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Construction of Molecular Subtype and Prognosis Prediction Model of Osteosarcoma Based on Aging-Related Genes. JOURNAL OF ONCOLOGY 2022; 2022:8177948. [PMID: 36157228 PMCID: PMC9507679 DOI: 10.1155/2022/8177948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/12/2022] [Accepted: 08/18/2022] [Indexed: 01/10/2023]
Abstract
Background Osteosarcoma (OS) is a rare form of malignant bone cancer that is usually detected in young adults and adolescents. This disease shows a poor prognosis owing to its metastatic status and resistance to chemotherapy. Hence, it is necessary to design a risk model that can successfully forecast the OS prognosis in patients. Methods The researchers retrieved the RNA sequencing data and follow-up clinical data related to OS patients from the TARGET and GEO databases, respectively. The coxph function in R software was used for carrying out the Univariate Cox regression analysis for deriving the aging-based genes related sto the OS prognosis. The researchers conducted consistency clustering using the ConcensusClusterPlus R package. The R software package ESTIMATE, MCPcounter, and GSVA packages were used for assessing the immune scores of various subtypes using the ssGSEA technique, respectively. The Univariate Cox and Lasso regression analyses were used for screening and developing a risk model. The ROC curves were constructed, using the pROC package. The performance of their developed risk model and designed survival curve was conducted, with the help of the Survminer package. Results The OS patients were classified into 2 categories, as per the aging-related genes. The results revealed that the Cluster 1 patients showed a better prognosis than the Cluster 2 patients. Both clusters showed different immune microenvironments. Additional screening of the prognosis-associated genes revealed the presence of 5 genes, i.e., ERCC4, GPX4, EPS8, TERT, and STAT5A, and these data were used for developing the risk model. This risk model categorized the training set samples into the high- and low-risk groups. The patients classified into the high-risk group showed a poor OS prognosis compared to the low-risk patients. The researchers verified the reliability and robustness of the designed 5-gene signature using the internal and external datasets. This risk model was able to effectively predict the prognosis even in the samples having differing clinical features. Compared with other models, the 5- gene model performs better in predicting the risk of osteosarcoma. Conclusion The 5-gene signature developed by the researchers in this study could be effectively used for forecasting the OS prognosis in patients.
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Nasrallah NA, Wiese BM, Sears CR. Xeroderma Pigmentosum Complementation Group C (XPC): Emerging Roles in Non-Dermatologic Malignancies. Front Oncol 2022; 12:846965. [PMID: 35530314 PMCID: PMC9069926 DOI: 10.3389/fonc.2022.846965] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
Xeroderma pigmentosum complementation group C (XPC) is a DNA damage recognition protein essential for initiation of global-genomic nucleotide excision repair (GG-NER). Humans carrying germline mutations in the XPC gene exhibit strong susceptibility to skin cancer due to defective removal via GG-NER of genotoxic, solar UV-induced dipyrimidine photoproducts. However, XPC is increasingly recognized as important for protection against non-dermatologic cancers, not only through its role in GG-NER, but also by participating in other DNA repair pathways, in the DNA damage response and in transcriptional regulation. Additionally, XPC expression levels and polymorphisms likely impact development and may serve as predictive and therapeutic biomarkers in a number of these non-dermatologic cancers. Here we review the existing literature, focusing on the role of XPC in non-dermatologic cancer development, progression, and treatment response, and highlight possible future applications of XPC as a prognostic and therapeutic biomarker.
