1
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Zhuang S, Yang Z, Cui Z, Zhang Y, Che F. Epigenetic alterations and advancement of lymphoma treatment. Ann Hematol 2024; 103:1435-1454. [PMID: 37581713 DOI: 10.1007/s00277-023-05395-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/29/2023] [Indexed: 08/16/2023]
Abstract
Lymphomas, complex and heterogeneous malignant tumors, originate from the lymphopoietic system. These tumors are notorious for their high recurrence rates and resistance to treatment, which leads to poor prognoses. As ongoing research has shown, epigenetic modifications like DNA methylation, histone modifications, non-coding RNA regulation, and RNA modifications play crucial roles in lymphoma pathogenesis. Epigenetic modification-targeting drugs have exhibited therapeutic efficacy and tolerability in both monotherapy and combination lymphoma therapy. This review discusses pathogenic mechanisms and potential epigenetic therapeutic targets in common lymphomas, offering new avenues for lymphoma diagnosis and treatment. We also discuss the shortcomings of current lymphoma treatments, while suggesting potential areas for future research, in order to improve the prediction and prognosis of lymphoma.
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Affiliation(s)
- Shuhui Zhuang
- Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang, China
- Department of Hematology, Linyi People's Hospital, Shandong University, Linyi, 276000, Shandong, China
| | - Zhaobo Yang
- Spine Surgery, Linyi People's Hospital, Shandong University, Linyi, 276000, Shandong, China
| | - Zhuangzhuang Cui
- Department of Hematology, Linyi People's Hospital, Shandong University, Linyi, 276000, Shandong, China
| | - Yuanyuan Zhang
- Department of Hematology, Linyi People's Hospital, Shandong University, Linyi, 276000, Shandong, China.
- Department of Hematology, Shandong Key Laboratory of Immunohematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, People's Republic of China.
| | - Fengyuan Che
- Department of Neurology, Central Laboratory and Key Laboratory of Neurophysiology, Linyi People's Hospital, Shandong University, Linyi, 276000, China.
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2
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Gu Y, Wang M, Gong Y, Li X, Wang Z, Wang Y, Jiang S, Zhang D, Li C. Unveiling breast cancer risk profiles: a survival clustering analysis empowered by an online web application. Future Oncol 2023; 19:2651-2667. [PMID: 38095059 DOI: 10.2217/fon-2023-0736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
Aim: To develop a shiny app for doctors to investigate breast cancer treatments through a new approach by incorporating unsupervised clustering and survival information. Materials & methods: Analysis is based on the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) dataset, which contains 1726 subjects and 22 variables. Cox regression was used to identify survival risk factors for K-means clustering. Logrank tests and C-statistics were compared across different cluster numbers and Kaplan-Meier plots were presented. Results & conclusion: Our study fills an existing void by introducing a unique combination of unsupervised learning techniques and survival information on the clinician side, demonstrating the potential of survival clustering as a valuable tool in uncovering hidden structures based on distinct risk profiles.
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Affiliation(s)
- Yuan Gu
- Department of Statistics, The George Washington University, Washington, DC 20052, USA
| | - Mingyue Wang
- Department of Mathematics, Syracuse University, Syracuse, NY 13244, USA
| | - Yishu Gong
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, NY 02115, USA
| | - Xin Li
- Department of Statistics, The George Washington University, Washington, DC 20052, USA
| | - Ziyang Wang
- Department of Computer Science, University of Oxford, Oxford, OX1 3QD, UK
| | - Yuli Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Song Jiang
- Department of Biochemistry, Huzhou Institute of Biological Products Co., Ltd., 313017, China
| | - Dan Zhang
- Department of Information Science and Engineering, Shandong University, Shan Dong, China
| | - Chen Li
- Department of Biology, Chemistry and Pharmacy, Free University of Berlin, Berlin, 14195, Germany
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3
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Thiel KW, Newtson AM, Devor EJ, Zhang Y, Malmrose PK, Bi J, Losh HA, Davies S, Smith LE, Padilla J, Leiva SM, Grueter CE, Breheny P, Hagan CR, Pufall MA, Gertz J, Guo Y, Leslie KK. Global expression analysis of endometrial cancer cells in response to progesterone identifies new therapeutic targets. J Steroid Biochem Mol Biol 2023; 234:106399. [PMID: 37716459 DOI: 10.1016/j.jsbmb.2023.106399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/06/2023] [Accepted: 09/12/2023] [Indexed: 09/18/2023]
Abstract
Progesterone prevents development of endometrial cancers through its receptor (PR) although the molecular mechanisms have yet to be fully characterized. In this study, we performed a global analysis of gene regulation by progesterone using human endometrial cancer cells that expressed PR endogenously or exogenously. We found progesterone strongly inhibits multiple components of the platelet derived growth factor receptor (PDGFR), Janus kinase (JAK), signal transducer and activator of transcription (STAT) pathway through PR. The PDGFR/JAK/STAT pathway signals to control numerous downstream targets including AP-1 transcription factors Fos and Jun. Treatment with inhibitors of the PDGFR/JAK/STAT pathway significantly blocked proliferation in multiple novel patient-derived organoid models of endometrial cancer, and activation of this pathway was found to be a poor prognostic signal for the survival of patients with endometrial cancer from The Cancer Genome Atlas. Our study identifies this pathway as central to the growth-limiting effects of progesterone in endometrial cancer and suggests that inhibitors of PDGFR/JAK/STAT should be considered for future therapeutic interventions.
