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Zhang Y, Zhang Y, Song J, Cheng X, Zhou C, Huang S, Zhao W, Zong Z, Yang L. Targeting the "tumor microenvironment": RNA-binding proteins in the spotlight in colorectal cancer therapy. Int Immunopharmacol 2024; 131:111876. [PMID: 38493688 DOI: 10.1016/j.intimp.2024.111876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/04/2024] [Accepted: 03/13/2024] [Indexed: 03/19/2024]
Abstract
Colorectal cancer (CRC) is the third most common cancer and has the second highest mortality rate among cancers. The development of CRC involves both genetic and epigenetic abnormalities, and recent research has focused on exploring the ex-transcriptome, particularly post-transcriptional modifications. RNA-binding proteins (RBPs) are emerging epigenetic regulators that play crucial roles in post-transcriptional events. Dysregulation of RBPs can result in aberrant expression of downstream target genes, thereby affecting the progression of colorectal tumors and the prognosis of patients. Recent studies have shown that RBPs can influence CRC pathogenesis and progression by regulating various components of the tumor microenvironment (TME). Although previous research on RBPs has primarily focused on their direct regulation of colorectal tumor development, their involvement in the remodeling of the TME has not been systematically reported. This review aims to highlight the significant role of RBPs in the intricate interactions within the CRC tumor microenvironment, including tumor immune microenvironment, inflammatory microenvironment, extracellular matrix, tumor vasculature, and CRC cancer stem cells. We also highlight several compounds under investigation for RBP-TME-based treatment of CRC, including small molecule inhibitors such as antisense oligonucleotides (ASOs), siRNAs, agonists, gene manipulation, and tumor vaccines. The insights gained from this review may lead to the development of RBP-based targeted novel therapeutic strategies aimed at modulating the TME, potentially inhibiting the progression and metastasis of CRC.
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Affiliation(s)
- Yiwei Zhang
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Nanchang University, No. 1 MinDe Road, 330006 Nanchang, China; Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, No. 1 Mingde Rd., Nanchang 330006, Jiangxi, China; Queen Mary School, Nanchang University, 330006 Nanchang, China
| | - Yujun Zhang
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Nanchang University, No. 1 MinDe Road, 330006 Nanchang, China; Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, No. 1 Mingde Rd., Nanchang 330006, Jiangxi, China
| | - Jingjing Song
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Nanchang University, No. 1 MinDe Road, 330006 Nanchang, China; Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, No. 1 Mingde Rd., Nanchang 330006, Jiangxi, China; School of Ophthalmology and Optometry of Nanchang University, China
| | - Xifu Cheng
- School of Ophthalmology and Optometry of Nanchang University, China
| | - Chulin Zhou
- The Second Clinical Medical College, Nanchang University, Nanchang 330006, China
| | - Shuo Huang
- The Second Clinical Medical College, Nanchang University, Nanchang 330006, China
| | - Wentao Zhao
- The 3rd Clinical Department of China Medical University, 10159 Shenyang, China
| | - Zhen Zong
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Nanchang University, No. 1 MinDe Road, 330006 Nanchang, China.
| | - Lingling Yang
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, No. 1 Mingde Rd., Nanchang 330006, Jiangxi, China.
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Coleman JC, Tattersall L, Yianni V, Knight L, Yu H, Hallett SR, Johnson P, Caetano AJ, Cosstick C, Ridley AJ, Gartland A, Conte MR, Grigoriadis AE. The RNA binding proteins LARP4A and LARP4B promote sarcoma and carcinoma growth and metastasis. iScience 2024; 27:109288. [PMID: 38532886 PMCID: PMC10963253 DOI: 10.1016/j.isci.2024.109288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 11/01/2023] [Accepted: 02/16/2024] [Indexed: 03/28/2024] Open
Abstract
RNA-binding proteins (RBPs) are emerging as important regulators of cancer pathogenesis. We reveal that the RBPs LARP4A and LARP4B are differentially overexpressed in osteosarcoma and osteosarcoma lung metastases, as well as in prostate cancer. Depletion of LARP4A and LARP4B reduced tumor growth and metastatic spread in xenografts, as well as inhibiting cell proliferation, motility, and migration. Transcriptomic profiling and high-content multiparametric analyses unveiled a central role for LARP4B, but not LARP4A, in regulating cell cycle progression in osteosarcoma and prostate cancer cells, potentially through modulating key cell cycle proteins such as Cyclins B1 and E2, Aurora B, and E2F1. This first systematic comparison between LARP4A and LARP4B assigns new pro-tumorigenic functions to LARP4A and LARP4B in bone and prostate cancer, highlighting their similarities while also indicating distinct functional differences. Uncovering clear biological roles for these paralogous proteins provides new avenues for identifying tissue-specific targets and potential druggable intervention.
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Affiliation(s)
- Jennifer C. Coleman
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, SE1 1UL UK
| | - Luke Tattersall
- The Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The University of Sheffield, Sheffield, S10 2RX UK
| | - Val Yianni
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Laura Knight
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Hongqiang Yu
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Sadie R. Hallett
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, SE1 1UL UK
| | - Philip Johnson
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Ana J. Caetano
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Charlie Cosstick
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Anne J. Ridley
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD UK
| | - Alison Gartland
- The Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The University of Sheffield, Sheffield, S10 2RX UK
| | - Maria R. Conte
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, SE1 1UL UK
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Kobayashi K, Kawazu M, Yoshimoto S, Ueno T, Omura G, Saito Y, Ando M, Ryo E, Sakyo A, Yoshida A, Yatabe Y, Mano H, Mori T. Genome Doubling Shapes High-Grade Transformation and Novel EWSR1::LARP4 Fusion Shows SOX10 Immunostaining in Hyalinizing Clear Cell Carcinoma of Salivary Gland. J Transl Med 2023; 103:100213. [PMID: 37479138 DOI: 10.1016/j.labinv.2023.100213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/04/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023] Open
Abstract
Hyalinizing clear cell carcinoma (HCCC) is a rare indolent malignant tumor of minor salivary gland origin with EWSR1::ATF1 rearrangement. Pathologically, the tumor cells possess a clear cytoplasm in a background of hyalinized stroma. Generally, the tumor cells are positive for p63 and p40 and negative for s100 and α-smooth muscle actin, suggesting that they differentiate into squamous epithelium and not into myoepithelium. In this study, we performed a detailed histopathological and genomic analysis of 6 cases of HCCC, including 2 atypical subtypes-a case of "high-grade transformation" and 1 "possessing a novel partner gene for EWSR1." We performed a sequential analysis of the primary and recurrent tumor by whole-exome sequencing, RNA sequencing, Sanger sequencing, and fluorescence in situ hybridization to investigate the effect of genomic changes on histopathology and clinical prognosis. A fusion gene involving the EWSR1 gene was detected in all cases. Five cases, including the "high-grade transformation," harbored a known EWSR1::ATF1 fusion gene; however, 1 case harbored a novel EWSR1::LARP4 fusion gene. This novel EWSR1::LARP4-fused HCCC has a SOX10-positive staining, which is different from the EWSR1::ATF1-fused HCCC. According to whole-exome sequencing and fluorescence in situ hybridization analysis, the "whole-genome doubling" and focal deletion involving CDKN2A, CDKN2B, and PTEN were detected in HCCC with "high-grade transformation." Conclusively, we identified a novel partner gene for EWSR1, LARP4, in indolent HCCC. Importantly, "high-grade transformation" and poor prognosis were caused by whole-genome doubling and subsequent genomic aberrations.
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Affiliation(s)
- Kenya Kobayashi
- Department of Otolaryngology, Head and Neck Surgery, The University of Tokyo, Tokyo, Japan; Department of Head and Neck Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Masahito Kawazu
- Division of Cell Therapy, Chiba Cancer Center, Chiba, Japan; Division of Cell Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Seiichi Yoshimoto
- Department of Head and Neck Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Toshihide Ueno
- Division of Cell Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Go Omura
- Department of Head and Neck Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Yuki Saito
- Department of Otolaryngology, Head and Neck Surgery, The University of Tokyo, Tokyo, Japan
| | - Mizuo Ando
- Department of Otolaryngology, Head and Neck Surgery, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Eigitsu Ryo
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
| | - Airi Sakyo
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Akihiko Yoshida
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan; Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Yasushi Yatabe
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan; Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Hiroyuki Mano
- Division of Cell Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Taisuke Mori
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan; Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan.
