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Wang Y, Shu M, Wang T, He T, Yuan J, Yang Y. Comprehensive characterization of somatic mutations associated with chimeric RNAs in human cancers. Int J Cancer 2024; 155:683-696. [PMID: 38613405 DOI: 10.1002/ijc.34955] [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: 11/03/2023] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024]
Abstract
Chimeric RNAs, which can arise from gene recombination at the DNA level or non-canonical splicing events at the RNA level, have been identified as important roles in human tumors. Dysregulated gene expression caused by somatic mutations and altered splicing patterns of oncogenes or tumor suppressor genes can contribute to the development of tumors. Therefore, investigating the formation mechanism of chimeric RNAs via somatic mutations is critical for understanding tumor pathogenesis. This project is the first to propose studying the association between somatic single nucleotide variants and chimeric RNAs, identifying around 2900 somatic SNVs affecting chimeric RNAs in pan-cancer level. The somatic SNVs on chimeric RNAs were commonly observed in various types of tumor tissues, providing a valuable resource for future study. Additionally, these SNVs show distinct tumor specificity, and those with high frequency had a significant impact on the survival time of patients with tumors. Further research revealed that somatic SNVs associated with chimeric RNA (chiR-SNVs) were typically found within 10 nt of the junction site of chimeric RNAs and had a particularly significant effect on chimeric RNAs from different chromosomes. The enrichment analysis revealed that chiR-SNVs were significantly overrepresented in oncogenes and genes related to RNA binding proteins involved in RNA splicing, which could imply that chiR-SNVs may disrupt the process of RNA splicing and induce the occurrence of chimeric RNAs. This study sheds light on the potential molecular interaction mechanism between somatic SNVs and chimeric RNAs, which opens up a new avenue for researching disease pathway and tumorigenesis development.
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Affiliation(s)
- Yuting Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Meng Shu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Tianqiang Wang
- Neurosurgery Department II Ward, Yidu Central Hospital of Weifang, Shandong, China
| | - Tongxin He
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jiapei Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yang Yang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Family Planning, The Second Hospital of Tianjin Medical University, Tianjin, China
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
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2
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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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Myers MA, Arnold BJ, Bansal V, Balaban M, Mullen KM, Zaccaria S, Raphael BJ. HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data. Genome Biol 2024; 25:130. [PMID: 38773520 PMCID: PMC11110434 DOI: 10.1186/s13059-024-03267-x] [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: 07/13/2023] [Accepted: 05/03/2024] [Indexed: 05/24/2024] Open
Abstract
Bulk DNA sequencing of multiple samples from the same tumor is becoming common, yet most methods to infer copy-number aberrations (CNAs) from this data analyze individual samples independently. We introduce HATCHet2, an algorithm to identify haplotype- and clone-specific CNAs simultaneously from multiple bulk samples. HATCHet2 extends the earlier HATCHet method by improving identification of focal CNAs and introducing a novel statistic, the minor haplotype B-allele frequency (mhBAF), that enables identification of mirrored-subclonal CNAs. We demonstrate HATCHet2's improved accuracy using simulations and a single-cell sequencing dataset. HATCHet2 analysis of 10 prostate cancer patients reveals previously unreported mirrored-subclonal CNAs affecting cancer genes.
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Affiliation(s)
- Matthew A Myers
- Department of Computer Science, Princeton University, Princeton, USA
| | - Brian J Arnold
- Center for Statistics and Machine Learning, Princeton University, Princeton, USA
| | - Vineet Bansal
- Princeton Research Computing, Princeton University, Princeton, NJ, USA
| | - Metin Balaban
- Department of Computer Science, Princeton University, Princeton, USA
| | - Katelyn M Mullen
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simone Zaccaria
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK.
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4
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Elfman J, Goins L, Heller T, Singh S, Wang YH, Li H. Discovery of a polymorphic gene fusion via bottom-up chimeric RNA prediction. Nucleic Acids Res 2024; 52:4409-4421. [PMID: 38587197 PMCID: PMC11077074 DOI: 10.1093/nar/gkae258] [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: 12/17/2022] [Accepted: 03/27/2024] [Indexed: 04/09/2024] Open
Abstract
Gene fusions and their chimeric products are commonly linked with cancer. However, recent studies have found chimeric transcripts in non-cancer tissues and cell lines. Large-scale efforts to annotate structural variations have identified gene fusions capable of generating chimeric transcripts even in normal tissues. In this study, we present a bottom-up approach targeting population-specific chimeric RNAs, identifying 58 such instances in the GTEx cohort, including notable cases such as SUZ12P1-CRLF3, TFG-ADGRG7 and TRPM4-PPFIA3, which possess distinct patterns across different ancestry groups. We provide direct evidence for an additional 29 polymorphic chimeric RNAs with associated structural variants, revealing 13 novel rare structural variants. Additionally, we utilize the All of Us dataset and a large cohort of clinical samples to characterize the association of the SUZ12P1-CRLF3-causing variant with patient phenotypes. Our study showcases SUZ12P1-CRLF3 as a representative example, illustrating the identification of elusive structural variants by focusing on those producing population-specific fusion transcripts.
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Affiliation(s)
- Justin Elfman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - Lynette Goins
- Department of Biological Sciences, Clemson University, Clemson, SC 29631, USA
| | - Tessa Heller
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - Sandeep Singh
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
- Computational Toxicology Facility, CSIR-Indian Institute of Toxicology Research, Lucknow, 226001, Uttar Pradesh, India
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - Hui Li
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
- Department of Pathology, University of Virginia, Charlottesville, VA 22903, USA
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5
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Shi X, Facemire L, Singh S, Kumar S, Cornelison R, Liang C, Qin F, Liu A, Lin S, Tang Y, Elfman J, Manley T, Bullock T, Haverstick DM, Wu P, Li H. UBA1-CDK16 : A Sex-Specific Chimeric RNA and Its Role in Immune Sexual Dimorphism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580120. [PMID: 38405903 PMCID: PMC10888732 DOI: 10.1101/2024.02.13.580120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
RNA processing mechanisms, such as alternative splicing and RNA editing, have been recognized as critical means to expand the transcriptome. Chimeric RNAs formed by intergenic splicing provide another potential layer of RNA diversification. By analyzing a large set of RNA-Seq data and validating results in over 1,200 blood samples, we identified UBA1-CDK16 , a female-specific chimeric transcript. Intriguingly, both parental genes, are expressed in males and females. Mechanistically, UBA1-CDK16 is produced by cis-splicing between the two adjacent X-linked genes, originating from the inactive X chromosome. A female-specific chromatin loop, formed between the junction sites, facilitates the alternative splicing of its readthrough precursor. This unique chimeric transcript exhibits evolutionary conservation, evolving to be female-specific from non-human primates to humans. Furthermore, our investigation reveals that UBA1-CDK16 is enriched in the myeloid lineage and plays a regulatory role in myeloid differentiation. Notably, female COVID-19 patients who tested negative for this chimeric transcript displayed higher counts of neutrophils, highlighting its potential role in disease pathogenesis. These findings support the notion that chimeric RNAs represent a new repertoire of transcripts that can be regulated independently from the parental genes, and a new class of RNA variance with potential implications in sexual dimorphism and immune responses.
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6
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Ploypetch S, Wongbandue G, Roytrakul S, Phaonakrop N, Prapaiwan N. Comparative Serum Proteome Profiling of Canine Benign Prostatic Hyperplasia before and after Castration. Animals (Basel) 2023; 13:3853. [PMID: 38136890 PMCID: PMC10740436 DOI: 10.3390/ani13243853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/18/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
BPH is the most prevalent prostatic condition in aging dogs. Nevertheless, clinical diagnosis and management remain inconsistent. This study employed in-solution digestion coupled with nano-liquid chromatography tandem mass spectrometry to assess serum proteome profiling of dogs with BPH and those dogs after castration. Male dogs were divided into two groups; control and BPH groups. In the BPH group, each dog was evaluated at two time points: Day 0 (BF subgroup) and Day 30 after castration (AT subgroup). In the BF subgroup, three proteins were significantly upregulated and associated with dihydrotestosterone: solute carrier family 5 member 5, tyrosine-protein kinase, and FRAT regulator of WNT signaling pathway 1. Additionally, the overexpression of polymeric immunoglobulin receptors in the BF subgroup hints at its potential as a novel protein linked to the BPH development process. Conversely, alpha-1-B glycoprotein (A1BG) displayed significant downregulation in the BF subgroup, suggesting A1BG's potential as a predictive protein for canine BPH. Finasteride was associated with increased proteins in the AT subgroup, including apolipoprotein C-I, apolipoprotein E, apolipoprotein A-II, TAO kinase 1, DnaJ homolog subfamily C member 16, PH domain and leucine-rich repeat protein phosphatase 1, neuregulin 1, and pseudopodium enriched atypical kinase 1. In conclusion, this pilot study highlighted alterations in various serum proteins in canine BPH, reflecting different pathological changes occurring in this condition. These proteins could be a source of potential non-invasive biomarkers for diagnosing this disease.
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Affiliation(s)
- Sekkarin Ploypetch
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (S.P.); (G.W.)
| | - Grisnarong Wongbandue
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (S.P.); (G.W.)
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.R.); (N.P.)
| | - Narumon Phaonakrop
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.R.); (N.P.)
| | - Nawarus Prapaiwan
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (S.P.); (G.W.)
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7
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Zhu Z, Guo Y, Liu Y, Ding R, Huang Z, Yu W, Cui L, Du P, Goel A, Liu C. ELK4 Promotes Colorectal Cancer Progression by Activating the Neoangiogenic Factor LRG1 in a Noncanonical SP1/3-Dependent Manner. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303378. [PMID: 37786278 PMCID: PMC10646254 DOI: 10.1002/advs.202303378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/08/2023] [Indexed: 10/04/2023]
Abstract
Although the MAPK/MEK/ERK pathway is prevalently activated in colorectal cancer (CRC), MEK/ERK inhibitors show limited efficiency in clinic. As a downstream target of MAPK, ELK4 is thought to work primarily by forming a complex with SRF. Whether ELK4 can serve as a potential therapeutic target is unclear and the transcriptional regulatory mechanism has not been systemically analyzed. Here, it is shown that ELK4 promotes CRC tumorigenesis. Integrated genomics- and proteomics-based approaches identified SP1 and SP3, instead of SRF, as cooperative functional partners of ELK4 at genome-wide level in CRC. Serum-induced phosphorylation of ELK4 by MAPKs facilitated its interaction with SP1/SP3. The pathological neoangiogenic factor LRG1 is identified as a direct target of the ELK4-SP1/SP3 complex. Furthermore, targeting the ELK4-SP1/SP3 complex by combination treatment with MEK/ERK inhibitor and the relatively specific SP1 inhibitor mithramycin A (MMA) elicited a synergistic antitumor effect on CRC. Clinically, ELK4 is a marker of poor prognosis in CRC. A 9-gene prognostic model based on the ELK4-SP1/3 complex-regulated gene set showed robust prognostic accuracy. The results demonstrate that ELK4 cooperates with SP1 and SP3 to transcriptionally regulate LRG1 to promote CRC tumorigenesis in an SRF-independent manner, identifying the ELK4-SP1/SP3 complex as a potential target for rational combination therapy.
