1
|
Wen T, Zhao S, Stingele J, Ravanat JL, Greenberg MM. Quantification of Intracellular DNA-Protein Cross-Links with N7-Methyl-2'-Deoxyguanosine and Their Contribution to Cytotoxicity. Chem Res Toxicol 2024; 37:814-823. [PMID: 38652696 PMCID: PMC11105979 DOI: 10.1021/acs.chemrestox.4c00076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The major product of DNA-methylating agents, N7-methyl-2'-deoxyguanosine (MdG), is a persistent lesion in vivo, but it is not believed to have a large direct physiological impact. However, MdG reacts with histone proteins to form reversible DNA-protein cross-links (DPCMdG), a family of DNA lesions that can significantly threaten cell survival. In this paper, we developed a tandem mass spectrometry method for quantifying the amounts of MdG and DPCMdG in nuclear DNA by taking advantage of their chemical lability and the concurrent release of N7-methylguanine. Using this method, we determined that DPCMdG is formed in less than 1% yield based upon the levels of MdG in methyl methanesulfonate (MMS)-treated HeLa cells. Despite its low chemical yield, DPCMdG contributes to MMS cytotoxicity. Consequently, cells that lack efficient DPC repair by the DPC protease SPRTN are hypersensitive to MMS. This investigation shows that the downstream chemical and biochemical effects of initially formed DNA damage can have significant biological consequences. With respect to MdG formation, the initial DNA lesion is only the beginning.
Collapse
Affiliation(s)
- Tingyu Wen
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
| | - Shubo Zhao
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Julian Stingele
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Jean-Luc Ravanat
- Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SyMMES, 38000 Grenoble, France
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
| |
Collapse
|
2
|
Cheng X, An J, Lou J, Gu Q, Ding W, Droby GN, Wang Y, Wang C, Gao Y, Anand JR, Shelton A, Satterlee AB, Mann B, Hsiao YC, Liu CW, Lu K, Hingtgen S, Wang J, Liu Z, Miller CR, Wu D, Vaziri C, Yang Y. Trans-lesion synthesis and mismatch repair pathway crosstalk defines chemoresistance and hypermutation mechanisms in glioblastoma. Nat Commun 2024; 15:1957. [PMID: 38438348 PMCID: PMC10912752 DOI: 10.1038/s41467-024-45979-5] [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: 12/11/2022] [Accepted: 02/08/2024] [Indexed: 03/06/2024] Open
Abstract
Almost all Glioblastoma (GBM) are either intrinsically resistant to the chemotherapeutical drug temozolomide (TMZ) or acquire therapy-induced mutations that cause chemoresistance and recurrence. The genome maintenance mechanisms responsible for GBM chemoresistance and hypermutation are unknown. We show that the E3 ubiquitin ligase RAD18 (a proximal regulator of TLS) is activated in a Mismatch repair (MMR)-dependent manner in TMZ-treated GBM cells, promoting post-replicative gap-filling and survival. An unbiased CRISPR screen provides an aerial map of RAD18-interacting DNA damage response (DDR) pathways deployed by GBM to tolerate TMZ genotoxicity. Analysis of mutation signatures from TMZ-treated GBM reveals a role for RAD18 in error-free bypass of O6mG (the most toxic TMZ-induced lesion), and error-prone bypass of other TMZ-induced lesions. Our analyses of recurrent GBM patient samples establishes a correlation between low RAD18 expression and hypermutation. Taken together we define molecular underpinnings for the hallmark tumorigenic phenotypes of TMZ-treated GBM.
Collapse
Affiliation(s)
- Xing Cheng
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Neuro-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Jing An
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
- Institute of Cancer Prevention and Treatment, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, China
| | - Jitong Lou
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Eli Lilly and Company, Indianapolis, IN, 46285, USA
| | - Qisheng Gu
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- Department of Immunology, Université Paris Cité, Paris, France
| | - Weimin Ding
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- Oncology Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Gaith Nabil Droby
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Yilin Wang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Chenghao Wang
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Yanzhe Gao
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jay Ramanlal Anand
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Abigail Shelton
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Andrew Benson Satterlee
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Breanna Mann
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Yun-Chung Hsiao
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Chih-Wei Liu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Shawn Hingtgen
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jiguang Wang
- Division of Life Science, Department of Chemical and Biological Engineering, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Hong Kong Center for Neurodegenerative Diseases, InnoHK, Hong Kong SAR, China
| | - Zhaoliang Liu
- Institute of Cancer Prevention and Treatment, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, China
| | - C Ryan Miller
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Pathology, Division of Neuropathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- Division of Oral and Craniofacial Health Science, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA.
| | - Yang Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA.
| |
Collapse
|
3
|
Cheng X, An J, Lou J, Gu Q, Ding W, Droby G, Wang Y, Wang C, Gao Y, Shelton A, Satterlee AB, Mann BE, Hsiao YC, Liu CW, Liu K, Hingtgen S, Wang J, Liu Z, Miller R, Wu D, Vaziri C, Yang Y. Trans-Lesion Synthesis and Mismatch Repair Pathway Crosstalk Defines Chemoresistance and Hypermutation Mechanisms in Glioblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562506. [PMID: 37905107 PMCID: PMC10614844 DOI: 10.1101/2023.10.16.562506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Almost all Glioblastoma (GBM) are either intrinsically resistant to the chemotherapeutical drug temozolomide (TMZ) or acquire therapy-induced mutations that cause chemoresistance and recurrence. The genome maintenance mechanisms responsible for GBM chemoresistance and hypermutation are unknown. We show that the E3 ubiquitin ligase RAD18 (a proximal regulator of TLS) is activated in a Mismatch repair (MMR)-dependent manner in TMZ-treated GBM cells, promoting post-replicative gap-filling and survival. An unbiased CRISPR screen provides a new aerial map of RAD18-interacting DNA damage response (DDR) pathways deployed by GBM to tolerate TMZ genotoxicity. Analysis of mutation signatures from TMZ-treated GBM reveals a role for RAD18 in error-free bypass of O6mG (the most toxic TMZ-induced lesion), and error-prone bypass of other TMZ-induced lesions. Our analyses of recurrent GBM patient samples establishes a correlation between low RAD18 expression and hypermutation. Taken together we define novel molecular underpinnings for the hallmark tumorigenic phenotypes of TMZ-treated GBM.
Collapse
Affiliation(s)
- Xing Cheng
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Neuro-Oncology, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, China
| | - Jing An
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Institute of Cancer Prevention and Treatment, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, China
| | - Jitong Lou
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Qisheng Gu
- Unit of Immunity and Pediatric Infectious Diseases, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
- Department of Immunology, Université Paris Cité, Paris, France
| | - Weimin Ding
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Oncology Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Gaith Droby
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Yilin Wang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Chenghao Wang
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yanzhe Gao
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Abigail Shelton
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Andrew Benson Satterlee
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC 27599
| | - Breanna Elizabeth Mann
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC 27599
| | - Yun-Chung Hsiao
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Chih-Wei Liu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kun Liu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Shawn Hingtgen
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC 27599
| | - Jiguang Wang
- Division of Life Science, Department of Chemical and Biological Engineering, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Hong Kong Center for Neurodegenerative Diseases, InnoHK, Hong Kong SAR, China
| | - Zhaoliang Liu
- Institute of Cancer Prevention and Treatment, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, China
| | - Ryan Miller
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Pathology, Division of Neuropathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Division of Oral and Craniofacial Health Science, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yang Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| |
Collapse
|
4
|
Cheng X, An J, Lou J, Gu Q, Ding W, Droby G, Wang Y, Wang C, Gao Y, Shelton A, Satterlee AB, Mann BE, Hsiao YC, Liu CW, Liu K, Hingtgen S, Wang J, Liu Z, Miller R, Wu D, Vaziri C, Yang Y. Trans-Lesion Synthesis and Mismatch Repair Pathway Crosstalk Defines Chemoresistance and Hypermutation Mechanisms in Glioblastoma. RESEARCH SQUARE 2023:rs.3.rs-2367368. [PMID: 37886584 PMCID: PMC10602147 DOI: 10.21203/rs.3.rs-2367368/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Almost all Glioblastoma (GBM) are either intrinsically resistant to the chemotherapeutical drug temozolomide (TMZ) or acquire therapy-induced mutations that cause chemoresistance and recurrence. The genome maintenance mechanisms responsible for GBM chemoresistance and hypermutation are unknown. We show that the E3 ubiquitin ligase RAD18 (a proximal regulator of TLS) is activated in a Mismatch repair (MMR)-dependent manner in TMZ-treated GBM cells, promoting post-replicative gap-filling and survival. An unbiased CRISPR screen provides a new aerial map of RAD18-interacting DNA damage response (DDR) pathways deployed by GBM to tolerate TMZ genotoxicity. Analysis of mutation signatures from TMZ-treated GBM reveals a role for RAD18 in error-free bypass of O6mG (the most toxic TMZ-induced lesion), and error-prone bypass of other TMZ-induced lesions. Our analyses of recurrent GBM patient samples establishes a correlation between low RAD18 expression and hypermutation. Taken together we define novel molecular underpinnings for the hallmark tumorigenic phenotypes of TMZ-treated GBM.
Collapse
Affiliation(s)
- Xing Cheng
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Neuro-Oncology, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, China
| | - Jing An
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Institute of Cancer Prevention and Treatment, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, China
| | - Jitong Lou
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Qisheng Gu
- Unit of Immunity and Pediatric Infectious Diseases, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
- Department of Immunology, Université Paris Cité, Paris, France
| | - Weimin Ding
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Oncology Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Gaith Droby
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Yilin Wang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Chenghao Wang
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yanzhe Gao
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Abigail Shelton
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Andrew Benson Satterlee
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC 27599
| | - Breanna Elizabeth Mann
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC 27599
| | - Yun-Chung Hsiao
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Chih-Wei Liu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kun Liu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Shawn Hingtgen
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC 27599
| | - Jiguang Wang
- Division of Life Science, Department of Chemical and Biological Engineering, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Hong Kong Center for Neurodegenerative Diseases, InnoHK, Hong Kong SAR, China
| | - Zhaoliang Liu
- Institute of Cancer Prevention and Treatment, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, China
| | - Ryan Miller
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Pathology, Division of Neuropathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Division of Oral and Craniofacial Health Science, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yang Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| |
Collapse
|
5
|
Danaeifar M, Negahdari B, Eslam HM, Zare H, Ghanaat M, Koushali SS, Malekshahi ZV. Polymeric nanoparticles for DNA vaccine-based cancer immunotherapy: a review. Biotechnol Lett 2023; 45:1053-1072. [PMID: 37335426 DOI: 10.1007/s10529-023-03383-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 03/28/2023] [Accepted: 04/11/2023] [Indexed: 06/21/2023]
Abstract
Cancer is one of the leading causes of death and mortality in the world. There is an essential need to develop new drugs or therapeutic approaches to manage treatment-resistant cancers. Cancer immunotherapy is a type of cancer treatment that uses the power of the body's immune system to prevent, control, and eliminate cancer. One of the materials used as a vaccine in immunotherapy is DNA. The application of polymeric nanoparticles as carriers for DNA vaccines could be an effective therapeutic approach to activate immune responses and increase antigen presentation efficiency. Various materials have been used as polymeric nanoparticles, including: chitosan, poly (lactic-co-glycolic acid), Polyethylenimine, dendrimers, polypeptides, and polyesters. Application of these polymer nanoparticles has several advantages, including increased vaccine delivery, enhanced antigen presentation, adjuvant effects, and more sustainable induction of the immune system. Besides many clinical trials and commercial products that were developed based on polymer nanoparticles, there is still a need for more comprehensive studies to increase the DNA vaccine efficiency in cancer immunotherapy using this type of carrier.
