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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] [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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Hafstað V, Häkkinen J, Larsson M, Staaf J, Vallon-Christersson J, Persson H. Improved detection of clinically relevant fusion transcripts in cancer by machine learning classification. BMC Genomics 2023; 24:783. [PMID: 38110872 PMCID: PMC10726539 DOI: 10.1186/s12864-023-09889-y] [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: 03/08/2023] [Accepted: 12/10/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Genomic rearrangements in cancer cells can create fusion genes that encode chimeric proteins or alter the expression of coding and non-coding RNAs. In some cancer types, fusions involving specific kinases are used as targets for therapy. Fusion genes can be detected by whole genome sequencing (WGS) and targeted fusion panels, but RNA sequencing (RNA-Seq) has the advantageous capability of broadly detecting expressed fusion transcripts. RESULTS We developed a pipeline for validation of fusion transcripts identified in RNA-Seq data using matched WGS data from The Cancer Genome Atlas (TCGA) and applied it to 910 tumors from 11 different cancer types. This resulted in 4237 validated gene fusions, 3049 of them with at least one identified genomic breakpoint. Utilizing validated fusions as true positive events, we trained a machine learning classifier to predict true and false positive fusion transcripts from RNA-Seq data. The final precision and recall metrics of the classifier were 0.74 and 0.71, respectively, in an independent dataset of 249 breast tumors. Application of this classifier to all samples with RNA-Seq data from these cancer types vastly extended the number of likely true positive fusion transcripts and identified many potentially targetable kinase fusions. Further analysis of the validated gene fusions suggested that many are created by intrachromosomal amplification events with microhomology-mediated non-homologous end-joining. CONCLUSIONS A classifier trained on validated fusion events increased the accuracy of fusion transcript identification in samples without WGS data. This allowed the analysis to be extended to all samples with RNA-Seq data, facilitating studies of tumor biology and increasing the number of detected kinase fusions. Machine learning could thus be used in identification of clinically relevant fusion events for targeted therapy. The large dataset of validated gene fusions generated here presents a useful resource for development and evaluation of fusion transcript detection algorithms.
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Affiliation(s)
- Völundur Hafstað
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University Cancer Centre, Lund, Sweden
| | - Jari Häkkinen
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University Cancer Centre, Lund, Sweden
| | - Malin Larsson
- Department of Physics, Chemistry and Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Linköping University, Linköping, Sweden
| | - Johan Staaf
- Faculty of Medicine, Department of Laboratory Medicine, Translational Cancer Research, Lund University Cancer Centre, Lund, Sweden
| | - Johan Vallon-Christersson
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University Cancer Centre, Lund, Sweden
| | - Helena Persson
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University Cancer Centre, Lund, Sweden.
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Hahn E, Xu B, Katabi N, Dogan S, Smith SM, Perez-Ordonez B, Patel PB, MacMillan C, Lubin DJ, Gagan J, Weinreb I, Bishop JA. Comprehensive Molecular Characterization of Polymorphous Adenocarcinoma, Cribriform Subtype: Identifying Novel Fusions and Fusion Partners. Mod Pathol 2023; 36:100305. [PMID: 37595638 DOI: 10.1016/j.modpat.2023.100305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/12/2023] [Accepted: 08/07/2023] [Indexed: 08/20/2023]
Abstract
Polymorphous adenocarcinoma (PAC) is a common, usually low-grade salivary gland carcinoma. While conventional PACs are most associated with PRKD1 p.E710D hotspot mutations, the cribriform subtype is often associated with gene fusions in PRKD1, PRKD2, or PRKD3. These fusions have been primarily identified by fluorescence in situ hybridization (FISH) analysis, with a minority evaluated by next-generation sequencing (NGS). Many of the reported fusions were detected by break-apart FISH probes and therefore have unknown partners or were negative by FISH altogether. In this study, we aimed to further characterize the fusions associated with PAC with NGS. Fifty-four PACs (exclusively cribriform and mixed/intermediate types to enrich the study for fusion-positive cases) were identified and subjected to NGS. Fifty-one cases were successfully sequenced, 28 of which demonstrated gene fusions involving PRKD1, PRKD2, or PRKD3. There were 10 cases with the PRKD1 p.E710D mutation. We identified a diverse group of fusion partners, including 13 novel partners, 3 of which were recurrent. The most common partners for the PRKD genes were ARID1A and ARID1B. The wide variety of involved genes is unlike in other salivary gland malignancies and warrants a broader strategy of sequencing for molecular confirmation for particularly challenging cases, as our NGS study shows.
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Affiliation(s)
- Elan Hahn
- Department of Pathology and Laboratory Medicine, Sinai Health System, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada.
| | - Bin Xu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nora Katabi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Snjezana Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Stephen M Smith
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada; Laboratory Medicine Program, University Health Network, Toronto General Hospital, Toronto, Ontario, Canada
| | - Bayardo Perez-Ordonez
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada; Laboratory Medicine Program, University Health Network, Toronto General Hospital, Toronto, Ontario, Canada
| | | | - Christina MacMillan
- Department of Pathology and Laboratory Medicine, Sinai Health System, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada
| | - Daniel J Lubin
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, Georgia
| | - Jeffrey Gagan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Ilan Weinreb
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada; Laboratory Medicine Program, University Health Network, Toronto General Hospital, Toronto, Ontario, Canada
| | - Justin A Bishop
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
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Hafstað V, Häkkinen J, Persson H. Fast and sensitive validation of fusion transcripts in whole-genome sequencing data. BMC Bioinformatics 2023; 24:359. [PMID: 37741966 PMCID: PMC10518092 DOI: 10.1186/s12859-023-05489-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023] Open
Abstract
BACKGROUND In cancer, genomic rearrangements can create fusion genes that either combine protein-coding sequences from two different partner genes or place one gene under the control of the promoter of another gene. These fusion genes can act as oncogenic drivers in tumor development and several fusions involving kinases have been successfully exploited as drug targets. Expressed fusions can be identified in RNA sequencing (RNA-Seq) data, but fusion prediction software often has a high fraction of false positive fusion transcript predictions. This is problematic for both research and clinical applications. RESULTS We describe a method for validation of fusion transcripts detected by RNA-Seq in matched whole-genome sequencing (WGS) data. Our pipeline uses discordant read pairs to identify supported fusion events and analyzes soft-clipped read alignments to determine genomic breakpoints. We have tested it on matched RNA-Seq and WGS data for both tumors and cancer cell lines and show that it can be used to validate both new predicted gene fusions and experimentally validated fusion events. It was considerably faster and more sensitive than using BreakDancer and Manta, software that is instead designed to detect many different types of structural variants on a genome-wide scale. CONCLUSIONS We have developed a fast and very sensitive pipeline for validation of gene fusions detected by RNA-Seq in matched WGS data. It can be used to identify high-quality gene fusions for further bioinformatic and experimental studies, including validation of genomic breakpoints and studies of the mechanisms that generate fusions. In a clinical setting, it could help find expressed gene fusions for personalized therapy.
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Affiliation(s)
- Völundur Hafstað
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University Cancer Centre, Lund, Sweden
| | - Jari Häkkinen
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University Cancer Centre, Lund, Sweden
| | - Helena Persson
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University Cancer Centre, Lund, Sweden.
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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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Vicente-Garcés C, Maynou J, Fernández G, Esperanza-Cebollada E, Torrebadell M, Català A, Rives S, Camós M, Vega-García N. Fusion InPipe, an integrative pipeline for gene fusion detection from RNA-seq data in acute pediatric leukemia. Front Mol Biosci 2023; 10:1141310. [PMID: 37363396 PMCID: PMC10288994 DOI: 10.3389/fmolb.2023.1141310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
RNA sequencing (RNA-seq) is a reliable tool for detecting gene fusions in acute leukemia. Multiple bioinformatics pipelines have been developed to analyze RNA-seq data, but an agreed gold standard has not been established. This study aimed to compare the applicability of 5 fusion calling pipelines (Arriba, deFuse, CICERO, FusionCatcher, and STAR-Fusion), as well as to define and develop an integrative bioinformatics pipeline (Fusion InPipe) to detect clinically relevant gene fusions in acute pediatric leukemia. We analyzed RNA-seq data by each pipeline individually and by Fusion InPipe. Each algorithm individually called most of the fusions with similar sensitivity and precision. However, not all rearrangements were called, suggesting that choosing a single pipeline might cause missing important fusions. To improve this, we integrated the results of the five algorithms in just one pipeline, Fusion InPipe, comparing the output from the agreement of 5/5, 4/5, and 3/5 algorithms. The maximum sensitivity was achieved with the agreement of 3/5 algorithms, with a global sensitivity of 95%, achieving a 100% in patients' data. Furthermore, we showed the necessity of filtering steps to reduce the false positive detection rate. Here, we demonstrate that Fusion InPipe is an excellent tool for fusion detection in pediatric acute leukemia with the best performance when selecting those fusions called by at least 3/5 pipelines.
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Affiliation(s)
- Clara Vicente-Garcés
- Pediatric Cancer Center Barcelona (PCCB), Institut de Recerca Sant Joan de Déu, Leukemia and Pediatric Hematology Disorders, Developmental Tumors Biology Group, Esplugues de Llobregat, Spain
| | - Joan Maynou
- Hospital Sant Joan de Déu Barcelona, Genetics Medicine Section, Esplugues de Llobregat, Spain
- Institut de Recerca Hospital Sant Joan de Déu, Neurogenetics and Molecular Medicine, Esplugues de Llobregat, Spain
| | - Guerau Fernández
- Hospital Sant Joan de Déu Barcelona, Genetics Medicine Section, Esplugues de Llobregat, Spain
- Institut de Recerca Hospital Sant Joan de Déu, Neurogenetics and Molecular Medicine, Esplugues de Llobregat, Spain
| | - Elena Esperanza-Cebollada
- Pediatric Cancer Center Barcelona (PCCB), Institut de Recerca Sant Joan de Déu, Leukemia and Pediatric Hematology Disorders, Developmental Tumors Biology Group, Esplugues de Llobregat, Spain
| | - Montserrat Torrebadell
- Pediatric Cancer Center Barcelona (PCCB), Institut de Recerca Sant Joan de Déu, Leukemia and Pediatric Hematology Disorders, Developmental Tumors Biology Group, Esplugues de Llobregat, Spain
- Hospital Sant Joan de Déu Barcelona, Hematology Laboratory, Esplugues de Llobregat, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red De Enfermedades Raras (CIBERER), Madrid, Spain
| | - Albert Català
- Pediatric Cancer Center Barcelona (PCCB), Institut de Recerca Sant Joan de Déu, Leukemia and Pediatric Hematology Disorders, Developmental Tumors Biology Group, Esplugues de Llobregat, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red De Enfermedades Raras (CIBERER), Madrid, Spain
- Pediatric Cancer Center Barcelona (PCCB), Hospital Sant Joan De Déu Barcelona, Leukemia and Lymphoma Unit, Barcelona, Spain
| | - Susana Rives
- Pediatric Cancer Center Barcelona (PCCB), Institut de Recerca Sant Joan de Déu, Leukemia and Pediatric Hematology Disorders, Developmental Tumors Biology Group, Esplugues de Llobregat, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red De Enfermedades Raras (CIBERER), Madrid, Spain
- Pediatric Cancer Center Barcelona (PCCB), Hospital Sant Joan De Déu Barcelona, Leukemia and Lymphoma Unit, Barcelona, Spain
| | - Mireia Camós
- Pediatric Cancer Center Barcelona (PCCB), Institut de Recerca Sant Joan de Déu, Leukemia and Pediatric Hematology Disorders, Developmental Tumors Biology Group, Esplugues de Llobregat, Spain
- Hospital Sant Joan de Déu Barcelona, Hematology Laboratory, Esplugues de Llobregat, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red De Enfermedades Raras (CIBERER), Madrid, Spain
| | - Nerea Vega-García
- Pediatric Cancer Center Barcelona (PCCB), Institut de Recerca Sant Joan de Déu, Leukemia and Pediatric Hematology Disorders, Developmental Tumors Biology Group, Esplugues de Llobregat, Spain
- Hospital Sant Joan de Déu Barcelona, Hematology Laboratory, Esplugues de Llobregat, Spain
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Collins K, Sholl LM, Vargas SO, Cornejo KM, Kravtsov O, Dickson BC, Idrees MT, Ulbright TM, Acosta AM. Testicular Juvenile Granulosa Cell Tumors Demonstrate Recurrent Loss of Chromosome 10 and Absence of Molecular Alterations Described in Ovarian Counterparts. Mod Pathol 2023; 36:100142. [PMID: 36813116 DOI: 10.1016/j.modpat.2023.100142] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/10/2023] [Accepted: 02/10/2023] [Indexed: 02/22/2023]
Abstract
Testicular juvenile granulosa cell tumors (JGCTs) are a rare type of sex cord-stromal tumor, accounting for <5% of all neoplasms of the prepubertal testis. Previous reports have demonstrated sex chromosome anomalies in a small subset of cases, but the molecular alterations associated with JGCTs remain largely undescribed. We evaluated 18 JGCTs using massive parallel DNA and RNA sequencing panels. The median patient age was <1 month (range, newborn to 5 months). The patients presented with scrotal or intra-abdominal masses/enlargement, and all underwent radical orchiectomy (17 unilateral and 1 bilateral). The median tumor size was 1.8 cm (range, 1.3-10.5 cm). Histologically, the tumors were purely cystic/follicular or mixed (ie, solid and cystic/follicular). All cases were predominantly epithelioid, with 2 exhibiting prominent spindle cell components. Nuclear atypia was mild or absent, and the median number of mitoses was 0.4/mm2 (range, 0-10/mm2). Tumors frequently expressed SF-1 (11/12 cases, 92%), inhibin (6/7 cases, 86%), calretinin (3/4 cases, 75%), and keratins (2/4 cases, 50%). Single-nucleotide variant analysis demonstrated the absence of recurrent mutations. RNA sequencing did not detect gene fusions in 3 cases that were sequenced successfully. Recurrent monosomy 10 was identified in 8 of 14 cases (57%) with interpretable copy number variant data, and multiple whole-chromosome gains were present in the 2 cases with significant spindle cell components. This study demonstrated that testicular JGCTs harbor recurrent loss of chromosome 10 and lack the GNAS and AKT1 variants described in their ovarian counterparts.
