1
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Liu S, Obert C, Yu YP, Zhao J, Ren BG, Liu JJ, Wiseman K, Krajacich BJ, Wang W, Metcalfe K, Smith M, Ben-Yehezkel T, Luo JH. Utility analyses of AVITI sequencing chemistry. BMC Genomics 2024; 25:778. [PMID: 39127634 DOI: 10.1186/s12864-024-10686-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in the genome and transcriptome sequencing of various organisms. Nevertheless, challenges with accuracy, lack of competitive options and prohibitive costs associated with high throughput parallel short-read sequencing persist. RESULTS Here, we conduct a comparative analysis using matched DNA and RNA short-reads assays between Element Biosciences' AVITI and Illumina's NextSeq 550 chemistries. Similar comparisons were evaluated for synthetic long-read sequencing for RNA and targeted single-cell transcripts between the AVITI and Illumina's NovaSeq 6000. For both DNA and RNA short-read applications, the study found that the AVITI produced significantly higher per sequence quality scores. For PCR-free DNA libraries, we observed an average 89.7% lower experimentally determined error rate when using the AVITI chemistry, compared to the NextSeq 550. For short-read RNA quantification, AVITI platform had an average of 32.5% lower error rate than that for NextSeq 550. With regards to synthetic long-read mRNA and targeted synthetic long read single cell mRNA sequencing, both platforms' respective chemistries performed comparably in quantification of genes and isoforms. The AVITI displayed a marginally lower error rate for long reads, with fewer chemistry-specific errors and a higher mutation detection rate. CONCLUSION These results point to the potential of the AVITI platform as a competitive candidate in high-throughput short read sequencing analyses when juxtaposed with the Illumina NextSeq 550.
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Affiliation(s)
- Silvia Liu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA.
- High Throughput Genome Center, University of Pittsburgh School of Medicine, Pittsburgh, USA.
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, USA.
| | - Caroline Obert
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA, 92121, USA
| | - Yan-Ping Yu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
- High Throughput Genome Center, University of Pittsburgh School of Medicine, Pittsburgh, USA
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Junhua Zhao
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA, 92121, USA
| | - Bao-Guo Ren
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
- High Throughput Genome Center, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Jia-Jun Liu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
- High Throughput Genome Center, University of Pittsburgh School of Medicine, Pittsburgh, USA
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Kelly Wiseman
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA, 92121, USA
| | - Benjamin J Krajacich
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA, 92121, USA
| | - Wenjia Wang
- Department of Biostatistics, University of Pittsburgh School of Public Health, Pittsburgh, USA
| | - Kyle Metcalfe
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA, 92121, USA
| | - Mat Smith
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA, 92121, USA
| | - Tuval Ben-Yehezkel
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA, 92121, USA
| | - Jian-Hua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA.
- High Throughput Genome Center, University of Pittsburgh School of Medicine, Pittsburgh, USA.
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, USA.
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2
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Kader M, Yu YP, Liu S, Luo JH. Immuno-targeting the ectopic phosphorylation sites of PDGFRA generated by MAN2A1-FER fusion in HCC. Hepatol Commun 2024; 8:e0511. [PMID: 39082961 DOI: 10.1097/hc9.0000000000000511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 06/30/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND HCC is one of the most lethal cancers for humans. Mannosidase alpha class 2A member 1 (MAN2A1)-FER is one of the most frequent oncogenic fusion genes in HCC. In this report, we showed that MAN2A1-FER ectopically phosphorylated the extracellular domains of PDGFRA, MET, AXL, and N-cadherin. The ectopic phosphorylation of these transmembrane proteins led to the activation of their kinase activities and initiated the activation cascades of their downstream signaling molecules. METHODS A panel of mouse monoclonal antibodies was developed to recognize the ectopic phosphorylation sites of PDGFRA. RESULTS AND CONCLUSIONS The analyses showed that these antibodies bound to the specific phosphotyrosine epitopes in the extracellular domain of PDGFRA with high affinity and specificity. The treatment of MAN2A1-FER-positive cancer HUH7 with one of the antibodies called 2-3B-G8 led to the deactivation of cell growth signaling pathways and cell growth arrest while having minimal impact on HUH7ko cells where MAN2A1-FER expression was disrupted. The treatment of 2-3B-G8 antibody also led to a large number of cell deaths of MAN2A1-FER-positive cancer cells such as HUH7, HEPG2, SNU449, etc., while the same treatment had no impact on HUH7ko cells. When severe combined immunodeficiency mice xenografted with HEPG2 or HUH7 were treated with monomethyl auristatin E-conjugated 2-3B-G8 antibody, it slowed the progression of tumor growth, eliminated the metastasis, and reduced the mortality, in comparison with the controls. Targeting the cancer-specific ectopic phosphorylation sites of PDGFRA induced by MAN2A1-FER may hold promise as an effective treatment for liver cancer.
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Affiliation(s)
- Muhamuda Kader
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yan-Ping Yu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- High Throughput Genome Center, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Silvia Liu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- High Throughput Genome Center, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jian-Hua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- High Throughput Genome Center, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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3
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Yu YP, Liu S, Geller D, Luo JH. Serum Fusion Transcripts to Assess the Risk of Hepatocellular Carcinoma and the Impact of Cancer Treatment through Machine Learning. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:1262-1271. [PMID: 38537933 PMCID: PMC11220925 DOI: 10.1016/j.ajpath.2024.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/05/2024] [Accepted: 02/21/2024] [Indexed: 04/10/2024]
Abstract
Hepatocellular carcinoma (HCC) is one of the most fatal malignancies. Early diagnosis of HCC is crucial in reducing the risk for mortality. This study analyzed a panel of nine fusion transcripts in serum samples from 61 patients with HCC and 75 patients with non-HCC conditions, using TaqMan real-time quantitative RT-PCR. Seven of the nine fusions frequently detected in patients with HCC included: MAN2A1-FER (100%), SLC45A2-AMACR (62.3%), ZMPSTE24-ZMYM4 (62.3%), PTEN-NOLC1 (57.4%), CCNH-C5orf30 (55.7%), STAMBPL1-FAS (26.2%), and PCMTD1-SNTG1 (16.4%). Machine-learning models were constructed based on serum fusion-gene levels to predict HCC in the training cohort, using the leave-one-out cross-validation approach. One machine-learning model, called the four fusion genes logistic regression model (MAN2A1-FER≤40, CCNH-C5orf30≤38, SLC45A2-AMACR≤41, and PTEN-NOLC1≤40), produced accuracies of 91.5% and 83.3% in the training and testing cohorts, respectively. When serum α-fetal protein level was incorporated into the machine-learning model, a two fusion gene (MAN2A1-FER≤40, CCNH-C5orf30≤38) + α-fetal protein logistic regression model was found to generate an accuracy of 94.8% in the training cohort. The same model resulted in 95% accuracy in both the testing and combined cohorts. Cancer treatment was associated with reduced levels of most of the serum fusion transcripts. Serum fusion-gene machine-learning models may serve as important tools in screening for HCC and in monitoring the impact of HCC treatment.
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Affiliation(s)
- Yan-Ping Yu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; High Throughput Genome Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Silvia Liu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; High Throughput Genome Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - David Geller
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jian-Hua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; High Throughput Genome Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.
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4
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Liu S, Obert C, Yu YP, Zhao J, Ren BG, Liu JJ, Wiseman K, Krajacich BJ, Wang W, Metcalfe K, Smith M, Ben-Yehezkel T, Luo JH. Utility Analyses of AVITI Sequencing Chemistry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590136. [PMID: 38712138 PMCID: PMC11071311 DOI: 10.1101/2024.04.18.590136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Background DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in the genome and transcriptome sequencing of various organisms. Nevertheless, challenges with accuracy, lack of competitive options and prohibitive costs associated with high throughput parallel short-read sequencing persist. Results Here, we conduct a comparative analysis using matched DNA and RNA short-reads assays between Element Biosciences' AVITI and Illumina's NextSeq 550 chemistries. Similar comparisons were evaluated for synthetic long-read sequencing for RNA and targeted single-cell transcripts between the AVITI and Illumina's NovaSeq 6000. For both DNA and RNA short-read applications, the study found that the AVITI produced significantly higher per sequence quality scores. For PCR-free DNA libraries, we observed an average 89.7% lower experimentally determined error rate when using the AVITI chemistry, compared to the NextSeq 550. For short-read RNA quantification, AVITI platform had an average of 32.5% lower error rate than that for NextSeq 550. With regards to synthetic long-read mRNA and targeted synthetic long read single cell mRNA sequencing, both platforms' respective chemistries performed comparably in quantification of genes and isoforms. The AVITI displayed a marginally lower error rate for long reads, with fewer chemistry-specific errors and a higher mutation detection rate. Conclusion These results point to the potential of the AVITI platform as a competitive candidate in high-throughput short read sequencing analyses when juxtaposed with the Illumina NextSeq 550.
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Affiliation(s)
- Silvia Liu
- Department of Pathology, University of Pittsburgh School of Medicine, United States
- High Throughput Genome Center, University of Pittsburgh School of Medicine, United States
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, United States
| | - Caroline Obert
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA 92121, United States
| | - Yan-Ping Yu
- Department of Pathology, University of Pittsburgh School of Medicine, United States
- High Throughput Genome Center, University of Pittsburgh School of Medicine, United States
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, United States
| | - Junhua Zhao
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA 92121, United States
| | - Bao-Guo Ren
- Department of Pathology, University of Pittsburgh School of Medicine, United States
- High Throughput Genome Center, University of Pittsburgh School of Medicine, United States
| | - Jia-Jun Liu
- Department of Pathology, University of Pittsburgh School of Medicine, United States
- High Throughput Genome Center, University of Pittsburgh School of Medicine, United States
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, United States
| | - Kelly Wiseman
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA 92121, United States
| | - Benjamin J Krajacich
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA 92121, United States
| | - Wenjia Wang
- Department of Biostatistics, University of Pittsburgh School of Public Health, United States
| | - Kyle Metcalfe
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA 92121, United States
| | - Mat Smith
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA 92121, United States
| | - Tuval Ben-Yehezkel
- Element Biosciences Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA 92121, United States
| | - Jian-Hua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, United States
- High Throughput Genome Center, University of Pittsburgh School of Medicine, United States
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, United States
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Wang W, Li Y, Ko S, Feng N, Zhang M, Liu JJ, Zheng S, Ren B, Yu YP, Luo JH, Tseng GC, Liu S. IFDlong: an isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.11.593690. [PMID: 38798496 PMCID: PMC11118288 DOI: 10.1101/2024.05.11.593690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Advancements in long-read transcriptome sequencing (long-RNA-seq) technology have revolutionized the study of isoform diversity. These full-length transcripts enhance the detection of various transcriptome structural variations, including novel isoforms, alternative splicing events, and fusion transcripts. By shifting the open reading frame or altering gene expressions, studies have proved that these transcript alterations can serve as crucial biomarkers for disease diagnosis and therapeutic targets. In this project, we proposed IFDlong, a bioinformatics and biostatistics tool to detect isoform and fusion transcripts using bulk or single-cell long-RNA-seq data. Specifically, the software performed gene and isoform annotation for each long-read, defined novel isoforms, quantified isoform expression by a novel expectation-maximization algorithm, and profiled the fusion transcripts. For evaluation, IFDlong pipeline achieved overall the best performance when compared with several existing tools in large-scale simulation studies. In both isoform and fusion transcript quantification, IFDlong is able to reach more than 0.8 Spearman's correlation with the truth, and more than 0.9 cosine similarity when distinguishing multiple alternative splicing events. In novel isoform simulation, IFDlong can successfully balance the sensitivity (higher than 90%) and specificity (higher than 90%). Furthermore, IFDlong has proved its accuracy and robustness in diverse in-house and public datasets on healthy tissues, cell lines and multiple types of diseases. Besides bulk long-RNA-seq, IFDlong pipeline has proved its compatibility to single-cell long-RNA-seq data. This new software may hold promise for significant impact on long-read transcriptome analysis. The IFDlong software is available at https://github.com/wenjiaking/IFDlong.
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Affiliation(s)
- Wenjia Wang
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Yuzhen Li
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Sungjin Ko
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA
| | - Ning Feng
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Manling Zhang
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Jia-Jun Liu
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA
| | - Songyang Zheng
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA
| | - Baoguo Ren
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA
| | - Yan P. Yu
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA
| | - Jian-Hua Luo
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - George C. Tseng
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Silvia Liu
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA
- Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA
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6
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Pan B, Cheng J, Tan W, Wu X, Fan Q, Fan L, Jiang M, Yu R, Cheng X, Deng Y. Pan-cancer analysis of LRRC59 with a focus on prognostic and immunological roles in hepatocellular carcinoma. Aging (Albany NY) 2024; 16:8171-8197. [PMID: 38738999 PMCID: PMC11131990 DOI: 10.18632/aging.205810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/09/2024] [Indexed: 05/14/2024]
Abstract
BACKGROUND LRRC59 is a leucine-rich repeats-containing protein located in the endoplasmic reticulum (ER), it serves as a prognostic marker in several cancers. However, there has been no systematic analysis of its role in the tumor immune microenvironment, nor its predictive value of prognosis and immunotherapy response in different cancers. METHODS A comprehensive pan-cancer analysis of LRRC59 was conducted from various databases to elucidate the associations between its expression and the prognosis of cancer, genetic alterations, tumor metabolism, and tumor immunity. Additionally, further functional assays were performed in hepatocellular carcinoma (HCC) to study its biological role in regulating cell proliferation, migration, apoptosis, cell cycle arrest, and sensitivity to immunotherapy. RESULTS The pan-cancer analysis reveals a significant upregulation of LRRC59 in pan-cancer, and its overexpression is correlated with unfavorable prognosis in cancer patients. LRRC59 is negatively correlated with immune cell infiltration, tumor purity estimation, and immune checkpoint genes. Finally, the validation in HCC demonstrates LRRC59 is significantly overexpressed in cancer tissue and cell lines, and its knockdown inhibits cell proliferation and migration, promotes cell apoptosis, induces cell cycle arrest, and enhances the sensitivity to immunotherapy in HCC cells. CONCLUSIONS LRRC59 emerges as a novel potential prognostic biomarker across malignancies, offering promise for anti-cancer drugs and immunotherapy.
