1
|
Li A, Gao H, Wu H, Xie Y, Jia Z, Yang Z, Zhang Z, Zhang X. Genetic association and functional implications of TLR4 rs1927914 polymorphism on colon cancer risk. BMC Cancer 2024; 24:858. [PMID: 39026223 DOI: 10.1186/s12885-024-12604-z] [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: 01/26/2024] [Accepted: 07/03/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND Colon cancer remains a major health concern worldwide, with genetic factors playing a crucial role in its development. Toll-like receptors (TLRs) has been implicated in various cancers, but their role in colon cancer is not well understood. This study aims to identify functional polymorphisms in the promoter and 3'UTR regions of TLRs and evaluate their association with colon cancer susceptibility. METHODS We conducted a case-control study involving 410 colon cancer patients and 410 healthy controls from the Chinese population. Genotyping of polymorphisms in TLR3, TLR4, TLR5 and TLR7 was performed using PCR-RFLP and TaqMan MGB probes. Using logistic regression analysis, we evaluated the association of TLRs polymorphisms and the susceptibility to colon cancer. To understand the biological implications of the TLR4 rs1927914 polymorphism, we conducted functional assays, including luciferase reporter assay and electrophoretic mobility shift assay (EMSA). RESULTS Our results demonstrated that the G-allele of the TLR4 rs1927914 polymorphism is significantly associated with a decreased risk of colon cancer (OR = 0.68, 95%CI = 0.50-0.91). Stratified analysis showed that TLR4 rs1927914 AG or GG genotype contributed to a decreased risk of colon cancer among younger individuals (OR = 0.52, 95%CI = 0.34-0.81), males (OR = 0.58, 95%CI = 0.38-0.87), non-smokers (OR = 0.58, 95%CI = 0.41-0.83) and non-drinker with OR (95%CI) of 0.66 (0.46-0.93). Functional assays demonstrated that in HCT116 and LOVO colon cancer cells, the luciferase activity driven by the TLR4 promoter with the rs1927914A allele was 5.43 and 2.07 times higher, respectively, compared to that driven by the promoter containing the rs1927914G allele. Electrophoretic mobility shift assay (EMSA) results indicated that the rs1927914G allele enhanced transcription factor binding. Using the transcription factor prediction tool, we found that the G allele facilitates binding of the repressive transcription factor Oct1, while the A allele does not. CONCLUSION The TLR4 rs1927914 polymorphism influence the susceptibility to colon cancer, with the G allele offering a protective effect through modulation of gene expression. These insights enhance our understanding of the genetic determinants of colon cancer risk and highlight TLR4 as a promising target for cancer prevention strategies.
Collapse
Affiliation(s)
- Ang Li
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China
- College of Life Science, North China University of Science and Technology, Tangshan, 063210, China
- Hebei Key Laboratory of Occupational Health and Safety for Coal Industry, Tangshan, 063210, China
| | - Hui Gao
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China
| | - Hongjiao Wu
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China
| | - Yuning Xie
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China
| | - Zhenxian Jia
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China
| | - Zhenbang Yang
- School of Basic Medical Sciences, North China University of Science and Technology, Tangshan, 063210, China
| | - Zhi Zhang
- Affliated Tangshan Gongren Hospital, North China University of Science and Technology, Tangshan, 063000, China
| | - Xuemei Zhang
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China.
- College of Life Science, North China University of Science and Technology, Tangshan, 063210, China.
- Hebei Key Laboratory of Occupational Health and Safety for Coal Industry, Tangshan, 063210, China.
| |
Collapse
|
2
|
Chen H, Chen M, Zeng B, Tang L, Nie Q, Jin X, Guo W, Chen L, Lin Y, Wang C, Fu F. Additional prognostic value of polymorphisms within the 3'-untranslated region of programmed cell death pathway genes in early-stage breast cancer. Front Immunol 2024; 15:1284579. [PMID: 38690279 PMCID: PMC11058218 DOI: 10.3389/fimmu.2024.1284579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 03/25/2024] [Indexed: 05/02/2024] Open
Abstract
Introduction The programmed cell death (PCD) pathway plays an important role in restricting cancer cell survival and proliferation. However, limited studies have investigated the association between genetic variants in the 3'-untranslated region of the PCD pathway genes and breast cancer outcomes. Methods In this study, we genotyped 28 potentially functional single nucleotide polymorphisms (SNPs) in 23 PCD pathway genes in 1,177 patients with early-stage breast cancer (EBC) from a Han Chinese population. The median follow-up period was 174 months. Results Among all the candidate SNPs, four independent SNPs (rs4900321 and rs7150025 in ATG2B, rs6753785 in BCL2L11, and rs2213181 in c-Kit) were associated with invasive disease-free survival (iDFS), distant disease-free survival (DDFS), breast cancer-specific survival (BCSS) and overall survival (OS), respectively. Further combined genotypes of these four SNPs revealed that the survival decreased as the number of unfavorable genotypes increased (Ptrend = 1.0 × 10-6, 8.5 × 10-8, 3.6 × 10-4, and 1.3 × 10-4 for iDFS, DDFS, BCSS, and OS, respectively). Receiver operating characteristic curve analysis demonstrated that incorporating unfavorable genotypes and clinicopathological variables improved the ability to predict EBC survival (P = 0.006, 0.004, 0.029, and 0.019 for iDFS, DDFS, BCSS, and OS, respectively). Additionally, rs6753785 and rs2213181 were associated with BCL2L11 and c-Kit mRNA expression, respectively. Conclusions Our results suggest that these four SNPs may act as novel biomarkers for EBC survival, possibly by modulating the expression of the corresponding genes.
Collapse
Affiliation(s)
- Hanxi Chen
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Minyan Chen
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Bangwei Zeng
- Administration Department of Nosocomial Infection, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Lili Tang
- Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Qian Nie
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Xuan Jin
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Wenhui Guo
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Lili Chen
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Yuxiang Lin
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Chuan Wang
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Fangmeng Fu
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| |
Collapse
|
3
|
Seyhan AA. Circulating microRNAs as Potential Biomarkers in Pancreatic Cancer-Advances and Challenges. Int J Mol Sci 2023; 24:13340. [PMID: 37686149 PMCID: PMC10488102 DOI: 10.3390/ijms241713340] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
There is an urgent unmet need for robust and reliable biomarkers for early diagnosis, prognosis, and prediction of response to specific treatments of many aggressive and deadly cancers, such as pancreatic cancer, and liquid biopsy-based miRNA profiling has the potential for this. MiRNAs are a subset of non-coding RNAs that regulate the expression of a multitude of genes post-transcriptionally and thus are potential diagnostic, prognostic, and predictive biomarkers and have also emerged as potential therapeutics. Because miRNAs are involved in the post-transcriptional regulation of their target mRNAs via repressing gene expression, defects in miRNA biogenesis pathway and miRNA expression perturb the expression of a multitude of oncogenic or tumor-suppressive genes that are involved in the pathogenesis of various cancers. As such, numerous miRNAs have been identified to be downregulated or upregulated in many cancers, functioning as either oncomes or oncosuppressor miRs. Moreover, dysregulation of miRNA biogenesis pathways can also change miRNA expression and function in cancer. Profiling of dysregulated miRNAs in pancreatic cancer has been shown to correlate with disease diagnosis, indicate optimal treatment options and predict response to a specific therapy. Specific miRNA signatures can track the stages of pancreatic cancer and hold potential as diagnostic, prognostic, and predictive markers, as well as therapeutics such as miRNA mimics and miRNA inhibitors (antagomirs). Furthermore, identified specific miRNAs and genes they regulate in pancreatic cancer along with downstream pathways can be used as potential therapeutic targets. However, a limited understanding and validation of the specific roles of miRNAs, lack of tissue specificity, methodological, technical, or analytical reproducibility, harmonization of miRNA isolation and quantification methods, the use of standard operating procedures, and the availability of automated and standardized assays to improve reproducibility between independent studies limit bench-to-bedside translation of the miRNA biomarkers for clinical applications. Here I review recent findings on miRNAs in pancreatic cancer pathogenesis and their potential as diagnostic, prognostic, and predictive markers.
Collapse
Affiliation(s)
- Attila A. Seyhan
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA;
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- Joint Program in Cancer Biology, Lifespan Health System and Brown University, Providence, RI 02912, USA
- Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
| |
Collapse
|
4
|
Wu L, Zhang Y, Zheng C, Zhao F, Lin Y. GEMIN4, a potential therapeutic targets for patients with basal-like subtype breast cancer. BMC Womens Health 2023; 23:396. [PMID: 37507701 PMCID: PMC10386636 DOI: 10.1186/s12905-023-02547-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Basal-like breast cancer (BLBC) takes up about 10-20% of all breast cancer(BC), what's more, BLBC has the lowest survival rate among all BC subtypes because of lacks of efficient treatment methods. We aimed to explore the molecules that can be used as diagnostic maker for BLBC at early stage and provide optimized treatment strategies for BLBC patients in this study. METHODS Apply weighted gene co-expression network analysis (WGCNA) to identify gene modules related to BLBC;The functional enrichment of candidate genes related to BLBC in the red module of Go data package and KEGG analysis;Overlapping cross analysis of URGs and WGCNA to identify candidate genes in each BC subtype;Divide BCBL patients into high-risk and low-risk groups, and analyze the two groups of overall survival (OS) and relapse free survival (RFS);Screening of GEMIN4 dependent cell lines; QRT PCR was used to verify the expression of GEMIN4 transfected with siRNA; CCK8 was used to determine the effect of GEMIN4 on cell viability; Positive cell count detected by BrdU staining;GO and KEGG enrichment analysis of GEMIN4. RESULTS The "red module" has the highest correlation with BLBC, with 913 promising candidate genes identified from the red module;913 red module candidate genes related to BLBC participated in multiple GO terms, and KEGG enrichment analysis results mainly enriched in estrogen signaling pathways and pathways in cancer;There are 386 overlapping candidate genes among the 913 "red module" genes identified by 1893 common URG and WGCNA;In BLBC patients, 9 highly expressed genes are associated with OS. Five highly expressed genes are associated with RFS. Kaplan Meier survival analysis suggests that high GEMIN4 expression levels are associated with poor prognosis in BLBC patients;The GEMIN4 gene dependency score in HCC1143 and CAL120 cell lines is negative and low; Si-GEMIN4-1 can significantly reduce the mRNA expression of GEMIN4; Si-GEMIN4 can inhibit cell viability; Si-GEMIN4 can reduce the number of positive cells;GO enrichment analysis showed that GEMIN4 is associated with DNA metabolism processes and adenylate binding; KEGG pathway enrichment analysis shows that GEMIN4 is related to ribosome biogenesis in eukaryotes. CONCLUSION We hypothesized that GEMIN4 may be the potential target for the treatment of BLBC.
Collapse
Affiliation(s)
- Liang Wu
- Department of Emergency Surgery, The Second Affiliated Hospital of Qiqihar Medical University, Heilongjiang Province, Qiqihar, People's Republic of China
| | - Yue Zhang
- Department of International Education School, Qiqihar Medical University, Heilongjiang Province, Qiqihar, People's Republic of China
| | - Chunlei Zheng
- Department of Surgical Oncology, The Second Affiliated Hospital of Qiqihar Medical University, Heilongjiang Province, Qiqihar, People's Republic of China
| | - Fuqiang Zhao
- Department of Surgical Oncology, The Second Affiliated Hospital of Qiqihar Medical University, Heilongjiang Province, Qiqihar, People's Republic of China
| | - Yan Lin
- Department of School of Basic Medicine, Qiqihar Medical University, Heilongjiang Province, Qiqihar, People's Republic of China.
| |
Collapse
|
5
|
Bortoletto AS, Parchem RJ. KRAS Hijacks the miRNA Regulatory Pathway in Cancer. Cancer Res 2023; 83:1563-1572. [PMID: 36946612 PMCID: PMC10183808 DOI: 10.1158/0008-5472.can-23-0296] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/01/2023] [Accepted: 03/20/2023] [Indexed: 03/23/2023]
Abstract
Extensive studies have focused on the misregulation of individual miRNAs in cancer. More recently, mutations in the miRNA biogenesis and processing machinery have been implicated in several malignancies. Such mutations can lead to global miRNA misregulation, which may promote many of the well-known hallmarks of cancer. Interestingly, recent evidence also suggests that oncogenic Kristen rat sarcoma viral oncogene homolog (KRAS) mutations act in part by modulating the activity of members of the miRNA regulatory pathway. Here, we highlight the vital role mutations in the miRNA core machinery play in promoting malignant transformation. Furthermore, we discuss how mutant KRAS can simultaneously impact multiple steps of miRNA processing and function to promote tumorigenesis. Although the ability of KRAS to hijack the miRNA regulatory pathway adds a layer of complexity to its oncogenic nature, it also provides a potential therapeutic avenue that has yet to be exploited in the clinic. Moreover, concurrent targeting of mutant KRAS and members of the miRNA core machinery represents a potential strategy for treating cancer.
