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Xu H, Zhang Y, Wang C, Fu Z, Lv J, Yang Y, Zhang Z, Qi Y, Meng K, Yuan J, Wang X. Research progress on the fanconi anemia signaling pathway in non-obstructive azoospermia. Front Endocrinol (Lausanne) 2024; 15:1393111. [PMID: 38846492 PMCID: PMC11153779 DOI: 10.3389/fendo.2024.1393111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/13/2024] [Indexed: 06/09/2024] Open
Abstract
Non-obstructive azoospermia (NOA) is a disease characterized by spermatogenesis failure and comprises phenotypes such as hypospermatogenesis, mature arrest, and Sertoli cell-only syndrome. Studies have shown that FA cross-linked anemia (FA) pathway is closely related to the occurrence of NOA. There are FA gene mutations in male NOA patients, which cause significant damage to male germ cells. The FA pathway is activated in the presence of DNA interstrand cross-links; the key step in activating this pathway is the mono-ubiquitination of the FANCD2-FANCI complex, and the activation of the FA pathway can repair DNA damage such as DNA double-strand breaks. Therefore, we believe that the FA pathway affects germ cells during DNA damage repair, resulting in minimal or even disappearance of mature sperm in males. This review summarizes the regulatory mechanisms of FA-related genes in male azoospermia, with the aim of providing a theoretical reference for clinical research and exploration of related genes.
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Affiliation(s)
- Haohui Xu
- Lin He’s Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining, China
- College of Second Clinical Medical, Jining Medical University, Jining, China
| | - Yixin Zhang
- Lin He’s Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining, China
- College of Second Clinical Medical, Jining Medical University, Jining, China
| | - Caiqin Wang
- Lin He’s Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining, China
- College of Second Clinical Medical, Jining Medical University, Jining, China
| | - Zhuoyan Fu
- Lin He’s Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining, China
- College of Clinical Medicine, Jining Medical University, Jining, China
| | - Jing Lv
- Lin He’s Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining, China
- College of Clinical Medicine, Jining Medical University, Jining, China
| | - Yufang Yang
- Lin He’s Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining, China
- College of Mental Health, Jining Medical University, Jining, China
| | - Zihan Zhang
- Lin He’s Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining, China
- College of Second Clinical Medical, Jining Medical University, Jining, China
| | - Yuanmin Qi
- Lin He’s Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining, China
- College of Clinical Medicine, Jining Medical University, Jining, China
| | - Kai Meng
- Lin He’s Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining, China
| | - Jinxiang Yuan
- Lin He’s Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining, China
| | - Xiaomei Wang
- College of Basic Medicine, Jining Medical University, Jining, China
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Ju Z, Xiang J, Xiao L, He Y, Zhang L, Wang Y, Lei R, Nie Y, Yang L, Miszczyk J, Zhou P, Huang R. TXNL4B regulates radioresistance by controlling the PRP3-mediated alternative splicing of FANCI. MedComm (Beijing) 2023; 4:e258. [PMID: 37168687 PMCID: PMC10165318 DOI: 10.1002/mco2.258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 05/13/2023] Open
Abstract
Ionizing radiation (IR) has been extensively used for cancer therapy, but the radioresistance hinders and undermines the radiotherapy efficacy in clinics greatly. Here, we reported that the spliceosomal protein thioredoxin-like 4B (TXNL4B) is highly expressed in lung tissues from lung cancer patients with radiotherapy. Lung cancer cells with TXNL4B knockdown illustrate increased sensitivity to IR. Mechanistically, TXNL4B interacts with RNA processing factor 3 (PRP3) and co-localizes in the nucleus post-IR. Nuclear localization of PRP3 promotes the alternative splicing of the Fanconi anemia group I protein (FANCI) transcript variants, FANCI-12 and FANCI-13. PRP3 regulates alternative splicing of FANCI toward the two variants, FANCI-12 and FANCI-13. Radioresistance was greatly enhanced through the combination of PRP31 and PRP8, the critical components of core spliceosome promoted by PRP3. Notably, the inhibition of PRP3 to suppress the production of FANCI-12 would deprive PRP31 and PRP8 of such interaction. As a result, cell cycle G2/M arrest was induced, DNA damage repair was delayed, and radiosensitivity was improved. Collectively, our study highlights potential novel underlying mechanisms of the involvement of TXNL4B and alternative splicing in radioresistance. The results would benefit potential cancer radiotherapy.