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Affiliation(s)
- Boyu Pan
- Department of Orthopaedics, The Third Hospital of Changsha, Changsha 410015, Hunan, China
- Department of Spine Surgery, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Jun Cheng
- Department of Spine Surgery, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Wei Tan
- Department of Spine Surgery, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Xin Wu
- Department of Spine Surgery, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Qizhi Fan
- Department of Spine Surgery, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Lei Fan
- Department of Orthopaedics, The Third Hospital of Changsha, Changsha 410015, Hunan, China
| | - Minghui Jiang
- Department of Orthopaedics, The Third Hospital of Changsha, Changsha 410015, Hunan, China
| | - Rong Yu
- Department of Orthopaedics, The Third Hospital of Changsha, Changsha 410015, Hunan, China
| | - Xiaoyun Cheng
- Department of Pulmonary and Critical Care Medicine, The Third Xiangya Hospital of Central South University, Changsha 410013, Hunan, China
| | - Youwen Deng
- Department of Spine Surgery, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
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7
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Landowski M, Gogoi P, Ikeda S, Ikeda A. Roles of transmembrane protein 135 in mitochondrial and peroxisomal functions - implications for age-related retinal disease. FRONTIERS IN OPHTHALMOLOGY 2024; 4:1355379. [PMID: 38576540 PMCID: PMC10993500 DOI: 10.3389/fopht.2024.1355379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Aging is the most significant risk factor for age-related diseases in general, which is true for age-related diseases in the eye including age-related macular degeneration (AMD). Therefore, in order to identify potential therapeutic targets for these diseases, it is crucial to understand the normal aging process and how its mis-regulation could cause age-related diseases at the molecular level. Recently, abnormal lipid metabolism has emerged as one major aspect of age-related symptoms in the retina. Animal models provide excellent means to identify and study factors that regulate lipid metabolism in relation to age-related symptoms. Central to this review is the role of transmembrane protein 135 (TMEM135) in the retina. TMEM135 was identified through the characterization of a mutant mouse strain exhibiting accelerated retinal aging and positional cloning of the responsible mutation within the gene, indicating the crucial role of TMEM135 in regulating the normal aging process in the retina. Over the past decade, the molecular functions of TMEM135 have been explored in various models and tissues, providing insights into the regulation of metabolism, particularly lipid metabolism, through its action in multiple organelles. Studies indicated that TMEM135 is a significant regulator of peroxisomes, mitochondria, and their interaction. Here, we provide an overview of the molecular functions of TMEM135 which is crucial for regulating mitochondria, peroxisomes, and lipids. The review also discusses the age-dependent phenotypes in mice with TMEM135 perturbations, emphasizing the importance of a balanced TMEM135 function for the health of the retina and other tissues including the heart, liver, and adipose tissue. Finally, we explore the potential roles of TMEM135 in human age-related retinal diseases, connecting its functions to the pathobiology of AMD.
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Affiliation(s)
- Michael Landowski
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, United States
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Purnima Gogoi
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, United States
| | - Sakae Ikeda
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, United States
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Akihiro Ikeda
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, United States
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, United States
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8
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Liu S, Yu YP, Ren BG, Ben-Yehezkel T, Obert C, Smith M, Wang W, Ostrowska A, Soto-Gutierrez A, Luo JH. Long-read single-cell sequencing reveals expressions of hypermutation clusters of isoforms in human liver cancer cells. eLife 2024; 12:RP87607. [PMID: 38206124 PMCID: PMC10945587 DOI: 10.7554/elife.87607] [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] [Indexed: 01/12/2024] Open
Abstract
The protein diversity of mammalian cells is determined by arrays of isoforms from genes. Genetic mutation is essential in species evolution and cancer development. Accurate long-read transcriptome sequencing at single-cell level is required to decipher the spectrum of protein expressions in mammalian organisms. In this report, we developed a synthetic long-read single-cell sequencing technology based on LOOPSeq technique. We applied this technology to analyze 447 transcriptomes of hepatocellular carcinoma (HCC) and benign liver from an individual. Through Uniform Manifold Approximation and Projection analysis, we identified a panel of mutation mRNA isoforms highly specific to HCC cells. The evolution pathways that led to the hyper-mutation clusters in single human leukocyte antigen molecules were identified. Novel fusion transcripts were detected. The combination of gene expressions, fusion gene transcripts, and mutation gene expressions significantly improved the classification of liver cancer cells versus benign hepatocytes. In conclusion, LOOPSeq single-cell technology may hold promise to provide a new level of precision analysis on the mammalian transcriptome.
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Affiliation(s)
- Silvia Liu
- Department of Pathology, University of PittsburghPittsburghUnited States
- High Throughput Genome Center, University of PittsburghPittsburghUnited States
- Pittsburgh Liver Research Center, University of PittsburghPittsburghUnited States
| | - Yan-Ping Yu
- Department of Pathology, University of PittsburghPittsburghUnited States
- High Throughput Genome Center, University of PittsburghPittsburghUnited States
- Pittsburgh Liver Research Center, University of PittsburghPittsburghUnited States
| | - Bao-Guo Ren
- Department of Pathology, University of PittsburghPittsburghUnited States
- High Throughput Genome Center, University of PittsburghPittsburghUnited States
- Pittsburgh Liver Research Center, University of PittsburghPittsburghUnited States
| | | | | | - Mat Smith
- Element Biosciences IncSan DiegoUnited States
| | - Wenjia Wang
- Biostatistics, University of PittsburghPittsburghUnited States
| | - Alina Ostrowska
- Department of Pathology, University of PittsburghPittsburghUnited States
- Pittsburgh Liver Research Center, University of PittsburghPittsburghUnited States
| | - Alejandro Soto-Gutierrez
- Department of Pathology, University of PittsburghPittsburghUnited States
- Pittsburgh Liver Research Center, University of PittsburghPittsburghUnited States
| | - Jian-Hua Luo
- Department of Pathology, University of PittsburghPittsburghUnited States
- High Throughput Genome Center, University of PittsburghPittsburghUnited States
- Pittsburgh Liver Research Center, University of PittsburghPittsburghUnited States
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9
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Desaunay M, Voisset E, Letard S, Roche P, De Sepulveda P. The Recurrent Liver MAN2A1-FER Oncoprotein Lacks Kinase Activity: Implications for the Use of Tyrosine Kinase Inhibitors. Cell Mol Gastroenterol Hepatol 2023; 17:667-669. [PMID: 38141924 PMCID: PMC10958342 DOI: 10.1016/j.jcmgh.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 12/25/2023]
Affiliation(s)
- Mathieu Desaunay
- Centre de Recherche en Cancérologie de Marseille, CRCM, Marseille, France; Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, Marseille, France; Signaling, Hematopoiesis and Mechanism of Oncogenesis Lab, Marseille, France
| | - Edwige Voisset
- Centre de Recherche en Cancérologie de Marseille, CRCM, Marseille, France; Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, Marseille, France; Signaling, Hematopoiesis and Mechanism of Oncogenesis Lab, Marseille, France
| | - Sebastien Letard
- Centre de Recherche en Cancérologie de Marseille, CRCM, Marseille, France; Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, Marseille, France; Signaling, Hematopoiesis and Mechanism of Oncogenesis Lab, Marseille, France
| | - Philippe Roche
- Centre de Recherche en Cancérologie de Marseille, CRCM, Marseille, France; Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, Marseille, France; High Throughput Screening (HiTS) Facility, Marseille, France
| | - Paulo De Sepulveda
- Centre de Recherche en Cancérologie de Marseille, CRCM, Marseille, France; Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, Marseille, France; Signaling, Hematopoiesis and Mechanism of Oncogenesis Lab, Marseille, France; OPALE Carnot Institute, Paris, France.
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10
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Zhang P, Xie X, Li C, Zhang C, Liang P. LRRC59 serves as a novel biomarker for predicting the progression and prognosis of bladder cancer. Cancer Med 2023; 12:19758-19776. [PMID: 37706625 PMCID: PMC10587936 DOI: 10.1002/cam4.6542] [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: 03/26/2023] [Revised: 06/28/2023] [Accepted: 09/05/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Leucine-rich repeat-containing protein 59 (LRRC59) is an endoplasmic reticulum membrane protein involved in various cancers, but its role in bladder cancer (BC) has not been reported. The aim of the present study was to investigate the role of LRRC59 protein in BC progression and prognosis. METHODS The expression profile and clinical significance were retrieved from BC patients in the Cancer Genome Atlas database. The methylation status of LRRC59 was analyzed by UALCAN and MethSurv databases. Potential signaling pathways and biological functions were explored by functional enrichment analysis. Immunocyte infiltration was evaluated by CIBERSORT analysis. The prognostic value of LRRC59 was evaluated by Kaplan-Meier and Cox regression analyses. Overall survival (OS) was predicted by the nomogram plot established in this study. LRRC59 expression in 10 pairs BC and adjacent noncancerous tissues were analyzed by immunohistochemistry (IHC). Cell proliferation, migration, and invasion were detected by CCK8, colony formation assay, transwell assay, and cell scratch assay, respectively. Proteins related to epithelial-mesenchymal transition and apoptosis were detected by western blot. RESULTS LRRC59 overexpression significantly decreased OS, disease-specific survival, and progress-free interval of BC patients. LRRC59 was a prognostic marker for OS and its hypomethylation status signified a poor prognosis. LRRC59 overexpression was correlated with infiltration of resting memory CD4 T cells, memory activated CD4 T cells, resting NK cells, macrophages M0, M1, M2, and neutrophils. IHC showed that the LRRC59 expression in BC tissue was significantly higher than that in adjacent noncancerous tissue. Knockdown of LRRC59 expression inhibited the proliferation of BC cells and reduced their migratory ability. Western blot showed that Snail and vimentin protein expressions decreased, while E-cadherin expressions increased. CONCLUSIONS LRRC59 expression can predict the outcome of BC independently and serve as a new biomarker for diagnosis.
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Affiliation(s)
- Peng Zhang
- Department of UrologyThe Second Affiliated Hospital of Chongqing Medical UniversityChongqingPeople's Republic of China
| | - Xiaodu Xie
- Department of UrologyThe Second Affiliated Hospital of Chongqing Medical UniversityChongqingPeople's Republic of China
| | - Chunming Li
- Department of Hepatobiliary SurgeryThe Second Affiliated Hospital of Chongqing Medical UniversityChongqingPeople's Republic of China
| | - Chaohua Zhang
- Department of Gastrointestinal SurgeryThe Second Affiliated Hospital of Chongqing Medical UniversityChongqingPeople's Republic of China
| | - Peihe Liang
- Department of UrologyThe Second Affiliated Hospital of Chongqing Medical UniversityChongqingPeople's Republic of China
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11
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Liu S, Yu YP, Ren BG, Ben-Yehezkel T, Obert C, Smith M, Wang W, Ostrowska A, Soto-Gutierrez A, Luo JH. Long-read single-cell sequencing reveals expressions of hypermutation clusters of isoforms in human liver cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.532991. [PMID: 36993628 PMCID: PMC10055174 DOI: 10.1101/2023.03.16.532991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
The protein diversity of mammalian cells is determined by arrays of isoforms from genes. Genetic mutation is essential in species evolution and cancer development. Accurate Long-read transcriptome sequencing at single-cell level is required to decipher the spectrum of protein expressions in mammalian organisms. In this report, we developed a synthetic long-read single-cell sequencing technology based on LOOPseq technique. We applied this technology to analyze 447 transcriptomes of hepatocellular carcinoma (HCC) and benign liver from an individual. Through Uniform Manifold Approximation and Projection (UMAP) analysis, we identified a panel of mutation mRNA isoforms highly specific to HCC cells. The evolution pathways that led to the hyper-mutation clusters in single human leukocyte antigen (HLA) molecules were identified. Novel fusion transcripts were detected. The combination of gene expressions, fusion gene transcripts, and mutation gene expressions significantly improved the classification of liver cancer cells versus benign hepatocytes. In conclusion, LOOPseq single-cell technology may hold promise to provide a new level of precision analysis on the mammalian transcriptome.
