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Sánchez-Marín D, Silva-Cázares MB, Porras-Reyes FI, García-Román R, Campos-Parra AD. Breaking paradigms: Long non-coding RNAs forming gene fusions with potential implications in cancer. Genes Dis 2024; 11:101136. [PMID: 38292185 PMCID: PMC10825296 DOI: 10.1016/j.gendis.2023.101136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/16/2023] [Accepted: 09/10/2023] [Indexed: 02/01/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) are non-coding RNAs longer than 200 nucleotides with dynamic regulatory functions. They interact with a wide range of molecules such as DNA, RNA, and proteins to modulate diverse cellular functions through several mechanisms and, if deregulated, they can lead to cancer development and progression. Recently, it has been described that lncRNAs are susceptible to form gene fusions with mRNAs or other lncRNAs, breaking the paradigm of gene fusions consisting mainly of protein-coding genes. However, their biological significance in the tumor phenotype is still uncertain. Therefore, their recent identification opens a new line of research to study their biological role in tumorigenesis, and their potential as biomarkers with clinical relevance or as therapeutic targets. The present study aimed to review the lncRNA fusions identified so far and to know which of them have been associated with a potential function. We address the current challenges to deepen their study as well as the reasons why they represent a future therapeutic window in cancer.
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Affiliation(s)
- David Sánchez-Marín
- Posgrado en Ciencias Biológicas, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, C.P. 04360, México
| | - Macrina Beatriz Silva-Cázares
- Unidad Académica Multidisciplinaria Región Altiplano, Universidad Autónoma de San Luis Potosí (UASLP), Carretera a Cedral Km 5+600, Ejido San José de la Trojes, Matehuala, San Luis Potosí, C.P. 78760, México
| | - Fany Iris Porras-Reyes
- Servicio de Anatomía Patológica, Instituto Nacional de Cancerología (INCan), Niño Jesús, Tlalpan, Ciudad de México, C.P. 14080, México
| | - Rebeca García-Román
- Instituto de Salud Pública, Universidad Veracruzana (UV), Av. Dr Luis, Dr. Castelazo Ayala s/n, Col. Industrial Ánimas, Xalapa, Veracruz, C.P. 91190, México
| | - Alma D. Campos-Parra
- Instituto de Salud Pública, Universidad Veracruzana (UV), Av. Dr Luis, Dr. Castelazo Ayala s/n, Col. Industrial Ánimas, Xalapa, Veracruz, C.P. 91190, México
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2
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Uro-Coste E. [Salivary gland tumours: When molecular biology resolves diagnostic dilemmas]. Ann Pathol 2024; 44:165-174. [PMID: 38555271 DOI: 10.1016/j.annpat.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/08/2024] [Indexed: 04/02/2024]
Affiliation(s)
- Emmanuelle Uro-Coste
- Service d'anatomie et cytologie pathologiques, institut universitaire du cancer-oncopole, 1, avenue Irène-Joliot-Curie, 31059 Toulouse cedex 9, France.
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3
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Schubert L, Le AT, Hinz TK, Navarro AC, Nelson-Taylor SK, Nemenoff RA, Heasley LE, Doebele RC. A functional sgRNA-CRISPR screening method for generating murine RET and NTRK1 rearranged oncogenes. Biol Open 2023; 12:bio059994. [PMID: 37470475 PMCID: PMC10445739 DOI: 10.1242/bio.059994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023] Open
Abstract
CRISPR/Cas9 gene editing represents a powerful tool for investigating fusion oncogenes in cancer biology. Successful experiments require that sgRNAs correctly associate with their target sequence and initiate double stranded breaks which are subsequently repaired by endogenous DNA repair systems yielding fusion chromosomes. Simple tests to ensure sgRNAs are functional are not generally available and often require single cell cloning to identify successful CRISPR-editing events. Here, we describe a novel method relying on acquisition of IL3-independence in Ba/F3 cells to identify sgRNA pairs that generate oncogenic gene rearrangements of the Ret and Ntrk1 tyrosine kinases. The rearrangements were confirmed with PCR, RT-PCR and sequencing and Ba/F3 cells harboring Ret or Ntrk1 rearrangements acquired sensitivity to RET and TRK inhibitors, respectively. Adenoviruses encoding Cas9 and sgRNA pairs inducing the Kif5b-Ret and Trim24-Ret rearrangements were intratracheally instilled into mice and yielded lung adenocarcinomas. A cell line (TR.1) established from a Trim24-Ret positive tumor exhibited high in vitro sensitivity to the RET inhibitors LOXO-292 and BLU-667 and orthotopic TR.1 cell-derived tumors underwent marked shrinkage upon LOXO-292 treatment. Thus, the method offers an efficient means to validate sgRNAs that successfully target their intended loci for the generation of novel, syngeneic murine oncogene-driven tumor models.
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Affiliation(s)
- Laura Schubert
- Departments of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045, USA
| | - Anh T. Le
- Departments of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045, USA
| | - Trista K. Hinz
- Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO80045, USA
| | - Andre C. Navarro
- Departments of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045, USA
| | - Sarah K. Nelson-Taylor
- Departments of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045, USA
| | - Raphael A. Nemenoff
- Departments of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045, USA
| | - Lynn E. Heasley
- Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO80045, USA
- Eastern Colorado VA Healthcare System, Rocky Mountain Regional VA Medical Center, Aurora, CO80045, USA
| | - Robert C. Doebele
- Departments of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO80045, USA
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González-Arreola RM, García-Romero A, Magaña-Torres MT, González-García JR. A novel approach for direct detection of the IGH::CRLF2 gene fusion by fluorescent in situ hybridization. Mol Cytogenet 2023; 16:19. [PMID: 37574565 PMCID: PMC10423412 DOI: 10.1186/s13039-023-00652-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/25/2023] [Indexed: 08/15/2023] Open
Abstract
BACKGROUND High expression of the Cytokine Receptor-Like Factor 2 (CRLF2) gene has been observed in patients with acute lymphoblastic leukemia BCR-ABL1-like subtype. Currently, there is no commercial system available for the direct detection of the IGH::CRLF2 fusion by fluorescent in situ hybridization (FISH), as there are for many other leukemia-related gene fusions. In an effort to verify the IGH::CRLF2 fusion, some researchers prepare home-grown FISH probes from bacterial artificial chromosome clones flanking the IGH and CRLF2 genes, which is the best alternative to confirm the fusion, however difficult to reproduce in most cytogenetic laboratories. RESULTS For the direct observation of the IGH::CRLF2 gene fusion we designed a methodological approach requiring the two commercially available IGH and CRLF2 break-apart probes. CONCLUSIONS Our methodological approach allows direct visualization of the IGH::CRLF2 gene fusion and has the potential to be used for identification of other gene fusions.