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Affiliation(s)
- Zhao Ju
- Department of Occupational and Environmental Health, Xiangya School of Public HealthCentral South UniversityChangshaHunanChina
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation MedicineAMMSBeijingChina
| | - Jing Xiang
- Department of Occupational and Environmental Health, Xiangya School of Public HealthCentral South UniversityChangshaHunanChina
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation MedicineAMMSBeijingChina
| | - Liang Xiao
- Faculty of Naval MedicineNaval Medical University (Second Military Medical University)ShanghaiChina
| | - Yan He
- Department of Ophthalmology, Hunan Clinical Research Center of Ophthalmic Disease, The Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Le Zhang
- Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Yin Wang
- Department of Occupational and Environmental Health, Xiangya School of Public HealthCentral South UniversityChangshaHunanChina
| | - Ridan Lei
- Department of Occupational and Environmental Health, Xiangya School of Public HealthCentral South UniversityChangshaHunanChina
| | - Yunfeng Nie
- Hunan Prevention and Treatment Institute for Occupational Diseases ChangshaChangshaHunanChina
| | - Long Yang
- Hunan Prevention and Treatment Institute for Occupational Diseases ChangshaChangshaHunanChina
| | - Justyna Miszczyk
- Department of Experimental Physics of Complex SystemsThe H. Niewodniczański Institute of Nuclear Physics, Polish Academy of SciencesKrakówPoland
| | - Pingkun Zhou
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation MedicineAMMSBeijingChina
| | - Ruixue Huang
- Department of Occupational and Environmental Health, Xiangya School of Public HealthCentral South UniversityChangshaHunanChina
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Mo JL, Liu JS, Xiao Q, Hong WX, Yin JY, Chen J, Liu ZQ. Association of variations in the Fanconi anemia complementation group and prognosis in Non-small cell lung cancer patients with Platinum-based chemotherapy. Gene 2022; 825:146398. [PMID: 35306114 DOI: 10.1016/j.gene.2022.146398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/08/2022] [Accepted: 03/04/2022] [Indexed: 11/19/2022]
Abstract
PURPOSE To explore the associations between FANC (FANCA, FANCC, FANCE, FANCF, and FANCJ) single nucleotide polymorphisms (SNPs) and prognosis of non-small cell lung cancer (NSCLC) patients with platinum-based chemotherapy. METHODS According to the inclusion criteria, we selected 395 DNA samples from NSCLC patients for genotyping and combined with clinical data for Cox regression analysis and stratification analyses to assess relationships between overall survival (OS) and progression free survival (PFS) with SNPs genotypes. RESULTS The results revealed that patients with FANCE rs6907678 TT genotype have a longer OS than TC and CC genotype (Additive model: P = 0.004, HR = 1.696, 95% CI = 1.186-2.425). In stratification analyses, Longer PFS is found in female, age ≤ 55 years old and non-smoking patients with FANCE rs6907678 TT genotype, and patients with TT genotypes were significantly had longer OS in male, age >55 years old, non-smoking, squamous cell carcinoma and stage IV stratification. CONCLUSION Our data demonstrates that patients with FANCE rs6907678 TT genotype are contributed to better prognosis. FANCE rs6907678 may be used as a clinical biomarker for predicting the prognosis of NSCLC patients with platinum-based chemotherapy.