Collapse
Affiliation(s)
- Angelina S. Bortoletto
- Center for Cell and Gene Therapy, Stem Cell and Regenerative Medicine Center, Department of Molecular and Cellular Biology, Department of Neuroscience, Translational Biology and Molecular Medicine Program, Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas
| | - Ronald J. Parchem
- Center for Cell and Gene Therapy, Stem Cell and Regenerative Medicine Center, Department of Molecular and Cellular Biology, Department of Neuroscience, Translational Biology and Molecular Medicine Program, Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas
| |
Collapse
|
6
|
Cytoskeleton Protein BmACT1 Is Potential for the Autophagic Function and Nuclear Localization of BmAtg4b in Bombyx mori. Cells 2023; 12:cells12060899. [PMID: 36980240 PMCID: PMC10047584 DOI: 10.3390/cells12060899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/24/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
Homologs of Autophagy-related (Atg) protein 4 are reported to cleave LC3 protein and facilitate autophagy occurrence differently in mammals, whereas their functions have not been investigated in insects. Three homologs, including BmAtg4a and its short form BmAtg4c as well as BmAtg4b, exist in Bombyx mori. Herein, the autophagic functions of BmAtg4a and BmAtg4b were investigated. qPCR detection found that BmAtg4a and BmAtg4b both peaked during larval-pupal metamorphosis when autophagy occurs robustly. Immunofluorescent staining showed that BmAtg4a was predominantly localized at the cytoplasm, while BmAtg4b had notable nuclear localization. Overexpression of BmAtg4a and BmAtg4b both slightly promoted basal autophagy but inhibited the autophagy induced by the infection of B. mori nucleopolyhedrovirus (BmNPV) and, thereby, its proliferation. In comparison, knockout of BmAtg4a or BmAtg4b significantly upregulated BmNPV-induced autophagy and its replication in BmN cells. Results of Co-immunoprecipitation associated with mass spectrum showed that the cytoskeleton protein B. mori actin A2 (BmACT2) and B. mori actin A1 (BmACT1) bound with BmAtg4a and BmAtg4b especially. Knockout of BmACT1 and BmACT2 inhibited BmAtg4b- and BmAtg4a-induced autophagy, respectively; moreover, knockout of BmACT1 reduced the ratio of cells with nuclear BmAtg4b. Of note, BmAtg4a and BmAtg4b had physical interaction, and they had an inhibitory effect on mutual autophagic function. In this work, we provide new insights into the autophagy machinery in insects as well as its function in the proliferation of BmNPV.
Collapse
|
7
|
Relationship between the Occurrence of Genetic Variants of Single Nucleotide Polymorphism in microRNA Processing Genes and the Risk of Developing Multiple Sclerosis. Biomedicines 2022; 10:biomedicines10123124. [PMID: 36551880 PMCID: PMC9776367 DOI: 10.3390/biomedicines10123124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/26/2022] [Accepted: 12/01/2022] [Indexed: 12/09/2022] Open
Abstract
Multiple sclerosis (MS) is an autoimmune demyelinating disorder of the central nervous system (CNS), which leads to disturbances in the conduction of nerve impulses, cognitive impairment, sensory and motor disturbances, as well as depressive symptoms. MS remains an incurable disease with a difficult diagnosis and unclear etiology. The aim of the analysis was to identify SNPs that may potentially be associated with an increased risk of developing MS. Blood samples were obtained from patients with MS (194 subjects) and age-matched healthy controls (188 subjects). The polymorphic variant frequencies of rs197412 T>C in GEMIN3, rs7813 G>A in GEMIN4, rs1106042 G>A in HIWI, rs10719 A>C in DROSHA, rs3742330 A>G in DICER1, rs11077 T>G in XPO5, rs14035 C>T in RAN, rs636832 G>A in AGO1 were determined in DNA using real-time PCR TaqMan® SNP Genotyping Assay. Our findings indicate that the GG AGO1 rs636832 and AA GEMIN4 rs7813 genotypes were associated with an increased risk of MS. Although our findings provide a clearer understanding of the pathogenesis of MS, further investigations are needed to better understand their potential for the evaluation of other miRNA processing genes believed to be associated with MS etiology.
Collapse
|
8
|
Xu Y, Wang C, Liu G, Zhao X, Qian Q, Li S, Mi X. Tetrahedral DNA framework based CRISPR electrochemical biosensor for amplification-free miRNA detection. Biosens Bioelectron 2022; 217:114671. [PMID: 36122469 DOI: 10.1016/j.bios.2022.114671] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/18/2022] [Accepted: 08/26/2022] [Indexed: 11/30/2022]
Abstract
microRNA (miRNA) is a kind of small non-coding RNA that has been regarded as potential biomarkers for cancers. Sensitive and specific detection of miRNA at low expression levels is highly desirable but remains challenging, especially for amplification-free and portable point of care (POC) diagnostics. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas13a has been recently discovered and used in the field of RNA detection. Nonetheless, most CRISPR/Cas13a-based methods were burdened with expensive equipment, time-consuming procedures, and complicated operations which were not suitable for POC analysis. In this work, we constructed a three-dimensional tetrahedral DNA framework based CRISPR-electrochemical biosensor (CRISPR-E). By combining tetrahedral DNA framework, CRISPR, and electrochemical biosensor, the process of activation, cleavage of Cas13a, and signal readout were all finished on the chip, and a simple, amplification-free and sensitive detection of miRNA-19b was realized. Under the optimal experimental conditions, a linear range from 10 pM to 104 pM with detection limit of 10 pM for miRNA-19b in buffer solution was achieved. Selectivity analysis indicated that our CRISPR-E had good distinguishing ability between miRNA-19b and miRNA-197. The results of miRNA-19b detection in mimic serum samples were consistent with that of the buffer solution. This all-on-chip strategy of our CRISPR-E is very suitable for POC testing.
Collapse
Affiliation(s)
- Yi Xu
- State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.
| | - Chenguang Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Gang Liu
- Key Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai, 201203, China
| | - Xiaoshuang Zhao
- State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China
| | - Qiuling Qian
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuainai Li
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianqiang Mi
- State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China; University of Chinese Academy of Sciences, Beijing, 100049, China; CAS Center for Excellence in Superconducting Electronics (CENSE), Shanghai, 200050, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
| |
Collapse
|
9
|
TLR4 regulatory region variants reduce the susceptibility of small-cell lung cancer in Chinese population. Eur J Cancer Prev 2022; 31:363-368. [PMID: 35579180 DOI: 10.1097/cej.0000000000000737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Toll-like receptors (TLRs) participate in the induction and regulation of immune responses and are closely related to the occurrence and development of small-cell lung cancer (SCLC). This study aimed to investigate the impact of polymorphisms in the regulatory regions of TLRs on the susceptibility of SCLC. METHODS The case-control study included 304 SCLC patients and 304 healthy controls. TLRs gene polymorphisms were genotyped by PCR-restrictive fragment length polymorphism analysis and TaqMan assay. Unconditional logistic regression was used to estimate odds ratio (OR) and its 95% confidence interval (95% CI). RESULTS Our results showed that TLR4 rs1927914 GG genotype and TLR4 rs7869402 TT genotype reduced the risk of SCLC with OR (95% CI) of 0.54 (0.32-0.90) and 0.47 (0.28-0.80), respectively. Stratified analysis suggested that TLR4 rs1927914 GG genotypes significantly reduced the risk of SCLC among male (OR = 0.35; 95% CI, 0.18-0.69; P < 0.01), the younger patients (OR = 0.49; 95% CI, 0.26-0.94; P = 0.03) and non-drinkers (OR = 0.47; 95% CI, 0.24-0.89; P = 0.02). TLR4 rs7869402 CT or TT genotype significantly reduced the susceptibility to SCLC among male patients (OR = 0.37; 95% CI, 0.19-0.71, P < 0.01), the younger patients (OR = 0.41; 95% CI, 0.22-0.79; P < 0.01), smokers (OR = 0.25; 95% CI, 0.10-0.60; P < 0.01) and drinkers (OR = 0.31; 95% CI, 0.11-0.88; P = 0.03). TLR3 rs5743303, TLR4 rs11536891, TLR5 rs1640816 and TLR7 rs3853839 had no significant correlation with the risk of SCLC. CONCLUSIONS These findings emphasized the important role of TLR4 in the development of SCLC.
Collapse
|
10
|
Almonaem ERA, Soliman DR, El Sayed MAM, Ahmed IA, Abdelrahman EG. Association between SNP rs59382073 in TBX2 3′ UTR and susceptibility to congenital heart diseases. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
11
|
Kandettu A, Adiga D, Devi V, Suresh PS, Chakrabarty S, Radhakrishnan R, Kabekkodu SP. Deregulated miRNA clusters in ovarian cancer: Imperative implications in personalized medicine. Genes Dis 2022; 9:1443-1465. [PMID: 36157483 PMCID: PMC9485269 DOI: 10.1016/j.gendis.2021.12.026] [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: 07/02/2021] [Revised: 12/04/2021] [Accepted: 12/31/2021] [Indexed: 11/25/2022] Open
Abstract
Ovarian cancer (OC) is one of the most common and fatal types of gynecological cancer. OC is usually detected at the advanced stages of the disease, making it highly lethal. miRNAs are single-stranded, small non-coding RNAs with an approximate size ranging around 22 nt. Interestingly, a considerable proportion of miRNAs are organized in clusters with miRNA genes placed adjacent to one another, getting transcribed together to result in miRNA clusters (MCs). MCs comprise two or more miRNAs that follow the same orientation during transcription. Abnormal expression of the miRNA cluster has been identified as one of the key drivers in OC. MC exists both as tumor-suppressive and oncogenic clusters and has a significant role in OC pathogenesis by facilitating cancer cells to acquire various hallmarks. The present review summarizes the regulation and biological function of MCs in OC. The review also highlights the utility of abnormally expressed MCs in the clinical management of OC.
Collapse
|
12
|
Chen S, Zhao J, Sakharov IY, Xu J, Xu C, Zhao S. An ultrasensitive multivariate signal amplification strategy based on microchip platform tailored for simultaneous quantification of multiple microRNAs in single cell. Biosens Bioelectron 2022; 203:114053. [PMID: 35121443 DOI: 10.1016/j.bios.2022.114053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 01/27/2022] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) play a very important regulatory role in life activities. Abnormal expression levels of miRNAs in cells are associated with various diseases, especially human cancer. Nevertheless, accurate detection of the copy numbers of various miRNA molecules in single cell is still a great challenge. In this study, an intracellular multivariate signal amplification strategy based on microchip platform was proposed, and an ultrasensitive single-cell analysis method was established for simultaneous quantification of absolute copy numbers of multiple miRNAs in a single cell. Using miRNA-21 and miRNA-141 as the analytical models of miRNAs, the detection limits of 1.0 and 2.0 fM were obtained. Based on the developed method, an analysis of 600 randomly acquired different types of cells was performed. The distribution of absolute copy numbers of miRNA-21 and miRNA-141 in six types of cells was obtained. It was found that the number of copies of miRNA-21 and miRNA-141 in different types of cancer cells showed different expression characteristics. The study results can help us more accurately understand cell-to-cell heterogeneity and the relationship between different miRNAs and different types of cancer at the single cell level.
Collapse
Affiliation(s)
- Shengyu Chen
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Science, Guangxi Normal University, Guilin, 541004, China
| | - Jingjin Zhao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Science, Guangxi Normal University, Guilin, 541004, China.
| | - Ivan Yu Sakharov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Jiayao Xu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Science, Guangxi Normal University, Guilin, 541004, China
| | - Chunhuan Xu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Science, Guangxi Normal University, Guilin, 541004, China
| | - Shulin Zhao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Science, Guangxi Normal University, Guilin, 541004, China.
| |
Collapse
|
13
|
Marinović S, Škrtić A, Catela Ivković T, Poljak M, Kapitanović S. Regulation of KRAS protein expression by miR-544a and KRAS-LCS6 polymorphism in wild-type KRAS sporadic colon adenocarcinoma. Hum Cell 2021; 34:1455-1465. [PMID: 34235620 DOI: 10.1007/s13577-021-00576-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/29/2021] [Indexed: 12/24/2022]
Abstract
Colorectal carcinoma (CRC) results from the accumulation of genetic mutations and alterations in signaling pathways. KRAS is mutated in 40% of CRC cases and is involved in increased tumor cells proliferation and survival. Although KRAS mutations are a dominant event in CRC tumorigenesis, increased wild-type KRAS expression has a similar effect on accelerated tumor growth. In this study, we investigated the KRAS status in correlation with clinicopathological features in sporadic CRC and more importantly the role of let-7a-5p and miR-544a-3p in the regulation of wild-type KRAS protein expression in the tumor center (T1) and invasive tumor front (T2). Analysis showed that 39.1% of tumor samples had KRAS mutations. In wild-type KRAS tumors, 62.0% were positive for KRAS protein expression and there was a higher percentage of KRAS-positive tumor cells and a higher intensity of immunohistochemical reaction in T2 than in T1 samples. This could not be attributed to differences in KRAS mRNA levels, suggesting regulation via miR-544a-3p expression which was significantly decreased in T2 samples. Furthermore, we demonstrated that tumor samples carrying the KRAS-LCS6 variant allele had significantly higher protein expression of the wild-type KRAS. Our results suggest the role of the KRAS-LCS6 polymorphism and miR-544a-3p expression in the regulation of wild-type KRAS protein expression in sporadic CRC.