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Affiliation(s)
- Zhehui Zhu
- Department of Colorectal and Anal SurgeryShanghai Colorectal Cancer Research CenterXinhua HospitalShanghai Jiao Tong University School of MedicineShanghai200092China
- Department of General SurgeryState Key Laboratory of Genetic EngineeringSchool of Life SciencesZhongshan HospitalFudan UniversityShanghai200438China
| | - Yuegui Guo
- Department of Colorectal and Anal SurgeryShanghai Colorectal Cancer Research CenterXinhua HospitalShanghai Jiao Tong University School of MedicineShanghai200092China
| | - Yun Liu
- Department of Colorectal and Anal SurgeryShanghai Colorectal Cancer Research CenterXinhua HospitalShanghai Jiao Tong University School of MedicineShanghai200092China
| | - Rui Ding
- Department of Colorectal and Anal SurgeryShanghai Colorectal Cancer Research CenterXinhua HospitalShanghai Jiao Tong University School of MedicineShanghai200092China
| | - Zhenyu Huang
- Department of Colorectal and Anal SurgeryShanghai Colorectal Cancer Research CenterXinhua HospitalShanghai Jiao Tong University School of MedicineShanghai200092China
| | - Wei Yu
- Department of General SurgeryState Key Laboratory of Genetic EngineeringSchool of Life SciencesZhongshan HospitalFudan UniversityShanghai200438China
| | - Long Cui
- Department of Colorectal and Anal SurgeryShanghai Colorectal Cancer Research CenterXinhua HospitalShanghai Jiao Tong University School of MedicineShanghai200092China
| | - Peng Du
- Department of Colorectal and Anal SurgeryShanghai Colorectal Cancer Research CenterXinhua HospitalShanghai Jiao Tong University School of MedicineShanghai200092China
| | - Ajay Goel
- Center for Gastrointestinal ResearchBaylor Scott & White Research Institute and Charles A. Sammons Cancer CenterBaylor University Medical CenterDepartment of Molecular Diagnostics and Experimental TherapeuticsBeckman Research Institute of City of Hope Comprehensive Cancer CenterDuarteCA91010USA
| | - Chen‐Ying Liu
- Department of Colorectal and Anal SurgeryShanghai Colorectal Cancer Research CenterXinhua HospitalShanghai Jiao Tong University School of MedicineShanghai200092China
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8
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Mukherjee S, Mukherjee SB, Frenkel-Morgenstern M. Functional and regulatory impact of chimeric RNAs in human normal and cancer cells. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1777. [PMID: 36633099 DOI: 10.1002/wrna.1777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 12/21/2022] [Accepted: 12/27/2022] [Indexed: 01/13/2023]
Abstract
Fusions of two genes can lead to the generation of chimeric RNAs, which may have a distinct functional role from their original molecules. Chimeric RNAs could encode novel functional proteins or serve as novel long noncoding RNAs (lncRNAs). The appearance of chimeric RNAs in a cell could help to generate new functionality and phenotypic diversity that might facilitate this cell to survive against new environmental stress. Several recent studies have demonstrated the functional roles of various chimeric RNAs in cancer progression and are considered as biomarkers for cancer diagnosis and sometimes even drug targets. Further, the growing evidence demonstrated the potential functional association of chimeric RNAs with cancer heterogeneity and drug resistance cancer evolution. Recent studies highlighted that chimeric RNAs also have functional potentiality in normal physiological processes. Several functionally potential chimeric RNAs were discovered in human cancer and normal cells in the last two decades. This could indicate that chimeric RNAs are the hidden layer of the human transcriptome that should be explored from the functional insights to better understand the functional evolution of the genome and disease development that could facilitate clinical practice improvements. This review summarizes the current knowledge of chimeric RNAs and highlights their functional, regulatory, and evolutionary impact on different cancers and normal physiological processes. Further, we will discuss the potential functional roles of a recently discovered novel class of chimeric RNAs named sense-antisense/cross-strand chimeric RNAs generated by the fusion of the bi-directional transcripts of the same gene. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Sumit Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Sunanda Biswas Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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Chang L, Deng E, Wang J, Zhou W, Ao J, Liu R, Su D, Fan X. Single-cell third-generation sequencing-based multi-omics uncovers gene expression changes governed by ecDNA and structural variants in cancer cells. Clin Transl Med 2023; 13:e1351. [PMID: 37517066 PMCID: PMC10387328 DOI: 10.1002/ctm2.1351] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 08/01/2023] Open
Abstract
BACKGROUND Cancer cells often exhibit large-scale genomic variations, such as circular extrachromosomal DNA (ecDNA) and structural variants (SVs), which have been highly correlated with the initiation and progression of cancer. Currently, no adequate method exists to unveil how these variations regulate gene expression in heterogeneous cancer cell populations at a single-cell resolution. METHODS Here, we developed a single-cell multi-omics sequencing method, scGTP-seq, to analyse ecDNA and SVs using long-read sequencing technologies. RESULTS AND CONCLUSIONS We demonstrated that our method can efficiently detect ecDNA and SVs and illustrated how these variations affect transcriptomic changes in various cell lines. Finally, we applied and validated this method in a clinical sample of hepatocellular carcinoma (HCC), demonstrating a feasible way to monitor the evolution of ecDNA and SVs during cancer progression.
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Affiliation(s)
- Lei Chang
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Innovation centre for Advanced Interdisciplinary MedicineThe Fifth Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
- Present address:
Department of Cellular and Molecular MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Enze Deng
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
| | - Jun Wang
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
| | - Wei Zhou
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
| | - Jian Ao
- Innovation centre for Advanced Interdisciplinary MedicineThe Fifth Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
| | - Rong Liu
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
| | - Dan Su
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
- The Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouGuangdong ProvinceP. R. China
| | - Xiaoying Fan
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Innovation centre for Advanced Interdisciplinary MedicineThe Fifth Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
- The Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouGuangdong ProvinceP. R. China
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10
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Myers MA, Arnold BJ, Bansal V, Mullen KM, Zaccaria S, Raphael BJ. HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548855. [PMID: 37502835 PMCID: PMC10370020 DOI: 10.1101/2023.07.13.548855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Multi-region DNA sequencing of primary tumors and metastases from individual patients helps identify somatic aberrations driving cancer development. However, most methods to infer copy-number aberrations (CNAs) analyze individual samples. We introduce HATCHet2 to identify haplotype- and clone-specific CNAs simultaneously from multiple bulk samples. HATCHet2 introduces a novel statistic, the mirrored haplotype B-allele frequency (mhBAF), to identify mirrored-subclonal CNAs having different numbers of copies of parental haplotypes in different tumor clones. HATCHet2 also has high accuracy in identifying focal CNAs and extends the earlier HATCHet method in several directions. We demonstrate HATCHet2's improved accuracy using simulations and a single-cell sequencing dataset. HATCHet2 analysis of 50 prostate cancer samples from 10 patients reveals previously-unreported mirrored-subclonal CNAs affecting cancer genes.
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Affiliation(s)
- Matthew A. Myers
- Department of Computer Science, Princeton University, Princeton, USA
| | - Brian J. Arnold
- Center for Statistics and Machine Learning, Princeton University, Princeton, USA
| | - Vineet Bansal
- Princeton Research Computing, Princeton University, Princeton, NJ, USA
| | - Katelyn M. Mullen
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simone Zaccaria
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
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11
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Arshadi A, Tolomeo D, Venuto S, Storlazzi CT. Advancements in Focal Amplification Detection in Tumor/Liquid Biopsies and Emerging Clinical Applications. Genes (Basel) 2023; 14:1304. [PMID: 37372484 PMCID: PMC10298061 DOI: 10.3390/genes14061304] [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: 05/17/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Focal amplifications (FAs) are crucial in cancer research due to their significant diagnostic, prognostic, and therapeutic implications. FAs manifest in various forms, such as episomes, double minute chromosomes, and homogeneously staining regions, arising through different mechanisms and mainly contributing to cancer cell heterogeneity, the leading cause of drug resistance in therapy. Numerous wet-lab, mainly FISH, PCR-based assays, next-generation sequencing, and bioinformatics approaches have been set up to detect FAs, unravel the internal structure of amplicons, assess their chromatin compaction status, and investigate the transcriptional landscape associated with their occurrence in cancer cells. Most of them are tailored for tumor samples, even at the single-cell level. Conversely, very limited approaches have been set up to detect FAs in liquid biopsies. This evidence suggests the need to improve these non-invasive investigations for early tumor detection, monitoring disease progression, and evaluating treatment response. Despite the potential therapeutic implications of FAs, such as, for example, the use of HER2-specific compounds for patients with ERBB2 amplification, challenges remain, including developing selective and effective FA-targeting agents and understanding the molecular mechanisms underlying FA maintenance and replication. This review details a state-of-the-art of FA investigation, with a particular focus on liquid biopsies and single-cell approaches in tumor samples, emphasizing their potential to revolutionize the future diagnosis, prognosis, and treatment of cancer patients.
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Affiliation(s)
| | | | | | - Clelia Tiziana Storlazzi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70125 Bari, Italy; (A.A.); (D.T.); (S.V.)
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12
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Liu CC, Wang XS. Are cis-spliced fusion proteins pathological in more aggressive luminal breast cancer? Oncotarget 2023; 14:595-596. [PMID: 37306551 PMCID: PMC10259257 DOI: 10.18632/oncotarget.28438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Indexed: 06/13/2023] Open
Affiliation(s)
| | - Xiao-Song Wang
- Correspondence to:Xiao-Song Wang, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA; Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15232, USA email
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13
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许 云, 苏 征, 郑 林, 张 孟, 谭 珺, 杨 亚, 张 梦, 徐 苗, 陈 铌, 陈 雪, 周 桥. [Read-through circular RNA rt-circ-HS promotes hypoxia inducible factor 1α expression and renal carcinoma cell proliferation, migration and invasiveness]. BEIJING DA XUE XUE BAO. YI XUE BAN = JOURNAL OF PEKING UNIVERSITY. HEALTH SCIENCES 2023; 55:217-227. [PMID: 37042131 PMCID: PMC10091263 DOI: 10.19723/j.issn.1671-167x.2023.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Indexed: 04/07/2024]
Abstract
OBJECTIVE To identify and characterize read-through RNAs and read-through circular RNAs (rt-circ-HS) derived from transcriptional read-through hypoxia inducible factor 1α (HIF1α) and small nuclear RNA activating complex polypeptide 1 (SNAPC1) the two adjacent genes located on chromosome 14q23, in renal carcinoma cells and renal carcinoma tissues, and to study the effects of rt-circ-HS on biological behavior of renal carcinoma cells and on regulation of HIF1α. METHODS Reverse transcription-polymerase chain reaction (RT-PCR) and Sanger sequencing were used to examine expression of read-through RNAs HIF1α-SNAPC1 and rt-circ-HS in different tumor cells. Tissue microarrays of 437 different types of renal cell carcinoma (RCC) were constructed, and chromogenic in situ hybridization (ISH) was used to investigate expression of rt-circ-HS in different RCC types. Small interference RNA (siRNA) and artificial overexpression plasmids were designed to examine the effects of rt-circ-HS on 786-O and A498 renal carcinoma cell proliferation, migration and invasiveness by cell counting kit 8 (CCK8), EdU incorporation and Transwell cell migration and invasion assays. RT-PCR and Western blot were used to exa-mine expression of HIF1α and SNAPC1 RNA and proteins after interference of rt-circ-HS with siRNA, respectively. The binding of rt-circ-HS with microRNA 539 (miR-539), and miR-539 with HIF1α 3' untranslated region (3' UTR), and the effects of these interactions were investigated by dual luciferase reporter gene assays. RESULTS We discovered a novel 1 144 nt rt-circ-HS, which was derived from read-through RNA HIF1α-SNAPC1 and consisted of HIF1α exon 2-6 and SNAPC1 exon 2-4. Expression of rt-circ-HS was significantly upregulated in 786-O renal carcinoma cells. ISH showed that the overall positive expression rate of rt-circ-HS in RCC tissue samples was 67.5% (295/437), and the expression was different in different types of RCCs. Mechanistically, rt-circ-HS promoted renal carcinoma cell proliferation, migration and invasiveness by functioning as a competitive endogenous inhibitor of miR-539, which we found to be a potent post-transcriptional suppressor of HIF1α, thus promoting expression of HIF1α. CONCLUSION The novel rt-circ-HS is highly expressed in different types of RCCs and acts as a competitive endogenous inhibitor of miR-539 to promote expression of its parental gene HIF1α and thus the proliferation, migration and invasion of renal cancer cells.