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Aikio E, Koivukoski S, Kallio E, Sadeesh N, Niskanen EA, Latonen L. Complementary analysis of proteome-wide proteomics reveals changes in RNA binding protein-profiles during prostate cancer progression. Cancer Rep (Hoboken) 2023; 6:e1886. [PMID: 37591798 PMCID: PMC10598248 DOI: 10.1002/cnr2.1886] [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: 04/28/2023] [Revised: 07/19/2023] [Accepted: 07/28/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Accumulating evidence indicates importance of RNA regulation in cancer. This includes events such as splicing, translation, and regulation of noncoding RNAs, functions which are governed by RNA binding proteins (RBPs). AIMS To find which RBPs could be relevant for prostate cancer, we performed systematic screening of RBP expression in clinical prostate cancer. METHODS AND RESULTS We interrogated four proteome-wide proteomics datasets including tumor samples of primary, castration resistant, and metastatic prostate cancer. We found that, while the majority of RBPs are expressed but not significantly altered during prostate cancer development and progression, expression of several RBPs increases in advanced disease. Interestingly, most of the differentially expressed RBPs are not targets of differential posttranscriptional phosphorylation during disease progression. The RBPs undergoing expression changes have functions in, especially, poly(A)-RNA binding, nucleocytoplasmic transport, and cellular stress responses, suggesting that these may play a role in formation of castration resistance. Pathway analyzes indicate that increased ribosome production and chromatin-related functions of RBPs are also linked to castration resistant and metastatic prostate cancers. We selected a group of differentially expressed RBPs and studied their role in cultured prostate cancer cells. With siRNA screens, several of these were indicated in survival (DDX6, EIF4A3, PABPN1), growth (e.g., EIF5A, HNRNPH2, LRRC47, and NVL), and migration (e.g., NOL3 and SLTM) of prostate cancer cells. Our analyzes further show that RRP9, a U3 small nucleolar protein essential for ribosome formation, undergoes changes at protein level during metastasis in prostate cancer. CONCLUSION In this work, we recognized significant molecular alterations in RBP profiles during development and evolution of prostate cancer. Our study further indicates several functionally significant RBPs warranting further investigation for their functions and possible targetability in prostate cancer.
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Affiliation(s)
- Erika Aikio
- Institute of BiomedicineUniversity of Eastern FinlandKuopioFinland
| | - Sonja Koivukoski
- Institute of BiomedicineUniversity of Eastern FinlandKuopioFinland
| | - Elina Kallio
- Institute of BiomedicineUniversity of Eastern FinlandKuopioFinland
| | - Nithin Sadeesh
- Institute of BiomedicineUniversity of Eastern FinlandKuopioFinland
| | | | - Leena Latonen
- Institute of BiomedicineUniversity of Eastern FinlandKuopioFinland
- Foundation for the Finnish Cancer InstituteHelsinkiFinland
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5
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Coleman JC, Hallett SR, Grigoriadis AE, Conte MR. LARP4A and LARP4B in cancer: The new kids on the block. Int J Biochem Cell Biol 2023; 161:106441. [PMID: 37356415 DOI: 10.1016/j.biocel.2023.106441] [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: 05/03/2023] [Revised: 06/09/2023] [Accepted: 06/17/2023] [Indexed: 06/27/2023]
Abstract
Recent developments have mounted a stunning body of evidence underlying the importance of RNA binding proteins (RBPs) in cancer research. In this minireview we focus on LARP4A and LARP4B, two paralogs belonging to the superfamily of La-related proteins, and provide a critical overview of current research, including their roles in cancer pathogenesis and cell proliferation, migration, cell cycle and apoptosis. We highlight current controversies surrounding LARP4A and LARP4B and conclude that their complex roles in tumorigenesis are cell-, tissue- and context-dependent, warning that caution must be exercised before categorising either protein as an oncoprotein or tumour-suppressor. We also reveal that LARP4A and LARP4B have often been confused with one another, adding uncertainty in delineating their functions. We suggest that further functional and mechanistic studies of LARP4 proteins present significant challenges for future investigations to recognise the vital contributions of these RBPs in cancer research.
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Affiliation(s)
- Jennifer C Coleman
- Centre for Craniofacial & Regenerative Biology, King's College London, London SE1 9RT, UK
| | - Sadie R Hallett
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | | | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK.
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6
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Sun L, Qiu Y, Ching WK, Zhao P, Zou Q. PCB: A pseudotemporal causality-based Bayesian approach to identify EMT-associated regulatory relationships of AS events and RBPs during breast cancer progression. PLoS Comput Biol 2023; 19:e1010939. [PMID: 36930678 PMCID: PMC10057809 DOI: 10.1371/journal.pcbi.1010939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 03/29/2023] [Accepted: 02/09/2023] [Indexed: 03/18/2023] Open
Abstract
During breast cancer metastasis, the developmental process epithelial-mesenchymal (EM) transition is abnormally activated. Transcriptional regulatory networks controlling EM transition are well-studied; however, alternative RNA splicing also plays a critical regulatory role during this process. Alternative splicing was proved to control the EM transition process, and RNA-binding proteins were determined to regulate alternative splicing. A comprehensive understanding of alternative splicing and the RNA-binding proteins that regulate it during EM transition and their dynamic impact on breast cancer remains largely unknown. To accurately study the dynamic regulatory relationships, time-series data of the EM transition process are essential. However, only cross-sectional data of epithelial and mesenchymal specimens are available. Therefore, we developed a pseudotemporal causality-based Bayesian (PCB) approach to infer the dynamic regulatory relationships between alternative splicing events and RNA-binding proteins. Our study sheds light on facilitating the regulatory network-based approach to identify key RNA-binding proteins or target alternative splicing events for the diagnosis or treatment of cancers. The data and code for PCB are available at: http://hkumath.hku.hk/~wkc/PCB(data+code).zip.
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Affiliation(s)
- Liangjie Sun
- Department of Mathematics, The University of Hong Kong, Hong Kong, China
| | - Yushan Qiu
- College of Mathematics and Statistics, Shenzhen University, Shenzhen, China
- * E-mail:
| | - Wai-Ki Ching
- Department of Mathematics, The University of Hong Kong, Hong Kong, China
| | - Pu Zhao
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
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7
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Mao Z, Nakamura F. Interaction of LARP4 to filamin A mechanosensing domain regulates cell migrations. Front Cell Dev Biol 2023; 11:1152109. [PMID: 37169020 PMCID: PMC10164935 DOI: 10.3389/fcell.2023.1152109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/14/2023] [Indexed: 05/13/2023] Open
Abstract
Filamin A (FLNA) is an actin cross-linking protein that mediates mechanotransduction. Force-dependent conformational changes of FLNA molecule expose cryptic binding site of FLNA, allowing interaction with partners such as integrin, smoothelin, and fimbacin. Here, we identified La-related protein 4 (LARP4) as a new FLNA mechanobinding partner. LARP4 specifically interacts with the cleft formed by C and D strands of immunoglobulin-like repeat 21 (R21) which is blocked by A strand of R20 without force. We validated the interaction between LARP4 and FLNA R21 both in vivo and in vitro. We also determined the critical amino acid that is responsible for the interaction and generated the non-FLNA-binding mutant LARP4 (F277A in human: F273A in mouse Larp4) that disrupts the interaction. Fluorescence recovery after photobleaching (FRAP) of GFP-labeled LARP4 in living cells demonstrated that mutant LARP4 diffuses faster than WT LARP4. Proximity ligation assay (PLA) also confirmed their interaction and disruption of actin polymerization diminishes the interaction. Data mining of RNAseq analysis of LARP4 knockdown (KD) HEK293T cells suggested that LARP4 is involved in morphogenesis and cell motility. Consistent with this prediction, we found that KD of LARP4 increases cell migration speed and expression of the F277A mutant LARP4 in LARP4-KD cells also leads to a higher cell migration speed compared to WT LARP4. These results demonstrated that the LARP4 interaction with FLNA regulates cell migration.
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8
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Albaradei S, Albaradei A, Alsaedi A, Uludag M, Thafar MA, Gojobori T, Essack M, Gao X. MetastaSite: Predicting metastasis to different sites using deep learning with gene expression data. Front Mol Biosci 2022; 9:913602. [PMID: 35936793 PMCID: PMC9353773 DOI: 10.3389/fmolb.2022.913602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/29/2022] [Indexed: 12/03/2022] Open
Abstract
Deep learning has massive potential in predicting phenotype from different omics profiles. However, deep neural networks are viewed as black boxes, providing predictions without explanation. Therefore, the requirements for these models to become interpretable are increasing, especially in the medical field. Here we propose a computational framework that takes the gene expression profile of any primary cancer sample and predicts whether patients’ samples are primary (localized) or metastasized to the brain, bone, lung, or liver based on deep learning architecture. Specifically, we first constructed an AutoEncoder framework to learn the non-linear relationship between genes, and then DeepLIFT was applied to calculate genes’ importance scores. Next, to mine the top essential genes that can distinguish the primary and metastasized tumors, we iteratively added ten top-ranked genes based upon their importance score to train a DNN model. Then we trained a final multi-class DNN that uses the output from the previous part as an input and predicts whether samples are primary or metastasized to the brain, bone, lung, or liver. The prediction performances ranged from AUC of 0.93–0.82. We further designed the model’s workflow to provide a second functionality beyond metastasis site prediction, i.e., to identify the biological functions that the DL model uses to perform the prediction. To our knowledge, this is the first multi-class DNN model developed for the generic prediction of metastasis to various sites.