Collapse
Affiliation(s)
- Mohsen Danaeifar
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Babak Negahdari
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Houra Mobaleghol Eslam
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamed Zare
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Momeneh Ghanaat
- Department of Microbiology, Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran
| | - Sekinehe Shokouhi Koushali
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Ziba Veisi Malekshahi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
6
|
Schmaltz LF, Koag MC, Kou Y, Zhang L, Lee S. Genotoxic effects of the major alkylation damage N7-methylguanine and methyl formamidopyrimidine. Biochem J 2023; 480:573-585. [PMID: 37078496 PMCID: PMC11061863 DOI: 10.1042/bcj20220460] [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: 08/31/2022] [Revised: 03/29/2023] [Accepted: 04/19/2023] [Indexed: 04/21/2023]
Abstract
Various alkylating agents are known to preferentially modify guanine in DNA, resulting in the formation of N7-alkylguanine (N7-alkylG) and the imidazole ring opened alkyl-formamidopyrimidine (alkyl-FapyG) lesions. Evaluating the mutagenic effects of N7-alkylG has been challenging due to the instability of the positively charged N7-alkylG. To address this issue, we developed a 2'-fluorine-mediated transition-state destabilization approach, which stabilizes N7-alkylG and prevents spontaneous depurination. We also developed a postsynthetic conversion of 2'-F-N7-alkylG DNA into 2'-F-alkyl-FapyG DNA. Using these methods, we incorporated site-specific N7-methylG and methyl-FapyG into pSP189 plasmid and determined their mutagenic properties in bacterial cells using the supF-based colony screening assay. The mutation frequency of N7-methylG was found to be less than 0.5%. Our crystal structure analysis revealed that N7-methylation did not significantly alter base pairing properties, as evidenced by a correct base pairing between 2'-F-N7-methylG and dCTP in Dpo4 polymerase catalytic site. In contrast, the mutation frequency of methyl-FapyG was 6.3%, highlighting the mutagenic nature of this secondary lesion. Interestingly, all mutations arising from methyl-FapyG in the 5'-GGT(methyl-FapyG)G-3' context were single nucleotide deletions at the 5'-G of the lesion. Overall, our results demonstrate that 2'-fluorination technology is a useful tool for studying the chemically labile N7-alkylG and alkyl-FapyG lesions.
Collapse
Affiliation(s)
- Lillian F Schmaltz
- From the Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Myong-Chul Koag
- From the Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Yi Kou
- From the Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Louis Zhang
- From the Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Seongmin Lee
- From the Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, U.S.A
| |
Collapse
|
7
|
Song J, He GN, Dai L. A comprehensive review on celastrol, triptolide and triptonide: Insights on their pharmacological activity, toxicity, combination therapy, new dosage form and novel drug delivery routes. Biomed Pharmacother 2023; 162:114705. [PMID: 37062220 DOI: 10.1016/j.biopha.2023.114705] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/01/2023] [Accepted: 04/12/2023] [Indexed: 04/18/2023] Open
Abstract
Celastrol, triptolide and triptonide are the most significant active ingredients of Tripterygium wilfordii Hook F (TWHF). In 2007, the 'Cell' journal ranked celastrol, triptolide, artemisinin, capsaicin and curcumin as the five natural drugs that can be developed into modern medicinal compounds. In this review, we collected relevant data from the Web of Science, PubMed and China Knowledge Resource Integrated databases. Some information was also acquired from government reports and conference papers. Celastrol, triptolide and triptonide have potent pharmacological activity and evident anti-cancer, anti-tumor, anti-obesity and anti-diabetes effects. Because these compounds have demonstrated unique therapeutic potential for acute and chronic inflammation, brain injury, vascular diseases, immune diseases, renal system diseases, bone diseases and cardiac diseases, they can be used as effective drugs in clinical practice in the future. However, celastrol, triptolide and triptonide have certain toxic effects on the liver, kidney, cholangiocyte heart, ear and reproductive system. These shortcomings limit their clinical application. Suitable combination therapy, new dosage forms and new routes of administration can effectively reduce toxicity and increase the effect. In recent years, the development of different targeted drug delivery formulations and administration routes of celastrol and triptolide to overcome their toxic effects and maximise their efficacy has become a major focus of research. However, in-depth investigation is required to elucidate the mechanisms of action of celastrol, triptolide and triptonide, and more clinical trials are required to assess the safety and clinical value of these compounds.
Collapse
Affiliation(s)
- Jing Song
- School of Pharmacy, Binzhou Medical University, Yantai, China; Shandong Yuze Pharmaceutical Industry Technology Research Institute Co., Ltd, Dezhou, China
| | - Guan-Nan He
- Shandong University of Traditional Chinese Medicine, Ji'nan 250014, China
| | - Long Dai
- School of Pharmacy, Binzhou Medical University, Yantai, China.
| |
Collapse
|
8
|
Wen T, Yang K, Greenberg MM. Local Alteration of Ionic Strength in a Nucleosome Core Particle and Its Effect on N7-Methyl-2'-deoxyguanosine Depurination. Biochemistry 2022; 61:2221-2228. [PMID: 36136907 PMCID: PMC9670023 DOI: 10.1021/acs.biochem.2c00342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Positively charged N-terminal histone tails play important roles in maintaining the nucleosome (and chromatin) structure and function. Charge alteration, including those imposed by post-translational modifications, impacts chromatin dynamics, protein binding, and the fate of DNA damage. There is evidence that N-terminal histone tails affect the local ionic environment within a nucleosome core particle (NCP), but this phenomenon is not well understood. Determining the modulation of the local ionic environment within an NCP by histone tails could help uncover the underlying mechanisms of their functions and effects. Utilizing bottom-up syntheses of NCPs containing wild-type or mutated histones and a fluorescent probe that is sensitive to the local ionic environment, we show that interaction with positively charged N-terminal tails increases the local ionic strength near nucleosomal DNA. The effect is diminished by replacing positively charged residues with neutral ones or deleting a tail in its entirety. Replacing the fluorescent probe with the major DNA methylation product, N7-methyl-2'-deoxyguanosine (MdG), revealed changes in the depurination rate constant varying inversely with local ionic strength. These data indicate that the MdG hydrolysis rates depend on and also inform on local ionic strength in an NCP. Overall, histone tail charge contributes to the complexity of the NCP structure and function by modulating the local ionic strength.
Collapse
Affiliation(s)
- Tingyu Wen
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Kun Yang
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| |
Collapse
|
9
|
Ryan BJ, Yang H, Bacurio JHT, Smith MR, Basu AK, Greenberg MM, Freudenthal BD. Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication. J Am Chem Soc 2022; 144:8054-8065. [PMID: 35499923 PMCID: PMC9097547 DOI: 10.1021/jacs.2c00193] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
N6-(2-Deoxy-α,β-d-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamido pyrimidine (Fapy•dG) is a prevalent form of genomic DNA damage. Fapy•dG is formed in greater amounts under anoxic conditions than the well-studied, chemically related 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxodGuo). Fapy•dG is more mutagenic in mammalian cells than 8-oxodGuo. A distinctive property of Fapy•dG is facile epimerization, but prior works with Fapy•dG analogues have precluded determining its effect on chemistry. We present crystallographic characterization of natural Fapy•dG in duplex DNA and as the template base for DNA polymerase β (Pol β). Fapy•dG adopts the β-anomer when base paired with cytosine but exists as a mixture of α- and β-anomers when promutagenically base paired with adenine. Rotation about the bond between the glycosidic nitrogen atom and the pyrimidine ring is also affected by the opposing nucleotide. Sodium cyanoborohydride soaking experiments trap the ring-opened Fapy•dG, demonstrating that ring opening and epimerization occur in the crystalline state. Ring opening and epimerization are facilitated by propitious water molecules that are observed in the structures. Determination of Fapy•dG mutagenicity in wild type and Pol β knockdown HEK 293T cells indicates that Pol β contributes to G → T transversions but also suppresses G → A transitions. Complementary kinetic studies have determined that Fapy•dG promotes mutagenesis by decreasing the catalytic efficiency of dCMP insertion opposite Fapy•dG, thus reducing polymerase fidelity. Kinetic studies have determined that dCMP incorporation opposite the β-anomer is ∼90 times faster than the α-anomer. This research identifies the importance of anomer dynamics, a feature unique to formamidopyrimidines, when considering the incorporation of nucleotides opposite Fapy•dG and potentially the repair of this structurally unusual lesion.
Collapse
Affiliation(s)
- Benjamin J Ryan
- Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Haozhe Yang
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Jan Henric T Bacurio
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Mallory R Smith
- Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Ashis K Basu
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| |
Collapse
|
10
|
Wang D, Wang X, Jiang Y, Cao S, Jin P, Pan H, Sun H, Sun Z, Chen J. Excited State Dynamics of Methylated Guanosine Derivatives Revealed by Femtosecond Time-resolved Spectroscopy. Photochem Photobiol 2022; 98:1008-1016. [PMID: 35203108 DOI: 10.1111/php.13612] [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: 11/29/2021] [Accepted: 02/20/2022] [Indexed: 11/28/2022]
Abstract
Methylated DNA/RNA nucleobases are important epigenetic marks in living species and play an important role for targeted therapies. Moreover, they could bring significant changes to the photo-stability of nucleic acid, leading these sites become mutational hotspots for disease such as skin cancer. While a number of studies have demonstrated the relationship between excited state dynamics and the biological function of methylated cytosine in DNA, investigations aimed at unraveling the excited state dynamics of methylated guanosine in RNA have been largely overlooked. In this work, influence of methylation on the excited state dynamics of guanosine is studied by using femtosecond time-resolved spectroscopy. Our results suggest that the effect of methyl substitution on the photophysical properties of guanosine is position sensitive. N1-methylguanosine shows very similar excited state dynamics as that in guanosine, while almost one order of magnitude longer lifetime of the La state is observed in N2, N2-dimethylguanosine. Notably, N7-methylation can lead to a new minimum on the La state, which shows a two orders of magnitude longer excited state lifetime compared with guanosine. These findings not only help understanding excited state dynamics of methylated guanosines, but also lay the foundation for further studying DNA/RNA strands incorporated with these bases.
Collapse
Affiliation(s)
- Danhong Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Xueli Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Yanrong Jiang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Simin Cao
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Peipei Jin
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Haifeng Pan
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Haitao Sun
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Zhenrong Sun
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi, 030006, China
| |
Collapse
|
11
|
Díaz-Muñoz M, Hernández-Muñoz R, Butanda-Ochoa A. Structure-activity features of purines and their receptors: implications in cell physiopathology. MOLECULAR BIOMEDICINE 2022; 3:5. [PMID: 35079944 PMCID: PMC8789959 DOI: 10.1186/s43556-022-00068-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/19/2022] [Indexed: 11/21/2022] Open
Abstract
The purine molecular structure consists of fused pyrimidine and imidazole rings. Purines are main pieces that conform the structure of nucleic acids which rule the inheritance processes. Purines also work as metabolic intermediates in different cell functions and as messengers in the signaling pathways throughout cellular communication. Purines, mainly ATP and adenosine (ADO), perform their functional and pharmacological properties because of their structural/chemical characteristics that make them either targets of mutagenesis, mother frameworks for designing molecules with controlled effects (e.g. anti-cancer), or chemical donors (e.g., of methyl groups, which represent a potential chemoprotective action against cancer). Purines functions also come from their effect on specific receptors, channel-linked and G-protein coupled for ATP, and exclusively G-coupled receptors for ADO (also known as ADORAs), which are involved in cell signaling pathways, there, purines work as chemical messengers with autocrine, paracrine, and endocrine actions that regulate cell metabolism and immune response in tumor progression which depends on the receptor types involved in these signals. Purines also have antioxidant and anti-inflammatory properties and participate in the cell energy homeostasis. Therefore, purine physiology is important for a variety of functions relevant to cellular health; thus, when these molecules present a homeostatic imbalance, the stability and survival of the cellular systems become compromised.
Collapse
Affiliation(s)
- Mauricio Díaz-Muñoz
- Departamento de Neurobiología Celular Y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, UNAM, Boulevard Juriquilla 3001, C.P. 76230, Juriquilla, Querétaro, México
| | - Rolando Hernández-Muñoz
- Departamento de Biología Celular Y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, UNAM, Ciudad Universitaria/Circuito Exterior, C.P. 04510, Ciudad de México, México
| | - Armando Butanda-Ochoa
- Departamento de Biología Celular Y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, UNAM, Ciudad Universitaria/Circuito Exterior, C.P. 04510, Ciudad de México, México.
| |
Collapse
|
12
|
Brovarets’ OO, Muradova A, Hovorun DM. Novel horizons of the conformationally-tautomeric transformations of the G·T base pairs: quantum-mechanical investigation. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2026510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ol’ha O. Brovarets’
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Alona Muradova
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| |
Collapse
|
13
|
Liu Y, Zhang X, Lv J, Zhang C, Chang X, Ye S, Wu J. A photocatalytic radical relay reaction of 2-methylthiolated phenylalkynones and potassium metabisulfite. Org Chem Front 2022. [DOI: 10.1039/d1qo01658j] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The generation of methylsufonyl-containing thioflavones through a radical relay reaction of methylthiolated phenylalkynones and potassium metabisulfite in the presence of sodium methylsulfinate under visible light irradiation is developed.