Collapse
Affiliation(s)
- Sonja Marinović
- Division of Molecular Medicine, Laboratory for Personalized Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | - Anita Škrtić
- Department of Pathology, Clinical Hospital Merkur, Zagreb, Croatia
| | - Tina Catela Ivković
- Division of Molecular Medicine, Laboratory for Personalized Medicine, Ruđer Bošković Institute, Zagreb, Croatia.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Mirko Poljak
- Department of Surgery, Clinical Hospital Merkur, Zagreb, Croatia
| | - Sanja Kapitanović
- Division of Molecular Medicine, Laboratory for Personalized Medicine, Ruđer Bošković Institute, Zagreb, Croatia.
| |
Collapse
|
14
|
Galka-Marciniak P, Urbanek-Trzeciak MO, Nawrocka PM, Kozlowski P. A pan-cancer atlas of somatic mutations in miRNA biogenesis genes. Nucleic Acids Res 2021; 49:601-620. [PMID: 33406242 PMCID: PMC7826265 DOI: 10.1093/nar/gkaa1223] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/28/2020] [Accepted: 12/04/2020] [Indexed: 02/07/2023] Open
Abstract
It is a well-known and intensively studied phenomenon that the levels of many miRNAs are differentiated in cancer. miRNA biogenesis and functional expression are complex processes orchestrated by many proteins cumulatively called miRNA biogenesis proteins. To characterize cancer somatic mutations in the miRNA biogenesis genes and investigate their potential impact on the levels of miRNAs, we analyzed whole-exome sequencing datasets of over 10 000 cancer/normal sample pairs deposited within the TCGA repository. We identified and characterized over 3600 somatic mutations in 29 miRNA biogenesis genes and showed that some of the genes are overmutated in specific cancers and/or have recurrent hotspot mutations (e.g. SMAD4 in PAAD, COAD and READ; DICER1 in UCEC; PRKRA in OV and LIN28B in SKCM). We identified a list of miRNAs whose level is affected by particular types of mutations in either SMAD4, SMAD2 or DICER1 and showed that hotspot mutations in the RNase domains in DICER1 not only decrease the level of 5p-miRNAs but also increase the level of 3p-miRNAs, including many well-known cancer-related miRNAs. We also showed an association of the mutations with patient survival. Eventually, we created an atlas/compendium of miRNA biogenesis alterations providing a useful resource for different aspects of biomedical research.
Collapse
Affiliation(s)
| | | | | | - Piotr Kozlowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| |
Collapse
|
15
|
Genetic variants in the regulation region of TLR4 reduce the gastric cancer susceptibility. Gene 2020; 767:145181. [PMID: 33007372 DOI: 10.1016/j.gene.2020.145181] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/30/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023]
Abstract
Gastric cancer (GC) is one of the most common cancers diagnosed in China. It has been suggested that the genetic polymorphisms of Toll-like receptors (TLRs) might be in close relation to tumorigenesis and development of gastric cancer. In this study, we performed a case-control study to investigate the genetic polymorphisms of TLR3, 4, 5, 7 with the genetic susceptibility of gastric cancer. TLRs gene polymorphisms in 471 gastric cancer (GC) patients and 471 healthy controls were analyzed by polymerase chain reaction-restrictive fragment length polymorphism (PCR-RFLP) analysis or TaqMan assays. Odds ratio (OR) and its 95% confidence interval (95%CI) were used to evaluate the association of TLR4 variants with the GC risk via unconditional logistic regression. Our results suggested that variant genotypes of TLR4 rs7869402 (OR = 0.61, 95%CI = 0.40-0.92, P = 0.02) and TLR4 rs7873784 (OR = 0.17, 95%CI = 0.09-0.33, P < 0.01) gene polymorphisms reduced the risk of GC. Stratified analysis showed that rs7869402 T-containing genotype significantly decreased the susceptibility of GC among females (OR = 0.38, 95%CI = 0.16-0.91, P = 0.03), older subjects (OR = 0.48, 95%CI = 0.26-0.87, P = 0.02), non-smokers (OR = 0.41, 95%CI = 0.23-0.71, P < 0.01) and non-drinkers (OR = 0.58, 95%CI = 0.30-0.78, P < 0.01). In case of rs7873784 polymorphism, C-containing genotype reduced the risk of GC among males (OR = 0.08, 95%CI = 0.03-0.21, P < 0.01), but not among females (OR = 0.53, 95%CI = 0.22-1.27, P = 0.15). As to the other four SNPs (TLR3 rs5743303, TLR4 rs1927914, TLR5 rs1640816 and TLR7 rs3853839), no significant correlations were found to be related to the risk of gastric carcinoma. Our research demonstrated the significance of TLRs polymorphisms in decreasing the risk of GC.
Collapse
|
16
|
Impact of Genetic Variation in TLR4 3'UTR on NSCLC Genetic Susceptibility. JOURNAL OF ONCOLOGY 2020; 2020:7593143. [PMID: 32351566 PMCID: PMC7171665 DOI: 10.1155/2020/7593143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/27/2020] [Accepted: 03/03/2020] [Indexed: 12/11/2022]
Abstract
Toll-like receptors (TLRs) are expressed not only in immune cells but also in a variety of tumor cells. Single-nucleotide polymorphisms (SNPs) located in the TLRs' promoter or the 3′ untranslated region may affect gene expression by affecting the activity of the promoter or regulating the binding of mRNA to miRNA. This study aimed to investigate the association of the SNPs in TLR genes with the susceptibility to NSCLC. This case-control study involved 700 lung cancer patients and 700 healthy controls. All individuals were genotyped for all selected SNPs in TLR genes using polymerase chain reaction (PCR) test-based restriction fragment length polymorphism (PCR-RFLP) and TaqMan SNP genotyping assay. The association of genetic variations in TLRs with the susceptibility to NSCLC was evaluated by unconditional logistic regression with OR (95% CI). After evaluating transcriptional factor or miRNA binding capability by bioinformatics methods, six TLRs were identified for further analysis. We did not find that TLR3 rs5743303, TLR4 rs1927914, TLR4 rs11536891, TLR5 rs1640816, and TLR7 rs3853839 were associated with NSCLC risk (P > 0.05). Our data showed that TLR4 rs7869402 C > T polymorphism reduced the risk of NSCLC with OR (95% CI) of 0.63 (0.45–0.89). When stratified by gender and age, the individuals carrying at least one rs7869402T allele significantly decreased the NSCLC risk among males (OR = 0.58, 95% CI = 0.38–0.87) and among youngsters (OR = 0.43, 95% CI = 0.27–0.69). Smoking stratification analysis showed that the rs7869402T allele-containing genotype reduced the risk of NSCLC with OR (95% CI) of 0.50 (0.29–0.87) among smokers but not among nonsmokers (P > 0.05). When the individuals were classed by the pathological type, we found that the rs7869402T-containing genotype was associated with the risk of adenocarcinoma (OR = 0.62, 95% CI = 0.41–0.92) but not with that of squamous cell carcinoma (OR = 0.71, 95% CI = 0.44–1.13) and other types (OR = 0.23, 95% CI = 0.03–1.70). Compared with the TLR4 Ars1927914-Crs7869402-Trs11536891 haplotype, the Grs1927914-Trs7869402-Trs11536891 haplotype was associated with a decreased risk for developing NSCLC with OR (95% CI) of 0.57 (0.41–0.80). These results indicated that the TLR4 rs7869402 variation affects the genetic susceptibility to NSCLC.
Collapse
|
17
|
Shao Y, Shen Y, Zhao L, Guo X, Niu C, Liu F. Association of microRNA biosynthesis genes XPO5 and RAN polymorphisms with cancer susceptibility: Bayesian hierarchical meta-analysis. J Cancer 2020; 11:2181-2191. [PMID: 32127945 PMCID: PMC7052917 DOI: 10.7150/jca.37150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 12/07/2019] [Indexed: 12/15/2022] Open
Abstract
XPO5/RAN-GTP complex mediates the nuclear transport of pre-miRNAs in the miRNA processing system, its altered expression is indicated to be correlated with cancer risk. Several studies have inspected the association between XPO5 or RAN polymorphisms and the risk of various cancers, but the findings remain controversial. A Bayesian hierarchical meta-analysis was carried out to review and analyze the effect of XPO5 and RAN polymorphisms on cancer risk. The association was estimated by calculating the logarithm of odds ratio (Log OR) and 95% credible interval (95% CrI). The expression quantitative trait loci (eQTL) analysis was used for in silico functional validation of the identified significant susceptibility loci. Consequently, 38 case-control studies (from 27 citations) with 27,459 cancer cases and 25,151controls were included in the meta-analysis of the five most prevalent SNPs (rs11077 A/C, rs2257082 G/A, rs3803012 A/G, rs14035 C/T, rs3809142 C/T). In the XPO5 gene rs11077 SNP, the minor C allele significantly increased the risk of cancer (Log OR = 0.120, 95% CrI = 0.013, 0.241), and a strong association between rs11077 SNP and cancer risk was also found in the dominant model (CC + AC vs. AA: Log OR = 0.132, 95% CrI = 0.009, 0.275). In addition, the minor GG genotype allele of the RAN gene rs3803012 SNP significantly increased the cancer risk (Log OR = 0.707, 95% CrI = 0.059, 1.385). Statistically significant associations between rs3803012 SNP and cancer risk were also observed in the recessive model (GG vs. AG + AA: Log OR = 0.708, 95% CrI = 0.059, 1.359). Furthermore, the eQTL analysis revealed that rs11077 SNP was significantly correlated with XPO5 mRNA expression, which provided additional biological basis for the observed positive association. Our results suggest that XPO5 rs11077 may be a possible functional susceptibility locus for cancer risk.
Collapse
Affiliation(s)
- Yi Shao
- Department of Epidemiology and Health Statistics, School of Public Health, Beijing Municipal Key Laboratory of Clinical Epidemiology, Capital Medical University, Beijing, China
| | - Yi Shen
- Department of Epidemiology and Health Statistics, School of Public Health, Beijing Municipal Key Laboratory of Clinical Epidemiology, Capital Medical University, Beijing, China
| | - Lei Zhao
- Department of Molecular Physiology and Biophysics, Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - Xudong Guo
- Department of Epidemiology and Health Statistics, School of Public Health, Beijing Municipal Key Laboratory of Clinical Epidemiology, Capital Medical University, Beijing, China
| | - Chen Niu
- Department of Epidemiology and Health Statistics, School of Public Health, Beijing Municipal Key Laboratory of Clinical Epidemiology, Capital Medical University, Beijing, China
| | - Fen Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Beijing Municipal Key Laboratory of Clinical Epidemiology, Capital Medical University, Beijing, China
| |
Collapse
|
18
|
Multiple genetic factors affecting the pharmacokinetic and pharmacodynamic processes of tacrolimus in Chinese myasthenia gravis patients. Eur J Clin Pharmacol 2020; 76:659-671. [PMID: 31955224 DOI: 10.1007/s00228-019-02803-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/20/2019] [Indexed: 12/14/2022]
Abstract
PURPOSE Tacrolimus is a novel effective immunosuppressant for myasthenia gravis (MG) patients. However, the narrow therapeutic window, and high inter- and intrapatient variation in bioavailability largely limited its clinical application. This article intended to find the SNPs influencing clinical outcome and discover the possible mechanisms. METHODS Based on the tagSNPs genotyped by Improved Multiple Ligase Detection Reaction, Plink 1.07 was used to find the SNPs having close interaction to tacrolimus serum concentration, QMG score changes or even reasonable drug dose. Then we searched several databases to predict the possible miRNA binding rs15524 sequence. Based on the prediction, dual-luciferase reporter assay and miRNA transfection were used to discover the mechanism of how SNP rs15524 controls tacrolimus serum concentration through influencing CYP3A5 expression. RESULTS In this article, we found multiple SNPs on CYP3A4, CYP3A5, FKBP1A, NFATC2 genes were predicted closely related to tacrolimus serum concentration, therapeutic effect which reflected by QMG score changes or even reasonable drug dose. After in silico miRNA selection, possible relationship between hsa-miR-500a and rs15524 was found. With the help of dual-luciferase reporter assay, wild-type rs15524 (T allele) was found having a stronger binding affinity for hsa-miR-500a. Higher expression of CYP3A5 may also led by lower hsa-miR-500a level. CONCLUSIONS SNP rs15524 may control CYP3A5 expression by affecting the binding affinity between CYP3A5 3'UTR and hsa-miR-500a. Wild type (T allele) 3'UTR of CYP3A5 has stronger binding affinity to hsa-miR-500a and cause lower CYP3A5 expression and higher tacrolimus serum concentration.