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Affiliation(s)
- Jun-Luan Mo
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, PR China; Shenzhen Center for Chronic Disease Control and Prevention, Shenzhen 518020, PR China
| | - Jia-Si Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, PR China; Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, PR China; Institute of Clinical Pharmacology, Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Central South University, Changsha 410078, PR China
| | - Qi Xiao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, PR China; Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, PR China; Institute of Clinical Pharmacology, Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Central South University, Changsha 410078, PR China
| | - Wen-Xu Hong
- Shenzhen Center for Chronic Disease Control and Prevention, Shenzhen 518020, PR China
| | - Ji-Ye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, PR China; Shenzhen Center for Chronic Disease Control and Prevention, Shenzhen 518020, PR China; Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, PR China; Institute of Clinical Pharmacology, Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Central South University, Changsha 410078, PR China
| | - Juan Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, PR China; Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, PR China.
| | - Zhao-Qian Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, PR China; Shenzhen Center for Chronic Disease Control and Prevention, Shenzhen 518020, PR China; Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, PR China; Institute of Clinical Pharmacology, Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Central South University, Changsha 410078, PR China.
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Expression and gene regulatory network of SNHG1 in hepatocellular carcinoma. BMC Med Genomics 2021; 14:28. [PMID: 33499863 PMCID: PMC7836560 DOI: 10.1186/s12920-021-00878-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 01/17/2021] [Indexed: 12/24/2022] Open
Abstract
Background Small nucleolar RNA host gene 1 (SNHG1), a long noncoding RNA (lncRNA), is a transcript that negatively regulates tumour suppressor genes, such as p53. Abnormal SNHG1 expression is associated with cell proliferation and cancer. We used sequencing data downloaded from Genomic Data Commons to analyse the expression and interaction networks of SNHG1 in hepatocellular carcinoma (HCC). Methods Expression was examined using the limma package of R and verified by Gene Expression Profiling Interactive Analysis. We also obtained miRNA expression data from StarBase to determine the lncRNA-miRNA-mRNA–related RNA regulatory network in HCC. Kaplan–Meier (KM) analysis was performed using the survival package of R. Gene Ontology annotation of genes was carried out using Metascape. Results We found that SNHG1 was overexpressed and often amplified in HCC patients. In addition, SNHG1 upregulation was associated with the promotion of several primary biological functions, including cell proliferation, transcription and protein binding. Moreover, we found similar trends of small nucleolar RNA host gene 1 (SNHG1), E2F8 (E2F transcription factor 8), FANCE (FA complementation group E) and LMNB2 (encodes lamin B2) expression. In the SNHG1-associated network, high expression levels of SNHG1 (log-rank P value = 0.0643), E2F8 (log-rank P value = 0.000048), FANCE (log-rank P value = 0.00125) and LMNB2 (log-rank P value = 0.0392) were significantly associated with poor survival. Single-cell analysis showed that E2F8 may play an important role in tumorigenesis or cancer development. Conclusions Our results highlight the benefit of utilizing multiple datasets to understand the functional potential regulatory networks of SNHG1 and the role of SNHG1 in tumours.
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Abstract
Background Aberrant methylation of DNA plays an important role in the pathogenesis of nasopharyngeal carcinoma (NPC). In the current study, we aimed to integrate three cohorts profile datasets to identify abnormally methylated-differentially expressed genes and pathways associated with NPC. Methods Data of gene expression microarrays (GSE53819, GSE412452) and gene methylation microarrays (GSE52068) obtained from the GEO database. Aberrantly methylated differentially expressed genes (DEGs) were obtained by GEO2R. The David database was utilized to perform enrichment and functional analysis regarding selected genes. To create a protein-protein interaction (PPI), STRING and Cytoscape software were utilized. The MCODE was used for module analysis of the PPI network. Results In total, 181 hypomethylation-high expression genes were identified, which were enriched in the biological mechanisms involved in the differentiation of endodermal cell, mitotic nuclear division, mitotic cell cycle process, chromosome segregation and cell cycle phase transition, etc. Pathway enrichment showed ECM-receptor interaction, PI3K-Akt signaling pathway, Focal adhesion, Protein digestion and absorption and Amoebiasis, etc. The top 3 hub genes of PPI network were FANCI, POSTN, and IFIH1. Additionally, 210 hypermethylation-low expression genes were identified, and our data revealed enrichment in biological processes including axoneme assembly, micro tubular formation, assembly of axonemal dynein complex, cilium movement and cilium organization, etc. Pathway analysis indicated enrichment in B cell receptor signaling pathway, Hematopoietic cell lineage, Leukocyte transendothelial migration, Complement and coagulation cascades and Fc gamma R-mediated phagocytosis, etc. The ZMYND10, PACRG and POU2AF1 were identified as the top three hub genes of PPI network. After validation in TCGA and GEPIA database, most hub genes remained significant. Patients with high expression of POSTN found to have shorter overall survival, while in patients with high expression of ZMYND10 and POU2AF1 longer overall survival was identified. Conclusions The data revealed novel aberrantly methylated-differentially expressed genes and pathways in NPC by bioinformatics analysis, potentially providing novel insights for the molecular mechanisms governing NPC progression. Hub genes including FANCI, POSTN, IFIH1, ZMYND10, PACRG and POU2AF1 might serve as novel biomarkers for precision diagnosis and providing medical treatment for patient with NPC.