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Affiliation(s)
- Silvia Liu
- Department of Pathology, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261
- High Throughput Genome Center, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261
- Pittsburgh Liver Research Center, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261
| | - Yan-Ping Yu
- Department of Pathology, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261
- High Throughput Genome Center, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261
- Pittsburgh Liver Research Center, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261
| | - Bao-Guo Ren
- Department of Pathology, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261
- High Throughput Genome Center, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261
- Pittsburgh Liver Research Center, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261
| | - Tuval Ben-Yehezkel
- Element Biosciences, Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA 92121
| | - Caroline Obert
- Element Biosciences, Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA 92121
| | - Mat Smith
- Element Biosciences, Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA 92121
| | - Wenjia Wang
- Biostatistics, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261
| | - Alina Ostrowska
- Department of Pathology, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261
- Pittsburgh Liver Research Center, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261
| | - Alejandro Soto-Gutierrez
- Department of Pathology, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261
- Pittsburgh Liver Research Center, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261
| | - Jian-Hua Luo
- Department of Pathology, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261
- High Throughput Genome Center, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261
- Pittsburgh Liver Research Center, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261
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12
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Salokas K, Dashi G, Varjosalo M. Decoding Oncofusions: Unveiling Mechanisms, Clinical Impact, and Prospects for Personalized Cancer Therapies. Cancers (Basel) 2023; 15:3678. [PMID: 37509339 PMCID: PMC10377698 DOI: 10.3390/cancers15143678] [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: 06/21/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Cancer-associated gene fusions, also known as oncofusions, have emerged as influential drivers of oncogenesis across a diverse range of cancer types. These genetic events occur via chromosomal translocations, deletions, and inversions, leading to the fusion of previously separate genes. Due to the drastic nature of these mutations, they often result in profound alterations of cellular behavior. The identification of oncofusions has revolutionized cancer research, with advancements in sequencing technologies facilitating the discovery of novel fusion events at an accelerated pace. Oncofusions exert their effects through the manipulation of critical cellular signaling pathways that regulate processes such as proliferation, differentiation, and survival. Extensive investigations have been conducted to understand the roles of oncofusions in solid tumors, leukemias, and lymphomas. Large-scale initiatives, including the Cancer Genome Atlas, have played a pivotal role in unraveling the landscape of oncofusions by characterizing a vast number of cancer samples across different tumor types. While validating the functional relevance of oncofusions remains a challenge, even non-driver mutations can hold significance in cancer treatment. Oncofusions have demonstrated potential value in the context of immunotherapy through the production of neoantigens. Their clinical importance has been observed in both treatment and diagnostic settings, with specific fusion events serving as therapeutic targets or diagnostic markers. However, despite the progress made, there is still considerable untapped potential within the field of oncofusions. Further research and validation efforts are necessary to understand their effects on a functional basis and to exploit the new targeted treatment avenues offered by oncofusions. Through further functional and clinical studies, oncofusions will enable the advancement of precision medicine and the drive towards more effective and specific treatments for cancer patients.
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Affiliation(s)
- Kari Salokas
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Giovanna Dashi
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
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13
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Drazdauskienė U, Kapustina Ž, Medžiūnė J, Dubovskaja V, Sabaliauskaitė R, Jarmalaitė S, Lubys A. Fusion sequencing via terminator-assisted synthesis (FTAS-seq) identifies TMPRSS2 fusion partners in prostate cancer. Mol Oncol 2023; 17:993-1006. [PMID: 37300660 DOI: 10.1002/1878-0261.13428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/26/2023] [Accepted: 04/03/2023] [Indexed: 06/12/2023] Open
Abstract
Genetic rearrangements that fuse an androgen-regulated promoter area with a protein-coding portion of an originally androgen-unaffected gene are frequent in prostate cancer, with the fusion between transmembrane serine protease 2 (TMPRSS2) and ETS transcription factor ERG (ERG) (TMPRSS2-ERG fusion) being the most prevalent. Conventional hybridization- or amplification-based methods can test for the presence of expected gene fusions, but the exploratory analysis of currently unknown fusion partners is often cost-prohibitive. Here, we developed an innovative next-generation sequencing (NGS)-based approach for gene fusion analysis termed fusion sequencing via terminator-assisted synthesis (FTAS-seq). FTAS-seq can be used to enrich the gene of interest while simultaneously profiling the whole spectrum of its 3'-terminal fusion partners. Using this novel semi-targeted RNA-sequencing technique, we were able to identify 11 previously uncharacterized TMPRSS2 fusion partners and capture a range of TMPRSS2-ERG isoforms. We tested the performance of FTAS-seq with well-characterized prostate cancer cell lines and utilized the technique for the analysis of patient RNA samples. FTAS-seq chemistry combined with appropriate primer panels holds great potential as a tool for biomarker discovery that can support the development of personalized cancer therapies.
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Affiliation(s)
| | | | | | | | | | - Sonata Jarmalaitė
- National Cancer Institute, Vilnius, Lithuania
- Institute of Biosciences, Life Sciences Center, Vilnius University, Lithuania
| | - Arvydas Lubys
- Thermo Fisher Scientific Baltics, Vilnius, Lithuania
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14
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Liu Z, Yan W, Liu S, Liu Z, Xu P, Fang W. Regulatory network and targeted interventions for CCDC family in tumor pathogenesis. Cancer Lett 2023; 565:216225. [PMID: 37182638 DOI: 10.1016/j.canlet.2023.216225] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/03/2023] [Accepted: 05/10/2023] [Indexed: 05/16/2023]
Abstract
CCDC (coiled-coil domain-containing) is a coiled helix domain that exists in natural proteins. There are about 180 CCDC family genes, encoding proteins that are involved in intercellular transmembrane signal transduction and genetic signal transcription, among other functions. Alterations in expression, mutation, and DNA promoter methylation of CCDC family genes have been shown to be associated with the pathogenesis of many diseases, including primary ciliary dyskinesia, infertility, and tumors. In recent studies, CCDC family genes have been found to be involved in regulation of growth, invasion, metastasis, chemosensitivity, and other biological behaviors of malignant tumor cells in various cancer types, including nasopharyngeal carcinoma, lung cancer, colorectal cancer, and thyroid cancer. In this review, we summarize the involvement of CCDC family genes in tumor pathogenesis and the relevant upstream and downstream molecular mechanisms. In addition, we summarize the potential of CCDC family genes as tumor therapy targets. The findings discussed here help us to further understand the role and the therapeutic applications of CCDC family genes in tumors.
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Affiliation(s)
- Zhen Liu
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315, Guangzhou, China.
| | - Weiwei Yan
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315, Guangzhou, China
| | - Shaohua Liu
- Department of General Surgery, Pingxiang People's Hospital, Pingxiang, Jiangxi, 337000, China
| | - Zhan Liu
- Department of Gastroenterology and Clinical Nutrition, The First Affiliated Hospital (People's Hospital of Hunan Province), Hunan Normal University, Changsha, 410002, China
| | - Ping Xu
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315, Guangzhou, China; Respiratory Department, Peking University Shenzhen Hospital, Shenzhen, 518034, China.
| | - Weiyi Fang
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315, Guangzhou, China.
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15
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Yu YP, Liu S, Ren BG, Nelson J, Jarrard D, Brooks JD, Michalopoulos G, Tseng G, Luo JH. Fusion Gene Detection in Prostate Cancer Samples Enhances the Prediction of Prostate Cancer Clinical Outcomes from Radical Prostatectomy through Machine Learning in a Multi-Institutional Analysis. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:392-403. [PMID: 36681188 PMCID: PMC10123524 DOI: 10.1016/j.ajpath.2022.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/29/2022] [Accepted: 12/12/2022] [Indexed: 01/20/2023]
Abstract
Prostate cancer remains one of the most fatal malignancies in men in the United States. Predicting the course of prostate cancer is challenging given that only a fraction of prostate cancer patients experience cancer recurrence after radical prostatectomy or radiation therapy. This study examined the expressions of 14 fusion genes in 607 prostate cancer samples from the University of Pittsburgh, Stanford University, and the University of Wisconsin-Madison. The profiling of 14 fusion genes was integrated with Gleason score of the primary prostate cancer and serum prostate-specific antigen level to develop machine-learning models to predict the recurrence of prostate cancer after radical prostatectomy. Machine-learning algorithms were developed by analysis of the data from the University of Pittsburgh cohort as a training set using the leave-one-out cross-validation method. These algorithms were then applied to the data set from the combined Stanford/Wisconsin cohort (testing set). The results showed that the addition of fusion gene profiling consistently improved the prediction accuracy rate of prostate cancer recurrence by Gleason score, serum prostate-specific antigen level, or a combination of both. These improvements occurred in both the training and testing cohorts and were corroborated by multiple models.
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Affiliation(s)
- Yan-Ping Yu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Silvia Liu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Bao-Guo Ren
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Joel Nelson
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - David Jarrard
- Department of Urology, University of Wisconsin School of Medicine, Madison, Wisconsin
| | - James D Brooks
- Department of Urology, Stanford University School of Medicine, Stanford, California
| | - George Michalopoulos
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - George Tseng
- Department of Biostatistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jian-Hua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.
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16
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Eickelschulte S, Riediger AL, Angeles AK, Janke F, Duensing S, Sültmann H, Görtz M. Biomarkers for the Detection and Risk Stratification of Aggressive Prostate Cancer. Cancers (Basel) 2022; 14:cancers14246094. [PMID: 36551580 PMCID: PMC9777028 DOI: 10.3390/cancers14246094] [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: 11/17/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Current strategies for the clinical management of prostate cancer are inadequate for a precise risk stratification between indolent and aggressive tumors. Recently developed tissue-based molecular biomarkers have refined the risk assessment of the disease. The characterization of tissue biopsy components and subsequent identification of relevant tissue-based molecular alterations have the potential to improve the clinical decision making and patient outcomes. However, tissue biopsies are invasive and spatially restricted due to tumor heterogeneity. Therefore, there is an urgent need for complementary diagnostic and prognostic options. Liquid biopsy approaches are minimally invasive with potential utility for the early detection, risk stratification, and monitoring of tumors. In this review, we focus on tissue and liquid biopsy biomarkers for early diagnosis and risk stratification of prostate cancer, including modifications on the genomic, epigenomic, transcriptomic, and proteomic levels. High-risk molecular alterations combined with orthogonal clinical parameters can improve the identification of aggressive tumors and increase patient survival.
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Affiliation(s)
- Samaneh Eickelschulte
- Junior Clinical Cooperation Unit, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Anja Lisa Riediger
- Junior Clinical Cooperation Unit, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Arlou Kristina Angeles
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Florian Janke
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Stefan Duensing
- Molecular Urooncology, Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Magdalena Görtz
- Junior Clinical Cooperation Unit, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Correspondence: ; Tel.: +49-6221-42-2603
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17
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Chira S, Nutu A, Isacescu E, Bica C, Pop L, Ciocan C, Berindan-Neagoe I. Genome Editing Approaches with CRISPR/Cas9 for Cancer Treatment: Critical Appraisal of Preclinical and Clinical Utility, Challenges, and Future Research. Cells 2022; 11:cells11182781. [PMID: 36139356 PMCID: PMC9496708 DOI: 10.3390/cells11182781] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/25/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
The increasing burden on human malignant diseases became a major concern for healthcare practitioners, that must deal with tumor relapse and the inability to efficiently treat metastasis, in addition to side effects. Throughout the decades, many therapeutic strategies have been employed to improve the clinical outcomes of cancer patients and great efforts have been made to develop more efficient and targeted medicines. The malignant cell is characterized by genetic and epigenetic modifications, therefore targeting those specific drivers of carcinogenesis is highly desirable. Among the genome editing technologies, CRISPR/Cas9 stood as a promising candidate for cancer treatment alternatives, due to its low complexity design. First described as a defense mechanism of bacteria against invading foreign DNA, later it was shown that CRISPR components can be engineered to target specific DNA sequences in a test tube, a discovery that was awarded later with the Nobel Prize in chemistry for its rapid expansion as a reliable genome editing tool in many fields of research, including medicine. The present paper aims of describing CRISPR/Cas9 potential targets for malignant disorders, and the approaches used for achieving this goal. Aside from preclinical studies, we also present the clinical trials that use CRISPR-based technology for therapeutic purposes of cancer. Finally, a summary of the presented studies adds a more focused view of the therapeutic value CRISPR/Cas9 holds and the associated shortcomings.
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18
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Wang QJ, Yuan XM. Role of coiled-coil domain containing proteins in development of gastric cancer. Shijie Huaren Xiaohua Zazhi 2022; 30:88-91. [DOI: 10.11569/wcjd.v30.i2.88] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Coiled-coil domain containing proteins (CCDCs) are a class of oligomeric proteins consisting of two or more coiled-coil domains. About 40 coiled coil family genes are associated with disease, and they can act as both pro-oncogenes and anti-oncogenes in the pathogenesis of tumors, regulating tumor proliferation, metastasis, angiogenesis, and apoptosis. Therefore, they are closely related to tumor development. This paper reviews the recent progress in the understanding of the role of CCDCs in gastric cancer, and explores their different roles and functions in the development of this malignancy.
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Affiliation(s)
- Qi-Ji Wang
- Graduate School, Shandong First Medical University and Shandong Academy of Medical Science, Jinan 250000, Shandong Province, China
| | - Xue-Min Yuan
- Department of Gastroenterology, Linyi People's Hospital, Linyi 276000, Shandong Province, China
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19
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Zuo Z, Yu Y, Ren B, Liu S, Nelson J, Wang Z, Tao J, Pradhan‐Sundd T, Bhargava R, Michalopoulos G, Chen Q, Zhang J, Ma D, Pennathur A, Luketich J, Satdarshan Monga P, Nalesnik M, Luo J. Oncogenic Activity of Solute Carrier Family 45 Member 2 and Alpha-Methylacyl-Coenzyme A Racemase Gene Fusion Is Mediated by Mitogen-Activated Protein Kinase. Hepatol Commun 2022; 6:209-222. [PMID: 34505419 PMCID: PMC8710797 DOI: 10.1002/hep4.1724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/23/2021] [Accepted: 02/28/2021] [Indexed: 11/09/2022] Open
Abstract
Chromosome rearrangement is one of the hallmarks of human malignancies. Gene fusion is one of the consequences of chromosome rearrangements. In this report, we show that gene fusion between solute carrier family 45 member 2 (SLC45A2) and alpha-methylacyl-coenzyme A racemase (AMACR) occurs in eight different types of human malignancies, with frequencies ranging from 45% to 97%. The chimeric protein is translocated to the lysosomal membrane and activates the extracellular signal-regulated kinase signaling cascade. The fusion protein promotes cell growth, accelerates migration, resists serum starvation-induced cell death, and is essential for cancer growth in mouse xenograft cancer models. Introduction of SLC45A2-AMACR into the mouse liver using a sleeping beauty transposon system and somatic knockout of phosphatase and TENsin homolog (Pten) generated spontaneous liver cancers within a short period. Conclusion: The gene fusion between SLC45A2 and AMACR may be a driving event for human liver cancer development.