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Affiliation(s)
- Katrina Collins
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Sara O Vargas
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts
| | - Kristine M Cornejo
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | | | - Brendan C Dickson
- Department of Pathology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Muhammad T Idrees
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Thomas M Ulbright
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Andrés M Acosta
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
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Shrestha M, Blay S, Liang S, Swanson D, Lerner-Ellis J, Dickson B, Wong A, Charames GS. Improving RNA fusion call confidence and reliability in molecular diagnostic testing. J Mol Diagn 2023; 25:320-330. [PMID: 36958423 DOI: 10.1016/j.jmoldx.2023.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/17/2023] [Accepted: 03/08/2023] [Indexed: 03/25/2023] Open
Abstract
Next-generation sequencing (NGS) is a superior method for detecting known and novel RNA fusions in formalin-fixed paraffin-embedded tissue over FISH and RT-PCR. However, confidence in fusion calling and true negatives may be compromised by poor RNA quality. Using a commercial panel of 507 genes and the recommended 3 million read threshold to accept results, two cases yielded false negatives while exceeding this recommendation during clinical validation. To develop a reliable quality control metric that better reflects internal sample quality and improve call confidence, gene expression across 361 patient tumor samples was evaluated to derive a set of 15 genes to serve as a proxy quality control (pQC). These 15 genes were assessed for their normalized expression using the sequencing data from each case and selected for robustness. A threshold of 11 pQC genes produced a 4.71% fail rate, selected for stringency as an acceptable level of repeat testing in the clinical setting, minimizing false negative calls. To increase the chance that low-quality samples pass pQC, a revision to the library preparation methodology was also tested, with 75% of previously failed samples passing pQC upon re-sequencing by increasing cDNA input. Taken together, an NGS analysis quality control tool is presented that serves as a surrogate for housekeeping genes and improves confidence in fusion calls.
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Affiliation(s)
- Mariusz Shrestha
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Sasha Blay
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 600 University Avenue, Toronto, ON, M5G 1X5, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - Sydney Liang
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - David Swanson
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - Jordan Lerner-Ellis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 600 University Avenue, Toronto, ON, M5G 1X5, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Brendan Dickson
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 600 University Avenue, Toronto, ON, M5G 1X5, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Andrew Wong
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - George S Charames
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 600 University Avenue, Toronto, ON, M5G 1X5, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada.
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9
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Singh S, Shi X, Ahmad SB, Manley T, Piczak C, Phung C, Sun Y, Lynch S, Sharma A, Li H. RTCpredictor: Identification of Read-Through Chimeric RNAs from RNA Sequencing Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526869. [PMID: 36778443 PMCID: PMC9915620 DOI: 10.1101/2023.02.02.526869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Read-through chimeric RNAs are gaining attention in cancer and other research fields, yet current tools often fail in predicting them. We have thus developed the first read-through chimeric RNA specific prediction method, RTCpredictor, utilizing a fast ripgrep algorithm to search for all possible exon-exon combinations of parental gene pairs. Compared with other ten popular tools, RTCpredictor achieved top performance on both simulated and real datasets. We randomly selected up to 30 candidate read-through chimeras predicted from each software method and experimentally validated a total of 109 read-throughs and on this set, RTCpredictor outperformed all the other methods. In addition, RTCpredictor ( https://github.com/sandybioteck/RTCpredictor ) has less memory requirements and faster execution time.
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10
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Collins K, Sholl LM, Siegmund S, Dickson BC, Colecchia M, Michalová K, Hwang M, Ulbright TM, Kao CS, van Leenders GJLH, Mehta V, Trpkov K, Yilmaz A, Cimadamore A, Matoso A, Epstein JI, Maclean F, Comperat E, Anderson WJ, Fletcher CDM, Acosta AM. Myoid gonadal stromal tumours are characterised by recurrent chromosome-level copy number gains: molecular assessment of a multi-institutional series. Histopathology 2023; 82:431-438. [PMID: 36226695 DOI: 10.1111/his.14825] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/06/2022] [Accepted: 10/08/2022] [Indexed: 01/27/2023]
Abstract
Myoid gonadal stromal tumours (MGST) represent a rare type of testicular sex cord-stromal tumour that has recently been recognised as a distinct entity by the World Health Organization (WHO) classification of genitourinary tumours. MGSTs affect adult men and have been reported to behave in an indolent fashion. Histologically, MGSTs are pure spindle cell neoplasms that coexpress SMA and S100 protein. Given that the molecular features of these neoplasms remain largely undescribed, we evaluated a multi-institutional series of MGSTs using DNA and RNA sequencing. This study included 12 tumours from 12 patients aged 28 to 57 years. Tumour sizes ranged from 0.6 to 4.3 cm. Aggressive histologic features, such as vascular invasion, necrosis, invasive growth, and atypical mitoses were invariably absent. Mitotic activity was low, with a median of less than 1 mitosis per 10 high power fields (HPF; maximum: 3 mitoses per 10 HPF). Molecular analyses did not identify recurrent mutations or gene fusions. All cases with interpretable copy number variant data (9/10 cases sequenced successfully) demonstrated a consistent pattern of chromosome arm-level and whole-chromosome-level copy number gains indicative of ploidy shifts, with recurrent gains involving chromosomes 3, 6, 7, 8, 9, 11, 12, 14q, 15q, 17, 18q, 20, and 21q. Similar findings have also been recognised in pure spindle cell and spindle-cell predominant sex cord-stromal tumours without S100 protein expression. MGSTs are characterised by ploidy shifts and may be part of a larger spectrum of spindle cell-predominant sex cord-stromal tumours, including cases without S100 protein expression.
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Affiliation(s)
- Katrina Collins
- Departments of Pathology of Indiana University School of Medicine, Indianapolis, IN, USA
| | - Lynette M Sholl
- Departments of Pathology of Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Stephanie Siegmund
- Departments of Pathology of Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Brendan C Dickson
- Departments of Pathology of Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Maurizio Colecchia
- Departments of Pathology of Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Michael Hwang
- Departments of Pathology of Indiana University School of Medicine, Indianapolis, IN, USA
| | - Thomas M Ulbright
- Departments of Pathology of Indiana University School of Medicine, Indianapolis, IN, USA
| | - Chia-Sui Kao
- Departments of Pathology of Stanford University, Stanford, CA, USA
| | | | - Vikas Mehta
- Departments of Pathology of University of Illinois at Chicago, Chicago, IL, USA
| | - Kiril Trpkov
- Departments of Pathology of Alberta Precision Laboratories and University of Calgary, Calgary, Alberta, Canada
| | - Asli Yilmaz
- Departments of Pathology of Alberta Precision Laboratories and University of Calgary, Calgary, Alberta, Canada
| | - Alessia Cimadamore
- Departments of Pathology of Polytechnic University of The Marche Region, Ancona, Italy
| | - Andres Matoso
- Departments of Pathology of The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Jonathan I Epstein
- Departments of Pathology of The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Fiona Maclean
- Departments of Pathology of Douglass Hanly Moir Pathology and Macquarie University, Sydney, Australia
| | - Eva Comperat
- Departments of Pathology of Tenon Hospital and Sorbonne University, Paris, France
| | - William J Anderson
- Departments of Pathology of Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Christopher D M Fletcher
- Departments of Pathology of Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Andrés M Acosta
- Departments of Pathology of Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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11
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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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12
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Molecular correlates of male germ cell tumors with overgrowth of components resembling somatic malignancies. Mod Pathol 2022; 35:1966-1973. [PMID: 36030288 DOI: 10.1038/s41379-022-01136-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 12/24/2022]
Abstract
A small subset of male germ cell tumors (GCT) demonstrates overgrowth of histologic components that resemble somatic malignancies (e.g., sarcoma, carcinoma). The presence of so-called "somatic-type" malignancies (SM) in GCT has been associated with chemotherapy-resistance and poor clinical outcomes in prior studies. However, the molecular characteristics of these tumors remain largely undescribed. In this study, we performed a multi-platform molecular analysis of GCTs with SM diagnosed in 36 male patients (primary site: testis, 29 and mediastinum, 7). The most common histologic types of SM were sarcoma and embryonic-type neuroectodermal tumor (ENT, formerly known as "PNET"), present in 61% and 31% of cases, respectively. KRAS and TP53 mutations were identified by DNA sequencing in 28% of cases each, with enrichment of TP53 mutations in mediastinal tumors (86%). Gains in the short arm of chromosome 12 were seen in 91% of cases, likely reflecting the presence of isochromosome 12p. Numerous copy number changes indicative of widespread aneuploidy were found in 94% of cases. Focal homozygous deletions and amplifications were also detected, including MDM2 amplifications in 16% of cases. Sequencing of paired samples in 8 patients revealed similar mutational and copy number profiles in the conventional GCT and SM components. Oncogenic gene fusions were not detected using RNA sequencing of SM components from 9 cases. DNA methylation analysis highlighted the distinct methylation profile of SM components that sets them apart from conventional GCT components. In conclusion, GCT with SM are characterized by widespread aneuploidy, a distinct epigenetic signature and the presence of mutations that are otherwise rare in testicular GCT without SM. The similarity of the mutational and DNA methylation profiles of different histologic types of SM suggests that the identification of SM components could be more important than their precise histologic subclassification, pending confirmation by further studies.
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13
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Acosta AM, McKenney JK, Sholl LM, Dickson BC, Matoso A, Lu H, Jo VY, Collins K, Ulbright TM, Fletcher CDM. Molecular assessment of paratesticular rhabdomyomas demonstrates recurrent findings, including a novel H3C2 p.K37I mutation. Mod Pathol 2022; 35:1921-1928. [PMID: 35842480 DOI: 10.1038/s41379-022-01134-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 12/24/2022]
Abstract
Rhabdomyomas are benign tumors with skeletal muscle differentiation that are broadly divided into cardiac and extracardiac types. The latter demonstrate a predilection for head and neck and genital locations and are further subclassified into adult-type rhabdomyoma (ATRM), fetal-type rhabdomyoma (FTRM) and genital rhabdomyoma (GRM). Most extracardiac rhabdomyomas that arise in paratesticular tissues have a somewhat distinctive morphology and have been termed sclerosing rhabdomyomas (SRM). Therefore, we hypothesized that these tumors may harbor recurrent genetic alterations. In this study, we assessed 15 paratesticular rhabdomyomas (11 initially classified as SRM, 2 cellular FTRM and 2 ATRM) using massively parallel DNA and RNA sequencing. Five of 14 successfully sequenced cases harbored a novel H3C2 p.K37I mutation (4 SRM and 1 ATRM). This mutation replaced a highly conserved lysine residue that is a target for epigenetic modifications and plays a role in regulation of DNA replication. Moreover, 4 tumors (2 cellular FTRM, 1 case initially diagnosed as SRM and 1 ATRM) had complex copy number profiles characterized by numerous chromosome-level and arm-level copy number gains, consistent with a ploidy shift. Rereview of the SRM with copy number gains demonstrated that it was significantly more cellular and had a more prominent fascicular architecture than the rest of the SRMs included in this series. Therefore, it was retrospectively reclassified as a cellular FTRM. In conclusion, this study demonstrated that paratesticular rhabdomyomas harbor recurrent somatic H3C2 p.K37I mutations and ploidy shifts.
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Affiliation(s)
- Andres M Acosta
- Department of Pathology, Brigham and Women's Hospital/Harvard Medical School, Boston, MA, USA.
| | - Jesse K McKenney
- Department of Pathology, Robert J. Tomsich Institute of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital/Harvard Medical School, Boston, MA, USA
| | - Brendan C Dickson
- Department of Pathology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Andres Matoso
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Haiyan Lu
- Department of Pathology, Robert J. Tomsich Institute of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Vickie Y Jo
- Department of Pathology, Brigham and Women's Hospital/Harvard Medical School, Boston, MA, USA
| | - Katrina Collins
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Thomas M Ulbright
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA
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14
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Costigan DC, Nucci MR, Dickson BC, Chang MC, Song S, Sholl LM, Hornick JL, Fletcher CD, Kolin DL. NTRK -Rearranged Uterine Sarcomas: Clinicopathologic Features of 15 Cases, Literature Review, and Risk Stratification. Am J Surg Pathol 2022; 46:1415-1429. [PMID: 35713627 PMCID: PMC9481736 DOI: 10.1097/pas.0000000000001929] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
NTRK -rearranged uterine sarcomas are rare spindle cell neoplasms that typically arise in the uterine cervix of young women. Some tumors recur or metastasize, but features which predict behavior have not been identified to date. Distinguishing these tumors from morphologic mimics is significant because patients with advanced stage disease may be treated with TRK inhibitors. Herein, we present 15 cases of NTRK- rearranged uterine sarcomas, the largest series to date. Median patient age was 35 years (range: 16 to 61). The majority arose in the uterine cervix (n=14) and all but 2 were organ-confined at diagnosis. Tumors were composed of an infiltrative, fascicular proliferation of spindle cells and most showed mild-to-moderate cytologic atypia. All were pan-TRK positive by immunohistochemistry (13/13); S100 (11/13) and CD34 (6/10) were usually positive. RNA or DNA sequencing found NTRK1 (10/13) and NTRK3 (3/13) fusions with partners TPR , TPM3 , EML4 , TFG , SPECC1L , C16orf72 , and IRF2BP2 . Unusual morphology was seen in 2 tumors which were originally diagnosed as unclassifiable uterine sarcomas, 1 of which also harbored TP53 mutations. Follow up was available for 9 patients, of whom 3 died of disease. By incorporating outcome data of previously reported tumors, adverse prognostic features were identified, including a mitotic index ≥8 per 10 high-power fields, lymphovascular invasion, necrosis, and NTRK3 fusion. Patients with tumors which lacked any of these 4 features had an excellent prognosis. This study expands the morphologic spectrum of NTRK -rearranged uterine sarcomas and identifies features which can be used for risk stratification.