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Affiliation(s)
- Rosa María González-Arreola
- Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco Mexico
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, CIBO-IMSS, Sierra Mojada #800, Colonia Independencia, CP 44340 Guadalajara, Jalisco Mexico
| | - Adriana García-Romero
- Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco Mexico
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, CIBO-IMSS, Sierra Mojada #800, Colonia Independencia, CP 44340 Guadalajara, Jalisco Mexico
| | - María Teresa Magaña-Torres
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, CIBO-IMSS, Sierra Mojada #800, Colonia Independencia, CP 44340 Guadalajara, Jalisco Mexico
| | - Juan Ramón González-García
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, CIBO-IMSS, Sierra Mojada #800, Colonia Independencia, CP 44340 Guadalajara, Jalisco Mexico
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van Belzen IAEM, Cai C, van Tuil M, Badloe S, Strengman E, Janse A, Verwiel ETP, van der Leest DFM, Kester L, Molenaar JJ, Meijerink J, Drost J, Peng WC, Kerstens HHD, Tops BBJ, Holstege FCP, Kemmeren P, Hehir-Kwa JY. Systematic discovery of gene fusions in pediatric cancer by integrating RNA-seq and WGS. BMC Cancer 2023; 23:618. [PMID: 37400763 DOI: 10.1186/s12885-023-11054-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 03/08/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND Gene fusions are important cancer drivers in pediatric cancer and their accurate detection is essential for diagnosis and treatment. Clinical decision-making requires high confidence and precision of detection. Recent developments show RNA sequencing (RNA-seq) is promising for genome-wide detection of fusion products but hindered by many false positives that require extensive manual curation and impede discovery of pathogenic fusions. METHODS We developed Fusion-sq to overcome existing disadvantages of detecting gene fusions. Fusion-sq integrates and "fuses" evidence from RNA-seq and whole genome sequencing (WGS) using intron-exon gene structure to identify tumor-specific protein coding gene fusions. Fusion-sq was then applied to the data generated from a pediatric pan-cancer cohort of 128 patients by WGS and RNA sequencing. RESULTS In a pediatric pan-cancer cohort of 128 patients, we identified 155 high confidence tumor-specific gene fusions and their underlying structural variants (SVs). This includes all clinically relevant fusions known to be present in this cohort (30 patients). Fusion-sq distinguishes healthy-occurring from tumor-specific fusions and resolves fusions in amplified regions and copy number unstable genomes. A high gene fusion burden is associated with copy number instability. We identified 27 potentially pathogenic fusions involving oncogenes or tumor-suppressor genes characterized by underlying SVs, in some cases leading to expression changes indicative of activating or disruptive effects. CONCLUSIONS Our results indicate how clinically relevant and potentially pathogenic gene fusions can be identified and their functional effects investigated by combining WGS and RNA-seq. Integrating RNA fusion predictions with underlying SVs advances fusion detection beyond extensive manual filtering. Taken together, we developed a method for identifying candidate gene fusions that is suitable for precision oncology applications. Our method provides multi-omics evidence for assessing the pathogenicity of tumor-specific gene fusions for future clinical decision making.
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Affiliation(s)
| | - Casey Cai
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Marc van Tuil
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Shashi Badloe
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Eric Strengman
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Alex Janse
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | | | - Lennart Kester
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Jan J Molenaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Jules Meijerink
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Weng Chuan Peng
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Bastiaan B J Tops
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
- Center for Molecular Medicine, UMC Utrecht and Utrecht University, Utrecht, The Netherlands.
| | - Jayne Y Hehir-Kwa
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
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Buglioni A, Caffes PL, Hessler MG, Mansfield AS, Lo YC. Clinical Utility Validation of an Automated Ultrarapid Gene Fusion Assay for NSCLC. JTO Clin Res Rep 2022; 3:100434. [PMID: 36536899 PMCID: PMC9758522 DOI: 10.1016/j.jtocrr.2022.100434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/13/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
Introduction Gene rearrangements are frequent oncologic drivers in NSCLC, and many are suitable for treatment with Food and Drug Administration-approved or experimental targeted therapies. We evaluated the accuracy, specimen acceptance profile, and limits of detection of a rapid fusion assay (Idylla GeneFusion Assay), a commercially available ultrarapid molecular assay, for its clinical utility. Methods A collection of 97 specimens which had previously undergone next-generation sequencing testing were analyzed using the rapid fusion assay. Accuracy was evaluated by sensitivity and specificity compared with the next-generation sequencing results. The performance characteristics were tested by using a variety of different clinically relevant specimen types. Limits of detection were assessed by evaluating different input of tumor percentage and material amount. Results The rapid fusion assay was found to have 100% sensitivity in detecting fusions of ALK, ROS1, RET, NTRK1, and MET exon 14 skipping and 83% sensitivity for NTRK2/3 fusions. There were 100% specificity in detecting fusions of ROS1, RET, NTRK2/3, and MET exon 14 skipping and 98% specificity for ALK. Testing was successful with formalin-fixed paraffin-embedded biopsy and surgical tissues, cell blocks from fine-needle aspiration and pleural fluid (down to 5% tumor content, 18 mm2 tissue scraped), cytology smears (≥300 cells), and previously extracted RNA (minimal 20 ng). Conclusions The rapid fusion assay is quick, accurate, and versatile, allowing reliable detection of ALK, ROS1, RET fusions, and MET exon 14 skipping in NSCLC, and NTRK fusions. Rapid molecular testing may expedite treatment with appropriate targeted therapies.
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Affiliation(s)
- Alessia Buglioni
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Patricia L. Caffes
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Mark G. Hessler
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Ying-Chun Lo
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
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Gray ER, Mordaka JM, Christoforou ER, von Bargen K, Potts ND, Xyrafaki C, Silva AL, Stolarek-Januszkiewicz M, Anton K, Powalowska PK, Andreazza S, Tomassini A, Palmer RN, Cooke A, Osborne RJ, Balmforth BW. Ultra-sensitive molecular detection of gene fusions from RNA using ASPYRE. BMC Med Genomics 2022; 15:215. [PMID: 36224552 PMCID: PMC9555097 DOI: 10.1186/s12920-022-01363-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/23/2022] [Indexed: 12/04/2022] Open
Abstract
Background RNA is a critical analyte for unambiguous detection of actionable mutations used to guide treatment decisions in oncology. Currently available methods for gene fusion detection include molecular or antibody-based assays, which suffer from either being limited to single-gene targeting, lack of sensitivity, or long turnaround time. The sensitivity and predictive value of next generation sequencing DNA-based assays to detect fusions by sequencing intronic regions is variable, due to the extensive size of introns. The required depth of sequencing and input nucleic acid required can be prohibitive; in addition it is not certain that predicted gene fusions are actually expressed. Results Herein we describe a method based on pyrophosphorolysis to include detection of gene fusions from RNA, with identical assay steps and conditions to detect somatic mutations in DNA [1], permitting concurrent assessment of DNA and RNA in a single instrument run. Conclusion The limit of detection was under 6 molecules/ 6 µL target volume. The workflow and instrumentation required are akin to PCR assays, and the entire assay from extracted nucleic acid to sample analysis can be completed within a single day. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01363-0.