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Affiliation(s)
- Ze‐Hua Zuo
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | - Yan‐Ping Yu
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
- Pittsburgh Liver Research Center of University of Pittsburgh Medical CenterPittsburghPAUSA
| | - Bao‐Guo Ren
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | - Silvia Liu
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
- Pittsburgh Liver Research Center of University of Pittsburgh Medical CenterPittsburghPAUSA
| | - Joel Nelson
- Department of UrologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | - Zhou Wang
- Department of UrologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | - Junyan Tao
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | | | - Rohit Bhargava
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | - George Michalopoulos
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
- Pittsburgh Liver Research Center of University of Pittsburgh Medical CenterPittsburghPAUSA
| | - Qi Chen
- Department of PharmacologyToxicology, and TherapeuticsUniversity of KansasKansas CityKSUSA
| | - Jun Zhang
- Department of MedicineUniversity of IowaIowa CityIAUSA
- Present address:
Department of MedicineUniversity of Kansas Medical CenterKansas CityKSUSA
| | - Deqin Ma
- Department of PathologyUniversity of IowaIowa CityIAUSA
| | - Arjun Pennathur
- Thoracic SurgeryUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | - James Luketich
- Thoracic SurgeryUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | - Paul Satdarshan Monga
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
- Pittsburgh Liver Research Center of University of Pittsburgh Medical CenterPittsburghPAUSA
| | - Michael Nalesnik
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | - Jian‐Hua Luo
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
- Pittsburgh Liver Research Center of University of Pittsburgh Medical CenterPittsburghPAUSA
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20
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Brūmele B, Mutso M, Telanne L, Õunap K, Spunde K, Abroi A, Kurg R. Human TRMT112-Methyltransferase Network Consists of Seven Partners Interacting with a Common Co-Factor. Int J Mol Sci 2021; 22:ijms222413593. [PMID: 34948388 PMCID: PMC8708615 DOI: 10.3390/ijms222413593] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/07/2021] [Accepted: 12/15/2021] [Indexed: 01/22/2023] Open
Abstract
Methylation is an essential epigenetic modification mainly catalysed by S-Adenosyl methionine-dependent methyltransferases (MTases). Several MTases require a cofactor for their metabolic stability and enzymatic activity. TRMT112 is a small evolutionary conserved protein that acts as a co-factor and activator for different MTases involved in rRNA, tRNA and protein methylation. Using a SILAC screen, we pulled down seven methyltransferases-N6AMT1, WBSCR22, METTL5, ALKBH8, THUMPD2, THUMPD3 and TRMT11-as interaction partners of TRMT112. We showed that TRMT112 stabilises all seven MTases in cells. TRMT112 and MTases exhibit a strong mutual feedback loop when expressed together in cells. TRMT112 interacts with its partners in a similar way; however, single amino acid mutations on the surface of TRMT112 reveal several differences as well. In summary, mammalian TRMT112 can be considered as a central "hub" protein that regulates the activity of at least seven methyltransferases.
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Affiliation(s)
| | | | | | | | | | | | - Reet Kurg
- Correspondence: ; Tel.: +372-737-5040
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21
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Liu S, Nalesnik MA, Singhi A, Wood-Trageser MA, Randhawa P, Ren BG, Humar A, Liu P, Yu YP, Tseng GC, Michalopoulos G, Luo JH. Transcriptome and Exome Analyses of Hepatocellular Carcinoma Reveal Patterns to Predict Cancer Recurrence in Liver Transplant Patients. Hepatol Commun 2021; 6:710-727. [PMID: 34725972 PMCID: PMC8948579 DOI: 10.1002/hep4.1846] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 10/06/2021] [Accepted: 10/10/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most lethal human cancers. Liver transplantation has been an effective approach to treat liver cancer. However, significant numbers of patients with HCC experience cancer recurrence, and the selection of suitable candidates for liver transplant remains a challenge. We developed a model to predict the likelihood of HCC recurrence after liver transplantation based on transcriptome and whole‐exome sequencing analyses. We used a training cohort and a subsequent testing cohort based on liver transplantation performed before or after the first half of 2012. We found that the combination of transcriptome and mutation pathway analyses using a random forest machine learning correctly predicted HCC recurrence in 86.8% of the training set. The same algorithm yielded a correct prediction of HCC recurrence of 76.9% in the testing set. When the cohorts were combined, the prediction rate reached 84.4% in the leave‐one‐out cross‐validation analysis. When the transcriptome analysis was combined with Milan criteria using the k‐top scoring pairs (k‐TSP) method, the testing cohort prediction rate improved to 80.8%, whereas the training cohort and the combined cohort prediction rates were 79% and 84.4%, respectively. Application of the transcriptome/mutation pathways RF model on eight tumor nodules from 3 patients with HCC yielded 8/8 consistency, suggesting a robust prediction despite the heterogeneity of HCC. Conclusion: The genome prediction model may hold promise as an alternative in selecting patients with HCC for liver transplant.
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Affiliation(s)
- Silvia Liu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michael A Nalesnik
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Aatur Singhi
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Parmjeet Randhawa
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Bao-Guo Ren
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Abhinav Humar
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Peng Liu
- Department of Biostatistics, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Yan-Ping Yu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - George Michalopoulos
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jian-Hua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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22
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Glenfield C, Innan H. Gene Duplication and Gene Fusion Are Important Drivers of Tumourigenesis during Cancer Evolution. Genes (Basel) 2021; 12:1376. [PMID: 34573358 PMCID: PMC8466788 DOI: 10.3390/genes12091376] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 02/07/2023] Open
Abstract
Chromosomal rearrangement and genome instability are common features of cancer cells in human. Consequently, gene duplication and gene fusion events are frequently observed in human malignancies and many of the products of these events are pathogenic, representing significant drivers of tumourigenesis and cancer evolution. In certain subsets of cancers duplicated and fused genes appear to be essential for initiation of tumour formation, and some even have the capability of transforming normal cells, highlighting the importance of understanding the events that result in their formation. The mechanisms that drive gene duplication and fusion are unregulated in cancer and they facilitate rapid evolution by selective forces akin to Darwinian survival of the fittest on a cellular level. In this review, we examine current knowledge of the landscape and prevalence of gene duplication and gene fusion in human cancers.
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Affiliation(s)
| | - Hideki Innan
- Department of Evolutionary Studies of Biosystems, SOKENDAI, The Graduate University for Advanced Studies, Shonan Village, Hayama, Kanagawar 240-0193, Japan;
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23
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Yu YP, Liu S, Nelson J, Luo JH. Detection of fusion gene transcripts in the blood samples of prostate cancer patients. Sci Rep 2021; 11:16995. [PMID: 34417538 PMCID: PMC8379170 DOI: 10.1038/s41598-021-96528-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/11/2021] [Indexed: 12/16/2022] Open
Abstract
Prostate cancer remains one of the most lethal cancers for men in the United States. The study aims to detect fusion transcripts in the blood samples of prostate cancer patients. We analyzed nine fusion transcripts including MAN2A1-FER, SLC45A2-AMACR, TRMT11-GRIK2, CCNH-C5orf30, mTOR-TP53BP1, KDM4-AC011523.2, TMEM135-CCDC67, LRRC59-FLJ60017 and Pten-NOLC1147 in the blood samples from 147 prostate cancer patients and 14 healthy individuals, using Taqman RT-PCR and Sanger's sequencing. Similar analyses were also performed on 25 matched prostate cancer samples for matched-sample evaluation. Eighty-two percent blood samples from the prostate cancer patients were positive for MAN2A1-FER transcript, while 41.5% and 38.8% blood samples from the prostate cancer patients were positive for SLC45A2-AMACR and Pten-NOLC1, respectively. CCNH-c5orf30 and mTOR-TP53BP1 had low detection rates, positive in only 5.4% and 4% of the blood samples from the prostate cancer patients. Only 2 blood samples were positive for KDM4B-AC011523.2 transcript. Overall, 89.8% patients were positive for at least one fusion transcript in their blood samples. The statistical analysis showed varied sensitivity of fusion transcript detection in the blood based on the types of fusions. In contrast, the blood samples from all healthy individuals were negative for the fusion transcripts. Detection of fusion transcripts in the blood samples of the prostate cancer patients may be a fast and cost-effective way to detect prostate cancer.
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Affiliation(s)
- Yan-Ping Yu
- Department of Pathology and Urology, School of Medicine, University of Pittsburgh, Scaife S-728, Pittsburgh, PA, 15261, USA
| | - Silvia Liu
- Department of Pathology and Urology, School of Medicine, University of Pittsburgh, Scaife S-728, Pittsburgh, PA, 15261, USA
| | - Joel Nelson
- Department of Pathology and Urology, School of Medicine, University of Pittsburgh, Scaife S-728, Pittsburgh, PA, 15261, USA
| | - Jian-Hua Luo
- Department of Pathology and Urology, School of Medicine, University of Pittsburgh, Scaife S-728, Pittsburgh, PA, 15261, USA.
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24
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Wei T, Lu J, Ma T, Huang H, Kocher JP, Wang L. Re-Evaluate Fusion Genes in Prostate Cancer. Cancer Inform 2021; 20:11769351211027592. [PMID: 34234399 PMCID: PMC8226361 DOI: 10.1177/11769351211027592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 06/06/2021] [Indexed: 11/15/2022] Open
Abstract
Background: Thousands of gene fusions have been reported in prostate cancer, but their
authenticity, incidence, and tumor specificity have not been thoroughly
evaluated, nor have their genomic characteristics been carefully
explored. Methods: We developed FusionVet to dedicatedly validate known fusion genes using
RNA-seq alignments. Using FusionVet, we re-assessed 2727 gene fusions
reported from 36 studies using the RNA-seq data generated by The Cancer
Genome Atlas (TCGA). We also explored their genomic characteristics and
interrogated the transcriptomic and DNA methylomic consequences of the E26
transformation-specific (ETS) fusions. Results: We found that nearly two-thirds of reported fusions are intra-chromosomal,
and 80% of them were formed between 2 protein-coding genes. Although most
(76%) genes were fused to only 1 partner, we observed many fusion hub genes
that have multiple fusion partners, including ETS family genes, androgen
receptor signaling pathway genes, tumor suppressor genes, and
proto-oncogenes. More than 90% of the reported fusions cannot be validated
by TCGA RNA-seq data. For those fusions that can be validated, 5% were
detected from tumor and normal samples with similar frequencies, and only 4%
(120 fusions) were tumor-specific. The occurrences of ERG,
ETV1, and ETV4 fusions were mutually
exclusive, and their fusion statuses were tightly associated with
overexpressions. Besides, we found ERG fusions were
significantly co-occurred with PTEN deletion but mutually
exclusive with common genomic alterations such as SPOP
mutation and FOXA1 mutation. Conclusions: Most of the reported fusion genes cannot be validated by TCGA samples. The
ETS family and androgen response genes were significantly enriched in
prostate cancer–specific fusion genes. Transcription activity was
significantly repressed, and the DNA methylation was significantly increased
in samples carrying ERG fusion.
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Affiliation(s)
- Ting Wei
- Division of Computational Biology, College of Medicine and Science, Mayo Clinic, Rochester, MN, USA
| | - Ji Lu
- Department of Urology, The First Hospital of Jilin University, Changchun, People's Republic of China
| | - Tao Ma
- Division of Computational Biology, College of Medicine and Science, Mayo Clinic, Rochester, MN, USA
| | - Haojie Huang
- Department of Biochemistry and Molecular Biology, College of Medicine and Science, Mayo Clinic, Rochester, MN, USA
| | - Jean-Pierre Kocher
- Division of Computational Biology, College of Medicine and Science, Mayo Clinic, Rochester, MN, USA
| | - Liguo Wang
- Division of Computational Biology, College of Medicine and Science, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, College of Medicine and Science, Mayo Clinic, Rochester, MN, USA.,Bioinformatics and Computational Biology Graduate Program, University of Minnesota Rochester, Rochester, MN, USA
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25
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Liu S, Wu I, Yu YP, Balamotis M, Ren B, Ben Yehezkel T, Luo JH. Targeted transcriptome analysis using synthetic long read sequencing uncovers isoform reprograming in the progression of colon cancer. Commun Biol 2021; 4:506. [PMID: 33907296 PMCID: PMC8079361 DOI: 10.1038/s42003-021-02024-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/09/2021] [Indexed: 02/02/2023] Open
Abstract
The characterization of human gene expression is limited by short read lengths, high error rates and large input requirements. Here, we used a synthetic long read (SLR) sequencing approach, LoopSeq, to generate accurate sequencing reads that span full length transcripts using standard short read data. LoopSeq identified isoforms from control samples with 99.4% accuracy and a 0.01% per-base error rate, exceeding the accuracy reported for other long-read technologies. Applied to targeted transcriptome sequencing from colon cancers and their metastatic counterparts, LoopSeq revealed large scale isoform redistributions from benign colon mucosa to primary colon cancer and metastatic cancer and identified several previously unknown fusion isoforms. Strikingly, single nucleotide variants (SNVs) occurred dominantly in specific isoforms and some SNVs underwent isoform switching in cancer progression. The ability to use short reads to generate accurate long-read data as the raw unit of information holds promise as a widely accessible approach in transcriptome sequencing.