Collapse
|
19
|
Huang X, Li Z, Lei J, Wang D, Zhang Y. Genetic polymorphism in DGCR8 is associated with late onset of preeclampsia. BMC MEDICAL GENETICS 2019; 20:151. [PMID: 31484500 PMCID: PMC6727569 DOI: 10.1186/s12881-019-0887-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/30/2019] [Indexed: 12/14/2022]
Abstract
Background PE (preeclampsia) is a heterogeneous disorder with early onset PE (EOPE) and late onset PE (LOPE) subtypes. Associations between maternal miRNAs biosynthesis genes polymorphisms and risk of PE have been previously observed. However, the impact of polymorphisms in DGCR8 which is indispensable in miRNA maturing processing on the susceptibility to preeclampsia (PE) has not been elucidated yet. We, therefore, conducted a case-control study to evaluate the impact of polymorphisms in DGCR8 on the risk of EOPE and LOPE. Methods A total of 66 patients diagnosed with EOPE, 206 with LOPE and 330 healthy controls were recruited. Five SNPs in DGCR8 were genotyped including rs1558496, rs1640299, rs720012, rs720014, and rs9606241. Logistic regression was used to estimate the OR and the 95% CI for the associations. Results Increased risk of LOPE has been observed among patients with rs1640299 TG genotype (OR = 1.98 (95%CI: 1.38, 2.87), p = 2.32e-4) and rs720014 TC genotype (OR = 2.49 (95%CI: 1.72, 3.60), p = 1.40e-7). The DGCR8 rs1558496/ rs1640299/ rs720012/ rs720014/ rs9606241 haplotype T-G-A-C-A and T-G-A-C-G were associated with increased risk of LOPE (OR = 2.20 (95%CI: 1.49, 3.25), p = 5.90e-5, and 1.58 (95%CI: 1.06, 2.36), p = 0.024, respectively). And the haplotype T-T-G-T-A was associated with lower risk of LOPE (OR = 0.74 (95%CI: 0.58, 0.95), p = 0.018). These significant associations retained after false-positive discovery rate correction. However, none of the tested SNPs or haplotypes in DGCR8 gene is associated with risk of EOPE (p > 0.05). Conclusions Polymorphisms in DGCR8 might participate in the pathological process of preeclampsia. The rs1640299 T > G and rs720014 T > C polymorphisms are associated with late onset preeclampsia susceptibility. Electronic supplementary material The online version of this article (10.1186/s12881-019-0887-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xin Huang
- Department of Preventive Medicine, School of Medicine, Hunan Normal University, 371 Tongzipo Road, Yuelu District, Changsha, 410013, Hunan, China
| | - Zuodong Li
- Department of Preventive Medicine, School of Medicine, Hunan Normal University, 371 Tongzipo Road, Yuelu District, Changsha, 410013, Hunan, China
| | - Jun Lei
- Department of Obstetrics and Gynecology, The Third Xiangya Hospital of Central South University, Changsha, 410013, Hunan, China
| | - Dapeng Wang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Guizhou Medical University, Guiyang, 550025, Guizhou, China
| | - Yujing Zhang
- Department of Preventive Medicine, School of Medicine, Hunan Normal University, 371 Tongzipo Road, Yuelu District, Changsha, 410013, Hunan, China.
| |
Collapse
|
20
|
Targeting ATG4 in Cancer Therapy. Cancers (Basel) 2019; 11:cancers11050649. [PMID: 31083460 PMCID: PMC6562779 DOI: 10.3390/cancers11050649] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 12/30/2022] Open
Abstract
Autophagy is a lysosome-mediated degradation pathway that enables the degradation and recycling of cytoplasmic components to sustain metabolic homoeostasis. Recently, autophagy has been reported to have an astonishing number of connections to cancer, as tumor cells require proficient autophagy in response to metabolic and therapeutic stresses to sustain cell proliferation. Autophagy-related gene 4 (ATG4) is essential for autophagy by affecting autophagosome formation through processing full-length microtubule-associated protein 1A/1B-light chain 3 (pro-LC3) and lipidated LC3. An increasing amount of evidence suggests that ATG4B expression is elevated in certain types of cancer, implying that ATG4B is a potential anticancer target. In this review, we address the central roles of ATG4B in the autophagy machinery and in targeted cancer therapy. Specifically, we discuss how pharmacologically inhibiting ATG4B can benefit cancer therapies.
Collapse
|
21
|
Orang AV, Petersen J, McKinnon RA, Michael MZ. Micromanaging aerobic respiration and glycolysis in cancer cells. Mol Metab 2019; 23:98-126. [PMID: 30837197 PMCID: PMC6479761 DOI: 10.1016/j.molmet.2019.01.014] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/22/2019] [Accepted: 01/30/2019] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Cancer cells possess a common metabolic phenotype, rewiring their metabolic pathways from mitochondrial oxidative phosphorylation to aerobic glycolysis and anabolic circuits, to support the energetic and biosynthetic requirements of continuous proliferation and migration. While, over the past decade, molecular and cellular studies have clearly highlighted the association of oncogenes and tumor suppressors with cancer-associated glycolysis, more recent attention has focused on the role of microRNAs (miRNAs) in mediating this metabolic shift. Accumulating studies have connected aberrant expression of miRNAs with direct and indirect regulation of aerobic glycolysis and associated pathways. SCOPE OF REVIEW This review discusses the underlying mechanisms of metabolic reprogramming in cancer cells and provides arguments that the earlier paradigm of cancer glycolysis needs to be updated to a broader concept, which involves interconnecting biological pathways that include miRNA-mediated regulation of metabolism. For these reasons and in light of recent knowledge, we illustrate the relationships between metabolic pathways in cancer cells. We further summarize our current understanding of the interplay between miRNAs and these metabolic pathways. This review aims to highlight important metabolism-associated molecular components in the hunt for selective preventive and therapeutic treatments. MAJOR CONCLUSIONS Metabolism in cancer cells is influenced by driver mutations but is also regulated by posttranscriptional gene silencing. Understanding the nuanced regulation of gene expression in these cells and distinguishing rapid cellular responses from chronic adaptive mechanisms provides a basis for rational drug design and novel therapeutic strategies.
Collapse
Affiliation(s)
- Ayla V Orang
- Flinders Centre for Innovation in Cancer, Flinders University, Flinders Medical Centre, Adelaide, South Australia 5042, Australia.
| | - Janni Petersen
- Flinders Centre for Innovation in Cancer, Flinders University, Flinders Medical Centre, Adelaide, South Australia 5042, Australia.
| | - Ross A McKinnon
- Flinders Centre for Innovation in Cancer, Flinders University, Flinders Medical Centre, Adelaide, South Australia 5042, Australia.
| | - Michael Z Michael
- Flinders Centre for Innovation in Cancer, Flinders University, Flinders Medical Centre, Adelaide, South Australia 5042, Australia.
| |
Collapse
|
22
|
Ruffalo M, Bar-Joseph Z. Protein interaction disruption in cancer. BMC Cancer 2019; 19:370. [PMID: 31014259 PMCID: PMC6823625 DOI: 10.1186/s12885-019-5532-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 03/27/2019] [Indexed: 12/18/2022] Open
Abstract
Background Most methods that integrate network and mutation data to study cancer focus on the effects of genes/proteins, quantifying the effect of mutations or differential expression of a gene and its neighbors, or identifying groups of genes that are significantly up- or down-regulated. However, several mutations are known to disrupt specific protein-protein interactions, and network dynamics are often ignored by such methods. Here we introduce a method that allows for predicting the disruption of specific interactions in cancer patients using somatic mutation data and protein interaction networks. Methods We extend standard network smoothing techniques to assign scores to the edges in a protein interaction network in addition to nodes. We use somatic mutations as input to our modified network smoothing method, producing scores that quantify the proximity of each edge to somatic mutations in individual samples. Results Using breast cancer mutation data, we show that predicted edges are significantly associated with patient survival and known ligand binding site mutations. In-silico analysis of protein binding further supports the ability of the method to infer novel disrupted interactions and provides a mechanistic explanation for the impact of mutations on key pathways. Conclusions Our results show the utility of our method both in identifying disruptions of protein interactions from known ligand binding site mutations, and in selecting novel clinically significant interactions.Supporting website with software and data: https://www.cs.cmu.edu/~mruffalo/mut-edge-disrupt/. Electronic supplementary material The online version of this article (10.1186/s12885-019-5532-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Matthew Ruffalo
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA. .,Machine Learning Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA.
| |
Collapse
|
23
|
Verma A, Singh V, Jaiswal PK, Mittal RD. Anomalies in MiRNAs Machinery Gene, GEMIN-4 Variants Suggest Renal Cell Carcinoma Risk: A Small Experimental Study from North India. Indian J Clin Biochem 2019; 34:45-51. [PMID: 30728672 DOI: 10.1007/s12291-017-0722-x] [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: 09/14/2017] [Accepted: 11/30/2017] [Indexed: 10/18/2022]
Abstract
GEMIN4 is a member of the GEMIN gene family which is involved in multiple pathologies including cancer. It is located on Chr17p13.3, the most notorious chromosome and a hotspot for various carcinomas. We therefore intend to find genetic variants of GEMIN4 gene associated with renal cell carcinoma risk (RCC). This study comprised 100 patients and 225 controls. Genotyping of GEMIN4 gene variants was done using Taqman® assay. The association of GEMIN4 variants and risk prediction of RCC was done by statistical analysis. Haplotype analysis was done to see the combined effect of variants on RCC. Patients carrying variant genotype, CC of GEMIN4 T/C rs7813 showed significant association whereas in case of GEMIN4 G/C rs910925 variant genotype, CC significant risk was found. GEMIN4 rs7813 T/C variant genotype, CC showed risk with smoking (p = 0.034). Our study gives a substantive support for the association between the GEMIN4 gene variants and RCC risk.
Collapse
Affiliation(s)
- Archana Verma
- Department of Urology and Renal Transplantation, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Raebareli Road, Lucknow, Uttar Pradesh 226014 India
| | - Vibha Singh
- Department of Urology and Renal Transplantation, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Raebareli Road, Lucknow, Uttar Pradesh 226014 India
| | - Praveen Kumar Jaiswal
- Department of Urology and Renal Transplantation, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Raebareli Road, Lucknow, Uttar Pradesh 226014 India
| | - Rama D Mittal
- Department of Urology and Renal Transplantation, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Raebareli Road, Lucknow, Uttar Pradesh 226014 India
| |
Collapse
|
24
|
Susceptibility to congenital heart defects associated with a polymorphism in TBX2 3' untranslated region in the Han Chinese population. Pediatr Res 2019; 85:378-383. [PMID: 30262811 DOI: 10.1038/s41390-018-0181-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 06/15/2018] [Accepted: 06/19/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Tbx2 plays a critical role in determining fates of cardiomyocytes. Little is known about the contribution of TBX2 3' untranslated region (UTR) variants to the risk of congenital heart defect (CHD). Thus, we aimed to determine the association of single-nucleotide polymorphisms (SNPs) in TBX2 3' UTR with CHD susceptibility. METHODS We recruited 1285 controls and 1241 CHD children from China. SNPs identification and genotyping were detected using Sanger Sequencing and SNaPshot. Stratified analysis was conducted to explore the association between rs59382073 polymorphism and CHD subtypes. Functional analyses were performed by luciferase assays in HEK-293T and H9c2 cells. RESULTS Among five TBX2 3'UTR variants identified, rs59382073 minor allele T carriers had a 1.89-fold increased CHD risk compared to GG genotype (95% CI = 1.48-2.46, P = 4.48 × 10-7). The most probable subtypes were right ventricular outflow tract obstruction, conotruncal, and septal defect. G to T variation decreased luciferase activity in cells. This discrepancy was exaggerated by miR-3940 and miR-708, while their corresponding inhibitors eliminated it. CONCLUSION T allele of rs59382073 in TBX2 3'UTR contributed to greater CHD risk in the Han Chinese population. G to T variation created binding sites for miR-3940 and miR-708 to inhibit gene expression.
Collapse
|
25
|
Yuan Y, Weidhaas JB. Functional microRNA binding site variants. Mol Oncol 2019; 13:4-8. [PMID: 30536617 PMCID: PMC6322190 DOI: 10.1002/1878-0261.12421] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/15/2018] [Accepted: 11/26/2018] [Indexed: 12/19/2022] Open
Abstract
Germline single nucleotide polymorphisms are one of the most common genetic variations. Polymorphisms that cause nonsynonymous mutations in gene coding regions are known to cause serious deleterious downstream effects. However, even polymorphisms in noncoding regions can have profound functional consequences by disrupting essential regulatory sites. Specifically, polymorphisms that alter microRNA binding sites can disrupt the regulation of hallmark biological pathways implicated in tumorigenesis and tumor progression. Many of these microRNA-associated polymorphisms (miR-SNPs) have recently been shown to be important biomarkers of cancer risk, prognosis, and treatment outcomes. This review will summarize the functional impact of key miR-SNPs and define a subset of miR-SNPs that may be clinically useful prognostic or predictive biomarkers.
Collapse
Affiliation(s)
- Ye Yuan
- Department of Radiation OncologyUCLALos AngelesCAUSA
| | | |
Collapse
|
26
|
Wu Z, Zhou H, He J, Li M, Ma X, Xue J, Li X, Fan X. G-triplex based molecular beacon with duplex-specific nuclease amplification for the specific detection of microRNA. Analyst 2019; 144:5201-5206. [DOI: 10.1039/c9an01075k] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Based on the G-triplex molecular beacon (MBG3), we have developed a duplex-specific nuclease signal amplification (DSNSA) assay for highly selective miRNA detection.