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Affiliation(s)
- Nawar Al Nasrallah
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Benjamin M. Wiese
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Catherine R. Sears
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
- Division of Pulmonary Medicine, Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis, IN, United States
- *Correspondence: Catherine R. Sears,
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Hu H, Liu S, Chu A, Chen J, Xing C, Jing J. Comprehensive analysis of ceRNA network of ERCC4 in colorectal cancer. PeerJ 2022; 9:e12647. [PMID: 34993023 PMCID: PMC8679902 DOI: 10.7717/peerj.12647] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/26/2021] [Indexed: 12/12/2022] Open
Abstract
Objective ERCC4 is one of the most significant molecules of Nucleotide Excision Repair (NER), which has been researched due to its high expression in colorectal cancer (CRC). This study aimed to find out the ceRNA (competitive endogenous RNA) network of ERCC4 in CRC. Methods and Materials Pan cancer mRNA expression of ERCC4 was evaluated using TCGA database. The protein expression of ERCC4 was evaluated based on the Human Protein Atlas (HPA). We screened DElncRNAs and DEmiRNAs in two groups of ERCC4high and ERCC4low expression in CRC. Then a lncRNA-miRNA-ERCC4 regulatory network was constructed based on DElncRNAs and DEmiRNAs using Starbase database and visualized by Cytoscape software. Kaplan-Meier analysis was performed to evaluate the prognostic value of the ceRNA network. Further, RT-PCR was performed to validate the expression of the representative molecules in the ceRNA network in CRC and normal tissues. The relationship between drug sensitivity and these molecules were also evaluated using RNAactDrug database. Results ERCC4 was overexpressed in a variety of tumors at mRNA levels, including CRC. High expression of ERCC4 was also observed on protein level in CRC. A total of 1,885 DElncRNAs and 68 DEmiRNAs were identified from CRC samples in ERCC4high and ERCC4low expression groups. Predicted by the Starbase database, we got interacting miRNAs and lncRNAs of ERCC4 from the DEmiRNAs and DElncRNAs, and a lncRNA-miRNA-ERCC4 regulatory network was constructed. Kaplan-Meier survival curves results showed that miR-200c-3p (hazard ratio [HR] = 0.62, P = 0.032), MALAT1 (HR = 1.54, P = 0.016), and AC005520.2 (hazard ratio [HR] = 1.75, P = 0.002) were significantly associated with the prognosis of CRC. After validation by RT-PCR, we found that ERCC4 and MALAT1 were up-regulated in CRC compared with normal tissues, while miR-200c-3p was down-regulated. A strong negative correlation was observed between MALAT1 and miR-200c-3p. Drug sensitivity analysis showed that ERCC4, miR-200c and MALAT1 were all associated with Cisplatin. Conclusion We constructed a ceRNA network of ERCC4 in CRC, of which the MALAT1-miR-200c-3p-ERCC4 axis may be involved in the development, prognosis and chemotherapy sensitivity of CRC. These findings might provide novel clues and insights on the molecular mechanisms of ERCC4 and NER pathway in CRC.
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Affiliation(s)
- Huixin Hu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China.,Department of Anorectal Surgery in Liaoning Province, the First Hospital of China Medical of China Medical University, Shenyang, China
| | - Songyi Liu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China.,Department of Anorectal Surgery in Liaoning Province, the First Hospital of China Medical of China Medical University, Shenyang, China
| | - Aining Chu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| | - Jing Chen
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| | - Chengzhong Xing
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China.,Department of Anorectal Surgery in Liaoning Province, the First Hospital of China Medical of China Medical University, Shenyang, China
| | - Jingjing Jing
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China
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Ghaderi-Zefrehi H, Rezaei M, Sadeghi F, Heiat M. Genetic polymorphisms in DNA repair genes and hepatocellular carcinoma risk. DNA Repair (Amst) 2021; 107:103196. [PMID: 34416543 DOI: 10.1016/j.dnarep.2021.103196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 05/23/2021] [Accepted: 07/26/2021] [Indexed: 01/27/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the most frequent types of tumors worldwide. Its occurrence and development have been related to various risk factors, such as chronic infection with hepatitis B or C viruses and alcohol addiction. DNA repair systems play a critical role in maintaining the integrity of the genome. Defects in these systems have been related to increased susceptibility to various types of cancer. Multiple genetic polymorphisms in genes of DNA repair systems have been reported that may affect DNA repair capacity (DRC) and modulate risk to cancer. Several studies have been conducted to assess the role of polymorphisms of DNA repair genes on the HCC risk. Identifying these polymorphisms and their association with HCC risk may help to improve prevention and treatment strategies. In this study, we review investigations that evaluated the association between genetic polymorphisms of DNA repair genes and risk of HCC.
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Affiliation(s)
- Hossein Ghaderi-Zefrehi
- Department of Clinical Biochemistry, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Maryam Rezaei
- Department of Clinical Biochemistry, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Farzin Sadeghi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Mohammad Heiat
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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Mehrabi S, Zolhavarieh M, Kiani A, Joughehdoust S. The relationship between risk factors of bladder cancer and tumor grade. GAZZETTA MEDICA ITALIANA ARCHIVIO PER LE SCIENZE MEDICHE 2020. [DOI: 10.23736/s0393-3660.19.04006-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Bioinformatics Analysis to Screen the Key Prognostic Genes in Tumor Microenvironment of Bladder Cancer. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6034670. [PMID: 32149116 PMCID: PMC7048919 DOI: 10.1155/2020/6034670] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 01/16/2020] [Indexed: 12/19/2022]
Abstract
Bladder cancer (BLCA) is the fifth most common cancer and has the features of low survival rate and high morbidity and mortality. The Cancer Genome Atlas (TCGA) is a pool of global gene expression profile and contains huge amounts of cancer genomics data, which makes it possible to inquire the relationship between gene expression and prognosis of a series of malignant tumors including BLCA. Immune and stromal cells are two major components of tumor microenvironment (TME) which play an important role in judging the prognosis of tumor and influencing the progression of malignant, inflammatory, and metabolic disorders. In our study, we conducted a quantitative analysis of immune and stromal elements based on the ESTIMATE algorithm and thus divided BLCA cases into high and low groups. Then the differentially expressed genes closely related to tumor prognosis between groups were identified and had been shown to correlate with immune response and stromal alterations, which was further confirmed by functional enrichment analysis and protein-protein interaction networks. We validated those genes through BLCA dates downloaded from ArrayExpress and thus got the marker genes to predict prognosis of BLCA. Additionally, immune cell infiltration analysis explored the correlation between the verified genes and immune cells. In conclusion, we identified a series of TME-related genes that assess the prognosis and explored the interaction between TME and tumor prognosis to guide clinical individualized treatment.
