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Lu S, Kim HS, Cao Y, Bedi K, Zhao L, Narayanan IV, Magnuson B, Gu Y, Yang J, Yi Z, Babaniamansour S, Shameon S, Xu C, Paulsen MT, Qiu P, Jeyarajan S, Ljungman M, Thomas D, Dou Y, Crawford H, di Magliano MP, Ge K, Yang B, Shi J. KMT2D links TGF-β signaling to noncanonical activin pathway and regulates pancreatic cancer cell plasticity. Int J Cancer 2023. [PMID: 37140208 DOI: 10.1002/ijc.34528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 03/02/2023] [Accepted: 03/13/2023] [Indexed: 05/05/2023]
Abstract
Although KMT2D, also known as MLL2, is known to play an essential role in development, differentiation, and tumor suppression, its role in pancreatic cancer development is not well understood. Here, we discovered a novel signaling axis mediated by KMT2D, which links TGF-β to the activin A pathway. We found that TGF-β upregulates a microRNA, miR-147b, which in turn leads to post-transcriptional silencing of KMT2D. Loss of KMT2D induces the expression and secretion of activin A, which activates a noncanonical p38 MAPK-mediated pathway to modulate cancer cell plasticity, promote a mesenchymal phenotype, and enhance tumor invasion and metastasis in mice. We observed a decreased KMT2D expression in human primary and metastatic pancreatic cancer. Furthermore, inhibition or knockdown of activin A reversed the protumoral role of KMT2D loss. These findings support a tumor-suppressive role of KMT2D in pancreatic cancer and identify miR-147b and activin A as novel therapeutic targets.
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Affiliation(s)
- Shuang Lu
- Department of Pathology & Clinical Labs, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
- Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Hong Sun Kim
- Department of Pathology & Clinical Labs, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Yubo Cao
- Department of Pathology & Clinical Labs, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Karan Bedi
- Department of Radiation Oncology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Lili Zhao
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Ishwarya Venkata Narayanan
- Department of Radiation Oncology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Brian Magnuson
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Yumei Gu
- Department of Pathology & Clinical Labs, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Jing Yang
- Department of Pathology & Clinical Labs, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Zhujun Yi
- Department of Pathology & Clinical Labs, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Sepideh Babaniamansour
- Department of Pathology & Clinical Labs, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Sargis Shameon
- Department of Pathology & Clinical Labs, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Chang Xu
- Department of Pathology & Clinical Labs, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Michelle T Paulsen
- Department of Radiation Oncology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Ping Qiu
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Sivakumar Jeyarajan
- Department of Pathology & Clinical Labs, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Mats Ljungman
- Department of Radiation Oncology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Dafydd Thomas
- Department of Pathology & Clinical Labs, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Yali Dou
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | | | | | - Kai Ge
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, Maryland, USA
| | - Bo Yang
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Jiaqi Shi
- Department of Pathology & Clinical Labs, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
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2
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Ljungman M. Transcription and genome integrity. DNA Repair (Amst) 2022; 118:103373. [PMID: 35914488 DOI: 10.1016/j.dnarep.2022.103373] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/16/2022] [Accepted: 07/17/2022] [Indexed: 11/03/2022]
Abstract
Transcription can cause genome instability by promoting R-loop formation but also act as a mutation-suppressing machinery by sensing of DNA lesions leading to the activation of DNA damage signaling and transcription-coupled repair. Recovery of RNA synthesis following the resolution of repair of transcription-blocking lesions is critical to avoid apoptosis and several new factors involved in this process have recently been identified. Some DNA repair proteins are recruited to initiating RNA polymerases and this may expediate the recruitment of other factors that participate in the repair of transcription-blocking DNA lesions. Recent studies have shown that transcription of protein-coding genes does not always give rise to spliced transcripts, opening the possibility that cells may use the transcription machinery in a splicing-uncoupled manner for other purposes including surveillance of the transcribed genome.
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Affiliation(s)
- Mats Ljungman
- Departments of Radiation Oncology and Environmental Health Sciences, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA.
