1
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Calamari ZT, Flynn JJ. Gene expression supports a single origin of horns and antlers in hoofed mammals. Commun Biol 2024; 7:509. [PMID: 38769090 PMCID: PMC11106249 DOI: 10.1038/s42003-024-06134-4] [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: 11/27/2020] [Accepted: 04/02/2024] [Indexed: 05/22/2024] Open
Abstract
Horns, antlers, and other bony cranial appendages of even-toed hoofed mammals (ruminant artiodactyls) challenge traditional morphological homology assessments. Cranial appendages all share a permanent bone portion with family-specific integument coverings, but homology determination depends on whether the integument covering is an essential component or a secondary elaboration of each structure. To enhance morphological homology assessments, we tested whether juvenile cattle horn bud transcriptomes share homologous gene expression patterns with deer antlers relative to pig outgroup tissues, treating the integument covering as a secondary elaboration. We uncovered differentially expressed genes that support horn and antler homology, potentially distinguish them from non-cranial-appendage bone and other tissues, and highlight the importance of phylogenetic outgroups in homology assessments. Furthermore, we found differentially expressed genes that could support a shared cranial neural crest origin for horns and antlers and expression patterns that refine our understanding of the timing of horn and antler differentiation.
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Affiliation(s)
- Zachary T Calamari
- Division of Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
- Richard Gilder Graduate School, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
- Department of Natural Sciences, Baruch College, City University of New York, 17 Lexington Avenue, Box A-920, New York, NY, 10010, USA.
| | - John J Flynn
- Division of Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
- Richard Gilder Graduate School, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
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2
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Mariani JN, Mansky B, Madsen PM, Salinas D, Kesmen D, Huynh NPT, Kuypers NJ, Kesel ER, Bates J, Payne C, Chandler-Militello D, Benraiss A, Goldman SA. Repression of developmental transcription factor networks triggers aging-associated gene expression in human glial progenitor cells. Nat Commun 2024; 15:3873. [PMID: 38719882 PMCID: PMC11079006 DOI: 10.1038/s41467-024-48118-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
Human glial progenitor cells (hGPCs) exhibit diminished expansion competence with age, as well as after recurrent demyelination. Using RNA-sequencing to compare the gene expression of fetal and adult hGPCs, we identify age-related changes in transcription consistent with the repression of genes enabling mitotic expansion, concurrent with the onset of aging-associated transcriptional programs. Adult hGPCs develop a repressive transcription factor network centered on MYC, and regulated by ZNF274, MAX, IKZF3, and E2F6. Individual over-expression of these factors in iPSC-derived hGPCs lead to a loss of proliferative gene expression and an induction of mitotic senescence, replicating the transcriptional changes incurred during glial aging. miRNA profiling identifies the appearance of an adult-selective miRNA signature, imposing further constraints on the expansion competence of aged GPCs. hGPC aging is thus associated with acquisition of a MYC-repressive environment, suggesting that suppression of these repressors of glial expansion may permit the rejuvenation of aged hGPCs.
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Affiliation(s)
- John N Mariani
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, 14642, USA.
| | - Benjamin Mansky
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Pernille M Madsen
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
- Center for Translational Neuromedicine, University of Copenhagen Faculty of Health, Copenhagen, 2200, Denmark
| | - Dennis Salinas
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Deniz Kesmen
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Nguyen P T Huynh
- Center for Translational Neuromedicine, University of Copenhagen Faculty of Health, Copenhagen, 2200, Denmark
| | - Nicholas J Kuypers
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Erin R Kesel
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Janna Bates
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Casey Payne
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Devin Chandler-Militello
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Abdellatif Benraiss
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Steven A Goldman
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, 14642, USA.
- Center for Translational Neuromedicine, University of Copenhagen Faculty of Health, Copenhagen, 2200, Denmark.
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3
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Chen Z, Li C, Huang H, Shi YL, Wang X. Research Progress of Aging-related MicroRNAs. Curr Stem Cell Res Ther 2024; 19:334-350. [PMID: 36892029 DOI: 10.2174/1574888x18666230308111043] [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: 10/22/2022] [Revised: 01/02/2023] [Accepted: 01/11/2023] [Indexed: 03/10/2023]
Abstract
Senescence refers to the irreversible state in which cells enter cell cycle arrest due to internal or external stimuli. The accumulation of senescent cells can lead to many age-related diseases, such as neurodegenerative diseases, cardiovascular diseases, and cancers. MicroRNAs are short non-coding RNAs that bind to target mRNA to regulate gene expression after transcription and play an important regulatory role in the aging process. From nematodes to humans, a variety of miRNAs have been confirmed to alter and affect the aging process. Studying the regulatory mechanisms of miRNAs in aging can further deepen our understanding of cell and body aging and provide a new perspective for the diagnosis and treatment of aging-related diseases. In this review, we illustrate the current research status of miRNAs in aging and discuss the possible prospects for clinical applications of targeting miRNAs in senile diseases.
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Affiliation(s)
- Zhongyu Chen
- School of Basic Medicine, Dali University, Dali, Yunnan, 671000, China
| | - Chenxu Li
- School of Basic Medicine, Dali University, Dali, Yunnan, 671000, China
| | - Haitao Huang
- School of Basic Medicine, Dali University, Dali, Yunnan, 671000, China
| | - Yi-Ling Shi
- School of Basic Medicine, Dali University, Dali, Yunnan, 671000, China
| | - Xiaobo Wang
- School of Basic Medicine, Dali University, Dali, Yunnan, 671000, China
- Key Laboratory of University Cell Biology, Dali, Yunnan, 671000, China
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4
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Liu Y, Chen K, Shou Y, Li S, Wang J, Zhang Q, Huang Z, Xu J, Li M, Liu D, Liang H, Yang H, Zhang X. circRARS synergises with IGF2BP3 to regulate RNA methylation recognition to promote tumour progression in renal cell carcinoma. Clin Transl Med 2023; 13:e1512. [PMID: 38073586 PMCID: PMC10711645 DOI: 10.1002/ctm2.1512] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 11/24/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
As the most prominent RNA modification, N6-methyladenosine (m6 A) participates in the regulation of tumour initiation and progression. Circular RNAs (circRNAs) also play crucial roles in ubiquitous life processes. Whether circRNAs are required for m6 A regulation in renal cell carcinoma (RCC) remains unclear. Meta-analysis and bioinformatics identified that IGF2BP3 was upregulated in RCC and indicated a worse prognosis. IGF2BP3 significantly promoted RCC progression in vitro and in vivo. Mechanistically, circRARS bound to KH1-KH2 domains of IGF2BP3 to enhance m6 A modification recognition. A 12-nt sequence (GUCUUCCAGCAA) was proven to be the IGF2BP3-binding site of circRARS. Additionally, CAPN15, CD44, HMGA2, TNRC6A and ZMIZ2 were screened to be the target genes regulated by the IGF2BP3/circRARS complex in an m6 A-dependent manner. Stabiliser proteins, including HuR, Matrin3 and pAbPC1, were recruited by circRARS, thereby increasing the mRNA stability of the forementioned five target genes. Consequently, the IGF2BP3/circRARS complex facilitated the lipid accumulation of RCC cells and promoted sunitinib resistance via target genes. circRARS synergised with IGF2BP3 to facilitate m6 A recognition, thereby promoting RCC progression. Thus, IGF2BP3 could be a potential biomarker for RCC diagnosis and prognosis and a therapeutic target.
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Affiliation(s)
- Yuenan Liu
- Department of UrologyUnion Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Institute of UrologyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
| | - Kailei Chen
- Department of UrologyUnion Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Institute of UrologyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
| | - Yi Shou
- Department of UrologyUnion Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Institute of UrologyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Department of UrologySir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouP. R. China
| | - Sen Li
- Department of UrologyUnion Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Institute of UrologyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
| | - Jun Wang
- Department of UrologyUnion Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Institute of UrologyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
| | - Qingyang Zhang
- Department of Biomedical InformaticsHarvard Medical SchoolBostonMassachusettsUSA
| | - Ziwei Huang
- Department of Breast and Thyroid SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
| | - Jiaju Xu
- Department of UrologyUnion Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Institute of UrologyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
| | - Mingfeng Li
- Department of UrologyUnion Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Institute of UrologyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
| | - Di Liu
- Department of UrologyUnion Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Institute of UrologyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
| | - Huageng Liang
- Department of UrologyUnion Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Institute of UrologyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
| | - Hongmei Yang
- Department of Pathogenic BiologySchool of Basic MedicineHuazhong University of Science and TechnologyWuhanP. R. China
| | - Xiaoping Zhang
- Department of UrologyUnion Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Institute of UrologyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Shenzhen Huazhong University of Science and Technology Research InstituteShenzhenP. R. China
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Yang R, Han J, Zhao S. LINC01082 Inhibits Non-Small Cell Lung Cancer by Targeting the miR-543/TNRC6A Axis. Biochem Genet 2023; 61:1585-1605. [PMID: 36719626 DOI: 10.1007/s10528-022-10313-5] [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: 07/28/2022] [Accepted: 12/09/2022] [Indexed: 02/01/2023]
Abstract
Non-small cell lung cancer (NSCLC) accounts for over 80% of lung cancer cases and have poor clinical outcomes. Increasing number of lncRNAs are reported to be implicated in the carcinogenesis of NSCLC. Previous lncRNA-seq results showed that LINC01082 was under-expressed in several cancer types. In the current study, we focused on the role of LINC01082 in NSCLC development. An online bioinformatics tool was utilized to assess the expression profile of LINC01082, miR-543, and TNRC6A in NSCLC samples. RT-qPCR analysis was performed for evaluating LINC01082, TNRC6A and miR-543 expression in cells (NSCLC cells vs. normal lung cells). Impact of LINC01082 upregulation on cell proliferation in vitro was investigated by MTT and EdU experiments. Transwell assay was applied to analyze the migration and invasion of NSCLC cells. The cell apoptosis after plasmid transfection was detected by flow cytometry. The interactions among LINC01082, miR-543 and TNRC6A were measured by RNA pulldown and luciferase reporter assays. We showed that LINC01082 levels were downregulated in NSCLC samples and NSCLC cells. Overexpression of LINC01082 inhibited NSCLC cell proliferation, migration and invasion and strengthened cell apoptosis. LINC01082 directly bound to miR-543, and miR-543 targeted TNRC6A. TNRC6A was downregulated and miR-543 was overexpressed in NSCLC cells. miR-543 inhibition suppressed malignant cellular behaviors. TNRC6A knockdown reversed the effects of LINC01082 on the malignant character of NSCLC cells. In conclusion, LINC01082 exerts an antioncogenic role in NSCLC via interaction with miR-543 to regulate TNRC6A expression.
