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Zhang P, Chen T, Yang M. Comparative analysis of prognosis and gene expression in prostate cancer patients with site-specific visceral metastases. Urol Oncol 2024; 42:160.e1-160.e10. [PMID: 38433022 DOI: 10.1016/j.urolonc.2024.01.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 03/05/2024]
Abstract
INTRODUCTION Prostate cancer patients with visceral metastases often exhibited poor prognoses. Few researches had compared the prognostic impact and gene expression profiles among distinct visceral metastatic sites. Therefore, we conducted a comprehensive study utilizing data from the Surveillance, Epidemiology, and End Results (SEER) database and the Gene Expression Omnibus database. PATIENTS AND METHODS We analyzed the prostate cancer-specific mortality (PCSM) risk for 8,170 patients diagnosed with metastatic prostate cancer (mPCa) between 2000 and 2019, utilizing data from the SEER 17 registry database. Patients with metastatic disease in nonregional lymph nodes, bones, brains, livers, and lungs were identified. Competing risks regression was employed to evaluate the effect of visceral metastatic disease sites on PCSM. Differentially expressed genes (DEGs) between visceral metastases were assessed using data from the GSE6752 dataset. A relative protein-protein interaction (PPI) network was constructed based on STRING analysis. Furthermore, we explored the distribution of DEGs in various normal tissues and tumor tissues using the Human Protein Atlas and GEPIA. RESULTS Competing risks regression analysis revealed that liver and lung metastases had a substantial impact on PCSM (hazard ratio 2.24, 95% confidence interval 1.70-2.95, P < 0.001; hazard ratio 1.30, 95% confidence interval 1.06-1.59, P = 0.012, respectively). Seven significant DEGs were identified from samples of liver and lung metastases (HERV-FRD, NUDT12, FAM63A, SCGB3A1, CEACAM6, LOC440416, SFTPB) and were associated with respiratory gaseous exchange, pulmonary surfactant metabolism, and fibronectin matrix formation in PPI network analysis. Notably, the expression levels of the three DEGs significantly upregulated in lung metastases were also found to be higher in normal lung tissues compared to normal liver tissues. CONCLUSION Patients diagnosed with mPCa and presenting with liver and/or lung metastases exhibit poorer prognoses. SCGB3A1, identified as a tumor suppressor gene, may contribute to the better survival prognosis observed in patients with prostate cancer lung metastases compared to those with liver metastases. The gene expression profiles in these two specific metastatic sites reveal a combination of both heterogeneity and homogeneity.
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Affiliation(s)
- Peng Zhang
- Department of Urology, Ningbo Medical Center Lihuili Hospital, Ningbo, Zhejiang, China.
| | - Tieding Chen
- Department of Urology, Ningbo Medical Center Lihuili Hospital, Ningbo, Zhejiang, China
| | - Ming Yang
- Department of Urology, Ningbo Medical Center Lihuili Hospital, Ningbo, Zhejiang, China
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Shi Q, Li X, Liu Y, Chen Z, He X. FLIBase: a comprehensive repository of full-length isoforms across human cancers and tissues. Nucleic Acids Res 2024; 52:D124-D133. [PMID: 37697439 PMCID: PMC10767943 DOI: 10.1093/nar/gkad745] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/14/2023] [Accepted: 08/31/2023] [Indexed: 09/13/2023] Open
Abstract
Regulatory processes at the RNA transcript level play a crucial role in generating transcriptome diversity and proteome composition in human cells, impacting both physiological and pathological states. This study introduces FLIBase (www.FLIBase.org), a specialized database that focuses on annotating full-length isoforms using long-read sequencing techniques. We collected and integrated long-read (351 samples) and short-read (12 469 samples) RNA sequencing data from diverse normal and cancerous human tissues and cells. The current version of FLIBase comprises a total of 983 789 full-length spliced isoforms, identified through long-read sequences and verified using short-read exon-exon splice junctions. Of these, 188 248 isoforms have been annotated, while 795 541 isoforms remain unannotated. By overcoming the limitations of short-read RNA sequencing methods, FLIBase provides an accurate and comprehensive representation of full-length transcripts. These comprehensive annotations empower researchers to undertake various downstream analyses and investigations. Importantly, FLIBase exhibits a significant advantage in identifying a substantial number of previously unannotated isoforms and tumor-specific RNA transcripts. These tumor-specific RNA transcripts have the potential to serve as a source of immunogenic recurrent neoantigens. This remarkable discovery holds tremendous promise for advancing the development of tailored RNA-based diagnostic and therapeutic strategies for various types of human cancer.