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Taylor SJ, Arends MJ, Langdon SP. Inhibitors of the Fanconi anaemia pathway as potential antitumour agents for ovarian cancer. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2020; 1:26-52. [PMID: 36046263 PMCID: PMC9400734 DOI: 10.37349/etat.2020.00003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/18/2019] [Indexed: 11/30/2022] Open
Abstract
The Fanconi anaemia (FA) pathway is an important mechanism for cellular DNA damage repair, which functions to remove toxic DNA interstrand crosslinks. This is particularly relevant in the context of ovarian and other cancers which rely extensively on interstrand cross-link generating platinum chemotherapy as standard of care treatment. These cancers often respond well to initial treatment, but reoccur with resistant disease and upregulation of DNA damage repair pathways. The FA pathway is therefore of great interest as a target for therapies that aim to improve the efficacy of platinum chemotherapies, and reverse tumour resistance to these. In this review, we discuss recent advances in understanding the mechanism of interstrand cross-link repair by the FA pathway, and the potential of the component parts as targets for therapeutic agents. We then focus on the current state of play of inhibitor development, covering both the characterisation of broad spectrum inhibitors and high throughput screening approaches to identify novel small molecule inhibitors. We also consider synthetic lethality between the FA pathway and other DNA damage repair pathways as a therapeutic approach.
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Affiliation(s)
- Sarah J Taylor
- Cancer Research UK Edinburgh Centre and Edinburgh Pathology, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, EH4 2XU Edinburgh, UK
| | - Mark J Arends
- Cancer Research UK Edinburgh Centre and Edinburgh Pathology, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, EH4 2XU Edinburgh, UK
| | - Simon P Langdon
- Cancer Research UK Edinburgh Centre and Edinburgh Pathology, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, EH4 2XU Edinburgh, UK
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Meng X, Yang S, Camp VJA. The Interplay Between the DNA Damage Response, RNA Processing and Extracellular Vesicles. Front Oncol 2020; 9:1538. [PMID: 32010626 PMCID: PMC6978769 DOI: 10.3389/fonc.2019.01538] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/19/2019] [Indexed: 12/13/2022] Open
Abstract
RNA processing was recently found to affect DNA damage response. The RNA processing factors THRAP3 and BCLAF1 play critical role in keeping DNA genomic stability by regulating the transcription, mRNA splicing and export of DNA repair proteins BRCA2, PALB2, Rad51, FANCD2, and FANCL in response to DNA damage. RNA processing factors THRAP3 and BCLAF1 play critical roles in maintaining DNA genomic stability. These factors regulate transcription, mRNA splicing and nuclear RNA export of DNA repair proteins BRCA2, PALB2, Rad51, FANCD2, and FANCL in response to DNA damage. Splicing factors SRSF10 and Sam68 were found to control the DNA damage agent-induced mRNA splicing of transcripts including BCLAF1, BRCA1, BCL2L1, CASP8, CHK2, and RBBP8 to regulate apoptosis, cell-cycle transition and DNA repair. Splicing factors and RNA binding proteins (RBPs) were also found to play a critical role in DNA/RNA hybrids (R-loops) formed during transcription and RNA processing to prevent RNA-induced genome instability. At the same time, DNA repair proteins FANCI and FANCD2 were found to regulate the nuclear localization of splicing factors SF3B1 in the DNA damage response. In addition, tumor-derived extracellular vesicles (Evs) enhanced by chemotherapeutic agents in cancer were found to promote cancer metastasis and drug resistance. Inhibiting Evs from cancer cells significantly reduced cancer metastasis and drug resistance. Furthermore, cross-talk between the DNA damage response and the immune response was observed including the enhancement of the efficacy of immune checkpoint blockade by PARP inhibitors and the effect of PD-L1 on mRNA stability of various mRNAs involved in DNA damage response by acting as a novel RNA binding protein to increase drug resistance in cancer cells. This review will introduce recent progress on the interplay of the DNA damage response, the RNA processing and the extracellular vesicles mediated metastasis.