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Affiliation(s)
- Ran Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, Henan, China
- Department of Thoracic Surgery, Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, No. 1 Huanbin North Road, Anyang, 455003, Henan, China
| | - Jinli Han
- Department of Clinical Laboratory, Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospita of Henan University of Science and Technology, No. 1 Huanbin North Road, Anyang, 455003, Henan, China
| | - Song Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, Henan, China.
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Sánchez-Alarcón J, Milić M, Bonassi S, Gómez-Arroyo S, Cortés-Eslava J, Flores-Márquez AR, Valencia-Sánchez RA, Valencia-Quintana R. Occupational exposure to pesticides: DNA damage in horticulturist from Nativitas, Tlaxcala in Mexico. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2023; 100:104141. [PMID: 37146670 DOI: 10.1016/j.etap.2023.104141] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/07/2023]
Abstract
Mexico is a country where agricultural activity is of great importance, but biomonitoring data are still scarce. With more intensive pesticides use per unit area/surface in horticultural productivity, there is a higher impact on environmental contamination and workers' health. Considering that exposure to various pesticide and pesticide mixtures represents an additional genotoxic risk, the appropriate characterization of exposure, confounding factors and the risk itself are very much needed. We compared genetic damage in 42 horticulturists and 46 unexposed controls (Nativitas, Tlaxcala) using alkaline comet (whole blood) and micronucleus (MN) test with nuclear abnormalities (NA) (buccal epithelial cells). Workers demonstrated significantly higher levels of damage (TI%=14.02 ± 2.49 vs. 5.37 ± 0.46; MN=10.14 ± 5.15 vs. 2.40 ± 0.20), with more than 90% of them not using protective clothing nor gloves during application. Combined DNA damage techniques and periodic monitoring together with educational programs for safe pesticide application is the best strategy to assess and prevent workers' health risks.
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Affiliation(s)
- Juana Sánchez-Alarcón
- Laboratorio "Rafael Villalobos-Pietrini" de Toxicología Genómica y Química Ambiental, Facultad de Agrobiología, Universidad Autónoma de Tlaxcala, CA Genética y Ambiente UATLX-CA 223, Red Temática de Toxicología de Plaguicidas, Tlaxcala 90120, Mexico
| | - Mirta Milić
- Mutagenesis Unit, Institute for Medical Research and Occupational Health, Ksaverska Cesta 2, 10 000 Zagreb, Croatia.
| | - Stefano Bonassi
- Department of Human Sciences and Quality of Life Promotion, San Raffaele University, 00166 Rome, Italy; Unit of Clinical and Molecular Epidemiology, IRCCS San Raffaele Roma, 00166 Rome, Italy
| | - Sandra Gómez-Arroyo
- Laboratorio de Genotoxicología y Mutagénesis Ambientales, Instituto de Ciencias de la Atmósfera y Cambio Climático, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, 04510 Ciudad de Mexico, Mexico
| | - Josefina Cortés-Eslava
- Laboratorio de Genotoxicología y Mutagénesis Ambientales, Instituto de Ciencias de la Atmósfera y Cambio Climático, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, 04510 Ciudad de Mexico, Mexico
| | - Ana Rosa Flores-Márquez
- Laboratorio de Genotoxicología y Mutagénesis Ambientales, Instituto de Ciencias de la Atmósfera y Cambio Climático, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, 04510 Ciudad de Mexico, Mexico
| | | | - Rafael Valencia-Quintana
- Laboratorio "Rafael Villalobos-Pietrini" de Toxicología Genómica y Química Ambiental, Facultad de Agrobiología, Universidad Autónoma de Tlaxcala, CA Genética y Ambiente UATLX-CA 223, Red Temática de Toxicología de Plaguicidas, Tlaxcala 90120, Mexico.
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Ye Q, Raese R, Luo D, Cao S, Wan YW, Qian Y, Guo NL. MicroRNA, mRNA, and Proteomics Biomarkers and Therapeutic Targets for Improving Lung Cancer Treatment Outcomes. Cancers (Basel) 2023; 15:cancers15082294. [PMID: 37190222 DOI: 10.3390/cancers15082294] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023] Open
Abstract
The majority of lung cancer patients are diagnosed with metastatic disease. This study identified a set of 73 microRNAs (miRNAs) that classified lung cancer tumors from normal lung tissues with an overall accuracy of 96.3% in the training patient cohort (n = 109) and 91.7% in unsupervised classification and 92.3% in supervised classification in the validation set (n = 375). Based on association with patient survival (n = 1016), 10 miRNAs were identified as potential tumor suppressors (hsa-miR-144, hsa-miR-195, hsa-miR-223, hsa-miR-30a, hsa-miR-30b, hsa-miR-30d, hsa-miR-335, hsa-miR-363, hsa-miR-451, and hsa-miR-99a), and 4 were identified as potential oncogenes (hsa-miR-21, hsa-miR-31, hsa-miR-411, and hsa-miR-494) in lung cancer. Experimentally confirmed target genes were identified for the 73 diagnostic miRNAs, from which proliferation genes were selected from CRISPR-Cas9/RNA interference (RNAi) screening assays. Pansensitive and panresistant genes to 21 NCCN-recommended drugs with concordant mRNA and protein expression were identified. DGKE and WDR47 were found with significant associations with responses to both systemic therapies and radiotherapy in lung cancer. Based on our identified miRNA-regulated molecular machinery, an inhibitor of PDK1/Akt BX-912, an anthracycline antibiotic daunorubicin, and a multi-targeted protein kinase inhibitor midostaurin were discovered as potential repositioning drugs for treating lung cancer. These findings have implications for improving lung cancer diagnosis, optimizing treatment selection, and discovering new drug options for better patient outcomes.
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Affiliation(s)
- Qing Ye
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506, USA
| | - Rebecca Raese
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506, USA
| | - Dajie Luo
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506, USA
| | - Shu Cao
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506, USA
| | - Ying-Wooi Wan
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506, USA
| | - Yong Qian
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Nancy Lan Guo
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506, USA
- Department of Occupational and Environmental Health Sciences, School of Public Health, West Virginia University, Morgantown, WV 26506, USA
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Chen W, Ru J, Wu T, Man D, Wu J, Wu L, Sun Y, Yu H, Li M, Zhang G, Zhu X, Tong R, Xiao H, Li Y, Yang B. MiR-652-3p promotes malignancy and metastasis of cancer cells via inhibiting TNRC6A in hepatocellular carcinoma. Biochem Biophys Res Commun 2023; 640:1-11. [PMID: 36495604 DOI: 10.1016/j.bbrc.2022.11.100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/21/2022] [Accepted: 11/30/2022] [Indexed: 12/07/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) was one of the most prevalent life-threatening cancers. Metastasis is the leading cause of cancer-related death in HCC. MiRNAs play essential roles in cancer metastasis. METHODS Expression of miR-652-3p in HCC was assessed. Function experiments of miR-652-3p and trinucleotide repeat-containing gene 6A protein (TNRC6A) were performed both in vitro and in vivo. mRNA sequencing, PCR, and western blot were performed to verify the target genes and pathway of miR-652-3p. The lung metastasis and xenograft cancer model in nude mice was established to investigate the effects of the miR-652-3p and TRNC6A on tumor metastasis in vivo. The relationship between the expression of the miR-652-3p, TNRC6A and the prognosis of HCC patients was analyzed. RESULTS Upregulated miR-652-3p was found in the tumor tissues of HCC, especially in metastatic HCC patients. Overexpression of miR-652-3p promoted and knockdown of miR-652-3p suppressed HCC metastasis both in vitro and in vivo. MiR-652-3p promoted HCC metastasis via regulating the EMT pathway. TNRC6A was identified as a direct target of miR-652-3p, and the knockdown of TNRC6A restored repressed EMT and HCC metastasis caused by the inhibition of miR-652-3p. Clinical results revealed that high expression of miR-652-3p and low expression of TNRC6A were positively correlated to shortened overall survival and disease-free survival in HCC patients. CONCLUSIONS MiR-652-3p promotes EMT and HCC metastasis by inhibiting TNRC6A expression in HCC. MiR-652-3p and TNRC6A may serve as potential biomarkers to predict prognosis in HCC patients with metastasis.
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Affiliation(s)
- Wei Chen
- General Practice Department, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
| | - Junnan Ru
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Tong Wu
- School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Da Man
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Jingbang Wu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Lijuan Wu
- General Practice Department, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
| | - Yujing Sun
- General Practice Department, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Hanxi Yu
- Health Management Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Min Li
- General Practice Department, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
| | - Gangwei Zhang
- General Practice Department, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
| | - Xingxin Zhu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Rongliang Tong
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Heng Xiao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Yanhua Li
- General Practice Department, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
| | - Beng Yang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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Xiong Q, Zhang Y, Li J, Zhu Q. Small Non-Coding RNAs in Human Cancer. Genes (Basel) 2022; 13:genes13112072. [PMID: 36360311 PMCID: PMC9690286 DOI: 10.3390/genes13112072] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
Small non-coding RNAs are widespread in the biological world and have been extensively explored over the past decades. Their fundamental roles in human health and disease are increasingly appreciated. Furthermore, a growing number of studies have investigated the functions of small non-coding RNAs in cancer initiation and progression. In this review, we provide an overview of the biogenesis of small non-coding RNAs with a focus on microRNAs, PIWI-interacting RNAs, and a new class of tRNA-derived small RNAs. We discuss their biological functions in human cancer and highlight their clinical application as molecular biomarkers or therapeutic targets.
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Affiliation(s)
- Qunli Xiong
- Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yaguang Zhang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Junjun Li
- Department of Radiation Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Qing Zhu
- Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
- Correspondence:
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10
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Farooq U, Notani D. Transcriptional regulation of INK4/ARF locus by cis and trans mechanisms. Front Cell Dev Biol 2022; 10:948351. [PMID: 36158211 PMCID: PMC9500187 DOI: 10.3389/fcell.2022.948351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/09/2022] [Indexed: 12/12/2022] Open
Abstract
9p21 locus is one of the most reproducible regions in genome-wide association studies (GWAS). The region harbors CDKN2A/B genes that code for p16INK4a, p15INK4b, and p14ARF proteins, and it also harbors a long gene desert adjacent to these genes. The polymorphisms that are associated with several diseases and cancers are present in these genes and the gene desert region. These proteins are critical cell cycle regulators whose transcriptional dysregulation is strongly linked with cellular regeneration, stemness, aging, and cancers. Given the importance of this locus, intense scientific efforts on understanding the regulation of these genes via promoter-driven mechanisms and recently, via the distal regulatory mechanism have provided major insights. In this review, we describe these mechanisms and propose the ways by which this locus can be targeted in pathologies and aging.