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Affiliation(s)
- 云屹 许
- 四川大学华西医院病理科,成都 610041Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - 征征 苏
- 四川大学华西医院病理科,成都 610041Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - 林茂 郑
- 四川大学华西医院病理科,成都 610041Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - 孟尼 张
- 四川大学华西医院病理科,成都 610041Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - 珺娅 谭
- 四川大学华西医院病理科,成都 610041Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
- 四川大学华西医院病理研究室,成都 610041Research Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - 亚蓝 杨
- 四川大学华西医院病理科,成都 610041Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - 梦鑫 张
- 四川大学华西医院病理科,成都 610041Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - 苗 徐
- 四川大学华西医院病理科,成都 610041Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - 铌 陈
- 四川大学华西医院病理科,成都 610041Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
- 四川大学华西医院病理研究室,成都 610041Research Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - 雪芹 陈
- 四川大学华西医院病理科,成都 610041Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
- 四川大学华西医院病理研究室,成都 610041Research Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - 桥 周
- 四川大学华西医院病理科,成都 610041Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
- 四川大学华西医院病理研究室,成都 610041Research Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
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Kosik P, Skorvaga M, Belyaev I. Preleukemic Fusion Genes Induced via Ionizing Radiation. Int J Mol Sci 2023; 24:ijms24076580. [PMID: 37047553 PMCID: PMC10095576 DOI: 10.3390/ijms24076580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Although the prevalence of leukemia is increasing, the agents responsible for this increase are not definitely known. While ionizing radiation (IR) was classified as a group one carcinogen by the IARC, the IR-induced cancers, including leukemia, are indistinguishable from those that are caused by other factors, so the risk estimation relies on epidemiological data. Several epidemiological studies on atomic bomb survivors and persons undergoing IR exposure during medical investigations or radiotherapy showed an association between radiation and leukemia. IR is also known to induce chromosomal translocations. Specific chromosomal translocations resulting in preleukemic fusion genes (PFGs) are generally accepted to be the first hit in the onset of many leukemias. Several studies indicated that incidence of PFGs in healthy newborns is up to 100-times higher than childhood leukemia with the same chromosomal aberrations. Because of this fact, it has been suggested that PFGs are not able to induce leukemia alone, but secondary mutations are necessary. PFGs also have to occur in specific cell populations of hematopoetic stem cells with higher leukemogenic potential. In this review, we describe the connection between IR, PFGs, and cancer, focusing on recurrent PFGs where an association with IR has been established.
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Affiliation(s)
- Pavol Kosik
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Milan Skorvaga
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Igor Belyaev
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
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15
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Wang Y, Huang Z, Sun M, Huang W, Xia L. ETS transcription factors: Multifaceted players from cancer progression to tumor immunity. Biochim Biophys Acta Rev Cancer 2023; 1878:188872. [PMID: 36841365 DOI: 10.1016/j.bbcan.2023.188872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/18/2023] [Accepted: 01/28/2023] [Indexed: 02/26/2023]
Abstract
The E26 transformation specific (ETS) family comprises 28 transcription factors, the majority of which are involved in tumor initiation and development. Serving as a group of functionally heterogeneous gene regulators, ETS factors possess a structurally conserved DNA-binding domain. As one of the most prominent families of transcription factors that control diverse cellular functions, ETS activation is modulated by multiple intracellular signaling pathways and post-translational modifications. Disturbances in ETS activity often lead to abnormal changes in oncogenicity, including cancer cell survival, growth, proliferation, metastasis, genetic instability, cell metabolism, and tumor immunity. This review systematically addresses the basics and advances in studying ETS factors, from their tumor relevance to clinical translational utility, with a particular focus on elucidating the role of ETS family in tumor immunity, aiming to decipher the vital role and clinical potential of regulation of ETS factors in the cancer field.
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Affiliation(s)
- Yufei Wang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
| | - Zhao Huang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei 430030, China
| | - Mengyu Sun
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
| | - Wenjie Huang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei 430030, China.
| | - Limin Xia
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China.
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16
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The Landscape of Expressed Chimeric Transcripts in the Blood of Severe COVID-19 Infected Patients. Viruses 2023; 15:v15020433. [PMID: 36851647 PMCID: PMC9958880 DOI: 10.3390/v15020433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
The ongoing COVID-19 pandemic caused by SARS-CoV-2 infections has quickly developed into a global public health threat. COVID-19 patients show distinct clinical features, and in some cases, during the severe stage of the condition, the disease severity leads to an acute respiratory disorder. In spite of several pieces of research in this area, the molecular mechanisms behind the development of disease severity are still not clearly understood. Recent studies demonstrated that SARS-CoV-2 alters the host cell splicing and transcriptional response to overcome the host immune response that provides the virus with favorable conditions to replicate efficiently within the host cells. In several disease conditions, aberrant splicing could lead to the development of novel chimeric transcripts that could promote the functional alternations of the cell. As severe SARS-CoV-2 infection was reported to cause abnormal splicing in the infected cells, we could expect the generation and expression of novel chimeric transcripts. However, no study so far has attempted to check whether novel chimeric transcripts are expressed in severe SARS-CoV-2 infections. In this study, we analyzed several publicly available blood transcriptome datasets of severe COVID-19, mild COVID-19, other severe respiratory viral infected patients, and healthy individuals. We identified 424 severe COVID-19 -specific chimeric transcripts, 42 of which were recurrent. Further, we detected 189 chimeric transcripts common to severe COVID-19 and multiple severe respiratory viral infections. Pathway and gene enrichment analysis of the parental genes of these two subsets of chimeric transcripts reveals that these are potentially involved in immune-related processes, interferon signaling, and inflammatory responses, which signify their potential association with immune dysfunction leading to the development of disease severity. Our study provides the first detailed expression landscape of chimeric transcripts in severe COVID-19 and other severe respiratory viral infections.
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17
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Elfman J, Goins L, Heller T, Singh S, Wang YH, Li H. Discovery of A Polymorphic Gene Fusion via Bottom-Up Chimeric RNA Prediction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526864. [PMID: 36778239 PMCID: PMC9915695 DOI: 10.1101/2023.02.02.526864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gene fusions and their chimeric products are typically considered hallmarks of cancer. However, recent studies have found chimeric transcripts in non-cancer tissues and cell lines. In addition, efforts to annotate structural variation at large scale have found examples of gene fusions with potential to produce chimeric transcripts in normal tissues. In this report, we provide a means for targeting population-specific chimeric RNAs to enrich for those generated by gene fusion events. We identify 57 such chimeric RNAs from the GTEx cohort, including SUZ12P1-CRLF3 and TFG-ADGRG7 , whose distribution we assessed across the populations of the 1000 Genomes Project. We reveal that SUZ12P1-CRLF3 results from a common complex structural variant in populations with African heritage, and identify its likely mechanism for formation. Additionally, we utilize a large cohort of clinical samples to characterize the SUZ12P1-CRLF3 chimeric RNA, and find an association between the variant and indications of Neurofibramatosis Type I. We present this gene fusion as a case study for identifying hard-to-find and potentially functional structural variants by selecting for those which produce population-specific fusion transcripts. KEY POINTS - Discovery of 57 polymorphic chimeric RNAs- Characterization of SUZ12P1-CRLF3 polymorphic chimeric RNA and corresponding rearrangement- Novel bottom-up approach to identify structural variants which produce transcribed gene fusions.
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18
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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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Zhou J, Guan X, Xu E, Zhou J, Xiong R, Yang Q. Chimeric RNA RRM2-C2orf48 plays an oncogenic role in the development of NNK-induced lung cancer. iScience 2022; 26:105708. [PMID: 36570773 PMCID: PMC9771722 DOI: 10.1016/j.isci.2022.105708] [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: 10/02/2022] [Revised: 10/24/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
Chimeric RNAs have been used as biomarkers and therapeutic targets for multiple types of cancers. However, less attention has been paid to their mechanism of action in neoplasia. Here, we reported that high-expressed chimeric RNA RRM2-C2orf48 was found in malignantly transformed BEAS-2B cells induced by 4-(methyl nitrosamine)-1-(3-pyridinyl)-1-butanone (NNK) in 74 lung cancer patients and several lung cancer cell lines. The expression level of RRM2-C2orf48 was significantly correlated with lymph node metastasis, distant metastasis, tumor-lymph node-metastasis (TNM) stage, and smoking. Overexpressing RRM2-C2orf48 promoted cell growth and accelerated the process of NNK-induced lung cancer. RRM2-C2orf48 knockdown inhibited the growth of RRM2-C2orf48-overexpressing BEAS-2B cells. Finally, we identified miR-219a-2-3p as a potential target of RRM2-C2orf48 in lung cancer. In summary, chimeric RNA RRM2-C2orf48 accelerated the process of NNK-induced lung cancer, and miR-219a-2-3p may be involved in this process.
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Affiliation(s)
- Jiazhen Zhou
- The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Xinchao Guan
- The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Enwu Xu
- Department of Thoracic Surgery, General Hospital of Southern Theater Command, PLA, Guangzhou 510010, PR China
| | - Jiaxin Zhou
- The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Rui Xiong
- The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Qiaoyuan Yang
- The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China,Corresponding author
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Cyrta J, Rosiene J, Bareja R, Kudman S, Al Zoughbi W, Motanagh S, Wilkes DC, Eng K, Zhang T, Sticca E, Mathew S, Rubin MA, Sboner A, Elemento O, Rubin BP, Imielinski M, Mosquera JM. Whole-genome characterization of myoepithelial carcinomas of the soft tissue. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006227. [PMID: 36577525 PMCID: PMC9808553 DOI: 10.1101/mcs.a006227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 10/28/2022] [Indexed: 12/30/2022] Open
Abstract
Myoepithelial carcinomas (MECs) of soft tissue are rare and aggressive tumors affecting young adults and children, but their molecular landscape has not been comprehensively explored through genome sequencing. Here, we present the whole-exome sequencing (WES), whole-genome sequencing (WGS), and RNA sequencing findings of two MECs. Patients 1 and 2 (P1, P2), both male, were diagnosed at 27 and 37 yr of age, respectively, with shoulder (P1) and inguinal (P2) soft tissue tumors. Both patients developed metastatic disease, and P2 died of disease. P1 tumor showed a rhabdoid cytomorphology and a complete loss of INI1 (SMARCB1) expression, associated with a homozygous SMARCB1 deletion. The tumor from P2 showed a clear cell/small cell morphology, retained INI1 expression and strong S100 positivity. By WES and WGS, tumors from both patients displayed low tumor mutation burdens, and no targetable alterations in cancer genes were detected. P2's tumor harbored an EWSR1::KLF15 rearrangement, whereas the tumor from P1 showed a novel ASCC2::GGNBP2 fusion. WGS evidenced a complex genomic event involving mainly Chromosomes 17 and 22 in the tumor from P1, which was consistent with chromoplexy. These findings are consistent with previous reports of EWSR1 rearrangements (50% of cases) in MECs and provide a genetic basis for the loss of SMARCB1 protein expression observed through immunohistochemistry in 10% of 40% of MEC cases. The lack of additional driver mutations in these tumors supports the hypothesis that these alterations are the key molecular events in MEC evolution. Furthermore, the presence of complex structural variant patterns, invisible to WES, highlights the novel biological insights that can be gained through the application of WGS to rare cancers.