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Affiliation(s)
- Eleanor R Gray
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | - Justyna M Mordaka
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | | | - Kristine von Bargen
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | - Nicola D Potts
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | - Christina Xyrafaki
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | - Ana-Luisa Silva
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | | | - Katarzyna Anton
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | - Paulina K Powalowska
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | - Simonetta Andreazza
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | - Alessandro Tomassini
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | - Rebecca N Palmer
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | - Aishling Cooke
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | - Robert J Osborne
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England
| | - Barnaby W Balmforth
- Biofidelity Ltd, 330 Cambridge Science Park, Milton road, CB4 0WN, Cambridge, England.
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Moreno DA, Becker AP, Scapulatempo-Neto C, Menezes W, Sheren J, Walter AM, Clara C, Machado HR, Oliveira RS, Neder L, Varella-Garcia M, Reis RM. NTRK2 gene fusions are uncommon in pilocytic astrocytoma. Mol Biol Rep 2022. [PMID: 35713800 DOI: 10.1007/s11033-022-07567-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 04/23/2022] [Accepted: 05/04/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Pilocytic astrocytoma is the most frequent pediatric glioma. Despite its overall good prognosis, complete surgical resection is sometimes unfeasible, especially for patients with deep-seated tumors. For these patients, the identification of targetable genetic alterations such as NTRK fusions, raised as a new hope for therapy. The presence of gene fusions involving NTRK2 has been rarely reported in pilocytic astrocytoma. The aim of the present study was to investigate the frequency of NTRK2 alterations in a series of Brazilian pilocytic astrocytomas. METHODS Sixty-nine pilocytic astrocytomas, previously characterized for BRAF and FGFR1 alterations were evaluated. The analysis of NTRK2 alterations was performed using a dual color break apart fluorescence in situ hybridization (FISH) assay. RESULTS NTRK2 fusions were successfully evaluated by FISH in 62 of the 69 cases. Neither evidence of NTRK2 gene rearrangements nor NTRK2 copy number alterations were found. CONCLUSIONS NTRK2 alterations are uncommon genetic events in pilocytic astrocytomas, regardless of patients' clinicopathological and molecular features.
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Agaimy A. [Mesenchymal tumors and tumor-like lesions of the gastrointestinal tract: an overview]. Pathologe 2022; 43:31-44. [PMID: 34919183 DOI: 10.1007/s00292-021-01040-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
Mesenchymal tumors and tumor-like lesions of the gastrointestinal (GI) tract are uncommon. They vary from reactive tumefactive lesions and benign neoplasms to highly aggressive sarcomas. Among them, GI stromal tumors (GISTs) are most common, followed, with less frequency, by smooth muscle and neurogenic tumors. The major challenge resides in correctly identifying GISTs and providing a comprehensive report (including risk assessment and genotyping) that represents the basis for an optimized surgical-oncological treatment and/or adjuvant therapy. On the other hand, the challenge of benign lesions is to find a good name (well understandable and reproducible diagnostic term) that helps avoid diagnostic ambiguity and prognostic uncertainty so that overprognostication and overtreatment can be prevented. Moreover, several recently described genetically defined benign and malignant entities need be correctly diagnosed due to their special "targeted" therapeutic options and to further characterize their clinicopathological and biological properties in the future. These recent entities include aggressive epithelioid inflammatory myofibroblastic sarcoma (ALK-RANBP2-driven), malignant gastrointestinal neuroectodermal tumor (EWSR1-ATF1/CREB-related), NTRK-rearranged neoplasms, and, most recently, colorectal NUTM1-rearranged sarcomas. This review highlights the major clinicopathological features of gastrointestinal mesenchymal lesions in light of recent developments.
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Affiliation(s)
- Abbas Agaimy
- Pathologisches Institut, Universitätsklinikum Erlangen, Krankenhausstraße 8-10, 91054, Erlangen, Deutschland.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Lilljebjörn H, Orsmark-Pietras C, Mitelman F, Hagström-Andersson A, Fioretos T. Transcriptomics paving the way for improved diagnostics and precision medicine of acute leukemia. Semin Cancer Biol 2021; 84:40-49. [PMID: 34606984 DOI: 10.1016/j.semcancer.2021.09.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 11/26/2022]
Abstract
Transcriptional profiling of acute leukemia, specifically by RNA-sequencing or whole transcriptome sequencing (WTS), has provided fundamental insights into its underlying disease biology and allows unbiased detection of oncogenic gene fusions, as well as of gene expression signatures that can be used for improved disease classification. While used as a research tool for many years, RNA-sequencing is becoming increasingly used in clinical diagnostics. Here, we highlight key transcriptomic studies of acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) that have improved our biological understanding of these heterogeneous malignant disorders and have paved the way for translation into clinical diagnostics. Recent single-cell transcriptomic studies of ALL and AML, which provide new insights into the cellular ecosystem of acute leukemia and point to future clinical utility, are also reviewed. Finally, we discuss current challenges that need to be overcome for a more wide-spread adoption of RNA-sequencing in clinical diagnostics and how this technology significantly can aid the identification of genetic alterations in current guidelines and of newly emerging disease entities, some of which are critical to identify because of the availability of targeted therapies, thereby paving the way for improved precision medicine of acute leukemia.
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Affiliation(s)
- Henrik Lilljebjörn
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.
| | - Christina Orsmark-Pietras
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden; Department of Clinical Genetics and Pathology, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
| | - Felix Mitelman
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anna Hagström-Andersson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Center for Translational Genomics, Lund University, Lund, Sweden; Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Center for Translational Genomics, Lund University, Lund, Sweden; Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden; Department of Clinical Genetics and Pathology, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden.
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12
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Rojo F, Colomer R, López-Ríos F, Bautista F, Álvarez R, de Álava E, Hladun R, Garrido P. [Multidisciplinary consensus on optimizing the detection of NTRK gene alterations in tumours]. Rev Esp Patol 2021; 54:250-62. [PMID: 34544555 DOI: 10.1016/j.patol.2021.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/16/2021] [Accepted: 05/13/2021] [Indexed: 11/21/2022]
Abstract
The recent identification of rearrangements of neurotrophic tyrosine receptor kinase (NTRK) genes and the development of specific fusion protein inhibitors, such as larotrectinib and entrectinib, have revolutionized the diagnostic and clinical management of patients presenting with tumours with these alterations. Tumours that harbour NTRK fusions are found in both adults and children and are either rare tumours with common NTRK fusions that may be diagnostic, or more common tumours with rare NTRK fusions. To assess the currently available evidence, 3key Spanish medical societies (the Spanish Society of Medical Oncology (SEOM), the Spanish Society of Pathology (SEAP) and the Spanish Society of Paediatric Haematology and Oncology (SEHOP) have brought together a group of experts to develop a consensus document that includes guidelines on the diagnostic, clinical and therapeutic aspects of NTRK-fusion tumours. It also discusses the challenges related to the routine detection of these genetic alterations in a mostly public health care system.