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Affiliation(s)
- Silvia Liu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
- High Throughput Genome Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Indira Wu
- Loop Genomics, Inc., San Jose, CA, 95138, USA
| | - Yan-Ping Yu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
- High Throughput Genome Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | | | - Baoguo Ren
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
- High Throughput Genome Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | | | - Jian-Hua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA.
- High Throughput Genome Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA.
- Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA.
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26
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Wang H, Liu H, Dai W, Luo S, Amos CI, Lee JE, Li X, Yue Y, Nan H, Wei Q. Association of genetic variants of TMEM135 and PEX5 in the peroxisome pathway with cutaneous melanoma-specific survival. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:396. [PMID: 33842617 PMCID: PMC8033299 DOI: 10.21037/atm-20-2117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Background Peroxisomes are ubiquitous and dynamic organelles that are involved in the metabolism of reactive oxygen species (ROS) and lipids. However, whether genetic variants in the peroxisome pathway genes are associated with survival in patients with melanoma has not been established. Therefore, our aim was to identify additional genetic variants in the peroxisome pathway that may provide new prognostic biomarkers for cutaneous melanoma (CM). Methods We assessed the associations between 8,397 common single-nucleotide polymorphisms (SNPs) in 88 peroxisome pathway genes and CM disease-specific survival (CMSS) in a two-stage analysis. For the discovery, we extracted the data from a published genome-wide association study from The University of Texas MD Anderson Cancer Center (MDACC). We then replicated the results in another dataset from the Nurse Health Study (NHS)/Health Professionals Follow-up Study (HPFS). Results Overall, 95 (11.1%) patients in the MDACC dataset and 48 (11.7%) patients in the NHS/HPFS dataset died of CM. We found 27 significant SNPs in the peroxisome pathway genes to be associated with CMSS in both datasets after multiple comparison correction using the Bayesian false-discovery probability method. In stepwise Cox proportional hazards regression analysis, with adjustment for other covariates and previously published SNPs in the MDACC dataset, we identified 2 independent SNPs (TMEM135 rs567403 C>G and PEX5 rs7969508 A>G) that predicted CMSS (P=0.003 and 0.031, respectively, in an additive genetic model). The expression quantitative trait loci analysis further revealed that the TMEM135 rs567403 GG and PEX5 rs7969508 GG genotypes were associated with increased and decreased levels of mRNA expression of their genes, respectively. Conclusions Once our findings are replicated by other investigators, these genetic variants may serve as novel biomarkers for the prediction of survival in patients with CM.
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Affiliation(s)
- Haijiao Wang
- Department of Gynecology Oncology, The First Hospital of Jilin University, Changchun, Jilin, China.,Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Wei Dai
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey E Lee
- Department of Surgical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Xin Li
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN, USA
| | - Ying Yue
- Department of Gynecology Oncology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Hongmei Nan
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN, USA
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC, USA
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27
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Hurst T, Chen SJ. Deciphering nucleotide modification-induced structure and stability changes. RNA Biol 2021; 18:1920-1930. [PMID: 33586616 DOI: 10.1080/15476286.2021.1882179] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Nucleotide modification in RNA controls a bevy of biological processes, including RNA degradation, gene expression, and gene editing. In turn, misregulation of modified nucleotides is associated with a host of chronic diseases and disorders. However, the molecular mechanisms driving these processes remain poorly understood. To partially address this knowledge gap, we used alchemical and temperature replica exchange molecular dynamics (TREMD) simulations on an RNA duplex and an analogous hairpin to probe the structural effects of modified and/or mutant nucleotides. The simulations successfully predict the modification/mutation-induced relative free energy change for complementary duplex formation, and structural analyses highlight mechanisms driving stability changes. Furthermore, TREMD simulations for a hairpin-forming RNA with and without modification provide reliable estimations of the energy landscape. Illuminating the impact of methylated and/or mutated nucleotides on the structure-function relationship and the folding energy landscape, the simulations provide insights into modification-induced alterations to the folding mechanics of the hairpin. The results here may be biologically significant as hairpins are widespread structure motifs that play critical roles in gene expression and regulation. Specifically, the tetraloop of the probed hairpin is phylogenetically abundant, and the stem mirrors a miRNA seed region whose modification has been implicated in epilepsy pathogenesis.
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Affiliation(s)
- Travis Hurst
- Department of Physics, Department of Biochemistry, and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
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28
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Pten-NOLC1 fusion promotes cancers involving MET and EGFR signalings. Oncogene 2020; 40:1064-1076. [PMID: 33323972 PMCID: PMC7880894 DOI: 10.1038/s41388-020-01582-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 11/03/2020] [Accepted: 11/20/2020] [Indexed: 02/07/2023]
Abstract
Inactivation of Pten gene through deletions and mutations leading to excessive pro-growth signaling pathway activations frequently occurs in cancers. Here, we report a Pten derived pro-cancer growth gene fusion Pten-NOLC1 originated from a chr10 genome rearrangement and identified through a transcriptome sequencing analysis of human cancers. Pten-NOLC1 fusion is present in primary human cancer samples and cancer cell lines from different organs. The product of Pten-NOLC1 is a nuclear protein that interacts and activates promoters of EGFR, c-MET, and their signaling molecules. Pten-NOLC1 promotes cancer proliferation, growth, invasion, and metastasis, and reduces the survival of animals xenografted with Pten-NOLC1-expressing cancer cells. Genomic disruption of Pten-NOLC1 induces cancer cell death, while genomic integration of this fusion gene into the liver coupled with somatic Pten deletion produces spontaneous liver cancers in mice. Our studies indicate that Pten-NOLC1 gene fusion is a driver for human cancers.
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29
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Li D, Xing Y, Tian T, Guo Y, Qian J. Overexpression of LRRC59 Is Associated with Poor Prognosis and Promotes Cell Proliferation and Invasion in Lung Adenocarcinoma. Onco Targets Ther 2020; 13:6453-6463. [PMID: 32753886 PMCID: PMC7342457 DOI: 10.2147/ott.s245336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/07/2020] [Indexed: 12/12/2022] Open
Abstract
Aim LRRC59 (leucine-rich repeat-containing protein 59) is a ribosome-binding protein that also interacts with fibroblast growth factors. Limited investigations revealed a possible role of LRRC59 in the aggressive phenotype of breast cancer. However, whether LRRC59 contributes to the progression of lung cancer remains unclear. Materials and Methods In this study, an online TCGA-based survival analysis software (GEPIA2) was used to estimate the prognostic value of LRRC59 mRNA expression level for lung cancer. Cell Counting Kit-8 assay, colony-forming assay, cell cycle analysis, and transwell assay were used to assess the biological functions of LRRC59 in lung cancer cells. Then, 94 lung adenocarcinoma (LUAD) patient tissues were collected to examine the expression level of LRRC59 by the tissue microarray (TMA)-based immunohistochemistry staining (IHC). Univariate Kaplan-Meier and multivariate Cox regression analyses were performed to evaluate the prognostic value of LRRC59 protein expression in LUAD. Results Higher mRNA level of LRRC59 was significantly associated with worse survival for lung adenocarcinoma, but not for lung squamous cell carcinoma. Knockdown of LRRC59 by shRNA apparently inhibited cell proliferation and colony formation in both H1299 and A549 cells. The G1/S phase arrest induced by LRRC59 depletion was observed in A549 and H1299 cells. Besides, the silencing of LRRC59 decreased cell migrative and invasive abilities. Moreover, TMA-based IHC showed that LRRC59 was highly expressed in LUAD tissues and closely associated with lymph node metastasis (P<0.001), TNM stage (P<0.001), and histological differentiation (P=0.007). Further multivariate analysis suggested that LRRC59 overexpression was an independent prognostic factor in LUAD. Conclusion LRRC59 may serve as a novel biomarkers and therapeutic target for LUAD clinical practice.
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Affiliation(s)
- Dong Li
- Department of Thoracic Surgery, Huzhou Central Hospital, Huzhou, Zhejiang, People's Republic of China
| | - Ying Xing
- Department of Gastroenterology, The 72nd Army Hospital of the People's Liberation Army of China, Huzhou, Zhejiang, People's Republic of China
| | - Tiannv Tian
- Huzhou University Schools of Nursing and Medicine, Huzhou University, Huzhou, Zhejiang, People's Republic of China
| | - Yanan Guo
- Huzhou University Schools of Nursing and Medicine, Huzhou University, Huzhou, Zhejiang, People's Republic of China
| | - Jing Qian
- Huzhou University Schools of Nursing and Medicine, Huzhou University, Huzhou, Zhejiang, People's Republic of China.,Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, Huzhou, Zhejiang, People's Republic of China
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30
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Rao SR, Alham NK, Upton E, McIntyre S, Bryant RJ, Cerundolo L, Bowes E, Jones S, Browne M, Mills I, Lamb A, Tomlinson I, Wedge D, Browning L, Sirinukunwattana K, Palles C, Hamdy FC, Rittscher J, Verrill C. Detailed Molecular and Immune Marker Profiling of Archival Prostate Cancer Samples Reveals an Inverse Association between TMPRSS2:ERG Fusion Status and Immune Cell Infiltration. J Mol Diagn 2020; 22:652-669. [PMID: 32229180 DOI: 10.1016/j.jmoldx.2020.02.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 08/28/2019] [Accepted: 02/04/2020] [Indexed: 01/02/2023] Open
Abstract
Prostate cancer is a significant global health issue, and limitations to current patient management pathways often result in overtreatment or undertreatment. New ways to stratify patients are urgently needed. We conducted a feasibility study of such novel assessments, looking for associations between genomic changes and lymphocyte infiltration. An innovative workflow using an in-house targeted sequencing panel, immune cell profiling using an image analysis pipeline, RNA sequencing, and exome sequencing in select cases was tested. Gene fusions were profiled by RNA sequencing in 27 of 27 cases, and a significantly higher tumor-infiltrating lymphocyte (TIL) count was noted in tumors without a TMPRSS2:ERG fusion compared with those with the fusion (P = 0.01). Although this finding was not replicated in a larger validation set (n = 436) of The Cancer Genome Atlas images, there was a trend in the same direction. Differential expression analysis of TIL-high and TIL-low tumors revealed the enrichment of both innate and adaptive immune response pathways. Mutations in mismatch repair genes (MLH1 and MSH6 mutations in 1 of 27 cases) were identified. We describe a potential immune escape mechanism in TMPRSS2:ERG fusion-positive tumors. Detailed profiling, as shown herein, can provide novel insights into tumor biology. Likely differences with findings with other cohorts are related to methods used to define region of interest, but this warrants further study in a larger cohort.
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Affiliation(s)
- Srinivasa R Rao
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Nasullah K Alham
- Big Data Institute, University of Oxford, Old Road Campus, Oxford, United Kingdom; Oxford National Institute for Health Research Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Elysia Upton
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Stacey McIntyre
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Richard J Bryant
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Lucia Cerundolo
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Emma Bowes
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom; Oxford National Institute for Health Research Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Stephanie Jones
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Molly Browne
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom; Oxford National Institute for Health Research Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Ian Mills
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Alastair Lamb
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Ian Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - David Wedge
- Big Data Institute, University of Oxford, Old Road Campus, Oxford, United Kingdom; Oxford National Institute for Health Research Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Lisa Browning
- Oxford National Institute for Health Research Oxford Biomedical Research Centre, Oxford, United Kingdom; Department of Cellular Pathology, Oxford University Hospitals National Health Service Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | | | - Claire Palles
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Jens Rittscher
- Big Data Institute, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Clare Verrill
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom; Oxford National Institute for Health Research Oxford Biomedical Research Centre, Oxford, United Kingdom; Department of Cellular Pathology, Oxford University Hospitals National Health Service Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom.
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31
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Li J, Xu C, Lee HJ, Ren S, Zi X, Zhang Z, Wang H, Yu Y, Yang C, Gao X, Hou J, Wang L, Yang B, Yang Q, Ye H, Zhou T, Lu X, Wang Y, Qu M, Yang Q, Zhang W, Shah NM, Pehrsson EC, Wang S, Wang Z, Jiang J, Zhu Y, Chen R, Chen H, Zhu F, Lian B, Li X, Zhang Y, Wang C, Wang Y, Xiao G, Jiang J, Yang Y, Liang C, Hou J, Han C, Chen M, Jiang N, Zhang D, Wu S, Yang J, Wang T, Chen Y, Cai J, Yang W, Xu J, Wang S, Gao X, Wang T, Sun Y. A genomic and epigenomic atlas of prostate cancer in Asian populations. Nature 2020; 580:93-99. [PMID: 32238934 DOI: 10.1038/s41586-020-2135-x] [Citation(s) in RCA: 181] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/17/2020] [Indexed: 12/24/2022]
Abstract
Prostate cancer is the second most common cancer in men worldwide1. Over the past decade, large-scale integrative genomics efforts have enhanced our understanding of this disease by characterizing its genetic and epigenetic landscape in thousands of patients2,3. However, most tumours profiled in these studies were obtained from patients from Western populations. Here we produced and analysed whole-genome, whole-transcriptome and DNA methylation data for 208 pairs of tumour tissue samples and matched healthy control tissue from Chinese patients with primary prostate cancer. Systematic comparison with published data from 2,554 prostate tumours revealed that the genomic alteration signatures in Chinese patients were markedly distinct from those of Western cohorts: specifically, 41% of tumours contained mutations in FOXA1 and 18% each had deletions in ZNF292 and CHD1. Alterations of the genome and epigenome were correlated and were predictive of disease phenotype and progression. Coding and noncoding mutations, as well as epimutations, converged on pathways that are important for prostate cancer, providing insights into this devastating disease. These discoveries underscore the importance of including population context in constructing comprehensive genomic maps for disease.