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Affiliation(s)
- Joanna Cyrta
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York 10021, USA;,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, New York, New York 10021, USA
| | - Joel Rosiene
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, New York, New York 10021, USA;,SUNY Downstate College of Medicine, Brooklyn, New York 11203, USA
| | - Rohan Bareja
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, New York, New York 10021, USA;,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York 10021, USA
| | - Sarah Kudman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York 10021, USA;,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, New York, New York 10021, USA
| | - Wael Al Zoughbi
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York 10021, USA;,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, New York, New York 10021, USA
| | - Samaneh Motanagh
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York 10021, USA;,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, New York, New York 10021, USA
| | - David C. Wilkes
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, New York, New York 10021, USA
| | - Kenneth Eng
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, New York, New York 10021, USA;,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York 10021, USA
| | - Tuo Zhang
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, New York, New York 10021, USA;,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York 10021, USA
| | - Evan Sticca
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, New York, New York 10021, USA;,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York 10021, USA
| | - Susan Mathew
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York 10021, USA
| | - Mark A. Rubin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York 10021, USA;,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, New York, New York 10021, USA
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York 10021, USA;,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, New York, New York 10021, USA;,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York 10021, USA
| | - Olivier Elemento
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York 10021, USA;,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, New York, New York 10021, USA;,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York 10021, USA
| | - Brian P. Rubin
- Department of Pathology, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Marcin Imielinski
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York 10021, USA;,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, New York, New York 10021, USA;,New York Genome Center, New York, New York 10013, USA
| | - Juan Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York 10021, USA;,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian, New York, New York 10021, USA;,New York Genome Center, New York, New York 10013, USA
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21
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PANAGOPOULOS IOANNIS, HEIM SVERRE. Neoplasia-associated Chromosome Translocations Resulting in Gene Truncation. Cancer Genomics Proteomics 2022; 19:647-672. [PMID: 36316036 PMCID: PMC9620447 DOI: 10.21873/cgp.20349] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/27/2022] Open
Abstract
Chromosomal translocations in cancer as well as benign neoplasias typically lead to the formation of fusion genes. Such genes may encode chimeric proteins when two protein-coding regions fuse in-frame, or they may result in deregulation of genes via promoter swapping or translocation of the gene into the vicinity of a highly active regulatory element. A less studied consequence of chromosomal translocations is the fusion of two breakpoint genes resulting in an out-of-frame chimera. The breaks then occur in one or both protein-coding regions forming a stop codon in the chimeric transcript shortly after the fusion point. Though the latter genetic events and mechanisms at first awoke little research interest, careful investigations have established them as neither rare nor inconsequential. In the present work, we review and discuss the truncation of genes in neoplastic cells resulting from chromosomal rearrangements, especially from seemingly balanced translocations.
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Affiliation(s)
- IOANNIS PANAGOPOULOS
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - SVERRE HEIM
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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22
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Chłopek M, Lasota J, Thompson LDR, Szczepaniak M, Kuźniacka A, Hińcza K, Kubicka K, Kaczorowski M, Newford M, Liu Y, Agaimy A, Biernat W, Durzyńska M, Dziuba I, Hartmann A, Inaguma S, Iżycka-Świeszewska E, Kato H, Kopczyński J, Michal M, Michal M, Pęksa R, Prochorec-Sobieszek M, Starzyńska A, Takahashi S, Wasąg B, Kowalik A, Miettinen M. Alterations in key signaling pathways in sinonasal tract melanoma. A molecular genetics and immunohistochemical study of 90 cases and comprehensive review of the literature. Mod Pathol 2022; 35:1609-1617. [PMID: 35978013 DOI: 10.1038/s41379-022-01122-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/01/2022] [Accepted: 06/01/2022] [Indexed: 11/09/2022]
Abstract
Sinonasal mucosal melanoma is a rare tumor arising within the nasal cavity, paranasal sinuses, or nasopharynx (sinonasal tract). This study evaluated 90 cases diagnosed in 29 males and 61 females with median age 68 years. Most tumors involved the nasal cavity and had an epithelioid morphology. Spectrum of research techniques used in this analysis includes targeted-DNA and -RNA next-generation sequencing, Sanger sequencing, fluorescence in situ hybridization and immunohistochemistry. Sinonasal melanomas were commonly driven by RAS (38/90, 42%), especially NRAS (n = 36) mutations and rarely (4/90, 4%) displayed BRAF pathogenic variants. BRAF/RAS mutants were more frequent among paranasal sinuses (10/14, 71%) than nasal (26/64, 41%) tumors. BRAF/RAS-wild type tumors occasionally harbored alterations of the key components and regulators of Ras-MAPK signaling pathway: NF1 mutations (1/17, 6%) or NF1 locus deletions (1/25, 4%), SPRED1 (3/25, 12%), PIK3CA (3/50, 6%), PTEN (4/50, 8%) and mTOR (1/50, 2%) mutations. These mutations often occurred in a mutually exclusive manner. In several tumors some of which were NRAS mutants, TP53 was deleted (6/48, 13%) and/or mutated (5/90, 6%). Variable nuclear accumulation of TP53, mirrored by elevated nuclear MDM2 expression was seen in >50% of cases. Furthermore, sinonasal melanomas (n = 7) including RAS/BRAF-wild type tumors (n = 5) harbored alterations of the key components and regulators of canonical WNT-pathway: APC (4/90, 4%), CTNNB1 (3/90, 3%) and AMER1 (1/90, 1%). Both, TERT promoter mutations (5/53, 9%) and fusions (2/40, 5%) were identified. The latter occurred in BRAF/RAS-wild type tumors. No oncogenic fusion gene transcripts previously reported in cutaneous melanomas were detected. Eight tumors including 7 BRAF/RAS-wild type cases expressed ADCK4::NUMBL cis-fusion transcripts. In summary, this study documented mutational activation of NRAS and other key components and regulators of Ras-MAPK signaling pathway such as SPRED1 in a majority of sinonasal melanomas.
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Affiliation(s)
- Małgorzata Chłopek
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.,Molecular Diagnostics, Holycross Cancer Center, Kielce, Poland
| | - Jerzy Lasota
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.
| | | | | | - Alina Kuźniacka
- Department of Biology and Genetics, Medical University of Gdańsk, Gdańsk, Poland
| | - Kinga Hińcza
- Molecular Diagnostics, Holycross Cancer Center, Kielce, Poland
| | - Kamila Kubicka
- Molecular Diagnostics, Holycross Cancer Center, Kielce, Poland
| | - Maciej Kaczorowski
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.,Department of Clinical and Experimental Pathology, Wrocław Medical University, Wrocław, Poland
| | - Michael Newford
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | - Yalan Liu
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | - Abbas Agaimy
- Institute of Pathology, University Hospital of Erlangen, Erlangen, Germany
| | - Wojciech Biernat
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Monika Durzyńska
- Department of Pathology, The Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Ireneusz Dziuba
- Faculty of Medicine, University of Technology, Katowice, Poland
| | - Arndt Hartmann
- Institute of Pathology, University Hospital of Erlangen, Erlangen, Germany
| | - Shingo Inaguma
- Department of Experimental Pathology and Tumor Biology, Nagoya City University Graduate School of Medical Sciences, Mizuho-cho, Mizuho-ku, Nagoya, Japan
| | - Ewa Iżycka-Świeszewska
- Department of Pathology and Neuropathology, Medical University of Gdańsk, Gdańsk, Poland
| | - Hiroyuki Kato
- Department of Experimental Pathology and Tumor Biology, Nagoya City University Graduate School of Medical Sciences, Mizuho-cho, Mizuho-ku, Nagoya, Japan
| | - Janusz Kopczyński
- Department of Surgical Pathology, Holycross Cancer Center, Kielce, Poland
| | - Michal Michal
- Sikl's Department of Pathology, University Hospital, Charles University in Prague, Medical Faculty in Plzeň, Plzeň, Czech Republic
| | - Michael Michal
- Sikl's Department of Pathology, University Hospital, Charles University in Prague, Medical Faculty in Plzeň, Plzeň, Czech Republic
| | - Rafał Pęksa
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Monika Prochorec-Sobieszek
- Department of Pathology, The Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Anna Starzyńska
- Department of Oral Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Satoru Takahashi
- Department of Experimental Pathology and Tumor Biology, Nagoya City University Graduate School of Medical Sciences, Mizuho-cho, Mizuho-ku, Nagoya, Japan
| | - Bartosz Wasąg
- Department of Biology and Genetics, Medical University of Gdańsk, Gdańsk, Poland
| | - Artur Kowalik
- Molecular Diagnostics, Holycross Cancer Center, Kielce, Poland.,Division of Medical Biology, Institute of Biology Jan Kochanowski University, Kielce, Poland
| | - Markku Miettinen
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
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23
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Zhou M, Ko M, Hoge AC, Luu K, Liu Y, Russell ML, Hannon WW, Zhang Z, Carrot-Zhang J, Beroukhim R, Van Allen EM, Choudhury AD, Nelson PS, Freedman ML, Taplin ME, Meyerson M, Viswanathan SR, Ha G. Patterns of structural variation define prostate cancer across disease states. JCI Insight 2022; 7:e161370. [PMID: 35943799 PMCID: PMC9536266 DOI: 10.1172/jci.insight.161370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/04/2022] [Indexed: 11/19/2022] Open
Abstract
The complex genomic landscape of prostate cancer evolves across disease states under therapeutic pressure directed toward inhibiting androgen receptor (AR) signaling. While significantly altered genes in prostate cancer have been extensively defined, there have been fewer systematic analyses of how structural variation shapes the genomic landscape of this disease across disease states. We uniformly characterized structural alterations across 531 localized and 143 metastatic prostate cancers profiled by whole genome sequencing, 125 metastatic samples of which were also profiled via whole transcriptome sequencing. We observed distinct significantly recurrent breakpoints in localized and metastatic castration-resistant prostate cancers (mCRPC), with pervasive alterations in noncoding regions flanking the AR, MYC, FOXA1, and LSAMP genes enriched in mCRPC and TMPRSS2-ERG rearrangements enriched in localized prostate cancer. We defined 9 subclasses of mCRPC based on signatures of structural variation, each associated with distinct genetic features and clinical outcomes. Our results comprehensively define patterns of structural variation in prostate cancer and identify clinically actionable subgroups based on whole genome profiling.
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Affiliation(s)
- Meng Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Minjeong Ko
- Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Anna C.H. Hoge
- Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Kelsey Luu
- Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Yuzhen Liu
- Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Magdalena L. Russell
- Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - William W. Hannon
- Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Zhenwei Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Pathology, UMass Memorial Medical Center, Worcester, Massachusetts, USA
| | - Jian Carrot-Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Rameen Beroukhim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Eliezer M. Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Atish D. Choudhury
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Peter S. Nelson
- Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Matthew L. Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Mary-Ellen Taplin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Srinivas R. Viswanathan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Gavin Ha
- Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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24
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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:genes13050741. [PMID: 35627126 PMCID: PMC9140685 DOI: 10.3390/genes13050741] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [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
- Correspondence:
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25
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Xu H, Fang M, Li C, Zuo B, Ren J, Zhang Y. BORIS-mediated generation of circular RNAs induces inflammation. Transl Oncol 2022; 18:101363. [PMID: 35182955 PMCID: PMC8857574 DOI: 10.1016/j.tranon.2022.101363] [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: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 11/04/2022] Open
Abstract
Cancer circRNAs can serve as a vaccine for cancer prevention. Cancer circRNAs activate TLR3 to stimulate NF-κB p65 and provoke inflammation. BORIS interactes with motifs adjacent to circRNA splicing sites. BORIS regulates the expression of circRNAs.
