-Hui Xiao
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
| | - Li-Qin Yang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
| | - Zia Ur Rahman
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Hao-Tian Wang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming, China
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27
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Fluoro-Chromogenic Labelling for Detection of MCM2 to Assess Proliferation Activity in HER2-amplified Breast Carcinomas. Appl Immunohistochem Mol Morphol 2018; 28:175-186. [PMID: 30358612 DOI: 10.1097/pai.0000000000000716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Minichromosome Maintenance Protein 2 (MCM2) is critical in initiating DNA replication during the cell division process. As expressed intensively in all phases of the active cell cycle, MCM2 has been proposed as a novel biomarker to determine cellular proliferation. We aimed at clarifying the prevalence and clinical significance of MCM2 in HER2-amplified breast cancer subtype. MCM2 expression was studied in 142 primary HER2-amplified breast carcinomas by applying a novel fluoro-chromogenic immunohistochemistry and tailored digital image analysis to determine labelling index (MCM2-LI). The presence of MCM2 was detected with HRP-conjugated polymer and visualized with 3, 3'-diaminobenzidine tetrahydrochloride, in cytokeratin (CK)-positive and Cy2-IgG-labelled breast cancer cells of epithelial origin. Stained slides were digitized by scanning sequentially under bright field (for MCM2) and fluorescence (for CK) illumination. Multilayer JPEG2000 images were analyzed with ImmunoRatio 2.5 (accessory in SlideVantage 1.2 software) utilizing its bright field and fluorescence image-blending mode to display MCM2-CK dual-positive cells. MCM2-LI was retrospectively compared with histopathologic characteristics and patients' clinical outcome. MCM2 protein-expressing cells (median MCM2-LI, 63.5%) were more frequent than those of Ki67 (median Ki67 labelling index, 33%). Significant correlations were found between high MCM2-LI, high Ki67 labelling index, negative hormone receptor (ER, PR) statuses, high grade of malignancy, and high cyclin E expression. MCM2-LI was not shown to be predictive of disease recurrence during the median follow-up of 5.3 years but was shown to be useful to distinguish aggressive-type HER2-amplified breast carcinomas with high malignancy grade and hormone receptor negativity. The fluoro-chromogenic double-labelling immunohistochemistry accompanied with digital image analysis provides an accurate carcinoma-specific determination of MCM2-LI on a single tumor section.
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28
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Hernández-Carralero E, Cabrera E, Alonso-de Vega I, Hernández-Pérez S, Smits VAJ, Freire R. Control of DNA Replication Initiation by Ubiquitin. Cells 2018; 7:E146. [PMID: 30241373 PMCID: PMC6211026 DOI: 10.3390/cells7100146] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 09/18/2018] [Accepted: 09/19/2018] [Indexed: 01/07/2023] Open
Abstract
Eukaryotic cells divide by accomplishing a program of events in which the replication of the genome is a fundamental part. To ensure all cells have an accurate copy of the genome, DNA replication occurs only once per cell cycle and is controlled by numerous pathways. A key step in this process is the initiation of DNA replication in which certain regions of DNA are marked as competent to replicate. Moreover, initiation of DNA replication needs to be coordinated with other cell cycle processes. At the molecular level, initiation of DNA replication relies, among other mechanisms, upon post-translational modifications, including the conjugation and hydrolysis of ubiquitin. An example is the precise control of the levels of the DNA replication initiation protein Cdt1 and its inhibitor Geminin by ubiquitin-mediated proteasomal degradation. This control ensures that DNA replication occurs with the right timing during the cell cycle, thereby avoiding re-replication events. Here, we review the events that involve ubiquitin signalling during DNA replication initiation, and how they are linked to human disease.
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Affiliation(s)
- Esperanza Hernández-Carralero
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Ofra s/n, 38320 La Laguna, Tenerife, Spain.
| | - Elisa Cabrera
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Ofra s/n, 38320 La Laguna, Tenerife, Spain.
| | - Ignacio Alonso-de Vega
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Ofra s/n, 38320 La Laguna, Tenerife, Spain.
| | - Santiago Hernández-Pérez
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Ofra s/n, 38320 La Laguna, Tenerife, Spain.
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
| | - Veronique A J Smits
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Ofra s/n, 38320 La Laguna, Tenerife, Spain.
| | - Raimundo Freire
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Ofra s/n, 38320 La Laguna, Tenerife, Spain.
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Tang X, Xu Y, Lu L, Jiao Y, Liu J, Wang L, Zhao H. Identification of key candidate genes and small molecule drugs in cervical cancer by bioinformatics strategy. Cancer Manag Res 2018; 10:3533-3549. [PMID: 30271202 PMCID: PMC6145638 DOI: 10.2147/cmar.s171661] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Purpose Cervical cancer (CC) is one of the most common malignant tumors among women. The present study aimed at integrating two expression profile datasets to identify critical genes and potential drugs in CC. Materials and methods Expression profiles, GSE7803 and GSE9750, were integrated using bioinformatics methods, including differentially expressed genes analysis, Kyoto Encyclopedia of Genes and Genomes pathway analysis, and protein–protein interaction (PPI) network construction. Subsequently, survival analysis was performed among the key genes using Gene Expression Profiling Interactive Analysis websites. Connectivity Map (CMap) was used to query potential drugs for CC. Results A total of 145 upregulated genes and 135 downregulated genes in CC were identified. The functional changes of these differentially expressed genes related to CC were mainly associated with cell cycle, DNA replication, p53 signaling pathway, and oocyte meiosis. A PPI network was identified by STRING with 220 nodes and 2,111 edges. Thirteen key genes were identified as the intersecting genes of the enrichment pathways and the top 20 nodes in PPI network. Survival analysis revealed that high mRNA expression of MCM2, PCNA, and RFC4 was significantly associated with longer overall survival, and the survival was significantly better in the low-expression RRM2 group. Moreover, CMap predicted nine small molecules as possible adjuvant drugs to treat CC. Conclusion Our study found key dysregulated genes involved in CC and potential drugs to combat it, which might provide insights into CC pathogenesis and might shed light on potential CC treatments.