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Affiliation(s)
- Xiangbing Meng
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States.,Holden Comprehensive Cancer Center, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Shujie Yang
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States.,Holden Comprehensive Cancer Center, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Vanessa J A Camp
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
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Fanconi Anemia complementation group C protein in metabolic disorders. Aging (Albany NY) 2019; 10:1506-1522. [PMID: 29930218 PMCID: PMC6046246 DOI: 10.18632/aging.101487] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 06/16/2018] [Indexed: 01/01/2023]
Abstract
Given importance of 22-Fanconi Anemia (FA) proteins together to act in a signaling pathway in preventing deleterious clinical symptoms, e.g. severe bone marrow failure, congenital defects, an early onset of aging and cancer, studies on each FA protein become increasingly attractive. However, an unbiased and systematic investigation of cellular effects resulting from each FA protein is missing. Here, we report roles of FA complementation C group protein (FANCC) in the protection from metabolic disorders. This study was prompted by the diabetes-prone feature displayed in FANCC knockout mice, which is not typically shown in patients with FA. We found that in cells expressing FANCC at different levels, there are representative alterations in metabolites associated with aging (glycine, citrulline, ornithine, L-asparagine, L-tyrosine, L-arginine, L-glutamine, L-leucine, L-isoleucine, L-valine, L-proline and L-alanine), Diabetes Mellitus (DM) (carbon monoxide, collagens, fatty acids, D-glucose, fumaric acid, 2-oxoglutaric acid, C3), inflammation (inosine, L-arginine, L-isoleucine, L-leucine, L-lysine, L-phenylalanine, hypoxanthine, L-methionine), and cancer ( L-methionine, sphingomyelin, acetyl-L-carnitine, L-aspartic acid, L-glutamic acid, niacinamide, phospho-rylethanolamine). We also found that FANCC can act in an FA-pathway-independent manner in tumor suppression. Collectively, featured-metabolic alterations are readouts of functional mechanisms underlying reduced tumorigenicity driven by FANCC, demonstrating close links among cancer, aging, inflammation and DM.
