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Cheng L, Yang C, Lu J, Huang M, Xie R, Lynch S, Elfman J, Huang Y, Liu S, Chen S, He B, Lin T, Li H, Chen X, Huang J. Oncogenic SLC2A11-MIF fusion protein interacts with polypyrimidine tract binding protein 1 to facilitate bladder cancer proliferation and metastasis by regulating mRNA stability. MedComm (Beijing) 2024; 5:e685. [PMID: 39156764 PMCID: PMC11324686 DOI: 10.1002/mco2.685] [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: 12/20/2023] [Revised: 07/03/2024] [Accepted: 07/14/2024] [Indexed: 08/20/2024] Open
Abstract
Chimeric RNAs, distinct from DNA gene fusions, have emerged as promising therapeutic targets with diverse functions in cancer treatment. However, the functional significance and therapeutic potential of most chimeric RNAs remain unclear. Here we identify a novel fusion transcript of solute carrier family 2-member 11 (SLC2A11) and macrophage migration inhibitory factor (MIF). In this study, we investigated the upregulation of SLC2A11-MIF in The Cancer Genome Atlas cohort and a cohort of patients from Sun Yat-Sen Memorial Hospital. Subsequently, functional investigations demonstrated that SLC2A11-MIF enhanced the proliferation, antiapoptotic effects, and metastasis of bladder cancer cells in vitro and in vivo. Mechanistically, the fusion protein encoded by SLC2A11-MIF interacted with polypyrimidine tract binding protein 1 (PTBP1) and regulated the mRNA half-lives of Polo Like Kinase 1, Roundabout guidance receptor 1, and phosphoinositide-3-kinase regulatory subunit 3 in BCa cells. Moreover, PTBP1 knockdown abolished the enhanced impact of SLC2A11-MIF on biological function and mRNA stability. Furthermore, the expression of SLC2A11-MIF mRNA is regulated by CCCTC-binding factor and stabilized through RNA N4-acetylcytidine modification facilitated by N-acetyltransferase 10. Overall, our findings revealed a significant fusion protein orchestrated by the SLC2A11-MIF-PTBP1 axis that governs mRNA stability during the multistep progression of bladder cancer.
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Affiliation(s)
- Liang Cheng
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
| | - Chenwei Yang
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
| | - Junlin Lu
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
| | - Ming Huang
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Clinical Research Center for Urological DiseasesDepartment of Urology, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Ruihui Xie
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Clinical Research Center for Urological DiseasesDepartment of Urology, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Sarah Lynch
- Department of PathologySchool of MedicineUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Justin Elfman
- Department of PathologySchool of MedicineUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Yuhang Huang
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
| | - Sen Liu
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
| | - Siting Chen
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
| | - Baoqing He
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
| | - Tianxin Lin
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Clinical Research Center for Urological DiseasesDepartment of Urology, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Hui Li
- Department of PathologySchool of MedicineUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Xu Chen
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Clinical Research Center for Urological DiseasesDepartment of Urology, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Jian Huang
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Clinical Research Center for Urological DiseasesDepartment of Urology, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
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Singh S, Shi X, Haddox S, Elfman J, Ahmad SB, Lynch S, Manley T, Piczak C, Phung C, Sun Y, Sharma A, Li H. RTCpredictor: identification of read-through chimeric RNAs from RNA sequencing data. Brief Bioinform 2024; 25:bbae251. [PMID: 38796690 PMCID: PMC11128028 DOI: 10.1093/bib/bbae251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/30/2024] [Accepted: 05/09/2024] [Indexed: 05/28/2024] Open
Abstract
Read-through chimeric RNAs are being recognized as a means to expand the functional transcriptome and contribute to cancer tumorigenesis when mis-regulated. However, current software tools often fail to predict them. We have developed RTCpredictor, utilizing a fast ripgrep tool to search for all possible exon-exon combinations of parental gene pairs. We also added exonic variants allowing searches containing common SNPs. To our knowledge, it is the first read-through chimeric RNA specific prediction method that also provides breakpoint coordinates. Compared with 10 other popular tools, RTCpredictor achieved high sensitivity on a simulated and three real datasets. In addition, RTCpredictor has less memory requirements and faster execution time, making it ideal for applying on large datasets.
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Affiliation(s)
- Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Xinrui Shi
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Samuel Haddox
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Justin Elfman
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Syed Basil Ahmad
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Sarah Lynch
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Tommy Manley
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Claire Piczak
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Christopher Phung
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Yunan Sun
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Aadi Sharma
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
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3
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Li H, Wang Q. Chimeric RNAs and their implication in prostate cancer. CANCER PATHOGENESIS AND THERAPY 2023; 1:216-219. [PMID: 38327838 PMCID: PMC10846317 DOI: 10.1016/j.cpt.2023.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 02/09/2024]
Abstract
•Chimeric ribonucleic acids (RNAs) form through gene fusion, trans-splicing, or cis-splicing between adjacent genes (cis-SAGe) mechanisms•Chimeric RNAs influence prostate cancer (PCa) progression by acting as long noncoding RNAs (lncRNAs) or circular RNAs (circRNAs), coding fusion proteins, and misregulating parental genes•Misregulated chimeric RNAs represent a novel repertoire for biomarkers and targets for PCa therapy.