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Affiliation(s)
- Danielle C. Costigan
- Division of Women’s and Perinatal Pathology, Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Marisa R. Nucci
- Division of Women’s and Perinatal Pathology, Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
| | - Brendan C. Dickson
- Department of Pathology, Mount Sinai Hospital and University of Toronto, Toronto, ON M5G 1X5
| | - Martin C. Chang
- Department of Pathology & Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, 05401
| | - Sharon Song
- Division of Women’s and Perinatal Pathology, Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
- Spectrum Healthcare Partners, Portland, Maine 04106
| | - Lynette M. Sholl
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
| | - Jason L. Hornick
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
| | | | - David L. Kolin
- Division of Women’s and Perinatal Pathology, Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
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15
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mRNA Capture Sequencing and RT-qPCR for the Detection of Pathognomonic, Novel, and Secondary Fusion Transcripts in FFPE Tissue: A Sarcoma Showcase. Int J Mol Sci 2022; 23:ijms231911007. [PMID: 36232302 PMCID: PMC9569610 DOI: 10.3390/ijms231911007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/12/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
We assess the performance of mRNA capture sequencing to identify fusion transcripts in FFPE tissue of different sarcoma types, followed by RT-qPCR confirmation. To validate our workflow, six positive control tumors with a specific chromosomal rearrangement were analyzed using the TruSight RNA Pan-Cancer Panel. Fusion transcript calling by FusionCatcher confirmed these aberrations and enabled the identification of both fusion gene partners and breakpoints. Next, whole-transcriptome TruSeq RNA Exome sequencing was applied to 17 fusion gene-negative alveolar rhabdomyosarcoma (ARMS) or undifferentiated round cell sarcoma (URCS) tumors, for whom fluorescence in situ hybridization (FISH) did not identify the classical pathognomonic rearrangements. For six patients, a pathognomonic fusion transcript was readily detected, i.e., PAX3-FOXO1 in two ARMS patients, and EWSR1-FLI1, EWSR1-ERG, or EWSR1-NFATC2 in four URCS patients. For the 11 remaining patients, 11 newly identified fusion transcripts were confirmed by RT-qPCR, including COPS3-TOM1L2, NCOA1-DTNB, WWTR1-LINC01986, PLAA-MOB3B, AP1B1-CHEK2, and BRD4-LEUTX fusion transcripts in ARMS patients. Additionally, recurrently detected secondary fusion transcripts in patients diagnosed with EWSR1-NFATC2-positive sarcoma were confirmed (COPS4-TBC1D9, PICALM-SYTL2, SMG6-VPS53, and UBE2F-ALS2). In conclusion, this study shows that mRNA capture sequencing enhances the detection rate of pathognomonic fusions and enables the identification of novel and secondary fusion transcripts in sarcomas.
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16
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An S, Koh HH, Chang ES, Choi J, Song JY, Lee MS, Choi YL. Unearthing novel fusions as therapeutic targets in solid tumors using targeted RNA sequencing. Front Oncol 2022; 12:892918. [PMID: 36033527 PMCID: PMC9399837 DOI: 10.3389/fonc.2022.892918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/13/2022] [Indexed: 11/24/2022] Open
Abstract
Detection of oncogenic fusion genes in cancers, particularly in the diagnosis of uncertain tumors, is crucial for determining effective therapeutic strategies. Although novel fusion genes have been discovered through sequencing, verifying their oncogenic potential remain difficult. Therefore, we evaluated the utility of targeted RNA sequencing in 165 tumor samples by identifying known and unknown fusions. Additionally, by applying additional criteria, we discovered eight novel fusion genes that are expected to process oncogenicity. Among the novel fusion genes, RAF1 fusion genes were detected in two cases. PTPRG-RAF1 fusion led to an increase in cell growth; while dabrafenib, a BRAF inhibitor, reduced the growth of cells expressing RAF1. This study demonstrated the utility of RNA panel sequencing as a theragnostic tool and established criteria for identifying oncogenic fusion genes during post-sequencing analysis.
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Affiliation(s)
- Sungbin An
- Department of Health Science and Technology, Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Sungkyunkwan University, Seoul, South Korea
- Laboratory of Molecular Pathology and Theranotics, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul, South Korea
| | - Hyun Hee Koh
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Eun Sol Chang
- Department of Health Science and Technology, Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Sungkyunkwan University, Seoul, South Korea
- Laboratory of Molecular Pathology and Theranotics, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul, South Korea
| | - Juyoung Choi
- Laboratory of Molecular Pathology and Theranotics, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul, South Korea
- Department of Digital Health, Samsung Advanced Institute for Health Sciences & Technology Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Sungkyunkwan University, Seoul, South Korea
| | - Ji-Young Song
- Laboratory of Molecular Pathology and Theranotics, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul, South Korea
| | - Mi-Sook Lee
- Department of Health Science and Technology, Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Sungkyunkwan University, Seoul, South Korea
- Laboratory of Molecular Pathology and Theranotics, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul, South Korea
- *Correspondence: Mi-Sook Lee, ; Yoon-La Choi,
| | - Yoon-La Choi
- Department of Health Science and Technology, Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Sungkyunkwan University, Seoul, South Korea
- Laboratory of Molecular Pathology and Theranotics, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul, South Korea
- Department of Pathology and Translational Genomics, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul, South Korea
- *Correspondence: Mi-Sook Lee, ; Yoon-La Choi,
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17
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Abstract
Distilling biologically meaningful information from cancer genome sequencing data requires comprehensive identification of somatic alterations using rigorous computational methods. As the amount and complexity of sequencing data have increased, so has the number of tools for analysing them. Here, we describe the main steps involved in the bioinformatic analysis of cancer genomes, review key algorithmic developments and highlight popular tools and emerging technologies. These tools include those that identify point mutations, copy number alterations, structural variations and mutational signatures in cancer genomes. We also discuss issues in experimental design, the strengths and limitations of sequencing modalities and methodological challenges for the future.
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18
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Acosta AM, Al-Obaidy KI, Sholl LM, Dickson BC, Lindeman NI, Hirsch MS, Collins K, Fletcher CD, Idrees MT. Sarcomatoid Yolk Sac Tumor Harbors Somatic Mutations That Are Otherwise Rare in Testicular Germ Cell Tumors. Am J Surg Pathol 2022; 46:701-712. [PMID: 35034041 DOI: 10.1097/pas.0000000000001865] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In testicular germ cell tumors (TGCTs), components with nonspecific sarcomatous features that express keratins and glypican 3 are classified as sarcomatoid yolk sac tumor (SYST). SYST is most frequently seen in metastatic sites after chemotherapy. Like so-called "somatic-type" malignancies arising in TGCTs, SYST is markedly resistant to systemic therapy and has a more aggressive clinical course than conventional types of TGCT. However, the clinicopathologic and molecular features of SYST remain incompletely described. This study evaluated a multi-institutional series of 20 SYSTs using massively parallel sequencing and p53 immunohistochemistry. The histologic and clinical characteristics of the cases were also assessed, including analyses of disease-specific outcomes. DNA sequencing identified somatic mutations in 12/20 cases (60%), including recurrent TP53 and RIF1 mutations (present in 4/20 cases, 20% each). In 3 of the 4 SYST with TP53 mutations, there was molecular evidence of loss of heterozygosity. Immunohistochemistry demonstrated diffuse overexpression of p53 protein in 3/4 (75%) cases with TP53 mutations. The remaining TP53-mutant case demonstrated multifocal overexpression of p53, suggestive of subclonal inactivation of the gene. Overexpression of p53 protein was not seen in any of 15 TP53 wild-type cases evaluated by immunohistochemistry. A subset of 4 cases underwent RNA sequencing (fusion panel), which demonstrated the absence of oncogenic gene fusions. A 2-tiered grading system based on 3 histologic parameters (cellularity, number of mitoses, and necrosis) demonstrated that high-grade SYSTs have a higher risk of disease-specific death compared to low-grade tumors. The risk of disease-specific mortality was also higher in SYSTs with somatic mutations. In conclusion, this study demonstrated that 60% of SYSTs harbor somatic oncogenic mutations that are otherwise rare in TGCTs, and the presence of these mutations is associated with an aggressive clinical course. In addition, the results presented herein suggest that grading SYSTs may be clinically relevant.
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Affiliation(s)
- Andres M Acosta
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Khaleel I Al-Obaidy
- Department of Pathology, Indiana University Health and Indiana University School of Medicine, Indianapolis, IN
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Brendan C Dickson
- Department of Pathology, Mount Sinai Hospital and University of Toronto, Toronto, ON, Canada
| | - Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Katrina Collins
- Department of Pathology, Indiana University Health and Indiana University School of Medicine, Indianapolis, IN
| | - Christopher D Fletcher
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Muhammad T Idrees
- Department of Pathology, Indiana University Health and Indiana University School of Medicine, Indianapolis, IN
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19
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Fusion Genes in Prostate Cancer: A Comparison in Men of African and European Descent. BIOLOGY 2022; 11:biology11050625. [PMID: 35625354 PMCID: PMC9137560 DOI: 10.3390/biology11050625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 11/21/2022]
Abstract
Simple Summary Men of African origin have a 2–3 times greater chance of developing prostate cancer than those of European origin, and of patients that are diagnosed with the disease, men of African descent are 2 times more likely to die compared to white men. Men of African origin are still greatly underrepresented in genetic studies and clinical trials. This, unfortunately, means that new discoveries in cancer treatment are missing key information on the group with a greater chance of mortality. A fusion gene is a hybrid gene formed from two previously independent genes. Fusion genes have been found to be common in all main types of human cancer. The objective of this study was to increase our knowledge of fusion genes in prostate cancer using computational approaches and to compare fusion genes between men of African and European origin. This identified novel gene fusions unique to men of African origin and suggested that this group has a greater number of fusion genes. Abstract Prostate cancer is one of the most prevalent cancers worldwide, particularly affecting men living a western lifestyle and of African descent, suggesting risk factors that are genetic, environmental, and socioeconomic in nature. In the USA, African American (AA) men are disproportionately affected, on average suffering from a higher grade of the disease and at a younger age compared to men of European descent (EA). Fusion genes are chimeric products formed by the merging of two separate genes occurring as a result of chromosomal structural changes, for example, inversion or trans/cis-splicing of neighboring genes. They are known drivers of cancer and have been identified in 20% of cancers. Improvements in genomics technologies such as RNA-sequencing coupled with better algorithms for prediction of fusion genes has added to our knowledge of specific gene fusions in cancers. At present AA are underrepresented in genomic studies of prostate cancer. The primary goal of this study was to examine molecular differences in predicted fusion genes in a cohort of AA and EA men in the context of prostate cancer using computational approaches. RNA was purified from prostate tissue specimens obtained at surgery from subjects enrolled in the study. Fusion gene predictions were performed using four different fusion gene detection programs. This identified novel putative gene fusions unique to AA and suggested that the fusion gene burden was higher in AA compared to EA men.
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20
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Saliba J, Church AJ, Rao S, Danos A, Furtado LV, Laetsch T, Zhang L, Nardi V, Lin WH, Ritter D, Madhavan S, Li MM, Griffith OL, Griffith M, Raca G, Roy A. Standardized Evidence-Based Approach for Assessment of Oncogenic and Clinical Significance of NTRK Fusions. Cancer Genet 2022; 264-265:50-59. [DOI: 10.1016/j.cancergen.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/13/2022] [Accepted: 03/07/2022] [Indexed: 11/17/2022]
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21
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Lacambra MD, Antonescu CR, Chit C, Chiu WK, Demicco EG, Ferguson PC, Swanson D, To KF, Zhang L, Dickson BC. Expanding the spectrum of mesenchymal neoplasms with NR1D1‐rearrangement. Genes Chromosomes Cancer 2022; 61:420-426. [DOI: 10.1002/gcc.23032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/29/2022] [Accepted: 02/01/2022] [Indexed: 11/08/2022] Open
Affiliation(s)
- Maribel D. Lacambra
- Department of Anatomic and Cellular Pathology Prince of UK Hospital, The Chinese University of Hong Kong
| | - Cristina R. Antonescu
- Department of Pathology Memorial Sloan Kettering Cancer Center New York New York United States
| | - Chow Chit
- Department of Anatomic and Cellular Pathology Prince of UK Hospital, The Chinese University of Hong Kong
| | - Wang Kei Chiu
- Department of Orthopedics and Traumatology Prince of UK Hospital, The Chinese University of Hong Kong
| | - Elizabeth G. Demicco
- Department of Pathology and Laboratory Medicine, Mount Sinai Health System; Department of Laboratory Medicine and Pathobiology University of Toronto Toronto Ontario Canada
| | - Peter C. Ferguson
- Department of Surgery, Mount Sinai Health System; Division of Orthopaedics, Department of Surgery University of Toronto Toronto Ontario Canada
| | - David Swanson
- Department of Pathology and Laboratory Medicine, Mount Sinai Health System; Department of Laboratory Medicine and Pathobiology University of Toronto Toronto Ontario Canada
| | - Ka Fai To
- Department of Anatomic and Cellular Pathology Prince of UK Hospital, The Chinese University of Hong Kong
| | - Lei Zhang
- Department of Anatomic and Cellular Pathology Prince of UK Hospital, The Chinese University of Hong Kong
| | - Brendan C. Dickson
- Department of Pathology and Laboratory Medicine, Mount Sinai Health System; Department of Laboratory Medicine and Pathobiology University of Toronto Toronto Ontario Canada
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22
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Davidson NM, Chen Y, Sadras T, Ryland GL, Blombery P, Ekert PG, Göke J, Oshlack A. JAFFAL: detecting fusion genes with long-read transcriptome sequencing. Genome Biol 2022; 23:10. [PMID: 34991664 PMCID: PMC8739696 DOI: 10.1186/s13059-021-02588-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 12/22/2021] [Indexed: 12/26/2022] Open
Abstract
In cancer, fusions are important diagnostic markers and targets for therapy. Long-read transcriptome sequencing allows the discovery of fusions with their full-length isoform structure. However, due to higher sequencing error rates, fusion finding algorithms designed for short reads do not work. Here we present JAFFAL, to identify fusions from long-read transcriptome sequencing. We validate JAFFAL using simulations, cell lines, and patient data from Nanopore and PacBio. We apply JAFFAL to single-cell data and find fusions spanning three genes demonstrating transcripts detected from complex rearrangements. JAFFAL is available at https://github.com/Oshlack/JAFFA/wiki .