Collapse
Affiliation(s)
- Yuyan Liu
- School of Pharmaceutical and Materials Engineering & Institute for Advanced Studies, Taizhou University, 1139 Shifu Avenue, Zhejiang 318000, China
| | - Xinyi Zhang
- School of Pharmaceutical and Materials Engineering & Institute for Advanced Studies, Taizhou University, 1139 Shifu Avenue, Zhejiang 318000, China
| | - Jiajing Lv
- School of Pharmaceutical and Materials Engineering & Institute for Advanced Studies, Taizhou University, 1139 Shifu Avenue, Zhejiang 318000, China
| | - Chao Zhang
- School of Pharmaceutical and Materials Engineering & Institute for Advanced Studies, Taizhou University, 1139 Shifu Avenue, Zhejiang 318000, China
| | - Xiaotong Chang
- School of Pharmaceutical and Materials Engineering & Institute for Advanced Studies, Taizhou University, 1139 Shifu Avenue, Zhejiang 318000, China
| | - Shengqing Ye
- School of Pharmaceutical and Materials Engineering & Institute for Advanced Studies, Taizhou University, 1139 Shifu Avenue, Zhejiang 318000, China
| | - Jie Wu
- School of Pharmaceutical and Materials Engineering & Institute for Advanced Studies, Taizhou University, 1139 Shifu Avenue, Zhejiang 318000, China
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
| |
Collapse
|
14
|
Nguyen VT, Nguyen QT, Pham NT, Nguyen DT, Pham TN, Tran NQ. An in vitro investigation into targeted paclitaxel delivery nanomaterials based on chitosan-Pluronic P123-biotin copolymer for inhibiting human breast cancer cells. J Drug Deliv Sci Technol 2021. [DOI: 10.1016/j.jddst.2021.102807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
15
|
Effect of N7-methylation on base pairing patterns of guanine: a DFT study. J Mol Model 2021; 27:184. [PMID: 34036469 DOI: 10.1007/s00894-021-04792-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/11/2021] [Indexed: 10/21/2022]
Abstract
In this paper, we aim to determine whether the N7-methylation can influence the base pairing properties of guanine by promoting the formation of guanine enol-tautomers. The keto- to -enol-tautomerization of N7-methylguanine (N7mG) and its base pairing patterns with all the canonical DNA bases have been investigated at the M06-2X/6-311+G(d,p) level of density functional theory. The barrier free energy calculations reveal that N7-methylation does not promote the keto- to enol- tautomerization of guanine. The Watson-Crick-like enol-N7mG:T1 or enol-N7mG:T2 base pair similar to what is observed experimentally is found to be energetically more stable than the keto-N7mG:T base pairs. However, the keto-N7mG:C1 which is structurally similar to the canonical G:C base pair is the most stable base pair among all the base pairs studied here. Thus, our calculations predict that N7mG would pair preferably with cytosine during DNA replication but there is also a probability that it can cause mutation through mispairing with thymine, in agreement with experimental observations.
Collapse
|
16
|
Translesion synthesis of the major nitrogen mustard-induced DNA lesion by human DNA polymerase η. Biochem J 2021; 477:4543-4558. [PMID: 33175093 DOI: 10.1042/bcj20200767] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 12/16/2022]
Abstract
Nitrogen mustards are among the first modern anticancer chemotherapeutics that are still widely used as non-specific anticancer alkylating agents. While the mechanism of action of mustard drugs involves the generation of DNA interstrand cross-links, the predominant lesions produced by these drugs are nitrogen half-mustard-N7-dG (NHMG) adducts. The bulky major groove lesion NHMG, if left unrepaired, can be bypassed by translesion synthesis (TLS) DNA polymerases. However, studies of the TLS past NHMG have not been reported so far. Here, we present the first synthesis of an oligonucleotide containing a site-specific NHMG. We also report kinetic and structural characterization of human DNA polymerase η (polη) bypassing NHMG. The templating NHMG slows dCTP incorporation ∼130-fold, while it increases the misincorporation frequency ∼10-30-fold, highlighting the promutagenic nature of NHMG. A crystal structure of polη incorporating dCTP opposite NHMG shows a Watson-Crick NHMG:dCTP base pair with a large propeller twist angle. The nitrogen half-mustard moiety fits snugly into an open cleft created by the Arg61-Trp64 loop of polη, suggesting a role of the Arg61-Trp64 loop in accommodating bulky major groove adducts during lesion bypass. Overall, our results presented here to provide first insights into the TLS of the major DNA adduct formed by nitrogen mustard drugs.
Collapse
|
17
|
Methylation-dependent MCM6 repression induced by LINC00472 inhibits triple-negative breast cancer metastasis by disturbing the MEK/ERK signaling pathway. Aging (Albany NY) 2021; 13:4962-4975. [PMID: 33668040 PMCID: PMC7950301 DOI: 10.18632/aging.103568] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/17/2020] [Indexed: 12/15/2022]
Abstract
Long noncoding RNAs (lncRNAs) have been identified to be dysregulated in multiple cancer types, which are speculated to be of vital significance in regulating several hallmarks of cancer biology. Triple-negative breast cancer (TNBC) is acknowledged as an aggressive subtype of breast cancer. In this study, we found the lncRNA LINC00472 was poorly expressed in TNBC tissues and cells. Overexpression of LINC00472 could inhibit the proliferation, invasion and migration of MDA-MB-231 cells. On the contrary, minichromosome maintenance complex component 6 (MCM6) was highly expressed in TNBC tissues and MDA-MB-231 cells due to suppressed methylation. LINC00472 induced site-specific DNA methylation and reduced the MCM6 expression by recruiting DNA methyltransferases into the MCM6 promoter. Since the restoration of MCM6 weakened the tumor-suppressive effect of LINC00472 on MDA-MB-231 cells, LINC00472 potentially acted as a tumor suppressor by inhibiting MCM6. In addition, in vivo experiments further substantiated that overexpression of LINC00472 inhibited tumor growth and metastasis to lungs by decreasing the expression of MCM6. Overall, the present study demonstrated that LINC00472-mediated epigenetic silencing of MCM6 contributes to the prevention of tumorigenesis and metastasis in TNBC, providing an exquisite therapeutic target for TNBC.
Collapse
|
18
|
Li W, Jin X, Guo S, Xu F, Su X, Jiang X, Wang G. Comprehensive analysis of prognostic immune-related genes in the tumor microenvironment of colorectal cancer. Aging (Albany NY) 2021; 13:5506-5524. [PMID: 33536348 PMCID: PMC7950244 DOI: 10.18632/aging.202479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/20/2020] [Indexed: 12/11/2022]
Abstract
In this study, we used the ESTIMATE algorithm to analyze clinical data and transcriptome profiles of 1635 colorectal cancer (CRC) samples from the Gene Expression Omnibus and The Cancer Genome Atlas databases and identify prognostic immune-related genes (IRGs). We identified 941 differentially expressed (4 downregulated and 937 upregulated) genes by comparing samples with high and low immune, stromal scores and tumor purity. LASSO Cox regression analyses showed that the risk score based on a ten-IRG signature was an independent prognostic factor in CRC. The nomogram with pathological stages (TNM) and the ten-IRG signature showed a C-index of 0.769 (95% CI, 0.717-0.821), and area under ROC curve values of 0.788, 0.782 and 0.789 for 1-, 3-, and 5-year OS, respectively. TIMER database analysis showed positive correlation between the ten prognostic IRGs and the levels of tumor-infiltrated immune cells, including CD4+ and CD8+ T cells, macrophages, neutrophils, and dendritic cells. These findings demonstrate that this novel ten-IRG signature correlates with the pathological stages and the levels of multiple tumor-infiltrated immune cell types. This makes the ten-IRG signature a potential prognostic factor for CRC patients.
Collapse
Affiliation(s)
- Wei Li
- Department of General Surgery, Hebei Key Laboratory of Colorectal Cancer Precision Diagnosis and Treatment, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xiaojing Jin
- Department of Emergency Medicine, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Shang Guo
- Department of General Surgery, Hebei Key Laboratory of Colorectal Cancer Precision Diagnosis and Treatment, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Fei Xu
- Department of General Surgery, Hebei Key Laboratory of Colorectal Cancer Precision Diagnosis and Treatment, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xingkai Su
- Department of General Surgery, Hebei Key Laboratory of Colorectal Cancer Precision Diagnosis and Treatment, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xia Jiang
- Department of General Surgery, Hebei Key Laboratory of Colorectal Cancer Precision Diagnosis and Treatment, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Guiqi Wang
- Department of General Surgery, Hebei Key Laboratory of Colorectal Cancer Precision Diagnosis and Treatment, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| |
Collapse
|
19
|
A novel five-lncRNA signature panel improves high-risk survival prediction in patients with cholangiocarcinoma. Aging (Albany NY) 2021; 13:2959-2981. [PMID: 33472169 PMCID: PMC7880389 DOI: 10.18632/aging.202446] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/23/2020] [Indexed: 12/21/2022]
Abstract
Cholangiocarcinoma (CCA) is a fatal disease with dismal survival rates. Long non-coding RNA (lncRNA) expression profiling as potential prognostic biomarkers play critical roles in tumor initiation, development, and poor prognosis. Identifying specific lncRNA to predict the prognosis of CCA patients in the early stages is very important for improving a patient’s survival. In the current study, we aimed to establish a novel risk-stratification lncRNA signature panel in CCA. The initial lncRNA discovery was identified in The Cancer Genome Atlas database (TCGA cohort). The Cox regression analysis was used to establish the lncRNA prognostic model and the receiver operating characteristic (ROC) curve analysis was performed to assess the specificity and sensitivity of the model. This was followed by independent validation of the lncRNA signature in the CCA patients from the First Affiliated Hospital of Wenzhou Medical University (WMU cohort). Furthermore, by using the Gene Ontology function and Kyoto Encyclopedia Gene and Genome pathway enrichment analysis, we explored the potential function of prognosis lncRNA. Finally, five lncRNA (HULC; AL359715.5; AC006504.8; AC090114.2; AP00943.4) were screened to establish the predictive model that significantly associated with poor overall survival(HR:4.879;95%CI,1.587-14.996;p=0.006). This five-lncRNA signature model showed excellent accuracy in the TCGA cohort (AUC=0.938), and also robustly predicted survival in the validation WMU cohort(AUC=0.816). Functional enrichment analysis suggested prognostic lncRNA was primarily associated with CCA-related biological processes. Our data established a novel lncRNA signature model for CCA risk-stratification and robust identification of CCA patients with poor molecular genotypes. Moreover, it revealed new molecular mechanisms of CCA.
Collapse
|
20
|
Gu M, Sun J, Zhang S, Chen J, Wang G, Ju S, Wang X. A novel methylation signature predicts inferior outcome of patients with PDAC. Aging (Albany NY) 2021; 13:2851-2863. [PMID: 33550277 PMCID: PMC7880369 DOI: 10.18632/aging.202347] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 11/10/2020] [Indexed: 04/07/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) will become the second most common cause of death in North America and Europe over the next 10 years owing to the lack of early diagnosis, poor treatment, and poor prognosis. This study evaluated the methylation array data of 184 patients with PDAC in The Cancer Genome Atlas database to explore methylation biomarkers related to patient outcome. Using Univariable Cox regression analysis and Lasso regression analysis method in the training dataset, it was found that the four DNA methylation markers (CCNT1, ITGB3, SDS, and HMOX2) were significantly correlated with the overall survival of patients with PDAC. Kaplan-Meier analysis showed that these four DNA methylation markers could significantly distinguish high-risk and low-risk patients. Receiver operating characteristic analysis further confirmed that the four DNA methylation markers had high sensitivity and specificity, which could predict the prognosis of patients. Moreover, there was a difference in the genetic mutations between high-risk and low-risk patients distinguished by the four-DNA methylation model, which can provide information for clinical treatment. Finally, compared with known biomarkers, the model was more accurate in predicting the prognosis of PDAC. This four-DNA methylation model has potential as a new independent prognostic indicator, and could be used for the diagnosis, monitoring, and precision medicine of pancreatic cancer.