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13
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Kojadinovic A, Laderian B, Mundi PS. Targeting TRK: A fast-tracked application of precision oncology and future directions. Crit Rev Oncol Hematol 2021; 165:103451. [PMID: 34389458 DOI: 10.1016/j.critrevonc.2021.103451] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/27/2021] [Accepted: 08/08/2021] [Indexed: 12/14/2022] Open
Abstract
The NTRK genes encode the tropomyosin-related receptor tyrosine kinases TrkA, TrkB and TrkC. TRK receptors regulate the proliferation, differentiation, and survival of many neuronal and non-neuronal glial cells during embryogenesis, thus playing a critical role in synaptic plasticity and the development of nociceptive pathways. Recurrent genomic alterations in NTRK genes, typically fusions involving the 3' region encoding the kinase domain juxtaposed to 5' sequences from numerous partner genes, occur at a low frequency in a wide diversity of adult and pediatric cancers. The contributions of the resulting constitutively activated kinase to oncogenesis and cancer progression are being elucidated. Larotrectinib and entrectinib are potent first-generation TRK inhibitors with IC50 values in the nanomolar range across cancer cell lines harboring NTRK fusions. Larotrectinib is highly selective for TRK receptors, whereas entrectinib also potently inhibits ROS1 and ALK. Clinical trials of both drugs demonstrated significant and durable responses in patients with tumors harboring NTRK alterations, leading to first of its kind cancer agnostic FDA approvals in the United States for drugs targeting a genomic alteration. Unfortunately, acquired resistance inevitably develops. The second-generation TRK inhibitors selitrectinib and repotrectinib are designed to overcome known mechanisms of resistance.
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Affiliation(s)
- Arsenije Kojadinovic
- Icahn School of Medicine at Mount Sinai, United States; James J. Peters VA Medical Center, United States
| | | | - Prabhjot S Mundi
- James J. Peters VA Medical Center, United States; Columbia University Irving Medical Center, United States.
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14
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Garrido P, Hladun R, de Álava E, Álvarez R, Bautista F, López-Ríos F, Colomer R, Rojo F. Multidisciplinary consensus on optimising the detection of NTRK gene alterations in tumours. Clin Transl Oncol 2021; 23:1529-1541. [PMID: 33620682 PMCID: PMC8238709 DOI: 10.1007/s12094-021-02558-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/24/2021] [Indexed: 12/21/2022]
Abstract
The recent identification of rearrangements of neurotrophic tyrosine receptor kinase (NTRK) genes and the development of specific fusion protein inhibitors, such as larotrectinib and entrectinib, have revolutionised the diagnostic and clinical management of patients presenting with tumours with these alterations. Tumours that harbour NTRK fusions are found in both adults and children; and they are either rare tumours with common NTRK fusions that may be diagnostic, or more prevalent tumours with rare NTRK fusions. To assess currently available evidence on this matter, three key Spanish medical societies (the Spanish Society of Medical Oncology (SEOM), the Spanish Society of Pathological Anatomy (SEAP), and the Spanish Society of Paediatric Haematology and Oncology (SEHOP) have brought together a group of experts to develop a consensus document that includes guidelines on the diagnostic, clinical, and therapeutic aspects of NTRK-fusion tumours. This document also discusses the challenges related to the routine detection of these genetic alterations in a mostly public Health Care System.
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Affiliation(s)
- P. Garrido
- Sociedad Española de Oncología Médica (SEOM), Departamento de Oncología Médica, Hospital Universitario Ramón y Cajal, Universidad de Alcalá, IRYCIS, CIBERONC, Madrid, Spain
| | - R. Hladun
- Sociedad Española de Hematología y Oncologías Pediátricas (SEHOP), Departamento de Oncología, Hematología y Trasplante de Progenitores Hematopoyéticos Pediátricos, Hospital Universitario Vall d’Hebron, Barcelona, Spain
| | - E. de Álava
- Sociedad Española de Anatomía Patológica (SEAP), Departamento de Citología e Histología Normal y Patológica, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBiS), CSIC, Facultad de Medicina, Universidad de Sevilla, CIBERONC, Sevilla, Spain
| | - R. Álvarez
- Sociedad Española de Oncología Médica (SEOM), Departamento de Oncología Médica, Hospital Universitario Gregorio Marañón. Instituto Investigación Sanitaria Gregorio Marañon (IISGM), Madrid, Spain
| | - F. Bautista
- Sociedad Española de Hematología y Oncologías Pediátricas (SEHOP), Oncología Pediátrica, Departamento de Hematología y Trasplante de Células Madre Hematopoyéticas, Hospital Universitario Infantil Niño Jesús, Madrid, Spain
| | - F. López-Ríos
- Sociedad Española de Anatomía Patológica (SEAP), Departamento de Patología, Laboratorio de Dianas Terapéuticas, Hospital Universitario HM Sanchinarro, CIBERONC, Madrid, Spain
| | - R. Colomer
- Sociedad Española de Oncología Médica (SEOM), Departamento de Oncología Médica, Hospital Universitario La Princesa, Universidad Autónoma de Madrid, Cátedra UAM-Fundación Instituto Roche de Medicina Personalizada de Precisión, Madrid, Spain
| | - F. Rojo
- Sociedad Española de Anatomía Patológica (SEAP), Departamento de Patología, IIS-Fundación Universitaria Jiménez Díaz, CIBERONC, Madrid, Spain
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15
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Bocciarelli C, Caumont C, Samaison L, Cariou M, Aline-Fardin A, Doucet L, Roudié J, Terris B, Merlio JP, Marcorelles P, Cappellen D, Uguen A. MSI-High RAS-BRAF wild-type colorectal adenocarcinomas with MLH1 loss have a high frequency of targetable oncogenic gene fusions whose diagnoses are feasible using methods easy-to-implement in pathology laboratories. Hum Pathol 2021; 114:99-109. [PMID: 34019865 DOI: 10.1016/j.humpath.2021.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 12/17/2022]
Abstract
Targetable kinase fusions are extremely rare (<1%) in colorectal cancers (CRCs), making their diagnosis challenging and often underinvestigated. They have been shown particularly frequently among MSI-High, BRAF/KRAS/NRAS wild-type CRCs with MLH1 loss (MLH1loss MSI-High wild-type). We searched for NTRK1, NTRK2, NTRK3, ALK, ROS1, BRAF, RET, and NRG1 kinase fusions in CRCs using methods easy-to-implement in pathology laboratories: immunohistochemistry (IHC), fluorescent in situ hybridization (FISH), and fully automated real-time PCR targeted analyses. RNA-sequencing analyses were used for confirmation. Among 84 selected MLH1 deficient (IHC) CRCs cases, MLH1loss MSI-High wild-type CRCs consisted first in 19 cases after Idylla™ analyses and finally in 18 cases (21%) after RNA-sequencing (detection of one additional KRASG12D mutation). FISH (and when relevant, IHC) analyses concluded in 5 NTRK1, 3 NTRK3, 1 ALK, 2 BRAF, and 2 RET FISH positive tumors. ALK and NTRK1 rearranged tumors were IHC positive, but pan-TRK IHC was negative in the 3 NTRK3 FISH positive tumors. RNA-sequencing analyses confirmed 12 of 13 fusions with only one false positive RET FISH result. Finally, 12/18 (67%) of MLH1loss MSI-High wild-type CRCs contained targetable kinase fusions. Our study demonstrates the feasibility, but also the cost-effectiveness, of a multistep but rapid diagnostic strategy based on nonsequencing methods to identify rare and targetable kinase fusions in patients with advanced CRCs, as well as the high prevalence of these kinase fusions in MLH1loss MSI-High wild-type CRCs. Nevertheless, confirmatory RNA-sequencing analyses are necessary in case of low FISH positive nuclei percentage to rule out FISH false-positive results.