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Affiliation(s)
- Xin Tang
- School of Rehabilitation, Kunming Medical University, Kunming, China
| | - Yicong Xu
- Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, China, .,Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Kunming, China,
| | - Lin Lu
- Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, China, .,Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Kunming, China,
| | - Yang Jiao
- Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, China, .,Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Kunming, China,
| | - Jianjun Liu
- Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, China, .,Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Kunming, China,
| | - Linlin Wang
- Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, China, .,Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Kunming, China,
| | - Hongbo Zhao
- Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, China, .,Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Kunming, China,
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Xu X, Huang L, Chan CH, Yu T, Miao R, Liu C. Assessing the clinical utility of genomic expression data across human cancers. Oncotarget 2018; 7:45926-45936. [PMID: 27322207 PMCID: PMC5216771 DOI: 10.18632/oncotarget.10002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/29/2016] [Indexed: 01/27/2023] Open
Abstract
Cancer molecular profiling provides better understanding of tumor mechanisms and helps to improve the existing cancer management. Here we present the gene expression signatures from ∼9000 human tumors with clinical information across 32 malignancies from The Cancer Genome Atlas project (TCGA). Major predictors from the RNA sequencing data that were significantly correlated with cancer survival were identified. The expression level of these prognostic genes revealed significant genomic pathways that were clinically relevant to survival outcomes across human cancers. Furthermore, it is shown that in most cancer types, combinations of these genomic signatures with clinical information might yield improved predictions. Thus, with respect to clinical utility, our study reveals the promising values of genomic data from the pan-cancer perspective.
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Affiliation(s)
- Xinsen Xu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Lei Huang
- 118 Lancaster Terrace, Brookline, MA, USA
| | - Chun Hei Chan
- Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | - Tao Yu
- Department of Neurosurgery, Peking University First Hospital, Beijing, China
| | - Runchen Miao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Chang Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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V S V, K R, V N S, Sara George P, K C, K J, S T, Sujathan K. DNA Replication Licensing Proteins for Early Detection of Lung Cancer. Asian Pac J Cancer Prev 2017; 18:3041-3047. [PMID: 29172277 PMCID: PMC5773789 DOI: 10.22034/apjcp.2017.18.11.3041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Background: To identify and characterize malignant and premalignant cells in sputum and matched tissue samples with reference to expression of minichromosome maintenance proteins (MCM2, MCM5) and cell division cycle protein 6 (CDC 6) and to assess their potential as biomarkers of premalignant and malignant lesions of the lung and associations with clinicopathological features. Methods: Expression of MCM2, MCM5 and 6 proteins in sputum samples and corresponding tissues was assessed by immunocytochemistry, and correlated with histological findings. Results: For characterization of malignant, metaplastic or dysplastic cells, CDC6 protein had the highest sensitivity of 87.7%. All the three markers together had a sensitivity of 94.4%. Furthermore these proteins could be employed to assess the proliferative potential of precancerous or atypical cells, as overexpression increasing with the stage of disease and degree of metastasis. Conclusion: The assessed markers can be utilized in routine cytopathology laboratories to supplement conventional morphological evaluation so that the sensitivity of sputum cytology can be enhanced. Potential applications in predicting the clinical behavior of lung lesions and predicting prognosis and survival deserve further attention.
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Affiliation(s)
- Veena V S
- Division of Pathology, Regional Cancer Centre, Medical College Campus, Thiruvananthapuram, India
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MCM2 expression in serrated polyps demonstrates aberrant cellular proliferation. Hum Pathol 2017; 63:177-183. [PMID: 28302537 DOI: 10.1016/j.humpath.2017.02.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/06/2017] [Accepted: 02/24/2017] [Indexed: 01/06/2023]
Abstract
In normal colonic epithelium, the proliferative zone is limited to the lower half of the colonic crypt. Evaluating the changes in the colonic epithelial proliferation can be useful in understanding pathophysiology of various diseases. Our aim was to investigate the proliferative compartment of serrated polyps (SPs) using MCM2, a protein involved in DNA replication, and assess for changes along the SP spectrum. Immunohistochemistry was performed on serrated polyps (16 microvesicular-type hyperplastic polyps (HP), 58 sessile serrated adenomas (SSA), 7 SSAs with dysplasia) and 6 sections of normal colon using anti-MCM2 antibody. Multiple sections of normal colon showed the following pattern for MCM2 and Ki-67 staining: positive nuclear staining of the lower half of the colonic crypts and/or slightly expanded to the lower two-thirds of the crypt. By MCM2, SPs show expansion of the proliferative compartments; 81.3% of HPs and 100% of SSAs showed some degree of full crypt MCM2 staining. SSAs with dysplasia showed consistent diffuse polyp staining. Aberrant staining in adjacent normal mucosa was also seen in SSAs with dysplasia and in a subset of non-dysplastic SSAs. By using MCM2, we show that serrated polyps exhibit changes in proliferation during progression along the pathway. HPs and SSAs show a similar highly proliferative profile. Aberrant proliferative cell staining patterns in adjacent normal colonic mucosa as seen in SSAs with dysplasia and a subset of SSAs suggest a field effect phenomenon. This indicates that changes in the colonic micro-environment may promote adenoma morphogenesis and predisposition to malignancy.