Collapse
Affiliation(s)
- Minqi Gu
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Jing Sun
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Shunhao Zhang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Jing Chen
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Guihua Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
- School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
- School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Xudong Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
- School of Public Health, Nantong University, Nantong, Jiangsu, China
| |
Collapse
|
21
|
Hsu LW, Huang KH, Chen MH, Fang WL, Chao Y, Lo SS, Li AFY, Wu CW, Shyr YM. Genetic alterations in gastric cancer patients according to sex. Aging (Albany NY) 2020; 13:376-388. [PMID: 33288737 PMCID: PMC7835020 DOI: 10.18632/aging.202142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/09/2020] [Indexed: 02/06/2023]
Abstract
To date, few reports have investigated the genetic alterations and clinicopathological features in gastric cancer (GC) according to sex. In total, 2673 GC patients receiving curative surgery were enrolled. Among the 2673 GC patients, 1979 (74.0%) patients were male. After propensity-score matching, 846 patients were enrolled for the analysis, including 423 males and 423 females. There was no significant difference in the clinicopathological features between the sexes. Regarding the initial recurrence pattern, the males were more likely to develop tumor recurrence and liver metastasis than the females, especially in stage III GC. Regarding the molecular analysis, the males had higher PD-L1 expression than the females, especially in stage III GC. In addition, the patients aged ≥ 65 years had higher PD-L1 expression than the patients younger than 65 years. The multivariate analysis demonstrated that sex was among the independent prognostic factors affecting overall survival (OS) and disease-free survival (DFS). Among the patients with liver metastases, PD-L1 expression was more common among the aged male patients. The males were associated with more tumor recurrence and higher PD-L1 expression than the females, especially in stage III GC. For GC patients with liver metastases, PD-L1 testing is recommended, especially among aged male patients.
Collapse
Affiliation(s)
- Li-Wen Hsu
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Kuo-Hung Huang
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Ming-Huang Chen
- School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Center of Immuno-Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Wen-Liang Fang
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yee Chao
- School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Center of Immuno-Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Su-Shun Lo
- School of Medicine, National Yang-Ming University, Taipei, Taiwan.,National Yang-Ming University Hospital, Yilan, Taiwan
| | - Anna Fen-Yau Li
- School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Pathology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chew-Wun Wu
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Ming Shyr
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| |
Collapse
|
22
|
Chen J, Zheng Y, Wang H, Zhang D, Zhao L, Yu D, Lin Z, Zhang T. Cause of death among patients with colorectal cancer: a population-based study in the United States. Aging (Albany NY) 2020; 12:22927-22948. [PMID: 33289707 PMCID: PMC7746372 DOI: 10.18632/aging.104022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/19/2020] [Indexed: 12/20/2022]
Abstract
CRC (Colorectal cancer) is one of the most common causes of death worldwide and in the US (United States). In this study, we aim to perform a population-based analysis on the cause of death among patients with CRC in the US. A total of 834,510 CRC patients diagnosed between 1975 and 2016 in the US were selected from the SEER (Surveillance, Epidemiology, and End Results) program. Causes of death among CRC patients were characterized and SMRs (standardized mortality ratios) of death from non-cancer causes were calculated. Among all CRC patients included in this study, a total of 531,507 deaths were recorded, of which 51.3% were due to CRC, 10.3% were due to other cancers, and 38.4% were due to non-cancer causes. Recently, there has been a relative decrease in index-cancer deaths and an increase in non-cancer causes among CRC patients. The mortality risk from non-cancer rises with accumulating age and longer follow-up time. Cardiovascular diseases are the most prevalent non-cancer causes, accounting for 20.3% of all deaths among CRC patients. Compared with the general population, the mortality rate of non-cancer deaths among CRC patients is doubled (SMR, 2.02; 95% confidence interval, 2.01-2.03).
Collapse
Affiliation(s)
- Jiayuan Chen
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yongqiang Zheng
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.,State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou 510060, China
| | - Haihong Wang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Dejun Zhang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Lei Zhao
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Dandan Yu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Zhenyu Lin
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Tao Zhang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| |
Collapse
|
23
|
Zhang W, Yang B, Weng L, Li J, Bai J, Wang T, Wang J, Ye J, Jing H, Jiao Y, Chen X, Liu H, Zeng YX. Single cell sequencing reveals cell populations that predict primary resistance to imatinib in chronic myeloid leukemia. Aging (Albany NY) 2020; 12:25337-25355. [PMID: 33226961 PMCID: PMC7803567 DOI: 10.18632/aging.104136] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 09/20/2020] [Indexed: 01/12/2023]
Abstract
The treatment of chronic myeloid leukemia (CML), a disease caused by t(9;22)(q34;q11) reciprocal translocation, has advanced largely through the use of targeted tyrosine kinase inhibitors (TKIs). To identify molecular differences that might distinguish TKI responders from non-responders, we performed single cell RNA sequencing on cells (n = 41,723 cells) obtained from the peripheral blood of four CML patients at different stages of treatment to generate single cell expression profiles. Analysis of our single cell expression profiles in conjunction with those previously obtained from the bone marrow of additional CML patients and healthy donors (total = 69,263 cells) demonstrated that imatinib treatment significantly altered leukocyte population compositions in both responders and non-responders, and affected the expression profiles of multiple cell populations, including non-neoplastic cell types. Notably, in imatinib poor-responders, patient-specific pre-treatment unique stem/progenitor cells became enriched in peripheral blood compared to the responders. These results indicate that resistance to TKIs might be intrinsic in some CML patients rather than acquired, and that non-neoplastic immune cell types may also play vital roles in dispersing the responsiveness of patients to TKIs. Furthermore, these results demonstrated the potential utility of peripheral blood as a diagnostic tool in the TKI sensitivity of CML patients.
Collapse
Affiliation(s)
- Weilong Zhang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing 100191, China.,State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Beibei Yang
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Linqian Weng
- Department of Hematology, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Jiangtao Li
- Department of Hematology, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Jiefei Bai
- Department of Hematology, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Ting Wang
- Department of Hematology, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Jingwen Wang
- Department of Hematology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Jin Ye
- Department of Hematology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Hongmei Jing
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing 100191, China
| | - Yuchen Jiao
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xixi Chen
- Genetron Health (Beijing) Co. Ltd., Beijing 102206, China.,Children’s Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Hui Liu
- Department of Hematology, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Yi-Xin Zeng
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.,Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong Province, China
| |
Collapse
|
24
|
Zou Y, Lu Q, Yao Q, Dong D, Chen B. Identification of novel prognostic biomarkers in renal cell carcinoma. Aging (Albany NY) 2020; 12:25304-25318. [PMID: 33234734 PMCID: PMC7803519 DOI: 10.18632/aging.104131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/29/2020] [Indexed: 12/15/2022]
Abstract
Objective: To identify novel prognostic biomarkers in renal cell carcinoma (RCC). Results: 12 coding genes and one miRNA were finally identified as prognostic biomarkers. All of them were related to a poor prognosis. Lower expression levels of the coding genes were observed in higher clinical stages. Prognostic signatures including 7 biomarkers were identified. Patients in the high-risk group had worse survival than those in the low-risk group. The areas under the curves in different years indicated that it was a valuable signature in prognosis. It was found that elevated WDR72 inhibited the survival and invasion of 786-O and 769P cells in vitro. Conclusions: Thirteen prognostic biomarkers of RCC were identified. Among them, 7 biomarkers comprised a signature to evaluate the RCC prognosis. WDR72 was a cancer suppressor and a potential therapeutic target in RCC. Methods: Differentially expressed genes/miRNAs (DEGs/DEMs) and prognosis-related genes/miRNAs were acquired from public database. Prognostic biomarkers were identified by overlapping the significant DEGs/DEMs and prognosis-related genes/miRNAs. The associations between these biomarkers and the clinical stages were analyzed. All of these prognostic biomarkers were further investigated with multi-variable Cox regression. Finally, the inhibitory effect of WDR72 on the growth and invasion of RCC cells was studied.
Collapse
Affiliation(s)
- Yuanzhang Zou
- Department of Urology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Qiu Lu
- Department of Urology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Qin Yao
- Department of Urology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Di Dong
- Department of Urology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Binghai Chen
- Department of Urology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu, China
| |
Collapse
|
25
|
Zhang Y, Zhou H, Zhang M, Xing L, Yang C, Xia B, Lou G. Integrated analysis of a competing endogenous RNA network reveals an 11-lncRNA prognostic signature in ovarian cancer. Aging (Albany NY) 2020; 12:25153-25171. [PMID: 33223503 PMCID: PMC7803494 DOI: 10.18632/aging.104116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/09/2020] [Indexed: 01/22/2023]
Abstract
Long noncoding RNA (lncRNA) can function as a competing endogenous RNA (ceRNA) involved in tumor initiation and progression. However, the prognostic roles of lncRNAs in the integrated analysis of the ceRNA network in ovarian cancer (OVC) are still lacking. This study aimed to identify lncRNAs associated with the prognosis of OVC. Differential expression analysis and WGCNA were used to screen OVC-specific RNAs. A lncRNA-miRNA-mRNA regulatory network consisting of 201 lncRNAs, 85 miRNA and 146 mRNAs was constructed, and functional enrichment and protein-protein network analyses were performed. Then, the OVC-specific RNAs were submitted to Cox regression analysis. Twelve differentially expressed lncRNAs and mRNAs were identified as significantly associated with OS of OVC patients. Meanwhile, 11 lncRNAs (including C4A-AS1, LINC02408, LINC00488) were established as prognostic risk formulas. The low-risk group had better OS and DFS than the high-risk group (P <0.01). Univariate and multivariate Cox regression analyses revealed the 11-lncRNA risk score as an independent prognostic factor. A prognostic nomogram was developed based on independent prognostic factors. Our data provide evidence that the 11-lncRNA signature could serve as an independent prognostic indicator. This study also suggests that these 11 lncRNAs potentially participate in the progression of OVC.
Collapse
Affiliation(s)
- Yongjian Zhang
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| | - Hu Zhou
- Department of Gynecology Oncology, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230001, Anhui Province, China
| | - Meiyin Zhang
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| | - Linan Xing
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| | - Chang Yang
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| | - Bairong Xia
- Department of Gynecology Oncology, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230001, Anhui Province, China
| | - Ge Lou
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| |
Collapse
|
26
|
Li P, Wang L, Li P, Hu F, Cao Y, Tang D, Ye G, Li H, Wang D. Silencing lncRNA XIST exhibits antiproliferative and proapoptotic effects on gastric cancer cells by up-regulating microRNA-132 and down-regulating PXN. Aging (Albany NY) 2020; 13:14469-14481. [PMID: 33154189 PMCID: PMC8202840 DOI: 10.18632/aging.103635] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 06/25/2020] [Indexed: 02/07/2023]
Abstract
The present study aims to elucidate the potential therapeutic role of lncRNA XIST in gastric cancer through regulation of microRNA-132 (miR-132) and paxillin (PXN) expression. The study employed 65 gastric cancer tissue specimens and SGC7901 cell lines. Our results demonstrated that expression of lncRNA XIST and PXN was significantly elevated while the expression of miR-132 was significantly reduced in gastric cancer tissues. Dual-luciferase, RNA pull-down and RIP assays demonstrated that lncRNA XIST up-regulated the PXN expression by competitively binding to miR-132. Moreover, silencing of lncRNA XIST and up-regulation of miR-132 could suppress tumor formation ability, cell proliferation and migration, but enhanced apoptosis in gastric cancer. However, the overexpression of PXN achieved the opposite tumor-promotive effect. Meanwhile, rescue experiments suggested that silencing of lncRNA XIST could reverse the tumor-promotive effect exerted by either miR-132 inhibitor or PXN. Taken together, the present study demonstrates lncRNA XIST as a novel oncogenic lncRNA in gastric cancer, highlighting its therapeutic role in this disease.