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Affiliation(s)
- Umer Farooq
- Genetics and Development, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, India
- The University of Trans-Disciplinary Health Sciences and Technology, Bangalore, India
- *Correspondence: Umer Farooq, ; Dimple Notani,
| | - Dimple Notani
- Genetics and Development, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, India
- *Correspondence: Umer Farooq, ; Dimple Notani,
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11
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Ghafouri-Fard S, Khoshbakht T, Hussen BM, Baniahmad A, Branicki W, Taheri M, Eghbali A. Emerging Role of Non-Coding RNAs in Senescence. Front Cell Dev Biol 2022; 10:869011. [PMID: 35865636 PMCID: PMC9294638 DOI: 10.3389/fcell.2022.869011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Senescence is defined as a gradual weakening of functional features of a living organism. Cellular senescence is a process that is principally aimed to remove undesirable cells by prompting tissue remodeling. This process is also regarded as a defense mechanism induced by cellular damage. In the course of oncogenesis, senescence can limit tumor progression. However, senescence participates in the pathoetiology of several disorders such as fibrotic disorders, vascular disorders, diabetes, renal disorders and sarcopenia. Recent studies have revealed contribution of different classes of non-coding RNAs in the cellular senescence. Long non-coding RNAs, microRNAs and circular RNAs are three classes of these transcripts whose contributions in this process have been more investigated. In the current review, we summarize the available literature on the impact of these transcripts in the cellular senescence.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Iraq
- Center of Research and Strategic Studies, Lebanese French University, Erbil, Iraq
| | - Aria Baniahmad
- Institute of Human Genetics, Jena University Hospitals, Jena, Germany
- *Correspondence: Aria Baniahmad, ; Mohammad Taheri, ; Ahmad Eghbali,
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospitals, Jena, Germany
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Aria Baniahmad, ; Mohammad Taheri, ; Ahmad Eghbali,
| | - Ahmad Eghbali
- Anesthesiology Research Center, Mofid Children Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Aria Baniahmad, ; Mohammad Taheri, ; Ahmad Eghbali,
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12
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Valencia-Quintana R, Bahena-Ocampo IU, González-Castañeda G, Bonilla E, Milić M, Bonassi S, Sánchez-Alarcón J. miRNAs: A potentially valuable tool in pesticide toxicology assessment-current experimental and epidemiological data review. CHEMOSPHERE 2022; 295:133792. [PMID: 35104543 DOI: 10.1016/j.chemosphere.2022.133792] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
miRNAs are responsible for the regulation of many cellular processes such as development, cell differentiation, proliferation, apoptosis, and tumor growth. Several studies showed that they can also serve as specific, stable, and sensitive markers of chemical exposure. In this review, current experimental and epidemiological data evidencing deregulation in miRNA expression in response to fungicides, insecticides or herbicides were analyzed. As shown by Venn's diagrams, miR-363 and miR-9 deregulation is associated with fungicide exposure in vitro and in vivo, while let-7, miR-155, miR-181 and miR-21 were found to be commonly deregulated by at least three different insecticides. Furthermore, let-7, miR-30, miR-126, miR-181 and miR-320 were commonly deregulated by 3 different herbicides. Notably, these 5 miRNAs were also found to be deregulated by one or more insecticides, suggesting their participation in the cellular response to pesticides, regardless of their chemical structure. All these miRNAs have been proposed as potential biomarkers for fungicide, insecticide, or herbicide exposure. These results allow us to improve our understanding of the molecular mechanisms of toxicity upon pesticide exposure, although further studies are needed to confirm these miRNAs as definitive (not potential) biomarkers of pesticide exposure.
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Affiliation(s)
- Rafael Valencia-Quintana
- Laboratorio "Rafael Villalobos-Pietrini" de Toxicología Genómica y Química Ambiental, Facultad de Agrobiología, Universidad Autónoma de Tlaxcala, CA Ambiente y Genética UATLX-CA-223 Red Temática de Toxicología de Plaguicidas, Tlaxcala, 90000, Mexico.
| | | | | | - Edmundo Bonilla
- Departamento de Ciencias de La Salud, UAM-Iztapalapa, Mexico.
| | - Mirta Milić
- Mutagenesis Unit, Institute for Medical Research and Occupational Health, Zagreb, 10000, Croatia.
| | - Stefano Bonassi
- Department of Human Sciences and Quality of Life Promotion, San Raffaele University, Rome, 00166, Italy; Unit of Clinical and Molecular Epidemiology IRCCS San Raffaele Pisana, Rome, 00166, Italy.
| | - Juana Sánchez-Alarcón
- Laboratorio "Rafael Villalobos-Pietrini" de Toxicología Genómica y Química Ambiental, Facultad de Agrobiología, Universidad Autónoma de Tlaxcala, CA Ambiente y Genética UATLX-CA-223 Red Temática de Toxicología de Plaguicidas, Tlaxcala, 90000, Mexico.
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13
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Zhang D, Li Y, Lei Y, Yang H, Huang L, Chen X, Zhou Z, Huang C, Zhou Y, Feng R, Xiong XD, Yuan Y, Cui H, Zheng HL, Sun X, Liu X, Xu S. Circular RNA circRNF169 functions as a miR-30c-5p sponge to promote cellular senescence. Biochem Biophys Res Commun 2022; 604:88-95. [PMID: 35303684 DOI: 10.1016/j.bbrc.2022.03.041] [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: 01/07/2022] [Accepted: 03/08/2022] [Indexed: 11/02/2022]
Abstract
Circular RNAs (circRNAs), characterized as single-stranded closed circular RNA molecules, have been established to exert pivotal functions in various biological or pathological processes. Nonetheless, the effects and underlying mechanisms concerning circRNAs on the aging and aging-related diseases remain elusive. We herein compared the expression patterns of circRNAs in young and senescent mouse embryonic fibroblasts (MEFs), and uncovered that circRNF169 was dramatically up-regulated in senescent MEFs compared with that in young MEFs. Therefore, we further digged into the role and potential mechanisms of circRNF169 in the senescence of MEFs. The results of senescence-associate-β-galactosidase staining and BrdU incorporation assay showed that silencing of circRNF169 significantly delayed MEFs senescence and promoted cell proliferation, while ectopic expression of circRNF169 exhibited the opposite effects. Moreover, the dual-luciferase reporter assay confirmed that circRNF169 acted as an endogenous miR-30c-5p sponge, which accelerated cellular senescence by sequestering and inhibiting miR-30c-5p activity. Taken together, our results suggested that circRNF169 exerted a crucial role in cellular senescence through sponging miR-30c-5p and represented a promising target for aging intervention.
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Affiliation(s)
- Dingyuan Zhang
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Yuting Li
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Yiting Lei
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Haiqing Yang
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Linying Huang
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Xue Chen
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Zhihao Zhou
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Cuiyi Huang
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Yantao Zhou
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Ruolan Feng
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Xing-Dong Xiong
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Yuan Yuan
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Hongjing Cui
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Hui-Ling Zheng
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Xuerong Sun
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Xinguang Liu
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China.
| | - Shun Xu
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China.
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14
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Shen W, He J, Hou T, Si J, Chen S. Common Pathogenetic Mechanisms Underlying Aging and Tumor and Means of Interventions. Aging Dis 2022; 13:1063-1091. [PMID: 35855334 PMCID: PMC9286910 DOI: 10.14336/ad.2021.1208] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/07/2021] [Indexed: 11/22/2022] Open
Abstract
Recently, there has been an increase in the incidence of malignant tumors among the older population. Moreover, there is an association between aging and cancer. During the process of senescence, the human body suffers from a series of imbalances, which have been shown to further accelerate aging, trigger tumorigenesis, and facilitate cancer progression. Therefore, exploring the junctions of aging and cancer and searching for novel methods to restore the junctions is of great importance to intervene against aging-related cancers. In this review, we have identified the underlying pathogenetic mechanisms of aging-related cancers by comparing alterations in the human body caused by aging and the factors that trigger cancers. We found that the common mechanisms of aging and cancer include cellular senescence, alterations in proteostasis, microbiota disorders (decreased probiotics and increased pernicious bacteria), persistent chronic inflammation, extensive immunosenescence, inordinate energy metabolism, altered material metabolism, endocrine disorders, altered genetic expression, and epigenetic modification. Furthermore, we have proposed that aging and cancer have common means of intervention, including novel uses of common medicine (metformin, resveratrol, and rapamycin), dietary restriction, and artificial microbiota intervention or selectively replenishing scarce metabolites. In addition, we have summarized the research progress of each intervention and revealed their bidirectional effects on cancer progression to compare their reliability and feasibility. Therefore, the study findings provide vital information for advanced research studies on age-related cancers. However, there is a need for further optimization of the described methods and more suitable methods for complicated clinical practices. In conclusion, targeting aging may have potential therapeutic effects on aging-related cancers.
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Affiliation(s)
- Weiyi Shen
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, Zhejiang, China.
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang, China.
- Prevention and Treatment Research Center for Senescent Disease, Zhejiang University School of Medicine, Zhejiang, China
| | - Jiamin He
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, Zhejiang, China.
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang, China.
- Prevention and Treatment Research Center for Senescent Disease, Zhejiang University School of Medicine, Zhejiang, China
| | - Tongyao Hou
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, Zhejiang, China.
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang, China.
- Prevention and Treatment Research Center for Senescent Disease, Zhejiang University School of Medicine, Zhejiang, China
- Correspondence should be addressed to: Dr. Shujie Chen (), Dr. Jianmin Si () and Dr. Tongyao Hou (), Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang, China
| | - Jianmin Si
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, Zhejiang, China.
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang, China.
- Prevention and Treatment Research Center for Senescent Disease, Zhejiang University School of Medicine, Zhejiang, China
- Correspondence should be addressed to: Dr. Shujie Chen (), Dr. Jianmin Si () and Dr. Tongyao Hou (), Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang, China
| | - Shujie Chen
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, Zhejiang, China.
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang, China.