Collapse
Affiliation(s)
- Zhifang Wu
- College of Chemistry and Chemical Engineering
- Gannan Normal University
- Ganzhou 341000
- P. R. China
| | - Hui Zhou
- College of Chemistry and Chemical Engineering
- Gannan Normal University
- Ganzhou 341000
- P. R. China
| | - Juan He
- College of Chemistry and Chemical Engineering
- Gannan Normal University
- Ganzhou 341000
- P. R. China
| | - Mei Li
- College of Chemistry and Chemical Engineering
- Gannan Normal University
- Ganzhou 341000
- P. R. China
| | - Xiaoming Ma
- College of Chemistry and Chemical Engineering
- Gannan Normal University
- Ganzhou 341000
- P. R. China
| | - Jun Xue
- College of Chemistry and Chemical Engineering
- Gannan Normal University
- Ganzhou 341000
- P. R. China
| | - Xun Li
- College of Chemistry and Chemical Engineering
- Gannan Normal University
- Ganzhou 341000
- P. R. China
| | - Xiaolin Fan
- College of Chemistry and Chemical Engineering
- Gannan Normal University
- Ganzhou 341000
- P. R. China
| |
Collapse
|
27
|
Zhu Y, Zhang M, Wang F, Lu J, Chen R, Xie Q, Sun J, Xue J, Hao C, Lin S. The calcineurin regulatory subunit polymorphism and the treatment efficacy of tacrolimus for idiopathic membranous nephropathy. Int Immunopharmacol 2018; 65:422-428. [PMID: 30388516 DOI: 10.1016/j.intimp.2018.10.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 10/11/2018] [Accepted: 10/25/2018] [Indexed: 12/12/2022]
Abstract
Tacrolimus is considered to be one of the main therapeutic options for idiopathic membranous nephropathy (IMN). This study aimed to investigate the association of variants in genes encoding the binding protein and the drug target (calcineurin) of tacrolimus with the efficacy in IMN patients and the potential mechanism. Sixty-seven IMN patients treated with tacrolimus were enrolled retrospectively. Sanger sequencing was performed to search for variants in all exons of the genes in 8 IMN patients and genotype for the detected variants in the other 59 patients. The molecular mechanism underlying the relationship between the variants and the efficacy was explored in human peripheral blood mononuclear cells (PBMCs) and other cell lines. Single nucleotide polymorphism rs875 (T > C) in the 3'untranslated region (3'UTR) of PPP3R1 encoding calcineurin regulatory subunit was found to be associated with the treatment efficacy of tacrolimus for IMN. Patients carrying TT genotype had a significantly higher remission rate than those carrying TC/CC genotype (83% vs. 47%, P = 0.008). Western blot showed that the TT genotype carriers exhibited reduced PPP3R1 protein levels in PBMCs (P = 0.02). Compared with C allele, T allele displayed increased binding affinity for miR-582-5p in the luciferase reporter assay (P < 0.001). Moreover, knockdown of PPP3R1 in Jurkat T cell line enhanced the immunosuppressive effect of tacrolimus. Our study revealed the association of PPP3R1 3'UTR polymorphism rs875 with the efficacy of tacrolimus in IMN patients. The functional polymorphism might alter PPP3R1 expression via modulating the interaction of miR-582-5p with PPP3R1, which further affected the immunosuppressive effect of tacrolimus.
Collapse
Affiliation(s)
- Ying Zhu
- Department of Nephrology, Huashan Hospital, Fudan University, Shanghai, China
| | - Min Zhang
- Department of Nephrology, Huashan Hospital, Fudan University, Shanghai, China
| | - Fan Wang
- Department of Nephrology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jianda Lu
- Department of Nephrology, Huashan Hospital, Fudan University, Shanghai, China
| | - Ruiying Chen
- Department of Nephrology, Huashan Hospital, Fudan University, Shanghai, China
| | - Qionghong Xie
- Department of Nephrology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jing Sun
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China.
| | - Jun Xue
- Department of Nephrology, Huashan Hospital, Fudan University, Shanghai, China.
| | - Chuanming Hao
- Department of Nephrology, Huashan Hospital, Fudan University, Shanghai, China
| | - Shanyan Lin
- Department of Nephrology, Huashan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
28
|
Salgado E, Bian X, Feng A, Shim H, Liang Z. HDAC9 overexpression confers invasive and angiogenic potential to triple negative breast cancer cells via modulating microRNA-206. Biochem Biophys Res Commun 2018; 503:1087-1091. [PMID: 29936177 DOI: 10.1016/j.bbrc.2018.06.120] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 06/20/2018] [Indexed: 12/31/2022]
Abstract
Triple negative breast cancer (TNBC) is among the most aggressive breast cancer subtypes with poor prognosis. The purpose of this study is to better understand the molecular basis of TNBC as well as develop new therapeutic strategies. Our results demonstrate that HDAC9 is overexpressed in TNBC compared to non-TNBC cell lines and tissues and is inversely proportional with miR-206 expression levels. We show that HDAC9 selective inhibition blocked the invasion of TNBC cells in vitro and repressed the angiogenesis shown via in vivo Matrigel plug assays. Subsequent HDAC9 siRNA knockdown was then shown to restore miR-206 while also decreasing VEGF and MAPK3 levels. Furthermore, the inhibition of miR-206 neutralized the action of HDAC9 siRNA on decreasing VEGF and MAPK3 levels. This study highlights HDAC9 as a mediator of cell invasion and angiogenesis in TNBC cells through VEGF and MAPK3 by modulating miR-206 expression and suggests that selective inhibition of HDAC9 may be an efficient route for TNBC therapy.
Collapse
Affiliation(s)
- Eric Salgado
- Molecular and Systems Pharmacology Graduate Studies Program, Emory University, Atlanta, GA, 30322, USA; Department of Radiation Oncology, Emory University, Atlanta, GA, 30322, USA
| | - Xuehai Bian
- Department of Radiation Oncology, Emory University, Atlanta, GA, 30322, USA; Department of Thyroid Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Amber Feng
- Department of Radiation Oncology, Emory University, Atlanta, GA, 30322, USA
| | - Hyunsuk Shim
- Molecular and Systems Pharmacology Graduate Studies Program, Emory University, Atlanta, GA, 30322, USA; Department of Radiation Oncology, Emory University, Atlanta, GA, 30322, USA; Winship Cancer Institute, Emory University, Atlanta, GA, 30322, USA.
| | - Zhongxing Liang
- Department of Radiation Oncology, Emory University, Atlanta, GA, 30322, USA; Winship Cancer Institute, Emory University, Atlanta, GA, 30322, USA.
| |
Collapse
|
29
|
Bermisheva MA, Takhirova ZR, Gilyazova IR, Khusnutdinova EK. MicroRNA Biogenesis Pathway Gene Polymorphisms Are Associated with Breast Cancer Risk. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418040051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
30
|
Zhang L, Ye Y, Tu H, Hildebrandt MA, Zhao L, Heymach JV, Roth JA, Wu X. MicroRNA-related genetic variants in iron regulatory genes, dietary iron intake, microRNAs and lung cancer risk. Ann Oncol 2018; 28:1124-1129. [PMID: 28453699 DOI: 10.1093/annonc/mdx046] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Background Genetic variations in MicroRNA (miRNA) binding sites may alter structural accessibility of miRNA binding sites to modulate risk of cancer. This large-scale integrative multistage study was aimed to evaluate the interplay of genetic variations in miRNA binding sites of iron regulatory pathway, dietary iron intake and lung cancer (LC) risk. Patients and methods The interplay of genetic variant, dietary iron intake and LC risk was assessed in large-scale case-control study. Functional characterization of the validated SNP and analysis of target miRNAs were performed. Results We found that the miRNA binding site SNP rs1062980 in 3' UTR of Iron-Responsive Element Binding protein 2 gene (IREB2) was associated with a 14% reduced LC risk (P value = 4.9×10 - 9). Comparing to AA genotype, GG genotype was associated with a 27% reduced LC risk. This association was evident in males and ever-smokers but not in females and never-smokers. Higher level of dietary iron intake was significantly associated with 39% reduced LC risk (P value = 2.0×10 - 8). This association was only present in individuals with AG + AA genotypes with a 46% reduced risk (P value = 1.0×10 - 10), but not in GG genotype. The eQTL-analysis showed that rs1062980 significantly alters IREB2 expression level. Rs1062980 is predicted to alter a miR-29 binding site on IREB2 and indeed the expression of miR-29 is inversely correlated with IREB2 expression. Further, we found that higher circulating miR-29a level was significantly associated with 78% increased LC risk. Conclusion The miRNA binding site SNP rs1062980 in iron regulatory pathway, which may alter the expression of IREB2 potentially through modulating the binding of miR-29a, together with dietary iron intake may modify risk of LC both individually and jointly. These discoveries reveal novel pathway for understanding lung cancer tumorigenesis and risk stratification.
Collapse
Affiliation(s)
- L Zhang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Y Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - H Tu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - M A Hildebrandt
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - L Zhao
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, USA.,Department of Radiation Oncology, The Forth Military Medical University, XiAn, China
| | - J V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, 2130 West Holcombe Boulevard, Houston, Texas 77030, USA
| | - J A Roth
- Department of Thoracic & Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - X Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, USA
| |
Collapse
|
31
|
Zhang Y, Zhang L, Li R, Chang DW, Ye Y, Minna JD, Roth JA, Han B, Wu X. Genetic variations in cancer-related significantly mutated genes and lung cancer susceptibility. Ann Oncol 2018; 28:1625-1630. [PMID: 28383694 DOI: 10.1093/annonc/mdx161] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Indexed: 12/13/2022] Open
Abstract
Background Cancer initiation and development are driven by key mutations in driver genes. Applying high-throughput sequencing technologies and bioinformatic analyses, The Cancer Genome Atlas (TCGA) project has identified panels of somatic mutations that contributed to the etiology of various cancers. However, there are few studies investigating the germline genetic variations in these significantly mutated genes (SMGs) and lung cancer susceptibility. Patients and methods We comprehensively evaluated 1655 tagged single nucleotide polymorphisms (SNPs) located in 127 SMGs identified by TCGA, and test their association with lung cancer risk in large-scale case-control study. Functional effect of the validated SNPs, gene mutation frequency and pathways were analyzed. Results We found 11 SNPs in 8 genes showed consistent association (P < 0.1) and 8 SNPs significantly associated with lung cancer risk (P < 0.05) in both discovery and validation phases. The most significant association was rs10412613 in PPP2R1A, with the minor G allele associated with a decreased risk of lung cancer [odds ratio = 0.91, 95% confidence interval (CI): 0.87-0.96, P = 2.3 × 10-4]. Cumulative analysis of risk score built as a weight sum of the 11 SNPs showed consistently elevated risk with increasing risk score (P for trend = 9.5 × 10-9). In stratified analyses, the association of PPP2R1A:rs10412613 and lung cancer risk appeared stronger among population of younger age at diagnosis and never smokers. The expression quantitative trait loci analysis indicated that rs10412613, rs10804682, rs635469 and rs6742399 genotypes significantly correlated with the expression of PPP2R1A, ATR, SETBP1 and ERBB4, respectively. From TCGA data, expression of the identified genes was significantly different in lung tumors compared with normal tissues, and the genes' highest mutation frequency was found in lung cancers. Integrative pathway analysis indicated the identified genes were mainly involved in AKT/NF-κB regulatory pathway suggesting the underlying biological processes. Conclusion This study revealed novel genetic variants in SMGs associated with lung cancer risk, which might contribute to elucidating the biological network involved in lung cancer development.
Collapse
Affiliation(s)
- Y Zhang
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, USA.,Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - L Zhang
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, USA
| | - R Li
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, USA.,Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - D W Chang
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, USA
| | - Y Ye
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, USA
| | - J D Minna
- Harmon Center for Therapeutic Oncology, University of Texas Southwestern Medical Center, Dallas
| | - J A Roth
- Department of Thoracic & Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, USA
| | - B Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - X Wu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, USA
| |
Collapse
|
32
|
Genome-Wide Mapping of SNPs in Non-coding RNAs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1094:39-48. [DOI: 10.1007/978-981-13-0719-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
33
|
Li J, Huang J, Yang X, Yang Y, Quan K, Xie N, Wu Y, Ma C, Wang K. Two-Color-Based Nanoflares for Multiplexed MicroRNAs Imaging in Live Cells. Nanotheranostics 2018; 2:96-105. [PMID: 29291166 PMCID: PMC5743841 DOI: 10.7150/ntno.22960] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 10/30/2017] [Indexed: 12/26/2022] Open
Abstract
MicroRNAs (miRNAs) have become an ideal biomarker candidate for early diagnosis of diseases. But various diseases involve changes in the expression of different miRNAs. Therefore, multiplexed assay of miRNAs in live cells can provide critical information for our better understanding of their roles in cells and further validating of their function in clinical diagnoses. Simultaneous detection of multiple biomarkers could effectively improve the accuracy of early cancer diagnosis. Here, we develop the two-color-based nanoflares for simultaneously detecting two distinct miRNA targets inside live cells. The nanoflares consist of gold nanoparticles (AuNPs) functionalized with a dense shell of recognition sequences hybridized to two short fluorophore-labeled DNA molecules, termed “flares”. In this conformation, the close proximity of the fluorophore to the AuNPs surface leads to quenching of the fluorescence. However, when target miRNAs bind to the recognition sequence, the concomitant displacement of the flare can be detected as a corresponding increase in fluorescence. The results demonstrate that the two-color-based nanoflares can simultaneously detect miR-21 and miR-141 expression levels in various live cancer cells successfully. Compared to the traditional single-color-based nanoflares, the two-color-based nanoflares could offer more reliable and practical information for cancer detection, improving the accuracy of early disease diagnosis.