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Affiliation(s)
- Nadia M Davidson
- Peter MacCallum Cancer Centre, Victoria, Australia.
- School of BioSciences, University of Melbourne, Victoria, Australia.
- The Walter and Eliza Hall Institute, Victoria, Australia.
| | - Ying Chen
- Genome Institute of Singapore, Singapore, Singapore
| | - Teresa Sadras
- Peter MacCallum Cancer Centre, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Georgina L Ryland
- Peter MacCallum Cancer Centre, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
- Centre for Cancer Research, University of Melbourne, Victoria, Australia
| | - Piers Blombery
- Peter MacCallum Cancer Centre, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Paul G Ekert
- Peter MacCallum Cancer Centre, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
- Children's Cancer Institute, Lowy Cancer Centre, UNSW, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW, Sydney, NSW, Australia
- Murdoch Children's Research Institute, Victoria, Australia
| | - Jonathan Göke
- Genome Institute of Singapore, Singapore, Singapore
- National Cancer Centre Singapore, Singapore, Singapore
| | - Alicia Oshlack
- Peter MacCallum Cancer Centre, Victoria, Australia.
- School of BioSciences, University of Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia.
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23
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Kerbs P, Vosberg S, Krebs S, Graf A, Blum H, Swoboda A, Batcha AMN, Mansmann U, Metzler D, Heckman CA, Herold T, Greif PA. Fusion gene detection by RNA-sequencing complements diagnostics of acute myeloid leukemia and identifies recurring NRIP1-MIR99AHG rearrangements. Haematologica 2022; 107:100-111. [PMID: 34134471 PMCID: PMC8719081 DOI: 10.3324/haematol.2021.278436] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/03/2021] [Indexed: 12/04/2022] Open
Abstract
Identification of fusion genes in clinical routine is mostly based on cytogenetics and targeted molecular genetics, such as metaphase karyotyping, fluorescence in situ hybridization and reverse-transcriptase polymerase chain reaction. However, sequencing technologies are becoming more important in clinical routine as processing time and costs per sample decrease. To evaluate the performance of fusion gene detection by RNAsequencing compared to standard diagnostic techniques, we analyzed 806 RNA-sequencing samples from patients with acute myeloid leukemia using two state-of-the-art software tools, namely Arriba and FusionCatcher. RNA-sequencing detected 90% of fusion events that were reported by routine with high evidence, while samples in which RNA-sequencing failed to detect fusion genes had overall lower and inhomogeneous sequence coverage. Based on properties of known and unknown fusion events, we developed a workflow with integrated filtering strategies for the identification of robust fusion gene candidates by RNA-sequencing. Thereby, we detected known recurrent fusion events in 26 cases that were not reported by routine and found discrepancies in evidence for known fusion events between routine and RNA-sequencing in three cases. Moreover, we identified 157 fusion genes as novel robust candidates and comparison to entries from ChimerDB or Mitelman Database showed novel recurrence of fusion genes in 14 cases. Finally, we detected the novel recurrent fusion gene NRIP1- MIR99AHG resulting from inv(21)(q11.2;q21.1) in nine patients (1.1%) and LTN1-MX1 resulting from inv(21)(q21.3;q22.3) in two patients (0.25%). We demonstrated that NRIP1-MIR99AHG results in overexpression of the 3' region of MIR99AHG and the disruption of the tricistronic miRNA cluster miR-99a/let-7c/miR-125b-2. Interestingly, upregulation of MIR99AHG and deregulation of the miRNA cluster, residing in the MIR99AHG locus, are known mechanisms of leukemogenesis in acute megakaryoblastic leukemia. Our findings demonstrate that RNA-sequencing has a strong potential to improve the systematic detection of fusion genes in clinical applications and provides a valuable tool for fusion discovery.
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Affiliation(s)
- Paul Kerbs
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich; and; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Vosberg
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich; and; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Anja Swoboda
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Aarif M N Batcha
- Department of Medical Data Processing, Biometry and Epidemiology, LMU Munich, Munich, Germany
| | - Ulrich Mansmann
- Department of Medical Data Processing, Biometry and Epidemiology, LMU Munich, Munich, Germany
| | - Dirk Metzler
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Caroline A Heckman
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich; and; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp A Greif
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich; and; German Cancer Research Center (DKFZ), Heidelberg, Germany.
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24
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Hoogstrate Y, Komor MA, Böttcher R, van Riet J, van de Werken HJG, van Lieshout S, Hoffmann R, van den Broek E, Bolijn AS, Dits N, Sie D, van der Meer D, Pepers F, Bangma CH, van Leenders GJLH, Smid M, French PJ, Martens JWM, van Workum W, van der Spek PJ, Janssen B, Caldenhoven E, Rausch C, de Jong M, Stubbs AP, Meijer GA, Fijneman RJA, Jenster GW. Fusion transcripts and their genomic breakpoints in polyadenylated and ribosomal RNA-minus RNA sequencing data. Gigascience 2021; 10:6458609. [PMID: 34891161 PMCID: PMC8673554 DOI: 10.1093/gigascience/giab080] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/08/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Fusion genes are typically identified by RNA sequencing (RNA-seq) without elucidating the causal genomic breakpoints. However, non-poly(A)-enriched RNA-seq contains large proportions of intronic reads that also span genomic breakpoints. RESULTS We have developed an algorithm, Dr. Disco, that searches for fusion transcripts by taking an entire reference genome into account as search space. This includes exons but also introns, intergenic regions, and sequences that do not meet splice junction motifs. Using 1,275 RNA-seq samples, we investigated to what extent genomic breakpoints can be extracted from RNA-seq data and their implications regarding poly(A)-enriched and ribosomal RNA-minus RNA-seq data. Comparison with whole-genome sequencing data revealed that most genomic breakpoints are not, or minimally, transcribed while, in contrast, the genomic breakpoints of all 32 TMPRSS2-ERG-positive tumours were present at RNA level. We also revealed tumours in which the ERG breakpoint was located before ERG, which co-existed with additional deletions and messenger RNA that incorporated intergenic cryptic exons. In breast cancer we identified rearrangement hot spots near CCND1 and in glioma near CDK4 and MDM2 and could directly associate this with increased expression. Furthermore, in all datasets we find fusions to intergenic regions, often spanning multiple cryptic exons that potentially encode neo-antigens. Thus, fusion transcripts other than classical gene-to-gene fusions are prominently present and can be identified using RNA-seq. CONCLUSION By using the full potential of non-poly(A)-enriched RNA-seq data, sophisticated analysis can reliably identify expressed genomic breakpoints and their transcriptional effects.
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Affiliation(s)
- Youri Hoogstrate
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands.,Department of Neurology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
| | - Malgorzata A Komor
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands
| | - René Böttcher
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands.,Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain
| | - Job van Riet
- Department of Medical Oncology, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | - Harmen J G van de Werken
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands.,Cancer Computational Biology Center, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | | | | | - Evert van den Broek
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands.,Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen 9713GZ, The Netherlands
| | - Anne S Bolijn
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands
| | - Natasja Dits
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
| | - Daoud Sie
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands
| | | | | | - Chris H Bangma
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
| | | | - Marcel Smid
- Department of Medical Oncology, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | - Pim J French
- Department of Neurology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | | | - Peter J van der Spek
- Department of Pathology, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | | | | | | | | | - Andrew P Stubbs
- Department of Pathology, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands
| | - Remond J A Fijneman
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands
| | - Guido W Jenster
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
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25
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Detroja R, Gorohovski A, Giwa O, Baum G, Frenkel-Morgenstern M. ChiTaH: a fast and accurate tool for identifying known human chimeric sequences from high-throughput sequencing data. NAR Genom Bioinform 2021; 3:lqab112. [PMID: 34859212 PMCID: PMC8633610 DOI: 10.1093/nargab/lqab112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/21/2021] [Accepted: 11/22/2021] [Indexed: 12/16/2022] Open
Abstract
Fusion genes or chimeras typically comprise sequences from two different genes. The chimeric RNAs of such joined sequences often serve as cancer drivers. Identifying such driver fusions in a given cancer or complex disease is important for diagnosis and treatment. The advent of next-generation sequencing technologies, such as DNA-Seq or RNA-Seq, together with the development of suitable computational tools, has made the global identification of chimeras in tumors possible. However, the testing of over 20 computational methods showed these to be limited in terms of chimera prediction sensitivity, specificity, and accurate quantification of junction reads. These shortcomings motivated us to develop the first ‘reference-based’ approach termed ChiTaH (Chimeric Transcripts from High–throughput sequencing data). ChiTaH uses 43,466 non–redundant known human chimeras as a reference database to map sequencing reads and to accurately identify chimeric reads. We benchmarked ChiTaH and four other methods to identify human chimeras, leveraging both simulated and real sequencing datasets. ChiTaH was found to be the most accurate and fastest method for identifying known human chimeras from simulated and sequencing datasets. Moreover, especially ChiTaH uncovered heterogeneity of the BCR-ABL1 chimera in both bulk and single-cells of the K-562 cell line, which was confirmed experimentally.
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Affiliation(s)
- Rajesh Detroja
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Alessandro Gorohovski
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Olawumi Giwa
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Gideon Baum
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
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26
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LaHaye S, Fitch JR, Voytovich KJ, Herman AC, Kelly BJ, Lammi GE, Arbesfeld JA, Wijeratne S, Franklin SJ, Schieffer KM, Bir N, McGrath SD, Miller AR, Wetzel A, Miller KE, Bedrosian TA, Leraas K, Varga EA, Lee K, Gupta A, Setty B, Boué DR, Leonard JR, Finlay JL, Abdelbaki MS, Osorio DS, Koo SC, Koboldt DC, Wagner AH, Eisfeld AK, Mrózek K, Magrini V, Cottrell CE, Mardis ER, Wilson RK, White P. Discovery of clinically relevant fusions in pediatric cancer. BMC Genomics 2021; 22:872. [PMID: 34863095 PMCID: PMC8642973 DOI: 10.1186/s12864-021-08094-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022] Open
Abstract
Background Pediatric cancers typically have a distinct genomic landscape when compared to adult cancers and frequently carry somatic gene fusion events that alter gene expression and drive tumorigenesis. Sensitive and specific detection of gene fusions through the analysis of next-generation-based RNA sequencing (RNA-Seq) data is computationally challenging and may be confounded by low tumor cellularity or underlying genomic complexity. Furthermore, numerous computational tools are available to identify fusions from supporting RNA-Seq reads, yet each algorithm demonstrates unique variability in sensitivity and precision, and no clearly superior approach currently exists. To overcome these challenges, we have developed an ensemble fusion calling approach to increase the accuracy of identifying fusions. Results Our Ensemble Fusion (EnFusion) approach utilizes seven fusion calling algorithms: Arriba, CICERO, FusionMap, FusionCatcher, JAFFA, MapSplice, and STAR-Fusion, which are packaged as a fully automated pipeline using Docker and Amazon Web Services (AWS) serverless technology. This method uses paired end RNA-Seq sequence reads as input, and the output from each algorithm is examined to identify fusions detected by a consensus of at least three algorithms. These consensus fusion results are filtered by comparison to an internal database to remove likely artifactual fusions occurring at high frequencies in our internal cohort, while a “known fusion list” prevents failure to report known pathogenic events. We have employed the EnFusion pipeline on RNA-Seq data from 229 patients with pediatric cancer or blood disorders studied under an IRB-approved protocol. The samples consist of 138 central nervous system tumors, 73 solid tumors, and 18 hematologic malignancies or disorders. The combination of an ensemble fusion-calling pipeline and a knowledge-based filtering strategy identified 67 clinically relevant fusions among our cohort (diagnostic yield of 29.3%), including RBPMS-MET, BCAN-NTRK1, and TRIM22-BRAF fusions. Following clinical confirmation and reporting in the patient’s medical record, both known and novel fusions provided medically meaningful information. Conclusions The EnFusion pipeline offers a streamlined approach to discover fusions in cancer, at higher levels of sensitivity and accuracy than single algorithm methods. Furthermore, this method accurately identifies driver fusions in pediatric cancer, providing clinical impact by contributing evidence to diagnosis and, when appropriate, indicating targeted therapies. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08094-z.