- Prevention and Treatment Research Center for Senescent Disease, Zhejiang University School of Medicine, Zhejiang, China
- Correspondence should be addressed to: Dr. Shujie Chen (), Dr. Jianmin Si () and Dr. Tongyao Hou (), Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang, China
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15
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Wu D, Tan H, Su W, Cheng D, Wang G, Wang J, Ma DA, Dong GM, Sun P. MZF1 mediates oncogene-induced senescence by promoting the transcription of p16 INK4A. Oncogene 2022; 41:414-426. [PMID: 34773072 PMCID: PMC8758531 DOI: 10.1038/s41388-021-02110-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 01/27/2023]
Abstract
Oncogene induced senescence is a tumor suppressing defense mechanism, in which the cell cycle-dependent protein kinase (CDK) inhibitor p16INK4A (encoded by the CDKN2A gene) plays a key role. We previously reported that a transcriptional co-activator chromodomain helicase DNA binding protein 7 (CHD7) mediates oncogenic ras-induced senescence by inducing transcription of the p16INK4A gene. In the current study, we identified myeloid zinc finger 1 (MZF1) as the transcriptional factor that recruits CHD7 to the p16INK4A promoter, where it mediates oncogenic ras-induced p16INK4A transcription and senescence through CHD7, in primary human cells from multiple origins. Moreover, the expression of MZF1 is induced by oncogenic ras in senescent cells through the c-Jun and Ets1 transcriptional factors upon their activation by the Ras-Raf-1-MEK-ERK signaling pathway. In non-small cell lung cancer (NSCLC) and pancreatic adenocarcinoma (PAAD) where activating ras mutations occur frequently, reduced MZF1 expression is observed in tumors, as compared to corresponding normal tissues, and correlates with poor patient survival. Analysis of single cell RNA-sequencing data from PAAD patients revealed that among the tumor cells with normal RB expression levels, those with reduced levels of MZF1 are more likely to express lower p16INK4A levels. These findings have identified novel signaling components in the pathway that mediates induction of the p16INK4A tumor suppressor and the senescence response, and suggested that MZF1 is a potential tumor suppressor in at least some cancer types, the loss of which contributes to the inactivation of the p16INK4A/RB pathway and disruption of senescence in tumor cells with intact RB.
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Affiliation(s)
- Dan Wu
- Departments of Cancer Biology, Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, NC 27157, USA
| | - Hua Tan
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Weijun Su
- Nankai University School of Medicine, Tianjin, China
| | - Dongmei Cheng
- Departments of Cancer Biology, Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, NC 27157, USA
| | - Guanwen Wang
- Departments of Cancer Biology, Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, NC 27157, USA,Nankai University School of Medicine, Tianjin, China
| | - Juan Wang
- Departments of Cancer Biology, Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, NC 27157, USA,Nankai University School of Medicine, Tianjin, China
| | - Ding A. Ma
- Departments of Cancer Biology, Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, NC 27157, USA
| | - George M. Dong
- Departments of Cancer Biology, Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, NC 27157, USA
| | - Peiqing Sun
- Department of Cancer Biology, Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-, Salem, NC, 27157, USA.
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16
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Footprints of microRNAs in Cancer Biology. Biomedicines 2021; 9:biomedicines9101494. [PMID: 34680611 PMCID: PMC8533183 DOI: 10.3390/biomedicines9101494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs involved in post-transcriptional gene regulation. Over the past years, various studies have demonstrated the role of aberrant miRNA expression in the onset of cancer. The mechanisms by which miRNA exerts its cancer-promoting or inhibitory effects are apparent through the various cancer hallmarks, which include selective proliferative advantage, altered stress response, vascularization, invasion and metastasis, metabolic rewiring, the tumor microenvironment and immune modulation; therefore, this review aims to highlight the association between miRNAs and the various cancer hallmarks by dissecting the mechanisms of miRNA regulation in each hallmark separately. It is hoped that the information presented herein will provide further insights regarding the role of cancer and serve as a guideline to evaluate the potential of microRNAs to be utilized as biomarkers and therapeutic targets on a larger scale in cancer research.
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17
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Yan L, Xie X, Niu BX, Wu MT, Tong WQ, He SY, Huang CY, Zhao WC, Li G, Li NS, Jiang JL. Involvement of miR-199a-3p/DDR1 in vascular endothelial cell senescence in diabetes. Eur J Pharmacol 2021; 908:174317. [PMID: 34270989 DOI: 10.1016/j.ejphar.2021.174317] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/21/2021] [Accepted: 07/07/2021] [Indexed: 10/20/2022]
Abstract
Endothelial cell dysfunction is a prominent feature of diabetic cardiovascular complications, and endothelial cell senescence is considered to be an important contributor to endothelial dysfunction. Discoidin domain receptor 1 (DDR1) has been reported to be involved in atherogenesis and cerebral ischemia/reperfusion injury. In this study, we aimed to explore the role of DDR1 in endothelial cell senescence under diabetic conditions and elucidate the underlying mechanisms. A diabetic rat model was established by a single intraperitoneal injection of streptozocin (STZ) (60 mg/kg), which showed an increase in senescence-associated β-galactosidase (SA-β-gal) staining signal of thoracic aortic endothelium, impaired vascular structure and function, accompanied by an up-regulation of DDR1. Next, we verified the role of DDR1 in endothelial senescence and the underlying mechanisms in high glucose-treated human umbilical vein endothelial cells (HUVECs). Consistent with the in vivo findings, high glucose induced endothelial senescence, impaired endothelial function and elevated DDR1 expression, accompanied by the elevation of senescence-related genes p53 and p21 expression, and these effects were reversed by DDR1 siRNA. DDR1 has been documented to be a potential target of miR-199a-3p. Here, we found that miR-199a-3p was down-regulated by high glucose in the aorta tissue and HUVECs, while miR-199a-3p mimic significantly suppressed increased endothelial senescence and elevated DDR1 induced by high glucose. In conclusion, our data demonstrated that miR-199a-3p/DDR1/p53/p21 signaling pathway was involved in endothelial senescence under diabetic conditions, and therapeutic targeting DDR1 would be exploited to inhibit endothelial senescence owing to high glucose exposure.
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Affiliation(s)
- Li Yan
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China; Departments of Pharmacy, Wuhan Asia General Hospital, Wuhan, 430056, China
| | - Xu Xie
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China
| | - Bing-Xuan Niu
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China
| | - Mei-Ting Wu
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China
| | - Wei-Qiang Tong
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China
| | - Shuang-Yi He
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China
| | - Chu-Yi Huang
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China
| | - Wei-Chen Zhao
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China
| | - Ge Li
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China
| | - Nian-Sheng Li
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China
| | - Jun-Lin Jiang
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China; Provincial Key Laboratory of Cardiovascular Research, Central South University, Changsha, 410078, China.
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18
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Chang A, Liu L, Ashby JM, Wu D, Chen Y, O'Neill SS, Huang S, Wang J, Wang G, Cheng D, Tan X, Petty WJ, Pasche BC, Xiang R, Zhang W, Sun P. Recruitment of KMT2C/MLL3 to DNA Damage Sites Mediates DNA Damage Responses and Regulates PARP Inhibitor Sensitivity in Cancer. Cancer Res 2021; 81:3358-3373. [PMID: 33853832 DOI: 10.1158/0008-5472.can-21-0688] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/26/2021] [Accepted: 03/31/2021] [Indexed: 11/16/2022]
Abstract
When recruited to promoters, histone 3 lysine 4 (H3K4) methyltransferases KMT2 (KMT2A-D) activate transcription by opening chromatin through H3K4 methylation. Here, we report that KMT2 mutations occur frequently in non-small cell lung cancer (NSCLC) and are associated with high mutation loads and poor survival. KMT2C regulated DNA damage responses (DDR) through direct recruitment to DNA damage sites by Ago2 and small noncoding DNA damage response RNA, where it mediates H3K4 methylation, chromatin relaxation, secondary recruitment of DDR factors, and amplification of DDR signals along chromatin. Furthermore, by disrupting homologous recombination (HR)-mediated DNA repair, KMT2C/D mutations sensitized NSCLC to Poly(ADP-ribose) polymerase inhibitors (PARPi), whose efficacy is unclear in NSCLC due to low BRCA1/2 mutation rates. These results demonstrate a novel, transcription-independent role of KMT2C in DDR and identify high-frequency KMT2C/D mutations as much-needed biomarkers for PARPi therapies in NSCLC and other cancers with infrequent BRCA1/2 mutations. SIGNIFICANCE: This study uncovers a critical role for KMT2C in DDR via direct recruitment to DNA damage sites, identifying high-frequency KMT2C/D mutations as biomarkers for response to PARP inhibition in cancer.
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Affiliation(s)
- Antao Chang
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina.,Nankai University School of Medicine, Tianjin, China
| | - Liang Liu
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina.,Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina
| | - Justin M Ashby
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina
| | - Dan Wu
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina
| | - Yanan Chen
- Nankai University School of Medicine, Tianjin, China
| | - Stacey S O'Neill
- Department of Pathology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina
| | - Shan Huang
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina.,Nankai University School of Medicine, Tianjin, China
| | - Juan Wang
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina.,Nankai University School of Medicine, Tianjin, China
| | - Guanwen Wang
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina.,Nankai University School of Medicine, Tianjin, China
| | - Dongmei Cheng
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina
| | - Xiaoming Tan
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina.,Department of Respiratory Disease, South Campus, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - W J Petty
- Department of Internal Medicine, Division of Hematology and Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina
| | - Boris C Pasche
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina
| | - Rong Xiang
- Nankai University School of Medicine, Tianjin, China
| | - Wei Zhang
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina. .,Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina
| | - Peiqing Sun
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina.
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MacDonagh L, Gallagher MF, Ffrench B, Gasch C, Gray SG, Reidy M, Nicholson S, Leonard N, Ryan R, Young V, O'Leary JJ, Cuffe S, Finn SP, O'Byrne KJ, Barr MP. MicroRNA expression profiling and biomarker validation in treatment-naïve and drug resistant non-small cell lung cancer. Transl Lung Cancer Res 2021; 10:1773-1791. [PMID: 34012792 PMCID: PMC8107736 DOI: 10.21037/tlcr-20-959] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Background In the absence of targetable mutations or immune checkpoints, cisplatin-doublet chemotherapy remains the standard of care in non-small cell lung cancer (NSCLC). Drug resistance has however become a significant clinical challenge. Exploring a role for small non-coding microRNAs (miRNA) as biomarker candidates in cisplatin resistant (CisR) lung cancer is lacking and warrants further investigation. Methods miRNA expression profiling was assessed in a panel of cisplatin sensitive and resistant NSCLC cell lines and validated by qPCR. Modulation of altered miRNAs was studied using antagomiRs and pre-miRs while functional assays were used to assess cisplatin response. The translational relevance of these miRNAs as potential biomarkers was assessed in serum and matched normal and tumour lung tissues from chemo-naïve NSCLC patients, in addition to xenograft formalin-fixed paraffin-embedded (FFPE) tumours derived from cisplatin sensitive and resistant cell lines. Results Differential expression of a 5-miR signature (miR-30a-3p, miR-30b-5p, miR-30c-5p, miR-34a-5p, miR-4286) demonstrated their ability to distinguish between normal and tumour lung tissue and between NSCLC histologies. In squamous cell carcinoma (SqCC), tissue miRNA expression was associated with poor survival. miR-4286 showed promise as a blood-based diagnostic biomarker that could distinguish between adenocarcinoma and SqCC histologies. In a xenograft model of cisplatin resistance, using 7-9 week old female NOD/SCID mice (NOD.CB17-Prkdcscid/NCrCrl), a 5-miRNA panel showed altered expression between sensitive and resistant tumours. Conclusions This study identified a panel of miRNAs which may have diagnostic and prognostic potential as novel biomarkers in lung cancer and furthermore, may have a predictive role in monitoring the emergence of resistance to cisplatin.