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Affiliation(s)
- Kristina W Thiel
- Department of Obstetrics and Gynecology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA; Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | - Andreea M Newtson
- Department of Obstetrics and Gynecology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA; Department of Obstetrics and Gynecology, University of Nebraska, Omaha, NE, USA
| | - Eric J Devor
- Department of Obstetrics and Gynecology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA; Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | - Yuping Zhang
- Department of Obstetrics and Gynecology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Paige K Malmrose
- Department of Obstetrics and Gynecology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Jianling Bi
- Department of Obstetrics and Gynecology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Haley A Losh
- Department of Obstetrics and Gynecology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Suzy Davies
- Department of Neurosciences, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Lane E Smith
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, USA
| | - Jamie Padilla
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, USA
| | - Stephanie M Leiva
- Department of Obstetrics and Gynecology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Chad E Grueter
- Department of Internal Medicine, Carver College of Medicine, the University of Iowa, Iowa City, IA, USA
| | - Patrick Breheny
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA; Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - Christy R Hagan
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Miles A Pufall
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, IA, USA
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Yan Guo
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, USA
| | - Kimberly K Leslie
- Department of Obstetrics and Gynecology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA; Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA; Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, USA.
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4
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Yu H, Jiang L, Li CI, Ness S, Piccirillo SGM, Guo Y. Somatic mutation effects diffused over microRNA dysregulation. Bioinformatics 2023; 39:btad520. [PMID: 37624931 PMCID: PMC10474951 DOI: 10.1093/bioinformatics/btad520] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/14/2023] [Accepted: 08/23/2023] [Indexed: 08/27/2023] Open
Abstract
MOTIVATION As an important player in transcriptome regulation, microRNAs may effectively diffuse somatic mutation impacts to broad cellular processes and ultimately manifest disease and dictate prognosis. Previous studies that tried to correlate mutation with gene expression dysregulation neglected to adjust for the disparate multitudes of false positives associated with unequal sample sizes and uneven class balancing scenarios. RESULTS To properly address this issue, we developed a statistical framework to rigorously assess the extent of mutation impact on microRNAs in relation to a permutation-based null distribution of a matching sample structure. Carrying out the framework in a pan-cancer study, we ascertained 9008 protein-coding genes with statistically significant mutation impacts on miRNAs. Of these, the collective miRNA expression for 83 genes showed significant prognostic power in nine cancer types. For example, in lower-grade glioma, 10 genes' mutations broadly impacted miRNAs, all of which showed prognostic value with the corresponding miRNA expression. Our framework was further validated with functional analysis and augmented with rich features including the ability to analyze miRNA isoforms; aggregative prognostic analysis; advanced annotations such as mutation type, regulator alteration, somatic motif, and disease association; and instructive visualization such as mutation OncoPrint, Ideogram, and interactive mRNA-miRNA network. AVAILABILITY AND IMPLEMENTATION The data underlying this article are available in MutMix, at http://innovebioinfo.com/Database/TmiEx/MutMix.php.
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Affiliation(s)
- Hui Yu
- Department of Public Health, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, U.S.A
| | - Limin Jiang
- Department of Public Health, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, U.S.A
| | - Chung-I Li
- Department of Statistics, National Cheng Kung University, Tainan 701401, Taiwan
| | - Scott Ness
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87109, United States
| | - Sara G M Piccirillo
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87109, United States
| | - Yan Guo
- Department of Public Health, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, U.S.A
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5
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Chronological horse herd optimization-based gene selection with deep learning towards survival prediction using PAN-Cancer gene-expression data. Biomed Signal Process Control 2023. [DOI: 10.1016/j.bspc.2023.104696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
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6
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Jiang L, Yu H, Guo Y. Modeling the relationship between gene expression and mutational signature. QUANTITATIVE BIOLOGY 2023; 11:31-43. [PMID: 37032811 PMCID: PMC10078980 DOI: 10.15302/j-qb-022-0309] [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] [Indexed: 04/11/2023]
Abstract
Background Mutational signatures computed from somatic mutations, allow an in-depth understanding of tumorigenesis and may illuminate early prevention strategies. Many studies have shown the regulation effects between somatic mutation and gene expression dysregulation. Methods We hypothesized that there are potential associations between mutational signature and gene expression. We capitalized upon RNA-seq data to model 49 established mutational signatures in 33 cancer types. Both accuracy and area under the curve were used as performance measures in five-fold cross-validation. Results A total of 475 models using unconstrained genes, and 112 models using protein-coding genes were selected for future inference purposes. An independent gene expression dataset on lung cancer smoking status was used for validation which achieved over 80% for both accuracy and area under the curve. Conclusion These results demonstrate that the associations between gene expression and somatic mutations can translate into the associations between gene expression and mutational signatures.