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Affiliation(s)
- Claire Bocciarelli
- CHU de la Martinique, Service d'anatomie et Cytologie Pathologiques, Fort-de-France, F-97261, France.
| | - Charline Caumont
- CHU Bordeaux, Department of Tumor Biology, Pessac, F-33600, France; Inserm U1053 BaRITOn, Univ Bordeaux, Bordeaux, F-33000, France.
| | | | - Mélanie Cariou
- Registre des Cancers Digestifs du Finistère EA7479 SPURBO, Université de Bretagne Occidentale Brest, F-29200, France.
| | - Aude Aline-Fardin
- CHU de la Martinique, Service d'anatomie et Cytologie Pathologiques, Fort-de-France, F-97261, France.
| | - Laurent Doucet
- CHRU Brest, Service d'anatomie et Cytologie Pathologiques, Brest, F-29200, France.
| | - Jean Roudié
- CHU de la Martinique, Service de Chirurgie Digestive, Fort-de-France, F-97261, France.
| | - Benoît Terris
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Paris Centre, Hôpital Cochin, Service d'anatomie et Cytologie Pathologiques, Paris, F-75014, France.
| | - Jean-Philippe Merlio
- CHU Bordeaux, Department of Tumor Biology, Pessac, F-33600, France; Inserm U1053 BaRITOn, Univ Bordeaux, Bordeaux, F-33000, France.
| | - Pascale Marcorelles
- CHRU Brest, Service d'anatomie et Cytologie Pathologiques, Brest, F-29200, France.
| | - David Cappellen
- CHU Bordeaux, Department of Tumor Biology, Pessac, F-33600, France; Inserm U1053 BaRITOn, Univ Bordeaux, Bordeaux, F-33000, France.
| | - Arnaud Uguen
- CHU de la Martinique, Service d'anatomie et Cytologie Pathologiques, Fort-de-France, F-97261, France; Univ Brest, Inserm, CHU de Brest, LBAI, UMR1227, Brest, 29200, France.
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16
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Uguen A, Csanyi-Bastien M, Sabourin JC, Penault-Llorca F, Adam J. [How to test for NTRK gene fusions: A practical approach for pathologists]. Ann Pathol 2021; 41:387-398. [PMID: 33846022 DOI: 10.1016/j.annpat.2021.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/06/2021] [Accepted: 03/10/2021] [Indexed: 11/29/2022]
Abstract
The recent availability of targeted anti-TRK therapies represents a new opportunity to treat patients with advanced cancers harboring NTRK gene fusions. In this article, we present an update on the practical modalities of implementing a "NTRK testing" to search for these fusions in view of the performances and availability of the different testing methods and the epidemiological characteristics of the tumors liable to present the NTRK1, NTRK2 or NTRK3 gene fusions.
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Affiliation(s)
- Arnaud Uguen
- Inserm, CHU de Brest, LBAI, UMR1227, Université Brest, 29200 Brest, France; Service d'anatomie et cytologie pathologiques, CHRU Brest, 29200 Brest, France.
| | | | | | - Frédérique Penault-Llorca
- Inserm U1240, département d'anatomie et de cytologie pathologiques, centre Jean-Perrin, université Clermont-Auvergne, 63011 Clermont-Ferrand, France
| | - Julien Adam
- Service d'anatomie et cytologie pathologiques, Hôpital Saint-Joseph, 75014 Paris, France
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17
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Szulzewsky F, Holland EC, Vasioukhin V. YAP1 and its fusion proteins in cancer initiation, progression and therapeutic resistance. Dev Biol 2021; 475:205-221. [PMID: 33428889 DOI: 10.1016/j.ydbio.2020.12.018] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/14/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023]
Abstract
YAP1 is a transcriptional co-activator whose activity is controlled by the Hippo signaling pathway. In addition to important functions in normal tissue homeostasis and regeneration, YAP1 has also prominent functions in cancer initiation, aggressiveness, metastasis, and therapy resistance. In this review we are discussing the molecular functions of YAP1 and its roles in cancer, with a focus on the different mechanisms of de-regulation of YAP1 activity in human cancers, including inactivation of upstream Hippo pathway tumor suppressors, regulation by intersecting pathways, miRNAs, and viral oncogenes. We are also discussing new findings on the function and biology of the recently identified family of YAP1 gene fusions, that constitute a new type of activating mutation of YAP1 and that are the likely oncogenic drivers in several subtypes of human cancers. Lastly, we also discuss different strategies of therapeutic inhibition of YAP1 functions.