Collapse
Affiliation(s)
- Jing Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Yanjing Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Ke Quan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Nuli Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Yanan Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Changbei Ma
- State Key Laboratory of Medical Genetics & School of Life Science, Central South University, Changsha, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| |
Collapse
|
34
|
Zhang GM, Wang MY, Liu YN, Zhu Y, Wan FN, Wei QY, Ye DW. Functional variants in the low-density lipoprotein receptor gene are associated with clear cell renal cell carcinoma susceptibility. Carcinogenesis 2017; 38:1241-1248. [PMID: 29029037 DOI: 10.1093/carcin/bgx098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 09/21/2017] [Indexed: 12/17/2022] Open
Abstract
Recent studies indicate that abnormal levels of low-density lipoprotein (LDL), which is an important component of dyslipidaemia, are associated with alterations to cancer risk, including that of renal cell carcinoma (RCC). Single nucleotide polymorphisms at microRNA-binding sites contribute to cancer susceptibility and progression by affecting the messenger RNA (mRNA) function of target genes. In this case-control study, we examined the frequency of six potentially functional single nucleotide polymorphisms in the LDL receptor gene (LDLR) in 1004 clear cell RCC (ccRCC) patients and 1065 cancer-free subjects. Logistic regression analyses estimated odds ratios (ORs) and 95% confidence intervals (CIs). The association between genetic variants and levels of LDLR mRNA and protein was also evaluated. Compared with the CC genotype, multivariate logistic regression analysis showed that the LDLR rs2738464 variant GG genotype was associated with a significantly decreased ccRCC risk (P = 0.002, OR: 0.605, 95% CI: 0.439-0.833). Further functional experiments showed that the rs2738464 variant G allele affected miR-330 regulation of the LDLR 3'-untranslated region (UTR), increasing LDLR mRNA levels in patient kidney tissues. These findings suggest that LDLR rs2738464 may affect the affinity of miR-330 binding to the LDLR 3'-UTR, thus regulating LDLR expression and contributing to ccRCC risk.
Collapse
Affiliation(s)
- Gui-Ming Zhang
- Department of Urology, The Affiliated Hospital of Qingdao University, China.,Department of Urology, Fudan University Shanghai Cancer Center, China.,Department of Oncology, Shanghai Medical College, Fudan University, China
| | - Meng-Yun Wang
- Department of Oncology, Shanghai Medical College, Fudan University, China.,Cancer Institute, Fudan University Shanghai Cancer Center, China
| | - Ya-Nan Liu
- Department of Urology, The Affiliated Hospital of Qingdao University, China
| | - Yao Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, China.,Department of Oncology, Shanghai Medical College, Fudan University, China
| | - Fang-Ning Wan
- Department of Urology, Fudan University Shanghai Cancer Center, China.,Department of Oncology, Shanghai Medical College, Fudan University, China
| | - Qing-Yi Wei
- Cancer Institute, Fudan University Shanghai Cancer Center, China.,Duke Cancer Institute, Duke University Medical Center, USA
| | - Ding-Wei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, China.,Department of Oncology, Shanghai Medical College, Fudan University, China
| |
Collapse
|
35
|
Wu N, Zhang X, Tian J, Yu S, Qiao Y. Association of GEMIN4 gene polymorphism and the risk of cancer: a meta-analysis. Onco Targets Ther 2017; 10:5263-5271. [PMID: 29138579 PMCID: PMC5679687 DOI: 10.2147/ott.s147204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Gem-associated protein 4 (GEMIN4) gene is a key regulator for the miRNA biogenesis processes. Recent studies have demonstrated that some single-nucleotide polymorphisms (SNPs) in GEMIN4 gene are associated with the risk of cancer, but the results are still controversial. Therefore, we conducted a meta-analysis to analyze the association between three major SNPs (rs2740348, rs7813, and rs3744741) in the GEMIN4 gene and the risk of cancer. Relevant articles were searched in Web of Science, PubMed, Cochrane Library, Chinese Wan Fang, and Chinese National Knowledge Infrastructure databases. Pooled odds ratio (OR) with 95% confidence interval (CI) was calculated to quantitatively estimate the association. Publication bias and sensitivity analyses were undertaken to evaluate the stability of the results. Overall, the pooled results showed that rs2740348 involving 3,604 cases and 3,770 controls was significantly associated with increased cancer risk (GG vs GC/CC: OR =1.16, 95% CI =1.05-1.29, P=0.004) and rs7813 involving 4,729 cases and 4,562 controls was also related to increased cancer risk (TT vs TC/CC: OR =1.12, 95% CI =1.03-1.22, P=0.009). However, there was no significant association between rs3744741 and cancer risk under overall genetic models. In conclusion, our study has demonstrated that rs2740348 and rs7813 are associated with increased risk of cancer, and they may be new biomarkers for predicting cancer risk.
Collapse
Affiliation(s)
- Nan Wu
- The Core Laboratory for Public Health Science and Practice, The First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Xiaowei Zhang
- The Core Laboratory for Public Health Science and Practice, The First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Jinlong Tian
- The Core Laboratory for Public Health Science and Practice, The First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Shuang Yu
- The Core Laboratory for Public Health Science and Practice, The First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Ying Qiao
- The Core Laboratory for Public Health Science and Practice, The First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| |
Collapse
|
36
|
Qi X, Wang Y, Hou J, Huang Y. A Single Nucleotide Polymorphism in HPGD Gene Is Associated with Prostate Cancer Risk. J Cancer 2017; 8:4083-4086. [PMID: 29187884 PMCID: PMC5706011 DOI: 10.7150/jca.22025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 08/26/2017] [Indexed: 01/18/2023] Open
Abstract
Introduction: The HPGD gene was associated with some cancers, such as colorectal, breast, prostate, and bladder. However, detailed role of 15-hydroxyprostaglandin dehydrogenase (HPGD) gene remain unclear in prostate cancer. The study was to investigate the correlation between rs8752 that located in the 3'untranslated region (UTR) of the 15-hydroxyprostaglandin dehydrogenase (HPGD) gene and prostate cancer (PCa) risk. Materials and Methods: 109 patients from the First Affiliate Hospital of Soochow University were recruited. According to the results of pathologic diagnosis, all patients were divided into two groups (prostate cancer and benign prostatic hyperplasia). The single-nucleotide polymorphism (SNP) rs8752 was genotyped in all samples by direct sequencing. Results: 54 prostate cancer and 55 BPH patients were included with a median age of 70.41 and 67.62 years, respectively. No statistically significant difference between two groups in patient criteria. The frequency of the GG homozygote and AG+GG genotype were 37.74% and 62.26% in 54 prostate cancer samples, while in 55BPH patients, values were 62.50% and 37.50%. Compared with the GG genotype, the combined GA+AA genotypes had a significantly higher risk of prostate cancer (OR = 2.750; 95% CI: 1.266-5.971, p = 0.011). Furthermore, the risk effect was obtained in subgroups of PCa patient group, the AA+AG genotypes significantly associated with the higher Gleason score samples (AA+AG vs GG: OR = 3.50, 95%CI = 1.106-11.072, p = 0.033) and the risk of pathological stage (AA+AG vs GG: OR = 4.00, 95%CI = 1.253-12.767, p = 0.019). Conclusions: rs8752 in the 3'untranslated region (UTR) of the 15-hydroxyprostaglandin dehydrogenase (HPGD) gene was found to be responsible for the susceptibility to prostate cancer in Chinese individuals.
Collapse
Affiliation(s)
- Xiaofei Qi
- Department of Urology, the First Affiliate Hospital of Soochow University, Suzhou, China
| | - Yu Wang
- Department of Urology, the First Affiliate Hospital of Soochow University, Suzhou, China
| | - Jianquan Hou
- Department of Urology, the First Affiliate Hospital of Soochow University, Suzhou, China
| | - Yuhua Huang
- Department of Urology, the First Affiliate Hospital of Soochow University, Suzhou, China
| |
Collapse
|
37
|
Assis J, Pereira C, Nogueira A, Pereira D, Carreira R, Medeiros R. Genetic variants as ovarian cancer first-line treatment hallmarks: A systematic review and meta-analysis. Cancer Treat Rev 2017; 61:35-52. [PMID: 29100168 DOI: 10.1016/j.ctrv.2017.10.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 10/02/2017] [Accepted: 10/07/2017] [Indexed: 01/13/2023]
Abstract
BACKGROUND The potential predictive value of genetic polymorphisms in ovarian cancer first-line treatment is inconsistently reported. We aimed to review ovarian cancer pharmacogenetic studies to update and summarize the available data and to provide directions for further research. METHODS A systematic review followed by a meta-analysis was conducted on cohort studies assessing the involvement of genetic polymorphisms in ovarian cancer first-line treatment response retrieved through a MEDLINE database search by November 2016. Studies were pooled and summary estimates and 95% confidence intervals (CI) were calculated using random or fixed-effects models as appropriate. RESULTS One hundred and forty-two studies gathering 106871 patients were included. Combined data suggested that GSTM1-null genotype patients have a lower risk of death compared to GSTM1-wt carriers, specifically in advanced stages (hazard ratio (HR), 0.68; 95% CI, 0.48-0.97) and when submitted to platinum-based chemotherapy (aHR, 0.61; 95% CI, 0.39-0.94). ERCC1 rs11615 and rs3212886 might have also a significant impact in treatment outcome (aHR, 0.67; 95% CI, 0.51-0.89; aHR, 1.28; 95% CI, 1.01-1.63, respectively). Moreover, ERCC2 rs13181 and rs1799793 showed a distinct ethnic behavior (Asians: aHR, 1.41; 95% CI, 0.80-2.49; aHR, 1.07; 95% CI, 0.62-1.86; Caucasians: aHR, 0.10; 95% CI, 0.01-0.96; aHR, 0.18; 95% CI, 0.05-0.68, respectively). CONCLUSION(S) The definition of integrative predictive models should encompass genetic information, especially regarding GSTM1 homozygous deletion. Justifying additional pharmacogenetic investigation are variants in ERCC1 and ERCC2, which highlight the DNA Repair ability to ovarian cancer prognosis. Further knowledge could aid to understand platinum-treatment failure and to tailor chemotherapy strategies.
Collapse
Affiliation(s)
- Joana Assis
- Molecular Oncology and Viral Pathology Group - Research Center, Portuguese Institute of Oncology, Porto, Portugal; FMUP, Faculty of Medicine of Porto University, Porto, Portugal
| | - Carina Pereira
- Molecular Oncology and Viral Pathology Group - Research Center, Portuguese Institute of Oncology, Porto, Portugal; CINTESIS, Center for Health Technology and Services Research, FMUP, Porto, Portugal
| | - Augusto Nogueira
- Molecular Oncology and Viral Pathology Group - Research Center, Portuguese Institute of Oncology, Porto, Portugal; FMUP, Faculty of Medicine of Porto University, Porto, Portugal
| | - Deolinda Pereira
- Oncology Department, Portuguese Institute of Oncology, Porto, Portugal
| | - Rafael Carreira
- Centre of Biological Engineering, University of Minho, Braga, Portugal; SilicoLife, Lda, Braga, Portugal
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group - Research Center, Portuguese Institute of Oncology, Porto, Portugal; Research Department, Portuguese League Against Cancer (NRNorte), Porto, Portugal; CEBIMED, Faculty of Health Sciences of Fernando Pessoa University, Porto, Portugal.
| |
Collapse
|
38
|
Wang X, Ivan M, Hawkins SM. The role of MicroRNA molecules and MicroRNA-regulating machinery in the pathogenesis and progression of epithelial ovarian cancer. Gynecol Oncol 2017; 147:481-487. [PMID: 28866430 DOI: 10.1016/j.ygyno.2017.08.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/03/2017] [Accepted: 08/26/2017] [Indexed: 12/20/2022]
Abstract
MicroRNA molecules are small, single-stranded RNA molecules that function to regulate networks of genes. They play important roles in normal female reproductive tract biology, as well as in the pathogenesis and progression of epithelial ovarian cancer. DROSHA, DICER, and Argonaute proteins are components of the microRNA-regulatory machinery and mediate microRNA production and function. This review discusses aberrant expression of microRNA molecules and microRNA-regulating machinery associated with clinical features of epithelial ovarian cancer. Understanding the regulation of microRNA molecule production and function may facilitate the development of novel diagnostic and therapeutic strategies to improve the prognosis of women with epithelial ovarian cancer. Additionally, understanding microRNA molecules and microRNA-regulatory machinery associations with clinical features may influence prevention and early detection efforts.