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Affiliation(s)
- Qili Shi
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xinrong Li
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yizhe Liu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Zhiao Chen
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China
| | - Xianghuo He
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China
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3
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Zhou BW, Wu QQ, Mauki DH, Wang X, Zhang SR, Yin TT, Chen FL, Li C, Liu YH, Wang GD, Zhang YP. Germline gene fusions across species reveal the chromosomal instability regions and cancer susceptibility. iScience 2023; 26:108431. [PMID: 38205119 PMCID: PMC10777377 DOI: 10.1016/j.isci.2023.108431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/24/2023] [Accepted: 11/08/2023] [Indexed: 01/12/2024] Open
Abstract
The canine transmissible venereal tumor (CTVT) is a clonal cell-mediated cancer with a long evolutionary history and extensive karyotype rearrangements in its genome. However, little is known about its genetic similarity to human tumors. Here, using multi-omics data we identified 11 germline gene fusions (GGFs) in CTVT, which showed higher genetic susceptibility than others. Additionally, we illustrate a mechanism of a complex gene fusion of three gene segments (HSD17B4-DMXL1-TNFAIP8) that we refer to "greedy fusion". Our findings also provided evidence that expressions of GGFs are downregulated during the tumor regressive phase, which is associated with DNA methylation level. This study presents a comprehensive landscape of gene fusions (GFs) in CTVT, which offers a valuable genetic resource for exploring potential genetic mechanisms underlying the development of cancers in both dogs and humans.
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Affiliation(s)
- Bo-Wen Zhou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Qing-Qin Wu
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan 650500, China
| | - David H. Mauki
- Institute of Neurological Disease, National-Local Joint Engineering Research Center of Translational Medicine, State Key Lab of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xuan Wang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Shu-Run Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Fang-Liang Chen
- Kunming Police Dog Base of the Ministry of Public Security, Kunming, Yunnan 650204, China
| | - Chao Li
- State Key Laboratory for Conservation and Utilization of Bio-Resource, Yunnan University, Kunming, Yunnan 650500, China
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
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Dondi A, Lischetti U, Jacob F, Singer F, Borgsmüller N, Coelho R, Heinzelmann-Schwarz V, Beisel C, Beerenwinkel N. Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer. Nat Commun 2023; 14:7780. [PMID: 38012143 PMCID: PMC10682465 DOI: 10.1038/s41467-023-43387-9] [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: 01/23/2023] [Accepted: 11/07/2023] [Indexed: 11/29/2023] Open
Abstract
Understanding the complex background of cancer requires genotype-phenotype information in single-cell resolution. Here, we perform long-read single-cell RNA sequencing (scRNA-seq) on clinical samples from three ovarian cancer patients presenting with omental metastasis and increase the PacBio sequencing depth to 12,000 reads per cell. Our approach captures 152,000 isoforms, of which over 52,000 were not previously reported. Isoform-level analysis accounting for non-coding isoforms reveals 20% overestimation of protein-coding gene expression on average. We also detect cell type-specific isoform and poly-adenylation site usage in tumor and mesothelial cells, and find that mesothelial cells transition into cancer-associated fibroblasts in the metastasis, partly through the TGF-β/miR-29/Collagen axis. Furthermore, we identify gene fusions, including an experimentally validated IGF2BP2::TESPA1 fusion, which is misclassified as high TESPA1 expression in matched short-read data, and call mutations confirmed by targeted NGS cancer gene panel results. With these findings, we envision long-read scRNA-seq to become increasingly relevant in oncology and personalized medicine.