Collapse
Affiliation(s)
- Ping Li
- Department of General Surgery, Huaian Tumor Hospital, Huaian Hospital of Huaian City, Huaian, 223200, P.R. China
- Department of Experimental Surgery-Cancer Metastasis, Medical Faculty Mannheim, Ruprecht Karls University, Mannheim 68167, Germany
| | - Liuhua Wang
- Department of General Surgery, Northern Jiangsu Province Hospital, Clinical Medical College, Institute of General Surgery - Yangzhou, Yangzhou University, Yangzhou 225000, P.R. China
| | - Pengfei Li
- Department of General Surgery, Huaian Tumor Hospital, Huaian Hospital of Huaian City, Huaian, 223200, P.R. China
| | - Fangyong Hu
- Department of General Surgery, Huaian Tumor Hospital, Huaian Hospital of Huaian City, Huaian, 223200, P.R. China
| | - Yi Cao
- Department of Experimental Surgery-Cancer Metastasis, Medical Faculty Mannheim, Ruprecht Karls University, Mannheim 68167, Germany
| | - Dong Tang
- Department of General Surgery, Northern Jiangsu Province Hospital, Clinical Medical College, Institute of General Surgery - Yangzhou, Yangzhou University, Yangzhou 225000, P.R. China
| | - Gang Ye
- Department of General Surgery, Jiangdu People's Hospital of Yangzhou, Yangzhou 225200, P.R. China
| | - Hongbo Li
- Department of General Surgery, Jiangdu People's Hospital of Yangzhou, Yangzhou 225200, P.R. China
| | - Daorong Wang
- Department of General Surgery, Northern Jiangsu Province Hospital, Clinical Medical College, Institute of General Surgery - Yangzhou, Yangzhou University, Yangzhou 225000, P.R. China
| |
Collapse
|
27
|
Gene expression-based clinical predictions in lung adenocarcinoma. Aging (Albany NY) 2020; 12:15492-15503. [PMID: 32756002 PMCID: PMC7467359 DOI: 10.18632/aging.103721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 07/06/2020] [Indexed: 12/25/2022]
Abstract
Mining disease-related genes contributes momentously to handling lung adenocarcinoma (LUAD). But genetic complexity and tumor heterogeneity severely get in the way. Fortunately, new light has been shed by dramatic progress of bioinformatic technology in the past decades. In this research, we investigated relationships between gene expression and clinical features of LUAD via integrative bioinformatic analysis. First, we applied limma and DESeq2 packages to analyze differentially expressed genes (DEGs) of LUAD from GEO database and TCGA project (tumor tissues versus normal tissues), and acquired 180 down-regulated DEGs and 52 up-regulated DEGs. Then, we investigated genetic and biological assignment of theses DEGs by Bioconductor packages and STRING database. We found these DEGs were distributed dispersedly among chromosomes, enriched observably in extracellular matrix-related processes, and weighted hierarchically in interaction network. Finally, we established DEGs-based statistical models for evaluating TNM stage and survival status of LUAD. And these models (logistic regression models for TNM parameter and Cox regression models for survival probability) all possessed fine predictive efficacy (C-indexes: T, 0.740; N, 0.687; M, 0.823; overall survival, 0.678; progression-free survival, 0.611). In summary, we have successfully established gene expression-based models for assessing clinical characteristics of LUAD, which will assist its pathogenesis investigation and clinical intervention.
Collapse
|
28
|
Wu G, Wang Q, Xu Y, Li Q, Cheng L. A new survival model based on ferroptosis-related genes for prognostic prediction in clear cell renal cell carcinoma. Aging (Albany NY) 2020; 12:14933-14948. [PMID: 32688345 PMCID: PMC7425493 DOI: 10.18632/aging.103553] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/04/2020] [Indexed: 12/21/2022]
Abstract
In this study, we analyzed the clinical significance of ferroptosis-related genes (FRGs) in 32 cancer types in the GSCA database. We detected a 2-82% mutation rate among 36 FRGs. In clear cell renal cell carcinoma (ccRCC; n=539) tissues from the The Cancer Genome Atlas database, 30 of 36 FRGs were differentially expressed (up- or down-regulated) compared to normal kidney tissues (n=72). Consensus clustering analysis identified two clusters of FRGs based on similar co-expression in ccRCC tissues. We then used LASSO regression analysis to build a new survival model based on five risk-related FRGs (CARS, NCOA4, FANCD2, HMGCR, and SLC7A11). Receiver operating characteristic curve analysis confirmed good prognostic performance of the new survival model with an area under the curve of 0.73. High FANCD2, CARS, and SLC7A11 expression and low HMGCR and NCOA4 expression were associated with high-risk ccRCC patients. Multivariate analysis showed that risk score, age, stage, and grade were independent risk factors associated with prognosis in ccRCC. These findings demonstrate that this five risk-related FRG-based survival model accurately predicts prognosis in ccRCC patients, and suggest FRGs are potential prognostic biomarkers and therapeutic targets in several cancer types.
Collapse
Affiliation(s)
- Guangzhen Wu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Qifei Wang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yingkun Xu
- Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Quanlin Li
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indianapolis, IN 46202, USA.,Department of Urology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| |
Collapse
|
29
|
Zhang Z, Weng W, Huang W, Wu B, Zhou Y, Zhang J, Deng T, Ye W, Zhang J, Ao J, Zhang Q, Shi K. A novel molecular-clinicopathologic nomogram to improve prognosis prediction of hepatocellular carcinoma. Aging (Albany NY) 2020; 12:12896-12920. [PMID: 32611831 PMCID: PMC7377850 DOI: 10.18632/aging.103350] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 05/20/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND Emerging evidence suggests that long non-coding RNA (lncRNA) plays a crucial part in the development and progress of hepatocellular carcinoma (HCC). The objective was to develop novel molecular-clinicopathological prediction methods for overall survival (OS) and recurrence of HCC. RESULTS An 8-lncRNA-based classifier for OS and a 14-lncRNA-based classifier for recurrence were developed by LASSO COX regression analysis, both of which had high accuracy. The tdROC of OS-nomogram and recurrence-nomogram indicates the satisfactory accuracy and predictive power. The classifiers and nomograms for predicting OS and recurrence of HCC were validated in the Test and GEO cohorts. CONCLUSIONS These two lncRNA-based classifiers could be independent prognostic factors for OS and recurrence. The molecule-clinicopathological nomograms based on the classifiers could increase the prognostic value. METHODS HCC lncRNA expression profiles from the cancer genome atlas (TCGA) were randomly divided into 1:1 training and test cohorts. Based on least absolute shrinkage and selection operator method (LASSO) COX regression model, lncRNA-based classifiers were established to predict OS and recurrence, respectively. OS-nomogram and recurrence-nomogram were developed by combining lncRNA-based classifiers and clinicopathological characterization to predict OS and recurrence, respectively. The prognostic value was accessed by the time-dependent receiver operating characteristic (tdROC) and the concordance index (C-index).
Collapse
Affiliation(s)
- Zhongjing Zhang
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou 325015, Zhejiang Province, PR China
| | - Wanqing Weng
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou 325015, Zhejiang Province, PR China
| | - Weiguo Huang
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou 325015, Zhejiang Province, PR China
| | - Boda Wu
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou 325015, Zhejiang Province, PR China
| | - Yi Zhou
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou 325015, Zhejiang Province, PR China
| | - Jie Zhang
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou 325015, Zhejiang Province, PR China
| | - Tuo Deng
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou 325015, Zhejiang Province, PR China
| | - Wen Ye
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou 325015, Zhejiang Province, PR China
| | - Jiecheng Zhang
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou 325015, Zhejiang Province, PR China
| | - Jianyang Ao
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou 325015, Zhejiang Province, PR China
| | - Qiyu Zhang
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou 325015, Zhejiang Province, PR China
| | - Keqing Shi
- Precision Medical Center Laboratory, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou 325015, Zhejiang Province, PR China
| |
Collapse
|
30
|
Genetic variant of COL11A2 gene is functionally associated with developmental dysplasia of the hip in Chinese Han population. Aging (Albany NY) 2020; 12:7694-7703. [PMID: 32396528 PMCID: PMC7244083 DOI: 10.18632/aging.103040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/10/2020] [Indexed: 12/27/2022]
Abstract
OBJECTIVES Developmental dysplasia of the hip (DDH) is a common skeletal disorder. This study was conducted to demonstrate the association between DDH and a polymorphism rs9277935 of COL11A2 gene. RESULTS A significant difference in genotype distribution in a recessive model (TT+GT vs. GG) between two groups (P=0.017) was demonstrated. Analysis in female patients showed significantly greater frequency of minor allele G(0.49 vs. 0.43, p=0.024) and significantly higher distribution of GG genotype (p=0.006). DDH patients were found to have significantly lower COL11A2 expression than controls. Moreover, DDH patients with rs9277935 genotype TT have a significantly increased expression of COL11A2 than those with genotype GG. COL11A2 demonstrated chondrogenic properties in vitro. CONCLUSION Polymorphism rs9277935 of gene COL11A2 is a functional variant regulating the expression and the chondrogenic properties of COL11A2 in DDH in Chinese Han population. METHODS A case-control candidate gene association study was conducted in 945 patients (350 radiologically confirmed DDH patients and 595 healthy controls). Difference of COL11A2 expression in hip joint tissue was compared between the patients and the controls. Allelic difference in Col11a2 expression by rs9277935 was assessed with luciferase activity. Chondrogenic effects of Col11a2 signaling on BMSCs were also determined in vitro.
Collapse
|
31
|
Pluronic P123 modified nano micelles loaded with doxorubicin enhanced tumor-suppressing effect on drug-resistant breast cancer cells. Aging (Albany NY) 2020; 12:8289-8300. [PMID: 32396524 PMCID: PMC7244042 DOI: 10.18632/aging.103138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 03/31/2020] [Indexed: 01/27/2023]
Abstract
OBJECTIVE Nano micelles (NMs) have been widely used for various biomedical applications due to its unique physiochemical properties. This study aimed to investigated the anti-tumor effect of doxorubicin (Dox)-loaded Pluronic P123 (P123) and PEG2000-DSPE mixed NMs in drug-resistant breast cancer cells. RESULTS The expression of P-gp and MDR1 gene was highly expressed in MCF-7R but not MCF-7 cells. The cellular uptake of P123-PEG2000-DSPE (Dox) was higher than that of free Dox and PEG2000-DSPE (Dox) in MCF-7R cells. Furthermore, compared with free Dox, both PEG2000-DSPE (Dox) and P123-PEG2000-DSPE (Dox) significantly diminished cell viability, and promoted cell apoptosis in MCF-7R cells. In addition, the P123-modified NMs obviously inhibited the expression of P-gp and MDR1. CONCLUSIONS P123-PEG2000-DSPE (Dox) had a superior anti-tumor activity than PEG2000-DSPE (Dox) in MCF-7R cells through P-gp-mediated drug excretion and drug resistance mechanisms. METHODS The PEG2000-DSPE NMs (PEG2000-DSPE), P123 and PEG2000-DSPE mixed NMs (P123-PEG2000-DSPE), Dox-loaded PEG2000-DSPE NMs (PEG2000-DSPE (Dox)), and Dox-loaded Pluronic P123 and PEG2000-DSPE mixed NMs (P123-PEG2000-DSPE (Dox)) were prepared, and then the morphologies and the size distribution of PEG2000-DSPE (Dox) and P123-PEG2000-DSPE (Dox) were observed by transmission electron microscopy (TEM) and dynamic light scattering (DLS), respectively.
Collapse
|
32
|
Jiang L, Yang H, Chen T, Zhu X, Ye J, Lv K. Identification of HMG-box family establishes the significance of SOX6 in the malignant progression of glioblastoma. Aging (Albany NY) 2020; 12:8084-8106. [PMID: 32388501 PMCID: PMC7244032 DOI: 10.18632/aging.103127] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 03/30/2020] [Indexed: 12/20/2022]
Abstract
Glioblastoma multiforme (GBM) is the most malignant neuroepithelial primary brain tumor and its mean survival time is 15 months after diagnosis. This study undertook to investigate the genome-wide and transcriptome-wide analyses of human high mobility group box (HMG-box) TF (transcript factor) families / HOX, TOX, FOX, HMG and SOX gene families, and their relationships to GBM. According to the TCGA-GBM profile analysis, differentially expressed HOX, FOX, HMG and SOX gene families (62 DEmRNA) were found in this study. We also analyzed DEmRNA (HMG-box related genes) co-expressed eight DElncRNA in GBM, and constructed a ceRNA network analysis as well. We constructed 50 DElncRNA-DEmiRNA-DEmRNA (HMG-box related genes) pairs between GBM and normal tissues. Then, risk genes SOX6 and SOX21 expression were correlated with immune infiltration levels in GBM. SOX6 also had a strong association with MAPT, GSK3B, FYN and DPYSL4, suggesting that they might be functional members in GBM.