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7
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Ding Y, Li X, Li J. COVID-19–associated lncRNAs as predictors of survival in uterine corpus endometrial carcinoma: A prognostic model. Front Genet 2022; 13:986453. [PMID: 36147497 PMCID: PMC9486303 DOI: 10.3389/fgene.2022.986453] [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: 07/05/2022] [Accepted: 08/08/2022] [Indexed: 12/05/2022] Open
Abstract
Background: Patients with uterine corpus endometrial carcinoma (UCEC) may be susceptible to the coronavirus disease-2019 (COVID-19). Long non–coding RNAs take on a critical significance in UCEC occurrence, development, and prognosis. Accordingly, this study aimed to develop a novel model related to COVID-19–related lncRNAs for optimizing the prognosis of endometrial carcinoma. Methods: The samples of endometrial carcinoma patients and the relevant clinical data were acquired in the Carcinoma Genome Atlas (TCGA) database. COVID-19–related lncRNAs were analyzed and obtained by coexpression. Univariate, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analyses were performed to establish a COVID-19–related lncRNA risk model. Kaplan–Meier analysis, principal component analysis (PCA), and functional enrichment annotation were used to analyze the risk model. Finally, the potential immunotherapeutic signatures and drug sensitivity prediction targeting this model were also discussed. Results: The risk model comprising 10 COVID-19–associated lncRNAs was identified as a predictive ability for overall survival (OS) in UCEC patients. PCA analysis confirmed a reliable clustering ability of the risk model. By regrouping the patients with this model, different clinic-pathological characteristics, immunotherapeutic response, and chemotherapeutics sensitivity were also observed in different groups. Conclusion: This risk model was developed based on COVID-19–associated lncRNAs which would be conducive to the precise treatment of patients with UCEC.
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Affiliation(s)
- Yang Ding
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shatin, HongKong, China
| | - Xia Li
- Department of Obstetrics and Gynaecology, Heze Municipal Hospital, Heze, Shandong, China
| | - Jiena Li
- Department of Obstetrics and Gynaecology, Heze Municipal Hospital, Heze, Shandong, China
- *Correspondence: Jiena Li, ; Liqun Zhu,
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8
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Pu J, Yu H, Guo Y. A Novel Strategy to Identify Prognosis-Relevant Gene Sets in Cancers. Genes (Basel) 2022; 13:862. [PMID: 35627247 PMCID: PMC9141699 DOI: 10.3390/genes13050862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 11/16/2022] Open
Abstract
Molecular prognosis markers hold promise for improved prediction of patient survival, and a pathway or gene set may add mechanistic interpretation to their prognostic prediction power. In this study, we demonstrated a novel strategy to identify prognosis-relevant gene sets in cancers. Our study consists of a first round of gene-level analyses and a second round of gene-set-level analyses, in which the Composite Gene Expression Score critically summarizes a surrogate expression value at gene set level and a permutation procedure is exerted to assess prognostic significance of gene sets. An optional differential coexpression module is appended to the two phases of survival analyses to corroborate and refine prognostic gene sets. Our strategy was demonstrated in 33 cancer types across 32,234 gene sets. We found oncogenic gene sets accounted for an increased proportion among the final gene sets, and genes involved in DNA replication and DNA repair have ubiquitous prognositic value for multiple cancer types. In summary, we carried out the largest gene set based prognosis study to date. Compared to previous similar studies, our approach offered multiple improvements in design and methodology implementation. Functionally relevant gene sets of ubiquitous prognostic significance in multiple cancer types were identified.