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Almadori G, Lauriola L, Coli A, Bussu F, Gallus R, Scannone D, Valentini V, Paludetti G, Carey TE, Ranelletti FO. Minichromosome maintenance protein 7 and geminin expression: Prognostic value in laryngeal squamous cell carcinoma in patients treated with radiotherapy and cetuximab. Head Neck 2016; 39:684-693. [PMID: 28032719 DOI: 10.1002/hed.24670] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 08/01/2016] [Accepted: 11/04/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Minichromosome maintenance protein 7 (MCM7) is a downstream of human epidermal growth receptor (HER1) signaling. We examined MCM7, geminin, and HER1 expression in patients with laryngeal squamous cell carcinoma (SCC) treated with radiotherapy and cetuximab. METHODS MCM7, geminin, and HER1 were evaluated by immunohistochemistry on 61 patients with laryngeal SCC. The follow-up (median, 32.1 months; range, 2-139 months) went from the beginning of therapy to tumor progression-free survival (PFS) and death (overall survival [OS]). RESULTS MCM7, but not geminin, was associated only with HER1 expression, whereas no association was found with other clinicopathological characteristics. Patients with MCM7 high - geminin high and MCM7 high - geminin low tumor status had a risk of progression 3.1 times and 17.7 times greater, respectively, than patients with MCM7 low - geminin high tumor status. Tumor site, MCM7, and geminin were independent determinants of PFS, whereas MCM7 was an independent prognostic marker of OS. CONCLUSION MCM7-geminin tumor status may be prognostic for patients with laryngeal SCC treated with cetuximab and radiotherapy. © 2016 Wiley Periodicals, Inc. Head Neck 39: 684-693, 2017.
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Affiliation(s)
- Giovanni Almadori
- Institute of Otolaryngology, Head and Neck Surgery, Catholic University of Sacred Heart, Rome, Italy
| | - Libero Lauriola
- Institute of Anatomic Pathology, Catholic University of Sacred Heart, Rome, Italy
| | - Antonella Coli
- Institute of Anatomic Pathology, Catholic University of Sacred Heart, Rome, Italy
| | - Francesco Bussu
- Institute of Otolaryngology, Head and Neck Surgery, Catholic University of Sacred Heart, Rome, Italy
| | - Roberto Gallus
- Institute of Otolaryngology, Head and Neck Surgery, Catholic University of Sacred Heart, Rome, Italy
| | - Domenico Scannone
- Institute of Anatomic Pathology, Catholic University of Sacred Heart, Rome, Italy
| | - Vincenzo Valentini
- Institute of Radiotherapy, Catholic University of Sacred Heart, Rome, Italy
| | - Gaetano Paludetti
- Institute of Otolaryngology, Head and Neck Surgery, Catholic University of Sacred Heart, Rome, Italy
| | - Thomas E Carey
- Laboratory of Head and Neck Center Biology, Department of Otolaryngology, Head and Neck Surgery, the University of Michigan, Ann Arbor, Michigan
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Ye Y, Xiao L, Wang SJ, Yue W, Yin QS, Sun MY, Xia W, Shao ZY, Zhang H. Up-regulation of REG3A in colorectal cancer cells confers proliferation and correlates with colorectal cancer risk. Oncotarget 2016; 7:3921-33. [PMID: 26646797 PMCID: PMC4826180 DOI: 10.18632/oncotarget.6473] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 11/25/2015] [Indexed: 12/31/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignancies in the world. Previous studies have investigated the altered expression of regenerating islet-derived 3 alpha (REG3A) in various cancers. We aimed at exploring the biological function and the underlying molecular mechanism of REG3A in CRC. In this study, REG3A was found elevated in CRC compared with normal tissues. Further, high REG3A expression level was correlated with bigger tumor size, poorer differentiation, higher tumor stage and lower survival rate. Knockdown of REG3A in two CRC cell lines, LOVO and RKO, significantly inhibited cell proliferation, and increased cells population in G1 phase and cell apoptotic rate. We also found that down-regulation of REG3A in CRC cells notably inhibited cell migration and invasion. Gene set enrichment analysis on The Cancer Genome Atlas dataset showed that Kyoto Encyclopedia of Genes and Genomes (KEGG) DNA replication and base excision repair (BER) pathways were correlative with the REG3A expression, which was further confirmed in CRC cells by Western blot. Moreover, we confirmed the interaction of REG3A and fibronectin in CRC cells. We also found that there was a positive correlation between REG3A expression level and the AKT and ERK1/2 phosphorylation status. These collective data indicated that REG3A overexpression promotes CRC tumorigenesis by activating AKT and ERK1/2 pathways. REG3A may serve as a promising therapeutic strategy for CRC.