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Affiliation(s)
- Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - James R Fitch
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Kyle J Voytovich
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Adam C Herman
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Benjamin J Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Grant E Lammi
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Jeremy A Arbesfeld
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Saranga Wijeratne
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Samuel J Franklin
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Kathleen M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Natalie Bir
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Sean D McGrath
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Anthony R Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Amy Wetzel
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Katherine E Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Tracy A Bedrosian
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Kristen Leraas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Elizabeth A Varga
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Kristy Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Ajay Gupta
- Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children's Hospital, Columbus, OH, USA
| | - Bhuvana Setty
- Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Daniel R Boué
- Department of Pathology, The Ohio State University, Columbus, OH, USA.,Department of Pathology, Nationwide Children's Hospital, Columbus, OH, USA
| | - Jeffrey R Leonard
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA.,Section of Neurosurgery, Nationwide Children's Hospital, Columbus, OH, USA
| | - Jonathan L Finlay
- Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Mohamed S Abdelbaki
- Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Diana S Osorio
- Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Selene C Koo
- Department of Pathology, The Ohio State University, Columbus, OH, USA.,Department of Pathology, Nationwide Children's Hospital, Columbus, OH, USA
| | - Daniel C Koboldt
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Alex H Wagner
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA.,Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Ann-Kathrin Eisfeld
- Division of Hematology, The Ohio State University, Columbus, OH, USA.,Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University, Columbus, OH, USA.,The Ohio State Comprehensive Cancer Center, Columbus, OH, USA
| | - Krzysztof Mrózek
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University, Columbus, OH, USA.,The Ohio State Comprehensive Cancer Center, Columbus, OH, USA
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA.,Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA. .,Department of Pediatrics, The Ohio State University, Columbus, OH, USA.
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27
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Balan J, Jenkinson G, Nair A, Saha N, Koganti T, Voss J, Zysk C, Barr Fritcher EG, Ross CA, Giannini C, Raghunathan A, Kipp BR, Jenkins R, Ida C, Halling KC, Blackburn PR, Dasari S, Oliver GR, Klee EW. SeekFusion - A Clinically Validated Fusion Transcript Detection Pipeline for PCR-Based Next-Generation Sequencing of RNA. Front Genet 2021; 12:739054. [PMID: 34745213 PMCID: PMC8569241 DOI: 10.3389/fgene.2021.739054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/24/2021] [Indexed: 11/13/2022] Open
Abstract
Detecting gene fusions involving driver oncogenes is pivotal in clinical diagnosis and treatment of cancer patients. Recent developments in next-generation sequencing (NGS) technologies have enabled improved assays for bioinformatics-based gene fusions detection. In clinical applications, where a small number of fusions are clinically actionable, targeted polymerase chain reaction (PCR)-based NGS chemistries, such as the QIAseq RNAscan assay, aim to improve accuracy compared to standard RNA sequencing. Existing informatics methods for gene fusion detection in NGS-based RNA sequencing assays traditionally use a transcriptome-based spliced alignment approach or a de-novo assembly approach. Transcriptome-based spliced alignment methods face challenges with short read mapping yielding low quality alignments. De-novo assembly-based methods yield longer contigs from short reads that can be more sensitive for genomic rearrangements, but face performance and scalability challenges. Consequently, there exists a need for a method to efficiently and accurately detect fusions in targeted PCR-based NGS chemistries. We describe SeekFusion, a highly accurate and computationally efficient pipeline enabling identification of gene fusions from PCR-based NGS chemistries. Utilizing biological samples processed with the QIAseq RNAscan assay and in-silico simulated data we demonstrate that SeekFusion gene fusion detection accuracy outperforms popular existing methods such as STAR-Fusion, TOPHAT-Fusion and JAFFA-hybrid. We also present results from 4,484 patient samples tested for neurological tumors and sarcoma, encompassing details on some novel fusions identified.
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Affiliation(s)
| | - Garrett Jenkinson
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Asha Nair
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Neiladri Saha
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Tejaswi Koganti
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Jesse Voss
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, United States
| | - Christopher Zysk
- Applied Genomics Division, Perkin Elmer, Waltham, MA, United States
| | | | - Christian A Ross
- Information Technology, Mayo Clinic, Rochester, MN, United States
| | - Caterina Giannini
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, United States
| | - Aditya Raghunathan
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, United States
| | - Benjamin R Kipp
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, United States
| | - Robert Jenkins
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, United States
| | - Cris Ida
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, United States
| | - Kevin C Halling
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, United States
| | - Patrick R Blackburn
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Surendra Dasari
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Gavin R Oliver
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Eric W Klee
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
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28
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Re-evaluating tumors of purported specialized prostatic stromal origin reveals molecular heterogeneity, including non-recurring gene fusions characteristic of uterine and soft tissue sarcoma subtypes. Mod Pathol 2021; 34:1763-1779. [PMID: 33986460 DOI: 10.1038/s41379-021-00818-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 12/14/2022]
Abstract
Tumors of purported specialized prostatic stromal origin comprise prostatic stromal sarcomas (PSS) and stromal tumors of uncertain malignant potential (STUMP). Prior studies have described their clinicopathologic characteristics, but the molecular features remain incompletely understood. Moreover, these neoplasms are morphologically heterogeneous and the lack of specific adjunctive markers of prostatic stromal lineage make precise definition more difficult, leading some to question whether they represent a specific tumor type. In this study, we used next-generation DNA and RNA sequencing to profile 25 primary prostatic mesenchymal neoplasms of possible specialized prostatic stromal origin, including cases originally diagnosed as PSS (11) and STUMP (14). Morphologically, the series comprised 20 cases with solid architecture (11 PSS and 9 STUMP) and 5 cases with phyllodes-like growth pattern (all STUMP). Combined DNA and RNA sequencing results demonstrated that 19/22 (86%) cases that underwent successful sequencing (either DNA or RNA) harbored pathogenic somatic variants. Except for TP53 alterations (6 cases), ATRX mutations (2 cases), and a few copy number variants (-13q, -14q, -16q and +8/8p), the findings were largely nonrecurrent. Eight gene rearrangements were found, and 4 (NAB2-STAT6, JAZF1-SUZ12, TPM3-NTRK1 and BCOR-MAML3) were useful for reclassification of the cases as specific entities. The present study shows that mesenchymal neoplasms of the prostate are morphologically and molecularly heterogeneous and include neoplasms that harbor genetic aberrations seen in specific mesenchymal tumors arising in other anatomic sites, including soft tissue and the uterus. These data suggest that tumors of purported specialized prostatic stromal origin may perhaps not represent a single diagnostic entity or specific disease group and that alternative diagnoses should be carefully considered.
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29
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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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30
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Lu B, Jiang R, Xie B, Wu W, Zhao Y. Fusion genes in gynecologic tumors: the occurrence, molecular mechanism and prospect for therapy. Cell Death Dis 2021; 12:783. [PMID: 34381020 PMCID: PMC8357806 DOI: 10.1038/s41419-021-04065-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/12/2022]
Abstract
Gene fusions are thought to be driver mutations in multiple cancers and are an important factor for poor patient prognosis. Most of them appear in specific cancers, thus satisfactory strategies can be developed for the precise treatment of these types of cancer. Currently, there are few targeted drugs to treat gynecologic tumors, and patients with gynecologic cancer often have a poor prognosis because of tumor progression or recurrence. With the application of massively parallel sequencing, a large number of fusion genes have been discovered in gynecologic tumors, and some fusions have been confirmed to be involved in the biological process of tumor progression. To this end, the present article reviews the current research status of all confirmed fusion genes in gynecologic tumors, including their rearrangement mechanism and frequency in ovarian cancer, endometrial cancer, endometrial stromal sarcoma, and other types of uterine tumors. We also describe the mechanisms by which fusion genes are generated and their oncogenic mechanism. Finally, we discuss the prospect of fusion genes as therapeutic targets in gynecologic tumors.
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Affiliation(s)
- Bingfeng Lu
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ruqi Jiang
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bumin Xie
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wu Wu
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yang Zhao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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31
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Downes CEJ, McClure BJ, Bruning JB, Page E, Breen J, Rehn J, Yeung DT, White DL. Acquired JAK2 mutations confer resistance to JAK inhibitors in cell models of acute lymphoblastic leukemia. NPJ Precis Oncol 2021; 5:75. [PMID: 34376782 PMCID: PMC8355279 DOI: 10.1038/s41698-021-00215-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/20/2021] [Indexed: 11/24/2022] Open
Abstract
Ruxolitinib (rux) Phase II clinical trials are underway for the treatment of high-risk JAK2-rearranged (JAK2r) B-cell acute lymphoblastic leukemia (B-ALL). Treatment resistance to targeted inhibitors in other settings is common; elucidating potential mechanisms of rux resistance in JAK2r B-ALL will enable development of therapeutic strategies to overcome or avert resistance. We generated a murine pro-B cell model of ATF7IP-JAK2 with acquired resistance to multiple type-I JAK inhibitors. Resistance was associated with mutations within the JAK2 ATP/rux binding site, including a JAK2 p.G993A mutation. Using in vitro models of JAK2r B-ALL, JAK2 p.G993A conferred resistance to six type-I JAK inhibitors and the type-II JAK inhibitor, CHZ-868. Using computational modeling, we postulate that JAK2 p.G993A enabled JAK2 activation in the presence of drug binding through a unique resistance mechanism that modulates the mobility of the conserved JAK2 activation loop. This study highlights the importance of monitoring mutation emergence and may inform future drug design and the development of therapeutic strategies for this high-risk patient cohort.
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Affiliation(s)
- Charlotte E J Downes
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Barbara J McClure
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, Australia
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - John B Bruning
- Institute of Photonics and Advanced Sensing, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Elyse Page
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - James Breen
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Computational and Systems Biology Program, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, Australia
- Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Jacqueline Rehn
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, Australia
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - David T Yeung
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, Australia
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, SA, Australia
| | - Deborah L White
- Cancer Program, Precision Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, Australia.
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia.
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia.
- Australian Genomics Health Alliance (AGHA), The Murdoch Children's Research Institute, Parkville, VIC, Australia.
- Australian and New Zealand Children's Oncology Group (ANZCHOG), Clayton, VIC, Australia.
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32
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Singh S, Li H. Comparative study of bioinformatic tools for the identification of chimeric RNAs from RNA Sequencing. RNA Biol 2021; 18:254-267. [PMID: 34142643 DOI: 10.1080/15476286.2021.1940047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Chimeric RNAs are gaining more and more attention as they have broad implications in both cancer and normal physiology. To date, over 40 chimeric RNA prediction methods have been developed to facilitate their identification from RNA sequencing data. However, a limited number of studies have been conducted to compare the performance of these tools; additionally, previous studies have become outdated as more software tools have been developed within the last three years. In this study, we benchmarked 16 chimeric RNA prediction software, including seven top performers in previous benchmarking studies, and nine that were recently developed. We used two simulated and two real RNA-Seq datasets, compared the 16 tools for their sensitivity, positive prediction value (PPV), F-measure, and also documented the computational requirements (time and memory). We noticed that none of the tools are inclusive, and their performance varies depending on the dataset and objects. To increase the detection of true positive events, we also evaluated the pair-wise combination of these methods to suggest the best combination for sensitivity and F-measure. In addition, we compared the performance of the tools for the identification of three classes (read-through, inter-chromosomal and intra-others) of chimeric RNAs. Finally, we performed TOPSIS analyses and ranked the weighted performance of the 16 tools.
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Affiliation(s)
- Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, USA.,Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, USA
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Dickson BC, Antonescu CR, Demicco EG, Leong I, Anderson ND, Swanson D, Zhang L, Fletcher CD, Hornick JL. Hybrid schwannoma-perineurioma frequently harbors VGLL3 rearrangement. Mod Pathol 2021; 34:1116-1124. [PMID: 33649458 PMCID: PMC8154639 DOI: 10.1038/s41379-021-00783-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 12/11/2022]
Abstract
Benign peripheral nerve tumors include schwannoma, neurofibroma, and perineurioma, as well as a recently recognized group of tumors with dual patterns of differentiation. The molecular pathogenesis of these so-called "hybrid" tumors remains poorly understood. Following identification of a novel CHD7-VGLL3 fusion gene in a hybrid schwannoma-perineurioma, we evaluated an expanded cohort of this tumor-type-as well as tumors with VGLL3 rearrangement identified from a curated molecular database-to characterize the prevalence of fusion genes among these tumors. Eighteen tumors met the inclusion criteria for this study. RNA sequencing identified VGLL3 rearrangement in 14 of these cases; the partner genes included CHD7 (ten cases), CHD9 (two cases), and MAMLD1 (two cases). Two cases possessed altogether unrelated fusions, including: DST-BRAF and SQSTM1-CDX1 fusion genes. Finally, two cases lacked identifiable fusion products. These findings highlight the molecular diversity of these neoplasms, with frequent rearrangement of VGLL3. More importantly, despite their dual pattern of differentiation, our results reveal the pathogenesis of hybrid schwannoma-perineurioma is unrelated to conventional schwannoma and perineurioma, thereby implying this tumor represents an altogether pathologically distinct entity.