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Affiliation(s)
- Somayah Albaradei
- Computer Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Asim Alsaedi
- King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
- King Abdulaziz Medical City, Jeddah, Saudi Arabia
| | - Mahmut Uludag
- Computer Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Maha A. Thafar
- Computer Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- College of Computers and Information Technology, Taif University, Taif, Saudi Arabia
| | - Takashi Gojobori
- Computer Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Magbubah Essack
- Computer Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Magbubah Essack, ; Xin Gao,
| | - Xin Gao
- Computer Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Magbubah Essack, ; Xin Gao,
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Zhang W, Zhang K. A transcriptomic signature for prostate cancer relapse prediction identified from the differentially expressed genes between TP53 mutant and wild-type tumors. Sci Rep 2022; 12:10561. [PMID: 35732666 PMCID: PMC9217948 DOI: 10.1038/s41598-022-14436-y] [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: 11/05/2021] [Accepted: 06/07/2022] [Indexed: 11/12/2022] Open
Abstract
For prostate cancer (PCa) patients, biochemical recurrence (BCR) is the first sign of disease relapse and the subsequent metastasis. TP53 mutations are relatively prevalent in advanced PCa forms. We aimed to utilize this knowledge to identify robust transcriptomic signatures for BCR prediction in patients with Gleason score ≥ 7 cancers, which cause most PCa deaths. Using the TCGA-PRAD dataset and the novel data-driven stochastic approach proposed in this study, we identified a 25-gene signature from the genes whose expression in tumors was associated with TP53 mutation statuses. The predictive strength of the signature was assessed by AUC and Fisher’s exact test p-value according to the output of support vector machine-based cross validation. For the TCGA-PRAD dataset, the AUC and p-value were 0.837 and 5 × 10–13, respectively. For five external datasets, the AUCs and p-values ranged from 0.632 to 0.794 and 6 × 10–2 to 5 × 10–5, respectively. The signature also performed well in predicting relapse-free survival (RFS). The signature-based transcriptomic risk scores (TRS) explained 28.2% of variation in RFS on average. The combination of TRS and clinicopathologic prognostic factors explained 23–72% of variation in RFS, with a median of 54.5%. Our method and findings are useful for developing new prognostic tools in PCa and other cancers.
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Affiliation(s)
- Wensheng Zhang
- Bioinformatics Core of Xavier NIH RCMI Center of Cancer Research, Xavier University of Louisiana, New Orleans, LA, 70125, USA.
| | - Kun Zhang
- Bioinformatics Core of Xavier NIH RCMI Center of Cancer Research, Xavier University of Louisiana, New Orleans, LA, 70125, USA. .,Department of Computer Science, Xavier University of Louisiana, New Orleans, LA, 70125, USA.
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10
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Identification of Candidate Genes Regulating Carcass Depth and Hind Leg Circumference in Simmental Beef Cattle Using Illumina Bovine Beadchip and Next-Generation Sequencing Analyses. Animals (Basel) 2022; 12:ani12091103. [PMID: 35565529 PMCID: PMC9102740 DOI: 10.3390/ani12091103] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 04/14/2022] [Accepted: 04/21/2022] [Indexed: 12/27/2022] Open
Abstract
Genome-wide association studies are a robust means of identifying candidate genes that regulate economically important traits in farm animals. The aim of this study is to identify single-nucleotide polymorphisms (SNPs) and candidate genes potentially related to carcass depth and hind leg circumference in Simmental beef cattle. We performed Illumina Bovine HD Beadchip (~670 k SNPs) and next-generation sequencing (~12 million imputed SNPs) analyses of data from 1252 beef cattle, to which we applied a linear mixed model. Using a statistical threshold (p = 0.05/number of SNPs identified) and adopting a false discovery rate (FDR), we identified many putative SNPs on different bovine chromosomes. We identified 12 candidate genes potentially annotated with the markers identified, including CDKAL1 and E2F3, related to myogenesis and skeletal muscle development. The identification of such genes in Simmental beef cattle will help breeders to understand and improve related traits, such as meat yield.
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11
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Li C, Zhang J, Yang X, Hu C, Chu T, Zhong R, Shen Y, Hu F, Pan F, Xu J, Lu J, Zheng X, Zhang H, Nie W, Han B, Zhang X. hsa_circ_0003222 accelerates stemness and progression of non-small cell lung cancer by sponging miR-527. Cell Death Dis 2021; 12:807. [PMID: 34433810 PMCID: PMC8387484 DOI: 10.1038/s41419-021-04095-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 06/19/2021] [Accepted: 06/21/2021] [Indexed: 12/24/2022]
Abstract
The relationship between circular RNA (circRNA) and cancer stem cells (CSCs) is uncertain. We have investigated the combined influence of CSCs, circRNA (hsa_circ_0003222), and immune checkpoint inhibitors in NSCLC progression and therapy resistance. We constructed lung CSCs (LCSCs; PC9 and A549). The effects of hsa_circ_0003222 in vitro were determined by cell counting, colony and sphere formation, and Transwell assays. A tumor xenograft model of metastasis and orthotopic model were built for in vivo analysis. We found that hsa_circ_0003222 was highly expressed in NSCLC tissues and LCSCs. Higher levels of hsa_circ_0003222 were associated with the stage, metastasis, and survival rate of patients with NSCLC. Reduced levels of hsa_circ_0003222 decreased tumor cell proliferation, migration, invasion, stemness-like properties, and chemoresistance. The silencing of hsa_circ_0003222 was found to downregulate PHF21B expression and its downstream, β-catenin by relieving the sponging effect of miR-527. Moreover, silencing hsa_circ_0003222 alleviated NSCLC resistance to anti-programmed cell death-ligand 1 (PD-L1)-based therapy in vivo. Our data demonstrate the significant role of hsa_circ_0003222 in NSCLC cell stemness-like properties. The manipulation of circRNAs in combination with anti-PD-L1 therapy may alleviate NSCLC stemness and progression.
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Affiliation(s)
- Changhui Li
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jiaqi Zhang
- Shanghai TCM-Integrated Institute of Vascular Anomalies, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200082, China
| | - Xiaohua Yang
- Central Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Cheng Hu
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Tianqing Chu
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Runbo Zhong
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yinchen Shen
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Fang Hu
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Pan
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jianlin Xu
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Lu
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoxuan Zheng
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Hai Zhang
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Nie
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.
| | - Baohui Han
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.
| | - Xueyan Zhang
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.
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12
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Xing Q, Liu S, Luan J, Wang Y, Ma L. A novel 13 RNA binding proteins (RBPs) signature could predict prostate cancer biochemical recurrence. Pathol Res Pract 2021; 225:153587. [PMID: 34419719 DOI: 10.1016/j.prp.2021.153587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/04/2021] [Accepted: 08/11/2021] [Indexed: 01/07/2023]
Abstract
BACKGROUND Cancer precision medicine requires biomarkers or signatures to predict prognosis and therapeutic benefits. Driven by this, we established a biochemical recurrence (BCR) predictive model for prostate cancer (PCA) patients based on RNA-binding proteins (RBPs). METHODS RNA-sequencing and corresponding clinicopathological data were downloaded from the Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. Univariate COX, LASSO and multivariate COX regression analyses were carried out to develop the BCR predictive riskScore model. Survival analysis, ROC curve, independent prognostic analysis, nomogram were also performed to evaluate this signature internally and externally. RESULTS A total of 13 RBPs including TRMT1L, WBP4, MBNL3, SMAD9, NSUN7, ENG9, PIWIL4, PEG10, CSDC2, HELZ2, CELF2, YBX2 and ESRP2 were eventually identified as BCR-related hub biomarkers and utilized to establish a riskScore. Further analysis including external and internal verification indicated that the patients with high riskScores had shorter time to BCR compared to those with low riskScores in both TCGA and GSE116918. The area under the curve (AUC) of the time-dependent receiver operator characteristic curve (ROC) of the predictive model exhibited a good predictive performance. The signature was also proven to be a valuable independent prognostic factor (all P < 0.05). We also established a nomogram based on the 13 RBPs to visualize the relationships between individual predictors and 1-, 3- and 5-year BCR for PCA. CONCLUSIONS Our results successfully screened out 13 RBPs as a robust BCR-predictive signature in PCA by external and internal verification, helping clinician predict patients' cancer progression status and promoting the specific individualized treatment than original clinical parameters.
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Affiliation(s)
- Qianwei Xing
- Department of Urology, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
| | - Shouyong Liu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Jiaochen Luan
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Yi Wang
- Department of Urology, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China.
| | - Limin Ma
- Department of Urology, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China.