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Affiliation(s)
- Lauren MacDonagh
- Thoracic Oncology Research Group, School of Medicine, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, St. James's Hospital and Trinity College Dublin, Dublin, Ireland
| | - Michael F Gallagher
- Histopathology Department, Sir Patrick Dun Laboratories, Central Pathology Laboratory, St. James's Hospital & Pathology Research Laboratory, Coombe Women and Infant's University Hospital, Dublin, Ireland
| | - Brendan Ffrench
- Histopathology Department, Sir Patrick Dun Laboratories, Central Pathology Laboratory, St. James's Hospital & Pathology Research Laboratory, Coombe Women and Infant's University Hospital, Dublin, Ireland
| | - Claudia Gasch
- Histopathology Department, Sir Patrick Dun Laboratories, Central Pathology Laboratory, St. James's Hospital & Pathology Research Laboratory, Coombe Women and Infant's University Hospital, Dublin, Ireland
| | - Steven G Gray
- Thoracic Oncology Research Group, School of Medicine, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, St. James's Hospital and Trinity College Dublin, Dublin, Ireland
| | - Marie Reidy
- Department of Histopathology, St. James's Hospital, Dublin, Ireland
| | | | - Niamh Leonard
- Department of Histopathology, St. James's Hospital, Dublin, Ireland
| | - Ronan Ryan
- Department of Cardiothoracic Surgery, St. James's Hospital, Dublin, Ireland
| | - Vincent Young
- Department of Cardiothoracic Surgery, St. James's Hospital, Dublin, Ireland
| | - John J O'Leary
- Histopathology Department, Sir Patrick Dun Laboratories, Central Pathology Laboratory, St. James's Hospital & Pathology Research Laboratory, Coombe Women and Infant's University Hospital, Dublin, Ireland
| | - Sinead Cuffe
- Thoracic Oncology Research Group, School of Medicine, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, St. James's Hospital and Trinity College Dublin, Dublin, Ireland.,Department of Medical Oncology, St James's Hospital, Dublin, Ireland
| | - Stephen P Finn
- Thoracic Oncology Research Group, School of Medicine, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, St. James's Hospital and Trinity College Dublin, Dublin, Ireland.,Department of Histopathology, St. James's Hospital, Dublin, Ireland
| | - Kenneth J O'Byrne
- Cancer & Ageing Research Program, Queensland University of Technology, Brisbane, Australia
| | - Martin P Barr
- Thoracic Oncology Research Group, School of Medicine, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, St. James's Hospital and Trinity College Dublin, Dublin, Ireland
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20
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Bae Y, Hwang JS, Shin YJ. miR-30c-1 encourages human corneal endothelial cells to regenerate through ameliorating senescence. Aging (Albany NY) 2021; 13:9348-9372. [PMID: 33744867 PMCID: PMC8064150 DOI: 10.18632/aging.202719] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 02/16/2021] [Indexed: 12/22/2022]
Abstract
In the present study, we studied the role of microRNA-30c-1 (miR-30c-1) on transforming growth factor beta1 (TGF-β1)-induced senescence of hCECs. hCECs were transfected by miR-30c-1 and treated with TGF-β1 to assess the inhibitory effect of miR-30c-1 on TGF-β1-induced senescence. Cell viability and proliferation rate in miR-30c-1-transfected cells was elevated compared with control. Cell cycle analysis revealed that cell abundance in S phase was elevated in miR-30c-1-treated cells compared with control. TGF-β1 increased the senescence of hCECs; however, this was ameliorated by miR-30c-1. TGF-β1 increased the size of hCECs, the ratio of senescence-associated beta-galactosidase-stained cells, secretion of senescence-associated secretory phenotype factors, the oxidative stress, and arrested the cell cycle, all of which were ameliorated by miR-30c-1 treatment. miR-30c-1 also suppressed a TGF-β1-induced depolarization of mitochondrial membrane potential and a TGF-β1 stimulated increase in levels of cleaved poly (ADP-ribose) polymerase (PARP), cleaved caspase 3, and microtubule-associated proteins 1A/1B light chain 3B II. In conclusion, miR-30c-1 promoted the proliferation of hCECs through ameliorating the TGF- β1-induced senescence of hCECs and reducing cell death of hCECs. Thus, miR-30c-1 may be a therapeutic target for hCECs regeneration.
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Affiliation(s)
- Younghwan Bae
- Department of Ophthalmology, Hallym University Medical Center, Hallym University College of Medicine, Seoul, Republic of Korea
| | - Jin Sun Hwang
- Department of Ophthalmology, Hallym University Medical Center, Hallym University College of Medicine, Seoul, Republic of Korea
| | - Young Joo Shin
- Department of Ophthalmology, Hallym University Medical Center, Hallym University College of Medicine, Seoul, Republic of Korea
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21
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Rivera HM, Muñoz EN, Osuna D, Florez M, Carvajal M, Gómez LA. Reciprocal Changes in miRNA Expression with Pigmentation and Decreased Proliferation Induced in Mouse B16F1 Melanoma Cells by L-Tyrosine and 5-Bromo-2'-Deoxyuridine. Int J Mol Sci 2021; 22:ijms22041591. [PMID: 33562431 PMCID: PMC7914888 DOI: 10.3390/ijms22041591] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/31/2020] [Accepted: 01/03/2021] [Indexed: 12/15/2022] Open
Abstract
Background: Many microRNAs have been identified as critical mediators in the progression of melanoma through its regulation of genes involved in different cellular processes such as melanogenesis, cell cycle control, and senescence. However, microRNAs’ concurrent participation in syngeneic mouse B16F1 melanoma cells simultaneously induced decreased proliferation and differential pigmentation by exposure to 5-Brd-2′-dU (5’Bromo-2-deoxyuridine) and L-Tyr (L-Tyrosine) respectively, is poorly understood. Aim: To evaluate changes in the expression of microRNAs and identify which miRNAs in-network may contribute to the functional bases of phenotypes of differential pigmentation and reduction of proliferation in B16F1 melanoma cells exposed to 5-Brd-2′-dU and L-Tyr. Methods: Small RNAseq evaluation of the expression profiles of miRNAs in B16F1 melanoma cells exposed to 5-Brd-2′-dU (2.5 μg/mL) and L-Tyr (5 mM), as well as the expression by qRT-PCR of some molecular targets related to melanogenesis, cell cycle, and senescence. By bioinformatic analysis, we constructed network models of regulation and co-expression of microRNAs. Results: We confirmed that stimulation or repression of melanogenesis with L-Tyr or 5-Brd-2′-dU, respectively, generated changes in melanin concentration, reduction in proliferation, and changes in expression of microRNAs 470-3p, 470-5p, 30d-5p, 129-5p, 148b-3p, 27b-3p, and 211-5p, which presented patterns of coordinated and reciprocal co-expression, related to changes in melanogenesis through their putative targets Mitf, Tyr and Tyrp1, and control of cell cycle and senescence: Cyclin D1, Cdk2, Cdk4, p21, and p27. Conclusions: These findings provide insights into the molecular biology of melanoma of the way miRNAs are coordinated and reciprocal expression that may operate in a network as molecular bases for understanding changes in pigmentation and decreased proliferation induced in B16F1 melanoma cells exposed to L-Tyr and 5-Brd-2′-dU.
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Affiliation(s)
- Hernán Mauricio Rivera
- Department of Medicine, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (H.M.R.); (E.N.M.)
- Molecular Physiology Group, Sub-Direction of Scientific and Technological Research, Direction of Public Health Research, National Institute of Health, Bogotá 111321, Colombia
| | - Esther Natalia Muñoz
- Department of Medicine, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (H.M.R.); (E.N.M.)
- Molecular Physiology Group, Sub-Direction of Scientific and Technological Research, Direction of Public Health Research, National Institute of Health, Bogotá 111321, Colombia
| | - Daniel Osuna
- Science Department, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (D.O.); (M.F.); (M.C.)
| | - Mauro Florez
- Science Department, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (D.O.); (M.F.); (M.C.)
| | - Michael Carvajal
- Science Department, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (D.O.); (M.F.); (M.C.)
| | - Luis Alberto Gómez
- Molecular Physiology Group, Sub-Direction of Scientific and Technological Research, Direction of Public Health Research, National Institute of Health, Bogotá 111321, Colombia
- Department of Physiological Sciences, Faculty of Medicine, Universidad Nacional de Colombia, Bogotá 111321, Colombia
- Correspondence:
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22
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Roupakia E, Markopoulos GS, Kolettas E. Genes and pathways involved in senescence bypass identified by functional genetic screens. Mech Ageing Dev 2021; 194:111432. [PMID: 33422562 DOI: 10.1016/j.mad.2021.111432] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 12/30/2020] [Accepted: 01/01/2021] [Indexed: 10/22/2022]
Abstract
Cellular senescence is a state of stable and irreversible cell cycle arrest with active metabolism, that normal cells undergo after a finite number of divisions (Hayflick limit). Senescence can be triggered by intrinsic and/or extrinsic stimuli including telomere shortening at the end of a cell's lifespan (telomere-initiated senescence) and in response to oxidative, genotoxic or oncogenic stresses (stress-induced premature senescence). Several effector mechanisms have been proposed to explain senescence programmes in diploid cells, including the induction of DNA damage responses, a senescence-associated secretory phenotype and epigenetic changes. Senescent cells display senescence-associated-β-galactosidase activity and undergo chromatin remodeling resulting in heterochromatinisation. Senescence is established by the pRb and p53 tumour suppressor networks. Senescence has been detected in in vitro cellular settings and in premalignant, but not malignant lesions in mice and humans expressing mutant oncogenes. Despite oncogene-induced senescence, which is believed to be a cancer initiating barrier and other tumour suppressive mechanisms, benign cancers may still develop into malignancies by bypassing senescence. Here, we summarise the functional genetic screens that have identified genes, uncovered pathways and characterised mechanisms involved in senescence evasion. These include cell cycle regulators and tumour suppressor pathways, DNA damage response pathways, epigenetic regulators, SASP components and noncoding RNAs.