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Affiliation(s)
- Ying Ye
- Central Laboratory, Shanghai Seventh People's Hospital, Shanghai, PR China
| | - Ling Xiao
- Central Laboratory, Shanghai Seventh People's Hospital, Shanghai, PR China
| | - Su-Juan Wang
- Central Laboratory, Shanghai Seventh People's Hospital, Shanghai, PR China
| | - Wei Yue
- Central Laboratory, Shanghai Seventh People's Hospital, Shanghai, PR China
| | - Qiao-Shan Yin
- Central Laboratory, Shanghai Seventh People's Hospital, Shanghai, PR China
| | - Meng-Yao Sun
- Central Laboratory, Shanghai Seventh People's Hospital, Shanghai, PR China.,Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai, PR China
| | - Wei Xia
- Department of Nuclear Medicine, Shanghai Seventh People's Hospital, Shanghai, PR China
| | - Zhi-Yi Shao
- Central Laboratory, Shanghai Seventh People's Hospital, Shanghai, PR China
| | - Hong Zhang
- Central Laboratory, Shanghai Seventh People's Hospital, Shanghai, PR China.,Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai, PR China
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Liu Z, Yang Z, Jiang S, Zou Q, Yuan Y, Li J, Li D, Liang L, Chen M, Chen S. MCM2 and TIP30 are prognostic markers in squamous cell/adenosquamous carcinoma and adenocarcinoma of the gallbladder. Mol Med Rep 2016; 14:4581-4592. [PMID: 27748889 PMCID: PMC5102005 DOI: 10.3892/mmr.2016.5851] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 09/30/2016] [Indexed: 12/29/2022] Open
Abstract
The clinicopathological and biological characteristics of squamous cell/adenosquamous carcinoma (SC/ASC) of the gallbladder remain to be fully elucidated, due to the fact that it is a rare gallbladder cancer subtype. In the current study, the expression of minichromosome maintenance complex component 2 (MCM2) and HIV‑1 tat interactive protein 2 (TIP30) was measured in 46 cases of SC/ASC and 80 adenocarcinomas (AC) using immunohistochemistry. Positive MCM2 and negative TIP30 expression were significantly associated with large tumor size, high TNM stage, invasion, lymph node metastasis and lack of surgical curability in SC/ASC and AC. Positive MCM2 and negative TIP30 expression were significantly associated with poor differentiation in AC, whereas only MCM2 was correlated with differentiation in SC/ASC. Univariate Kaplan‑Meier analysis demonstrated that positive MCM2 and negative TIP30 expression, the degree of differentiation, tumor size, TNM stage, invasion, lymph node metastasis and surgical curability were significantly associated with post‑operative survival in patients with SC/ASC and AC. Multivariate Cox regression analysis demonstrated that positive MCM2 and negative TIP30 expression, the degree of differentiation, tumor size, TNM stage, invasion, lymph node metastasis and lack of surgical curability were also independent predictors of poor prognosis in patients with SC/ASC and AC. These data suggest that positive MCM2 and negative TIP30 expression are closely correlated with the clinical, pathological and biological parameters, in addition to poor prognosis in patients with gallbladder cancer.
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Affiliation(s)
- Ziru Liu
- Department of Minimal Invasive Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Zhulin Yang
- Research Laboratory of Hepatobiliary Diseases, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Song Jiang
- Research Laboratory of Hepatobiliary Diseases, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Qiong Zou
- Department of Pathology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Yuan Yuan
- Department of Pathology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Jinghe Li
- Department of Pathology, Basic School of Medicine, Changsha, Hunan 410078, P.R. China
| | - Daiqiang Li
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Lufeng Liang
- Department of Hepatobiliary and Pancreatic Surgery, Hunan Provincial People's Hospital, Changsha, Hunan 410007, P.R. China
| | - Meigui Chen
- Department of Pathology, Loudi Central Hospital, Loudi, Hunan 417011, P.R. China
| | - Senlin Chen
- Department of Pathology, Hunan Provincial Tumor Hospital, Changsha, Hunan 410013, P.R. China
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Schimmack S, Lawrence B, Kenney B, Schmitz-Winnenthal H, Modlin IM, Kidd M. Minichromosome Maintenance Expression Defines Slow-Growing Gastroenteropancreatic Neuroendocrine Neoplasms. Transl Oncol 2016; 9:411-418. [PMID: 27751345 PMCID: PMC5067926 DOI: 10.1016/j.tranon.2016.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/13/2016] [Accepted: 07/13/2016] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND: Small intestinal neuroendocrine neoplasm (SI-NEN) proliferation is quantified by Ki67 measurements which capture G1-G2M phases of the cell cycle. G0 and early G1 phases, typical of slow-growing cells, can be detected by minichromosome maintenance protein (MCM) expression. We hypothesized that these replication licensing markers may provide clinically relevant information to augment Ki67 in low-grade neuroendocrine neoplasia. METHODS: Immunohistochemical staining (IHC), Western blot analysis, quantitative polymerase chain reaction, and copy number variations of MCM2, MCM3, and Ki67 were undertaken in SI-NENs (n = 22). MCM and Ki67 expression was compared by Kaplan-Meier survival analysis (tissue microarray, independent set [n = 55]). Forty-three pancreatic NENs and 14 normal tissues were included as controls. RESULTS: In SI-NENs, MCM2 (mean: 21.2%: range: 16%-25%) and MCM3 (28.7%: 22%-34%) were detected in significantly more cells than Ki67 (2.3%: 0%-7%, P < .01). MCM2 mRNA correlated with Ki67 IHC (P < .05). MCM3 protein expression was higher in metastases (38-fold) than in normal small intestine (P = .06) and was largely absent in normal neuroendocrine cells. There was considerable variation at the MCM copy number level (0-4 copies). MCM3 expression in proliferating cells significantly predicted overall survival (P < .002). Combinations of Ki67 and MCM2/3 in algorithms differentiated low and higher proliferative lesions (overall survival: 12 vs 6.1 years, P = .06). MCM expression was not informative in pancreatic NENs. CONCLUSION: MCMs are expressed in a higher proportion of NEN cells than Ki67 in slow-growing small intestinal lesions and correlate with survival. Assessment can be used to augment Ki67 to improve prognostic classification in these low-grade tumors.
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Affiliation(s)
- Simon Schimmack
- Gastrointestinal Pathobiology Research Group, Department of Gastrointestinal Surgery, Yale University School of Medicine, PO Box 208602, New Haven, CT, USA; University Hospital of General, Visceral and Transplantation-Surgery of Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Germany.
| | - Ben Lawrence
- Gastrointestinal Pathobiology Research Group, Department of Gastrointestinal Surgery, Yale University School of Medicine, PO Box 208602, New Haven, CT, USA.
| | - Barton Kenney
- Department of Pathology, Division of Gastrointestinal and Hepatic Pathology, Yale University School of Medicine, PO Box 208023, New Haven, CT, USA.
| | - Hubertus Schmitz-Winnenthal
- University Hospital of General, Visceral and Transplantation-Surgery of Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Germany.
| | - Irvin M Modlin
- Gastrointestinal Pathobiology Research Group, Department of Gastrointestinal Surgery, Yale University School of Medicine, PO Box 208602, New Haven, CT, USA.
| | - Mark Kidd
- Gastrointestinal Pathobiology Research Group, Department of Gastrointestinal Surgery, Yale University School of Medicine, PO Box 208602, New Haven, CT, USA.