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Sakasai R, Wakasugi M, Matsui T, Sunatani Y, Saijo M, Matsunaga T, Iwabuchi K. Camptothecin compromises transcription recovery and cell survival against cisplatin and ultraviolet irradiation regardless of transcription-coupled nucleotide excision repair. DNA Repair (Amst) 2022; 113:103318. [PMID: 35325630 DOI: 10.1016/j.dnarep.2022.103318] [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: 09/10/2021] [Revised: 02/18/2022] [Accepted: 03/07/2022] [Indexed: 11/28/2022]
Abstract
DNA-damaging anti-cancer drugs are used clinically to induce cell death by causing DNA strand breaks or DNA replication stress. Camptothecin (CPT) and cisplatin are commonly used anti-cancer drugs, and their combined use enhances the anti-tumour effects. However, the mechanism underlying this enhanced effect has not been well studied. In this study, we analysed the combined effect of CPT and cisplatin or ultraviolet (UV) and found that CPT suppresses transcription recovery after UV damage and induces the disappearance of the Cockayne syndrome group B (CSB) protein, a transcription-coupled nucleotide excision repair (TC-NER) factor. This CPT-induced disappearance of CSB expression was suppressed by proteasome and transcription inhibitors. Moreover, CSB ubiquitination was detected after CPT treatment in a transcription-dependent manner, suggesting that the transcription stress caused by CPT induces CSB ubiquitination, resulting in CSB undetectability. However, Cockayne syndrome group A (CSA) and CUL4A were not involved in the CPT-induced CSB undetectability, suggesting that CSB ubiquitination caused by CPT is regulated differently from the UV response. However, cisplatin or UV sensitivity was enhanced by CPT even in CSB- or CSA-knockout cells. Furthermore, the excessive CSB expression, which suppressed CSB ubiquitination, did not cancel the combined effect of CPT. These results suggest that CPT blocks the repair of cisplatin or UV-induced DNA damage regardless of TC-NER status. CPT possibly compromised the alternative repair pathways other than TC-NER, leading to the suppression of transcription recovery and enhancement of cell killing.
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Affiliation(s)
- Ryo Sakasai
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa 920-0293, Japan.
| | - Mitsuo Wakasugi
- Laboratory of Human Molecular Genetics, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Tadashi Matsui
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa 920-0293, Japan
| | - Yumi Sunatani
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa 920-0293, Japan
| | - Masafumi Saijo
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tsukasa Matsunaga
- Laboratory of Human Molecular Genetics, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Kuniyoshi Iwabuchi
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa 920-0293, Japan.
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Zhao P, Ma X, Cheng J, Chen H, Li L. Identification of the hub genes and transcription factor-miRNA axes involved in Helicobacter pylori-associated gastric cancer. Oncol Lett 2022; 23:89. [PMID: 35126731 PMCID: PMC8805177 DOI: 10.3892/ol.2022.13209] [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: 02/05/2020] [Accepted: 11/26/2021] [Indexed: 12/03/2022] Open
Abstract
It has been previously reported that transcription factor-microRNA (TF-miRNA) axes play a significant role in the carcinogenesis of several types of malignant tumor. However, there is a lack of research into the differences in the mechanism of Helicobacter pylori (HP)-positive [HP(+)] and HP-negative [HP(−)] gastric cancer. The aim of the present study was to identify the hub genes and TF-miRNA axes, and to determine the potential mechanisms involved in HP-associated gastric cancer. HP-associated mRNA and miRNA data, as well as the corresponding clinical information, was downloaded from The Cancer Genome Atlas database. Differentially expressed genes (DEGs) and DE miRNAs (DEMs) were then identified from the HP(+) and HP(−) cancer mRNA and miRNA datasets, respectively. Subsequently, gene set enrichment analysis and the protein-protein interaction (PPI) networks were investigated using the ClusterProfiler packages. Lastly, TF-miRNA-DEG networks were constructed using the miRWalk online tool. A total of 1,050 DEGs and 13 DEMs were identified from the normalized mRNA and miRNA expression datasets, respectively. In addition, 180 Gene Ontology terms and 30 Kyoto Encyclopedia of Genes and Genomes pathways were found to be enriched, while 6 hub genes were identified from the PPI analysis. Furthermore, 7 TF-miRNA interactions and 181 TF-miRNA-DEG axes were constructed using an integrated bioinformatics approach, while 2 TF-miRNA interactions (ZEB1-miRNA-144-3p and PAX2-miRNA-592) were confirmed using reverse transcription-quantitative PCR in samples from enrolled patients. Moreover, the ZEB1-miRNA-144-3p axis was further validated based on dual luciferase reporter assay results. In summary, an integrated bioinformatics approach was used to screen the significant molecular and regulatory axes, which may provide a novel direction to investigate the pathogenesis of gastric cancer associated with HP.