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Santos HBDP, Morais EFD, Cavalcante RB, Nogueira RLM, Nonaka CFW, Souza LBD, Freitas RDA. Immunoexpression of DNA base excision repair and nucleotide excision repair proteins in ameloblastomas, syndromic and non-syndromic odontogenic keratocysts and dentigerous cysts. Arch Oral Biol 2019; 110:104627. [PMID: 31862643 DOI: 10.1016/j.archoralbio.2019.104627] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/01/2019] [Accepted: 12/02/2019] [Indexed: 12/22/2022]
Abstract
OBJECTIVE To evaluate the immunoexpression of DNA base excision repair (BER) [apurinic/apyrimidinic endonuclease 1 (APE-1), X-ray repair cross complementing 1 (XRCC-1)] and nucleotide excision repair (NER) [xeroderma pigmentosum complementation group (XPF)] proteins in benign epithelial odontogenic lesions with different biological behaviors. DESIGN Thirty solid ameloblastomas, 30 non-syndromic odontogenic keratocysts (NSOKCs), 29 syndromic odontogenic keratocysts (SKOCs), 30 dentigerous cysts (DCs) and 20 dental follicles (DFs) were evaluated quantitatively for APE-1, XRCC-1 and XPF through immunohistochemistry. RESULTS Nuclear expression of APE-1 was significantly higher in NSOKCs, SOKCs, and ameloblastomas in comparison to DCs (p < 0.001). Nuclear expression of XRCC-1 was higher in NSOKCs and SOKCs than in DCs (p < 0.05). At the nuclear level, XPF expression was higher in NSOKCs and SOKCs than in DCs and ameloblastomas (p < 0.05). A statistically significant higher expression of APE-1 (nuclear), XRCC-1 (nuclear), and XPF (nuclear and cytoplasmic) was found in all odontogenic lesion samples as compared to DFs (p < 0.05). For all lesions, there was a positive correlation between nuclear expression of APE-1 and XRCC-1 or XPF (p < 0.05). CONCLUSIONS Our results suggest a potential involvement of APE-1, XRCC-1 and XPF proteins in the pathogenesis of benign epithelial odontogenic lesions, especially in those with more aggressive biological behavior, such as ameloblastomas, NSOKCs, and SOKCs. We also showed that the expression of APE-1 was positively correlated with the nuclear expression of XRCC-1 and XPF, which may suggest an interaction between the BER and NER pathways in all odontogenic lesions studied herein.