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13
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Bitaraf A, Razmara E, Bakhshinejad B, Yousefi H, Vatanmakanian M, Garshasbi M, Cho WC, Babashah S. The oncogenic and tumor suppressive roles of RNA-binding proteins in human cancers. J Cell Physiol 2021; 236:6200-6224. [PMID: 33559213 DOI: 10.1002/jcp.30311] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 01/14/2021] [Accepted: 01/22/2021] [Indexed: 12/17/2022]
Abstract
Posttranscriptional regulation is a mechanism for the cells to control gene regulation at the RNA level. In this process, RNA-binding proteins (RBPs) play central roles and orchestrate the function of RNA molecules in multiple steps. Accumulating evidence has shown that the aberrant regulation of RBPs makes contributions to the initiation and progression of tumorigenesis via numerous mechanisms such as genetic changes, epigenetic alterations, and noncoding RNA-mediated regulations. In this article, we review the effects caused by RBPs and their functional diversity in the malignant transformation of cancer cells that occurs through the involvement of these proteins in various stages of RNA regulation including alternative splicing, stability, polyadenylation, localization, and translation. Besides this, we review the various interactions between RBPs and other crucial posttranscriptional regulators such as microRNAs and long noncoding RNAs in the pathogenesis of cancer. Finally, we discuss the potential approaches for targeting RBPs in human cancers.
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Affiliation(s)
- Amirreza Bitaraf
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ehsan Razmara
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Babak Bakhshinejad
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hassan Yousefi
- Department of Biochemistry and Molecular Biology, LSUHSC School of Medicine, New Orleans, Louisiana, USA
| | - Mousa Vatanmakanian
- Department of Biochemistry and Molecular Biology, LSUHSC School of Medicine, New Orleans, Louisiana, USA
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - Sadegh Babashah
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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14
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Wang C, Li J. A Deep Learning Framework Identifies Pathogenic Noncoding Somatic Mutations from Personal Prostate Cancer Genomes. Cancer Res 2020; 80:4644-4654. [PMID: 32907840 DOI: 10.1158/0008-5472.can-20-1791] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/15/2020] [Accepted: 09/02/2020] [Indexed: 11/16/2022]
Abstract
Our understanding of noncoding mutations in cancer genomes has been derived primarily from mutational recurrence analysis by aggregating clinical samples on a large scale. These cohort-based approaches cannot directly identify individual pathogenic noncoding mutations from personal cancer genomes. Therefore, although most somatic mutations are localized in the noncoding cancer genome, their effects on driving tumorigenesis and progression have not been systematically explored and noncoding somatic alleles have not been leveraged in current clinical practice to guide personalized screening, diagnosis, and treatment. Here, we present a deep learning framework to capture pathogenic noncoding mutations in personal cancer genomes, which perturb gene regulation by altering chromatin architecture. We deployed the system specifically for localized prostate cancer by integrating large-scale prostate cancer genomes and the prostate-specific epigenome. We exhaustively evaluated somatic mutations in each patient's genome and agnostically identified thousands of somatic alleles altering the prostate epigenome. Functional genomic analyses subsequently demonstrated that affected genes displayed differential expression in prostate tumor samples, were vulnerable to expression alterations, and were convergent onto androgen receptor-mediated signaling pathways. Accumulation of pathogenic regulatory mutations in these affected genes was predictive of clinical observations, suggesting potential clinical utility of this approach. Overall, the deep learning framework has significantly expanded our view of somatic mutations in the vast noncoding genome, uncovered novel genes in localized prostate cancer, and will foster the development of personalized screening and therapeutic strategies for prostate cancer. SIGNIFICANCE: This study's characterization of the noncoding genome in prostate cancer reveals mutational signatures predictive of clinical observations, which may serve as a powerful prognostic tool in this disease.
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Affiliation(s)
- Cheng Wang
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, The Parker Institute for Cancer Immunotherapy, The Bakar Computational Health Sciences Institute, Department of Neurology, School of Medicine, University of California, San Francisco, San Francisco, California
| | - Jingjing Li
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, The Parker Institute for Cancer Immunotherapy, The Bakar Computational Health Sciences Institute, Department of Neurology, School of Medicine, University of California, San Francisco, San Francisco, California.
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15
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Abstract
RNA-binding proteins are important regulators of RNA metabolism and are of critical importance in all steps of the gene expression cascade. The role of aberrantly expressed RBPs in human disease is an exciting research field and the potential application of RBPs as a therapeutic target or a diagnostic marker represents a fast-growing area of research.Aberrant overexpression of the human RNA-binding protein La has been found in various cancer entities including lung, cervical, head and neck, and chronic myelogenous leukaemia. Cancer-associated La protein supports tumour-promoting processes such as proliferation, mobility, invasiveness and tumour growth. Moreover, the La protein maintains the survival of cancer cells by supporting an anti-apoptotic state that may cause resistance to chemotherapeutic therapy.The human La protein represents a multifunctional post-translationally modified RNA-binding protein with RNA chaperone activity that promotes processing of non-coding precursor RNAs but also stimulates the translation of selective messenger RNAs encoding tumour-promoting and anti-apoptotic factors. In our model, La facilitates the expression of those factors and helps cancer cells to cope with cellular stress. In contrast to oncogenes, able to initiate tumorigenesis, we postulate that the aberrantly elevated expression of the human La protein contributes to the non-oncogenic addiction of cancer cells. In this review, we summarize the current understanding about the implications of the RNA-binding protein La in cancer progression and therapeutic resistance. The concept of exploiting the RBP La as a cancer drug target will be discussed.
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Affiliation(s)
- Gunhild Sommer
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Regensburg, Germany
| | - Tilman Heise
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Regensburg, Germany
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16
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Lu H, Guo Q, Mao G, Zhu J, Li F. CircLARP4 Suppresses Cell Proliferation, Invasion and Glycolysis and Promotes Apoptosis in Non-Small Cell Lung Cancer by Targeting miR-135b. Onco Targets Ther 2020; 13:3717-3728. [PMID: 32440141 PMCID: PMC7210031 DOI: 10.2147/ott.s240399] [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: 11/28/2019] [Accepted: 02/16/2020] [Indexed: 12/14/2022] Open
Abstract
Background CircLARP4 is reported to act as a tumor suppressor in some cancers. However, the detailed roles and molecular basis of circLARP4 in non-small cell lung cancer (NSCLC) tumorigenesis are still unclear. The aim of the study is to explore the potential roles and molecular basis of circLARP4 in NSCLC tumorigenesis. Materials and Methods qRT-PCR was taken to detect circLARP4 and miR-135b expressions. MTT assay, transwell invasion assay and flow cytometry analysis were applied to evaluate cell proliferation, invasion and apoptosis, respectively. Glycolysis was assessed by measuring hexokinase2 (HK2) expression, glucose consumption and lactate production. Association between circLARP4 and miR-135a was examined by luciferase reporter and RIP assays. The changes of the phosphatase and tension homolog (PTEN)/protein kinase B (AKT)/hypoxia-inducible factor-1α (HIF-1α) pathway were evaluated by Western blot. The nude mouse xenograft models were applied to verify the regulation of circLARP4 in vivo. Results CircLARP4 was decreased in NSCLC tissues and cells. CircLARP4 overexpression blocked cell proliferation and invasion, and facilitated apoptosis in NSCLC cells. Meanwhile, circLARP4 overexpression suppressed glycolysis in NSCLC cells, as evidenced by the reduced HK2, glucose consumption and lactate production levels. Further analyses proved a downregulation of miR-135b by circLARP4 in a ceRNA-dependent manner in NSCLC cells. CircLARP4-mediated tumor suppression on NSCLC progression was partially overturned by overexpressing miR-135b. Moreover, we confirmed that circLARP4 had antitumor effect on xenograft tumors and downregulated miR-135b. Furthermore, circLARP4 overexpression inhibited the PTEN/AKT/HIF-1α pathway in NSCLC cells and xenograft tumors by downregulating miR-135b. Conclusion Our findings suggested that circLARP4 suppressed NSCLC progression by sponging miR-135b through inactivation of the PTEN/AKT/HIF-1α pathway, which broadens our understanding concerning the roles of circLARP4 in NSCLC tumorigenesis.
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Affiliation(s)
- Huawei Lu
- Department of General Thoracic Surgery, Zhoukou Central Hospital, Zhoukou 466000, Henan, People's Republic of China
| | - Qingwei Guo
- Department of General Thoracic Surgery, Zhoukou Central Hospital, Zhoukou 466000, Henan, People's Republic of China
| | - Guozhang Mao
- Department of General Thoracic Surgery, Zhoukou Central Hospital, Zhoukou 466000, Henan, People's Republic of China
| | - Junwei Zhu
- Department of General Thoracic Surgery, Zhoukou Central Hospital, Zhoukou 466000, Henan, People's Republic of China
| | - Fei Li
- Department of General Thoracic Surgery, Zhoukou Central Hospital, Zhoukou 466000, Henan, People's Republic of China
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17
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Li G, Ni A, Tang Y, Li S, Meng L. RNA binding proteins involved in regulation of protein synthesis to initiate biogenesis of secondary tumor in hepatocellular carcinoma in mice. PeerJ 2020; 8:e8680. [PMID: 32219019 PMCID: PMC7087493 DOI: 10.7717/peerj.8680] [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: 08/20/2019] [Accepted: 02/03/2020] [Indexed: 12/24/2022] Open
Abstract
Background The tumor microenvironment (TM) in close contact with cancer cells is highly related to tumor growth and cancer metastasis. This study is to explore the biogenesis mechanism of a secondary hepatocellular carcinoma (HCC) based on the function of RNA binding proteins (RBPs)-encoding genes in the physiological microenvironment (PM). Methods The healthy and HCC mice were used to isolate the PM, pre-tumor microenvironment (PTM), and TM. The samples were analyzed using the technology of RNA-seq and bioinformatics. The differentially expressed RBPs-encoding genes (DERs) and differentially expressed DERs-associated genes (DEDs) were screened to undergo GO and KEGG analysis. Results 18 DERs and DEDs were identified in the PTM vs. PM, 87 in the TM vs. PTM, and 87 in the TM vs. PM. Those DERs and DEDs participated in the regulation of gene expression at the levels of chromatin conformation, gene activation and silencing, splicing and degradation of mRNA, biogenesis of piRNA and miRNA, ribosome assemble, and translation of proteins. Conclusion The genes encoding RBPs and the relevant genes are involved in the transformation from PM to PTM, then constructing the TM by regulating protein synthesis. This regulation included whole process of biological genetic information transmission from chromatin conformation to gene activation and silencing to mRNA splicing to ribosome assemble to translation of proteins and degradation of mRNA. The abnormality of those functions in the organic microenvironments promoted the metastasis of HCC and initiated the biogenesis of a secondary HCC in a PM when the PM encountered the invasion of cancer cells.