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Affiliation(s)
- Jing Li
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Center for Translational Medicine, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory of Cell Engineering, Shanghai, China
| | - Chuanliang Xu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory of Cell Engineering, Shanghai, China
| | - Hyung Joo Lee
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Shancheng Ren
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory of Cell Engineering, Shanghai, China
| | - Xiaoyuan Zi
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | | | - Haifeng Wang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yongwei Yu
- Department of Pathology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Chenghua Yang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China.,CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaofeng Gao
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Jianguo Hou
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Linhui Wang
- Department of Urology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Bo Yang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Qing Yang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Huamao Ye
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Tie Zhou
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Xin Lu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yan Wang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Min Qu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Qingsong Yang
- Department of Radiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Wenhui Zhang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Nakul M Shah
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Erica C Pehrsson
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Shuo Wang
- Department of Urology, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Zengjun Wang
- State Key Laboratory of Reproductive Medicine and Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Jiang
- Department of Urology, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Yan Zhu
- Department of Pathology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Rui Chen
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Huan Chen
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Feng Zhu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Bijun Lian
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | | | - Yun Zhang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Chao Wang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yue Wang
- Shanghai Key Laboratory of Cell Engineering, Shanghai, China.,Department of Histology and Embryology, Second Military Medical University, Shanghai, China
| | - Guangan Xiao
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Junfeng Jiang
- Shanghai Key Laboratory of Cell Engineering, Shanghai, China.,Department of Histology and Embryology, Second Military Medical University, Shanghai, China
| | - Yue Yang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Chaozhao Liang
- Department of Urology, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jianquan Hou
- Department of Urology, First Affiliated Hospital of Soochow University, Suzhou, China
| | - Conghui Han
- Department of Urology, Xuzhou Central Hospital, The Affiliated Xuzhou Hospital of Medical College of Southeast University, Xuzhou, China
| | - Ming Chen
- Department of Urology, Zhongda Hospital, Southeast University, Nanjing, China
| | - Ning Jiang
- Department of Urology, Gongli Hospital, Second Military Medical University, Shanghai, China
| | - Dahong Zhang
- Department of Urology, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Song Wu
- Department of Urology Institute of Shenzhen University, Shenzhen Luohu People's Hospital, Shenzhen, China
| | - Jinjian Yang
- Department of Urology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tao Wang
- Department of Urology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yongliang Chen
- Department of Urology, Shaoxing Central Hospital, Shaoxing, China
| | - Jiantong Cai
- Department of Urology, Shishi Hospital, Shishi, China
| | - Wenzeng Yang
- Department of Urology, The Affiliated Hospital of Hebei University, Baoding, China
| | - Jun Xu
- Department of Urology, Huadong Hospital, Fudan University, Shanghai, China
| | - Shaogang Wang
- Department of Urology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology, Wuhan, China
| | - Xu Gao
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China. .,Shanghai Key Laboratory of Cell Engineering, Shanghai, China.
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA. .,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA.
| | - Yinghao Sun
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China. .,Shanghai Key Laboratory of Cell Engineering, Shanghai, China.
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32
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Kaushik I, Ramachandran S, Srivastava SK. CRISPR-Cas9: A multifaceted therapeutic strategy for cancer treatment. Semin Cell Dev Biol 2019; 96:4-12. [PMID: 31054324 PMCID: PMC6829064 DOI: 10.1016/j.semcdb.2019.04.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 12/20/2022]
Abstract
CRISPR-Cas9 is an RNA guided endonuclease that has revolutionized the ability to edit genome and introduce desired manipulations in the target genomic sequence. It is a flexible methodology and is capable of targeting multiple loci simultaneously. Owing to the fact that cancer is an amalgamation of several genetic mutations, application of CRISPR-Cas9 technology is considered as a novel strategy to combat cancer. Genetic and epigenetic modulations in cancer leads to development of resistance to conventional therapy options. Given the abundance of transcriptomic and genomic alterations in cancer, developing a strategy to decipher these alterations is critical. CRISPR-Cas9 system has proven to be a promising tool in generating cellular and animal models to mimic the mutations and understand their role in tumorigenesis. CRISPR-Cas9 is an upheaval in the field of cancer immunotherapy. Furthermore, CRISPR-Cas9 plays an important role in the development of whole genome libraries for cancer patients. This approach will help understand the diversity in genome variation among the patients and also, will provide multiple variables to scientists to investigate and improvise cancer therapy. This review will focus on the discovery of CRISPR-Cas9 system, mechanisms behind CRISPR technique and its current status as a potential tool for investigating the genomic mutations associated with all cancer types.
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Affiliation(s)
- Itishree Kaushik
- Department of Immunotherapeutics and Biotechnology and Center for Tumor Immunology and Targeted Cancer Therapy, Texas Tech University Health Sciences Center, Abilene, TX, 79601, USA
| | - Sharavan Ramachandran
- Department of Immunotherapeutics and Biotechnology and Center for Tumor Immunology and Targeted Cancer Therapy, Texas Tech University Health Sciences Center, Abilene, TX, 79601, USA
| | - Sanjay K Srivastava
- Department of Immunotherapeutics and Biotechnology and Center for Tumor Immunology and Targeted Cancer Therapy, Texas Tech University Health Sciences Center, Abilene, TX, 79601, USA.
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33
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Zhang L, Wang L, Lei M, Ma R, Yu F, Liu C, Yin D. Generation and identification of a thyroid cancer cell line with stable expression of CCDC67 and luciferase reporter genes. Oncol Lett 2019; 18:4495-4502. [PMID: 31611958 PMCID: PMC6781759 DOI: 10.3892/ol.2019.10839] [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: 12/08/2018] [Accepted: 07/09/2019] [Indexed: 11/06/2022] Open
Abstract
Coiled-coil domain containing 67 (CCDC67) gene is a tumor suppressor gene that exhibits a significant inhibitory effect on a variety of tumors. Our previous study demonstrated that the upregulation of CCDC67 gene in TPC-1 cells inhibited cell proliferation, migration and invasion, and promoted apoptosis in vitro. However, due to the lack of a suitable cell tool, these results were not validated in vivo. In the present study, a thyroid cancer cell line with stable expression of CCDC67 and luciferase reporter genes was generated and identified. Firstly, cDNA clones of the CCDC67 gene were obtained by reverse transcription using a custom-designed primer. The results of subsequent electrophoresis analysis and sequencing revealed that the cDNA clones of CCDC67 gene were obtained successfully, with a length of 1,862 bp. The lentiviral vectors, containing the CCDC67, luciferase reporter and puromycin acetyltransferase genes, were co-transfected with two plasmids that encode lentiviral structural proteins and envelope proteins into 293T cells. Following ultracentrifugation, the titer of lentivirus was determined by ELISA to be 5.0×108 TU/ml. The constructed lentiviral vector was used to transfect TPC-1 thyroid cancer cells, and stabilization was achieved by puromycin screening. The expression of CCDC67 gene, luciferase activity and tumorigenic ability of the generated cell line were detected. Reverse transcription-qPCR results demonstrated that the expression levels of CCDC67 gene in TPC-1 cells following transfection were increased 194,46.782-fold compared with those in the negative control group (P<0.01). A higher fluorescence intensity was detected in the generated cell line, while no detectable fluorescence was observed in untransfected TPC-1 cells. The tumorigenic ability of TPC-1-Luc-Puromycin-CCDC67 cells was verified by bioluminescence imaging and histopathological analysis using a pulmonary metastasis model. These results demonstrated that a thyroid cancer cell line with stable expression of CCDC67 and luciferase reporter genes was generated successfully. The TPC-1-Luc-Puromycin-CCDC67 cell line may be a helpful tool for further research on CCDC67 in vivo.
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Affiliation(s)
- Lele Zhang
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Thyroid Surgery, Key Discipline Laboratory of Clinical Medicine of Henan, Zhengzhou, Henan 450050, P.R. China
| | - Longlong Wang
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Thyroid Surgery, Key Discipline Laboratory of Clinical Medicine of Henan, Zhengzhou, Henan 450050, P.R. China
| | - Mengyuan Lei
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Thyroid Surgery, Key Discipline Laboratory of Clinical Medicine of Henan, Zhengzhou, Henan 450050, P.R. China
| | - Runsheng Ma
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Thyroid Surgery, Key Discipline Laboratory of Clinical Medicine of Henan, Zhengzhou, Henan 450050, P.R. China
| | - Fangqin Yu
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Thyroid Surgery, Key Discipline Laboratory of Clinical Medicine of Henan, Zhengzhou, Henan 450050, P.R. China
| | - Chenguang Liu
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Thyroid Surgery, Key Discipline Laboratory of Clinical Medicine of Henan, Zhengzhou, Henan 450050, P.R. China
| | - Detao Yin
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Thyroid Surgery, Key Discipline Laboratory of Clinical Medicine of Henan, Zhengzhou, Henan 450050, P.R. China
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34
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Yu YP, Tsung A, Liu S, Nalesnick M, Geller D, Michalopoulos G, Luo JH. Detection of fusion transcripts in the serum samples of patients with hepatocellular carcinoma. Oncotarget 2019; 10:3352-3360. [PMID: 31164957 PMCID: PMC6534357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/04/2019] [Indexed: 12/16/2022] Open
Abstract
Hepatocellular carcinoma is one of the most lethal cancers in the United States. Early detection of the disease is crucial for reducing the mortality of this malignancy. Recently, we identified a panel of fusion genes present in several types of human cancers, including hepatocellular carcinoma. Among 8 fusion genes, MAN2A1-FER, TRMT11-GRIK2 and CCNH-C5orf30 appear most frequently in hepatocellular carcinoma samples. In this study, we showed that the fusion transcripts of MAN2A1-FER, CCNH-C5orf30 and SLC45A2-AMACR were detected in the serum samples of liver cancer patients as circulating cell-free RNA. The distributions of these gene fusion RNA fragments largely matched those of the primary HCC samples. In contrast, the sera of all healthy individuals free of human malignancies were shown to be negative for these fusion genes. These results suggest that gene fusion RNA is frequently shed from liver cancer cells. The detection of serum cell-free fusion transcripts may provide a new approach to aid in the diagnosis, follow-up or therapy of liver cancers.
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Affiliation(s)
- Yan-Ping Yu
- 1Department of Pathology and Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Allan Tsung
- 1Department of Pathology and Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA,2Current address: Department of Surgery, Ohio State University School of Medicine, Columbus, Ohio 43210, USA
| | - Silvia Liu
- 1Department of Pathology and Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Michael Nalesnick
- 1Department of Pathology and Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - David Geller
- 1Department of Pathology and Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - George Michalopoulos
- 1Department of Pathology and Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Jian-Hua Luo
- 1Department of Pathology and Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
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35
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Yu YP, Tsung A, Liu S, Nalesnick M, Geller D, Michalopoulos G, Luo JH. Detection of fusion transcripts in the serum samples of patients with hepatocellular carcinoma. Oncotarget 2019. [DOI: 10.18632/oncotarget.26918] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Yan-Ping Yu
- Department of Pathology and Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Allan Tsung
- Department of Pathology and Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
- Current address: Department of Surgery, Ohio State University School of Medicine, Columbus, Ohio 43210, USA
| | - Silvia Liu
- Department of Pathology and Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Michael Nalesnick
- Department of Pathology and Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - David Geller
- Department of Pathology and Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - George Michalopoulos
- Department of Pathology and Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Jian-Hua Luo
- Department of Pathology and Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
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36
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Xing L, Zhang X, Tong D. Systematic Profile Analysis of Prognostic Alternative Messenger RNA Splicing Signatures and Splicing Factors in Head and Neck Squamous Cell Carcinoma. DNA Cell Biol 2019; 38:627-638. [PMID: 31025877 DOI: 10.1089/dna.2019.4644] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSC) is a common malignancy with high mortality and poor prognosis. Alternative splicing (AS) is a transcriptional regulation mechanism that generates multiple transcripts from same genes, and aberrant AS signatures of cancers can be predictive for prognosis. We identified the survival-related AS events and splicing factors (SFs) from the RNA sequencing data and the corresponding clinical information of an HNSC cohort downloaded from The Cancer Genome Atlas (TCGA) and SpliceSeq. The independent prognostic predictors were assessed by Cox proportional regression analysis, and the regulatory network of SFs and AS events was analyzed by Spearman's test and constructed. A total of 4626 survival-related AS events in 3280 genes were identified, and most were protective factors. Among the different types of splicing events, exon skip was the most frequent. The prognostic models were constructed for each type of AS, and the area under the curve of the receiver operating characteristic curve of the combined prognostic model was 0.765, indicating good predictive performance. Finally, a correlation network between SF and AS events was constructed. We identified prognostic predictors based on AS events that stratified HNSC patients into the high- and low-risk groups, and revealed splicing networks that provide insights into the underlying mechanisms.
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Affiliation(s)
- Lu Xing
- 1 Shandong Provincial Key Laboratory of Oral Tissue Regeneration, School of Stomatology, Shandong University, Jinan, China
| | - Xiaoqian Zhang
- 2 Department of Stomatology, Haiyuan College of Kunming Medical University, Kunming, China
| | - Dongdong Tong
- 3 Shandong Provincial Key Laboratory of Oral Tissue Regeneration, Department of Oral and Maxillofacial Surgery, School of Stomatology, Shandong University, Jinan, China
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37
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Tian X, Gu T, Patel S, Bode AM, Lee MH, Dong Z. CRISPR/Cas9 - An evolving biological tool kit for cancer biology and oncology. NPJ Precis Oncol 2019; 3:8. [PMID: 30911676 PMCID: PMC6423228 DOI: 10.1038/s41698-019-0080-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 01/18/2019] [Indexed: 12/13/2022] Open
Abstract
The development of genetic engineering in the 1970s marked a new frontier in genome-editing technology. Gene-editing technologies have provided a plethora of benefits to the life sciences. The clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/ Cas9) system is a versatile technology that provides the ability to add or remove DNA in the genome in a sequence-specific manner. Serious efforts are underway to improve the efficiency of CRISPR/Cas9 targeting and thus reduce off-target effects. Currently, various applications of CRISPR/Cas9 are used in cancer biology and oncology to perform robust site-specific gene editing, thereby becoming more useful for biological and clinical applications. Many variants and applications of CRISPR/Cas9 are being rapidly developed. Experimental approaches that are based on CRISPR technology have created a very promising tool that is inexpensive and simple for developing effective cancer therapeutics. This review discusses diverse applications of CRISPR-based gene-editing tools in oncology and potential future cancer therapies.