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Affiliation(s)
- Peng Zhao
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Xianxiong Ma
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Jiancheng Cheng
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Hengyu Chen
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Hainan Medical University, Haikou, Hainan 570100, P.R. China.,Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Lei Li
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
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The Tardigrade Damage Suppressor Protein Modulates Transcription Factor and DNA Repair Genes in Human Cells Treated with Hydroxyl Radicals and UV-C. BIOLOGY 2021; 10:biology10100970. [PMID: 34681069 PMCID: PMC8533384 DOI: 10.3390/biology10100970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/24/2021] [Accepted: 09/24/2021] [Indexed: 12/22/2022]
Abstract
Simple Summary The Ramazzottius varieornatus is known to be the most resilient invertebrate on Earth. Belonging to the phylum of Tardigrada, it can live in any habitat, from the deep sea to various terrestrial environments, surviving in extreme temperatures, severe dryness or air deprivation. This exceptional tolerance to extreme conditions is attributable to the Dsup protein, which is able to bind and “protect” the DNA of this micro-animal, allowing it to survive where most other forms of life would quickly die. By introducing Dsup in human cell cultures, we investigated how this protein operates in response to two different extreme conditions: oxidative stress and ultraviolet (UV) irradiation. We learned that Dsup increases cell survival by triggering significantly different cellular mechanisms. In cells treated with hydrogen peroxide, Dsup “physically” protects DNA and activates several detoxification pathways aimed to remove intracellular free radicals. In contrast to this, a direct protection of DNA is not exerted by Dsup after UV irradiation, but the protein seems to activate mechanisms of DNA damage repair more efficiently, promoting faster cell recovery and survival. Even though further studies are required, understanding the mechanisms associated with Dsup resistance to cell damage may represent an important benefit for humans and plants. Abstract The Ramazzottius varieornatus tardigrade is an extremotolerant terrestrial invertebrate with a length of 0.1–1.0 mm. These small animals show an extraordinary tolerance to extreme conditions such as high pressure, irradiation, chemicals and dehydration. These abilities are linked to a recently discovered damage suppressor protein (Dsup). Dsup is a nucleosome-binding protein that avoids DNA damage after X-ray and oxidative stress exposure without impairing cell life in Dsup-transfected animal and plant cells. The exact “protective” role of this protein is still under study. In human cells, we confirmed that Dsup confers resistance to UV-C and H2O2 exposure compared to untransfected cells. A different transcription factor activation was also observed. In addition, a different expression of endogenous genes involved in apoptosis, cell survival and DNA repair was found in Dsup+ cells after H2O2 and UV-C. In UV-C exposed cells, Dsup efficiently upregulates DNA damage repair genes, while H2O2 treatment only marginally involves the activation of pathways responsible for DNA repair in Dsup+ cells. These data are in agreement with the idea of a direct protective effect of the protein on DNA after oxidative stress. In conclusion, our data may help to outline the different mechanisms by which the Dsup protein works in response to different insults.
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Global analysis of RNA metabolism using bio-orthogonal labeling coupled with next-generation RNA sequencing. Methods 2018; 155:88-103. [PMID: 30529548 DOI: 10.1016/j.ymeth.2018.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 11/21/2022] Open
Abstract
Many open questions in RNA biology relate to the kinetics of gene expression and the impact of RNA binding regulatory factors on processing or decay rates of particular transcripts. Steady state measurements of RNA abundance obtained from RNA-seq approaches are not able to separate the effects of transcription from those of RNA decay in the overall abundance of any given transcript, instead only giving information on the (presumed steady-state) abundances of transcripts. Through the combination of metabolic labeling and high-throughput sequencing, several groups have been able to measure both transcription rates and decay rates of the entire transcriptome of an organism in a single experiment. This review focuses on the methodology used to specifically measure RNA decay at a global level. By comparing and contrasting approaches and describing the experimental protocols in a modular manner, we intend to provide both experienced and new researchers to the field the ability to combine aspects of various protocols to fit the unique needs of biological questions not addressed by current methods.