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Affiliation(s)
- Genliang Li
- Department of Biochemistry and Molecular Biology, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Anni Ni
- Department of Biochemistry and Molecular Biology, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Yulian Tang
- Department of Biochemistry and Molecular Biology, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Shubo Li
- Department of Biochemistry and Molecular Biology, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Lingzhang Meng
- Department of Biochemistry and Molecular Biology, Youjiang Medical University for Nationalities, Baise, Guangxi, China
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18
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Dai JY, Wang X, Wang B, Sun W, Jordahl KM, Kolb S, Nyame YA, Wright JL, Ostrander EA, Feng Z, Stanford JL. DNA methylation and cis-regulation of gene expression by prostate cancer risk SNPs. PLoS Genet 2020; 16:e1008667. [PMID: 32226005 PMCID: PMC7145271 DOI: 10.1371/journal.pgen.1008667] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 04/09/2020] [Accepted: 02/13/2020] [Indexed: 02/06/2023] Open
Abstract
Genome-wide association studies have identified more than 100 SNPs that increase the risk of prostate cancer (PrCa). We identify and compare expression quantitative trait loci (eQTLs) and CpG methylation quantitative trait loci (meQTLs) among 147 established PrCa risk SNPs in primary prostate tumors (n = 355 from a Seattle-based study and n = 495 from The Cancer Genome Atlas, TCGA) and tumor-adjacent, histologically benign samples (n = 471 from a Mayo Clinic study). The role of DNA methylation in eQTL regulation of gene expression was investigated by data triangulation using several causal inference approaches, including a proposed adaptation of the Causal Inference Test (CIT) for causal direction. Comparing eQTLs between tumors and benign samples, we show that 98 of the 147 risk SNPs were identified as eQTLs in the tumor-adjacent benign samples, and almost all 34 eQTL identified in tumor sets were also eQTLs in the benign samples. Three lines of results support the causal role of DNA methylation. First, nearly 100 of the 147 risk SNPs were identified as meQTLs in one tumor set, and almost all eQTLs in tumors were meQTLs. Second, the loss of eQTLs in tumors relative to benign samples was associated with altered DNA methylation. Third, among risk SNPs identified as both eQTLs and meQTLs, mediation analyses suggest that over two-thirds have evidence of a causal role for DNA methylation, mostly mediating genetic influence on gene expression. In summary, we provide a comprehensive catalog of eQTLs, meQTLs and putative cancer genes for known PrCa risk SNPs. We observe that a substantial portion of germline eQTL regulatory mechanisms are maintained in the tumor development, despite somatic alterations in tumor genome. Finally, our mediation analyses illuminate the likely intermediary role of CpG methylation in eQTL regulation of gene expression.
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Affiliation(s)
- James Y. Dai
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington School of Public Health, Seattle, Washington, United States of America
| | - Xiaoyu Wang
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
| | - Bo Wang
- Department of Laboratory Medicine, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Sun
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington School of Public Health, Seattle, Washington, United States of America
| | - Kristina M. Jordahl
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
| | - Suzanne Kolb
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
| | - Yaw A. Nyame
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Urology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Jonathan L. Wright
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Urology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Elaine A. Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, United States of America
| | - Ziding Feng
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington School of Public Health, Seattle, Washington, United States of America
| | - Janet L. Stanford
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, United States of America
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19
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Chen L, Pan X, Guo W, Gan Z, Zhang YH, Niu Z, Huang T, Cai YD. Investigating the gene expression profiles of cells in seven embryonic stages with machine learning algorithms. Genomics 2020; 112:2524-2534. [PMID: 32045671 DOI: 10.1016/j.ygeno.2020.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/26/2019] [Accepted: 02/07/2020] [Indexed: 12/15/2022]
Abstract
The development of embryonic cells involves several continuous stages, and some genes are related to embryogenesis. To date, few studies have systematically investigated changes in gene expression profiles during mammalian embryogenesis. In this study, a computational analysis using machine learning algorithms was performed on the gene expression profiles of mouse embryonic cells at seven stages. First, the profiles were analyzed through a powerful Monte Carlo feature selection method for the generation of a feature list. Second, increment feature selection was applied on the list by incorporating two classification algorithms: support vector machine (SVM) and repeated incremental pruning to produce error reduction (RIPPER). Through SVM, we extracted several latent gene biomarkers, indicating the stages of embryonic cells, and constructed an optimal SVM classifier that produced a nearly perfect classification of embryonic cells. Furthermore, some interesting rules were accessed by the RIPPER algorithm, suggesting different expression patterns for different stages.
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Affiliation(s)
- Lei Chen
- School of Life Sciences, Shanghai University, Shanghai 200444, China; College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China; Shanghai Key Laboratory of PMMP, East China Normal University, Shanghai 200241, China.
| | - XiaoYong Pan
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Key Laboratory of System Control and Information Processing, Ministry of Education of China, 200240 Shanghai, China.
| | - Wei Guo
- Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Zijun Gan
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Yu-Hang Zhang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Zhibin Niu
- College of Intelligence and Computing, Tianjin University, Tianjin 300072, China.
| | - Tao Huang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, China.
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20
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Hu Y, Gu J, Shen H, Shao T, Li S, Wang W, Yu Z. Circular RNA LARP4 correlates with decreased Enneking stage, better histological response, and prolonged survival profiles, and it elevates chemosensitivity to cisplatin and doxorubicin via sponging microRNA-424 in osteosarcoma. J Clin Lab Anal 2020; 34:e23045. [PMID: 31642110 PMCID: PMC7031593 DOI: 10.1002/jcla.23045] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/03/2019] [Accepted: 09/09/2019] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND This study aimed to evaluate the association of circular RNA La-related RNA-binding protein 4 (circ-LARP4) with clinical features and prognosis in osteosarcoma patients, and further explore its effect on chemosensitivity in osteosarcoma cells. METHODS Seventy-two osteosarcoma patients with Enneking stage IIA-IIB who underwent resection were consecutively enrolled, and then, tumor tissues and non-tumor tissues were obtained. Circ-LARP4 in tumor tissue/non-tumor tissue was detected by quantitative polymerase chain reaction. After circ-LARP4 overexpression and negative control overexpression plasmid transfection, relative cell viability (%) was evaluated by Cell Counting Kit-8 in MG63 cells treated by different concentrations of cisplatin, methotrexate, and doxorubicin, and IC50 was calculated. RESULTS Circ-LARP4 was downregulated in tumor tissue compared with non-tumor tissue and had a good value in distinguishing tumor tissue from non-tumor tissue with an area under curve of 0.829 (95% CI: 0.762-0.859). Meanwhile, tumor circ-LARP4 was negatively correlated with the Enneking stage. After resection, circ-LARP4 high expression patients showed an increased tumor cell necrosis rate to adjuvant chemotherapy compared to circ-LARP4 low expression patients, and circ-LARP4 high expression correlated with prolonged disease-free survival and overall survival. In vitro experiments revealed that circ-LARP4 overexpression elevated the chemosensitivity of MG63 cells to cisplatin and doxorubicin but not methotrexate, with decreased cisplatin IC50 and doxorubicin IC50 concentrations than negative control. Besides, miR-424 overexpression attenuated the chemosensitivity in circ-LARP4 overexpression-treated MG63 cells. CONCLUSION Circ-LARP4 high expression correlates with decreased Enneking stage and prolonged survival profiles, and it elevates chemosensitivity to cisplatin and doxorubicin via sponging miR-424 in osteosarcoma.