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Affiliation(s)
- Junyi Pu
- School of Life Sciences, Northwest University, Xi’an 710069, China;
| | - Hui Yu
- Comprehensive Cancer Center, New Mexico University, Albuquerque, NM 87131, USA;
| | - Yan Guo
- Comprehensive Cancer Center, New Mexico University, Albuquerque, NM 87131, USA;
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9
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Jia L, Zhang Y, Pu F, Yang C, Yang S, Yu J, Xu Z, Yang H, Zhou Y, Zhu S. Pseudogene AK4P1 promotes pancreatic ductal adenocarcinoma progression through relieving miR-375-mediated YAP1 degradation. Aging (Albany NY) 2022; 14:1983-2003. [PMID: 35220277 PMCID: PMC8908928 DOI: 10.18632/aging.203921] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/22/2022] [Indexed: 11/25/2022]
Abstract
Pseudogenes have been reported to play oncogenic or tumor-suppressive roles in cancer progression. However, the molecular mechanism of most pseudogenes in pancreatic ductal adenocarcinoma (PDAC) remains unknown. Herein, we characterized a novel pseudogene-miRNA-mRNA network associated with PDAC progression using bioinformatics analysis. After screening by dreamBase and GEPIA, 12 up-regulated and 7 down-regulated differentially expressed pseudogenes (DEPs) were identified. According to survival analysis, only elevated AK4P1 indicated a poor prognosis for PDAC patients. Moreover, we found that AK4 acts as a cognate gene of AK4P1 and also predicts worse survival for PDAC patients. Furthermore, 32 miRNAs were predicted to bind to AK4P1 by starBase, among which miR-375 was identified as the most potential binding miRNA of AK4P1. A total of 477 potential target genes of miR-375 were obtained by miRNet, in which 49 hub genes with node degree ≥ 20 were identified by STRING. Subsequent analysis for hub genes demonstrated that YAP1 may be a functional downstream target of AK4P1. To confirmed the above findings, microarray, and qRT-PCR assay revealed that YAP1 was dramatically upregulated in both PDAC cells and tissues. Functional experiments showed that knockdown of YAP1 significantly suppressed PDAC cells growth, increased apoptosis, and decreased the ability of invasion. In conclusion, amplification of AK4P1 may fuel the onset and development of PDAC by targeting YAP1 through competitively binding to miR-375, and serve as a promising biomarker and therapeutic target for PDAC.
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Affiliation(s)
- Lang Jia
- Organ Transplant Center, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- School of Clinical Medicine, Southwest Medical University, Luzhou 646000, China
| | - Yun Zhang
- Organ Transplant Center, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
| | - Feng Pu
- Organ Transplant Center, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
| | - Chong Yang
- Organ Transplant Center, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
| | - Shula Yang
- Organ Transplant Center, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
| | - Jinze Yu
- Organ Transplant Center, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
| | - Zihan Xu
- Organ Transplant Center, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
| | - Hongji Yang
- Organ Transplant Center, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 611731, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
| | - Yu Zhou
- Human Disease Gene Study Key Laboratory of Sichuan Province, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
| | - Shikai Zhu
- Organ Transplant Center, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 611731, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
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10
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Jiang L, Yu H, Ness S, Mao P, Guo F, Tang J, Guo Y. Comprehensive Analysis of Co-Mutations Identifies Cooperating Mechanisms of Tumorigenesis. Cancers (Basel) 2022; 14:415. [PMID: 35053577 PMCID: PMC8774165 DOI: 10.3390/cancers14020415] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 12/16/2022] Open
Abstract
Somatic mutations are one of the most important factors in tumorigenesis and are the focus of most cancer-sequencing efforts. The co-occurrence of multiple mutations in one tumor has gained increasing attention as a means of identifying cooperating mutations or pathways that contribute to cancer. Using multi-omics, phenotypical, and clinical data from 29,559 cancer subjects and 1747 cancer cell lines covering 78 distinct cancer types, we show that co-mutations are associated with prognosis, drug sensitivity, and disparities in sex, age, and race. Some co-mutation combinations displayed stronger effects than their corresponding single mutations. For example, co-mutation TP53:KRAS in pancreatic adenocarcinoma is significantly associated with disease specific survival (hazard ratio = 2.87, adjusted p-value = 0.0003) and its prognostic predictive power is greater than either TP53 or KRAS as individually mutated genes. Functional analyses revealed that co-mutations with higher prognostic values have higher potential impact and cause greater dysregulation of gene expression. Furthermore, many of the prognostically significant co-mutations caused gains or losses of binding sequences of RNA binding proteins or micro RNAs with known cancer associations. Thus, detailed analyses of co-mutations can identify mechanisms that cooperate in tumorigenesis.
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Affiliation(s)
- Limin Jiang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China;
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin 300350, China
| | - Hui Yu
- Department of Internal Medicine, Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA; (H.Y.); (S.N.); (P.M.)
| | - Scott Ness
- Department of Internal Medicine, Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA; (H.Y.); (S.N.); (P.M.)
| | - Peng Mao
- Department of Internal Medicine, Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA; (H.Y.); (S.N.); (P.M.)
| | - Fei Guo
- School of Computer Science and Engineering, Central South University, Changsha 410083, China;
| | - Jijun Tang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China;
| | - Yan Guo
- Department of Internal Medicine, Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA; (H.Y.); (S.N.); (P.M.)