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Expression of Minichromosome Maintenance Proteins in Actinic Keratosis and Squamous Cell Carcinoma. Appl Immunohistochem Mol Morphol 2016; 26:165-172. [PMID: 27299186 DOI: 10.1097/pai.0000000000000399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Minichromosome maintenance (MCM) proteins are a group of proteins involved in DNA replication and cell-cycle regulation. Because they are associated with DNA through G1 into S phase, MCM proteins are potentially specific indicators of cell proliferation that could be valuable markers of dysplasia, and preinvasive and invasive malignant tumors. To analyze MCM protein expression patterns in actinic keratosis (AK), Bowen disease (BD), and cutaneous squamous cell carcinoma (SCC), we performed immunohistochemical staining of MCM2, -5, and -7 on tissue microarray blocks from 91 AK, 50 BD, and 174 SCC samples. The distribution and semiquantitatively assessed number of positive cells were analyzed in relation to the type of the lesion and the SCC prognostic parameters (grade, diameter, and thickness). Basal expression of all 3 proteins was observed more frequently in AK, whereas the distribution in BD was predominantly diffuse (P<0.001). All 3 proteins showed peripheral distribution in most well-differentiated SCC and diffuse distribution in poorly differentiated tumors (P<0.001). Using the 50% cut-off value, there was a statistically significant difference among AK, BD, and SCC (P<0.001). In addition, all MCM proteins showed highly significant differences (P<0.001) between well-differentiated SCC and both moderately and poorly differentiated SCC. The diffuse distribution and 50% cut-off value of positive cells revealed statistically significant associations of all MCM proteins with SCC thicker than 6 mm. Our results suggest a role for MCM proteins in the progression of in situ keratinocytic lesions and their association with high-risk features in SCC.
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TU ZHENBO, HE DU, DENG XINZHOU, XIONG MENG, HUANG XIAOXING, LI XINRAN, HAO LING, DING QIANSHAN, ZHANG QIUPING. An eight-long non-coding RNA signature as a candidate prognostic biomarker for lung cancer. Oncol Rep 2016; 36:215-22. [DOI: 10.3892/or.2016.4817] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 02/22/2016] [Indexed: 11/05/2022] Open
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Tőkés T, Tőkés AM, Szentmártoni G, Kiszner G, Madaras L, Kulka J, Krenács T, Dank M. Expression of cell cycle markers is predictive of the response to primary systemic therapy of locally advanced breast cancer. Virchows Arch 2016; 468:675-86. [PMID: 27026269 DOI: 10.1007/s00428-016-1925-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 11/16/2015] [Accepted: 03/07/2016] [Indexed: 12/18/2022]
Abstract
We aimed to analyze to what extent expression of four cell cycle regulation markers-minichromosome maintenance protein (MCM2), Ki-67, cyclin A, and phosphohistone-H3 (PHH3)-predict response to primary systemic therapy in terms of pathological complete remission (pCR). In search of an accurate and reproducible scoring method, we compared computer-assisted (CA) and routine visual assessment (VA) of immunoreactivity. We included 57 patients with breast cancer in the study. The cell cycle markers were detected using immunohistochemistry on pre-therapy core biopsy samples. Parallel CA (validated by manual labeling) and standard VA were performed and compared for diagnostic agreement and predictive value for pCR. CA and VA results were dichotomized based on receiver operating characteristic analysis defined optimal cut-off values. "High" was defined by staining scores above the optimal cut-off, while "low" had staining scores below the optimal cut-off. The CA method resulted in significantly lower values for Ki-67 and MCM2 compared to VA (mean difference, -3.939 and -4.323). Diagnostic agreement was highest for cyclin A and PHH3 (-0.586 and -0.666, respectively). Regardless of the method (CA/VA) used, all tested markers were predictive of pCR. Optimal cut-off-based dichotomization improved diagnostic agreement between the CA and VA methods for every marker, in particular for MCM2 (κ = 1, p < 0.000). Cyclin A displayed excellent agreement (κ = 0.925; p < 0.000), while Ki-67 and PHH3 showed good agreement (κ = 0.789, p < 0.000 and κ = 0.794, p < 0.000, respectively). We found all cell cycle markers (Ki-67, MCM2, cyclin A, and PHH3) predictive of pCR. Diagnostic agreement between CA and VA was better at lower staining scores but improved after optimal cut-off-based dichotomization.
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Affiliation(s)
- Tímea Tőkés
- 1st Department of Internal Medicine, Oncological Division, Semmelweis University, Tömő utca 25-29, 4th floor, Budapest, 1083, Hungary
| | - Anna-Mária Tőkés
- MTA-SE Tumor Progression Research Group, 2nd Department of Pahtology, Semmelweis University, Üllői út 93, Budapest, 1091, Hungary.,2nd Department of Pathology, Semmelweis University, Üllői út 93, Budapest, 1091, Hungary
| | - Gyöngyvér Szentmártoni
- 1st Department of Internal Medicine, Oncological Division, Semmelweis University, Tömő utca 25-29, 4th floor, Budapest, 1083, Hungary
| | - Gergő Kiszner
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
| | - Lilla Madaras
- 2nd Department of Pathology, Semmelweis University, Üllői út 93, Budapest, 1091, Hungary
| | - Janina Kulka
- 2nd Department of Pathology, Semmelweis University, Üllői út 93, Budapest, 1091, Hungary
| | - Tibor Krenács
- MTA-SE Tumor Progression Research Group, 2nd Department of Pahtology, Semmelweis University, Üllői út 93, Budapest, 1091, Hungary.,1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
| | - Magdolna Dank
- 1st Department of Internal Medicine, Oncological Division, Semmelweis University, Tömő utca 25-29, 4th floor, Budapest, 1083, Hungary.