Circular RNAs (circRNAs), which are more stable than linear mRNAs and long non-coding RNAs (LncRNAs), are detected in body fluids such as plasma, serum, and exosomes. Disease-associated circRNAs have significant clinical roles due to their diagnostic and prognostic values. Brother of regulator of imprinting site (BORIS) promotes cancer progression and is specifically highly expressed in the majority of carcinoma. However, the mechanism underlying the regulation of circRNAs by the oncoprotein BORIS and their role in regulating inflammation and immunity remain to be further explored. Vaccines prepared from circRNAs extracted from cancer cells showed that circRNAs induced inflammation and prevented cancer progression. Serum from animals injected with cancer cell-derived circRNAs vigorously reacted with cells that expressed cancer-specific antigen BORIS or cancer extracted circRNAs. It has been implicated that cancer-related circRNAs could be used as antigens to activate immune responses to prevent cancers and stimulate NF-κB signaling pathway by up-regulating and inducing TLR3. In the study we also found that BORIS regulated the expression of circRNAs and interacted with RNA motifs and the CCCTC binding factor (CTCF) motif adjacent to circRNA splicing sites to enhance the formation of circRNAs. Thus, our study delineated the novel mechanism by which cancer-specific antigen BORIS regulated circRNAs and identified that circRNAs could serve as a vaccine for cancer prevention.
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Affiliation(s)
- Hao Xu
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou 310013, China
| | - Mengdie Fang
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou 310013, China
| | - Chao Li
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou 310013, China
| | - Bowen Zuo
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou 310013, China
| | - Juan Ren
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou 310013, China
| | - Yanmei Zhang
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou 310013, China.
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26
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Mukherjee S, Detroja R, Balamurali D, Matveishina E, Medvedeva Y, Valencia A, Gorohovski A, Frenkel-Morgenstern M. Computational analysis of sense-antisense chimeric transcripts reveals their potential regulatory features and the landscape of expression in human cells. NAR Genom Bioinform 2021; 3:lqab074. [PMID: 34458728 PMCID: PMC8386243 DOI: 10.1093/nargab/lqab074] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 07/02/2021] [Accepted: 08/20/2021] [Indexed: 12/11/2022] Open
Abstract
Many human genes are transcribed from both strands and produce sense-antisense gene pairs. Sense-antisense (SAS) chimeric transcripts are produced upon the coalescing of exons/introns from both sense and antisense transcripts of the same gene. SAS chimera was first reported in prostate cancer cells. Subsequently, numerous SAS chimeras have been reported in the ChiTaRS-2.1 database. However, the landscape of their expression in human cells and functional aspects are still unknown. We found that longer palindromic sequences are a unique feature of SAS chimeras. Structural analysis indicates that a long hairpin-like structure formed by many consecutive Watson-Crick base pairs appears because of these long palindromic sequences, which possibly play a similar role as double-stranded RNA (dsRNA), interfering with gene expression. RNA-RNA interaction analysis suggested that SAS chimeras could significantly interact with their parental mRNAs, indicating their potential regulatory features. Here, 267 SAS chimeras were mapped in RNA-seq data from 16 healthy human tissues, revealing their expression in normal cells. Evolutionary analysis suggested the positive selection favoring sense-antisense fusions that significantly impacted the evolution of their function and structure. Overall, our study provides detailed insight into the expression landscape of SAS chimeras in human cells and identifies potential regulatory features.
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Affiliation(s)
- Sumit Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Rajesh Detroja
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Deepak Balamurali
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Elena Matveishina
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russian Federation
- Institute of Bioengineering, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russian Federation
| | - Yulia A Medvedeva
- Institute of Bioengineering, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russian Federation
- Department of Biomedical Physics, Moscow Institute of Technology, Dolgoprudny 141701, Russian Federation
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), C/ Jordi Girona 29, 08034, Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Alessandro Gorohovski
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
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27
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Mukherjee S, Heng HH, Frenkel-Morgenstern M. Emerging Role of Chimeric RNAs in Cell Plasticity and Adaptive Evolution of Cancer Cells. Cancers (Basel) 2021; 13:4328. [PMID: 34503137 PMCID: PMC8431553 DOI: 10.3390/cancers13174328] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 12/12/2022] Open
Abstract
Gene fusions can give rise to somatic alterations in cancers. Fusion genes have the potential to create chimeric RNAs, which can generate the phenotypic diversity of cancer cells, and could be associated with novel molecular functions related to cancer cell survival and proliferation. The expression of chimeric RNAs in cancer cells might impact diverse cancer-related functions, including loss of apoptosis and cancer cell plasticity, and promote oncogenesis. Due to their recurrence in cancers and functional association with oncogenic processes, chimeric RNAs are considered biomarkers for cancer diagnosis. Several recent studies demonstrated that chimeric RNAs could lead to the generation of new functionality for the resistance of cancer cells against drug therapy. Therefore, targeting chimeric RNAs in drug resistance cancer could be useful for developing precision medicine. So, understanding the functional impact of chimeric RNAs in cancer cells from an evolutionary perspective will be helpful to elucidate cancer evolution, which could provide a new insight to design more effective therapies for cancer patients in a personalized manner.
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Affiliation(s)
- Sumit Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel;
| | - Henry H. Heng
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA;
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel;
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28
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Lu B, Jiang R, Xie B, Wu W, Zhao Y. Fusion genes in gynecologic tumors: the occurrence, molecular mechanism and prospect for therapy. Cell Death Dis 2021; 12:783. [PMID: 34381020 PMCID: PMC8357806 DOI: 10.1038/s41419-021-04065-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/12/2022]
Abstract
Gene fusions are thought to be driver mutations in multiple cancers and are an important factor for poor patient prognosis. Most of them appear in specific cancers, thus satisfactory strategies can be developed for the precise treatment of these types of cancer. Currently, there are few targeted drugs to treat gynecologic tumors, and patients with gynecologic cancer often have a poor prognosis because of tumor progression or recurrence. With the application of massively parallel sequencing, a large number of fusion genes have been discovered in gynecologic tumors, and some fusions have been confirmed to be involved in the biological process of tumor progression. To this end, the present article reviews the current research status of all confirmed fusion genes in gynecologic tumors, including their rearrangement mechanism and frequency in ovarian cancer, endometrial cancer, endometrial stromal sarcoma, and other types of uterine tumors. We also describe the mechanisms by which fusion genes are generated and their oncogenic mechanism. Finally, we discuss the prospect of fusion genes as therapeutic targets in gynecologic tumors.
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Affiliation(s)
- Bingfeng Lu
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ruqi Jiang
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bumin Xie
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wu Wu
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yang Zhao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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29
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Zheng L, Xu H, Di Y, Chen L, Liu J, Kang L, Gao L. ELK4 promotes the development of gastric cancer by inducing M2 polarization of macrophages through regulation of the KDM5A-PJA2-KSR1 axis. J Transl Med 2021; 19:342. [PMID: 34372882 PMCID: PMC8353876 DOI: 10.1186/s12967-021-02915-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 05/27/2021] [Indexed: 02/09/2023] Open
Abstract
Background We tried to elaborate the molecular mechanism of ETS-like transcription factor 4 (ELK4) affecting gastric cancer (GC) progression through M2 polarization of macrophages mediated by lysine-specific demethylase 5A (KDM5A)-Praja2 (PJA2)-kinase suppressor of ras 1 (KSR1) axis. Methods GC expression dataset was obtained from GEO database, and the downstream regulatory mechanism of ELK4 was predicted. Tumor-associated macrophages (TAMs) were isolated from GC tissues. The interaction among ELK4, KDM5A, PJA2 and KSR1 was analyzed by dual luciferase reporter gene, ChIP and Co-IP assays. The stability of KSR1 protein was detected by cycloheximide (CHX) treatment. After TAMs were co-cultured with HGC-27 cells, HGC-27 cell biological processes were assessed through gain- and loss-of function assays. Tumorigenicity was detected by tumorigenicity test in nude mice. Results In GC and TAMs, ELK4, KDM5A and KSR1 were highly expressed, while PJA2 was lowly expressed. M2 polarization of macrophages promoted the development of GC. ELK4 activated KDM5A by transcription and promoted macrophage M2 polarization. KDM5A inhibited the expression of PJA2 by removing H3K4me3 of PJA2 promoter, which promoted M2 polarization of macrophages. PJA2 reduced KSR1 by ubiquitination. ELK4 promoted the proliferative, migrative and invasive potentials of GC cells as well as the growth of GC xenografts by regulating KSR1. Conclusion ELK4 may reduce the PJA2-dependent inhibition of KSR1 by transcriptional activation of KDM5A to promote M2 polarization of macrophages, thus promoting the development of GC. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02915-1.
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Affiliation(s)
- Lei Zheng
- Department of Oncology, The First Hospital of Qinhuangdao, No. 258, Wenhua Road, Qinhuangdao, 066000, Hebei Province, People's Republic of China
| | - Hongmei Xu
- Department of Oncology, The First Hospital of Qinhuangdao, No. 258, Wenhua Road, Qinhuangdao, 066000, Hebei Province, People's Republic of China
| | - Ya Di
- Department of Oncology, The First Hospital of Qinhuangdao, No. 258, Wenhua Road, Qinhuangdao, 066000, Hebei Province, People's Republic of China
| | - Lanlan Chen
- Department of Oncology, The First Hospital of Qinhuangdao, No. 258, Wenhua Road, Qinhuangdao, 066000, Hebei Province, People's Republic of China
| | - Jiao Liu
- Department of Oncology, The First Hospital of Qinhuangdao, No. 258, Wenhua Road, Qinhuangdao, 066000, Hebei Province, People's Republic of China
| | - Liying Kang
- Department of Oncology, Tianjin Wuqing District People's Hospital, Tianjin, 301700, People's Republic of China
| | - Liming Gao
- Department of Oncology, The First Hospital of Qinhuangdao, No. 258, Wenhua Road, Qinhuangdao, 066000, Hebei Province, People's Republic of China.
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30
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Wang Y, Zou Q, Li F, Zhao W, Xu H, Zhang W, Deng H, Yang X. Identification of the cross-strand chimeric RNAs generated by fusions of bi-directional transcripts. Nat Commun 2021; 12:4645. [PMID: 34330918 PMCID: PMC8324879 DOI: 10.1038/s41467-021-24910-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 07/14/2021] [Indexed: 12/22/2022] Open
Abstract
A major part of the transcriptome complexity is attributed to multiple types of DNA or RNA fusion events, which take place within a gene such as alternative splicing or between different genes such as DNA rearrangement and trans-splicing. In the present study, using the RNA deep sequencing data, we systematically survey a type of non-canonical fusions between the RNA transcripts from the two opposite DNA strands. We name the products of such fusion events cross-strand chimeric RNA (cscRNA). Hundreds to thousands of cscRNAs can be found in human normal tissues, primary cells, and cancerous cells, and in other species as well. Although cscRNAs exhibit strong tissue-specificity, our analysis identifies thousands of recurrent cscRNAs found in multiple different samples. cscRNAs are mostly originated from convergent transcriptions of the annotated genes and their anti-sense DNA. The machinery of cscRNA biogenesis is unclear, but the cross-strand junction events show some features related to RNA splicing. The present study is a comprehensive survey of the non-canonical cross-strand RNA junction events, a resource for further characterization of the originations and functions of the cscRNAs.
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Affiliation(s)
- Yuting Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science, Beijing, China
| | - Qin Zou
- MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Fajin Li
- MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science, Beijing, China
| | - Wenwei Zhao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hui Xu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Wenhao Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xuerui Yang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China.