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Affiliation(s)
- Arthur Dondi
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Ulrike Lischetti
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058, Basel, Switzerland.
- University Hospital Basel and University of Basel, Ovarian Cancer Research, Department of Biomedicine, Hebelstrasse 20, 4031, Basel, Switzerland.
| | - Francis Jacob
- University Hospital Basel and University of Basel, Ovarian Cancer Research, Department of Biomedicine, Hebelstrasse 20, 4031, Basel, Switzerland
| | - Franziska Singer
- SIB Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058, Basel, Switzerland
- ETH Zurich, NEXUS Personalized Health Technologies, Wagistrasse 18, 8952, Schlieren, Switzerland
| | - Nico Borgsmüller
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Ricardo Coelho
- University Hospital Basel and University of Basel, Ovarian Cancer Research, Department of Biomedicine, Hebelstrasse 20, 4031, Basel, Switzerland
| | - Viola Heinzelmann-Schwarz
- University Hospital Basel and University of Basel, Ovarian Cancer Research, Department of Biomedicine, Hebelstrasse 20, 4031, Basel, Switzerland
- University Hospital Basel, Gynecological Cancer Center, Spitalstrasse 21, 4031, Basel, Switzerland
| | - Christian Beisel
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058, Basel, Switzerland.
| | - Niko Beerenwinkel
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058, Basel, Switzerland.
- SIB Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058, Basel, Switzerland.
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Wen X, Shen J, De Miglio MR, Zeng D, Sechi LA. Endogenous retrovirus group FRD member 1 is a potential biomarker for prognosis and immunotherapy for kidney renal clear cell carcinoma. Front Cell Infect Microbiol 2023; 13:1252905. [PMID: 37780849 PMCID: PMC10534008 DOI: 10.3389/fcimb.2023.1252905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 08/29/2023] [Indexed: 10/03/2023] Open
Abstract
Introduction The activation of endogenous retroviral (ERV) genes in kidney renal clear cell carcinoma (KIRC) suggests the necessity for further research on their functions. Methods In this study, KIRC and healthy cohorts were obtained from TGGA and GEO datasets. Subsequently, differential analysis and functional annotation were conducted using GO, KEGG, and GSEA. Clinical outcomes were then observed and utilized in the development of a nomogram. Results We observed the general low expression of ERVFRD-1 in KIRC tumors compared to normal tissue (P < 0.001) across multiple cohorts. Differential analysis and functional annotation using GO, KEGG, GSEA analysis revealed significant involvement of ERVFRD-1 in tumor immunoregulation: a close relation to the infiltration levels of mast cells and Treg cell (P < 0.001) and occurrence with a variety of immune markers. Methylation status was then applied to uncover potential mechanisms of ERVFRD-1 in KIRC. Notably, higher expression levels of ERVFRD-1 were associated with extended overall survival, disease-specific survival, and progression-free survival. Finally, based on Cox regression analysis, we constructed a nomogram incorporating ERVFRD-1, pathologic T, and age, which exhibited promising predictive power in assessing the survival outcomes of KIRC patients. Discussion To sum up, our study suggests that ERVFRD-1 plays a role in regulating immunological activity within the tumor microenvironment and is associated with overall survival in KIRC patients. ERVFRD-1 may therefore be a sensitive biomarker for diagnosis, immunotherapy, and prognosis assessment of KIRC.