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Affiliation(s)
- Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA; Seattle Tumor Translational Research Center, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Valeri Vasioukhin
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
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18
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Gaonkar KS, Marini F, Rathi KS, Jain P, Zhu Y, Chimicles NA, Brown MA, Naqvi AS, Zhang B, Storm PB, Maris JM, Raman P, Resnick AC, Strauch K, Taroni JN, Rokita JL. annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions. BMC Bioinformatics 2020; 21:577. [PMID: 33317447 PMCID: PMC7737294 DOI: 10.1186/s12859-020-03922-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 12/03/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Gene fusion events are significant sources of somatic variation across adult and pediatric cancers and are some of the most clinically-effective therapeutic targets, yet low consensus of RNA-Seq fusion prediction algorithms makes therapeutic prioritization difficult. In addition, events such as polymerase read-throughs, mis-mapping due to gene homology, and fusions occurring in healthy normal tissue require informed filtering, making it difficult for researchers and clinicians to rapidly discern gene fusions that might be true underlying oncogenic drivers of a tumor and in some cases, appropriate targets for therapy. RESULTS We developed annoFuse, an R package, and shinyFuse, a companion web application, to annotate, prioritize, and explore biologically-relevant expressed gene fusions, downstream of fusion calling. We validated annoFuse using a random cohort of TCGA RNA-Seq samples (N = 160) and achieved a 96% sensitivity for retention of high-confidence fusions (N = 603). annoFuse uses FusionAnnotator annotations to filter non-oncogenic and/or artifactual fusions. Then, fusions are prioritized if previously reported in TCGA and/or fusions containing gene partners that are known oncogenes, tumor suppressor genes, COSMIC genes, and/or transcription factors. We applied annoFuse to fusion calls from pediatric brain tumor RNA-Seq samples (N = 1028) provided as part of the Open Pediatric Brain Tumor Atlas (OpenPBTA) Project to determine recurrent fusions and recurrently-fused genes within different brain tumor histologies. annoFuse annotates protein domains using the PFAM database, assesses reciprocality, and annotates gene partners for kinase domain retention. As a standard function, reportFuse enables generation of a reproducible R Markdown report to summarize filtered fusions, visualize breakpoints and protein domains by transcript, and plot recurrent fusions within cohorts. Finally, we created shinyFuse for algorithm-agnostic interactive exploration and plotting of gene fusions. CONCLUSIONS annoFuse provides standardized filtering and annotation for gene fusion calls from STAR-Fusion and Arriba by merging, filtering, and prioritizing putative oncogenic fusions across large cancer datasets, as demonstrated here with data from the OpenPBTA project. We are expanding the package to be widely-applicable to other fusion algorithms and expect annoFuse to provide researchers a method for rapidly evaluating, prioritizing, and translating fusion findings in patient tumors.
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Affiliation(s)
- Krutika S Gaonkar
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Center for Thrombosis and Hemostasis, Mainz, Germany
| | - Komal S Rathi
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Payal Jain
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yuankun Zhu
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nicholas A Chimicles
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Miguel A Brown
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ammar S Naqvi
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Bo Zhang
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Phillip B Storm
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - John M Maris
- Division of Oncology, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Pichai Raman
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Adam C Resnick
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Konstantin Strauch
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Jaclyn N Taroni
- Alex's Lemonade Stand Foundation Childhood Cancer Data Lab, Philadelphia, PA, USA
| | - Jo Lynne Rokita
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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19
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Salami SS, Tosoian JJ, Nallandhighal S, Jones TA, Brockman S, Elkhoury FF, Bazzi S, Plouffe KR, Siddiqui J, Liu CJ, Kunju LP, Morgan TM, Natarajan S, Boonstra PS, Sumida L, Tomlins SA, Udager AM, Sisk AE, Marks LS, Palapattu GS. Serial Molecular Profiling of Low-grade Prostate Cancer to Assess Tumor Upgrading: A Longitudinal Cohort Study. Eur Urol 2020; 79:456-465. [PMID: 32631746 DOI: 10.1016/j.eururo.2020.06.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 06/17/2020] [Indexed: 11/26/2022]
Abstract
BACKGROUND The potential for low-grade (grade group 1 [GG1]) prostate cancer (PCa) to progress to high-grade disease remains unclear. OBJECTIVE To interrogate the molecular and biological features of low-grade PCa serially over time. DESIGN, SETTING, AND PARTICIPANTS Nested longitudinal cohort study in an academic active surveillance (AS) program. Men were on AS for GG1 PCa from 2012 to 2017. INTERVENTION Electronic tracking and resampling of PCa using magnetic resonance imaging/ultrasound fusion biopsy. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS ERG immunohistochemistry (IHC) and targeted DNA/RNA next-generation sequencing were performed on initial and repeat biopsies. Tumor clonality was assessed. Molecular data were compared between men who upgraded and those who did not upgrade to GG ≥ 2 cancer. RESULTS AND LIMITATIONS Sixty-six men with median age 64 yr (interquartile range [IQR], 59-69) and prostate-specific antigen 4.9 ng/mL (IQR, 3.3-6.4) underwent repeat sampling of a tracked tumor focus (median interval, 11 mo; IQR, 6-13). IHC-based ERG fusion status was concordant at initial and repeat biopsies in 63 men (95% vs expected 50%, p < 0.001), and RNAseq-based fusion and isoform expression were concordant in nine of 13 (69%) ERG+ patients, supporting focal resampling. Among 15 men who upgraded with complete data at both time points, integrated DNA/RNAseq analysis provided evidence of shared clonality in at least five cases. Such cases could reflect initial undersampling, but also support the possibility of clonal temporal progression of low-grade cancer. Our assessment was limited by sample size and use of targeted sequencing. CONCLUSIONS Repeat molecular assessment of low-grade tumors suggests that clonal progression could be one mechanism of upgrading. These data underscore the importance of serial tumor assessment in men pursuing AS of low-grade PCa. PATIENT SUMMARY We performed targeted rebiopsy and molecular testing of low-grade tumors on active surveillance. Our findings highlight the importance of periodic biopsy as a component of monitoring for cancer upgrading during surveillance.
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Affiliation(s)
- Simpa S Salami
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA.
| | - Jeffrey J Tosoian
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | | | - Tonye A Jones
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Scott Brockman
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA
| | - Fuad F Elkhoury
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Selena Bazzi
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA
| | - Komal R Plouffe
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Javed Siddiqui
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA; Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Chia-Jen Liu
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA; Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Lakshmi P Kunju
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Todd M Morgan
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Shyam Natarajan
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Philip S Boonstra
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Lauren Sumida
- Department of Pathology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Scott A Tomlins
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA; Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Aaron M Udager
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA; Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Anthony E Sisk
- Department of Pathology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Leonard S Marks
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Ganesh S Palapattu
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA; Department of Urology, Medical University of Vienna, Vienna, Austria
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20
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Stichel D, Schrimpf D, Casalini B, Meyer J, Wefers AK, Sievers P, Korshunov A, Koelsche C, Reuss DE, Reinhardt A, Ebrahimi A, Fernández-Klett F, Kessler T, Sturm D, Ecker J, Milde T, Herold-Mende C, Witt O, Pfister SM, Wick W, Jones DTW, von Deimling A, Sahm F. Routine RNA sequencing of formalin-fixed paraffin-embedded specimens in neuropathology diagnostics identifies diagnostically and therapeutically relevant gene fusions. Acta Neuropathol 2019; 138:827-35. [PMID: 31278449 DOI: 10.1007/s00401-019-02039-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/13/2019] [Accepted: 06/20/2019] [Indexed: 12/23/2022]
Abstract
Molecular markers have become pivotal in brain tumor diagnostics. Mutational analyses by targeted next-generation sequencing of DNA and array-based DNA methylation assessment with copy number analyses are increasingly being used in routine diagnostics. However, the broad variety of gene fusions occurring in brain tumors is marginally covered by these technologies and often only assessed by targeted assays. Here, we assessed the feasibility and clinical value of investigating gene fusions in formalin-fixed paraffin-embedded (FFPE) tumor tissues by next-generation mRNA sequencing in a routine diagnostic setting. After establishment and optimization of a workflow applicable in a routine setting, prospective diagnostic application in a neuropathology department for 26 months yielded relevant fusions in 66 out of 101 (65%) analyzed cases. In 43 (43%) cases, the fusions were of decisive diagnostic relevance and in 40 (40%) cases the fusion genes rendered a druggable target. A major strength of this approach was its ability to detect fusions beyond the canonical alterations for a given entity, and the unbiased search for any fusion event in cases with uncertain diagnosis and, thus, uncertain spectrum of expected fusions. This included both rare variants of established fusions which had evaded prior targeted analyses as well as the detection of previously unreported fusion events. While the impact of fusion detection on diagnostics is highly relevant, it is especially the detection of "druggable" fusions which will most likely provide direct benefit to the patients. The wider application of this approach for unbiased fusion identification therefore promises to be a major advance in identifying alterations with immediate impact on patient care.