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Affiliation(s)
- Yuhang Hu
- Department of OrthopedicsThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Jiaao Gu
- Department of OrthopedicsThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Hongtao Shen
- Department of OrthopedicsThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Tuo Shao
- Department of OrthopedicsThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Song Li
- Department of OrthopedicsThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Wei Wang
- Department of OrthopedicsThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Zhange Yu
- Department of OrthopedicsThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
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21
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The Butterfly Effect of RNA Alterations on Transcriptomic Equilibrium. Cells 2019; 8:cells8121634. [PMID: 31847302 PMCID: PMC6953095 DOI: 10.3390/cells8121634] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/11/2019] [Accepted: 12/11/2019] [Indexed: 12/17/2022] Open
Abstract
: Post-transcriptional regulation plays a key role in modulating gene expression, and the perturbation of transcriptomic equilibrium has been shown to drive the development of multiple diseases including cancer. Recent studies have revealed the existence of multiple post-transcriptional processes that coordinatively regulate the expression and function of each RNA transcript. In this review, we summarize the latest research describing various mechanisms by which small alterations in RNA processing or function can potentially reshape the transcriptomic landscape, and the impact that this may have on cancer development.
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22
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Haga RB, Garg R, Collu F, Borda D'Agua B, Menéndez ST, Colomba A, Fraternali F, Ridley AJ. RhoBTB1 interacts with ROCKs and inhibits invasion. Biochem J 2019; 476:2499-2514. [PMID: 31431478 PMCID: PMC6744581 DOI: 10.1042/bcj20190203] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/31/2022]
Abstract
RhoBTB1 is an atypical Rho GTPase with two BTB domains in addition to its Rho domain. Although most Rho GTPases regulate actin cytoskeletal dynamics, RhoBTB1 is not known to affect cell shape or motility. We report that RhoBTB1 depletion increases prostate cancer cell invasion and induces elongation in Matrigel, a phenotype similar to that induced by depletion of ROCK1 and ROCK2. We demonstrate that RhoBTB1 associates with ROCK1 and ROCK2 and its association with ROCK1 is via its Rho domain. The Rho domain binds to the coiled-coil region of ROCK1 close to its kinase domain. We identify two amino acids within the Rho domain that alter RhoBTB1 association with ROCK1. RhoBTB1 is a substrate for ROCK1, and mutation of putative phosphorylation sites reduces its association with Cullin3, a scaffold for ubiquitin ligases. We propose that RhoBTB1 suppresses cancer cell invasion through interacting with ROCKs, which in turn regulate its association with Cullin3. Via Cullin3, RhoBTB1 has the potential to affect protein degradation.
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Affiliation(s)
- Raquel B Haga
- Randall Centre of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, U.K
| | - Ritu Garg
- Randall Centre of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, U.K
| | - Francesca Collu
- Randall Centre of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, U.K
| | - Bárbara Borda D'Agua
- Randall Centre of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, U.K
| | - Sofia T Menéndez
- Randall Centre of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, U.K
| | - Audrey Colomba
- Randall Centre of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, U.K
| | - Franca Fraternali
- Randall Centre of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, U.K
| | - Anne J Ridley
- Randall Centre of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, U.K.
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, U.K
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23
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Mohibi S, Chen X, Zhang J. Cancer the'RBP'eutics-RNA-binding proteins as therapeutic targets for cancer. Pharmacol Ther 2019; 203:107390. [PMID: 31302171 DOI: 10.1016/j.pharmthera.2019.07.001] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/02/2019] [Indexed: 12/11/2022]
Abstract
RNA-binding proteins (RBPs) play a critical role in the regulation of various RNA processes, including splicing, cleavage and polyadenylation, transport, translation and degradation of coding RNAs, non-coding RNAs and microRNAs. Recent studies indicate that RBPs not only play an instrumental role in normal cellular processes but have also emerged as major players in the development and spread of cancer. Herein, we review the current knowledge about RNA binding proteins and their role in tumorigenesis as well as the potential to target RBPs for cancer therapeutics.
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Affiliation(s)
- Shakur Mohibi
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States
| | - Xinbin Chen
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States
| | - Jin Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States.
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24
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Cruz-Gallardo I, Martino L, Kelly G, Atkinson R, Trotta R, De Tito S, Coleman P, Ahdash Z, Gu Y, Bui TTT, Conte MR. LARP4A recognizes polyA RNA via a novel binding mechanism mediated by disordered regions and involving the PAM2w motif, revealing interplay between PABP, LARP4A and mRNA. Nucleic Acids Res 2019; 47:4272-4291. [PMID: 30820564 PMCID: PMC6486636 DOI: 10.1093/nar/gkz144] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 11/22/2022] Open
Abstract
LARP4A belongs to the ancient RNA-binding protein superfamily of La-related proteins (LARPs). In humans, it acts mainly by stabilizing mRNAs, enhancing translation and controlling polyA lengths of heterologous mRNAs. These activities are known to implicate its association with mRNA, protein partners and translating ribosomes, albeit molecular details are missing. Here, we characterize the direct interaction between LARP4A, oligoA RNA and the MLLE domain of the PolyA-binding protein (PABP). Our study shows that LARP4A-oligoA association entails novel RNA recognition features involving the N-terminal region of the protein that exists in a semi-disordered state and lacks any recognizable RNA-binding motif. Against expectations, we show that the La module, the conserved RNA-binding unit across LARPs, is not the principal determinant for oligoA interaction, only contributing to binding to a limited degree. Furthermore, the variant PABP-interacting motif 2 (PAM2w) featured in the N-terminal region of LARP4A was found to be important for both RNA and PABP recognition, revealing a new role for this protein-protein binding motif. Our analysis demonstrates the mutual exclusive nature of the PAM2w-mediated interactions, thereby unveiling a tantalizing interplay between LARP4A, polyA and PABP.
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Affiliation(s)
- Isabel Cruz-Gallardo
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
| | - Luigi Martino
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
| | - Geoff Kelly
- MRC Biomedical NMR Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - R Andrew Atkinson
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
- Centre for Biomolecular Spectroscopy, King’s College London, London SE1 1UL, UK
| | - Roberta Trotta
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
| | - Stefano De Tito
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
| | - Pierre Coleman
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
| | - Zainab Ahdash
- Department of Chemistry, King’s College London, London SE1 1DB, UK
| | - Yifei Gu
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
| | - Tam T T Bui
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
- Centre for Biomolecular Spectroscopy, King’s College London, London SE1 1UL, UK
| | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
- Centre for Biomolecular Spectroscopy, King’s College London, London SE1 1UL, UK
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25
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Abstract
Cancer is a serious health issue in the world due to a large body of cancer-related human deaths, and there is no current treatment available to efficiently treat the disease as the tumor is often diagnosed at a serious stage. Moreover, Cancer cells are often resistant to chemotherapy, radiotherapy, and molecular-targeted therapy. Upon further knowledge of mechanisms of tumorigenesis, aggressiveness, metastasis, and resistance to treatments, it is necessary to detect the disease at an earlier stage and for a better response to therapy. The hippo pathway possesses the unique capacity to lead to tumorigenesis. Mutations and altered expression of its core components (MST1/2, LATS1/2, YAP and TAZ) promote the migration, invasion, malignancy of cancer cells. The biological significance and deregulation of it have received a large body of interests in the past few years. Further understanding of hippo pathway will be responsible for cancer treatment. In this review, we try to discover the function of hippo pathway in different diversity of cancers, and discuss how Hippo pathway contributes to other cellular signaling pathways. Also, we try to describe how microRNAs, circRNAs, and ZNFs regulate hippo pathway in the process of cancer. It is necessary to find new therapy strategies for cancer.
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Affiliation(s)
- Yanyan Han
- Department of Pathology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, 2-5-1, Shikata-cho, Kita-ku, Okayama, 700-8558, Japan.
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26
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Cruz-Gallardo I, Martino L, Trotta R, De Tito S, Kelly G, Atkinson RA, Randazzo A, Conte MR. Resonance assignment of human LARP4A La module. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:169-172. [PMID: 30632004 PMCID: PMC6439165 DOI: 10.1007/s12104-019-09871-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/03/2019] [Indexed: 06/09/2023]
Abstract
Human LARP4A belongs to a superfamily of RNA binding proteins called La-related proteins (LARPs). Whilst being a positive regulator of protein synthesis and a promoter of mRNA stability, LARP4A also controls cell morphology and motility in human breast and prostate cancer cells. All LARPs share a characteristic RNA binding unit named the La-module, which despite a high level of primary structure conservation exhibits a great versatility in RNA target selection. Human LARP4A La-module is the most divergent compared with other LARPs and its RNA recognition properties have only recently started to be revealed. Given the key role of LARP4A protein in cancer cell biology, we have initiated a complete NMR characterisation of its La-module and here we report the assignment of 1H, 15N and 13C resonances resulting from our studies.
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Affiliation(s)
- Isabel Cruz-Gallardo
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
- Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK
| | - Luigi Martino
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Roberta Trotta
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Stefano De Tito
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Geoff Kelly
- MRC Biomedical NMR Centre, The Francis Crick Institute, London, NW1 1AT, UK
| | - R Andrew Atkinson
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
- Centre for Biomolecular Spectroscopy, King's College London, London, SE1 1UL, UK
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK.
- Centre for Biomolecular Spectroscopy, King's College London, London, SE1 1UL, UK.