Collapse
Affiliation(s)
- Lan Jiang
- Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu 241001, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu 241001, China
| | - Hui Yang
- Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu 241001, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu 241001, China
| | - Tianbing Chen
- Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu 241001, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu 241001, China
| | - Xiaolong Zhu
- Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu 241001, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu 241001, China
| | - Jingjing Ye
- Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu 241001, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu 241001, China
| | - Kun Lv
- Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu 241001, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu 241001, China
| |
Collapse
|
33
|
Zhu J, Tang B, Li J, Shi Y, Chen M, Lv X, Meng M, Weng Q, Zhang N, Fan K, Xu M, Ji J. Identification and validation of the angiogenic genes for constructing diagnostic, prognostic, and recurrence models for hepatocellular carcinoma. Aging (Albany NY) 2020; 12:7848-7873. [PMID: 32379058 PMCID: PMC7244068 DOI: 10.18632/aging.103107] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 03/09/2020] [Indexed: 12/24/2022]
Abstract
Since angiogenesis has an indispensable effect in the development and progression of tumors, in this study we aimed to identify angiogenic genes closely associated with prognosis of HCC to establish diagnostic, prognostic, and recurrence models. We analyzed 132 angiogenic genes and HCC-related RNA sequence data from the TCGA and ICGC databases by Cox and least absolute shrinkage and selection operator (LASSO) regression, and identified four angiogenic genes (ENFA3, EGF, MMP3 and AURKB) to establish prognosis, recurrence and diagnostic models and corresponding nomograms. The prognostic and recurrence models were determined to be independent predictors of prognosis and recurrence (P < 0.05). And compared with the low-risk group, patients in the high-risk group had worse overall survival (OS) rates in training cohort (P < 0.001) and validation cohort (P < 0.001), and higher recurrence rates in training cohort (P<0.001) and validation cohort (P=0.01). The diagnostic models have been validated to correctly distinguish HCC from normal samples and proliferative nodule samples. Through pharmacological analysis we identified piperlongumine as a drug for targeting angiogenesis, and it was validated to inhibit HCC cell proliferation and angiogenesis via the EGF/EGFR axis.
Collapse
Affiliation(s)
- Jinyu Zhu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China.,Department of Radiology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Bufu Tang
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China.,Department of Radiology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jie Li
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China.,Department of Radiology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yueli Shi
- Department of Pathology and Pathophysiology, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Minjiang Chen
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China.,Department of Radiology, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui 323000, China
| | - Xiuling Lv
- Department of Radiology, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui 323000, China
| | - Miaomiao Meng
- Department of Radiology, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui 323000, China
| | - Qiaoyou Weng
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China.,Department of Radiology, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui 323000, China
| | - Nannan Zhang
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China.,Department of Radiology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Kai Fan
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China.,Department of Radiology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Min Xu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China.,Department of Radiology, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui 323000, China
| | - Jiansong Ji
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China.,Department of Radiology, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui 323000, China
| |
Collapse
|
34
|
Sirt1 is regulated by miR-135a and involved in DNA damage repair during mouse cellular reprogramming. Aging (Albany NY) 2020; 12:7431-7447. [PMID: 32335545 PMCID: PMC7202538 DOI: 10.18632/aging.103090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 03/30/2020] [Indexed: 02/07/2023]
Abstract
Sirt1 facilitates the reprogramming of mouse somatic cells into induced pluripotent stem cells (iPSCs). It is regulated by micro-RNA and reported to be a target of miR-135a. However, their relationship and roles on cellular reprogramming remain unknown. In this study, we found negative correlations between miR-135a and Sirt1 during mouse embryonic stem cells differentiation and mouse embryonic fibroblasts reprogramming. We further found that the reprogramming efficiency was reduced by the overexpression of miR-135a precursor but induced by the miR-135a inhibitor. Co-immunoprecipitation followed by mass spectrometry identified 21 SIRT1 interacting proteins including KU70 and WRN, which were highly enriched for DNA damage repair. In accordance, Sirt1 activator resveratrol reduced DNA damage during the reprogramming process. Wrn was regulated by miR-135a and resveratrol partly rescued the impaired reprogramming efficiency induced by Wrn knockdown. This study showed Sirt1, being partly regulated by miR-135a, bound proteins involved in DNA damage repair and enhanced the iPSCs production.
Collapse
|
35
|
Wang HW, Ma KL, Liu H, Zhou JY. Reversal of multidrug resistance in leukemia cells using a transferrin-modified nanomicelle encapsulating both doxorubicin and psoralen. Aging (Albany NY) 2020; 12:6018-6029. [PMID: 32259795 PMCID: PMC7185111 DOI: 10.18632/aging.102992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 03/02/2020] [Indexed: 12/11/2022]
Abstract
To ameliorate multidrug resistance (MDR) observed in leukemia cells, nanomicelles modified by transferrin (Tf-M-DOX/PSO), coencapsulating doxorubicin (DOX) and psoralen (PSO), were designed, synthesized and tested in K562 and doxorubicin-resistant K562 (K562/DOX) cells. In vitro drug release kinetics for constructed nanomicelles were measured using high-performance liquid chromatography. Characterization of the produced nanomicelles was completed using transmission electron microscopy and dynamic light scattering. Uptake of the nanomicelles in K562 cells was investigated using both confocal microscopy and flow cytometry. Apoptosis levels as well as the expression of glycoprotein (P-gp) were analyzing by western blotting and flow cytometry. Cellular cytotoxicity resulting from the exposure of nanomicelles was evaluated using MTT assays. The nanomicelles all showed mild release of DOX in PBS solution. In K562/DOX cells, Tf-M-Dox/PSO exhibited higher uptake compared to the other nanomicelles observed. Furthermore, cellular cytotoxicity when exposed to Tf-M-Dox/PSO was 2.8 and 1.6-fold greater than observed in the unmodified DOX and Tf-nanomicelles loaded with DOX alone, respectively. Tf-M-Dox/PSO strongly increased apoptosis of K562/DOX cells. Finally, the reversal of the drug resistance when cells are exposed to Tf-M-DOX/PSO was associated with P-gp expression inhibition. The Tf-M-Dox/PSO nanomicelle showed a reversal of MDR, with enhanced cellular uptake and delivery release.
Collapse
Affiliation(s)
- He-Wen Wang
- Department of Pediatrics, Rizhao People's Hospital, Shandong, China
| | - Ke-Ling Ma
- Department of Pediatrics, Rizhao People's Hospital, Shandong, China
| | - Hua Liu
- Department of Pediatrics, Rizhao People's Hospital, Shandong, China
| | - Jia-Yun Zhou
- Department of Pediatrics, Rizhao People's Hospital, Shandong, China
| |
Collapse
|
36
|
Ye J, Liu L, Xu X, Wen Y, Li P, Cheng B, Cheng S, Zhang L, Ma M, Qi X, Liang C, Kafle OP, Wu C, Wang S, Wang X, Ning Y, Chu X, Niu L, Zhang F. A genome-wide multiphenotypic association analysis identified candidate genes and gene ontology shared by four common risky behaviors. Aging (Albany NY) 2020; 12:3287-3297. [PMID: 32090979 PMCID: PMC7066886 DOI: 10.18632/aging.102812] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 01/25/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Risky behaviors can lead to huge economic and health losses. However, limited efforts are paid to explore the genetic mechanisms of risky behaviors. RESULT MASH analysis identified a group of target genes for risky behaviors, such as APBB2, MAPT and DCC. For GO enrichment analysis, FUMA detected multiple risky behaviors related GO terms and brain related diseases, such as regulation of neuron differentiation (adjusted P value = 2.84×10-5), autism spectrum disorder (adjusted P value =1.81×10-27) and intelligence (adjusted P value =5.89×10-15). CONCLUSION We reported multiple candidate genes and GO terms shared by the four risky behaviors, providing novel clues for understanding the genetic mechanism of risky behaviors. METHODS Multivariate Adaptive Shrinkage (MASH) analysis was first applied to the GWAS data of four specific risky behaviors (automobile speeding, drinks per week, ever-smoker, number of sexual partners) to detect the common genetic variants shared by the four risky behaviors. Utilizing genomic functional annotation data of SNPs, the SNPs detected by MASH were then mapped to target genes. Finally, gene set enrichment analysis of the identified candidate genes were conducted by the FUMA platform to obtain risky behaviors related gene ontology (GO) terms as well as diseases and traits, respectively.
Collapse
Affiliation(s)
- Jing Ye
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xiaoqiao Xu
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Ping Li
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Bolun Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Lu Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Mei Ma
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xin Qi
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Chujun Liang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Om Prakash Kafle
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Cuiyan Wu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Sen Wang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xi Wang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yujie Ning
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xiaomeng Chu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Lin Niu
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| |
Collapse
|
37
|
Cheng S, Li C, Xie W, Miao Y, Guo J, Wang J, Zhang Y. Integrated analysis of DNA methylation and mRNA expression profiles to identify key genes involved in the regrowth of clinically non-functioning pituitary adenoma. Aging (Albany NY) 2020; 12:2408-2427. [PMID: 32015217 PMCID: PMC7041752 DOI: 10.18632/aging.102751] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/07/2020] [Indexed: 12/15/2022]
Abstract
Tumour regrowth is a key characteristic of clinically non-functioning pituitary adenoma (NFPA). No applicable prognosis evaluation method is available for post-operative patients. We aimed to identify DNA methylation biomarkers that can facilitate prognosis evaluation. Genome-wide DNA methylation and mRNA microarray analyses were performed for tumour samples from 71 NFPA patients. Differentially expressed genes and methylated genes were identified based on the regrowth vs non-regrowth grouping. There were 139 genes that showed alterations in methylation status and expression level, and only 13 genes showed a negative correlation. The progression-free analysis found that FAM90A1, ETS2, STAT6, MYT1L, ING2 and KCNK1 are related to tumour regrowth. A prognosis-prediction model was built based on all 13 genes from integrated analysis, and the 6-gene model achieved the best area under the receiver operating characteristic curves (AUC) of 0.820, compared with 0.785 and 0.568 for the 13-gene and 7-gene models, respectively. Our prognostic biomarkers were validated by pyrosequencing and RT-PCR. FAM90A1 and ING2 was found to be independent prognostic factors of tumour regrowth with univariate Cox regression. The DNA methylation and expression levels of FAM90A1 and ING2 are associated with tumour regrowth, and may serve as biomarkers for predicting the prognosis of patients with NFPA.
Collapse
Affiliation(s)
- Sen Cheng
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Chuzhong Li
- Beijing Neurosurgical Institute, Beijing Tiantan Hospital Affiliated to Capital Medical University, Beijing Institute for Brain Disorders Brain Tumour Center, China National Clinical Research Center for Neurological Diseases, Key Laboratory of Central Nervous System Injury Research, Beijing 100070, China
| | - Weiyan Xie
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Yazhou Miao
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Jing Guo
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Jichao Wang
- People's Hospital of Xin Jiang Uygur Autonomous Region, Urumqi 830001, China
| | - Yazhuo Zhang
- Beijing Neurosurgical Institute, Beijing Tiantan Hospital Affiliated to Capital Medical University, Beijing Institute for Brain Disorders Brain Tumour Center, China National Clinical Research Center for Neurological Diseases, Key Laboratory of Central Nervous System Injury Research, Beijing 100070, China
| |
Collapse
|
38
|
Ieong C, Yang H, Ma J, Lai W. Prognostic significance of X-linked inhibitor of apoptosis protein in patients with gastrointestinal tract cancers: A meta-analysis. Medicine (Baltimore) 2020; 99:e18497. [PMID: 32118702 PMCID: PMC7478481 DOI: 10.1097/md.0000000000018497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The aim of this meta-analysis was to systematically evaluate the prognostic significance of X-linked inhibitor of apoptosis protein (XIAP) in patients with gastrointestinal tract (GIT) cancers. METHODS PubMed, Web of Science, EMBASE, Cochrane Library and China National Knowledge Infrastructure were searched for potentially eligible literature. The baseline characteristics and relevant data were extracted. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated to assess the prognostic role of XIAP in patients with GIT cancers. RESULTS Twelve studies with 2,477 patients were included. The pooled HRs of higher expression of XIAP for overall survival (OS) and recurrence free survival (RFS) in patients with GIT cancers were 1.64 (95% CI, 1.27-2.13) and 1.06 (95% CI, 0.96-1.16), respectively. Subgroup analysis and sensitivity analysis were also performed. No significant publication bias was found. CONCLUSION Our results suggested that XIAP could be a prognostic marker for OS but not RFS in patients with GIT cancers. Higher expression of XIAP was related to poorer OS. These findings may help evaluate the prognosis of patients and assist future research on novel therapeutic strategies of GIT cancers by targeting XIAP. However, more well-designed studies are warranted to verify the results.