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21
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Supplee JG, Milan MSD, Lim LP, Potts KT, Sholl LM, Oxnard GR, Paweletz CP. Sensitivity of next-generation sequencing assays detecting oncogenic fusions in plasma cell-free DNA. Lung Cancer 2019; 134:96-9. [PMID: 31320002 DOI: 10.1016/j.lungcan.2019.06.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 01/25/2023]
Abstract
OBJECTIVES Plasma genotyping represents an opportunity for convenient detection of clinically actionable mutations in advanced cancer patients, such has been well-documented in non-small cell lung cancer (NSCLC). Oncogenic gene fusions are complex variants that may be more challenging to detect by next-generation sequencing (NGS) of plasma cell-free DNA (cfDNA). Rigorous evaluation of plasma NGS assays in the detection of fusions is needed to maximize clinical utility. MATERIALS AND METHODS Additional plasma was collected from patients with advanced NSCLC and ALK, ROS1, or RET gene fusions in tissue who had undergone clinical plasma NGS using Guardant360™(G360, Guardant Health). We then sequenced extracted cfDNA with a plasma NGS kit focused on known driver mutations in NSCLC (ctDx-Lung, Resolution Bioscience) with cloud-based bioinformatic analysis and blinded variant calling. RESULTS Of 16 patients assayed known to harbor anALK, ROS1, or RET in tumor, G360 detected fusions in 7 cases, ctDx-Lung detected fusions in 13 cases, and 3 cases were detected by neither. Of the 7 fusions detected by both assays, G360 reported lower mutant allelic fractions (AF). In cases missed by G360, tumor derived TP53 mutations were often detected confirming presence of tumor DNA. Raw sequencing data showed that inverted or out-of-frame variants were overrepresented in cases detected using ctDx-Lung but not by G360. CONCLUSION Focusing on complex, clinically actionable mutations using tumor as a reference standard allows for evaluation of technical differences in plasma NGS assays that may impact clinical performance. Noting the heterogeneity of fusion sequences observed in NSCLC, we hypothesize that differences in hybrid capture techniques and bioinformatic calling may be sources of variations in sensitivity among these assays.
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22
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Abstract
Structural gene fusion rearrangements leading to aberrant signaling are frequently detected in many cancer types. Gene fusions have significant prognostic and predictive value and are screened as part of molecular pathology testing for patient management. Many bioinformatic approaches have been developed to detect fusion mutations including whole-genome sequencing, targeted-based hybridization capture, and transcriptome-based approaches. Here we describe the most commonly used experimental methods to sequence and identify gene fusions using either DNA or RNA. We contrast experimental approaches both in the research and diagnostic setting and describe typical bioinformatic pipelines and software packages used to identify fusions.
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Affiliation(s)
- Jan Schröder
- Peter MacCallum Cancer Center, Melbourne, VIC, Australia
| | - Amit Kumar
- Peter MacCallum Cancer Center, Melbourne, VIC, Australia
| | - Stephen Q Wong
- Peter MacCallum Cancer Center, Melbourne, VIC, Australia.
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23
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Zorofchian S, El-Achi H, Yan Y, Esquenazi Y, Ballester LY. Characterization of genomic alterations in primary central nervous system lymphomas. J Neurooncol 2018; 140:509-517. [PMID: 30171453 DOI: 10.1007/s11060-018-2990-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/22/2018] [Indexed: 01/01/2023]
Abstract
PURPOSE Primary central nervous system lymphoma (PCNSL) is a non-Hodgkin lymphoma that affects the central nervous system (CNS). Although previous studies have reported the most common mutated genes in PCNSL, including MYD88 and CD79b, our understanding of genetic characterizations in primary CNS lymphomas is limited. The aim of this study was to perform a retrospective analysis investigating the most frequent mutation types, and their frequency, in PCNSL. METHODS Fifteen patients with a diagnosis of PCNSL from our institution were analyzed for mutations in 406 genes and rearrangements in 31 genes by next generation sequencing (NGS). RESULTS Missense mutations were identified as the most common mutation type (32%) followed by frame shift mutations (23%). The highest mutation rate was reported in the MYD88 (33.3%), CDKN2A/B (33.3%), and TP53 (26.7%) genes. Intermediate tumor mutation burden (TMB) and high TMB was detected in 13.3% and 26.7% of PCNSL, respectively. The most frequent gene rearrangement involved the IGH-BCL6 genes (20%). CONCLUSIONS This study shows the most common genetic alterations in PCNSL as determined by a commercial next generation sequencing assay. MYD88 and CD79b are frequently mutated in PCNSL, IGH-BCL6 is the most frequent gene rearrangement and approximately 1/4 of cases show a high TMB. Mutations in multiple genes, in addition to high TMB and gene rearrangements, highlights the complex molecular heterogeneity of PCNSL. Knowledge about genetic alterations in PCNSL can inform the development of novel targets for diagnosis and treatment.
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Affiliation(s)
- Soheil Zorofchian
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center, 6431 Fannin St., MSB 2.136, Houston, TX, 77030, USA
| | - Hanadi El-Achi
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center, 6431 Fannin St., MSB 2.136, Houston, TX, 77030, USA
| | - Yuanqing Yan
- Vivian L. Smith Department of Neurosurgery, University of Texas Health Science Center, 6431 Fannin St., MSB 2.136, Houston, TX, 77030, USA
| | - Yoshua Esquenazi
- Vivian L. Smith Department of Neurosurgery, University of Texas Health Science Center, 6431 Fannin St., MSB 2.136, Houston, TX, 77030, USA.
| | - Leomar Y Ballester
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center, 6431 Fannin St., MSB 2.136, Houston, TX, 77030, USA. .,Vivian L. Smith Department of Neurosurgery, University of Texas Health Science Center, 6431 Fannin St., MSB 2.136, Houston, TX, 77030, USA.