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27
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Egiz M, Usui T, Ishibashi M, Zhang X, Shigeta S, Toyoshima M, Kitatani K, Yaegashi N. La-Related Protein 4 as a Suppressor for Motility of Ovarian Cancer Cells. TOHOKU J EXP MED 2019; 247:59-67. [PMID: 30686809 DOI: 10.1620/tjem.247.59] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The La-related proteins (LARPs) are a family of RNA binding proteins that control the degradation and stabilization of RNAs. As emerging research reveals the biology of each LARP, it is evident that LARPs are dysregulated in some types of cancer. Upregulation of cell motility potentiates the metastatic potential of ovarian cancer cells; however, the roles of LARPs in cell motility remain unknown. In the present study, we investigated the roles of LARPs in the progression of ovarian cancer using SKOV3 human ovarian cancer cells and a public database that integrates microarray-based gene expression data and clinical data. To explore the involvement of LARPs in the cell motility, we performed RNA interference screening for LARP mRNAs in SKOV3 cells. The screening identified LARP4 as a potential suppressor of the formation of lamellipodia. Conversely, enforced expression of LARP4 suppressed the formation of lamellipodia. Moreover, cell migration was significantly increased in LARP4-depleted SKOV3 cells. Mechanistically, LARP4 depletion was associated with the decrease in RhoA protein expression. These results suggest that LARP4 may limit RhoA-dependent cell motility. In a mouse xenograft model with SKOV3 cells, LARP4 depletion potentiated peritoneal metastasis. Upon analysis of a public database of patients with ovarian cancer, the LARP4 mRNA-high expression group (n = 166) showed longer overall survival compared with the LARP4 mRNA-low expression group (n = 489), implying a positive correlation of LARP4 mRNA levels in ovarian cancer tissues with patient prognosis. Taken together, we propose that LARP4 could suppress motility and metastatic potential of ovarian cancer cells.
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Affiliation(s)
- Mahy Egiz
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Tohoku University
- Department of Obstetrics and Gynecology, Menoufia University Graduate School of Medicine
| | - Toshinori Usui
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Tohoku University
| | - Masumi Ishibashi
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Tohoku University
| | - Xuewei Zhang
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Tohoku University
| | - Shogo Shigeta
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Tohoku University
| | - Masafumi Toyoshima
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Tohoku University
| | - Kazuyuki Kitatani
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Tohoku University
- Tohoku Medical Megabank Organization, Tohoku University
- Laboratory of Immunopharmacology, Faculty of Pharmaceutical Sciences, Setsunan University
| | - Nobuo Yaegashi
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Tohoku University
- Tohoku Medical Megabank Organization, Tohoku University
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28
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Fyn Regulates Binding Partners of Cyclic-AMP Dependent Protein Kinase A. Proteomes 2018; 6:proteomes6040037. [PMID: 30274258 PMCID: PMC6313912 DOI: 10.3390/proteomes6040037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 12/03/2022] Open
Abstract
The cAMP-dependent protein kinase A (PKA) is a serine/threonine kinase involved in many fundamental cellular processes, including migration and proliferation. Recently, we found that the Src family kinase Fyn phosphorylates the catalytic subunit of PKA (PKA-C) at Y69, thereby increasing PKA kinase activity. We also showed that Fyn induced the phosphorylation of cellular proteins within the PKA preferred target motif. This led to the hypothesis that Fyn could affect proteins in complex with PKA. To test this, we employed a quantitative mass spectrometry approach to identify Fyn-dependent binding partners in complex with PKA-C. We found Fyn enhanced the binding of PKA-C to several cytoskeletal regulators that localize to the centrosome and Golgi apparatus. Three of these Fyn-induced PKA interactors, AKAP9, PDE4DIP, and CDK5RAP2, were validated biochemically and were shown to exist in complex with Fyn and PKA in a glioblastoma cell line. Intriguingly, the complexes formed between PKA-C and these known AKAPs were dependent upon Fyn catalytic activity and expression levels. In addition, we identified Fyn-regulated phosphorylation sites on proteins in complex with PKA-C. We also identified and biochemically validated a novel PKA-C interactor, LARP4, which complexed with PKA in the absence of Fyn. These results demonstrate the ability of Fyn to influence the docking of PKA to specific cellular scaffolds and suggest that Fyn may affect the downstream substrates targeted by PKA.
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29
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Advances of circular RNAs in carcinoma. Biomed Pharmacother 2018; 107:59-71. [PMID: 30077838 DOI: 10.1016/j.biopha.2018.07.164] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 07/29/2018] [Accepted: 07/31/2018] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) are a type of non-coding RNAs with single-stranded closed structure. The rapid development of high-throughput sequencing technology has allowed for the widespread presence of circRNAs in transcriptomes. Moreover, increasing studies have identified a correlation between circRNAs and different cancers. In addition, most circRNAs are dysregulated in various cancers, and some of them have been reported be vital in the occurrence and development of tumors. For example, ciRS-7 plays a role in tumor promotion and circ-ITCH acts as a tumor suppressor. This review summarizes the latest progressions in the field regarding the functions of circRNAs in relation with cancers, and anticipates the emerging roles of circRNAs and future challenges in cancer research.
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30
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Del Favero G, Woelflingseder L, Janker L, Neuditschko B, Seriani S, Gallina P, Sbaizero O, Gerner C, Marko D. Deoxynivalenol induces structural alterations in epidermoid carcinoma cells A431 and impairs the response to biomechanical stimulation. Sci Rep 2018; 8:11351. [PMID: 30054545 PMCID: PMC6063857 DOI: 10.1038/s41598-018-29728-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 07/12/2018] [Indexed: 12/12/2022] Open
Abstract
Morphology together with the capability to respond to surrounding stimuli are key elements governing the spatial interaction of living cells with the environment. In this respect, biomechanical stimulation can trigger significant physiological cascades that can potentially modulate toxicity. Deoxynivalenol (DON, vomitoxin) is one of the most prevalent mycotoxins produced by Fusarium spp. and it was used to explore the delicate interaction between biomechanical stimulation and cytotoxicity in A431 cells. In fact, in addition of being a food contaminant, DON is a relevant toxin for several organ systems. The combination between biomechanical stimulation and the mycotoxin revealed how DON can impair crucial functions affecting cellular morphology, tubulin and lysosomes at concentrations even below those known to be cytotoxic in routine toxicity studies. Sub-toxic concentrations of DON (0.1-1 μM) impaired the capability of A431 cells to respond to a biomechanical stimulation that normally sustains trophic effects in these cells. Moreover, the effects of DON (0.1-10 μM) were partially modulated by the application of uniaxial stretching (0.5 Hz, 24 h, 15% deformation). Ultimately, proteomic analysis revealed the potential of DON to alter several proteins necessary for cell adhesion and cytoskeletal modulation suggesting a molecular link between biomechanics and the cytotoxic potential of the mycotoxin.
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Affiliation(s)
- Giorgia Del Favero
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Währingerstr. 38-40, 1090, Vienna, Austria.
| | - Lydia Woelflingseder
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Währingerstr. 38-40, 1090, Vienna, Austria
| | - Lukas Janker
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 38-40, 1090, Vienna, Austria
| | - Benjamin Neuditschko
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 38-40, 1090, Vienna, Austria
| | - Stefano Seriani
- Department of Engineering and Architecture, University of Trieste Via A, Valerio 10, 34127, Trieste, Italy
- Robotik und Mechatronik Zentrum, Deutsches Zentrum für Luft- und Raumfahrt e.V. (DLR), Oberpfaffenhofen, Germany
| | - Paolo Gallina
- Department of Engineering and Architecture, University of Trieste Via A, Valerio 10, 34127, Trieste, Italy
| | - Orfeo Sbaizero
- Department of Engineering and Architecture, University of Trieste Via A, Valerio 10, 34127, Trieste, Italy
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 38-40, 1090, Vienna, Austria
| | - Doris Marko
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Währingerstr. 38-40, 1090, Vienna, Austria
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31
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Cortesi M, Llamosas E, Henry CE, Kumaran RYA, Ng B, Youkhana J, Ford CE. I-AbACUS: a Reliable Software Tool for the Semi-Automatic Analysis of Invasion and Migration Transwell Assays. Sci Rep 2018; 8:3814. [PMID: 29491372 PMCID: PMC5830488 DOI: 10.1038/s41598-018-22091-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 02/16/2018] [Indexed: 12/17/2022] Open
Abstract
The quantification of invasion and migration is an important aspect of cancer research, used both in the study of the molecular processes involved in this collection of diseases and the evaluation of the efficacy of new potential treatments. The transwell assay, while being one of the most widely used techniques for the evaluation of these characteristics, shows a high dependence on the operator's ability to correctly identify the cells and a low protocol standardization. Here we present I-AbACUS, a software tool specifically designed to aid the analysis of transwell assays that automatically and specifically recognizes cells in images of stained membranes and provides the user with a suggested cell count. A complete description of this instrument, together with its validation against the standard analysis technique for this assay is presented. Furthermore, we show that I-AbACUS is versatile and able to elaborate images containing cells with different morphologies and that the obtained results are less dependent on the operator and their experience. We anticipate that this instrument, freely available (Gnu Public Licence GPL v2) at www.marilisacortesi.com as a standalone application, could significantly improve the quantification of invasion and migration of cancer cells.