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Zhang S, Zhao H, Ng MK. Functional Module Analysis for Gene Coexpression Networks with Network Integration. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015; 12:1146-60. [PMID: 26451826 PMCID: PMC4664071 DOI: 10.1109/tcbb.2015.2396073] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Network has been a general tool for studying the complex interactions between different genes, proteins, and other small molecules. Module as a fundamental property of many biological networks has been widely studied and many computational methods have been proposed to identify the modules in an individual network. However, in many cases, a single network is insufficient for module analysis due to the noise in the data or the tuning of parameters when building the biological network. The availability of a large amount of biological networks makes network integration study possible. By integrating such networks, more informative modules for some specific disease can be derived from the networks constructed from different tissues, and consistent factors for different diseases can be inferred. In this paper, we have developed an effective method for module identification from multiple networks under different conditions. The problem is formulated as an optimization model, which combines the module identification in each individual network and alignment of the modules from different networks together. An approximation algorithm based on eigenvector computation is proposed. Our method outperforms the existing methods, especially when the underlying modules in multiple networks are different in simulation studies. We also applied our method to two groups of gene coexpression networks for humans, which include one for three different cancers, and one for three tissues from the morbidly obese patients. We identified 13 modules with three complete subgraphs, and 11 modules with two complete subgraphs, respectively. The modules were validated through Gene Ontology enrichment and KEGG pathway enrichment analysis. We also showed that the main functions of most modules for the corresponding disease have been addressed by other researchers, which may provide the theoretical basis for further studying the modules experimentally.
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Paduano F, Forbes AG. Extended LineSets: a visualization technique for the interactive inspection of biological pathways. BMC Proc 2015; 9:S4. [PMID: 26361500 PMCID: PMC4547339 DOI: 10.1186/1753-6561-9-s6-s4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Biologists make use of pathway visualization tools for a range of tasks, including investigating inter-pathway connectivity and retrieving details about biological entities and interactions. Some of these tasks require an understanding of the hierarchical nature of elements within the pathway or the ability to make comparisons between multiple pathways. We introduce a technique inspired by LineSets that enables biologists to fulfill these tasks more effectively. RESULTS We introduce a novel technique, Extended LineSets, to facilitate new explorations of biological pathways. Our technique incorporates intuitive graphical representations of different levels of information and includes a well-designed set of user interactions for selecting, filtering, and organizing biological pathway data gathered from multiple databases. CONCLUSIONS Based on interviews with domain experts and an analysis of two use cases, we show that our technique provides functionality not currently enabled by current techniques, and moreover that it helps biologists to better understand both inter-pathway connectivity and the hierarchical structure of biological elements within the pathways.
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Affiliation(s)
- Francesco Paduano
- Department of Computer Science M/C 152, University of Illinois at Chicago, 851 S. Morgan, Room 1120, Chicago 60607-7053, IL, USA
| | - Angus Graeme Forbes
- Department of Computer Science M/C 152, University of Illinois at Chicago, 851 S. Morgan, Room 1120, Chicago 60607-7053, IL, USA
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Abd El-Rehim DM, Gayyed MF. Does Immunohistochemistry for Discovered on GIST1 and Minichromosome Maintenance Protein7 Provide Additional Clinicopathological Value in Gastrointestinal Stromal Tumors? World J Oncol 2015; 6:355-363. [PMID: 28983330 PMCID: PMC5624661 DOI: 10.14740/wjon918w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2015] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The aim of the study was to investigate the expression of discovered on GIST 1 (DOG1) and minichromosome maintenance protein 7 (MCM7) in addition to the traditional markers, C-KIT and Ki-67, in gastrointestinal stromal tumors (GISTs) to specify the diagnosis and to evaluate their clinicopathological significance in GIST patients. METHODS Hematoxylin and eosin sections of 43 GISTs were re-examined to review histopathological criteria and risk stratification of these tumors. Immunohistochemistry for DOG1, C-KIT, MCM7, Ki-67 antibodies was performed. RESULTS Positive DOG1 and C-KIT expressions were found in 42 (97.7%) and 39 (90.7%) of cases, respectively. DOG1 and C-KIT expression scores were significantly correlated (P < 0.001). Among four C-KIT-negative GISTs, three cases were DOG1-positive. DOG1 was more sensitive and specific than C-KIT in the diagnosis of GISTs. High DOG1 expression scores were significantly associated with tumor size (P = 0.023) and risk (P = 0.037). Significant positive correlation was noted between MCM7 and Ki-67 labeling indices (LIs) (P < 0.001, r = 0.885). MCM7 demonstrated higher proliferation LIs than Ki-67. Significant associations were found between MCM7 and Ki-67 LIs and tumor size (P = 0.001 and 0.003 respectively), mitotic rate (P < 0.001 both) and risk stratification (P < 0.001 both) with a stepwise increase in MCM7 LIs with increasing tumor risk. CONCLUSION DOG1 is an important diagnostic tool for GISTs particularly in C-KIT-negative tumors. It may have a role in GISTs tumorogenesis and progression. Despite the established clinicopathological value of Ki-67 in GISTs, detection of MCM7 expression is recommended as a prognostic adjunct, given its better sensitivity for cellular proliferation and stepwise association with tumor risk.