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Affiliation(s)
- Xueli Tian
- Basic Medical College, Zhengzhou University, 450001 Zhengzhou, Henan China
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, 450008 Zhengzhou, Henan China
| | - Tingxuan Gu
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, 450008 Zhengzhou, Henan China
| | - Satyananda Patel
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, 450008 Zhengzhou, Henan China
| | - Ann M. Bode
- The Hormel Institute, University of Minnesota, Austin, 55912 USA
| | - Mee-Hyun Lee
- Basic Medical College, Zhengzhou University, 450001 Zhengzhou, Henan China
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, 450008 Zhengzhou, Henan China
- The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, China
| | - Zigang Dong
- Basic Medical College, Zhengzhou University, 450001 Zhengzhou, Henan China
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, 450008 Zhengzhou, Henan China
- The Hormel Institute, University of Minnesota, Austin, 55912 USA
- The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, China
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38
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Yu YP, Liu P, Nelson J, Hamilton RL, Bhargava R, Michalopoulos G, Chen Q, Zhang J, Ma D, Pennathur A, Luketich J, Nalesnik M, Tseng G, Luo JH. Identification of recurrent fusion genes across multiple cancer types. Sci Rep 2019; 9:1074. [PMID: 30705370 PMCID: PMC6355770 DOI: 10.1038/s41598-019-38550-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/27/2018] [Indexed: 01/21/2023] Open
Abstract
Chromosome changes are one of the hallmarks of human malignancies. Chromosomal rearrangement is frequent in human cancers. One of the consequences of chromosomal rearrangement is gene fusions in the cancer genome. We have previously identified a panel of fusion genes in aggressive prostate cancers. In this study, we showed that 6 of these fusion genes are present in 7 different types of human malignancies with variable frequencies. Among them, the CCNH-C5orf30 and TRMT11-GRIK2 gene fusions were found in breast cancer, colon cancer, non-small cell lung cancer, esophageal adenocarcinoma, glioblastoma multiforme, ovarian cancer and liver cancer, with frequencies ranging from 12.9% to 85%. In contrast, four other gene fusions (mTOR-TP53BP1, TMEM135-CCDC67, KDM4-AC011523.2 and LRRC59-FLJ60017) are less frequent. Both TRMT11-GRIK2 and CCNH-C5orf30 are also frequently present in lymph node metastatic cancer samples from the breast, colon and ovary. Thus, detecting these fusion transcripts may have significant biological and clinical implications in cancer patient management.
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Affiliation(s)
- Yan-Ping Yu
- Departments of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Peng Liu
- Departments of Biostatistics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Joel Nelson
- Departments of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Ronald L Hamilton
- Departments of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Rohit Bhargava
- Departments of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - George Michalopoulos
- Departments of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Qi Chen
- Department of Pharmacology, Toxicology & Therapeutics, University of Kansas, Kansas City, KS, 66160, USA
| | - Jun Zhang
- Department of Medicine, University of Iowa, Iowa City, Iowa, 52242, USA
| | - Deqin Ma
- Department of Pathology, University of Iowa, Iowa City, Iowa, 52242, USA
| | - Arjun Pennathur
- Departments of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - James Luketich
- Departments of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Michael Nalesnik
- Departments of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - George Tseng
- Departments of Biostatistics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Jian-Hua Luo
- Departments of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA.
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39
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Dorris ER, Tazzyman SJ, Moylett J, Ramamoorthi N, Hackney J, Townsend M, Muthana M, Lewis MJ, Pitzalis C, Wilson AG. The Autoimmune Susceptibility Gene C5orf30 Regulates Macrophage-Mediated Resolution of Inflammation. THE JOURNAL OF IMMUNOLOGY 2019; 202:1069-1078. [PMID: 30659109 DOI: 10.4049/jimmunol.1801155] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 12/10/2018] [Indexed: 12/19/2022]
Abstract
Genetic variants in C5orf30 have been associated with development of the autoimmune conditions primary biliary cirrhosis and rheumatoid arthritis. In rheumatoid arthritis, C5orf30 expression is cell-specific, with highest expression found in macrophages and synovial fibroblasts. C5orf30 is highly expressed in inflamed joints and is a negative regulator of tissue damage in a mouse model of inflammatory arthritis. Transcriptomic analysis from ultrasound-guided synovial biopsy of inflamed joints in a well characterized clinical cohort of newly diagnosed, disease-modifying antirheumatic drugs-naive rheumatoid arthritis patients was used to determine the clinical association of C5orf30 expression with disease activity. A combined molecular and computational biology approach was used to elucidate C5orf30 function in macrophages both in vitro and in vivo. Synovial expression of C5orf30 is inversely correlated with both clinical measures of rheumatoid arthritis disease activity and with synovial TNF mRNA expression. C5orf30 plays a role in regulating macrophage phenotype and is differentially turned over in inflammatory and anti-inflammatory macrophages. Inhibition of C5orf30 reduces wound healing/repair-associated functions of macrophages, reduces signaling required for resolution of inflammation, and decreases secretion of anti-inflammatory mediators. In an animal model of wound healing (zebrafish), C5orf30 inhibition increases the recruitment of macrophages to the wound site. Finally, we demonstrate that C5orf30 skews macrophage immunometabolism, demonstrating a mechanism for C5orf30-mediated immune regulation.
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Affiliation(s)
- Emma R Dorris
- University College Dublin Centre for Arthritis Research, Conway Institute, University College Dublin, Dublin D04 W6F6, Ireland;
| | | | - John Moylett
- University College Dublin Centre for Arthritis Research, Conway Institute, University College Dublin, Dublin D04 W6F6, Ireland
| | - Nandhini Ramamoorthi
- Biomarker Discovery OMNI, Genentech Research and Early Development, San Francisco, CA 94080; and
| | - Jason Hackney
- Biomarker Discovery OMNI, Genentech Research and Early Development, San Francisco, CA 94080; and
| | - Michael Townsend
- Biomarker Discovery OMNI, Genentech Research and Early Development, San Francisco, CA 94080; and
| | | | - Myles J Lewis
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry and Barts Health National Health Service Trust, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Costantino Pitzalis
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry and Barts Health National Health Service Trust, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Anthony G Wilson
- University College Dublin Centre for Arthritis Research, Conway Institute, University College Dublin, Dublin D04 W6F6, Ireland
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40
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Vasilieva EN, Laptev IG, Sergiev PV, Dontsova OA. The Common Partner of Several Methyltransferases Modifying the Components of The Eukaryotic Translation Apparatus. Mol Biol 2018. [DOI: 10.1134/s0026893318060171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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41
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Yang J, Chen Y, Lu J, Wang X, Wang L, Liang J, Sun ZS. Identification and characterization of novel fusion genes in prostate cancer by targeted RNA capture and next-generation sequencing. Acta Biochim Biophys Sin (Shanghai) 2018; 50:1166-1172. [PMID: 30307468 DOI: 10.1093/abbs/gmy112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Indexed: 11/13/2022] Open
Abstract
Gene fusions play critical roles in the development and progression of prostate cancer, and have been used as molecular biomarkers for diagnosis of the malignant disease. To further explore the novel fusions in prostate cancer, we performed targeted RNA capture and next-generation sequencing in a cohort of 52 prostate cancer patients, identified and validated 14 fusion events (7 types of fusion genes) in 12 cases, including three novel fusion genes. We characterized a chromosome rearrangement-induced trigenic KLK2-DGKB-ETV1 fusion, which may function as a non-coding RNA to upregulate the expression of the wild-type ETV1 protein in the tumor tissue. Additionally, we detected two novel fusion forms of HNRNPA2B1-ETV1 and SLC45A2-AMACR fusions, respectively. Interestingly, fusion events participated by kinase genes, which frequently occurred in other human cancers, were not present in these prostate cancer cases, suggesting discrepant gene fusion patterns in different cancers. These findings expand the genetic spectrum of prostate cancer and provide insight into diagnosis of this prevalent disease.
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Affiliation(s)
- Jie Yang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Yun Chen
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jingxiao Lu
- Biobank of the Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Xingxing Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Lu Wang
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, Nanjing, China
| | - Jialong Liang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Zhong Sheng Sun
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
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Boriack-Sjodin PA, Ribich S, Copeland RA. RNA-modifying proteins as anticancer drug targets. Nat Rev Drug Discov 2018; 17:435-453. [PMID: 29773918 DOI: 10.1038/nrd.2018.71] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
All major biological macromolecules (DNA, RNA, proteins and lipids) undergo enzyme-catalysed covalent modifications that impact their structure, function and stability. A variety of covalent modifications of RNA have been identified and demonstrated to affect RNA stability and translation to proteins; these mechanisms of translational control have been termed epitranscriptomics. Emerging data suggest that some epitranscriptomic mechanisms are altered in human cancers as well as other human diseases. In this Review, we examine the current understanding of RNA modifications with a focus on mRNA methylation, highlight their possible roles in specific cancer indications and discuss the emerging potential of RNA-modifying proteins as therapeutic targets.
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Panigrahi P, Jere A, Anamika K. FusionHub: A unified web platform for annotation and visualization of gene fusion events in human cancer. PLoS One 2018; 13:e0196588. [PMID: 29715310 PMCID: PMC5929557 DOI: 10.1371/journal.pone.0196588] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 04/16/2018] [Indexed: 12/15/2022] Open
Abstract
Gene fusion is a chromosomal rearrangement event which plays a significant role in cancer due to the oncogenic potential of the chimeric protein generated through fusions. At present many databases are available in public domain which provides detailed information about known gene fusion events and their functional role. Existing gene fusion detection tools, based on analysis of transcriptomics data usually report a large number of fusion genes as potential candidates, which could be either known or novel or false positives. Manual annotation of these putative genes is indeed time-consuming. We have developed a web platform FusionHub, which acts as integrated search engine interfacing various fusion gene databases and simplifies large scale annotation of fusion genes in a seamless way. In addition, FusionHub provides three ways of visualizing fusion events: circular view, domain architecture view and network view. Design of potential siRNA molecules through ensemble method is another utility integrated in FusionHub that could aid in siRNA-based targeted therapy. FusionHub is freely available at https://fusionhub.persistent.co.in.
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Affiliation(s)
| | - Abhay Jere
- LABS, Persistent Systems, Pingala-Aryabhata, Erandwane, Pune, India
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Zhao S, Løvf M, Carm KT, Bakken AC, Hoff AM, Skotheim RI. Novel transcription-induced fusion RNAs in prostate cancer. Oncotarget 2018; 8:49133-49143. [PMID: 28467780 PMCID: PMC5564755 DOI: 10.18632/oncotarget.17099] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 04/03/2017] [Indexed: 12/21/2022] Open
Abstract
Prostate cancer is a clinically and pathologically heterogeneous disease with a broad spectrum of molecular abnormalities in the genome and transcriptome. One key feature is the involvement of chromosomal rearrangements creating fusion genes. Recent RNA-sequencing technology has uncovered that fusions which are not caused by chromosomal rearrangements, but rather meditated at transcription level, are common in both healthy and diseased cells. Such fusion transcripts have been proven highly associated with prostate cancer development and progression. To discover novel fusion transcripts, we analyzed RNA sequencing data from 44 primary prostate tumors and matched benign tissues from The Cancer Genome Atlas. Twenty-one high-confident candidates were significantly enriched in malignant vs. benign samples. Thirteen of the candidates have not previously been described in prostate cancer, and among them, five long intergenic non-coding RNAs are involved as fusion partners. Their expressions were validated in 50 additional prostate tumor samples and seven prostate cancer cell lines. For four fusion transcripts, we found a positive correlation between their expression and the expression of the 3′ partner gene. Among these, differential exon usage and qRT-PCR analyses in particular support that SLC45A3-ELK4 is mediated by an RNA polymerase read-through mechanism.