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Affiliation(s)
- Xiaofen Wen
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Department of Medical Oncology, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Jiaxin Shen
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Department of Hematology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Maria Rosaria De Miglio
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - De Zeng
- Department of Medical Oncology, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Leonardo A. Sechi
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Struttura Complessa (SC) Microbiologia e Virologia, Azienda Ospedaliera Universitaria, Sassari, Italy
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6
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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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7
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Ren Y, Tseng E, Smith TPL, Hiendleder S, Williams JL, Low WY. Long read isoform sequencing reveals hidden transcriptional complexity between cattle subspecies. BMC Genomics 2023; 24:108. [PMID: 36915055 PMCID: PMC10012480 DOI: 10.1186/s12864-023-09212-9] [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: 12/07/2022] [Accepted: 02/27/2023] [Indexed: 03/16/2023] Open
Abstract
The Iso-Seq method of full-length cDNA sequencing is suitable to quantify differentially expressed genes (DEGs), transcripts (DETs) and transcript usage (DTU). However, the higher cost of Iso-Seq relative to RNA-seq has limited the comparison of both methods. Transcript abundance estimated by RNA-seq and deep Iso-Seq data for fetal liver from two cattle subspecies were compared to evaluate concordance. Inter-sample correlation of gene- and transcript-level abundance was higher within technology than between technologies. Identification of DEGs between the cattle subspecies depended on sequencing method with only 44 genes identified by both that included 6 novel genes annotated by Iso-Seq. There was a pronounced difference between Iso-Seq and RNA-seq results at transcript-level wherein Iso-Seq revealed several magnitudes more transcript abundance and usage differences between subspecies. Factors influencing DEG identification included size selection during Iso-Seq library preparation, average transcript abundance, multi-mapping of RNA-seq reads to the reference genome, and overlapping coordinates of genes. Some DEGs called by RNA-seq alone appear to be sequence duplication artifacts. Among the 44 DEGs identified by both technologies some play a role in immune system, thyroid function and cell growth. Iso-Seq revealed hidden transcriptional complexity in DEGs, DETs and DTU genes between cattle subspecies previously missed by RNA-seq.
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Affiliation(s)
- Yan Ren
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, Adelaide, SA, 5371, Australia
| | | | - Timothy P L Smith
- U.S. Meat Animal Research Center, USDA-ARS, Clay Center, Clay Center, Nebraska, USA
| | - Stefan Hiendleder
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, Adelaide, SA, 5371, Australia.,Robinson Research Institute, The University of Adelaide, North Adelaide, Adelaide, SA, 5006, Australia
| | - John L Williams
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, Adelaide, SA, 5371, Australia.,Department of Animal Science, Food and Nutrition, Università Cattolica del Sacro Cuore, 29122, Piacenza, Italy
| | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, Adelaide, SA, 5371, Australia.
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Dorney R, Dhungel BP, Rasko JEJ, Hebbard L, Schmitz U. Recent advances in cancer fusion transcript detection. Brief Bioinform 2022; 24:6918739. [PMID: 36527429 PMCID: PMC9851307 DOI: 10.1093/bib/bbac519] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/11/2022] [Accepted: 10/31/2022] [Indexed: 12/23/2022] Open
Abstract
Extensive investigation of gene fusions in cancer has led to the discovery of novel biomarkers and therapeutic targets. To date, most studies have neglected chromosomal rearrangement-independent fusion transcripts and complex fusion structures such as double or triple-hop fusions, and fusion-circRNAs. In this review, we untangle fusion-related terminology and propose a classification system involving both gene and transcript fusions. We highlight the importance of RNA-level fusions and how long-read sequencing approaches can improve detection and characterization. Moreover, we discuss novel bioinformatic tools to identify fusions in long-read sequencing data and strategies to experimentally validate and functionally characterize fusion transcripts.