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Affiliation(s)
- Eugenia Roupakia
- Laboratory of Biology, School of Medicine, Faculty of Health Sciences, University of Ioannina, Ioannina, 45100, Greece; Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Ioannina, 45110, Greece
| | - Georgios S Markopoulos
- Laboratory of Biology, School of Medicine, Faculty of Health Sciences, University of Ioannina, Ioannina, 45100, Greece; Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Ioannina, 45110, Greece
| | - Evangelos Kolettas
- Laboratory of Biology, School of Medicine, Faculty of Health Sciences, University of Ioannina, Ioannina, 45100, Greece; Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Ioannina, 45110, Greece.
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23
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Zhu J, Zhou Y, Zhu S, Li F, Xu J, Zhang L, Shu H. circRNA circ_102049 Implicates in Pancreatic Ductal Adenocarcinoma Progression through Activating CD80 by Targeting miR-455-3p. Mediators Inflamm 2021; 2021:8819990. [PMID: 33505218 PMCID: PMC7811564 DOI: 10.1155/2021/8819990] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/27/2020] [Accepted: 12/13/2020] [Indexed: 12/27/2022] Open
Abstract
Emerging evidence has shown that circular RNAs (circRNAs) and DNA methylation play important roles in the causation and progression of cancers. However, the roles of circRNAs and abnormal methylation genes in the tumorigenesis of pancreatic ductal adenocarcinoma (PDAC) are still largely unknown. Expression profiles of circRNA, gene methylation, and mRNA were downloaded from the GEO database, and differentially expressed genes were obtained via GEO2R, and a ceRNA network was constructed based on circRNA-miRNA pairs and miRNA-mRNA pairs. Inflammation-associated genes were collected from the GeneCards database. Then, functional enrichment analysis and protein-protein interaction (PPI) networks of inflammation-associated methylated expressed genes were investigated using Metascape and STRING databases, respectively, and visualized in Cytoscape. Hub genes of PPI networks were identified using the NetworkAnalyzer plugin. Also, we analyzed the methylation, protein expression levels, and prognostic value of hub genes in PDAC patients through the UALCAN, Human Protein Atlas (HPA), and Kaplan-Meier plotter databases, respectively. The circRNA_102049/miR-455-3p/CD80 axis was identified by the ceRNA network and hub genes. In vitro and in vivo experiments were performed to evaluate the functions of circRNA_102049. The regulatory mechanisms of circRNA_102049 and miR-455-3p were explored by RT-PCR, western blot, and dual-luciferase assays. In the present study, twelve hub genes (STAT1, CCND1, KRAS, CD80, ICAM1, ESR1, RAF1, RPS6KA2, KDM6B, TNRC6A, FOSB, and DNM1) were determined from the PPI networks. Additionally, the circRNA_102049 was upregulated in PDAC cell lines. Functionally, the knockdown of circRNA_102049 by siRNAs inhibited cell growth, inflammatory factors, and migratory and invasive potential and promoted cell apoptosis. Mechanistically, circRNA_102049 functioned as a sponge of miR-455-3p and partially reversed the effect of miR-455-3p and consequently upregulated CD80 expression. Our findings showed that circRNA_102049 and methylated hub genes play an important role in the proliferation, apoptosis, migration, invasion, and inflammatory response of PDAC, which might be selected as a promising prognostic marker and therapeutic target for PDAC.
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Affiliation(s)
- Jie Zhu
- Medical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Yong Zhou
- Medical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Shanshan Zhu
- Medical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Fei Li
- Medical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Jiajia Xu
- Medical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Liming Zhang
- Medical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Hairong Shu
- Department of Medical Service, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
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24
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The cross-talk between signaling pathways, noncoding RNAs and DNA damage response: Emerging players in cancer progression. DNA Repair (Amst) 2021; 98:103036. [PMID: 33429260 DOI: 10.1016/j.dnarep.2020.103036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023]
Abstract
The DNA damage response (DDR) pathway's primary purpose is to maintain the genome structure's integrity and stability. A great deal of effort has done to understand the exact molecular mechanisms of non-coding RNAs, such as lncRNA, miRNAs, and circRNAs, in distinct cellular and genomic processes and cancer progression. In this regard, the ncRNAs possible regulatory role in DDR via modulation of key components expression and controlling repair signaling pathway activation is validated. Therefore, in this article, we will discuss the latest developments of ncRNAs contribution in different aspects of DNA repair through regulation of ATM-ATR, P53, and other regulatory signaling pathways.
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25
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Shen Y, Yang Y, Li Y. MiR-133a acts as a tumor suppressor in lung cancer progression by regulating the LASP1 and TGF-β/Smad3 signaling pathway. Thorac Cancer 2020; 11:3473-3481. [PMID: 33074595 PMCID: PMC7705923 DOI: 10.1111/1759-7714.13678] [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: 07/19/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND MiR-133a has been confirmed to be involved in the development of multiple cancers including non-small cell lung cancer (NSCLC). However, the precise molecular mechanism has not yet been fully elucidated. The purpose of this study was to investigate the functional role and underlying mechanism of miR-133a in the progression of NSCLC. METHODS Quantitative real-time PCR (qRT-PCR) was performed to measure miR-133a and LASP1 expression in NSCLC tissues and cells. 3-(4, 5-dimethyl-2-thiazolyl)-2, 5-diphenyl-2H-tetrazolium bromide (MTT) assay was used to detect cell viability. The protein levels were measured by western blot. The tumor growth was measured by xenograft tumor formation assay. RESULTS miR-133a was significantly decreased while LASP1 was increased in NSCLC tissues and cells compared with control groups. Moreover, overexpression of miR-133a suppressed cell viability, whereas miR-133a knockdown enhanced the viability of A549 cells. More importantly, LASP1 was verified as a direct target of miR-133a. Moreover, overexpression of miR-133a inhibited the epithelial-mesenchymal transition (EMT) and TGF-β/Smad3 pathways by regulating LASP1 in vitro. In addition, miR-133a mimic suppressed tumor growth by modulating the TGF-β/Smad3 pathway in vivo. CONCLUSIONS In conclusion, miR-133a acted as a tumor suppressor in lung cancer progression by regulating the LASP1 and TGF-β/Smad3 signaling pathway.
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Affiliation(s)
- Yuyao Shen
- Department of Respiratory Medicine, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Yan Yang
- Department of Respiratory Medicine, Shan Dong Chest Hospital, Jinan, China
| | - Yahua Li
- Department of Respiratory Medicine, The Third Hospital of Hebei Medical University, Shijiazhuang, China
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Arumugam T, Ghazi T, Chuturgoon A. Fumonisin B 1 Epigenetically Regulates PTEN Expression and Modulates DNA Damage Checkpoint Regulation in HepG2 Liver Cells. Toxins (Basel) 2020; 12:toxins12100625. [PMID: 33007920 PMCID: PMC7601513 DOI: 10.3390/toxins12100625] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/19/2020] [Accepted: 08/27/2020] [Indexed: 12/13/2022] Open
Abstract
Fumonisin B1 (FB1), a Fusarium-produced mycotoxin, is found in various foods and feeds. It is a well-known liver carcinogen in experimental animals; however, its role in genotoxicity is controversial. The current study investigated FB1-triggered changes in the epigenetic regulation of PTEN and determined its effect on DNA damage checkpoint regulation in human liver hepatoma G2 (HepG2) cells. Following treatment with FB1 (IC50: 200 µM; 24 h), the expression of miR-30c, KDM5B, PTEN, H3K4me3, PI3K, AKT, p-ser473-AKT, CHK1, and p-ser280-CHK1 was measured using qPCR and/or Western blot. H3K4me3 enrichment at the PTEN promoter region was assayed via a ChIP assay and DNA damage was determined using an ELISA. FB1 induced oxidative DNA damage. Total KDM5B expression was reduced, which subsequently increased the total H3K4me3 and the enrichment of H3K4me3 at PTEN promoters. Increased H3K4me3 induced an increase in PTEN transcript levels. However, miR-30c inhibited PTEN translation. Thus, PI3K/AKT signaling was activated, inhibiting CHK1 activity via phosphorylation of its serine 280 residue preventing the repair of damaged DNA. In conclusion, FB1 epigenetically modulates the PTEN/PI3K/AKT signaling cascade, preventing DNA damage checkpoint regulation, and induces significant DNA damage.
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Pudova EA, Krasnov GS, Nyushko KM, Kobelyatskaya AA, Savvateeva MV, Poloznikov AA, Dolotkazin DR, Klimina KM, Guvatova ZG, Simanovsky SA, Gladysh NS, Tokarev AT, Melnikova NV, Dmitriev AA, Alekseev BY, Kaprin AD, Kiseleva MV, Snezhkina AV, Kudryavtseva AV. miRNAs expression signature potentially associated with lymphatic dissemination in locally advanced prostate cancer. BMC Med Genomics 2020; 13:129. [PMID: 32948204 PMCID: PMC7500008 DOI: 10.1186/s12920-020-00788-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 08/31/2020] [Indexed: 02/08/2023] Open
Abstract
Background Prostate cancer is one of the most common and socially significant cancers among men. The aim of our study was to reveal changes in miRNA expression profiles associated with lymphatic dissemination in prostate cancer and to identify the most prominent miRNAs as potential prognostic markers for future studies. Methods High-throughput miRNA sequencing was performed for 44 prostate cancer specimens taken from Russian patients, with and without lymphatic dissemination (N1 – 20 samples; N0 – 24 samples). Results We found at least 18 microRNAs with differential expression between N0 and N1 sample groups: miR-182-5p, miR-183-5p, miR-96-5p, miR-25-3p, miR-93-5p, miR-7-5p, miR-615-3p, miR-10b, miR-1248 (N1-miRs; elevated expression in N1 cohort; p < 0.05); miR-1271-5p, miR-184, miR-222-3p, miR-221-5p, miR-221-3p, miR-455-3p, miR-143-5p, miR-181c-3p and miR-455-5p (N0-miRs; elevated expression in N0; p < 0.05). The expression levels of N1-miRs were highly correlated between each other (the same is applied for N0-miRs) and the expression levels of N0-miRs and N1-miRs were anti-correlated. The tumor samples can be divided into two groups depending on the expression ratio between N0-miRs and N1-miRs. Conclusions We found the miRNA expression signature associated with lymphatic dissemination, in particular on the Russian patient cohort. Many of these miRNAs are well-known players in either oncogenic transformation or tumor suppression. Further experimental studies with extended sampling are required to validate these results.