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11
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Song Z, Wang J. LncRNA ASMTL-AS1/microRNA-1270 differentiate prognostic groups in gastric cancer and influence cell proliferation, migration and invasion. Bioengineered 2022; 13:1507-1517. [PMID: 34986743 PMCID: PMC8805870 DOI: 10.1080/21655979.2021.2021063] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The objective of this study was to determine the expression levels of ASMTL-AS1 and miR-1270 in gastric cancer, and to explore whether ASMTL-AS1 and miR-1270 is associated with cancer prognosis and progression or not. ASMTL-AS1 and miR-1270 expression were quantified in gastric cancer tissues and adjacent normal tissues (n = 167) and cell lines. The potential of ASMTL-AS1 and miR-1270 as prognostic biomarkers was evaluated by the receiver operating characteristic (ROC) curve, Kaplan-Meier, and multivariate Cox regression analyses. The binding between ASMTL-AS1 and miR-1270 was verified by the Luciferase reporter assay and RNA pull-down assay. Functional roles of ASMTL-AS1/miR-1270 on cells were investigated in HGC-27 and NCI-N87 cells by MTS viability, Transwell migration, and Matrigel invasion assay. ASMTL-AS1 was significantly downregulated while miR-1270 was upregulated in gastric cancer tissues as compared with normal tissue and cell lines. According to the studies, ASMTL-AS1 and miR-1270 were related to unfavorable clinical parameters, such as the advanced TNM stage. Downregulated ASMTL-AS1 and upregulated miR-1270 were associated with reduced 5-year overall survival. Functional studies suggested that ASMTL-AS1 inhibits proliferation, migration, and invasion of HGC-27 and NCI-N87 cells by regulation of miR-1270. In summary, ASMTL-AS1 and miR-1270 are associated with poor prognosis of patients with gastric cancer. ASMTL-AS1 inhibited gastric cancer progression by regulating miR-1270. Therefore, ASMTL-AS1/miR-1270 may be a potential prognostic biomarker and novel strategy for gastric cancer targeted therapy.
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Affiliation(s)
- Zhenhe Song
- Department of Gastroenterology, Weihai Municipal Hospital, Cheeloo College of Medicine, Shandong University, Weihai, Shandong, China
| | - Jian Wang
- Department of Laboratory, Yidu Central Hospital of Weifang, Weifang, Shandong, China
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12
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Wu Y, Guo Y, Yu H, Guo T. RNA editing affects cis-regulatory elements and predicts adverse cancer survival. Cancer Med 2021; 10:6114-6127. [PMID: 34319007 PMCID: PMC8419749 DOI: 10.1002/cam4.4146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND RNA editing exerts critical impacts on numerous biological processes and thus are implicated in crucial human phenotypes, including tumorigenesis and prognosis. While previous studies have analyzed aggregate RNA editing activity at the sample level and associated it with overall cancer survival, there is not yet a large-scale disease-specific survival study to examine genome-wide RNA editing sites' prognostic value taking into account the host gene expression and clinical variables. METHODS In this study, we solved comprehensive Cox proportional models of disease-specific survival on individual RNA-editing sites plus host gene expression and critical demographic covariates. This allowed us to interrogate the prognostic value of a large number of RNA-editing sites at single-nucleotide resolution. RESULTS As a result, we identified 402 gene-proximal RNA-editing sites that generally predict adverse cancer survival. For example, an RNA-editing site residing in ZNF264 indicates poor survival of uterine corpus endometrial carcinoma, with a hazard ratio of 2.13 and an adjusted p-value of 4.07 × 10-7 . Some of these prognostic RNA-editing sites mediate the binding of RNA binding proteins and microRNAs, thus propagating their impacts to extensive regulatory targets. CONCLUSIONS In conclusion, RNA editing affects cis-regulatory elements and predicts adverse cancer survival.