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Affiliation(s)
- Sen Zhao
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, Oslo, Norway.,Center for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marthe Løvf
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, Oslo, Norway.,Center for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Kristina Totland Carm
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, Oslo, Norway.,Center for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anne Cathrine Bakken
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, Oslo, Norway.,Center for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Andreas M Hoff
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, Oslo, Norway.,Center for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Rolf I Skotheim
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, Oslo, Norway.,Center for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Informatics, Faculty of Natural Science and Mathematics, University of Oslo, Oslo, Norway
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45
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Cozar J, Robles-Fernandez I, Martinez-Gonzalez L, Pascual-Geler M, Rodriguez-Martinez A, Serrano M, Lorente J, Alvarez-Cubero M. Genetic markers a landscape in prostate cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 775:1-10. [DOI: 10.1016/j.mrrev.2017.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/21/2017] [Accepted: 11/28/2017] [Indexed: 12/19/2022]
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46
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Chen ZH, Yu YP, Tao J, Liu S, Tseng G, Nalesnik M, Hamilton R, Bhargava R, Nelson JB, Pennathur A, Monga SP, Luketich JD, Michalopoulos GK, Luo JH. MAN2A1-FER Fusion Gene Is Expressed by Human Liver and Other Tumor Types and Has Oncogenic Activity in Mice. Gastroenterology 2017; 153:1120-1132.e15. [PMID: 28245430 PMCID: PMC5572118 DOI: 10.1053/j.gastro.2016.12.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/16/2016] [Accepted: 12/23/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Human tumors and liver cancer cell lines express the product of a fusion between the first 13 exons in the mannosidase α class 2A member 1 gene (MAN2A1) and the last 6 exons in the FER tyrosine kinase gene (FER), called MAN2A1-FER. We investigated whether MAN2A1-FER is expressed by human liver tumors and its role in liver carcinogenesis. METHODS We performed reverse transcription polymerase chain reaction analyses of 102 non-small cell lung tumors, 61 ovarian tumors, 70 liver tumors, 156 glioblastoma multiform samples, 27 esophageal adenocarcinomas, and 269 prostate cancer samples, as well as 10 nontumor liver tissues and 20 nontumor prostate tissues, collected at the University of Pittsburgh. We also measured expression by 15 human cancer cell lines. We expressed a tagged form of MAN2A1-FER in NIH3T3 and HEP3B (liver cancer) cells; Golgi were isolated for analysis. MAN2A1-FER was also overexpressed in PC3 or DU145 (prostate cancer), NIH3T3 (fibroblast), H23 (lung cancer), and A-172 (glioblastoma multiforme) cell lines and knocked out in HUH7 (liver cancer) cells. Cells were analyzed for proliferation and in invasion assays, and/or injected into flanks of severe combined immunodeficient mice; xenograft tumor growth and metastasis were assessed. Mice with hepatic deletion of PTEN were given tail-vein injections of MAN2A1-FER. RESULTS We detected MAN2A1-FER messenger RNA and fusion protein (114 kD) in the hepatocellular carcinoma cell line HUH7, as well as in liver tumors, esophageal adenocarcinoma, glioblastoma multiforme, prostate tumors, non-small cell lung tumors, and ovarian tumors, but not nontumor prostate or liver tissues. MAN2A1-FER protein retained the signal peptide for Golgi localization from MAN2A1 and translocated from the cytoplasm to Golgi in cancer cell lines. MAN2A1-FER had tyrosine kinase activity almost 4-fold higher than that of wild-type FER, and phosphorylated the epidermal growth factor receptor at tyrosine 88 in its N-terminus. Expression of MAN2A1-FER in 4 cell lines led to epidermal growth factor receptor activation of BRAF, MEK, and AKT; HUH7 cells with MAN2A1-FER knockout had significant decreases in phosphorylation of these proteins. Cell lines that expressed MAN2A1-FER had increased proliferation, colony formation, and invasiveness and formed larger (>2-fold) xenograft tumors in mice, with more metastases, than cells not expressing the fusion protein. HUH7 cells with MAN2A1-FER knockout formed smaller xenograft tumors, with fewer metastases, than control HUH7 cells. HUH7, A-172, and PC3 cells that expressed MAN2A1-FER were about 2-fold more sensitive to the FER kinase inhibitor crizotinib and the epidermal growth factor receptor kinase inhibitor canertinib; these drugs slowed growth of xenograft tumors from MAN2A1-FER cells and prevented their metastasis in mice. Hydrodynamic tail-vein injection of MAN2A1-FER resulted in rapid development of liver cancer in mice with hepatic disruption of Pten. CONCLUSIONS Many human tumor types and cancer cell lines express the MAN2A1-FER fusion, which increases proliferation and invasiveness of cancer cell lines and has liver oncogenic activity in mice.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Cell Line, Tumor
- Cell Movement
- Cell Proliferation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Crizotinib
- Dose-Response Relationship, Drug
- Enzyme Activation
- ErbB Receptors/genetics
- ErbB Receptors/metabolism
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Neoplastic
- Gene Fusion
- Golgi Apparatus/enzymology
- Humans
- Liver Neoplasms/drug therapy
- Liver Neoplasms/enzymology
- Liver Neoplasms/genetics
- Liver Neoplasms/pathology
- Mice
- Mice, Knockout
- Mice, SCID
- Morpholines/pharmacology
- NIH 3T3 Cells
- Neoplasm Invasiveness
- Neoplasm Transplantation
- Oncogene Proteins, Fusion/antagonists & inhibitors
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Oncogenes
- PTEN Phosphohydrolase/deficiency
- PTEN Phosphohydrolase/genetics
- Phosphorylation
- Protein Kinase Inhibitors/pharmacology
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Protein-Tyrosine Kinases/genetics
- Protein-Tyrosine Kinases/metabolism
- Pyrazoles/pharmacology
- Pyridines/pharmacology
- RNA Interference
- Time Factors
- Transfection
- Tumor Burden
- alpha-Mannosidase/antagonists & inhibitors
- alpha-Mannosidase/genetics
- alpha-Mannosidase/metabolism
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Affiliation(s)
- Zhang-Hui Chen
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Yan P Yu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Junyan Tao
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Silvia Liu
- Department of Biostatistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - George Tseng
- Department of Biostatistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Michael Nalesnik
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Ronald Hamilton
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Rohit Bhargava
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Joel B Nelson
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Arjun Pennathur
- Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Satdarshan P Monga
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - James D Luketich
- Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - George K Michalopoulos
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jian-Hua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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Targeting genomic rearrangements in tumor cells through Cas9-mediated insertion of a suicide gene. Nat Biotechnol 2017; 35:543-550. [PMID: 28459452 PMCID: PMC5462845 DOI: 10.1038/nbt.3843] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 03/08/2017] [Indexed: 11/08/2022]
Abstract
Specifically targeting genomic rearrangements and mutations in tumor cells remains an elusive goal in cancer therapy. Here, we used Cas9-based genome editing to introduce the gene encoding the prodrug-converting enzyme herpes simplex virus type 1 thymidine kinase (HSV1-tk) into the genomes of cancer cells carrying unique sequences resulting from genome rearrangements. Specifically, we targeted the breakpoints of TMEM135-CCDC67 and MAN2A1-FER fusions in human prostate cancer or hepatocellular carcinoma cells in vitro and in mouse xenografts. We designed one adenovirus to deliver the nickase Cas9D10A and guide RNAs targeting the breakpoint sequences, and another to deliver an EGFP-HSV1-tk construct flanked by sequences homologous to those surrounding the breakpoint. Infection with both viruses resulted in breakpoint-dependent expression of EGFP-tk and ganciclovir-mediated apoptosis. When mouse xenografts were treated with adenoviruses and ganciclovir, all animals showed decreased tumor burden and no mortality during the study. Thus, Cas9-mediated suicide-gene insertion may be a viable genotype-specific cancer therapy.
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48
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Bourgeois G, Létoquart J, van Tran N, Graille M. Trm112, a Protein Activator of Methyltransferases Modifying Actors of the Eukaryotic Translational Apparatus. Biomolecules 2017; 7:biom7010007. [PMID: 28134793 PMCID: PMC5372719 DOI: 10.3390/biom7010007] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 01/16/2017] [Accepted: 01/18/2017] [Indexed: 12/17/2022] Open
Abstract
Post-transcriptional and post-translational modifications are very important for the control and optimal efficiency of messenger RNA (mRNA) translation. Among these, methylation is the most widespread modification, as it is found in all domains of life. These methyl groups can be grafted either on nucleic acids (transfer RNA (tRNA), ribosomal RNA (rRNA), mRNA, etc.) or on protein translation factors. This review focuses on Trm112, a small protein interacting with and activating at least four different eukaryotic methyltransferase (MTase) enzymes modifying factors involved in translation. The Trm112-Trm9 and Trm112-Trm11 complexes modify tRNAs, while the Trm112-Mtq2 complex targets translation termination factor eRF1, which is a tRNA mimic. The last complex formed between Trm112 and Bud23 proteins modifies 18S rRNA and participates in the 40S biogenesis pathway. In this review, we present the functions of these eukaryotic Trm112-MTase complexes, the molecular bases responsible for complex formation and substrate recognition, as well as their implications in human diseases. Moreover, as Trm112 orthologs are found in bacterial and archaeal genomes, the conservation of this Trm112 network beyond eukaryotic organisms is also discussed.
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Affiliation(s)
- Gabrielle Bourgeois
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau CEDEX, France.
| | - Juliette Létoquart
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau CEDEX, France.
- De Duve Institute, Université Catholique de Louvain, avenue Hippocrate 75, 1200 Brussels, Belgium.
| | - Nhan van Tran
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau CEDEX, France.
| | - Marc Graille
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau CEDEX, France.
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49
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Zuo ZH, Yu YP, Martin A, Luo JH. Cellular stress response 1 down-regulates the expression of epidermal growth factor receptor and platelet-derived growth factor receptor through inactivation of splicing factor 3A3. Mol Carcinog 2016; 56:315-324. [PMID: 27148859 DOI: 10.1002/mc.22494] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 02/19/2016] [Accepted: 04/13/2016] [Indexed: 12/19/2022]
Abstract
Cellular stress response 1 (CSR1) is a tumor suppressor gene that plays an important role in regulating cell death. In this report, we show that the N-terminus of CSR1 interacts with splicing factor 3A, subunit 3 (SF3A3). The SF3A3 binding motif was identified in the region of amino acids 62-91 of CSR1 through cell-free binding analyses. The interaction between CSR1 and SF3A3 led to migration of SF3A3 from nucleus to cytoplasm. The cytoplasmic redistribution of SF3A3 significantly reduced the splicing efficiency of epidermal growth factor receptor and platelet-derived growth factor receptor. Induction of CSR1 or down-regulation of SF3A3 also significantly reduced the splicing activity of oxytocin reporter gene both in vivo and in vitro. Mutant CSR1 that lacks the SF3A3 binding motif contained no RNA splicing regulatory activity, while the peptide corresponding to the SF3A3 binding motif in CSR1 interfered with the wild-type CSR1 mediated inhibition of RNA splicing. Interaction of CSR1 and SF3A3 is essential for CSR1 mediated cell death. To our knowledge, this is the first report demonstrating that RNA splicing is negatively regulated by redistribution of a splicing factor. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ze-Hua Zuo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Yan P Yu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Amantha Martin
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jian-Hua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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50
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Liu S, Tsai WH, Ding Y, Chen R, Fang Z, Huo Z, Kim S, Ma T, Chang TY, Priedigkeit NM, Lee AV, Luo J, Wang HW, Chung IF, Tseng GC. Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data. Nucleic Acids Res 2015; 44:e47. [PMID: 26582927 PMCID: PMC4797269 DOI: 10.1093/nar/gkv1234] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 10/24/2015] [Indexed: 12/31/2022] Open
Abstract
Background: Fusion transcripts are formed by either fusion genes (DNA level) or trans-splicing events (RNA level). They have been recognized as a promising tool for diagnosing, subtyping and treating cancers. RNA-seq has become a precise and efficient standard for genome-wide screening of such aberration events. Many fusion transcript detection algorithms have been developed for paired-end RNA-seq data but their performance has not been comprehensively evaluated to guide practitioners. In this paper, we evaluated 15 popular algorithms by their precision and recall trade-off, accuracy of supporting reads and computational cost. We further combine top-performing methods for improved ensemble detection. Results: Fifteen fusion transcript detection tools were compared using three synthetic data sets under different coverage, read length, insert size and background noise, and three real data sets with selected experimental validations. No single method dominantly performed the best but SOAPfuse generally performed well, followed by FusionCatcher and JAFFA. We further demonstrated the potential of a meta-caller algorithm by combining top performing methods to re-prioritize candidate fusion transcripts with high confidence that can be followed by experimental validation. Conclusion: Our result provides insightful recommendations when applying individual tool or combining top performers to identify fusion transcript candidates.
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Affiliation(s)
- Silvia Liu
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261, USA Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Wei-Hsiang Tsai
- Institute of Biomedical Informatics, National Yang-Ming University, No. 155, Sec. 2, Linong Street, Beitou District, Taipei 112, Taiwan
| | - Ying Ding
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261, USA Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Rui Chen
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261, USA
| | - Zhou Fang
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261, USA
| | - Zhiguang Huo
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261, USA
| | - SungHwan Kim
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261, USA
| | - Tianzhou Ma
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261, USA
| | - Ting-Yu Chang
- Institute of Microbiology and Immunology, National Yang-Ming University, No. 155, Sec. 2, Linong Street, Beitou District, Taipei 112, Taiwan
| | - Nolan Michael Priedigkeit
- Molecular Pharmacology, School of Medicine, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Adrian V Lee
- Magee-Women's Research Institute, 204 Craft Avenue, Pittsburgh, PA 15213, USA
| | - Jianhua Luo
- Department of Pathology, School of Medicine, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Hsei-Wei Wang
- Institute of Biomedical Informatics, National Yang-Ming University, No. 155, Sec. 2, Linong Street, Beitou District, Taipei 112, Taiwan Institute of Microbiology and Immunology, National Yang-Ming University, No. 155, Sec. 2, Linong Street, Beitou District, Taipei 112, Taiwan Center for Systems and Synthetic Biology, National Yang-Ming University, No. 155, Sec. 2, Linong Street, Beitou District, Taipei 112, Taiwan
| | - I-Fang Chung
- Institute of Biomedical Informatics, National Yang-Ming University, No. 155, Sec. 2, Linong Street, Beitou District, Taipei 112, Taiwan Center for Systems and Synthetic Biology, National Yang-Ming University, No. 155, Sec. 2, Linong Street, Beitou District, Taipei 112, Taiwan
| | - George C Tseng
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261, USA Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15213, USA
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