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Affiliation(s)
- Ryley Dorney
- epartment of Molecular & Cell Biology, College of Public Health, Medical & Vet Sciences, James Cook University, Douglas, QLD 4811, Australia,Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns 4878, Australia
| | - Bijay P Dhungel
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia,Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2006, Australia,Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns 4878, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia,Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Lionel Hebbard
- epartment of Molecular & Cell Biology, College of Public Health, Medical & Vet Sciences, James Cook University, Douglas, QLD 4811, Australia,Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, Sydney, New South Wales, Australia
| | - Ulf Schmitz
- Corresponding author. Ulf Schmitz, Department of Molecular and Cell Biology, College of Public Health, Medical and Vet Sciences, James Cook University, Douglas, QLD 4811, Australia. E-mail:
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Ono Y, Hamada M, Asai K. PBSIM3: a simulator for all types of PacBio and ONT long reads. NAR Genom Bioinform 2022; 4:lqac092. [PMID: 36465498 PMCID: PMC9713900 DOI: 10.1093/nargab/lqac092] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 11/02/2022] [Accepted: 11/12/2022] [Indexed: 12/03/2022] Open
Abstract
Long-read sequencers, such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) sequencers, have improved their read length and accuracy, thereby opening up unprecedented research. Many tools and algorithms have been developed to analyze long reads, and rapid progress in PacBio and ONT has further accelerated their development. Together with the development of high-throughput sequencing technologies and their analysis tools, many read simulators have been developed and effectively utilized. PBSIM is one of the popular long-read simulators. In this study, we developed PBSIM3 with three new functions: error models for long reads, multi-pass sequencing for high-fidelity read simulation and transcriptome sequencing simulation. Therefore, PBSIM3 is now able to meet a wide range of long-read simulation requirements.
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Affiliation(s)
- Yukiteru Ono
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8561, Japan
| | - Michiaki Hamada
- Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 63-520, 3-4-1, Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Institute for Medical-Oriented Structural Biology, Waseda University, 2-2, Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- Graduate School of Medicine, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan
| | - Kiyoshi Asai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8561, Japan
- Artificial Intelligence Research Center (AIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, 135-0064 Tokyo, Japan
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Wu L, Yang J, Ke RS, Liu Y, Guo P, Feng L, Li Z, Li Z. Impact of lncRNA SOX9-AS1 overexpression on the prognosis and progression of intrahepatic cholangiocarcinoma. Clin Res Hepatol Gastroenterol 2022; 46:101999. [PMID: 35870795 DOI: 10.1016/j.clinre.2022.101999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Intrahepatic cholangiocarcinoma (ICC) is a latent and malignant tumor with a dismal prognosis. This study was to evaluate the clinical relevance and therapeutic potential of SOX9-AS1 expression in ICC. METHODS The cancerous tissues and adjacent normal tissues were collected from ICC patients. Blood samples from ICC, hepatocellular carcinoma (HCC) group, the extrahepatic cholangiocarcinoma (ECC) group and the healthy controls were collected. SOX9-AS1 levels were evaluated in tissues (versus normal tissues) and plasma samples (versus plasma from HCC and ECC by quantitative real-time RT-PCR. The diagnostic value of SOX9-AS1 for ICC was estimated using receiver operating characteristic (ROC) curves. The relevancy between SOX9-AS1 expression and overall survival or recurrence-free survival was assessed by Kaplan-Meier curves multivariate analyses. The overexpression and knockdown of SOX9-AS1 on cell behavior were assessed by CCK-8 and transwell assay. RESULTS SOX9-AS1 levels were increased in ICC, both in the tissues and the cell lines. The upregulation of SOX9-AS1 showed a highly discriminative profile, distinguishing ICC patients from healthy subjects or HCC or ECC patients. Upregulation of SOX9-AS1 was related to shorter overall survival and recurrence-free survival. Muli-variate analysis revealed that SOX9-AS1 expression was an independent prognostic purpose factor of worst overall survival and recurrence-free survival. CONCLUSIONS SOX9-AS1 drives tumor growth and metastasis in ICC. SOX9-AS1 may be applied as a new diagnostic and prognostic purposed marker, in addition to a promising therapeutic target in ICC.
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Affiliation(s)
- Lupeng Wu
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China
| | - Jingrui Yang
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China
| | - Rui-Sheng Ke
- Department of General Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China
| | - Yujian Liu
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China
| | - Ping Guo
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China
| | - Liuxing Feng
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China
| | - Zhimin Li
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China.
| | - Zhimin Li
- Department of Hepatobiliary Pancreatic Vascular Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China.