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Affiliation(s)
- Yuan‐Ming Wu
- School of Basic Medical SciencesGuizhou Medical UniversityGuiyangChina
- Stem Cell and Tissue Engineering Research CenterGuizhou Medical UniversityGuizhouChina
| | - Yan Guo
- Comprehensive Cancer CenterUniversity of New MexicoAlbuquerqueNMUSA
| | - Hui Yu
- Comprehensive Cancer CenterUniversity of New MexicoAlbuquerqueNMUSA
| | - Tao Guo
- Guizhou Provincial People’s HospitalGuiyangChina
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13
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Qi X, Liu Z, Zhang Q, Yang M, Wan Y, Huang J, Xu L. Systematic analysis of the function and prognostic value of RNA binding proteins in Colon Adenocarcinoma. J Cancer 2021; 12:2537-2549. [PMID: 33854615 PMCID: PMC8040719 DOI: 10.7150/jca.50407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 02/17/2021] [Indexed: 12/22/2022] Open
Abstract
Background: Abnormal expression of RNA-binding proteins (RBPs) is closely related to tumorigenesis, progression, and prognosis. This study performed systematic bioinformatic analysis of RBPs abnormally expressed in colon adenocarcinoma (COAD) using the Cancer Genome Atlas (TCGA) database to screen prognostic markers and potential therapeutic targets. Methods: First, the gene expression data from COAD samples were used to screen out differentially expressed RBPs for functional enrichment analysis and to visualize interaction relationships. Second, RBPs that were significantly related to prognosis were screened through univariate and multivariate Cox regression analysis to construct a prognostic model. The prediction performance of the prognostic model was evaluated by survival analysis and receiver operating characteristic (ROC) curve analysis. It addition, it was verified in the test cohort. The Human Protein Atlas (HPA) online database was used to verify the expression levels of RBPs in the prognostic model. Results: The study identified 181 differentially expressed RBPs and analyzed their interaction and functional enrichment, which were mainly related to non-coding RNA processing, ribosome biogenesis, RNA metabolic processes, RNA phosphodiester bond hydrolysis, and alternative mRNA splicing. Five RBPs related to prognosis were used to construct a prognostic model, and its predictive ability was verified by the test cohort. ROC curve analysis showed that the prognostic model had good sensitivity and specificity. Independent prognostic analysis showed that risk scores could be used as independent prognostic factors for COAD. Conclusion: This study constructed a reliable prognostic model by analyzing COAD differentially expressed RBPs, facilitating the screening of COAD prognostic markers and therapeutic targets.
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Affiliation(s)
- Xuewei Qi
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Zeyu Liu
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Qiaoli Zhang
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Ming Yang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Yuxiang Wan
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jinchang Huang
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China.,Institute of Acupuncture and Moxibustion in Cancer Care, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Lin Xu
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
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14
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Mizdrak M, Tičinović Kurir T, Božić J. The Role of Biomarkers in Adrenocortical Carcinoma: A Review of Current Evidence and Future Perspectives. Biomedicines 2021; 9:174. [PMID: 33578890 PMCID: PMC7916711 DOI: 10.3390/biomedicines9020174] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/07/2021] [Accepted: 02/08/2021] [Indexed: 12/18/2022] Open
Abstract
Adrenocortical carcinoma (ACC) is a rare endocrine malignancy arising from the adrenal cortex often with unexpected biological behavior. It can occur at any age, with two peaks of incidence: in the first and between fifth and seventh decades of life. Although ACC are mostly hormonally active, precursors and metabolites, rather than end products of steroidogenesis are produced by dedifferentiated and immature malignant cells. Distinguishing the etiology of adrenal mass, between benign adenomas, which are quite frequent in general population, and malignant carcinomas with dismal prognosis is often unfeasible. Even after pathohistological analysis, diagnosis of adrenocortical carcinomas is not always straightforward and represents a great challenge for experienced and multidisciplinary expert teams. No single imaging method, hormonal work-up or immunohistochemical labelling can definitively prove the diagnosis of ACC. Over several decades' great efforts have been made in finding novel reliable and available diagnostic and prognostic factors including steroid metabolome profiling or target gene identification. Despite these achievements, the 5-year mortality rate still accounts for approximately 75% to 90%, ACC is frequently diagnosed in advanced stages and therapeutic options are unfortunately limited. Therefore, imperative is to identify new biological markers that can predict patient prognosis and provide new therapeutic options.
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Affiliation(s)
- Maja Mizdrak
- Department of Nephrology and Hemodialysis, University Hospital of Split, 21000 Split, Croatia;
- Department of Pathophysiology, University of Split School of Medicine, 21000 Split, Croatia;
| | - Tina Tičinović Kurir
- Department of Pathophysiology, University of Split School of Medicine, 21000 Split, Croatia;
- Department of Endocrinology, Diabetes and Metabolic Disorders, University Hospital of Split, 21000 Split, Croatia
| | - Joško Božić
- Department of Pathophysiology, University of Split School of Medicine, 21000 Split, Croatia;
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15
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Zhang D, Guo Y, Xie N. Prognostic value and co-expression patterns of metabolic pathways in cancers. BMC Genomics 2020; 21:860. [PMID: 33372594 PMCID: PMC7771089 DOI: 10.1186/s12864-020-07251-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Abnormal metabolic pathways have been considered as one of the hallmarks of cancer. While numerous metabolic pathways have been studied in various cancers, the direct link between metabolic pathway gene expression and cancer prognosis has not been established. RESULTS Using two recently developed bioinformatics analysis methods, we evaluated the prognosis potential of metabolic pathway expression and tumor-vs-normal dysregulations for up to 29 metabolic pathways in 33 cancer types. Results show that increased metabolic gene expression within tumors corresponds to poor cancer prognosis. Meta differential co-expression analysis identified four metabolic pathways with significant global co-expression network disturbance between tumor and normal samples. Differential expression analysis of metabolic pathways also demonstrated strong gene expression disturbance between paired tumor and normal samples. CONCLUSION Taken together, these results strongly suggested that metabolic pathway gene expressions are disturbed after tumorigenesis. Within tumors, many metabolic pathways are upregulated for tumor cells to activate corresponding metabolisms to sustain the required energy for cell division.