Collapse
Affiliation(s)
- Xiyin Wang
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Mircea Ivan
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States; Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Shannon M Hawkins
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, United States; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States.
| |
Collapse
|
39
|
An Integrating Approach for Genome-Wide Screening of MicroRNA Polymorphisms Mediated Drug Response Alterations. Int J Genomics 2017; 2017:1674827. [PMID: 28480217 PMCID: PMC5396474 DOI: 10.1155/2017/1674827] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 12/20/2016] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of evolutionarily conserved small noncoding RNAs, ~22 nt in length, and found in diverse organisms and play important roles in the regulation of mRNA translation and degradation. It was shown that miRNAs were involved in many key biological processes through regulating the expression of targets. Genetic polymorphisms in miRNA target sites may alter miRNA regulation and therefore result in the alterations of the drug targets. Recent studies have demonstrated that SNPs in miRNA target sites can affect drug efficiency. However, there are still a large number of specific genetic variants related to drug efficiency that are yet to be discovered. We integrated large scale of genetic variations, drug targets, gene interaction networks, biological pathways, and seeds region of miRNA to identify miRNA polymorphisms affecting drug response. In addition, harnessing the abundant high quality biological network/pathways, we evaluated the cascade distribution of tarSNP impacts. We showed that the predictions can uncover most of the known experimentally supported cases as well as provide informative candidates complementary to existing methods/tools. Although there are several existing databases predicting the gain or loss of targeting function of miRNA mediated by SNPs, such as PolymiRTS, miRNASNP, MicroSNiPer, and MirSNP, none of them evaluated the influences of tarSNPs on drug response alterations. We developed a user-friendly online database of this approach named Mir2Drug.
Collapse
|
40
|
Tian X, Han Y, Yu L, Luo B, Hu Z, Li X, Yang Z, Wang X, Huang W, Wang H, Zhang Q, Ma D. Decreased expression of ALDH5A1 predicts prognosis in patients with ovarian cancer. Cancer Biol Ther 2017; 18:245-251. [PMID: 28346042 DOI: 10.1080/15384047.2017.1295175] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Aldehyde dehydrogenase 5 family, member A1 (ALDH5A1) belongs to the superfamily of aldehyde dehydrogenases (ALDHs). However, the prognostic value of ALDH5A1 in ovarian cancer remains unclear. The aim of this study was to explore the relationship between ALDH5A1 and the prognosis of patients with ovarian cancer (OC). We compared the expression of ALDH5A1 in OC to that innormal controls, using GSE40595 profiling data. Tissue microarray analysis was conducted for192 OC patients, 14 adjacent normal ovary tissues, and 2 normal ovary tissues. Using the "Kaplan-Meier plotter" (KM plotter) database, updated gene expression data and survival information of a total of 1583 OC patients were used to evaluate the prognostic value of ALDH5A1 in OC patients. We found that ALDH5A1 mRNA expression was downregulated in OC patients compared with that innormal tissues. In survival analyses, we found that ALDH5A1 was positively linked to prognosis in patients with OC, particularly in those with serous ovarian cancer (SOC). In addition, high Ctranscription activity of ALDH5A1 was correlated with better overall survival in SOC patients expressing mutatedTP53, but not in those expressing wild-type TP53. In pathological grades II/III, a high mRNA level of ALDH5A1 was associated with improved overall survival. The positive association between ALDH5A1 and prognosis was found not only in early stages(I and II), but also in advanced stages (III and IV) of SOC patients. results indicate that ALDH5A1 is an excellent predictive factor of OC and may play crucial roles in OC progression.
Collapse
Affiliation(s)
- Xun Tian
- a Cancer Biology Research Center, Key Laboratory of Cancer Invasion and Metastasis of the Ministry of Education, Tongji Hospital , Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Yingyan Han
- b Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College , Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Lan Yu
- a Cancer Biology Research Center, Key Laboratory of Cancer Invasion and Metastasis of the Ministry of Education, Tongji Hospital , Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Bo Luo
- c Department of Pathology, The Central Hospital of Wuhan, Tongji Medical College , Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Zheng Hu
- a Cancer Biology Research Center, Key Laboratory of Cancer Invasion and Metastasis of the Ministry of Education, Tongji Hospital , Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China.,d Department of Gynecological Oncology , The First Affiliated Hospital of Sun Yat-sen University, Yuexiu , Guangzhou , Guangdong , China
| | - Xiong Li
- e Department of Obstetrics and Gynecology, Key Laboratory for Molecular Diagnosis of Hubei Province , The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Zongyuan Yang
- a Cancer Biology Research Center, Key Laboratory of Cancer Invasion and Metastasis of the Ministry of Education, Tongji Hospital , Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Xin Wang
- a Cancer Biology Research Center, Key Laboratory of Cancer Invasion and Metastasis of the Ministry of Education, Tongji Hospital , Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Wanqiu Huang
- a Cancer Biology Research Center, Key Laboratory of Cancer Invasion and Metastasis of the Ministry of Education, Tongji Hospital , Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Hui Wang
- b Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College , Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Qinghua Zhang
- e Department of Obstetrics and Gynecology, Key Laboratory for Molecular Diagnosis of Hubei Province , The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Ding Ma
- b Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College , Huazhong University of Science and Technology , Wuhan , Hubei , China
| |
Collapse
|
41
|
Association between Polymorphism of Exportin-5 and Susceptibility to Lead Poisoning in a Chinese Population. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 14:ijerph14010036. [PMID: 28042866 PMCID: PMC5295287 DOI: 10.3390/ijerph14010036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/11/2016] [Accepted: 12/14/2016] [Indexed: 12/28/2022]
Abstract
Lead (Pb) is one of the major contaminants in many industries, and imposes hazardous effects on multiple human organs and systems. Studies have shown that lead is able to induce the alteration of microRNA (miRNA) expression in serum and organs. In this study we investigated whether polymorphisms in miRNA-regulating genes were associated with the risk of lead exposure. We genotyped seven single-nucleotide polymorphisms (SNPs) in 113 lead-sensitive and 113 lead-resistant lead-related Chinese workers by Taqman analysis. The lead-sensitive group showed a significantly higher blood lead level (BLL) than the resistant group based on unconditional logistic regression results. One SNP in XPO5 extron (rs2257082) was significantly associated with lead-poisoning (p = 0.022, odds rate (OR) = 1.63, 95% confidence interval (CI) = 1.07-2.47 in the C allele compared to the T allele). There were no significant associations between the other six SNPs and the blood lead levels. Therefore, polymorphism rs2257082 could be used to distinguish lead-resistant and lead-susceptible populations, and to develop more specific and accurate preventions.
Collapse
|
42
|
Li MP, Hu YD, Hu XL, Zhang YJ, Yang YL, Jiang C, Tang J, Chen XP. MiRNAs and miRNA Polymorphisms Modify Drug Response. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:ijerph13111096. [PMID: 27834829 PMCID: PMC5129306 DOI: 10.3390/ijerph13111096] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/17/2016] [Accepted: 10/31/2016] [Indexed: 12/13/2022]
Abstract
Differences in expression of drug response-related genes contribute to inter-individual variation in drugs’ biological effects. MicroRNAs (miRNAs) are small noncoding RNAs emerging as new players in epigenetic regulation of gene expression at post-transcriptional level. MiRNAs regulate the expression of genes involved in drug metabolism, drug transportation, drug targets and downstream signal molecules directly or indirectly. MiRNA polymorphisms, the genetic variations affecting miRNA expression and/or miRNA-mRNA interaction, provide a new insight into the understanding of inter-individual difference in drug response. Here, we provide an overview of the recent progress in miRNAs mediated regulation of biotransformation enzymes, drug transporters, and nuclear receptors. We also describe the implications of miRNA polymorphisms in cancer chemotherapy response.
Collapse
Affiliation(s)
- Mu-Peng Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Yao-Dong Hu
- Department of Cardiology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi 046000, China.
| | - Xiao-Lei Hu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Yan-Jiao Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Yong-Long Yang
- Haikou People's Hospital and Affiliated Haikou Hospital of Xiangya Medical School, Central South University, Haikou 570311, China.
| | - Chun Jiang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Jie Tang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Xiao-Ping Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| |
Collapse
|
43
|
Sun Y, Tao W, Huang M, Wu X, Gu J. Genetic variants in telomere-maintenance genes are associated with ovarian cancer risk and outcome. J Cell Mol Med 2016; 21:510-518. [PMID: 28233473 PMCID: PMC5323825 DOI: 10.1111/jcmm.12995] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/19/2016] [Indexed: 01/02/2023] Open
Abstract
Most ovarian cancer patients present at an advanced stage with poor prognosis. Telomeres play a critical role in protecting chromosomes stability. The associations of genetic variants in telomere maintenance genes and ovarian cancer risk and outcome are unclear. We genotyped 137 single nucleotide polymorphisms (SNPs) in telomere-maintenance genes in 417 ovarian cancer cases and 417 matched healthy controls to evaluate their associations with cancer risk, survival and therapeutic response. False discovery rate Q-value was calculated to account for multiple testing. Eleven SNPs from two genes showed nominally significant associations with the risks of ovarian cancer. The most significant SNP was TEP1: rs2228026 with participants carrying at least one variant allele exhibiting a 3.28-fold (95% CI: 1.72-6.29; P < 0.001, Q = 0.028) increased ovarian cancer risk, which remained significant after multiple testing adjusting. There was also suggested evidence for the associations of SNPs with outcome, although none of the associations had a Q < 0.05. Seven SNPs from two genes showed associations with ovarian cancer survival (P < 0.05). The strongest association was found in TNKS gene (rs10093972, hazard ratio = 1.88; 95% CI: 1.20-2.92; P = 0.006, Q = 0.076). Five SNPs from four genes showed suggestive associations with therapeutic response (P < 0.05). In a survival tree analysis, TEP1:rs10143407 was the primary factor contributing to overall survival. Unfavourable genotype analysis showed a cumulative effect of significant SNPs on ovarian cancer risk, survival and therapeutic response. Genetic variations in telomere-maintenance genes may be associated with ovarian cancer risk and outcome.
Collapse
Affiliation(s)
- Yuhui Sun
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wade Tao
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maosheng Huang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jian Gu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| |
Collapse
|
44
|
Role of let-7 family microRNA in breast cancer. Noncoding RNA Res 2016; 1:77-82. [PMID: 30159414 PMCID: PMC6096426 DOI: 10.1016/j.ncrna.2016.10.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 10/29/2016] [Accepted: 10/29/2016] [Indexed: 02/06/2023] Open
Abstract
Metastasis and resistance to therapy significantly contribute to cancer-related deaths. Growing body of evidence suggest that altered expression of microRNAs (miRNAs) is one of the root cause of adverse clinical outcome. miRNAs such as let-7 are the new fine tuners of signaling cascade and cellular processes which regulates the genes in post-transcriptional manner. In this review, we described the regulation of let-7 expression and the involvement of molecular factors in this process. We discussed the mechanism by which let-7 alter the expression of genes involved in the process of tumorigenesis. Further, we listed the pathways targeted by let-7 to reduce the burden of the tumor. In addition, we described the role of let-7 in breast cancer metastasis and stemness properties. This article will provide the in-depth insight into the biology of let-7 miRNA and its role in the breast cancer progression.
Collapse
|
45
|
Peckham-Gregory EC, Thapa DR, Martinson J, Duggal P, Penugonda S, Bream JH, Chang PY, Dandekar S, Chang SC, Detels R, Martínez-Maza O, Zhang ZF, Hussain SK. MicroRNA-related polymorphisms and non-Hodgkin lymphoma susceptibility in the Multicenter AIDS Cohort Study. Cancer Epidemiol 2016; 45:47-57. [PMID: 27701053 DOI: 10.1016/j.canep.2016.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/12/2016] [Accepted: 09/19/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND MicroRNAs, small non-coding RNAs involved in gene regulation, are implicated in lymphomagenesis. We evaluated whether genetic variations in microRNA coding regions, binding sites, or biogenesis genes (collectively referred to as miRNA-SNPs) were associated with risk of AIDS-associated non-Hodgkin lymphoma (AIDS-NHL), and serum levels of four lymphoma-related microRNAs. METHODS Twenty-five miRNA-SNPs were genotyped in 180 AIDS-NHL cases and 529 HIV-infected matched controls from the Multicenter AIDS Cohort Study (MACS), and real-time polymerase chain reaction was used to quantify serum microRNA levels. Adjusted odds ratios (ORs) estimated using conditional logistic regression evaluated associations between miRNA-SNPs and AIDS-NHL risk. A semi-Bayes shrinkage approach was employed to reduce likelihood of false-positive associations. Adjusted mean ratios (MR) calculated using linear regression assessed associations between miRNA-SNPs and serum microRNA levels. RESULTS DDX20 rs197412, a non-synonymous miRNA biogenesis gene SNP, was associated with AIDS-NHL risk (OR=1.34 per minor allele; 95% CI: 1.02-1.75), and higher miRNA-222 serum levels nearing statistical significance (MR=1.21 per minor allele; 95% CI: 0.98-1.49). MiRNA-196a2 rs11614913 was associated with decreased central nervous system (CNS) AIDS-NHL (CT vs. CC OR=0.52; 95% CI: 0.27-0.99). The minor allele of HIF1A rs2057482, which creates a miRNA-196a2 binding site, was associated with systemic AIDS-NHL risk (OR=1.73 per minor allele; 95% CI: 1.12-2.67), and decreased CNS AIDS-NHL risk (OR=0.49 per minor allele; 95% CI: 0.25-0.94). CONCLUSIONS This study suggests that a few miRNA-SNPs are associated with AIDS-NHL risk and may modulate miRNA expression. These results support a role for miRNA in AIDS-NHL and may highlight pathways to be targeted for risk stratification or therapeutics.