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11
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Leshkowitz D, Kedmi M, Fried Y, Pilzer D, Keren-Shaul H, Ainbinder E, Dassa B. Exploring differential exon usage via short- and long-read RNA sequencing strategies. Open Biol 2022; 12:220206. [PMID: 36168804 PMCID: PMC9516339 DOI: 10.1098/rsob.220206] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Alternative splicing produces various mRNAs, and thereby various protein products, from one gene, impacting a wide range of cellular activities. However, accurate reconstruction and quantification of full-length transcripts using short-reads is limited, due to their length. Long-reads sequencing technologies may provide a solution by sequencing full-length transcripts. We explored the use of both Illumina short-reads and two long Oxford Nanopore Technology (cDNA and Direct RNA) RNA-Seq reads for detecting global differential splicing during mouse embryonic stem cell differentiation, applying several bioinformatics strategies: gene-based, isoform-based and exon-based. We detected the strongest similarity among the sequencing platforms at the gene level compared to exon-based and isoform-based. Furthermore, the exon-based strategy discovered many differential exon usage (DEU) events, mostly in a platform-dependent manner and in non-differentially expressed genes. Thus, the platforms complemented each other in the ability to detect DEUs (i.e. long-reads exhibited an advantage in detecting DEUs at the UTRs, and short-reads detected more DEUs). Exons within 20 genes, detected in one or more platforms, were here validated by PCR, including key differentiation genes, such as Mdb3 and Aplp1. We provide an important analysis resource for discovering transcriptome changes during stem cell differentiation and insights for analysing such data.
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Affiliation(s)
- Dena Leshkowitz
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Merav Kedmi
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yael Fried
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 76100, Israel
| | - David Pilzer
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hadas Keren-Shaul
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Elena Ainbinder
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Bareket Dassa
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 76100, Israel
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12
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Loo SK, Yates ME, Yang S, Oesterreich S, Lee AV, Wang X. Fusion-Associated Carcinomas of the Breast: Diagnostic, Prognostic, and Therapeutic Significance. Genes Chromosomes Cancer 2022; 61:261-273. [PMID: 35106856 DOI: 10.1002/gcc.23029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 11/11/2022] Open
Abstract
Recurrent gene fusions comprise a class of viable genetic targets in solid tumors that have culminated several recent break-through cancer therapies. Their role in breast cancer, however, remains largely underappreciated due to the complexity of genomic rearrangements in breast malignancy. Just recently, we and others have identified several recurrent gene fusions in breast cancer with important clinical and biological implications. Examples of the most significant recurrent gene fusions to date include 1) ESR1-CCDC170 gene fusions in luminal B and endocrine resistant breast cancer that exert oncogenic function via modulating the HER2/HER3/SRC complex, 2) ESR1 exon 6 fusions in metastatic disease that drive estrogen-independent ER transcriptional activity, 3) BCL2L14-ETV6 fusions in a more aggressive form of the triple negative subtype that prime epithelial-mesenchymal transition and endow paclitaxel resistance, 4) the ETV6-NTRK3 fusion in secretory breast carcinoma that constitutively activates NTRK3 kinase, 5) the oncogenic MYB-NFIB fusion as a genetic driver underpinning adenoid cystic carcinomas of the breast that activates MYB pathway, and 6) the NOTCH/MAST kinase gene fusions that activate NOTCH and MAST signaling. Importantly, these fusions are enriched in more aggressive and lethal breast cancer presentations and appear to confer therapeutic resistance. Thus, these gene fusions could be utilized as genetic biomarkers to identify patients that require more intensive treatment and surveillance. In addition, kinase fusions are currently being evaluated in breast cancer clinical trials and on-going mechanistic investigation is exposing therapeutic vulnerabilities in patients with fusion positive disease. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Suet Kee Loo
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Megan E Yates
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA, USA.,Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sichun Yang
- Center for Proteomics and Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| | - Steffi Oesterreich
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adrian V Lee
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xiaosong Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
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