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Affiliation(s)
- Brendan C. Dickson
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, 600 University Ave, Toronto, Ontario, Canada M5G 1X5; Department of Pathobiology and Laboratory Medicine, University of Toronto, Toronto, Ontario, Canada,Corresponding Authors: Brendan C. Dickson, MD, MSc, Pathology & Laboratory Medicine, Mount Sinai Hospital, 600 University Ave, Suite 6.500.12.5, Toronto, Ontario, Canada M5G 1X5, P: (416) 586-4800 / F: (416) 586-8628, ; Jason L. Hornick, MD, PhD, Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA 02115, P: (617) 525-7257 / F: (617) 566-3897,
| | | | - Elizabeth G. Demicco
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, 600 University Ave, Toronto, Ontario, Canada M5G 1X5; Department of Pathobiology and Laboratory Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Iona Leong
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, 600 University Ave, Toronto, Ontario, Canada M5G 1X5; Department of Pathobiology and Laboratory Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Nathaniel D. Anderson
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - David Swanson
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, 600 University Ave, Toronto, Ontario, Canada M5G 1X5; Department of Pathobiology and Laboratory Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lei Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher D.M. Fletcher
- Department of Pathology, Brigham and Women’s Hospital, 75 Francis Street, Boston, Massachusetts, USA, 02115; Harvard Medical School, Boston, Massachusetts, USA
| | - Jason L. Hornick
- Department of Pathology, Brigham and Women’s Hospital, 75 Francis Street, Boston, Massachusetts, USA, 02115; Harvard Medical School, Boston, Massachusetts, USA,Corresponding Authors: Brendan C. Dickson, MD, MSc, Pathology & Laboratory Medicine, Mount Sinai Hospital, 600 University Ave, Suite 6.500.12.5, Toronto, Ontario, Canada M5G 1X5, P: (416) 586-4800 / F: (416) 586-8628, ; Jason L. Hornick, MD, PhD, Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA 02115, P: (617) 525-7257 / F: (617) 566-3897,
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34
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Challenging conventional karyotyping by next-generation karyotyping in 281 intensively treated patients with AML. Blood Adv 2021; 5:1003-1016. [PMID: 33591326 DOI: 10.1182/bloodadvances.2020002517] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 12/10/2020] [Indexed: 12/19/2022] Open
Abstract
Although copy number alterations (CNAs) and translocations constitute the backbone of the diagnosis and prognostication of acute myeloid leukemia (AML), techniques used for their assessment in routine diagnostics have not been reconsidered for decades. We used a combination of 2 next-generation sequencing-based techniques to challenge the currently recommended conventional cytogenetic analysis (CCA), comparing the approaches in a series of 281 intensively treated patients with AML. Shallow whole-genome sequencing (sWGS) outperformed CCA in detecting European Leukemia Net (ELN)-defining CNAs and showed that CCA overestimated monosomies and suboptimally reported karyotype complexity. Still, the concordance between CCA and sWGS for all ELN CNA-related criteria was 94%. Moreover, using in silico dilution, we showed that 1 million reads per patient would be enough to accurately assess ELN-defining CNAs. Total genomic loss, defined as a total loss ≥200 Mb by sWGS, was found to be a better marker for genetic complexity and poor prognosis compared with the CCA-based definition of complex karyotype. For fusion detection, the concordance between CCA and whole-transcriptome sequencing (WTS) was 99%. WTS had better sensitivity in identifying inv(16) and KMT2A rearrangements while showing limitations in detecting lowly expressed PML-RARA fusions. Ligation-dependent reverse transcription polymerase chain reaction was used for validation and was shown to be a fast and reliable method for fusion detection. We conclude that a next-generation sequencing-based approach can replace conventional CCA for karyotyping, provided that efforts are made to cover lowly expressed fusion transcripts.
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35
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Thomas C, Soschinski P, Zwaig M, Oikonomopoulos S, Okonechnikov K, Pajtler KW, Sill M, Schweizer L, Koch A, Neumann J, Schüller U, Sahm F, Rauschenbach L, Keyvani K, Proescholdt M, Riemenschneider MJ, Segewiß J, Ruckert C, Grauer O, Monoranu CM, Lamszus K, Patrizi A, Kordes U, Siebert R, Kool M, Ragoussis J, Foulkes WD, Paulus W, Rivera B, Hasselblatt M. The genetic landscape of choroid plexus tumors in children and adults. Neuro Oncol 2021; 23:650-660. [PMID: 33249490 DOI: 10.1093/neuonc/noaa267] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Choroid plexus tumors (CPTs) are intraventricular brain tumors predominantly arising in children but also affecting adults. In most cases, driver mutations have not been identified, although there are reports of frequent chromosome-wide copy-number alterations and TP53 mutations, especially in choroid plexus carcinomas (CPCs). METHODS DNA methylation profiling and RNA-sequencing was performed in a series of 47 CPTs. Samples comprised 35 choroid plexus papillomas (CPPs), 6 atypical choroid plexus papillomas (aCPPs) and 6 CPCs plus three recurrences thereof. Targeted TP53 and TERT promotor sequencing was performed in all samples. Whole exome sequencing (WES) and linked-read whole genome sequencing (WGS) was performed in 25 and 4 samples, respectively. RESULTS Tumors comprised the molecular subgroups "pediatric A" (N=11), "pediatric B" (N=12) and "adult" (N=27). Copy-number alterations mainly represented whole-chromosomal alterations with subgroup-specific enrichments (gains of Chr1, 2 and 21q in "pediatric B" and gains of Chr5 and 9 and loss of Chr21q in "adult"). RNA sequencing yielded a novel CCDC47-PRKCA fusion transcript in one adult choroid plexus papilloma patient with aggressive clinical course; an underlying Chr17 inversion was demonstrated by linked-read WGS. WES and targeted sequencing showed TP53 mutations in 7/47 CPTs (15%), five of which were children. On the contrary, TERT promoter mutations were encountered in 7/28 adult patients (25%) and associated with shorter progression-free survival (log-rank test, p=0.015). CONCLUSION Pediatric CPTs lack recurrent driver alterations except for TP53, whereas CPTs in adults show TERT promoter mutations or a novel CCDC47-PRKCA gene fusion, being associated with a more unfavorable clinical course.
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Affiliation(s)
- Christian Thomas
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Patrick Soschinski
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Melissa Zwaig
- McGill University Genome Centre, Department of Human Genetics, McGill University, Montreal, Canada
| | - Spyridon Oikonomopoulos
- McGill University Genome Centre, Department of Human Genetics, McGill University, Montreal, Canada
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, University Hospital, Heidelberg, Germany
| | - Martin Sill
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
| | - Leonille Schweizer
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany, Partner Site Charité Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Arend Koch
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany, Partner Site Charité Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Julia Neumann
- Department of Neuropathology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Department of Neuropathology, University Hospital Hamburg-Eppendorf, Hamburg, Germany.,Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Laurèl Rauschenbach
- Department of Neurosurgery and Spine Surgery, University Hospital Essen, University Duisburg-Essen, Essen, Germany.,DKFZ Division Translational Neurooncology, DKTK partner site, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Kathy Keyvani
- Institute of Neuropathology, University of Duisburg-Essen, Essen, Germany
| | - Martin Proescholdt
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Neurosurgery, Regensburg University Hospital, Regensburg, Germany
| | | | - Jochen Segewiß
- Institute of Human Genetics, University Hospital Münster, Münster, Germany
| | - Christian Ruckert
- Institute of Human Genetics, University Hospital Münster, Münster, Germany
| | - Oliver Grauer
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | | | - Katrin Lamszus
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Annarita Patrizi
- Schaller Research Group Leader at the German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Uwe Kordes
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany.,Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Jiannis Ragoussis
- McGill University Genome Centre, Department of Human Genetics, McGill University, Montreal, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Werner Paulus
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Barbara Rivera
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
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Apostolides M, Jiang Y, Husić M, Siddaway R, Hawkins C, Turinsky AL, Brudno M, Ramani AK. MetaFusion: A high-confidence metacaller for filtering and prioritizing RNA-seq gene fusion candidates. Bioinformatics 2021; 37:3144-3151. [PMID: 33944895 DOI: 10.1093/bioinformatics/btab249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 03/04/2021] [Accepted: 05/03/2021] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Current fusion detection tools use diverse calling approaches and provide varying results, making selection of the appropriate tool challenging. Ensemble fusion calling techniques appear promising; however, current options have limited accessibility and function. RESULTS MetaFusion is a flexible meta-calling tool that amalgamates outputs from any number of fusion callers. Individual caller results are standardized by conversion into the new file type Common Fusion Format (CFF). Calls are annotated, merged using graph clustering, filtered, and ranked to provide a final output of high confidence candidates. MetaFusion consistently achieves higher precision and recall than individual callers on real and simulated datasets, and reaches up to 100% precision, indicating that ensemble calling is imperative for high confidence results. MetaFusion uses FusionAnnotator to annotate calls with information from cancer fusion databases, and is provided with a benchmarking toolkit to calibrate new callers. AVAILABILITY MetaFusion is freely available at https://github.com/ccmbioinfo/MetaFusion. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Michael Apostolides
- Centre for Computational Medicine, The Hospital For Sick Children, Toronto, ON, Canada
| | - Yue Jiang
- Centre for Computational Medicine, The Hospital For Sick Children, Toronto, ON, Canada
| | - Mia Husić
- Centre for Computational Medicine, The Hospital For Sick Children, Toronto, ON, Canada
| | - Robert Siddaway
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Cynthia Hawkins
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Division of Pathology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Andrei L Turinsky
- Centre for Computational Medicine, The Hospital For Sick Children, Toronto, ON, Canada
| | - Michael Brudno
- Centre for Computational Medicine, The Hospital For Sick Children, Toronto, ON, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada.,University Health Network, Toronto, ON, Canada
| | - Arun K Ramani
- Centre for Computational Medicine, The Hospital For Sick Children, Toronto, ON, Canada
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Newtson A, Reyes H, Devor EJ, Goodheart MJ, Bosquet JG. Identification of Novel Fusion Transcripts in High Grade Serous Ovarian Cancer. Int J Mol Sci 2021; 22:ijms22094791. [PMID: 33946483 PMCID: PMC8125626 DOI: 10.3390/ijms22094791] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/11/2022] Open
Abstract
Fusion genes are structural chromosomal rearrangements resulting in the exchange of DNA sequences between genes. This results in the formation of a new combined gene. They have been implicated in carcinogenesis in a number of different cancers, though they have been understudied in high grade serous ovarian cancer. This study used high throughput tools to compare the transcriptome of high grade serous ovarian cancer and normal fallopian tubes in the interest of identifying unique fusion transcripts within each group. Indeed, we found that there were significantly more fusion transcripts in the cancer samples relative to the normal fallopian tubes. Following this, the role of fusion transcripts in chemo-response and overall survival was investigated. This led to the identification of fusion transcripts significantly associated with overall survival. Validation was performed with different analytical platforms and different algorithms to find fusion transcripts.
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Affiliation(s)
- Andreea Newtson
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA; (M.J.G.); (J.G.B.)
- Correspondence: ; Tel.: +1-319-356-2015
| | - Henry Reyes
- Department of Obstetrics and Gynecology, University of Buffalo, Buffalo, NY 14260, USA;
| | - Eric J. Devor
- Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA;
- Department of Obstetrics and Gynecology, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
| | - Michael J. Goodheart
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA; (M.J.G.); (J.G.B.)
- Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA;
| | - Jesus Gonzalez Bosquet
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA; (M.J.G.); (J.G.B.)
- Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA;
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Liu Z, Chen X, Roberts R, Huang R, Mikailov M, Tong W. Unraveling Gene Fusions for Drug Repositioning in High-Risk Neuroblastoma. Front Pharmacol 2021; 12:608778. [PMID: 33967751 PMCID: PMC8105087 DOI: 10.3389/fphar.2021.608778] [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: 09/21/2020] [Accepted: 03/23/2021] [Indexed: 11/13/2022] Open
Abstract
High-risk neuroblastoma (NB) remains a significant therapeutic challenge facing current pediatric oncology patients. Structural variants such as gene fusions have shown an initial promise in enhancing mechanistic understanding of NB and improving survival rates. In this study, we performed a comprehensive in silico investigation on the translational ability of gene fusions for patient stratification and treatment development for high-risk NB patients. Specifically, three state-of-the-art gene fusion detection algorithms, including ChimeraScan, SOAPfuse, and TopHat-Fusion, were employed to identify the fusion transcripts in a RNA-seq data set of 498 neuroblastoma patients. Then, the 176 high-risk patients were further stratified into four different subgroups based on gene fusion profiles. Furthermore, Kaplan-Meier survival analysis was performed, and differentially expressed genes (DEGs) for the redefined high-risk group were extracted and functionally analyzed. Finally, repositioning candidates were enriched in each patient subgroup with drug transcriptomic profiles from the LINCS L1000 Connectivity Map. We found the number of identified gene fusions was increased from clinical the low-risk stage to the high-risk stage. Although the technical concordance of fusion detection algorithms was suboptimal, they have a similar biological relevance concerning perturbed pathways and regulated DEGs. The gene fusion profiles could be utilized to redefine high-risk patient subgroups with significant onset age of NB, which yielded the improved survival curves (Log-rank p value ≤ 0.05). Out of 48 enriched repositioning candidates, 45 (93.8%) have antitumor potency, and 24 (50%) were confirmed with either on-going clinical trials or literature reports. The gene fusion profiles have a discrimination power for redefining patient subgroups in high-risk NB and facilitate precision medicine-based drug repositioning implementation.