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Affiliation(s)
- Elena A Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Kirill M Nyushko
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | | | - Maria V Savvateeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey A Poloznikov
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Daniyar R Dolotkazin
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Kseniya M Klimina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Zulfiya G Guvatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergey A Simanovsky
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Boris Y Alekseev
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Andrey D Kaprin
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Marina V Kiseleva
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | | | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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28
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Chen S, Thorne RF, Zhang XD, Wu M, Liu L. Non-coding RNAs, guardians of the p53 galaxy. Semin Cancer Biol 2020; 75:72-83. [PMID: 32927018 DOI: 10.1016/j.semcancer.2020.09.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/26/2020] [Accepted: 09/01/2020] [Indexed: 12/12/2022]
Abstract
The TP53 gene is arguably the most important tumor suppressor gene known, contributing multifaceted roles to the process of tumor development. Its protein product p53, is a crucial sequence-specific transcription factor which regulates the expression of a large network of protein-coding genes, as well as thousands of noncoding RNAs (ncRNAs), notably microRNAs and long ncRNAs (lncRNAs). Through a variety of direct and indirect mechanisms, ncRNAs in turn modulate p53 levels and activity. Here the numbers of studies are steadily building which link the contributions of dysregulated ncRNAs to tumorigenesis via their participation throughout the p53 regulatory network. In this review, we will examine how the principal forms of ncRNAs, namely microRNAs, lncRNAs and circular RNAs (circRNAs) function as either effectors or regulators amongst the diversity of p53's cellular responses. We first discuss the more recently discovered connections between miRNAs and p53 signaling before focusing on the remarkable diversity of crosstalk evident between lncRNAs and p53, and subsequently, developing reports linking circRNAs to p53. Highlighted throughout the review are the mechanistic impacts of dysregulated ncRNAs on p53 functions as well as the possible prognostic implications of these interactions. We also describe the emerging connections between ncRNAs and the often-perplexing functions of mutant p53. Finally, in the context of p53 therapeutic approaches, we describe some of the challenges in ncRNA research and their potential for translation.
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Affiliation(s)
- Song Chen
- Translational Research Institute, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou, 450003, China; Molecular Pathology Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450053, China; Institute of Medicinal Biotechnology, Jiangsu College of Nursing, Huai'an, Jiangsu, 223300, China
| | - Rick F Thorne
- Translational Research Institute, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou, 450003, China; Molecular Pathology Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450053, China; School of Environmental and Life Sciences, the University of Newcastle, NSW, 2258, Australia
| | - Xu Dong Zhang
- Translational Research Institute, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou, 450003, China; Molecular Pathology Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450053, China; School of Biomedical Sciences and Pharmacy, the University of Newcastle, NSW, 2308, Australia
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou, 450003, China; Molecular Pathology Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450053, China; The First Affiliated Hospital of University of Science and Technology of China, Hefei, 230027, China.
| | - Lianxin Liu
- The First Affiliated Hospital of University of Science and Technology of China, Hefei, 230027, China.
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Zhou L, Zhang Z, Huang Z, Nice E, Zou B, Huang C. Revisiting cancer hallmarks: insights from the interplay between oxidative stress and non-coding RNAs. MOLECULAR BIOMEDICINE 2020; 1:4. [PMID: 35006436 PMCID: PMC8603983 DOI: 10.1186/s43556-020-00004-1] [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: 06/11/2020] [Accepted: 07/21/2020] [Indexed: 02/08/2023] Open
Abstract
Cancer is one of the most common disease worldwide, with complex changes and certain traits which have been described as “The Hallmarks of Cancer.” Despite increasing studies on in-depth investigation of these hallmarks, the molecular mechanisms associated with tumorigenesis have still not yet been fully defined. Recently, accumulating evidence supports the observation that microRNAs and long noncoding RNAs (lncRNAs), two main classes of noncoding RNAs (ncRNAs), regulate most cancer hallmarks through their binding with DNA, RNA or proteins, or encoding small peptides. Reactive oxygen species (ROS), the byproducts generated during metabolic processes, are known to regulate every step of tumorigenesis by acting as second messengers in cancer cells. The disturbance in ROS homeostasis leads to a specific pathological state termed “oxidative stress”, which plays essential roles in regulation of cancer progression. In addition, the interplay between oxidative stress and ncRNAs is found to regulate the expression of multiple genes and the activation of several signaling pathways involved in cancer hallmarks, revealing a potential mechanistic relationship involving ncRNAs, oxidative stress and cancer. In this review, we provide evidence that shows the essential role of ncRNAs and the interplay between oxidative stress and ncRNAs in regulating cancer hallmarks, which may expand our understanding of ncRNAs in the cancer development from the new perspective.
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Affiliation(s)
- Li Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
| | - Zhe Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
| | - Zhao Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
| | - Edouard Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia
| | - Bingwen Zou
- Department of Thoracic Oncology and Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China.
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China. .,School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, P.R. China.
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30
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Yazbeck AM, Stadler PF, Tout K, Fallmann J. Automatic curation of large comparative animal MicroRNA datasets. Bioinformatics 2020; 35:4553-4559. [PMID: 30993337 DOI: 10.1093/bioinformatics/btz271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/11/2019] [Accepted: 04/10/2019] [Indexed: 12/22/2022] Open
Abstract
MOTIVATION MicroRNAs form an important class of RNA regulators that has been studied extensively. The miRBase and Rfam database provide rich, frequently updated information on both pre-miRNAs and their mature forms. These data sources, however, rely on individual data submission and thus are neither complete nor consistent in their coverage across different miRNA families. Quantitative studies of miRNA evolution therefore are difficult or impossible on this basis. RESULTS We present here a workflow and a corresponding implementation, MIRfix, that automatically curates miRNA datasets by improving alignments of their precursors, the consistency of the annotation of mature miR and miR* sequence, and the phylogenetic coverage. MIRfix produces alignments that are comparable across families and sets the stage for improved homology search as well as quantitative analyses. AVAILABILITY AND IMPLEMENTATION MIRfix can be downloaded from https://github.com/Bierinformatik/MIRfix. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ali M Yazbeck
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, D-04107 Leipzig, Germany.,Doctoral School of Science and Technology, Center for Biotechnology Research, Lebanese University, Hadath Campus, Beirut, Lebanon.,Helmholtz Centre for Environmental Research - UFZ, Young Investigators Group Bioinformatics and Transcriptomics, D-04318 Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, D-04107 Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, University Leipzig, D-04107 Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, D-04103 Leipzig, Germany.,Institute for Theoretical Chemistry, University of Vienna, A-1090 Wien, Austria.,Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia.,Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Kifah Tout
- Doctoral School of Science and Technology, Center for Biotechnology Research, Lebanese University, Hadath Campus, Beirut, Lebanon
| | - Jörg Fallmann
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, D-04107 Leipzig, Germany
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31
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Ma X, Zheng Q, Zhao G, Yuan W, Liu W. Regulation of cellular senescence by microRNAs. Mech Ageing Dev 2020; 189:111264. [PMID: 32450085 DOI: 10.1016/j.mad.2020.111264] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 04/26/2020] [Accepted: 05/15/2020] [Indexed: 12/15/2022]
Abstract
Cellular senescence is mainly characterized as a stable proliferation arrest and a senescence associated secretory phenotype (SASP). Senescence is triggered by diverse stimuli such as telomere shortening, oxidative stress, oncogene activation and DNA damage, and consequently contributes to multiple physiology and pathology outcomes, including embryonic development, wound healing and tumor suppression as well as aging or age-associated diseases. Interestingly, therapeutic clearance of senescent cells in tissues has recently been demonstrated to be beneficial for extending a healthy lifespan and for improving numerous age-related disorders. However the molecular mechanisms of senescence regulation remain partially understood. Theoretically, senescence is tightly regulated by a vast number of molecules, among which the p16 and p53 pathways are the most classical. In addition, intracellular cellular calcium signaling has emerged as a key regulator of senescence. In the last few decades, a growing number of studies have demonstrated that microRNAs (miRNAs, small non-coding RNAs) are strongly implicated in controlling senescence, especially at the transcriptional and post-transcriptional levels. In this review we will discuss the involvement of miRNAs in modulating senescence through the major p16, p53, SASP and calcium signaling pathways, thus aiming to reveal the mechanisms of how miRNAs regulate cellular senescence.
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Affiliation(s)
- Xingjie Ma
- Department of Intensive Care, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China; Department of the Central Laboratory, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225000, China
| | - Qingbin Zheng
- Department of Intensive Care, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Guangming Zhao
- Department of Intensive Care, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Wenjie Yuan
- Department of Intensive Care, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Weili Liu
- Department of Intensive Care, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China.
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32
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Tan H, Kim P, Sun P, Zhou X. miRactDB characterizes miRNA-gene relation switch between normal and cancer tissues across pan-cancer. Brief Bioinform 2020; 22:5840023. [PMID: 32436932 DOI: 10.1093/bib/bbaa089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/05/2020] [Accepted: 04/26/2020] [Indexed: 12/26/2022] Open
Abstract
It has been increasingly accepted that microRNA (miRNA) can both activate and suppress gene expression, directly or indirectly, under particular circumstances. Yet, a systematic study on the switch in their interaction pattern between activation and suppression and between normal and cancer conditions based on multi-omics evidences is not available. We built miRactDB, a database for miRNA-gene interaction, at https://ccsm.uth.edu/miRactDB, to provide a versatile resource and platform for annotation and interpretation of miRNA-gene relations. We conducted a comprehensive investigation on miRNA-gene interactions and their biological implications across tissue types in both tumour and normal conditions, based on TCGA, CCLE and GTEx databases. We particularly explored the genetic and epigenetic mechanisms potentially contributing to the positive correlation, including identification of miRNA binding sites in the gene coding sequence (CDS) and promoter regions of partner genes. Integrative analysis based on this resource revealed that top-ranked genes derived from TCGA tumour and adjacent normal samples share an overwhelming part of biological processes, which are quite different than those from CCLE and GTEx. The most active miRNAs predicted to target CDS and promoter regions are largely overlapped. These findings corroborate that adjacent normal tissues might have undergone significant molecular transformations towards oncogenesis before phenotypic and histological change; and there probably exists a small yet critical set of miRNAs that profoundly influence various cancer hallmark processes. miRactDB provides a unique resource for the cancer and genomics communities to screen, prioritize and rationalize their candidates of miRNA-gene interactions, in both normal and cancer scenarios.