Collapse
Affiliation(s)
- Chengcheng Ieong
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University
| | - Hong Yang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University
| | - Junpeng Ma
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wenli Lai
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University
| |
Collapse
|
39
|
Low-abundance mutations in colorectal cancer patients and healthy adults. Aging (Albany NY) 2020; 12:808-824. [PMID: 31927530 PMCID: PMC6977685 DOI: 10.18632/aging.102657] [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: 09/07/2019] [Accepted: 12/24/2019] [Indexed: 11/25/2022]
Abstract
Detecting low-abundance mutations is very important for cancer diagnosis and treatment. Here we describe an improved targeted sequencing analysis that dramatically increases sequencing depth. Seven colorectal cancer (CRC) patients and seven healthy adults were enrolled in this study. We examined genetic mutations in tissue samples from the central and peripheral regions of tumors from the CRC patients and in blood cells from the healthy adults. We observed that each CRC carried larger numbers of mutations more than previously estimated. These included numerous deletion mutations in the tumor tissue. While the cellular morphology in the surrounding normal colonic tissues was healthy, these cells also carried many mutations. Similarly, the blood cells from the healthy donors carried numerous mutations. These findings shed new light on the processes of tumorigenesis and aging, and also present a potentially effective method for detecting low-abundance mutations for cancer diagnosis and targeted treatments.
Collapse
|
40
|
Wang J, Chen X, Tian Y, Zhu G, Qin Y, Chen X, Pi L, Wei M, Liu G, Li Z, Chen C, Lv Y, Cai G. Six-gene signature for predicting survival in patients with head and neck squamous cell carcinoma. Aging (Albany NY) 2020; 12:767-783. [PMID: 31927533 PMCID: PMC6977678 DOI: 10.18632/aging.102655] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/24/2019] [Indexed: 12/21/2022]
Abstract
The prognosis of head and neck squamous cell carcinoma (HNSCC) patients remains poor. High-throughput sequencing data have laid a solid foundation for identifying genes related to cancer prognosis, but a gene marker is needed to predict clinical outcomes in HNSCC. In our study, we downloaded RNA Seq, single nucleotide polymorphism, copy number variation, and clinical follow-up data from TCGA. The samples were randomly divided into training and test. In the training set, we screened genes and used random forests for feature selection. Gene-related prognostic models were established and validated in a test set and GEO verification set. Six genes (PEX11A, NLRP2, SERPINE1, UPK, CTTN, D2HGDH) were ultimately obtained through random forest feature selection. Cox regression analysis confirmed the 6-gene signature is an independent prognostic factor in HNSCC patients. This signature effectively stratified samples in the training, test, and external verification sets (P < 0.01). The 5-year survival AUC in the training and verification sets was greater than 0.74. Thus, we have constructed a 6-gene signature as a new prognostic marker for predicting survival of HNSCC patients.
Collapse
Affiliation(s)
- Juncheng Wang
- Department of Otolaryngology, Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Xun Chen
- Department of Oral and Maxillofacial Surgery, First Affiliated Hospital of Quanzhou, Fujian Medical University, Quanzhou 362000, People's Republic of China
| | - Yuxi Tian
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008 People's Republic of China
| | - Gangcai Zhu
- Department of Otolaryngology, Head and Neck Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, People's Republic of China
| | - Yuexiang Qin
- Department of Health Management, The Third Xiangya Hospital, Central South University, Changsha 410011, People's Republic of China
| | - Xuan Chen
- Department of Stomatology, Changzheng Hospital, Second Military Medcial University, Shanghai 200003, People's Republic of China
| | - Leiming Pi
- Department of Otolaryngology, Head and Neck Surgery, HeYuan People's Hospital, Jinan University, He Yuan,517000, People's Republic of China
| | - Ming Wei
- Department of Otolaryngology, Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Guancheng Liu
- Department of Otolaryngology, Head and Neck Surgery, Affiliated Hospital of Guilin University, Guilin 541000, People's Republic of China
| | - Zhexuan Li
- Department of Otolaryngology, Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Changhan Chen
- Department of Otolaryngology, Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Yunxia Lv
- Department of Thyroid Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, People's Republic of China
| | - Gengming Cai
- Department of Otolaryngology, Head and Neck Surgery, First Affiliated Hospital of Quanzhou, Fujian Medical University, Quanzhou 362000, People's Republic of China
| |
Collapse
|
41
|
Shao N, Su H, Ye D. Conditional disease-free survival in high-risk renal cell carcinoma treated with sunitinib. Aging (Albany NY) 2019; 11:11490-11503. [PMID: 31825895 PMCID: PMC6932878 DOI: 10.18632/aging.102549] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/19/2019] [Indexed: 04/19/2023]
Abstract
BACKGROUND Disease-free survival (DFS) did not reflect accurate individual prognosis after initial diagnosis. As conditional DFS (CDFS) could provide dynamic prognostic information, we evaluated CDFS in these patients treated with or without sunitinib. RESULTS A total of 1329 patients with median follow-up 6.54 years were enrolled. CDFS improved continuously with disease-free survivorship increasing in both sunitinib and placebo group with minimal difference. In placebo arm, the CDFS of surviving to five year after living 1, 2, 3, and 4 years were 65%, 78%, 87%, and 95% (observed 5-year DFS: 51%). Dynamic changes of HR showed adjuvant sunitinib decrease relapse risks during the first 1.5 years after surgery (P < 0.03). CONCLUSIONS Our study provided contemporary data of CDFS and change of relapse HR in high-risk ccRCC patients after adjuvant sunitinib or placebo. The remarkable improvement in CDFS highlighted the importance of disease-free interval as a strong indicator in patient counseling and surveillance planning. MATERIALS AND METHODS The primary end point was CDFS and the second end point was smooth hazard ratios (HR) for the prediction of relapses. The differences of conditional survival were compared with the calculation of d value.
Collapse
Affiliation(s)
- Ning Shao
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Hengchuan Su
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| |
Collapse
|
42
|
A twenty gene-based gene set variation score reflects the pathological progression from cirrhosis to hepatocellular carcinoma. Aging (Albany NY) 2019; 11:11157-11169. [PMID: 31811111 PMCID: PMC6932912 DOI: 10.18632/aging.102518] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/18/2019] [Indexed: 02/07/2023]
Abstract
The molecular mechanism of the pathological progression from cirrhosis to hepatocellular carcinoma (HCC) remains elusive. In the present study, tissue samples from normal liver, cirrhosis and HCC were subjected to differentially gene expression analysis, weighted gene correlation network analysis to identify the twenty hub genes (TOP2A, CDC20, PTTG1, CDCA5, CCNB2, PRC1, KIF20A, SF3B4, HSP90AB1, FOXD2, PLOD3, CCT3, SETDB1, VPS45, SPDL1, RACGAP1, MED24, KIAA0101, ZNF282, and USP21) in the pathological progression from cirrhosis to HCC. Each sample was calculated a hub gene set variation analysis (HGSVA) score using Gene Set Variation Analysis, The HGSVA score significantly increased with progression from cirrhosis to HCC, and this result was validated in two independent data sets. Moreover, this score may be used as a blood-based marker for HCC and is an independent prognostic factor of recurrence-free survival (RFS) and overall survival (OS). High expression of the hub genes may be driven by hypomethylation. The twenty gene-based gene set variation score may reflect the pathological progression from cirrhosis to HCC and is an independent prognostic factor for both OS and RFS.
Collapse
|
43
|
Koag MC, Jung H, Kou Y, Lee S. Bypass of the Major Alkylative DNA Lesion by Human DNA Polymerase η. Molecules 2019; 24:molecules24213928. [PMID: 31683505 PMCID: PMC6864850 DOI: 10.3390/molecules24213928] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 01/13/2023] Open
Abstract
A wide range of endogenous and exogenous alkylating agents attack DNA to generate various alkylation adducts. N7-methyl-2-deoxyguanosine (Fm7dG) is the most abundant alkylative DNA lesion. If not repaired, Fm7dG can undergo spontaneous depurination, imidazole ring-opening, or bypass by translesion synthesis DNA polymerases. Human DNA polymerase η (polη) efficiently catalyzes across Fm7dG in vitro, but its structural basis is unknown. Herein, we report a crystal structure of polη in complex with templating Fm7dG and an incoming nonhydrolyzable dCTP analog, where a 2'-fluorine-mediated transition destabilization approach was used to prevent the spontaneous depurination of Fm7dG. The structure showed that polη readily accommodated the Fm7dG:dCTP base pair with little conformational change of protein and DNA. In the catalytic site, Fm7dG and dCTP formed three hydrogen bonds with a Watson-Crick geometry, indicating that the major keto tautomer of Fm7dG is involved in base pairing. The polη-Fm7dG:dCTP structure was essentially identical to the corresponding undamaged structure, which explained the efficient bypass of the major methylated lesion. Overall, the first structure of translesion synthesis DNA polymerase bypassing Fm7dG suggests that in the catalytic site of Y-family DNA polymerases, small N7-alkylguanine adducts may be well tolerated and form the canonical Watson-Crick base pair with dCTP through their keto tautomers.
Collapse
Affiliation(s)
- Myong-Chul Koag
- The Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, 2409 University Avenue, TX 78712, USA.
| | - Hunmin Jung
- The Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, 2409 University Avenue, TX 78712, USA.
| | - Yi Kou
- The Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, 2409 University Avenue, TX 78712, USA.
| | - Seongmin Lee
- The Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, 2409 University Avenue, TX 78712, USA.
| |
Collapse
|
44
|
Yang K, Sun H, Lowder L, Varadarajan S, Greenberg MM. Reactivity of N3-Methyl-2'-Deoxyadenosine in Nucleosome Core Particles. Chem Res Toxicol 2019; 32:2118-2124. [PMID: 31565933 PMCID: PMC6803048 DOI: 10.1021/acs.chemrestox.9b00299] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
N3-Methyl-2′-deoxyadenosine
(MdA) is the major dA methylation
product in duplex DNA. MdA blocks DNA replication and undergoes depurination
at significantly higher rates than the native nucleotide from which
it is derived. Recent reports on the effects of the nucleosome core
particle (NCP) environment on the reactivity of N7-methyl-2′-deoxyguanosine
(MdG) inspired this investigation concerning the reactivity of MdA
in NCPs. NCPs containing MdA at selected positions were produced using
a strategy in which the minor groove binding Me-Lex molecule serves
as a sequence specific methylating agent. Hydrolysis of the glycosidic
bond in MdA to form abasic sites (AP) is suppressed in a NCP. Experiments
using histone variants indicate that the proximal, highly basic N-terminal
tails are partially responsible for the decreased depurination rate
constant. MdA also forms cross-links with histone proteins. The levels
of MdA-histone DNA–protein cross-links (DPCMdA)
decrease significantly over time and are replaced by those involving
AP. The time dependent decrease in DPCMdA is attributed
to the reversibility of their formation and the relatively rapid rate
of AP formation from MdA. Overall, MdA reactivity in NCPs qualitatively
resembles that of MdG.