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Affiliation(s)
- Zhichao Liu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, United States
| | - Xi Chen
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, United States
| | - Ruth Roberts
- ApconiX, BioHub at Alderley Park, Alderley Edge, United Kingdom.,University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Mike Mikailov
- Office of Science and Engineering Labs, Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, MD, United States
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, United States
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Morton LM, Karyadi DM, Stewart C, Bogdanova TI, Dawson ET, Steinberg MK, Dai J, Hartley SW, Schonfeld SJ, Sampson JN, Maruvka YE, Kapoor V, Ramsden DA, Carvajal-Garcia J, Perou CM, Parker JS, Krznaric M, Yeager M, Boland JF, Hutchinson A, Hicks BD, Dagnall CL, Gastier-Foster JM, Bowen J, Lee O, Machiela MJ, Cahoon EK, Brenner AV, Mabuchi K, Drozdovitch V, Masiuk S, Chepurny M, Zurnadzhy LY, Hatch M, Berrington de Gonzalez A, Thomas GA, Tronko MD, Getz G, Chanock SJ. Radiation-related genomic profile of papillary thyroid carcinoma after the Chernobyl accident. Science 2021; 372:science.abg2538. [PMID: 33888599 DOI: 10.1126/science.abg2538] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/25/2021] [Indexed: 12/13/2022]
Abstract
The 1986 Chernobyl nuclear power plant accident increased papillary thyroid carcinoma (PTC) incidence in surrounding regions, particularly for radioactive iodine (131I)-exposed children. We analyzed genomic, transcriptomic, and epigenomic characteristics of 440 PTCs from Ukraine (from 359 individuals with estimated childhood 131I exposure and 81 unexposed children born after 1986). PTCs displayed radiation dose-dependent enrichment of fusion drivers, nearly all in the mitogen-activated protein kinase pathway, and increases in small deletions and simple/balanced structural variants that were clonal and bore hallmarks of nonhomologous end-joining repair. Radiation-related genomic alterations were more pronounced for individuals who were younger at exposure. Transcriptomic and epigenomic features were strongly associated with driver events but not radiation dose. Our results point to DNA double-strand breaks as early carcinogenic events that subsequently enable PTC growth after environmental radiation exposure.
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Affiliation(s)
- Lindsay M Morton
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.
| | - Danielle M Karyadi
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Chip Stewart
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tetiana I Bogdanova
- Laboratory of Morphology of the Endocrine System, V. P. Komisarenko Institute of Endocrinology and Metabolism of the National Academy of Medical Sciences of Ukraine, Kyiv 04114, Ukraine
| | - Eric T Dawson
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.,Nvidia Corporation, Santa Clara, CA 95051, USA
| | - Mia K Steinberg
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Jieqiong Dai
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Stephen W Hartley
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sara J Schonfeld
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Joshua N Sampson
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Yosef E Maruvka
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vidushi Kapoor
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Dale A Ramsden
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Juan Carvajal-Garcia
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Joel S Parker
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Marko Krznaric
- Department of Surgery and Cancer, Imperial College London, Charing Cross Hospital, London W6 8RF, UK
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Joseph F Boland
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Casey L Dagnall
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Julie M Gastier-Foster
- Nationwide Children's Hospital, Biospecimen Core Resource, Columbus, OH 43205, USA.,Departments of Pathology and Pediatrics, Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Jay Bowen
- Nationwide Children's Hospital, Biospecimen Core Resource, Columbus, OH 43205, USA
| | - Olivia Lee
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mitchell J Machiela
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Elizabeth K Cahoon
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Alina V Brenner
- Radiation Effects Research Foundation, Hiroshima 732-0815, Japan
| | - Kiyohiko Mabuchi
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Vladimir Drozdovitch
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sergii Masiuk
- Radiological Protection Laboratory, Institute of Radiation Hygiene and Epidemiology, National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine, Kyiv 04050, Ukraine
| | - Mykola Chepurny
- Radiological Protection Laboratory, Institute of Radiation Hygiene and Epidemiology, National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine, Kyiv 04050, Ukraine
| | - Liudmyla Yu Zurnadzhy
- Laboratory of Morphology of the Endocrine System, V. P. Komisarenko Institute of Endocrinology and Metabolism of the National Academy of Medical Sciences of Ukraine, Kyiv 04114, Ukraine
| | - Maureen Hatch
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Amy Berrington de Gonzalez
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Gerry A Thomas
- Department of Surgery and Cancer, Imperial College London, Charing Cross Hospital, London W6 8RF, UK
| | - Mykola D Tronko
- Department of Fundamental and Applied Problems of Endocrinology, V. P. Komisarenko Institute of Endocrinology and Metabolism of the National Academy of Medical Sciences of Ukraine, Kyiv 04114, Ukraine
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Center for Cancer Research and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Stephen J Chanock
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.
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40
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Qiu Q, Zhou Q, Luo A, Li X, Li K, Li W, Yu M, Amanullah M, Lu B, Lu W, Liu P, Lu Y. Integrated analysis of virus and host transcriptomes in cervical cancer in Asian and Western populations. Genomics 2021; 113:1554-1564. [PMID: 33785400 DOI: 10.1016/j.ygeno.2021.03.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 03/09/2021] [Accepted: 03/26/2021] [Indexed: 12/31/2022]
Abstract
Race may influence vulnerability to HPV variants in viral infection and perisistence. Integrated analysis of the virus and host transcriptomes from different populations provides an unprecedented opportunity to understand these racial disparities in the prevalence of HPV and cervical cancers. We performed RNA-Seq analysis of 90 tumors and 39 adjacent normal tissues from cervical cancer patients at Zhejiang University (ZJU) in China, and conducted a comparative analysis with RNA-Seq data of 286 cervical cancers from TCGA. We found a modestly higher rate of HPV positives and HPV integrations in TCGA than in ZJU. In addition to LINC00393 and HSPB3 as new common integration hotspots in both cohorts, we found new hotspots such as SH2D3C and CASC8 in TCGA, and SCGB1A1 and ABCA1 in ZJU. We described the first, to our knowledge, virus-transcriptome-based classification of cervical cancer associated with clinical outcome. Particularly, patients with expressed E5 performed better than those without E5 expression. However, the constituents of these virus-transcriptome-based tumor subtypes differ dramatically between the two cohorts. We further characterized the immune infiltration landscapes between different HPV statuses and revealed significantly elevated levels of regulatory T cells and M0 macrophages in HPV positive tumors, which were associated with poor prognosis. These findings increase our understanding of the racial disparities in the prevalence of HPV and its associated cervical cancers between the two cohorts, and also have important implications in the classification of tumor subtypes, prognosis, and anti-cancer immunotherapy in cervical cancer.
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Affiliation(s)
- Qiongzi Qiu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310002, China
| | - Qing Zhou
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310002, China
| | - Aoran Luo
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310002, China
| | - Xufan Li
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China
| | - Kezhen Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Wenfeng Li
- Department of Radiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Mengqian Yu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310002, China
| | - Md Amanullah
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310002, China
| | - Bingjian Lu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310002, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Weiguo Lu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310002, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310029, China.
| | - Pengyuan Liu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310029, China; Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Yan Lu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310002, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310029, China.
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41
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Landscape of Chimeric RNAs in Non-Cancerous Cells. Genes (Basel) 2021; 12:genes12040466. [PMID: 33805149 PMCID: PMC8064075 DOI: 10.3390/genes12040466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 11/21/2022] Open
Abstract
Gene fusions and their products (RNA and protein) have been traditionally recognized as unique features of cancer cells and are used as ideal biomarkers and drug targets for multiple cancer types. However, recent studies have demonstrated that chimeric RNAs generated by intergenic alternative splicing can also be found in normal cells and tissues. In this study, we aim to identify chimeric RNAs in different non-neoplastic cell lines and investigate the landscape and expression of these novel candidate chimeric RNAs. To do so, we used HEK-293T, HUVEC, and LO2 cell lines as models, performed paired-end RNA sequencing, and conducted analyses for chimeric RNA profiles. Several filtering criteria were applied, and the landscape of chimeric RNAs was characterized at multiple levels and from various angles. Further, we experimentally validated 17 chimeric RNAs from different classifications. Finally, we examined a number of validated chimeric RNAs in different cancer and non-cancer cells, including blood from healthy donors, and demonstrated their ubiquitous expression pattern.
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42
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Taniue K, Akimitsu N. Fusion Genes and RNAs in Cancer Development. Noncoding RNA 2021; 7:10. [PMID: 33557176 PMCID: PMC7931065 DOI: 10.3390/ncrna7010010] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 02/07/2023] Open
Abstract
Fusion RNAs are a hallmark of some cancers. They result either from chromosomal rearrangements or from splicing mechanisms that are non-chromosomal rearrangements. Chromosomal rearrangements that result in gene fusions are particularly prevalent in sarcomas and hematopoietic malignancies; they are also common in solid tumors. The splicing process can also give rise to more complex RNA patterns in cells. Gene fusions frequently affect tyrosine kinases, chromatin regulators, or transcription factors, and can cause constitutive activation, enhancement of downstream signaling, and tumor development, as major drivers of oncogenesis. In addition, some fusion RNAs have been shown to function as noncoding RNAs and to affect cancer progression. Fusion genes and RNAs will therefore become increasingly important as diagnostic and therapeutic targets for cancer development. Here, we discuss the function, biogenesis, detection, clinical relevance, and therapeutic implications of oncogenic fusion genes and RNAs in cancer development. Further understanding the molecular mechanisms that regulate how fusion RNAs form in cancers is critical to the development of therapeutic strategies against tumorigenesis.
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Affiliation(s)
- Kenzui Taniue
- Isotope Science Center, The University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Cancer Genomics and Precision Medicine, Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido 078-8510, Japan
| | - Nobuyoshi Akimitsu
- Isotope Science Center, The University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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43
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Pseudosarcomatous myofibroblastic proliferations of the urinary bladder are neoplasms characterized by recurrent FN1-ALK fusions. Mod Pathol 2021; 34:469-477. [PMID: 32908253 DOI: 10.1038/s41379-020-00670-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/21/2020] [Accepted: 08/21/2020] [Indexed: 11/08/2022]
Abstract
Pseudosarcomatous myofibroblastic proliferation is a descriptive term that designates a group of clinically indolent genitourinary lesions that most commonly arise in the urinary bladder. Given that pseudosarcomatous myofibroblastic proliferation may show morphologic overlap with inflammatory myofibroblastic tumor, the relationship, if any, between the two entities has been unclear. Moreover, pseudosarcomatous myofibroblastic proliferations are known to be positive for ALK immunohistochemistry in a subset of cases, although an inconsistent association with ALK rearrangement (ranging from 0 to 60%) has been reported. The objectives of this study were to determine the frequency of ALK rearrangement and to identify fusion partners using fluorescence in situ hybridization (FISH) and targeted RNA sequencing studies in a contemporary series of 30 pseudosarcomatous myofibroblastic proliferations of the urinary bladder, as well as to investigate ROS1 status by immunohistochemistry. ALK immunohistochemistry was positive in 70% (21/30) of pseudosarcomatous myofibroblastic proliferations; ROS1 immunohistochemistry was consistently negative (0/28). ALK rearrangements were detected by FISH in 86% (18/21) of cases, correlating with ALK immunohistochemical positivity in all but 3 cases. Of eight cases confirmed to be ALK rearranged by FISH, targeted RNA-sequencing detected FN1-ALK fusions in seven (88%) cases, which involved exons 20-26 of FN1 (5') and exon 18-19 of ALK (3'). In conclusion, ALK rearrangements are frequent in pseudosarcomatous myofibroblastic proliferations, typically involving exon 19, and FN1 appears to be a consistent fusion partner. Given the significant clinicopathologic differences between inflammatory myofibroblastic tumor and pseudosarcomatous myofibroblastic proliferation, our findings provide further support for classification of pseudosarcomatous myofibroblastic proliferation as a distinct clinicopathologic entity, and propose the alternate terminology "pseudosarcomatous myofibroblastic neoplasm of the genitourinary tract."
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44
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Liu Q, Hu Y, Stucky A, Fang L, Zhong JF, Wang K. LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing. BMC Genomics 2020; 21:793. [PMID: 33372596 PMCID: PMC7771079 DOI: 10.1186/s12864-020-07207-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 10/29/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Long-read RNA-Seq techniques can generate reads that encompass a large proportion or the entire mRNA/cDNA molecules, so they are expected to address inherited limitations of short-read RNA-Seq techniques that typically generate < 150 bp reads. However, there is a general lack of software tools for gene fusion detection from long-read RNA-seq data, which takes into account the high basecalling error rates and the presence of alignment errors. RESULTS In this study, we developed a fast computational tool, LongGF, to efficiently detect candidate gene fusions from long-read RNA-seq data, including cDNA sequencing data and direct mRNA sequencing data. We evaluated LongGF on tens of simulated long-read RNA-seq datasets, and demonstrated its superior performance in gene fusion detection. We also tested LongGF on a Nanopore direct mRNA sequencing dataset and a PacBio sequencing dataset generated on a mixture of 10 cancer cell lines, and found that LongGF achieved better performance to detect known gene fusions over existing computational tools. Furthermore, we tested LongGF on a Nanopore cDNA sequencing dataset on acute myeloid leukemia, and pinpointed the exact location of a translocation (previously known in cytogenetic resolution) in base resolution, which was further validated by Sanger sequencing. CONCLUSIONS In summary, LongGF will greatly facilitate the discovery of candidate gene fusion events from long-read RNA-Seq data, especially in cancer samples. LongGF is implemented in C++ and is available at https://github.com/WGLab/LongGF .