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31
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Singh S, Li H. Comparative study of bioinformatic tools for the identification of chimeric RNAs from RNA Sequencing. RNA Biol 2021; 18:254-267. [PMID: 34142643 DOI: 10.1080/15476286.2021.1940047] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Chimeric RNAs are gaining more and more attention as they have broad implications in both cancer and normal physiology. To date, over 40 chimeric RNA prediction methods have been developed to facilitate their identification from RNA sequencing data. However, a limited number of studies have been conducted to compare the performance of these tools; additionally, previous studies have become outdated as more software tools have been developed within the last three years. In this study, we benchmarked 16 chimeric RNA prediction software, including seven top performers in previous benchmarking studies, and nine that were recently developed. We used two simulated and two real RNA-Seq datasets, compared the 16 tools for their sensitivity, positive prediction value (PPV), F-measure, and also documented the computational requirements (time and memory). We noticed that none of the tools are inclusive, and their performance varies depending on the dataset and objects. To increase the detection of true positive events, we also evaluated the pair-wise combination of these methods to suggest the best combination for sensitivity and F-measure. In addition, we compared the performance of the tools for the identification of three classes (read-through, inter-chromosomal and intra-others) of chimeric RNAs. Finally, we performed TOPSIS analyses and ranked the weighted performance of the 16 tools.
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Affiliation(s)
- Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, USA.,Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, USA
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32
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Wang MY, Huang M, Wang CY, Tang XY, Wang JG, Yang YD, Xiong X, Gao CW. Transcriptome Analysis Reveals MFGE8-HAPLN3 Fusion as a Novel Biomarker in Triple-Negative Breast Cancer. Front Oncol 2021; 11:682021. [PMID: 34211850 PMCID: PMC8239224 DOI: 10.3389/fonc.2021.682021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/24/2021] [Indexed: 12/27/2022] Open
Abstract
Background Triple-negative breast cancer (TNBC) is a highly aggressive cancer with poor prognosis. The lack of effective targeted therapies for TNBC remains a profound clinical challenge. Fusion transcripts play critical roles in carcinogenesis and serve as valuable diagnostic and therapeutic targets in cancer. The present study aimed to identify novel fusion transcripts in TNBC. Methods We analyzed the RNA sequencing data of 360 TNBC samples to identify and filter fusion candidates through SOAPfuse and ChimeraScan analysis. The characteristics, including recurrence, fusion type, chromosomal localization, TNBC subgroup distribution, and clinicopathological correlations, were analyzed in all candidates. Furthermore, we selected the promising fusion transcript and predicted its fusion type and protein coding capacity. Results Using the RNA sequencing data, we identified 189 fusion transcripts in TNBC, among which 22 were recurrent fusions. Compared to para-tumor tissues, TNBC tumor tissues accumulated more fusion events, especially in high-grade tumors. Interestingly, these events were enriched at specific chromosomal loci, and the distribution pattern varied in different TNBC subtypes. The vast majority of fusion partners were discovered on chromosomes 1p, 11q, 19p, and 19q. Besides, fusion events mainly clustered on chromosome 11 in the immunomodulatory subtype and chromosome 19 in the luminal androgen receptor subtype of TNBC. Considering the tumor specificity and frameshift mutation, we selected MFGE8-HAPLN3 as a novel biomarker and further validated it in TNBC samples using PCR and Sanger sequencing. Further, we successfully identified three types of MFGE8-HAPLN3 (E6-E2, E5-E3, and E6-E3) and predicted the ORF of E6-E2, which could encode a protein of 712 amino acids, suggesting its critical role in TNBC. Conclusions Improved bioinformatic stratification and comprehensive analysis identified the fusion transcript MFGE8-HAPLN3 as a novel biomarker with promising clinical application in the future.
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Affiliation(s)
- Meng-Yuan Wang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Man Huang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Chao-Yi Wang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Xiao-Ying Tang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Jian-Gen Wang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Yong-De Yang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Xin Xiong
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Chao-Wei Gao
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, Chongqing, China
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Panagopoulos I, Heim S. Interstitial Deletions Generating Fusion Genes. Cancer Genomics Proteomics 2021; 18:167-196. [PMID: 33893073 DOI: 10.21873/cgp.20251] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/16/2022] Open
Abstract
A fusion gene is the physical juxtaposition of two different genes resulting in a structure consisting of the head of one gene and the tail of the other. Gene fusion is often a primary neoplasia-inducing event in leukemias, lymphomas, solid malignancies as well as benign tumors. Knowledge about fusion genes is crucial not only for our understanding of tumorigenesis, but also for the diagnosis, prognostication, and treatment of cancer. Balanced chromosomal rearrangements, in particular translocations and inversions, are the most frequent genetic events leading to the generation of fusion genes. In the present review, we summarize the existing knowledge on chromosome deletions as a mechanism for fusion gene formation. Such deletions are mostly submicroscopic and, hence, not detected by cytogenetic analyses but by array comparative genome hybridization (aCGH) and/or high throughput sequencing (HTS). They are found across the genome in a variety of neoplasias. As tumors are increasingly analyzed using aCGH and HTS, it is likely that more interstitial deletions giving rise to fusion genes will be found, significantly impacting our understanding and treatment of cancer.
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Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway;
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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34
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Guan W, Zhou L, Li Y, Yang E, Liu Y, Lv N, Fu L, Ding Y, Wang N, Fang N, Liu Q, Wang B, Li F, Zhang J, Wang M, Wang L, Jing Y, Li Y, Yu L. Profiling of somatic mutations and fusion genes in acute myeloid leukemia patients with FLT3-ITD or FLT3-TKD mutation at diagnosis reveals distinct evolutionary patterns. Exp Hematol Oncol 2021; 10:27. [PMID: 33836835 PMCID: PMC8033687 DOI: 10.1186/s40164-021-00207-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/04/2021] [Indexed: 12/26/2022] Open
Abstract
Background The receptor tyrosine kinase FLT3 with internal tandem duplications within the juxtamembrane domain (FLT3-ITD) is a poor prognostic factor; however, the prognostic significance of missense mutation in the tyrosine kinase domain (FLT3-TKD) is controversial. Furthermore, the accompanying mutations and fusion genes with FLT3 mutations are unclear in acute myeloid leukemia (AML). Methods We investigated FLT3 mutations and their correlation with other gene mutations and gene fusions through two RNA-seq based next-generation sequencing (NGS) method and prognostic impact in 207 de novo AML patients. Results FLT3-ITD mutations were positive in 58 patients (28%), and FLT3-TKD mutations were positive in 20 patients (9.7%). FLT3-ITD was associated with a higher white blood cell count (WBC, mean 72.9 × 109/L vs. 24.2 × 109/L, P = 0.000), higher bone marrow blasts (mean 65.9% vs. 56.0%, P = 0.024), and NK-AML (normal karyotype) (64.8% vs. 48.4%, P = 0.043). NPM1 and DNMT3A mutations were enriched in FLT3-ITD (53.5% vs. 15.3%, P = 0.000; 34.6% vs. 13%, P = 0.003). However, the mutations of CEBPA were excluded in FLT3-AML (3.8% vs. 0% vs. 19.8%, P = 0.005). Mutations of Ras and TP53 were unlikely associated with FLT3-ITD (1.9% vs. 20.6%, P = 0.006; 0% vs. 6.1%, P = 0.04). The common fusion genes (> 10%) in FLT3-ITD had MLL-rearrangement and NUP98-rearrangement, while the common fusion genes in FLT3-TKD had AML1-ETO and MLL-rearrangement. Two novel fusion genes PRDM16-SKI and EFAN2-ZNF238 were identified in FLT3-ITD patients. Gene fusions and NPM1 mutation were mutually excluded in FLT3-ITD and FLT3-TKD patients. Their patterns of mutual exclusivity and cooperation among mutated genes suggest that additional driver genetic alterations are required and reveal two evolutionary patterns of FLT3 pathogenesis. Patients with FLT3-ITD had a lower CR (complete remission) rate, lower 3-year OS (overall survival), DFS (disease-free survival), and EFS (event-free survival) compared to FLT3wtAML. NK-AML with FLT3-ITD had a lower 3-year OS, DFS, and EFS than those without, while FLT3-TKD did not influence the survival in whole cohort and NK-AML. Besides, we found that FLT3-ITD/TET2 bimutation defined a poor prognostic subgroup. Conclusions Our study offers deep insights into the molecular pathogenesis and biology of AML with FLT3-ITD and FLT3-TKD by providing the profiles of concurrent molecular alterations and the clinical impact of FLT3-ITD and FLT3-TKD on AML patients.
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Affiliation(s)
- Wei Guan
- Department of Hematology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Lei Zhou
- Department of Hematology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Yan Li
- Department of Hematology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China.,Department of Hematology, Peking University Third Hospital, 49 North Garden Road, Beijing, 100191, China
| | - Erna Yang
- Department of Hematology and Oncology, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Carlson International Cancer Center, Shenzhen University General Hospital, Shenzhen University Health Science Center, 1098 Xueyuan AVE, Shenzhen, 518060, China
| | - Yangyang Liu
- Beijing USCI Medical Laboratory Co., Ltd, Beijing, China
| | - Na Lv
- Department of Hematology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China.,Department of Hematology and Oncology, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Carlson International Cancer Center, Shenzhen University General Hospital, Shenzhen University Health Science Center, 1098 Xueyuan AVE, Shenzhen, 518060, China
| | - Lin Fu
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Yi Ding
- Department of Hematology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Nan Wang
- Department of Hematology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Nan Fang
- Beijing USCI Medical Laboratory Co., Ltd, Beijing, China
| | - Qian Liu
- Beijing USCI Medical Laboratory Co., Ltd, Beijing, China
| | - Binan Wang
- Beijing USCI Medical Laboratory Co., Ltd, Beijing, China
| | - Fuwei Li
- Beijing USCI Medical Laboratory Co., Ltd, Beijing, China
| | - Juan Zhang
- Beijing USCI Medical Laboratory Co., Ltd, Beijing, China
| | - Maoquan Wang
- School of Medicine, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Lili Wang
- Department of Hematology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Yu Jing
- Department of Hematology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Yonghui Li
- Department of Hematology and Oncology, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Carlson International Cancer Center, Shenzhen University General Hospital, Shenzhen University Health Science Center, 1098 Xueyuan AVE, Shenzhen, 518060, China
| | - Li Yu
- Department of Hematology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China. .,Department of Hematology and Oncology, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Carlson International Cancer Center, Shenzhen University General Hospital, Shenzhen University Health Science Center, 1098 Xueyuan AVE, Shenzhen, 518060, China.
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35
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Landscape of Chimeric RNAs in Non-Cancerous Cells. Genes (Basel) 2021; 12:genes12040466. [PMID: 33805149 PMCID: PMC8064075 DOI: 10.3390/genes12040466] [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: 02/22/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 11/21/2022] Open
Abstract
Gene fusions and their products (RNA and protein) have been traditionally recognized as unique features of cancer cells and are used as ideal biomarkers and drug targets for multiple cancer types. However, recent studies have demonstrated that chimeric RNAs generated by intergenic alternative splicing can also be found in normal cells and tissues. In this study, we aim to identify chimeric RNAs in different non-neoplastic cell lines and investigate the landscape and expression of these novel candidate chimeric RNAs. To do so, we used HEK-293T, HUVEC, and LO2 cell lines as models, performed paired-end RNA sequencing, and conducted analyses for chimeric RNA profiles. Several filtering criteria were applied, and the landscape of chimeric RNAs was characterized at multiple levels and from various angles. Further, we experimentally validated 17 chimeric RNAs from different classifications. Finally, we examined a number of validated chimeric RNAs in different cancer and non-cancer cells, including blood from healthy donors, and demonstrated their ubiquitous expression pattern.