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Hamilton G, Rath B. Pharmacogenetics of platinum-based chemotherapy in non-small cell lung cancer: predictive validity of polymorphisms of ERCC1. Expert Opin Drug Metab Toxicol 2017; 14:17-24. [PMID: 29226731 DOI: 10.1080/17425255.2018.1416095] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION The efficacy of platinum-based chemotherapy for patients with non-small cell lung cancer (NSCLC) is limited by chemoresistance. Platinum drugs damage DNA by introducing intrastrand and interstrand crosslinks which result in cell death. Excision repair cross-complementing 1 (ERCC1) is a member of the nucleotide excision repair (NER) pathway which erases such defects. Single nucleotide polymorphisms (SNPs) in ERCC1 impair this activity and have been suggested to predict the response to chemotherapy. Area covered: Among the polymorphisms of proteins involved in uptake, metabolism, cytotoxicity and efflux of platinum drugs, codon 118 C/T and C8092A in ERCC1 are the best characterized SNPs studied for their predictive power. Here, the divergent results for studies of these markers in NSCLC are summarized and the reasons for this contradictory data discussed. Expert opinion: Cytotoxicity of platinum compounds comprise complex cellular processes for which DNA repair may not constitute the rate limiting step. These drugs are administered as doublets to histologically diverse patients and, furthermore, the NER pathway in ERCC1 wildtype cohorts may be still impaired by the chemotherapeutics applied. At present, assessment of a limited number of polymorphism in DNA repair proteins is not reliably associated with response to treatment in NSCLC patients.
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Affiliation(s)
- Gerhard Hamilton
- a Department of Surgery , Medical University of Vienna , Vienna , Austria
| | - Barbara Rath
- a Department of Surgery , Medical University of Vienna , Vienna , Austria
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Eskandari E, Rezaifar A, Hashemi M. XPG Asp1104His, XRCC2 Rs3218536 A/G and RAD51 135G/C Gene Polymorphisms and Colorectal Cancer Risk: A Meta-Analysis. Asian Pac J Cancer Prev 2017; 18:1805-1813. [PMID: 28749109 PMCID: PMC5648383 DOI: 10.22034/apjcp.2017.18.7.1805] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background: DNA repair mechanisms are crucial for sustaining DNA integrity and preventing carcinogenesis. The xeroderma pigmentosum group G (XPG), X-ray repair cross complementing group 2 (XRCC2) and RAD51 are candidate genes for DNA repair pathways. Methods: We performed a meta-analysis of 26 studies that assessed the impact of XPG Asp1104His, XRCC2 rs3218536 A/G and RAD51 135G/C polymorphisms on colorectal cancer (CRC) risk. This study included 10288 CRC patients and 11885 controls, and odds ratio (OR) with its 95% confidence interval (CI) were used to calculate the strength of association. Results: The results of overall meta-analysis suggested an association between the XPG Asp1104His polymorphism and CRC susceptibility in allele (OR=1.06; 95% CI=1.01-1.12) and heterozygote model (OR=1.16; 95%CI=1.02-1.31). In the subgroup analysis based on ethnicity and source of control, we found significantly increased CRC cancer risk in Asians (OR=1.12, 95%CI=1.04-1.21) and in hospital-based (OR=1.22, 95%CI=1.08-1.38) populations. Moreover, the RAD51 135 G/C polymorphism increased the risk of CRC in total using allele (OR=1.21) and recessive models (OR=1.62). However, XRCC2 rs3218536 A/G was not associated with the risk of CRC in total or in subgroups. Conclusions: According to the results of our meta-analysis, the XPG Asp1104His and RAD51 135 G/C polymorphisms might influence colorectal cancer risk.
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Affiliation(s)
- Ebrahim Eskandari
- Genetic of Non-Communicable Disease Research Center, School of Medicine, University of Medical Sciences, Zahedan, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran.
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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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