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Affiliation(s)
- Dan Zhang
- Biobank, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen, 518035, China
| | - Yan Guo
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, 87131, USA
| | - Ni Xie
- Biobank, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen, 518035, China.
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16
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Xu B, Mei J, Ji W, Bian Z, Jiao J, Sun J, Shao J. LncRNA SNHG3, a potential oncogene in human cancers. Cancer Cell Int 2020; 20:536. [PMID: 33292213 PMCID: PMC7640707 DOI: 10.1186/s12935-020-01608-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/15/2020] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are composed of > 200 nucleotides; they lack the ability to encode proteins but play important roles in a variety of human tumors. A large number of studies have shown that dysregulated expression of lncRNAs is related to tumor oncogenesis and progression. Emerging evidence shows that SNHG3 is a novel oncogenic lncRNA that is abnormally expressed in various tumors, including osteosarcoma, liver cancer, lung cancer, etc. SNHG3 primarily competes as a competitive endogenous RNA (ceRNA) that targets tumor suppressor microRNAs (miRNAs) and ceRNA mechanisms that regulate biological processes of tumors. In addition, abnormal expression of SNHG3 is significantly correlated with patient clinical features. Upregulation of SNHG3 contributes to biological functions, including tumor cell proliferation, migration, invasion and EMT. Therefore, SNHG3 may represent a potential diagnostic and prognostic biomarker, as well as a novel therapeutic target.
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Affiliation(s)
- Bin Xu
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, Wuxi, 214023, Jiangsu, China
| | - Jie Mei
- Department of Oncology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, P. R. China
| | - Wei Ji
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, Wuxi, 214023, Jiangsu, China
| | - Zheng Bian
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, Wuxi, 214023, Jiangsu, China
| | - Jiantong Jiao
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, Wuxi, 214023, Jiangsu, China
| | - Jun Sun
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, Wuxi, 214023, Jiangsu, China.
| | - Junfei Shao
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, Wuxi, 214023, Jiangsu, China.
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17
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Yang Q, Chu W, Yang W, Cheng Y, Chu C, Pan X, Ye J, Cao J, Gan S, Cui X. Identification of RNA Transcript Makers Associated With Prognosis of Kidney Renal Clear Cell Carcinoma by a Competing Endogenous RNA Network Analysis. Front Genet 2020; 11:540094. [PMID: 33193613 PMCID: PMC7593646 DOI: 10.3389/fgene.2020.540094] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/04/2020] [Indexed: 12/16/2022] Open
Abstract
Objective This study aims to identify several RNA transcripts associated with the prognosis of kidney renal clear cell carcinoma (KIRC). Methods The differentially expressed mRNAs, lncRNAs, and miRNAs (DEmRNAs, DElncRNAs, and DEmiRNAs) between KIRC cases and controls were screened based on an RNA-seq dataset from The Cancer Genome Atlas (TCGA) database. Subsequently, miRcode, miRDB, and TargetScan database were used to predict interactions between lncRNAs, miRNAs and target mRNAs. Then, a ceRNA network was built using miRNAs-mRNAs and lncRNAs-miRNAs pairs. Functional analysis of mRNAs in ceRNA was performed. Finally, the survival analysis of RNA transcripts in ceRNA network and correlation analysis for key RNA regulators were carried out. Results There were 1527 DElncRNAs, 54 DEmiRNAs, and 2321 DEmRNAs. A ceRNA network was constructed among 81 lncRNAs, 9 miRNAs, and 197 mRNAs. Functional analysis showed that numerous mRNAs were significantly associated with regulation of cellular glucuronidation. In addition, 35 lncRNAs, 84 mRNAs and two miRNAs were significantly corelated to the survival of patients with KIRC (P < 0.05). Among them, miRNA-21 and miRNA-155 were negatively related to three lncRNAs (LINC00472, SLC25A5.AS1, and TCL6). Seven mRNA targets of miRNA-21 (FASLG, FGF1, TGFBI, ALX1, SLC30A10, ADCY2, and ABAT) and 12 mRNAs targets of miRNA-155 (STXBP5L, SCG2, SPI1, C12orf40, TYRP1, CTHRC1, TDO2, PTPRQ, TRPM8, ERMP1, CD36, and ST9SIA4) also acted as prognostic biomarkers for KIRC patients. Conclusion We screened numerous novel prognosis-related RNA markers for KIRC patients by a ceRNA network analysis, providing deeper understandings of prognostic values of RNA transcripts for KIRC.