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Soares AB, Altemani A, de Oliveira TR, de Oliveira Fonseca Rodrigues F, Ribeiro-Silva A, Soave DF, Passador-Santos F, Brum ST, Napimoga MH, de Araújo VC. Comparison of the blood and lymphatic microvessel density of pleomorphic adenoma and Basal cell adenoma. Clin Med Insights Pathol 2015; 8:17-21. [PMID: 25987856 PMCID: PMC4405080 DOI: 10.4137/cpath.s23035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 01/12/2015] [Accepted: 01/12/2015] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Pleomorphic adenoma (PA) is the most common tumor of the salivary gland, while basal cell adenoma (BCA) is an uncommon neoplasm. Blood and lymphatic vessels are crucial for tumor metabolism. The aim of this study was to compare the blood and lymphatic vascular density and vascular and endothelial growth factor (VEGF) expression in PA and BCA tumors. In addition, cell proliferation was evaluated in these tumors. METHODS Blood and lymphatic vessel content, VEGF expression, and cell proliferation were analyzed in 30 cases of PA and 13 cases of BCA by immu-nohistochemistry using antibodies for CD34, CD105, D2–40, VEGF, and Mcm−2. RESULTS Regarding CD34 and CD105 expression, PA demonstrated a high vascularity and a low number of positive vessels, respectively. D2–40-positive lymphatic vessels were mainly located in the tumor capsules, with small intratumoral lymphatic vessels observed occasionally. VEGF expression revealed a remarkably heterogeneous immunoreactivity, alternating from weak or negative to positive or intense. BCA presented significantly higher CD34, CD34, CD105, D2–40, and VEGF expression compared to PA. No significant difference was found in cell proliferation between the tumors. CONCLUSION Although PA and BCA are considered part of the same spectrum of differentiation, this study showed that the blood and lymphatic vascularization of these tumors is different.
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Affiliation(s)
- Andresa Borges Soares
- Department of Oral Pathology, São Leopoldo Mandic Institute and Research Center, Campinas, São Paulo, Brazil
| | - Albina Altemani
- Department of Pathology, School of Medicine, State University of Campinas (UNICAMP), São Paulo, Brazil
| | - Thais Ribeiro de Oliveira
- Department of Oral Pathology, São Leopoldo Mandic Institute and Research Center, Campinas, São Paulo, Brazil
| | | | - Alfredo Ribeiro-Silva
- Department of Pathology, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Danilo Figueiredo Soave
- Department of Pathology, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Fabricio Passador-Santos
- Department of Oral Pathology, São Leopoldo Mandic Institute and Research Center, Campinas, São Paulo, Brazil
| | - Suellen Trentin Brum
- Department of Oral Pathology, São Leopoldo Mandic Institute and Research Center, Campinas, São Paulo, Brazil
| | - Marcelo Henrique Napimoga
- Department of Oral Pathology, São Leopoldo Mandic Institute and Research Center, Campinas, São Paulo, Brazil
| | - Vera Cavalcanti de Araújo
- Department of Oral Pathology, São Leopoldo Mandic Institute and Research Center, Campinas, São Paulo, Brazil
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Correlation of MCM2 detection with stage and virology of cervical cancer. Int J Biol Markers 2014; 29:e363-71. [PMID: 24706378 DOI: 10.5301/jbm.5000081] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2014] [Indexed: 11/20/2022]
Abstract
UNLABELLED The highly conserved mini-chromosome maintenance proteins (MCM) are important in the initiation of DNA replication. Few studies have correlated MCM expression with the progression of cancer. OBJECTIVES (i) To analyze the expression of MCM2 in cervical cancer; (ii) to correlate MCM2 expression with the clinical tumor staging according to FIGO classification, and (iii) to relate HPV type to MCM2 expression. METHODS Tissue micro-arrays (TMA) from patients with invasive cervical cancer and controls were analyzed. Human papillomavirus (HPV) DNA detection and HPV types were determined by in situ hybridization, PCR, and sequencing. MCM2 expression was analyzed by immunohistochemistry. RESULTS The most prevalent HPV types found in invasive cancer were HPV 16 (66.6%), followed by HPV 33 (11.8%), and HPV 35 (3.6%). An increased (p<0.05) expression of MCM2 was found in invasive cervical cancers compared to controls. Moreover, a strong correlation was found between the MCM2-positive cells and the presence of HPV DNA detected by in situ hybridization. No statistically significant difference was observed between MCM2 expression and FIGO stage. CONCLUSIONS The present study shows that HPV-infected cells strongly express MCM2; nevertheless, our data suggests that MCM2 is not a good biomarker when comparing the different clinical stages of cervical cancer.
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Hua C, Zhao G, Li Y, Bie L. Minichromosome Maintenance (MCM) Family as potential diagnostic and prognostic tumor markers for human gliomas. BMC Cancer 2014; 14:526. [PMID: 25046975 PMCID: PMC4223428 DOI: 10.1186/1471-2407-14-526] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/15/2014] [Indexed: 12/15/2022] Open
Abstract
Background Gliomas are the most common type of all central nervous system tumors. Almost all patients diagnosed with these tumors have a poor prognostic outcome. We aimed to identify novel glioma prognosis-associated candidate genes. Methods We applied WebArrayDB software to span platform integrate and analyze the microarray datasets. We focused on a subset of the significantly up-regulated genes, the minichromosome maintenance (MCM) family. We used frozen glioma samples to predict the relationship between the expression of MCMs and patients outcome by qPCR and western blot. Results We found that MCMs expression was significantly up-regulated in glioma samples. MCM2-7 and MCM10 expressions were associated with WHO tumor grade. High MCM2 mRNA expression appeared to be strongly associated with poor overall survival in patients with high grade glioma. Furthermore, we report that MCM7 is strongly correlated with patient outcome in patients with WHO grade II-IV tumor. MCM3 expression was found to be up-regulated in glioma and correlated with overall survival in patients with WHO grade III tumor. MCM2, MCM3 and MCM7 expression levels were of greater prognostic relevance than histological diagnosis according to the current WHO classification system. Conclusions High expression of MCM 2, MCM3 and MCM7 mRNA correlated with poor outcome and may be clinically useful molecular prognostic markers in glioma.