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Allione A, Pardini B, Viberti C, Oderda M, Allasia M, Gontero P, Vineis P, Sacerdote C, Matullo G. The prognostic value of basal DNA damage level in peripheral blood lymphocytes of patients affected by bladder cancer. Urol Oncol 2018; 36:241.e15-241.e23. [DOI: 10.1016/j.urolonc.2018.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 01/04/2018] [Accepted: 01/09/2018] [Indexed: 10/18/2022]
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Holcomb N, Goswami M, Han SG, Clark S, Orren DK, Gairola CG, Mellon I. Exposure of Human Lung Cells to Tobacco Smoke Condensate Inhibits the Nucleotide Excision Repair Pathway. PLoS One 2016; 11:e0158858. [PMID: 27391141 PMCID: PMC4938567 DOI: 10.1371/journal.pone.0158858] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/22/2016] [Indexed: 12/19/2022] Open
Abstract
Exposure to tobacco smoke is the number one risk factor for lung cancer. Although the DNA damaging properties of tobacco smoke have been well documented, relatively few studies have examined its effect on DNA repair pathways. This is especially true for the nucleotide excision repair (NER) pathway which recognizes and removes many structurally diverse DNA lesions, including those introduced by chemical carcinogens present in tobacco smoke. The aim of the present study was to investigate the effect of tobacco smoke on NER in human lung cells. We studied the effect of cigarette smoke condensate (CSC), a surrogate for tobacco smoke, on the NER pathway in two different human lung cell lines; IMR-90 lung fibroblasts and BEAS-2B bronchial epithelial cells. To measure NER, we employed a slot-blot assay to quantify the introduction and removal of UV light-induced 6–4 photoproducts and cyclobutane pyrimidine dimers. We find a dose-dependent inhibition of 6–4 photoproduct repair in both cell lines treated with CSC. Additionally, the impact of CSC on the abundance of various NER proteins and their respective RNAs was investigated. The abundance of XPC protein, which is required for functional NER, is significantly reduced by treatment with CSC while the abundance of XPA protein, also required for NER, is unaffected. Both XPC and XPA RNA levels are modestly reduced by CSC treatment. Finally, treatment of cells with MG-132 abrogates the reduction in the abundance of XPC protein produced by treatment with CSC, suggesting that CSC enhances proteasome-dependent turnover of the protein that is mediated by ubiquitination. Together, these findings indicate that tobacco smoke can inhibit the same DNA repair pathway that is also essential for the removal of some of the carcinogenic DNA damage introduced by smoke itself, increasing the DNA damage burden of cells exposed to tobacco smoke.
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Affiliation(s)
- Nathaniel Holcomb
- Department of Toxicology and Cancer Biology, The Markey Cancer Center, University of Kentucky, Lexington, Kentucky, United States of America
| | - Mamta Goswami
- Department of Toxicology and Cancer Biology, The Markey Cancer Center, University of Kentucky, Lexington, Kentucky, United States of America
| | - Sung Gu Han
- Toxicology Laboratory, Department of Food Science and Biotechnology of Animal Resources, College of Animal Bioscience and Technology, Konkuk University, Seoul, Republic of Korea
| | - Samuel Clark
- Department of Toxicology and Cancer Biology, The Markey Cancer Center, University of Kentucky, Lexington, Kentucky, United States of America
| | - David K. Orren
- Department of Toxicology and Cancer Biology, The Markey Cancer Center, University of Kentucky, Lexington, Kentucky, United States of America
| | - C. Gary Gairola
- Department of Toxicology and Cancer Biology, The Markey Cancer Center, University of Kentucky, Lexington, Kentucky, United States of America
| | - Isabel Mellon
- Department of Toxicology and Cancer Biology, The Markey Cancer Center, University of Kentucky, Lexington, Kentucky, United States of America
- * E-mail:
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Insulin-like growth factor-1 receptor regulates repair of ultraviolet B-induced DNA damage in human keratinocytes in vivo. Mol Oncol 2016; 10:1245-54. [PMID: 27373487 DOI: 10.1016/j.molonc.2016.06.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 05/24/2016] [Accepted: 06/07/2016] [Indexed: 11/23/2022] Open
Abstract
The activation status of the insulin-like growth factor-1 receptor (IGF-1R) regulates the cellular response of keratinocytes to ultraviolet B (UVB) exposure, both in vitro and in vivo. Geriatric skin is deficient in IGF-1 expression resulting in an aberrant IGF-1R-dependent UVB response which contributes to the development of aging-associated squamous cell carcinoma. Furthermore, our lab and others have reported that geriatric keratinocytes repair UVB-induced DNA damage less efficiently than young adult keratinocytes. Here, we show that IGF-1R activation influences DNA damage repair in UVB-irradiated keratinocytes. Specifically, in the absence of IGF-1R activation, the rate of DNA damage repair following UVB-irradiation was significantly slowed (using immortalized human keratinocytes) or inhibited (using primary human keratinocytes). Furthermore, inhibition of IGF-1R activity in human skin, using either ex vivo explant cultures or in vivo xenograft models, suppressed DNA damage repair. Primary keratinocytes with an inactivated IGF-1R also exhibited lower steady-state levels of nucleotide excision repair mRNAs. These results suggest that deficient UVB-induced DNA repair in geriatric keratinocytes is due in part to silenced IGF-1R activation in geriatric skin and provide a mechanism for how the IGF-1 pathway plays a role in the initiation of squamous cell carcinoma in geriatric patients.
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Ma Y, Deng XD, Feng Y, Zhang W, Wang SX, Liu Y, Liu H. Association of XPF Levels and Genetic Polymorphism with Susceptibility to Ischemic Stroke. J Mol Neurosci 2016; 59:168-76. [DOI: 10.1007/s12031-016-0729-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/02/2016] [Indexed: 11/28/2022]
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