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Affiliation(s)
- Marilisa Cortesi
- Laboratory of Cellular and Molecular Engineering "S. Cavalcanti", Department of Electrical, Electronic and Information Engineering "G. Marconi" (DEI), University of Bologna, Cesena, Italy.
| | - Estelle Llamosas
- Gynaecological Cancer Research Group, Lowy Cancer Research Centre and School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Claire E Henry
- Gynaecological Cancer Research Group, Lowy Cancer Research Centre and School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Raani-Yogeeta A Kumaran
- Gynaecological Cancer Research Group, Lowy Cancer Research Centre and School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Benedict Ng
- Adult Cancer Program, Lowy Cancer Research Center, Prince of Wales Clinical School, University of New South Wales, Sydney, Australia
| | - Janet Youkhana
- Adult Cancer Program, Lowy Cancer Research Center, Prince of Wales Clinical School, University of New South Wales, Sydney, Australia
| | - Caroline E Ford
- Gynaecological Cancer Research Group, Lowy Cancer Research Centre and School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, Australia.
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32
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Maraia RJ, Mattijssen S, Cruz-Gallardo I, Conte MR. The La and related RNA-binding proteins (LARPs): structures, functions, and evolving perspectives. WILEY INTERDISCIPLINARY REVIEWS. RNA 2017; 8:10.1002/wrna.1430. [PMID: 28782243 PMCID: PMC5647580 DOI: 10.1002/wrna.1430] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 01/02/2023]
Abstract
La was first identified as a polypeptide component of ribonucleic protein complexes targeted by antibodies in autoimmune patients and is now known to be a eukaryote cell-ubiquitous protein. Structure and function studies have shown that La binds to a common terminal motif, UUU-3'-OH, of nascent RNA polymerase III (RNAP III) transcripts and protects them from exonucleolytic decay. For precursor-tRNAs, the most diverse and abundant of these transcripts, La also functions as an RNA chaperone that helps to prevent their misfolding. Related to this, we review evidence that suggests that La and its link to RNAP III were significant in the great expansions of the tRNAomes that occurred in eukaryotes. Four families of La-related proteins (LARPs) emerged during eukaryotic evolution with specialized functions. We provide an overview of the high-resolution structural biology of La and LARPs. LARP7 family members most closely resemble La but function with a single RNAP III nuclear transcript, 7SK, or telomerase RNA. A cytoplasmic isoform of La protein as well as LARPs 6, 4, and 1 function in mRNA metabolism and translation in distinct but similar ways, sometimes with the poly(A)-binding protein, and in some cases by direct binding to poly(A)-RNA. New structures of LARP domains, some complexed with RNA, provide novel insights into the functional versatility of these proteins. We also consider LARPs in relation to ancestral La protein and potential retention of links to specific RNA-related pathways. One such link may be tRNA surveillance and codon usage by LARP-associated mRNAs. WIREs RNA 2017, 8:e1430. doi: 10.1002/wrna.1430 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Richard J. Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
- Commissioned Corps, U.S. Public Health Service, Rockville, MD USA
| | - Sandy Mattijssen
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
| | - Isabel Cruz-Gallardo
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
| | - Maria R. Conte
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
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33
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Zhang J, Liu H, Hou L, Wang G, Zhang R, Huang Y, Chen X, Zhu J. Circular RNA_LARP4 inhibits cell proliferation and invasion of gastric cancer by sponging miR-424-5p and regulating LATS1 expression. Mol Cancer 2017; 16:151. [PMID: 28893265 PMCID: PMC5594516 DOI: 10.1186/s12943-017-0719-3] [Citation(s) in RCA: 410] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/31/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Non-coding RNAs (ncRNAs) have been shown to regulate gene expression involved in tumor progression of multiple malignancies. Our previous studies indicated that large tumor suppressor kinase 1 (LATS1), a core part of Hippo signaling pathway, functions as a tumor suppressor in gastric cancer (GC). But, the underlying molecular mechanisms by which ncRNAs modulate LATS1 expression in GC remain undetermined. METHODS The correlation of LATS1 and has-miR-424-5p (miR-424) expression with clinicopathological characteristics and prognosis of GC patients was analyzed by TCGA RNA-sequencing data. A novel circular RNA_LARP4 (circLARP4) was identified to sponge miR-424 by circRNA expression profile and bioinformatic analysis. The binding site between miR-424 and LATS1 or circLARP4 was verified using dual luciferase assay and RNA immunoprecipitation (RIP) assay. The expression and localization of circLARP4 in GC tissues were investigated by fluorescence in situ hybridization (FISH). MTT, colony formation, Transwell and EdU assays were performed to assess the effects of miR-424 or circLARP4 on cell proliferation and invasion. RESULTS Increased miR-424 expression or decreased LATS1 expression was associated with pathological stage and unfavorable prognosis of GC patients. Ectopic expression of miR-424 promoted proliferation and invasion of GC cells by targeting LATS1 gene. Furthermore, circLARP4 was mainly localized in the cytoplasm and inhibited biological behaviors of GC cells by sponging miR-424. The expression of circLARP4 was downregulated in GC tissues and represented an independent prognostic factor for overall survival of GC patients. CONCLUSION circLARP4 may act as a novel tumor suppressive factor and a potential biomarker in GC.
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Affiliation(s)
- Jing Zhang
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, No. 600 Yishan Road, Shanghai, 200233, China
| | - Hui Liu
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, No. 600 Yishan Road, Shanghai, 200233, China
| | - Lidan Hou
- Department of Gastroenterology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ge Wang
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, No. 600 Yishan Road, Shanghai, 200233, China
| | - Rui Zhang
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, No. 600 Yishan Road, Shanghai, 200233, China
| | - Yanxia Huang
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, No. 600 Yishan Road, Shanghai, 200233, China
| | - Xiaoyu Chen
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, No. 600 Yishan Road, Shanghai, 200233, China
| | - Jinshui Zhu
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, No. 600 Yishan Road, Shanghai, 200233, China.
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34
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Hu Z, Yau C, Ahmed AA. A pan-cancer genome-wide analysis reveals tumour dependencies by induction of nonsense-mediated decay. Nat Commun 2017; 8:15943. [PMID: 28649990 PMCID: PMC5490262 DOI: 10.1038/ncomms15943] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 05/15/2017] [Indexed: 12/12/2022] Open
Abstract
Nonsense-mediated decay (NMD) eliminates transcripts with premature termination codons. Although NMD-induced loss-of-function has been shown to contribute to the genesis of particular cancers, its global functional consequence in tumours has not been characterized. Here we develop an algorithm to predict NMD and apply it on somatic mutations reported in The Cancer Genome Atlas. We identify more than 73 K mutations that are predicted to elicit NMD (NMD-elicit). NMD-elicit mutations in tumour suppressor genes (TSGs) are associated with significant reduction in gene expression. We discover cancer-specific NMD-elicit signatures in TSGs and cancer-associated genes. Our analysis reveals a previously unrecognized dependence of hypermutated tumours on hypofunction of genes that are involved in chromatin remodelling and translation. Half of hypermutated stomach adenocarcinomas are associated with NMD-elicit mutations of the translation initiators LARP4B and EIF5B. Our results unravel strong therapeutic opportunities by targeting tumour dependencies on NMD-elicit mutations.
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Affiliation(s)
- Zhiyuan Hu
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DU, UK
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Oxford OX3 9DU, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Christopher Yau
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Ahmed Ashour Ahmed
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DU, UK
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Oxford OX3 9DU, UK
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Pereira B, Billaud M, Almeida R. RNA-Binding Proteins in Cancer: Old Players and New Actors. Trends Cancer 2017; 3:506-528. [PMID: 28718405 DOI: 10.1016/j.trecan.2017.05.003] [Citation(s) in RCA: 459] [Impact Index Per Article: 65.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/04/2017] [Accepted: 05/05/2017] [Indexed: 12/15/2022]
Abstract
RNA-binding proteins (RBPs) are key players in post-transcriptional events. The combination of versatility of their RNA-binding domains with structural flexibility enables RBPs to control the metabolism of a large array of transcripts. Perturbations in RBP-RNA networks activity have been causally associated with cancer development, but the rational framework describing these contributions remains fragmented. We review here the evidence that RBPs modulate multiple cancer traits, emphasize their functional diversity, and assess future trends in the study of RBPs in cancer.
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Affiliation(s)
- Bruno Pereira
- i3S - Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-465 Porto, Portugal.
| | - Marc Billaud
- Clinical and Experimental Model of Lymphomagenesis, Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1052, Centre National de la Recherche Scientifique (CNRS) Unité 5286, Centre Léon Bérard, Université Claude Bernard Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Raquel Almeida
- i3S - Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-465 Porto, Portugal; Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; Biology Department, Faculty of Sciences of the University of Porto, 4169-007 Porto, Portugal
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