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Affiliation(s)
- Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Qiong Wang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
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Oreper D, Klaeger S, Jhunjhunwala S, Delamarre L. The peptide woods are lovely, dark and deep: Hunting for novel cancer antigens. Semin Immunol 2023; 67:101758. [PMID: 37027981 DOI: 10.1016/j.smim.2023.101758] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 04/08/2023]
Abstract
Harnessing the patient's immune system to control a tumor is a proven avenue for cancer therapy. T cell therapies as well as therapeutic vaccines, which target specific antigens of interest, are being explored as treatments in conjunction with immune checkpoint blockade. For these therapies, selecting the best suited antigens is crucial. Most of the focus has thus far been on neoantigens that arise from tumor-specific somatic mutations. Although there is clear evidence that T-cell responses against mutated neoantigens are protective, the large majority of these mutations are not immunogenic. In addition, most somatic mutations are unique to each individual patient and their targeting requires the development of individualized approaches. Therefore, novel antigen types are needed to broaden the scope of such treatments. We review high throughput approaches for discovering novel tumor antigens and some of the key challenges associated with their detection, and discuss considerations when selecting tumor antigens to target in the clinic.
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Affiliation(s)
- Daniel Oreper
- Genentech, 1 DNA way, South San Francisco, 94080 CA, USA.
| | - Susan Klaeger
- Genentech, 1 DNA way, South San Francisco, 94080 CA, USA.
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Singh S, Shi X, Ahmad SB, Manley T, Piczak C, Phung C, Sun Y, Lynch S, Sharma A, Li H. RTCpredictor: Identification of Read-Through Chimeric RNAs from RNA Sequencing Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526869. [PMID: 36778443 PMCID: PMC9915620 DOI: 10.1101/2023.02.02.526869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Read-through chimeric RNAs are gaining attention in cancer and other research fields, yet current tools often fail in predicting them. We have thus developed the first read-through chimeric RNA specific prediction method, RTCpredictor, utilizing a fast ripgrep algorithm to search for all possible exon-exon combinations of parental gene pairs. Compared with other ten popular tools, RTCpredictor achieved top performance on both simulated and real datasets. We randomly selected up to 30 candidate read-through chimeras predicted from each software method and experimentally validated a total of 109 read-throughs and on this set, RTCpredictor outperformed all the other methods. In addition, RTCpredictor ( https://github.com/sandybioteck/RTCpredictor ) has less memory requirements and faster execution time.
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Dorney R, Dhungel BP, Rasko JEJ, Hebbard L, Schmitz U. Recent advances in cancer fusion transcript detection. Brief Bioinform 2022; 24:6918739. [PMID: 36527429 PMCID: PMC9851307 DOI: 10.1093/bib/bbac519] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/11/2022] [Accepted: 10/31/2022] [Indexed: 12/23/2022] Open
Abstract
Extensive investigation of gene fusions in cancer has led to the discovery of novel biomarkers and therapeutic targets. To date, most studies have neglected chromosomal rearrangement-independent fusion transcripts and complex fusion structures such as double or triple-hop fusions, and fusion-circRNAs. In this review, we untangle fusion-related terminology and propose a classification system involving both gene and transcript fusions. We highlight the importance of RNA-level fusions and how long-read sequencing approaches can improve detection and characterization. Moreover, we discuss novel bioinformatic tools to identify fusions in long-read sequencing data and strategies to experimentally validate and functionally characterize fusion transcripts.
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Affiliation(s)
- Ryley Dorney
- epartment of Molecular & Cell Biology, College of Public Health, Medical & Vet Sciences, James Cook University, Douglas, QLD 4811, Australia,Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns 4878, Australia
| | - Bijay P Dhungel
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia,Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2006, Australia,Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns 4878, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia,Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Lionel Hebbard
- epartment of Molecular & Cell Biology, College of Public Health, Medical & Vet Sciences, James Cook University, Douglas, QLD 4811, Australia,Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, Sydney, New South Wales, Australia
| | - Ulf Schmitz
- Corresponding author. Ulf Schmitz, Department of Molecular and Cell Biology, College of Public Health, Medical and Vet Sciences, James Cook University, Douglas, QLD 4811, Australia. E-mail:
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7
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Sun Y, Li H. Chimeric RNAs Discovered by RNA Sequencing and Their Roles in Cancer and Rare Genetic Diseases. Genes (Basel) 2022; 13:741. [PMID: 35627126 PMCID: PMC9140685 DOI: 10.3390/genes13050741] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/13/2022] [Accepted: 04/20/2022] [Indexed: 12/30/2022] Open
Abstract
Chimeric RNAs are transcripts that are generated by gene fusion and intergenic splicing events, thus comprising nucleotide sequences from different parental genes. In the past, Northern blot analysis and RT-PCR were used to detect chimeric RNAs. However, they are low-throughput and can be time-consuming, labor-intensive, and cost-prohibitive. With the development of RNA-seq and transcriptome analyses over the past decade, the number of chimeric RNAs in cancer as well as in rare inherited diseases has dramatically increased. Chimeric RNAs may be potential diagnostic biomarkers when they are specifically expressed in cancerous cells and/or tissues. Some chimeric RNAs can also play a role in cell proliferation and cancer development, acting as tools for cancer prognosis, and revealing new insights into the cell origin of tumors. Due to their abilities to characterize a whole transcriptome with a high sequencing depth and intergenically identify spliced chimeric RNAs produced with the absence of chromosomal rearrangement, RNA sequencing has not only enhanced our ability to diagnose genetic diseases, but also provided us with a deeper understanding of these diseases. Here, we reviewed the mechanisms of chimeric RNA formation and the utility of RNA sequencing for discovering chimeric RNAs in several types of cancer and rare inherited diseases. We also discussed the diagnostic, prognostic, and therapeutic values of chimeric RNAs.
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Affiliation(s)
- Yunan Sun
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA;
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA;
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
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