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Khor ES, Wong PF. The roles of MTOR and miRNAs in endothelial cell senescence. Biogerontology 2020; 21:517-530. [PMID: 32246301 DOI: 10.1007/s10522-020-09876-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/30/2020] [Indexed: 12/11/2022]
Abstract
Accumulation of senescent cells in vascular endothelium is known to contribute to vascular aging and increases the risk of developing cardiovascular diseases. The involvement of classical pathways such as p53/p21 and p16/pRB in cellular senescence are well described but there are emerging evidence supporting the increasingly important role of mammalian target of rapamycin (MTOR) as driver of cellular senescence via these pathways or other effector molecules. MicroRNAs (miRNAs) are a highly conserved group of small non-coding RNAs (18-25 nucleotides), instrumental in modulating the expression of target genes associated with various biological and cellular processes including cellular senescence. The inhibition of MTOR activity is predominantly linked to cellular senescence blunting and prolonged lifespan in model organisms. To date, known miRNAs regulating MTOR in endothelial cell senescence remain limited. Herein, this review discusses the roles of MTOR and MTOR-associated miRNAs in regulating endothelial cell senescence, including the crosstalk between MTOR Complex 1 (MTORC1) and cell cycle pathways and the emerging role of MTORC2 in cellular senescence. New insights on how MTOR and miRNAs coordinate underlying molecular mechanisms of endothelial senescence will provide deeper understanding and clarity to the complexity of the regulation of cellular senescence.
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Affiliation(s)
- Eng-Soon Khor
- Department of Pharmacology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Pooi-Fong Wong
- Department of Pharmacology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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Gramantieri L, Pollutri D, Gagliardi M, Giovannini C, Quarta S, Ferracin M, Casadei-Gardini A, Callegari E, De Carolis S, Marinelli S, Benevento F, Vasuri F, Ravaioli M, Cescon M, Piscaglia F, Negrini M, Bolondi L, Fornari F. MiR-30e-3p Influences Tumor Phenotype through MDM2/ TP53 Axis and Predicts Sorafenib Resistance in Hepatocellular Carcinoma. Cancer Res 2020; 80:1720-1734. [PMID: 32015093 DOI: 10.1158/0008-5472.can-19-0472] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/29/2019] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
Abstract
The molecular background of hepatocellular carcinoma (HCC) is highly heterogeneous, and biomarkers predicting response to treatments are an unmet clinical need. We investigated miR-30e-3p contribution to HCC phenotype and response to sorafenib, as well as the mutual modulation of TP53/MDM2 pathway, in HCC tissues and preclinical models. MiR-30e-3p was downregulated in human and rat HCCs, and its downregulation associated with TP53 mutations. TP53 contributed to miR-30e-3p biogenesis, and MDM2 was identified among its target genes, establishing an miR-30e-3p/TP53/MDM2 feedforward loop and accounting for miR-30e-3p dual role based on TP53 status. EpCAM, PTEN, and p27 were demonstrated as miR-30e-3p additional targets mediating its contribution to stemness and malignant features. In a preliminary cohort of patients with HCC treated with sorafenib, increased miR-30e-3p circulating levels predicted the development of resistance. In conclusion, molecular background dictates miR-30e-3p dual behavior in HCC. Mdm2 targeting plays a predominant tumor suppressor function in wild-type TP53 contexts, whereas other targets such as PTEN, p27, and EpCAM gain relevance and mediate miR-30e-3p oncogenic role in nonfunctional TP53 backgrounds. Increased circulating levels of miR-30e-3p predict the development of sorafenib resistance in a preliminary series of patients with HCC and deserve future investigations. SIGNIFICANCE: The dual role of miR-30e-3p in HCC clarifies how the molecular context dictates the tumor suppressor or oncogenic function played by miRNAs.
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Affiliation(s)
- Laura Gramantieri
- Center for Applied Biomedical Research, St.Orsola-Malpighi University Hospital, Bologna, Italy.
| | - Daniela Pollutri
- Center for Applied Biomedical Research, St.Orsola-Malpighi University Hospital, Bologna, Italy
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Martina Gagliardi
- Center for Applied Biomedical Research, St.Orsola-Malpighi University Hospital, Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Catia Giovannini
- Center for Applied Biomedical Research, St.Orsola-Malpighi University Hospital, Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Santina Quarta
- Department of Medicine, University of Padua, Padua, Italy
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Andrea Casadei-Gardini
- Division of Oncology, Department of Oncology and Hematology, University of Modena and Reggio Emilia, Modena, Italy
| | - Elisa Callegari
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Sabrina De Carolis
- Center for Applied Biomedical Research, St.Orsola-Malpighi University Hospital, Bologna, Italy
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Sara Marinelli
- Center for Applied Biomedical Research, St.Orsola-Malpighi University Hospital, Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Francesca Benevento
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Francesco Vasuri
- Pathology Unit, St.Orsola-Malpighi University Hospital, Bologna, Italy
| | - Matteo Ravaioli
- General Surgery and Transplant Unit, St.Orsola-Malpighi University Hospital, Bologna, Italy
| | - Matteo Cescon
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
- General Surgery and Transplant Unit, St.Orsola-Malpighi University Hospital, Bologna, Italy
| | - Fabio Piscaglia
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Massimo Negrini
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Luigi Bolondi
- Center for Applied Biomedical Research, St.Orsola-Malpighi University Hospital, Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Francesca Fornari
- Center for Applied Biomedical Research, St.Orsola-Malpighi University Hospital, Bologna, Italy.
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
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35
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Pretreatment Cancer-Related Cognitive Impairment-Mechanisms and Outlook. Cancers (Basel) 2019; 11:cancers11050687. [PMID: 31100985 PMCID: PMC6562730 DOI: 10.3390/cancers11050687] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/06/2019] [Accepted: 05/14/2019] [Indexed: 12/25/2022] Open
Abstract
Cognitive changes are common in patients with active cancer and during its remission. This has largely been blamed on therapy-related toxicities and diagnosis-related stress, with little attention paid to the biological impact of cancer itself. A plethora of clinical studies demonstrates that cancer patients experience cognitive impairment during and after treatment. However, recent studies show that a significant portion of patients with non-central nervous system (CNS) tumors experience cognitive decline prior to treatment, suggesting a role for tumor-derived factors in modulating cognition and behavior. Cancer-related cognitive impairment (CRCI) negatively impacts a patient’s quality of life, reduces occupational and social functioning, and increases morbidity and mortality. Furthermore, patients with cancer cachexia frequently experience a stark neurocognitive decline, suggesting peripheral tumors exert an enduring toll on the brain during this chronic paraneoplastic syndrome. However, the scarcity of research on cognitive impairment in non-CNS cancers makes it difficult to isolate psychosocial, genetic, behavioral, and pathophysiological factors in CRCI. Furthermore, clinical models of CRCI are frequently confounded by complicated drug regimens that inherently affect neurocognitive processes. The severity of CRCI varies considerably amongst patients and highlights its multifactorial nature. Untangling the biological aspects of CRCI from genetic, psychosocial, and behavioral factors is non-trivial, yet vital in understanding the pathogenesis of CRCI and discovering means for therapeutic intervention. Recent evidence demonstrating the ability of peripheral tumors to alter CNS pathways in murine models is compelling, and it allows researchers to isolate the underlying biological mechanisms from the confounding psychosocial stressors found in the clinic. This review summarizes the state of the science of CRCI independent of treatment and focuses on biological mechanisms in which peripheral cancers modulate the CNS.
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36
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Lujambio A, Banito A. Functional screening to identify senescence regulators in cancer. Curr Opin Genet Dev 2019; 54:17-24. [PMID: 30877988 DOI: 10.1016/j.gde.2019.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/01/2019] [Indexed: 12/12/2022]
Abstract
Cellular senescence is implicated in numerous biological processes, and can play pleiotropic, sometimes opposing, roles in cancer. Several triggers, cell types, contexts, and senescence-associated phenotypes introduce a multitude of possibilities when studying this process and its biological consequences. Recent studies continue to characterize cellular senescence at different levels, using a combination of functional screens, in silico analysis, omics characterizations and more targeted studies. However, a comprehensive analysis of its context-dependent effects and multiple phenotypes is required. Application of state-of-the-art and emerging technologies will increase our understanding of this complex process and better guide future strategies to harness senescence to our advantage, or to target it when detrimental.
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Affiliation(s)
- Amaia Lujambio
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, USA; Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, USA; Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, USA
| | - Ana Banito
- Hopp Children's Cancer Center (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Klinge CM. Non-Coding RNAs in Breast Cancer: Intracellular and Intercellular Communication. Noncoding RNA 2018; 4:E40. [PMID: 30545127 PMCID: PMC6316884 DOI: 10.3390/ncrna4040040] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/29/2018] [Accepted: 12/04/2018] [Indexed: 02/07/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are regulators of intracellular and intercellular signaling in breast cancer. ncRNAs modulate intracellular signaling to control diverse cellular processes, including levels and activity of estrogen receptor α (ERα), proliferation, invasion, migration, apoptosis, and stemness. In addition, ncRNAs can be packaged into exosomes to provide intercellular communication by the transmission of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) to cells locally or systemically. This review provides an overview of the biogenesis and roles of ncRNAs: small nucleolar RNA (snRNA), circular RNAs (circRNAs), PIWI-interacting RNAs (piRNAs), miRNAs, and lncRNAs in breast cancer. Since more is known about the miRNAs and lncRNAs that are expressed in breast tumors, their established targets as oncogenic drivers and tumor suppressors will be reviewed. The focus is on miRNAs and lncRNAs identified in breast tumors, since a number of ncRNAs identified in breast cancer cells are not dysregulated in breast tumors. The identity and putative function of selected lncRNAs increased: nuclear paraspeckle assembly transcript 1 (NEAT1), metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), steroid receptor RNA activator 1 (SRA1), colon cancer associated transcript 2 (CCAT2), colorectal neoplasia differentially expressed (CRNDE), myocardial infarction associated transcript (MIAT), and long intergenic non-protein coding RNA, Regulator of Reprogramming (LINC-ROR); and decreased levels of maternally-expressed 3 (MEG3) in breast tumors have been observed as well. miRNAs and lncRNAs are considered targets of therapeutic intervention in breast cancer, but further work is needed to bring the promise of regulating their activities to clinical use.
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Affiliation(s)
- Carolyn M Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA.
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Sun L, Guo Z, Sun J, Li J, Dong Z, Zhang Y, Chen J, Kan Q, Yu Z. MiR-133a acts as an anti-oncogene in Hepatocellular carcinoma by inhibiting FOSL2 through TGF-β/Smad3 signaling pathway. Biomed Pharmacother 2018; 107:168-176. [DOI: 10.1016/j.biopha.2018.07.151] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/16/2018] [Accepted: 07/30/2018] [Indexed: 01/27/2023] Open
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