Collapse
Affiliation(s)
- Erin C Peckham-Gregory
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles (UCLA), Box 951772, 71-267 CHS, Los Angeles, CA 90095-1772, USA.
| | - Dharma R Thapa
- Departments of Obstetrics and Gynecology, and Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, UCLA, Box 951740, 153 BSRB, Los Angeles, CA 90095-1740, USA
| | - Jeremy Martinson
- Department of Infectious Disease and Microbiology, Graduate School of Public Health, University of Pittsburgh, 403 Parran Hall, 130 DeSoto Street, Pittsburgh, PA 15261, USA
| | - Priya Duggal
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe Street, Room E6539, Baltimore, MD 21205, USA
| | - Sudhir Penugonda
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, 645 North Michigan Avenue, Suite 900, Chicago, IL 60611, USA
| | - Jay H Bream
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe Street, Room E5624, Baltimore, MD 21205, USA
| | - Po-Yin Chang
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles (UCLA), Box 951772, 71-267 CHS, Los Angeles, CA 90095-1772, USA
| | - Sugandha Dandekar
- The UCLA Genotyping and Sequencing Core, Department of Human Genetics, David Geffen School of Medicine, UCLA, CHS 36-125, 650 Charles E Young Drive South, Los Angeles, CA 90095, USA
| | - Shen-Chih Chang
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles (UCLA), Box 951772, 71-267 CHS, Los Angeles, CA 90095-1772, USA
| | - Roger Detels
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles (UCLA), Box 951772, 71-267 CHS, Los Angeles, CA 90095-1772, USA
| | - Otoniel Martínez-Maza
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles (UCLA), Box 951772, 71-267 CHS, Los Angeles, CA 90095-1772, USA; Departments of Obstetrics and Gynecology, and Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, UCLA, Box 951740, 153 BSRB, Los Angeles, CA 90095-1740, USA; Jonsson Comprehensive Cancer Center, UCLA, Box 951740, 153 BSRB, Los Angeles, CA 90095-1740, USA; UCLA AIDS Institute, UCLA, Box 951740, 153 BSRB, Los Angeles, CA 90095-1740, USA
| | - Zuo-Feng Zhang
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles (UCLA), Box 951772, 71-267 CHS, Los Angeles, CA 90095-1772, USA
| | - Shehnaz K Hussain
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles (UCLA), Box 951772, 71-267 CHS, Los Angeles, CA 90095-1772, USA; Department of Medicine and Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, 8700 Beverly Blvd, West Hollywood, CA 90048, USA
| |
Collapse
|
46
|
Fang X, Yin Z, Li X, Xia L, Zhou B. Polymorphisms in GEMIN4 and AGO1 Genes Are Associated with the Risk of Lung Cancer: A Case-Control Study in Chinese Female Non-Smokers. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:ijerph13100939. [PMID: 27669275 PMCID: PMC5086678 DOI: 10.3390/ijerph13100939] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 09/06/2016] [Accepted: 09/19/2016] [Indexed: 02/07/2023]
Abstract
MicroRNA biosynthesis genes can affect the regulatory effect of global microRNAs to target mRNA and hence influence the genesis and development of human cancer. Here, we selected five single nucleotide polymorphisms (SNPs) (rs7813, rs2740349, rs2291778, rs910924, rs595961) in two key microRNA biosynthesis genes (GEMIN4 and AGO1) and systematically evaluated the association between these SNPs, the gene-environment interaction and lung cancer risk. To control the impact of cigarette smoking on lung cancer, we recruited Chinese female non-smokers for the study. The total number of lung cancer cases and cancer-free controls were 473 and 395 in the case-control study. Four SNPs showed statistically significant associations with lung cancer risk. After Bonferroni correction, rs7813 and rs595961 were evidently still associated with lung cancer risk. In the stratified analysis, our results revealed that all five SNPs were associated with the risk of lung adenocarcinoma; after Bonferroni correction, significant association was maintained for rs7813, rs910924 and rs595961. Haplotype analysis showed GEMIN4 haplotype C-A-G-T was a protective haplotype for lung cancer. In the combined unfavorable genotype analysis, with the increasing number of unfavorable genotypes, a progressively increased gene-dose effect was observed in lung adenocarcinoma. We also found that individuals exposed to cooking oil fumes showed a relatively high risk of lung cancer, but no interactions were found between cooking oil fume exposure or passive smoking exposure with these SNPs, either on an additive scale or a multiplicative scale. Overall, this is the first study showing that rs7813 and rs595961 could be meaningful as genetic markers for lung cancer risk.
Collapse
Affiliation(s)
- Xue Fang
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110122, China.
- Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang 110122, China.
| | - Zhihua Yin
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110122, China.
- Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang 110122, China.
| | - Xuelian Li
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110122, China.
- Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang 110122, China.
| | - Lingzi Xia
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110122, China.
- Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang 110122, China.
| | - Baosen Zhou
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110122, China.
- Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang 110122, China.
| |
Collapse
|
47
|
Variation in the Dicer and RAN Genes Are Associated with Survival in Patients with Hepatocellular Carcinoma. PLoS One 2016; 11:e0162279. [PMID: 27611467 PMCID: PMC5017754 DOI: 10.1371/journal.pone.0162279] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 08/20/2016] [Indexed: 01/14/2023] Open
Abstract
Single-nucleotide polymorphisms (SNPs) in microRNA machinery genes might affect microRNA processing and subsequently impact tumorigenesis. The aim of this study was to investigate the associations between SNPs in microRNA machinery genes and hepatocellular carcinoma (HCC) in a Korean population. Genotyping of six SNPs in microRNA machinery genes was performed using blood samples from 147 patients with HCC and 209 healthy control subjects. None of the six SNPs in microRNA machinery genes were significantly associated with HCC development. However, among the models for six polymorphic loci—DICER (rs3742330 and rs13078), DROSHA (rs10719 and rs6877842), RAN (rs14035) and XPO5 (rs11077)—one allele combination (A-A-T-C-C-C) showed synergistic effects in terms of an increased risk of HCC development (odds ratio = 8.881, 95% confidence interval [CI] = 1.889–41.750; P = 0.002). Multivariate Cox proportional hazard regression analysis showed a significant survival benefit for the DICER rs3742330 GG compared with the AA type (hazard ratio [HR], 0.314; 95% CI, 0.135–0.730; P = 0.007) and for the RAN rs14035 CT compared with the CC genotype (HR, 0.587; 95% CI, 0.349–0.987; P = 0.044). Although we found no direct association between DICER (rs3742330 and rs13078), DROSHA (rs10719 and rs6877842), RAN (rs14035) or XPO5 (rs11077) polymorphisms and HCC risk, we demonstrated that DICER (rs3742330) and RAN (rs14035) were associated with the survival of HCC patients. Future studies with larger samples are needed to determine associations of SNPs in microRNA machinery genes with HCC risk and prognosis.
Collapse
|
48
|
Unraveling the roles of Atg4 proteases from autophagy modulation to targeted cancer therapy. Cancer Lett 2016; 373:19-26. [DOI: 10.1016/j.canlet.2016.01.022] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/12/2016] [Accepted: 01/12/2016] [Indexed: 11/22/2022]
|
49
|
Li R, Pu X, Chang JY, Ye Y, Komaki R, Minna JD, Roth JA, Han B, Wu X. MiRNA-Related Genetic Variations Associated with Radiotherapy-Induced Toxicities in Patients with Locally Advanced Non-Small Cell Lung Cancer. PLoS One 2016; 11:e0150467. [PMID: 26991123 PMCID: PMC4798772 DOI: 10.1371/journal.pone.0150467] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 02/15/2016] [Indexed: 12/12/2022] Open
Abstract
Severe radiation-induced toxicities limit treatment efficacy and compromise outcomes of lung cancer. We aimed to identify microRNA-related genetic variations as biomarkers for the prediction of radiotherapy-induced acute toxicities. We genotyped 233 SNPs (161 in microRNA binding site and 72 in processing gene) and analyzed their associations with pneumonitis and esophagitis in 167 stage III NSCLC patients received definitive radiation therapy. Sixteen and 11 SNPs were associated with esophagitis and pneumonitis, respectively. After multiple comparison correction, RPS6KB2:rs10274, SMO:rs1061280, SMO:rs1061285 remained significantly associated with esophagitis, while processing gene DGCR8:rs720014, DGCR8:rs3757, DGCR8:rs1633445 remained significantly associated with pneumonitis. Patients with the AA genotype of RPS6KB2:rs10274 had an 81% reduced risk of developing esophagitis (OR: 0.19, 95% CI: 0.07–0.51, p = 0.001, q = 0.06). Patients with the AG+GG genotype of SMO:rs1061280 had an 81% reduced risk of developing esophagitis (OR: 0.19, 95% CI: 0.07–0.53, p = 0.001, q = 0.06). Patients with the GG+GA genotype of DGCR8:rs720014 had a 3.54-fold increased risk of pneumonitis (OR: 3.54, 95% CI: 1.65–7.61, p <0.05, q <0.1). Significantly cumulative effects of the top SNPs were observed for both toxicities (P-trend <0.001). Using bioinformatics tools, we found that the genotype of rs10274 was associated with altered expression of the RPS6KB2 gene. Gene-based analysis showed DGCR8 (p = 0.010) and GEMIN4 (p = 0.039) were the top genes associated with the risk of developing pneumonitis. Our results provide strong evidence that microRNA-related genetic variations contribute to the development of radiotherapy-induced acute esophagitis and pneumonitis and could thus serve as biomarkers to help accurately predict radiotherapy-induced toxicity in NSCLC patients.
Collapse
Affiliation(s)
- Rong Li
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, West Huaihai Road 241, Shanghai, China
| | - Xia Pu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Joe Y. Chang
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Yuanqing Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Ritsuko Komaki
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - John D. Minna
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, United States of America
| | - Jack A. Roth
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, West Huaihai Road 241, Shanghai, China
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail:
| |
Collapse
|
50
|
Zhu W, Zhao J, He J, Qi D, Wang L, Ma X, Liu P. Genetic variants in the MicroRNA biosynthetic pathway Gemin3 and Gemin4 are associated with a risk of cancer: a meta-analysis. PeerJ 2016; 4:e1724. [PMID: 27019773 PMCID: PMC4806601 DOI: 10.7717/peerj.1724] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/01/2016] [Indexed: 01/22/2023] Open
Abstract
The effects of the microRNA (miRNA) processing genes Gemin3 and Gemin4 on cellular signaling pathways could have a major impact on the risk of cancer. Several studies concerning the association between the Gemin3 rs197412, Gemin4 rs7813 and Gemin4 rs2740348 polymorphisms with cancer susceptibility have been published. The present meta-analysis summarized this evidence and evaluated the precision of these relationships. Relevant studies (published prior to December 16th, 2015) without language restriction were identified using the PubMed, Web of Science and China National Knowledge Infrastructure (CNKI) on-line databases. The data were extracted from the eligible studies and were processed using Stata 12.0 software. Seven studies (2,588 cases and 2,549 controls) indicated that the rs7813 polymorphism was significantly associated with increased cancer risk (TT vs TC + CC, OR = 1.18 95% CI [1.05–1.32]). Six studies (1,314 cases and 1,244 controls) indicated that rs2740348 was associated with an increased cancer risk (GG vs. GC + CC, OR = 1.41 95% CI [1.00–1.83]). However the rs197412 polymorphism was not associated with an increased cancer risk (OR = 0.97 95% CI [0.80–1.19]). Our results suggest that the Gemin4 rs7813 T > C and rs2740348 G > C polymorphisms are associated with cancer susceptibility.
Collapse
Affiliation(s)
- Wenbo Zhu
- Public Health, Southeast University , Nanjing, Jiangsu , China
| | - Jun Zhao
- National Research Institute for Family Planning, National Research Institute for Family Planning , Beijing , China
| | - Jieyu He
- Public Health, Southeast University , Nanjing, Jiangsu , China
| | - Daxun Qi
- National Research Institute for Family Planning, National Research Institute for Family Planning , Beijing , China
| | - Lina Wang
- Public Health, Southeast University , Nanjing, Jiangsu , China
| | - Xu Ma
- National Research Institute for Family Planning, National Research Institute for Family Planning , Beijing , China
| | - Pei Liu
- Public Health, Southeast University , Nanjing, Jiangsu , China
| |
Collapse
|