Collapse
Affiliation(s)
- Kun Yang
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
| | - Huabing Sun
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
| | - Leah Lowder
- Department of Chemistry and Biochemistry , University of North Carolina Wilmington , 601 South College Road , Wilmington , North Carolina 28403 , United States
| | - Sridhar Varadarajan
- Department of Chemistry and Biochemistry , University of North Carolina Wilmington , 601 South College Road , Wilmington , North Carolina 28403 , United States
| | - Marc M Greenberg
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
| |
Collapse
|
45
|
Kou Y, Koag MC, Lee S. Promutagenicity of 8-Chloroguanine, A Major Inflammation-Induced Halogenated DNA Lesion. Molecules 2019; 24:molecules24193507. [PMID: 31569643 PMCID: PMC6804246 DOI: 10.3390/molecules24193507] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 09/26/2019] [Accepted: 09/26/2019] [Indexed: 12/18/2022] Open
Abstract
Chronic inflammation is closely associated with cancer development. One possible mechanism for inflammation-induced carcinogenesis is DNA damage caused by reactive halogen species, such as hypochlorous acid, which is released by myeloperoxidase to kill pathogens. Hypochlorous acid can attack genomic DNA to produce 8-chloro-2′-deoxyguanosine (ClG) as a major lesion. It has been postulated that ClG promotes mutagenic replication using its syn conformer; yet, the structural basis for ClG-induced mutagenesis is unknown. We obtained crystal structures and kinetics data for nucleotide incorporation past a templating ClG using human DNA polymerase β (polβ) as a model enzyme for high-fidelity DNA polymerases. The structures showed that ClG formed base pairs with incoming dCTP and dGTP using its anti and syn conformers, respectively. Kinetic studies showed that polβ incorporated dGTP only 15-fold less efficiently than dCTP, suggesting that replication across ClG is promutagenic. Two hydrogen bonds between syn-ClG and anti-dGTP and a water-mediated hydrogen bond appeared to facilitate mutagenic replication opposite the major halogenated guanine lesion. These results suggest that ClG in DNA promotes G to C transversion mutations by forming Hoogsteen base pairing between syn-ClG and anti-G during DNA synthesis.
Collapse
Affiliation(s)
- Yi Kou
- The Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, 2409 University Avenue, Austin, TX 78712, USA.
| | - Myong-Chul Koag
- The Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, 2409 University Avenue, Austin, TX 78712, USA.
| | - Seongmin Lee
- The Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, 2409 University Avenue, Austin, TX 78712, USA.
| |
Collapse
|
46
|
Yang K, Greenberg MM. DNA-Protein Cross-Link Formation in Nucleosome Core Particles Treated with Methyl Methanesulfonate. Chem Res Toxicol 2019; 32:2144-2151. [PMID: 31532638 DOI: 10.1021/acs.chemrestox.9b00314] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
N7-Methyl-2'-deoxyguanosine (MdG) is the major damage product in DNA produced by methylating agents, but it often thought to be nontoxic and nonmutagenic. MdG is chemically unstable. An abasic site (AP) is the major product produced from MdG under physiologically relevant conditions. AP formation is frequently considered to be responsible for the cytotoxic effects of MdG, but the reaction is suppressed in nucleosome core particles (NCPs). Recently, it was discovered that histone proteins form reversible DNA-protein cross-links (DPCs) with MdG in reconstituted NCPs, as well as in methylmethanesulfonate (MMS) treated cells. In this study, the formation and reactivity of MdG in MMS treated NCPs was examined at single nucleotide resolution. Sequences consisting of three or more consecutive dGs are more reactive with MMS. The efficiency and selectivity of MdG formation by MMS is largely unaffected within a NCP, although reactivity at several dGs is ∼1.5-2.5-fold higher in NCPs. DPC formation from MdG (DPCMdG) predominates over AP at all positions within the NCP. With few exceptions, DPCMdG yield is strongly dependent upon the accessibility of the major groove containing MdG to lysine-rich histone N-terminal tails. These data indicate that histone-MdG DPC formation will depend upon DNA sequence and translational position within an NCP.
Collapse
Affiliation(s)
- Kun Yang
- Department of Chemistry , Johns Hopkins University , 3400 N. Charles Street , Baltimore , Maryland 21218 , United States
| | - Marc M Greenberg
- Department of Chemistry , Johns Hopkins University , 3400 N. Charles Street , Baltimore , Maryland 21218 , United States
| |
Collapse
|
47
|
He FS, Gong X, Rojsitthisak P, Wu J. Direct C–H Methylsulfonylation of Alkenes with the Insertion of Sulfur Dioxide. J Org Chem 2019; 84:13159-13163. [DOI: 10.1021/acs.joc.9b01729] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Fu-Sheng He
- School of Pharmaceutical and Materials Engineering and Institute for Advanced Studies, Taizhou University, 1139 Shifu Avenue, Taizhou 318000, China
| | - Xinxing Gong
- Department of Chemistry, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Pornchai Rojsitthisak
- Department of Food and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Chulalongkorn University, 254 Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Jie Wu
- School of Pharmaceutical and Materials Engineering and Institute for Advanced Studies, Taizhou University, 1139 Shifu Avenue, Taizhou 318000, China
- Department of Chemistry, Fudan University, 2005 Songhu Road, Shanghai 200438, China
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| |
Collapse
|
48
|
Qin S, Wang J, Zhou C, Xu Y, Zhang Y, Wang X, Wang S. The influence of interleukin 28B polymorphisms on the risk of hepatocellular carcinoma among patients with HBV or HCV infection: An updated meta-analysis. Medicine (Baltimore) 2019; 98:e17275. [PMID: 31568008 PMCID: PMC6756689 DOI: 10.1097/md.0000000000017275] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 06/14/2019] [Accepted: 08/28/2019] [Indexed: 12/22/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) of the interleukin 28B (IL28B) gene has proven to be associated with the clinical outcome of patients with chronic hepatitis virus B or C (HBV or HCV) infections. However, whether IL28B SNPs have an influence on the risk of hepatocellular carcinoma (HCC) among patients with HBV or HCV infection remains controversial. Therefore, this study aims to determine the association between IL28B polymorphisms and the risk of HCC in individuals with HBV or HCV infection.PubMed, EMBASE, and Chinese National Knowledge Infrastructure (CNKI) databases were used to identify studies meeting the selection requirements using the terms "interleukin 28B", "IFN-lambda-3", "IFNL3", "single nucleotide polymorphisms", "SNPs", "hepatocellular carcinoma", "HCC", "liver cancer".A total of 24 eligible original studies (1 cohort study and 23 case-control studies) involved 20238 individuals (HCC group = 8725 vs control group = 11,513) were included. Both IL28B rs12979860 CC and rs8099917 TT genotypes were significantly associated with a decreased risk of HCC among patients with HBV or HCV infection (OR = 0.71, 95% CI = 0.57-0.88; OR = 0.82, 95% CI = 0.72-0.94, respectively). Egger test and Begg test revealed no' publication bias (P > .05). Sensitivity analyses suggested the robustness of the results in this meta-analysis.Both IL28B rs12979860 CC and rs8099917 TT genotypes are protective factors for the development of HCC among patients with HBV or HCV infection. Future prospective studies examining the impact of IL28B polymorphisms on the risk of HCC and investigating the underlying mechanism for the protective role of IL28B polymorphisms in HCC development are warranted.
Collapse
Affiliation(s)
- Shaoyou Qin
- Department of Gastroenterology and Hepatology, China-Japan Union Hospital of Jilin University
| | - Jiangbin Wang
- Department of Gastroenterology and Hepatology, China-Japan Union Hospital of Jilin University
| | - Changyu Zhou
- Department of Gastroenterology and Hepatology, China-Japan Union Hospital of Jilin University
| | - Yan Xu
- Department of Gastroenterology and Hepatology, China-Japan Union Hospital of Jilin University
| | - Yonggui Zhang
- Department of Gastroenterology and Hepatology, China-Japan Union Hospital of Jilin University
| | - Xu Wang
- Department of Gastroenterology and Hepatology, China-Japan Union Hospital of Jilin University
| | - Song Wang
- Department of Urology, the First Hospital of Jilin University, Changchun, China
| |
Collapse
|
49
|
Jiang L, Zhang Y, Yang Z, Liang F, Wu J, Wang R. A comparison of clinical outcomes between simultaneous integrated boost (SIB) versus sequential boost (SEQ) intensity modulated radiation therapy (IMRT) for head and neck cancer: A meta-analysis. Medicine (Baltimore) 2019; 98:e16942. [PMID: 31441887 PMCID: PMC6716705 DOI: 10.1097/md.0000000000016942] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The optimal intensity modulated radiation therapy (IMRT) technique for head and neck cancer (HNC) has not been determined yet. The present study aimed to compare the clinical outcomes of the simultaneous integrated boost (SIB)-IMRT versus the sequential boost (SEQ)-IMRT in HNC. METHODS A meta-analysis of 7 studies involving a total of 1049 patients was carried out to compare the treatment outcomes together with severe acute adverse effects of the SIB-IMRT versus the SEQ-IMRT in HNC patients. RESULTS Comparison of the SIB-IMRT and SEQ-IMRT showed no significant difference in the measurement of overall survival (OS) (hazard ratio [HR] 0.94; 95% confidence inerval [CI], 0.70-1.27; P = .71), progression free survival (PFS) (HR 1.03; 95% CI, 0.82-1.30; P = .79), locoregional recurrence free survival (LRFS) (HR 0.98; 95% CI, 0.65-1.47; P = .91), and distance metastasis free survival (DMFS) (HR 0.87; 95% CI, 0.50-1.53; P = .63). Moreover, there were no significant differences in adverse effect occurrence between the SIB-IMRT and SEQ-IMRT groups. CONCLUSION SIB-IMRT and SEQ-IMRT can provide comparable outcomes in the treatment of patients afflicted by HNC. Both IMRT techniques were found to carry a similar risk of severe acute adverse effect. SIB-IMRT may have advantages due to its convenience and short-course of treatment; however, the optimum fractionation and prescribed dose remained unclear. Furthermore, both IMRT techniques can be advocated as the technique of choice for HNC. Treatment plan should be individualized for patients.
Collapse
|
50
|
Zhang F, Yin Y, Xu T. Cinobufotalin injection combined with chemotherapy for the treatment of advanced NSCLC in China: A PRISMA-compliant meta-analysis of 29 randomized controlled trials. Medicine (Baltimore) 2019; 98:e16969. [PMID: 31464940 PMCID: PMC6736171 DOI: 10.1097/md.0000000000016969] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND AND OBJECTIVE Cinobufotalin injection (CFI), a kind of Chinese medicine, has been considered as a promising complementary therapy option for advanced non-small cell lung cancer (NSCLC), but their efficacy and safety remain controversial. This study aimed to systematically evaluate the efficacy and safety of CFI and chemotherapy-combined therapy for advanced NSCLC. METHODS Clinical trials were searched from Web of Science, Cochrane Library, PubMed, Embase, China National Knowledge Infrastructure (CNKI), Chinese Biological Medicine Database (CBM), Chinese Medical Citation Index (CMCI), Wanfang database and Chinese Scientific Journal Database (VIP). Main measurements, including therapeutic efficacy, quality of life (QoL) and adverse events, were extracted from the retrieved publications and were systematically evaluated. RESULTS The 29 trials including 2300 advanced NSCLC patients were involved in this study. Compared with chemotherapy alone, its combination with CFI significantly prolonged the patients' 1-, 2- and 3-year overall survival rate (OS) (1-year OS, OR = 1.94, 95% CI = 1.42-2.65, P < .0001; 2-year OS, OR = 2.31, 95% CI = 1.55-3.45, P < .0001; 3-year OS, OR = 4.69, 95% CI = 1.78-12.39, P = .002) and improved patients' overall response (ORR, OR = 1.84, CI = 1.54-2.18, P < .00001), disease control rate (DCR, OR = 2.09, 95% CI = 1.68-2.60, P < .00001) and QoL (quality of life improved rate, QIR, OR = 2.64, 95% CI = 1.98-3.52, P < .00001; karnofsky performance score, KPS, OR = 10.97, 95% CI = 5.48-16.47, P < .0001). Most adverse events caused by chemotherapy were obviously alleviated (P < .05) when CFI was also applied to patients. CONCLUSION The combination of CFI and chemotherapy is safe, and is more effective in treating NSCLC than chemotherapy alone. Therefore, CFI mediated therapy could be recommended as an adjuvant treatment method for NSCLC.
Collapse
Affiliation(s)
| | - Yantong Yin
- Department of Respiratory Medicine, Liaocheng People's Hospital, Liaocheng, Shandong Province, China
| | | |
Collapse
|