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Li J, Tseng CS, Federico A, Ivankovic F, Huang YS, Ciccodicola A, Swanson MS, Yu P. SFMetaDB: a comprehensive annotation of mouse RNA splicing factor RNA-Seq datasets. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2017:4161772. [PMID: 29220461 PMCID: PMC5737203 DOI: 10.1093/database/bax071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/15/2017] [Indexed: 02/07/2023]
Abstract
Although the number of RNA-Seq datasets deposited publicly has increased over the past few years, incomplete annotation of the associated metadata limits their potential use. Because of the importance of RNA splicing in diseases and biological processes, we constructed a database called SFMetaDB by curating datasets related with RNA splicing factors. Our effort focused on the RNA-Seq datasets in which splicing factors were knocked-down, knocked-out or over-expressed, leading to 75 datasets corresponding to 56 splicing factors. These datasets can be used in differential alternative splicing analysis for the identification of the potential targets of these splicing factors and other functional studies. Surprisingly, only ∼15% of all the splicing factors have been studied by loss- or gain-of-function experiments using RNA-Seq. In particular, splicing factors with domains from a few dominant Pfam domain families have not been studied. This suggests a significant gap that needs to be addressed to fully elucidate the splicing regulatory landscape. Indeed, there are already mouse models available for ∼20 of the unstudied splicing factors, and it can be a fruitful research direction to study these splicing factors in vitro and in vivo using RNA-Seq. Database URL:http://sfmetadb.ece.tamu.edu/
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Affiliation(s)
- Jin Li
- Department of Electrical and Computer Engineering.,TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Ching-San Tseng
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Antonio Federico
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, Naples, Italy.,Department of Science and Technology, University of Naples "Parthenope", Naples, Italy
| | - Franjo Ivankovic
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Yi-Shuian Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Alfredo Ciccodicola
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, Naples, Italy.,Department of Science and Technology, University of Naples "Parthenope", Naples, Italy
| | - Maurice S Swanson
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Peng Yu
- Department of Electrical and Computer Engineering.,TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX 77843, USA
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Panneerselvam J, Xie G, Che R, Su M, Zhang J, Jia W, Fei P. Distinct Metabolic Signature of Human Bladder Cancer Cells Carrying an Impaired Fanconi Anemia Tumor-Suppressor Signaling Pathway. J Proteome Res 2016; 15:1333-41. [PMID: 26956768 DOI: 10.1021/acs.jproteome.6b00076] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Metabolic profiling has great potential to help the diagnosis and prognosis of cancer patients. Fanconi Anemia (FA) tumor-suppressor signaling has been instrumental in understanding human tumorigenesis. However, this instrumental understanding has never been demonstrated at the metabolic level. Here, we show that impaired FA signaling can lead cells to exhibit metabolic signatures of tumorigenesis. This is consistent with our original studies of the roles of FA signaling in suppressing non-FA tumorigenesis at functional and genetic levels. Using ultraperformance liquid chromatography-mass spectroscopy and gas chromatography-mass spectrometry, we characterized metabolic alterations in bladder cancer cells carrying an intact or impaired FA pathway. The latter was obtained by ectopically expressing FAVL (FAVL-high), which we previously found to be capable of inactivating FA signaling. A total of 18 metabolites, end products of cell proliferation or apoptosis, were significantly different between FAVL-high and -low cells. Methionine, phenylalanine, and threonine, resulting from a tumorigenic process, were substantially increased in FAVL-high cells. With this study, we achieved genomic, functional, and metabolomic characterization of the roles of FA signaling in the development of human cancer. Furthermore, this study provides novel insights into how to translate FA basic research into strategies for producing effective biomarkers in human cancer diagnosis and prognosis.
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Affiliation(s)
- Jayabal Panneerselvam
- University of Hawaii Cancer Center, University of Hawaii , Honolulu, Hawaii, 96813 United States
| | - Guoxiang Xie
- University of Hawaii Cancer Center, University of Hawaii , Honolulu, Hawaii, 96813 United States
| | - Raymond Che
- University of Hawaii Cancer Center, University of Hawaii , Honolulu, Hawaii, 96813 United States
| | - Mingming Su
- University of Hawaii Cancer Center, University of Hawaii , Honolulu, Hawaii, 96813 United States
| | - Jun Zhang
- Department of Laboratory Medicine and Pathology, Mayo Clinic Foundation , Rochester, Minnesota, 55905 United States
| | - Wei Jia
- University of Hawaii Cancer Center, University of Hawaii , Honolulu, Hawaii, 96813 United States
| | - Peiwen Fei
- University of Hawaii Cancer Center, University of Hawaii , Honolulu, Hawaii, 96813 United States
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Ding JJ, Wang G, Shi WX, Zhou HH, Zhao EF. Promoter Hypermethylation of FANCF and Susceptibility and Prognosis of Epithelial Ovarian Cancer. Reprod Sci 2015; 23:24-30. [DOI: 10.1177/1933719115612136] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Jia-Jia Ding
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, China
| | - Guan Wang
- Department of Gynecology, Tianjin central Hospital of Obstetrics and Gynecology, Tianjin, China
| | - Wen-Xin Shi
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, China
| | - Hong-Hui Zhou
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, China
| | - En-Feng Zhao
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, China
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