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Shi Y, Yuan J, Rraklli V, Maxymovitz E, Cipullo M, Liu M, Li S, Westerlund I, Bedoya-Reina OC, Bullova P, Rorbach J, Juhlin CC, Stenman A, Larsson C, Kogner P, O’Sullivan MJ, Schlisio S, Holmberg J. Aberrant splicing in neuroblastoma generates RNA-fusion transcripts and provides vulnerability to spliceosome inhibitors. Nucleic Acids Res 2021; 49:2509-2521. [PMID: 33555349 PMCID: PMC7969022 DOI: 10.1093/nar/gkab054] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 01/14/2021] [Accepted: 01/21/2021] [Indexed: 11/12/2022] Open
Abstract
The paucity of recurrent mutations has hampered efforts to understand and treat neuroblastoma. Alternative splicing and splicing-dependent RNA-fusions represent mechanisms able to increase the gene product repertoire but their role in neuroblastoma remains largely unexplored. Here we investigate the presence and possible roles of aberrant splicing and splicing-dependent RNA-fusion transcripts in neuroblastoma. In addition, we attend to establish whether the spliceosome can be targeted to treat neuroblastoma. Through analysis of RNA-sequenced neuroblastoma we show that elevated expression of splicing factors is a strong predictor of poor clinical outcome. Furthermore, we identified >900 primarily intrachromosomal fusions containing canonical splicing sites. Fusions included transcripts from well-known oncogenes, were enriched for proximal genes and in chromosomal regions commonly gained or lost in neuroblastoma. As a proof-of-principle that these fusions can generate altered gene products, we characterized a ZNF451-BAG2 fusion, producing a truncated BAG2-protein which inhibited retinoic acid induced differentiation. Spliceosome inhibition impeded neuroblastoma fusion expression, induced apoptosis and inhibited xenograft tumor growth. Our findings elucidate a splicing-dependent mechanism generating altered gene products in neuroblastoma and show that the spliceosome is a potential target for clinical intervention.
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Affiliation(s)
- Yao Shi
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Juan Yuan
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Vilma Rraklli
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Eva Maxymovitz
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, SE-171-65 Solna, Sweden
| | - Mingzhi Liu
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Shuijie Li
- Department of Microbiology, Tumor- and Cellbiology, Karolinska Institutet, Solnavägen 9, SE-171 65 Solna, Sweden
| | - Isabelle Westerlund
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Oscar C Bedoya-Reina
- Department of Microbiology, Tumor- and Cellbiology, Karolinska Institutet, Solnavägen 9, SE-171 65 Solna, Sweden
| | - Petra Bullova
- Department of Microbiology, Tumor- and Cellbiology, Karolinska Institutet, Solnavägen 9, SE-171 65 Solna, Sweden
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, SE-171-65 Solna, Sweden
| | - C Christofer Juhlin
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska (CCK), Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Adam Stenman
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska (CCK), Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Catharina Larsson
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska (CCK), Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Per Kogner
- Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Maureen J O’Sullivan
- Department of Histopathology, Our Lady's Children's Hospital, Dublin, Ireland
- Trinity Translational Medicine Institute, Trinity College, Dublin, Ireland
| | - Susanne Schlisio
- Department of Microbiology, Tumor- and Cellbiology, Karolinska Institutet, Solnavägen 9, SE-171 65 Solna, Sweden
| | - Johan Holmberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
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Scaravilli M, Koivukoski S, Latonen L. Androgen-Driven Fusion Genes and Chimeric Transcripts in Prostate Cancer. Front Cell Dev Biol 2021; 9:623809. [PMID: 33634124 PMCID: PMC7900491 DOI: 10.3389/fcell.2021.623809] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/14/2021] [Indexed: 12/15/2022] Open
Abstract
Androgens are steroid hormones governing the male reproductive development and function. As such, androgens and the key mediator of their effects, androgen receptor (AR), have a leading role in many diseases. Prostate cancer is a major disease where AR and its transcription factor function affect a significant number of patients worldwide. While disease-related AR-driven transcriptional programs are connected to the presence and activity of the receptor itself, also novel modes of transcriptional regulation by androgens are exploited by cancer cells. One of the most intriguing and ingenious mechanisms is to bring previously unconnected genes under the control of AR. Most often this occurs through genetic rearrangements resulting in fusion genes where an androgen-regulated promoter area is combined to a protein-coding area of a previously androgen-unaffected gene. These gene fusions are distinctly frequent in prostate cancer compared to other common solid tumors, a phenomenon still requiring an explanation. Interestingly, also another mode of connecting androgen regulation to a previously unaffected gene product exists via transcriptional read-through mechanisms. Furthermore, androgen regulation of fusion genes and transcripts is not linked to only protein-coding genes. Pseudogenes and non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs) can also be affected by androgens and de novo functions produced. In this review, we discuss the prevalence, molecular mechanisms, and functional evidence for androgen-regulated prostate cancer fusion genes and transcripts. We also discuss the clinical relevance of especially the most common prostate cancer fusion gene TMPRSS2-ERG, as well as present open questions of prostate cancer fusions requiring further investigation.
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Affiliation(s)
- Mauro Scaravilli
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Sonja Koivukoski
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Leena Latonen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
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38
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Liu CC, Veeraraghavan J, Tan Y, Kim JA, Wang X, Loo SK, Lee S, Hu Y, Wang XS. A Novel Neoplastic Fusion Transcript, RAD51AP1-DYRK4, Confers Sensitivity to the MEK Inhibitor Trametinib in Aggressive Breast Cancers. Clin Cancer Res 2021; 27:785-798. [PMID: 33172895 PMCID: PMC7934498 DOI: 10.1158/1078-0432.ccr-20-2769] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/18/2020] [Accepted: 11/04/2020] [Indexed: 01/19/2023]
Abstract
PURPOSE Luminal B breast tumors are more aggressive estrogen receptor-positive (ER+) breast cancers characterized by aggressive clinical behavior and a high risk of metastatic dissemination. The underlying pathologic molecular events remain poorly understood with a paucity of actionable genetic drivers, which hinders the development of new treatment strategies. EXPERIMENTAL DESIGN We performed large-scale RNA sequencing analysis to identify chimerical transcripts preferentially expressed in luminal B breast cancer. The lead candidate was validated by reverse transcription PCR in breast cancer tissues. The effects of inducible ectopic expression or genetic silencing were assessed by phenotypic assays such as MTS, transwell, and transendothelial migration assays, and by clonogenic assays to assess MEK inhibitor sensitivity. Subcellular fractionation, Western blots, and immunoprecipitation were performed to characterize the protein products and elucidate the engaged mechanisms. RESULTS Here we report a novel tumor-specific chimeric transcript RAD51AP1-DYRK4 preferentially expressed in luminal B tumors. Analysis of 200 ER+ breast tumors detected RAD51AP1-DYRK4 overexpression in 19 tumors (9.5%), which is markedly enriched in the luminal B tumors (17.5%). Ectopic expression of RAD51AP1-DYRK4, but not wild-type RAD51AP1, leads to marked activation of MEK/ERK signaling, and endows increased cell motility and transendothelial migration. More importantly, RAD51AP1-DYRK4 appears to endow increased sensitivity to the MEK inhibitor trametinib through attenuating compensatory activation of HER2/PI3K/AKT under MEK inhibition. CONCLUSIONS This discovery sheds light on a new area of molecular pathobiology of luminal B tumors and implies potential new therapeutic opportunities for more aggressive breast tumors overexpressing this fusion.
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Affiliation(s)
- Chia-Chia Liu
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jamunarani Veeraraghavan
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Ying Tan
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Jin-Ah Kim
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Xian Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Suet Kee Loo
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sanghoon Lee
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yiheng Hu
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Xiao-Song Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania.
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
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39
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Chen W, Cui W, Qiu Y, Cui D. Research Progress of Chimeric RNA and Health. Health (London) 2021. [DOI: 10.4236/health.2021.134036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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40
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Minati R, Perreault C, Thibault P. A Roadmap Toward the Definition of Actionable Tumor-Specific Antigens. Front Immunol 2020; 11:583287. [PMID: 33424836 PMCID: PMC7793940 DOI: 10.3389/fimmu.2020.583287] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/30/2020] [Indexed: 12/15/2022] Open
Abstract
The search for tumor-specific antigens (TSAs) has considerably accelerated during the past decade due to the improvement of proteogenomic detection methods. This provides new opportunities for the development of novel antitumoral immunotherapies to mount an efficient T cell response against one or multiple types of tumors. While the identification of mutated antigens originating from coding exons has provided relatively few TSA candidates, the possibility of enlarging the repertoire of targetable TSAs by looking at antigens arising from non-canonical open reading frames opens up interesting avenues for cancer immunotherapy. In this review, we outline the potential sources of TSAs and the mechanisms responsible for their expression strictly in cancer cells. In line with the heterogeneity of cancer, we propose that discrete families of TSAs may be enriched in specific cancer types.
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Affiliation(s)
- Robin Minati
- École Normale Supérieure de Lyon, Université Claude Bernard Lyon I, Université de Lyon, Lyon, France
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Department of Chemistry, Université de Montréal, Montréal, QC, Canada
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41
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CircRNAs and Fusion-circRNAs in cancer: New players in an old game. Cell Signal 2020; 75:109747. [DOI: 10.1016/j.cellsig.2020.109747] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/13/2020] [Accepted: 08/18/2020] [Indexed: 12/12/2022]
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42
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Pederzoli F, Bandini M, Marandino L, Ali SM, Madison R, Chung J, Ross JS, Necchi A. Targetable gene fusions and aberrations in genitourinary oncology. Nat Rev Urol 2020; 17:613-625. [PMID: 33046892 DOI: 10.1038/s41585-020-00379-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2020] [Indexed: 12/14/2022]
Abstract
Gene fusions result from either structural chromosomal rearrangement or aberrations caused by splicing or transcriptional readthrough. The precise and distinctive presence of fusion genes in neoplastic tissues and their involvement in multiple pathways central to cancer development, growth and survival make them promising targets for personalized therapy. In genitourinary malignancies, rearrangements involving the E26 transformation-specific family of transcription factors have emerged as very frequent alterations in prostate cancer, especially the TMPRSS2-ERG fusion. In renal malignancies, Xp11 and t(6;11) translocations are hallmarks of a distinct pathological group of tumours described as microphthalmia-associated transcription factor family translocation-associated renal cell carcinomas. Novel druggable fusion events have been recognized in genitourinary malignancies, leading to the activation of several clinical trials. For instance, ALK-rearranged renal cell carcinomas have shown responses to alectinib and crizotinib. Erdafitinib has been tested for the treatment of FGFR-rearranged bladder cancer. Other anti-fibroblast growth factor receptor 3 (FGFR3) compounds are showing promising results in the treatment of bladder cancer, including infigratinib and pemigatinib, and all are currently in clinical trials.