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Affiliation(s)
- Qiwei Yang
- Department of Urology, Gongli Hospital, Shanghai, China.,Department of Urology, The Third Affiliated Hospital of Naval Military Medical University (Eastern Hepatobiliary Surgery Hospital), Shanghai, China
| | - Weiwei Chu
- Laboratory of Nano Biomedicine and International Joint Cancer Institute, Second Military Medical University, Shanghai, China
| | - Wei Yang
- Department of Urology, The Third Affiliated Hospital of Naval Military Medical University (Eastern Hepatobiliary Surgery Hospital), Shanghai, China
| | - Yanqiong Cheng
- Department of Pharmaceutical College, Naval Military Medical University, Shanghai, China
| | - Chuanmin Chu
- Department of Urology, The Third Affiliated Hospital of Naval Military Medical University (Eastern Hepatobiliary Surgery Hospital), Shanghai, China
| | - Xiuwu Pan
- Department of Urology, Gongli Hospital, Shanghai, China
| | - Jianqing Ye
- Department of Urology, The Third Affiliated Hospital of Naval Military Medical University (Eastern Hepatobiliary Surgery Hospital), Shanghai, China
| | - Jianwei Cao
- Department of Urology, The Third Affiliated Hospital of Naval Military Medical University (Eastern Hepatobiliary Surgery Hospital), Shanghai, China
| | - Sishun Gan
- Department of Urology, The Third Affiliated Hospital of Naval Military Medical University (Eastern Hepatobiliary Surgery Hospital), Shanghai, China
| | - Xingang Cui
- Department of Urology, Gongli Hospital, Shanghai, China.,Department of Urology, The Third Affiliated Hospital of Naval Military Medical University (Eastern Hepatobiliary Surgery Hospital), Shanghai, China
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18
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Mei J, Hao L, Wang H, Xu R, Liu Y, Zhu Y, Liu C. Systematic characterization of non-coding RNAs in triple-negative breast cancer. Cell Prolif 2020; 53:e12801. [PMID: 32249490 PMCID: PMC7260065 DOI: 10.1111/cpr.12801] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/03/2020] [Accepted: 03/11/2020] [Indexed: 12/17/2022] Open
Abstract
Triple‐negative breast cancer (TNBC) is one of the most aggressive subtypes of breast cancer with negativity for oestrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor (HER2). Non‐coding RNAs (ncRNAs) make up most of the transcriptome and are widely present in eukaryotic cells. In recent years, emerging evidence suggests that ncRNAs, mainly microRNAs (miRNAs), long ncRNAs (lncRNAs) and circular RNAs (circRNAs), play prominent roles in the tumorigenesis and development of TNBC, but the functions of most ncRNAs have not been fully described. In this review, we systematically elucidate the general characteristics and biogenesis of miRNAs, lncRNAs and circRNAs, discuss the emerging functions of these ncRNAs in TNBC and present future perspectives in clinical practice.
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Affiliation(s)
- Jie Mei
- Department of Oncology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Leiyu Hao
- Department of Physiology, Nanjing Medical University, Nanjing, China
| | - Huiyu Wang
- Department of Oncology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Rui Xu
- Department of Physiology, Nanjing Medical University, Nanjing, China
| | - Yan Liu
- Department of Physiology, Nanjing Medical University, Nanjing, China
| | - Yichao Zhu
- Department of Physiology, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Chaoying Liu
- Department of Oncology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, China
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19
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Shulman ED, Elkon R. Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data. Nucleic Acids Res 2019; 47:10027-10039. [PMID: 31501864 PMCID: PMC6821429 DOI: 10.1093/nar/gkz781] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 08/27/2019] [Accepted: 09/01/2019] [Indexed: 12/22/2022] Open
Abstract
Alternative polyadenylation (APA) is emerging as an important layer of gene regulation because the majority of mammalian protein-coding genes contain multiple polyadenylation (pA) sites in their 3′ UTR. By alteration of 3′ UTR length, APA can considerably affect post-transcriptional gene regulation. Yet, our understanding of APA remains rudimentary. Novel single-cell RNA sequencing (scRNA-seq) techniques allow molecular characterization of different cell types to an unprecedented degree. Notably, the most popular scRNA-seq protocols specifically sequence the 3′ end of transcripts. Building on this property, we implemented a method for analysing patterns of APA regulation from such data. Analyzing multiple datasets from diverse tissues, we identified widespread modulation of APA in different cell types resulting in global 3′ UTR shortening/lengthening and enhanced cleavage at intronic pA sites. Our results provide a proof-of-concept demonstration that the huge volume of scRNA-seq data that accumulates in the public domain offers a unique resource for the exploration of APA based on a very broad collection of cell types and biological conditions.
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Affiliation(s)
- Eldad David Shulman
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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