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Affiliation(s)
| | | | | | - Li Bie
- Department of Neurosurgery of the First Clinical Hospital, Jilin University, 71 Xinmin St, Changchun, Jilin 130021, China.
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Bilyk KT, Cheng CHC. RNA-seq analyses of cellular responses to elevated body temperature in the high Antarctic cryopelagic nototheniid fish Pagothenia borchgrevinki. Mar Genomics 2014; 18 Pt B:163-71. [PMID: 24999838 DOI: 10.1016/j.margen.2014.06.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 06/17/2014] [Accepted: 06/17/2014] [Indexed: 11/18/2022]
Abstract
Through evolution in the isolated, freezing (-1.9°C) Southern Ocean, Antarctic notothenioid fish have become cold-adapted as well as cold-specialized. Notothenioid cold specialization is most evident in their limited tolerance to heat challenge, and an apparent loss of the near universal inducible heat shock (HSP70) response. Beyond these it remains unclear how broadly cold specialization pervades the underlying tissue-wide cellular responses. We report the first analysis of massively parallel RNA sequencing (RNA-seq) to identify gene expression changes in the liver in response to elevated body temperature of a high-latitude Antarctic nototheniid, the highly cold-adapted and cold-specialized cryopelagic bald notothen, Pagothenia borchgrevinki. From a large (14,873) mapped set of qualified, annotated liver transcripts, we identified hundreds of significantly differentially expressed genes following two and four days of 4°C exposure, suggesting substantial transcriptional reorganization in the liver when body temperature was raised 5°C above native water temperature. Most notably, and in sharp contrast to heat stressed non-polar fish species, was a widespread down-regulation of nearly all classes of molecular chaperones including HSP70, as well as polyubiquitins that are associated with proteosomal degradation of damaged proteins. In parallel, genes involved in the cell cycle were down-regulated by day two of 4°C exposure, signifying slowing cellular proliferation; by day four, genes associated with transcriptional and translational machineries were down-regulated, signifying general slowing of protein biosynthesis. The log2 fold differential transcriptional changes are generally of small magnitudes but significant, and in total portray a broad down turn of cellular activities in response to four days of elevated body temperature in the cold-specialized bald notothen.
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Affiliation(s)
- Kevin T Bilyk
- Department of Animal Biology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - C-H Christina Cheng
- Department of Animal Biology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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Abstract
DNA replication must be tightly regulated to ensure that the genome is accurately duplicated during each cell cycle. When these regulatory mechanisms fail, replicative stress and DNA damage ensue. Activated oncogenes promote replicative stress, inducing a DNA damage response (DDR) early in tumorigenesis. Senescence or apoptosis result, forming a barrier against tumour progression. This may provide a selective pressure for acquisition of mutations in the DDR pathway during tumorigenesis. Despite its potential importance in early cancer development, the precise nature of oncogene-induced replicative stress remains poorly understood. Here, we review our current understanding of replication initiation and its regulation, describe mechanisms by which activated oncogenes might interfere with these processes and discuss how replicative stress might contribute to the genomic instability seen in cancers.
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Affiliation(s)
- Stephanie A Hills
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, Herts, EN6 3LD, UK
| | - John F X Diffley
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, Herts, EN6 3LD, UK.
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Wang SC. PCNA: a silent housekeeper or a potential therapeutic target? Trends Pharmacol Sci 2014; 35:178-86. [PMID: 24655521 DOI: 10.1016/j.tips.2014.02.004] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Revised: 02/17/2014] [Accepted: 02/18/2014] [Indexed: 11/18/2022]
Abstract
Proliferating cell nuclear antigen (PCNA) is known as a molecular marker for proliferation given its role in replication. Three identical molecules of PCNA form a molecular sliding clamp around the DNA double helix. This provides an essential platform on which multiple proteins are dynamically recruited and coordinately regulated. Over the past decade, new research has provided a deeper comprehension of PCNA as a coordinator of essential cellular functions for cell growth, death, and maintenance. Although the biology of PCNA in proliferation has been comprehensively reviewed, research progress in unveiling the potential of targeting PCNA for disease treatment has not been systematically discussed. Here we briefly summarize the basic structural and functional characteristics of PCNA, and then discuss new developments in its protein interactions, trimer formation, and signaling regulation that open the door to possible therapeutic targeting of PCNA.
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Affiliation(s)
- Shao-Chun Wang
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
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von Knebel Doeberitz M, Reuschenbach M, Schmidt D, Bergeron C. Biomarkers for cervical cancer screening: the role of p16INK4ato highlight transforming HPV infections. Expert Rev Proteomics 2014; 9:149-63. [DOI: 10.1586/epr.12.13] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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50
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Jackson AP, Laskey RA, Coleman N. Replication proteins and human disease. Cold Spring Harb Perspect Biol 2014; 6:cshperspect.a013060. [PMID: 23881941 DOI: 10.1101/cshperspect.a013060] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this article, we discuss the significance of DNA replication proteins in human disease. There is a broad range of mutations in genes encoding replication proteins, which result in several distinct clinical disorders that share common themes. One group of replication proteins, the MCMs, has emerged as effective biomarkers for early detection of a range of common cancers. They offer practical and theoretical advantages over other replication proteins and have been developed for widespread clinical use.
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Affiliation(s)
- Andrew P Jackson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
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