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Affiliation(s)
- Filippo Pederzoli
- Urological Research Institute (URI), Unit of Urology, IRCCS Ospedale San Raffaele, Vita-Salute San Raffaele University, Milan, Italy.
| | - Marco Bandini
- Urological Research Institute (URI), Unit of Urology, IRCCS Ospedale San Raffaele, Vita-Salute San Raffaele University, Milan, Italy
| | - Laura Marandino
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Siraj M Ali
- Foundation Medicine Inc., Cambridge, MA, USA
| | | | - Jon Chung
- Foundation Medicine Inc., Cambridge, MA, USA
| | - Jeffrey S Ross
- Foundation Medicine Inc., Cambridge, MA, USA.,Upstate Medical University, Syracuse, NY, USA
| | - Andrea Necchi
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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43
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Friedrich S, Sonnhammer ELL. Fusion transcript detection using spatial transcriptomics. BMC Med Genomics 2020; 13:110. [PMID: 32753032 PMCID: PMC7437936 DOI: 10.1186/s12920-020-00738-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 06/11/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Fusion transcripts are involved in tumourigenesis and play a crucial role in tumour heterogeneity, tumour evolution and cancer treatment resistance. However, fusion transcripts have not been studied at high spatial resolution in tissue sections due to the lack of full-length transcripts with spatial information. New high-throughput technologies like spatial transcriptomics measure the transcriptome of tissue sections on almost single-cell level. While this technique does not allow for direct detection of fusion transcripts, we show that they can be inferred using the relative poly(A) tail abundance of the involved parental genes. METHOD We present a new method STfusion, which uses spatial transcriptomics to infer the presence and absence of poly(A) tails. A fusion transcript lacks a poly(A) tail for the 5' gene and has an elevated number of poly(A) tails for the 3' gene. Its expression level is defined by the upstream promoter of the 5' gene. STfusion measures the difference between the observed and expected number of poly(A) tails with a novel C-score. RESULTS We verified the STfusion ability to predict fusion transcripts on HeLa cells with known fusions. STfusion and C-score applied to clinical prostate cancer data revealed the spatial distribution of the cis-SAGe SLC45A3-ELK4 in 12 tissue sections with almost single-cell resolution. The cis-SAGe occurred in disease areas, e.g. inflamed, prostatic intraepithelial neoplastic, or cancerous areas, and occasionally in normal glands. CONCLUSIONS STfusion detects fusion transcripts in cancer cell line and clinical tissue data, and distinguishes chimeric transcripts from chimeras caused by trans-splicing events. With STfusion and the use of C-scores, fusion transcripts can be spatially localised in clinical tissue sections on almost single cell level.
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Affiliation(s)
- Stefanie Friedrich
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, 17121, Solna, Sweden.
| | - Erik L L Sonnhammer
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, 17121, Solna, Sweden
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44
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Elfman J, Pham LP, Li H. The relationship between chimeric RNAs and gene fusions: Potential implications of reciprocity in cancer. J Genet Genomics 2020; 47:341-348. [PMID: 33008771 DOI: 10.1016/j.jgg.2020.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/09/2020] [Accepted: 04/20/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Justin Elfman
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, 22904 USA
| | - Lam-Phong Pham
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22904 USA
| | - Hui Li
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, 22904 USA; Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22904 USA.
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45
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Wu H, Singh S, Xie Z, Li X, Li H. Landscape characterization of chimeric RNAs in colorectal cancer. Cancer Lett 2020; 489:56-65. [PMID: 32534173 DOI: 10.1016/j.canlet.2020.05.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/22/2020] [Accepted: 05/27/2020] [Indexed: 12/31/2022]
Abstract
Gene fusions and their fusion products have been recognized as ideal biomarkers and drug targets for cancer. However, few recurrent gene fusions were found in colorectal cancer (CRC), despite comprehensive studies. We believe that chimeric RNAs, in the absence of chromosomal rearrangement, may represent a new repertoire of biomarkers and/or therapeutic targets in CRC. In this study, we aim to identify such recurrent chimeric RNAs, and investigate their clinical implications. To do so, we performed extensive data mining for chimeric RNAs using The Cancer Genome Atlas CRC RNA-Seq datasets. Multiple filtering criteria were applied, and the landscape of chimeric RNAs at multiple levels, from various angles, was analyzed. Eleven frequent, cancer biased chimeric RNAs were validated. The expression of RRM2-C2orf48 correlates with poor clinical outcomes, while the expression of parental RRM2 and C2orf48 correlates with positive clinical outcomes. Mechanistically, it is a product of cis-splicing between adjacent genes. Silencing of RRM2-C2orf48 resulted in reduced cellular proliferation in colon cancer cells, whereas overexpressed chimera promoted cell proliferation. These findings suggest that frequent chimeric RNAs are present in CRCs, and that chimeric RNAs may have different expression profiles and functions from parental genes, thus representing a new repertoire of biomarkers and therapeutic targets.
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Affiliation(s)
- Hao Wu
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, China; Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA; Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan, 410013, China
| | - Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
| | - Zhongqiu Xie
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
| | - Xiaorong Li
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan, 410013, China
| | - 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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Abstract
Chimeric RNAs are hybrid transcripts containing exons from two separate genes. Chimeric RNAs are traditionally considered to be transcribed from fusion genes caused by chromosomal rearrangement. These canonical chimeric RNAs are well characterized to be expressed in a cancer-unique pattern and/or act as oncogene products. However, benefited by the development of advanced deep sequencing technologies, novel types of non-canonical chimeric RNAs have been discovered to be generated from intergenic splicing without genomic aberrations. They can be formed through trans-splicing or cis-splicing between adjacent genes (cis-SAGe) mechanisms. Non-canonical chimeric RNAs are widely detected in normal physiology, although several have been shown to have a cancer-specific expression pattern. Further studies have indicated that some of them play fundamental roles in controlling cell growth and motility, and may have functions independent of the parental genes. These discoveries are unveiling a new layer of the functional transcriptome and are also raising the possibility of utilizing non-canonical chimeric RNAs as cancer diagnostic markers and therapeutic targets. In this chapter, we will overview different categories of chimeric RNAs and their expression in various types of cancerous and normal samples. Acknowledging that chimeric RNAs are not unique to cancer, we will discuss both bioinformatic and biological methods to identify credible cancer-specific chimeric RNAs. Furthermore, we will describe downstream methods to explore their molecular processing mechanisms and potential functions. A better understanding of the biogenesis mechanisms and functional products of cancer-specific chimeric RNAs will pave ways for the development of novel cancer biomarkers and therapeutic targets.
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Affiliation(s)
- Xinrui Shi
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Emily Lin
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Hui Li
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, United States; Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, United States.
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47
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Ding S, Li S, Zhang S, Li Y. Genetic Alterations and Checkpoint Expression: Mechanisms and Models for Drug Discovery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1248:227-250. [PMID: 32185713 DOI: 10.1007/978-981-15-3266-5_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this chapter, we will sketch a story that begins with the breakdown of chromosome homeostasis and genomic stability. Genomic alterations may render tumor cells eternal life at the expense of immunogenicity. Although antitumor immunity can be primed through neoantigens or inflammatory signals, tumor cells have evolved countermeasures to evade immune surveillance and strike back by modulating immune checkpoint related pathways. At present, monoclonal antibody drugs targeting checkpoints like PD-1 and CTLA-4 have significantly prolonged the survival of a variety of cancer patients, and thus have marked a great achievement in the history of antitumor therapy. Nevertheless, this is not the end of the story. As the relationship between genomic alteration and checkpoint expression is being delineated though the advances of preclinical animal models and emerging technologies, novel checkpoint targets are on the way to be discovered.
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Affiliation(s)
- Shuai Ding
- The State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Department of Rheumatology and Immunology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Model Animal Research Center of Nanjing University, Nanjing, Jiangsu, 210061, China
| | - Siqi Li
- The State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Department of Rheumatology and Immunology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Model Animal Research Center of Nanjing University, Nanjing, Jiangsu, 210061, China
| | - Shujie Zhang
- The State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Department of Rheumatology and Immunology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Model Animal Research Center of Nanjing University, Nanjing, Jiangsu, 210061, China
| | - Yan Li
- The State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Department of Rheumatology and Immunology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Model Animal Research Center of Nanjing University, Nanjing, Jiangsu, 210061, China.
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48
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Singh S, Qin F, Kumar S, Elfman J, Lin E, Pham LP, Yang A, Li H. The landscape of chimeric RNAs in non-diseased tissues and cells. Nucleic Acids Res 2020; 48:1764-1778. [PMID: 31965184 PMCID: PMC7038929 DOI: 10.1093/nar/gkz1223] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 12/13/2019] [Accepted: 01/20/2020] [Indexed: 12/17/2022] Open
Abstract
Chimeric RNAs and their encoded proteins have been traditionally viewed as unique features of neoplasia, and have been used as biomarkers and therapeutic targets for multiple cancers. Recent studies have demonstrated that chimeric RNAs also exist in non-cancerous cells and tissues, although large-scale, genome-wide studies of chimeric RNAs in non-diseased tissues have been scarce. Here, we explored the landscape of chimeric RNAs in 9495 non-diseased human tissue samples of 53 different tissues from the GTEx project. Further, we established means for classifying chimeric RNAs, and observed enrichment for particular classifications as more stringent filters are applied. We experimentally validated a subset of chimeric RNAs from each classification and demonstrated functional relevance of two chimeric RNAs in non-cancerous cells. Importantly, our list of chimeric RNAs in non-diseased tissues overlaps with some entries in several cancer fusion databases, raising concerns for some annotations. The data from this study provides a large repository of chimeric RNAs present in non-diseased tissues, which can be used as a control dataset to facilitate the identification of true cancer-specific chimeras.
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Affiliation(s)
- Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Fujun Qin
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Shailesh Kumar
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Justin Elfman
- 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
| | - Emily Lin
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Lam-Phong Pham
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Amy Yang
- Department of Pathology, 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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GOLT1A-KISS1 fusion is associated with metastasis in adenoid cystic carcinomas. Biochem Biophys Res Commun 2020; 526:70-77. [PMID: 32192769 DOI: 10.1016/j.bbrc.2020.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 03/01/2020] [Indexed: 11/21/2022]
Abstract
Genetic alterations can drive carcinogenesis. Numerous studies have shown that gene fusion is associated with cancer progression and could provide valuable biomarkers for clinical diagnosis or targets for cancer therapy. Adenoid cystic carcinoma (ACC) is a rare form of adenocarcinoma, characterized by frequent local recurrence and high rates of distant metastasis, ultimately resulting in low survival rates. Owing to the lack of effective therapeutic targets and limited biomarkers for diagnosis, a deeper understanding of the molecular basis of ACC is urgently needed. Here, we show that gene fusion is associated with ACC metastasis. We identified a metastasis suppressor KISS1 fused with a close-by gene, GOLT1A, in highly metastatic ACC cell lines and human specimens. Such fusion blocks KISS1 translation, but not transcription, by introducing 5' upstream open reading frames (uORFs) in the GOLT1A-KISS1 fusion transcript. Deletion of these uORFs rescued KISS1 expression and reduced invasion and migration of metastatic ACC cells. We also detected GOLT1A-KISS1 fusion transcripts in other types of highly metastatic cancer cell lines. Taken together, our results highlight the significance of this novel GOLT1A-KISS1 gene fusion in tumor metastasis and provide a valuable biomarker for clinical diagnosis and future therapeutic targeting of ACC.
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Abstract
Exosomes are considered as sources of disease biomarkers since they are stable carriers of genetic material and proteins. We recently demonstrated that chimeric RNA in exosomes derived from patient fluids can be detected and further used for disease diagnosis. Here we describe a systematic method to obtain exosomes from body fluids for detecting expression of specific chimeric RNA based on a RT-qPCR strategy.
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Affiliation(s)
- Xiurong Ke
- Cancer Research Center, Shantou University Medical College, Shantou, Guangdong, China
- Laboratory for Translational Surgical Oncology, Department of Surgery, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Xiao Xiong
- Cancer Research Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Yusheng Lin
- Cancer Research Center, Shantou University Medical College, Shantou, Guangdong, China
- Department of Hematology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Hao Zhang
- Institute of Precision Cancer and Pathology, Jinan University Medical College, Guangzhou, Guangdong, China.
- Department of Pathology, Jinan University Medical College, Guangzhou, Guangdong, China.
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