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Affiliation(s)
- Qian Liu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Yu Hu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Andres Stucky
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Li Fang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Jiang F Zhong
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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45
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Rao AA, Madejska AA, Pfeil J, Paten B, Salama SR, Haussler D. ProTECT-Prediction of T-Cell Epitopes for Cancer Therapy. Front Immunol 2020; 11:483296. [PMID: 33244314 PMCID: PMC7683782 DOI: 10.3389/fimmu.2020.483296] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 10/13/2020] [Indexed: 12/21/2022] Open
Abstract
Somatic mutations in cancers affecting protein coding genes can give rise to potentially therapeutic neoepitopes. These neoepitopes can guide Adoptive Cell Therapies and Peptide- and RNA-based Neoepitope Vaccines to selectively target tumor cells using autologous patient cytotoxic T-cells. Currently, researchers have to independently align their data, call somatic mutations and haplotype the patient’s HLA to use existing neoepitope prediction tools. We present ProTECT, a fully automated, reproducible, scalable, and efficient end-to-end analysis pipeline to identify and rank therapeutically relevant tumor neoepitopes in terms of potential immunogenicity starting directly from raw patient sequencing data, or from pre-processed data. The ProTECT pipeline encompasses alignment, HLA haplotyping, mutation calling (single nucleotide variants, short insertions and deletions, and gene fusions), peptide:MHC binding prediction, and ranking of final candidates. We demonstrate the scalability, efficiency, and utility of ProTECT on 326 samples from the TCGA Prostate Adenocarcinoma cohort, identifying recurrent potential neoepitopes from TMPRSS2-ERG fusions, and from SNVs in SPOP. We also compare ProTECT with results from published tools. ProTECT can be run on a standalone computer, a local cluster, or on a compute cloud using a Mesos backend. ProTECT is highly scalable and can process TCGA data in under 30 min per sample (on average) when run in large batches. ProTECT is freely available at https://www.github.com/BD2KGenomics/protect.
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Affiliation(s)
- Arjun A Rao
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States.,Computational Genomics Lab, University of California, Santa Cruz, Santa Cruz, CA, United States.,UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Ada A Madejska
- Computational Genomics Lab, University of California, Santa Cruz, Santa Cruz, CA, United States.,Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, Santa Cruz, CA, United States
| | - Jacob Pfeil
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States.,Computational Genomics Lab, University of California, Santa Cruz, Santa Cruz, CA, United States.,UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Benedict Paten
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States.,Computational Genomics Lab, University of California, Santa Cruz, Santa Cruz, CA, United States.,UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Sofie R Salama
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States.,UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, United States.,Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - David Haussler
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States.,Computational Genomics Lab, University of California, Santa Cruz, Santa Cruz, CA, United States.,UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, United States.,Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, United States
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46
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Koboldt DC. Best practices for variant calling in clinical sequencing. Genome Med 2020; 12:91. [PMID: 33106175 PMCID: PMC7586657 DOI: 10.1186/s13073-020-00791-w] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 10/08/2020] [Indexed: 02/08/2023] Open
Abstract
Next-generation sequencing technologies have enabled a dramatic expansion of clinical genetic testing both for inherited conditions and diseases such as cancer. Accurate variant calling in NGS data is a critical step upon which virtually all downstream analysis and interpretation processes rely. Just as NGS technologies have evolved considerably over the past 10 years, so too have the software tools and approaches for detecting sequence variants in clinical samples. In this review, I discuss the current best practices for variant calling in clinical sequencing studies, with a particular emphasis on trio sequencing for inherited disorders and somatic mutation detection in cancer patients. I describe the relative strengths and weaknesses of panel, exome, and whole-genome sequencing for variant detection. Recommended tools and strategies for calling variants of different classes are also provided, along with guidance on variant review, validation, and benchmarking to ensure optimal performance. Although NGS technologies are continually evolving, and new capabilities (such as long-read single-molecule sequencing) are emerging, the “best practice” principles in this review should be relevant to clinical variant calling in the long term.
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Affiliation(s)
- Daniel C Koboldt
- Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, OH, USA. .,Department of Pediatrics, The Ohio State University, Columbus, OH, USA.
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47
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Sakamoto Y, Xu L, Seki M, Yokoyama TT, Kasahara M, Kashima Y, Ohashi A, Shimada Y, Motoi N, Tsuchihara K, Kobayashi SS, Kohno T, Shiraishi Y, Suzuki A, Suzuki Y. Long-read sequencing for non-small-cell lung cancer genomes. Genome Res 2020; 30:1243-1257. [PMID: 32887687 PMCID: PMC7545141 DOI: 10.1101/gr.261941.120] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 04/09/2020] [Indexed: 12/23/2022]
Abstract
Here, we report the application of a long-read sequencer, PromethION, for analyzing human cancer genomes. We first conducted whole-genome sequencing on lung cancer cell lines. We found that it is possible to genotype known cancerous mutations, such as point mutations. We also found that long-read sequencing is particularly useful for precisely identifying and characterizing structural aberrations, such as large deletions, gene fusions, and other chromosomal rearrangements. In addition, we identified several medium-sized structural aberrations consisting of complex combinations of local duplications, inversions, and microdeletions. These complex mutations occurred even in key cancer-related genes, such as STK11, NF1, SMARCA4, and PTEN. The biological relevance of those mutations was further revealed by epigenome, transcriptome, and protein analyses of the affected signaling pathways. Such structural aberrations were also found in clinical lung adenocarcinoma specimens. Those structural aberrations were unlikely to be reliably detected by conventional short-read sequencing. Therefore, long-read sequencing may contribute to understanding the molecular etiology of patients for whom causative cancerous mutations remain unknown and therapeutic strategies are elusive.
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Affiliation(s)
- Yoshitaka Sakamoto
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Liu Xu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Toshiyuki T Yokoyama
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Masahiro Kasahara
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Yukie Kashima
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba 277-8577, Japan.,Division of Translational Genomics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba 277-8577, Japan
| | - Akihiro Ohashi
- Division of Translational Genomics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba 277-8577, Japan
| | - Yoko Shimada
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Noriko Motoi
- Department of Pathology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Katsuya Tsuchihara
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba 277-8577, Japan
| | - Susumu S Kobayashi
- Division of Translational Genomics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba 277-8577, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Yuichi Shiraishi
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Ayako Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan.,Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba 277-8577, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
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48
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Zou Y, Turashvili G, Soslow RA, Park KJ, Croce S, McCluggage WG, Stewart CJR, Oda Y, Oliva E, Young RH, Da Cruz Paula A, Dessources K, Ashley CW, Hensley ML, Yip S, Weigelt B, Benayed R, Antonescu CR, Lee CH, Chiang S. High-grade transformation of low-grade endometrial stromal sarcomas lacking YWHAE and BCOR genetic abnormalities. Mod Pathol 2020; 33:1861-1870. [PMID: 32317704 PMCID: PMC8288077 DOI: 10.1038/s41379-020-0535-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/19/2020] [Accepted: 03/19/2020] [Indexed: 01/27/2023]
Abstract
High-grade histologic transformation of low-grade endometrial stromal sarcoma (LGESS) is rare. Here, we describe the clinicopathologic features and gene fusion status of 12 cases (11 primary uterine corpus and 1 primary vaginal), 11 diagnosed prospectively from 2016, and 1 retrospectively collected. Targeted RNA sequencing and/or fluorescence in situ hybridization was employed in all cases. High-grade transformation was seen at the time of initial diagnosis in eight patients and at the time of recurrence in four patients, 4-11 years after initial diagnosis of LGESS. High-grade morphology consisted of generally uniform population of round to epithelioid cells with enlarged nuclei one to two times larger than a lymphocyte, visible nucleoli, and increased mitotic index (range, 6-30; median, 16 per 10 high-power fields); there was often an associated sclerotic and/or myxoid stroma. Estrogen receptor, progesterone receptor, and CD10 expression was absent or significantly decreased (compared with the low-grade component) in the high-grade foci of five tumors. One tumor demonstrated positive (diffuse and strong) cyclin D1 and BCOR staining. p53 staining was wild type in both components of all eight tumors tested. JAZF1-SUZ12 (n = 6), JAZF1-PHF1 (n = 3), EPC1-PHF1, (n = 1), or BRD8-PHF1 (n = 1) fusions were detected in 11 tumors; no fusions were found in one by targeted RNA sequencing. Patients presented with FIGO stages I (n = 4), II (n = 4), III (n = 1), and IV disease (n = 2). Median overall survival calculated from the time of histologic transformation was 22 months (range, 8 months to 8 years) with five patients who died of disease 8-18 months after transformation. High-grade transformation may occur in LGESS with JAZF1 and PHF1 rearrangements at the time of or years after initial diagnosis. Such high-grade transformation is characterized by nuclear enlargement, prominent nucleoli, and increased mitotic index compared with typical LGESS. Histologic high-grade transformation may herald aggressive behavior.
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Affiliation(s)
- Youran Zou
- Department of Pathology, Oakland Medical Center, Kaiser Permanente, Oakland, CA, USA
| | - Gulisa Turashvili
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Pathology and Laboratory Medicine, University of Toronto, Toronto, ON, Canada
| | - Robert A Soslow
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kay J Park
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sabrina Croce
- Department of Biopathology, Institut Bergonié, Comprehensive Cancer Center, Bordeaux, France
| | - W Glenn McCluggage
- Department of Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland, UK
| | - Colin J R Stewart
- Department of Pathology, King Edward Memorial Hospital, Perth, WA, Australia
- School of Women's and Infants' Health, University of Western Australia, Perth, WA, Australia
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Esther Oliva
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Robert H Young
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Arnaud Da Cruz Paula
- Department of Surgery, Gynecologic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kimberly Dessources
- Department of Surgery, Gynecologic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charles W Ashley
- Department of Surgery, Gynecologic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martee L Hensley
- Department of Medicine, Gynecologic Medical Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, BC Cancer, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cristina R Antonescu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cheng-Han Lee
- Department of Pathology and Laboratory Medicine, BC Cancer, Vancouver, BC, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
| | - Sarah Chiang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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49
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Human transcription factor and protein kinase gene fusions in human cancer. Sci Rep 2020; 10:14169. [PMID: 32843691 PMCID: PMC7447636 DOI: 10.1038/s41598-020-71040-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/30/2020] [Indexed: 11/26/2022] Open
Abstract
Oncogenic gene fusions are estimated to account for up-to 20% of cancer morbidity. Recently sequence-level studies have established oncofusions throughout all tissue types. However, the functional implications of the identified oncofusions have often not been investigated. In this study, identified oncofusions from a fusion detection approach (DEEPEST) were analyzed in detail. Of the 28,863 oncofusions, we found almost 30% are expected to produce functional proteins with features from both parent genes. Kinases and transcription factors were the main gene families of the protein producing fusions. Considering their role as initiators, actors, and termination points of cellular signaling pathways, we focused our in-depth analyses on them. Domain architecture of the fusions and their wild-type interactors suggests that abnormal molecular context of protein domains caused by fusion events may unlock the oncogenic potential of the wild type counterparts of the fusion proteins. To understand overall oncofusion effects, we performed differential expression analysis using TCGA cancer project samples. Results indicated oncofusion-specific alterations in gene expression levels, and lower expression levels of components of key cellular pathways, in particular signal transduction and transcription regulation. The sum of results suggests that kinase and transcription factor oncofusions deregulate cellular signaling, possibly via acquiring novel functions.
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50
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Chrisinger JSA, Wehrli B, Dickson BC, Fasih S, Hirbe AC, Shultz DB, Zadeh G, Gupta AA, Demicco EG. Epithelioid and spindle cell rhabdomyosarcoma with FUS-TFCP2 or EWSR1-TFCP2 fusion: report of two cases. VIRCHOWS ARCHIV : AN INTERNATIONAL JOURNAL OF PATHOLOGY 2020. [PMID: 32556562 DOI: 10.1007/s00428‐020‐02870‐0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The WHO Classification of Tumors of Soft Tissue and Bone divides rhabdomyosarcoma (RMS) into alveolar, embryonal, pleomorphic, and spindle cell/sclerosing types. Advances in molecular diagnostics have allowed for further refinement of RMS classification including the identification of new subtypes. Very rare RMS with epithelioid and spindle cell morphology, female predominance, marked osseous predilection, ALK expression, EWSR1/FUS-TFCP2 gene fusions, and highly aggressive clinical behavior have recently been recognized with only 23 cases reported in the English language literature. Herein, we report two additional cases with detailed clinicopathologic description and molecular confirmation. In brief, two young women presented each with a primary bone tumor-one with a frontal bone tumor and another with an osseous pelvic tumor. Both tumors showed epithelioid to spindle cell morphology, ALK expression, and EWSR1/FUS-TFCP2 gene fusions. Both patients died of disease less than 17 months from diagnosis despite administration of multiple lines of aggressive treatment. In addition, we review the literature and discuss differential diagnostic and potential treatment considerations.
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Affiliation(s)
- John S A Chrisinger
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Bret Wehrli
- Department of Pathology and Laboratory Medicine, London Health Sciences Centre, Western University, London, ON, Canada
| | - Brendan C Dickson
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Samir Fasih
- Princess Margaret Cancer Centre, Division of Medical Oncology, University of Toronto, Toronto, ON, Canada
| | - Angela C Hirbe
- Division of Medical Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - David B Shultz
- Department of Radiation Oncology, Princess Margaret Cancer Centre & Department of Radiation Oncology, University of Toronto, Toronto, Canada
| | - Gelareh Zadeh
- Division of Neurosurgery, University Health Network, University of Toronto, Toronto, ON, Canada
- MacFeeters-Hamilton Center for Neuro-Oncology, Princess Margaret Cancer Center, Toronto, ON, Canada
| | - Abha A Gupta
- Princess Margaret Cancer Centre, Division of Medical Oncology, University of Toronto, Toronto, ON, Canada
- Division of Haematology/Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Elizabeth G Demicco
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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