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24
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Vaughn CP, Costa JL, Feilotter HE, Petraroli R, Bagai V, Rachiglio AM, Marino FZ, Tops B, Kurth HM, Sakai K, Mafficini A, Bastien RRL, Reiman A, Le Corre D, Boag A, Crocker S, Bihl M, Hirschmann A, Scarpa A, Machado JC, Blons H, Sheils O, Bramlett K, Ligtenberg MJL, Cree IA, Normanno N, Nishio K, Laurent-Puig P. Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: a multi-institutional research study. BMC Cancer 2018; 18:828. [PMID: 30115026 PMCID: PMC6097211 DOI: 10.1186/s12885-018-4736-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 08/09/2018] [Indexed: 12/30/2022] Open
Abstract
Background Gene fusion events resulting from chromosomal rearrangements play an important role in initiation of lung adenocarcinoma. The recent association of four oncogenic driver genes, ALK, ROS1, RET, and NTRK1, as lung tumor predictive biomarkers has increased the need for development of up-to-date technologies for detection of these biomarkers in limited amounts of material. Methods We describe here a multi-institutional study using the Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel to interrogate previously characterized lung tumor samples. Results Reproducibility between laboratories using diluted fusion-positive cell lines was 100%. A cohort of lung clinical research samples from different origins (tissue biopsies, tissue resections, lymph nodes and pleural fluid samples) were used to evaluate the panel. We observed 97% concordance for ALK (28/30 positive; 71/70 negative samples), 95% for ROS1 (3/4 positive; 19/18 negative samples), and 93% for RET (2/1 positive; 13/14 negative samples) between the AmpliSeq assay and other methodologies. Conclusion This methodology enables simultaneous detection of multiple ALK, ROS1, RET, and NTRK1 gene fusion transcripts in a single panel, enhanced by an integrated analysis solution. The assay performs well on limited amounts of input RNA (10 ng) and offers an integrated single assay solution for detection of actionable fusions in lung adenocarcinoma, with potential savings in both cost and turn-around-time compared to the combination of all four assays by other methods. Electronic supplementary material The online version of this article (10.1186/s12885-018-4736-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cecily P Vaughn
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - José Luis Costa
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal. .,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal. .,Medical Faculty of the University of Porto, Porto, Portugal.
| | - Harriet E Feilotter
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | | | | | - Anna Maria Rachiglio
- Laboratory of Pharmacogenomics, Centro di Ricerche Oncologiche di Mercogliano (CROM)-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Federica Zito Marino
- Pathology Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Bastiaan Tops
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Henriette M Kurth
- Viollier AG, Department of Genetics/Molecular Biology, Basel, Switzerland
| | - Kazuko Sakai
- Department of Genome Biology, Kinki University Faculty of Medicine, Osaka, Japan
| | - Andrea Mafficini
- ARC-NET: Centre for Applied Research on Cancer, Department of Pathology and Diagnostic, University and Hospital Trust of Verona, Verona, Italy
| | - Roy R L Bastien
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - Anne Reiman
- Centre for Sport, Exercise and Life Sciences, Coventry University, Coventry, UK
| | - Delphine Le Corre
- University Paris Descartes, Paris, France.,Biology Department, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou Hospital, Paris, France
| | - Alexander Boag
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Susan Crocker
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Michel Bihl
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | | | - Aldo Scarpa
- ARC-NET: Centre for Applied Research on Cancer, Department of Pathology and Diagnostic, University and Hospital Trust of Verona, Verona, Italy
| | - José Carlos Machado
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,Medical Faculty of the University of Porto, Porto, Portugal
| | - Hélène Blons
- University Paris Descartes, Paris, France.,Biology Department, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou Hospital, Paris, France
| | - Orla Sheils
- Trinity Translational Medicine Institute (TTMI), Trinity College Dublin, Dublin, Ireland
| | | | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ian A Cree
- Department of Pathology, University Hospitals Coventry and Warwickshire, Walsgrave, Coventry, UK
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Kazuto Nishio
- Department of Genome Biology, Kinki University Faculty of Medicine, Osaka, Japan
| | - Pierre Laurent-Puig
- University Paris Descartes, Paris, France.,Biology Department, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou Hospital, Paris, France
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25
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Iturriaga EA, Alvarez MI, Eslava AP, Papp T. Expression Vectors and Gene Fusions for the Directed Modification of the Carotenoid Biosynthesis Pathway in Mucor circinelloides. Methods Mol Biol 2018; 1852:239-56. [PMID: 30109635 DOI: 10.1007/978-1-4939-8742-9_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Several fungal species, particularly some included in the Mucoromycotina, have been used to develop fermentation processes for the production of β-carotene. Oxygenated derivatives of β-carotene (xanthophylls) are desirable value-added products, and the preference by the market of carotenoids from biological sources has increased the research in different carotenoid-producing organisms. We currently use Mucor circinelloides f. lusitanicus as a model organism to develop strains with an increased content of new and more valuable carotenoids. The main carotenoid accumulated by M. circinelloides is β-carotene, although it has some hydroxylase activity and produces low amounts of zeaxanthin. On the other hand, in astaxanthin-producing organisms two enzymatic activities are required for the production of astaxanthin from β-carotene: a hydroxylase and a ketolase. In this chapter, we delineate part of our efforts to construct genetically modified strains that could advance in the improvement of carotenoid accumulation by this fungus and the diversification of its carotenoid content. Accordingly, we describe detailed and empirically tested protocols for the construction of functional expression vectors and gene fusions.
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26
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Bailey PC, Schudoma C, Jackson W, Baggs E, Dagdas G, Haerty W, Moscou M, Krasileva KV. Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions. Genome Biol 2018; 19:23. [PMID: 29458393 PMCID: PMC5819176 DOI: 10.1186/s13059-018-1392-6] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 01/16/2018] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The plant immune system is innate and encoded in the germline. Using it efficiently, plants are capable of recognizing a diverse range of rapidly evolving pathogens. A recently described phenomenon shows that plant immune receptors are able to recognize pathogen effectors through the acquisition of exogenous protein domains from other plant genes. RESULTS We show that plant immune receptors with integrated domains are distributed unevenly across their phylogeny in grasses. Using phylogenetic analysis, we uncover a major integration clade, whose members underwent repeated independent integration events producing diverse fusions. This clade is ancestral in grasses with members often found on syntenic chromosomes. Analyses of these fusion events reveals that homologous receptors can be fused to diverse domains. Furthermore, we discover a 43 amino acid long motif associated with this dominant integration clade which is located immediately upstream of the fusion site. Sequence analysis reveals that DNA transposition and/or ectopic recombination are the most likely mechanisms of formation for nucleotide binding leucine rich repeat proteins with integrated domains. CONCLUSIONS The identification of this subclass of plant immune receptors that is naturally adapted to new domain integration will inform biotechnological approaches for generating synthetic receptors with novel pathogen "baits."
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Affiliation(s)
- Paul C Bailey
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | | | - William Jackson
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Erin Baggs
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Gulay Dagdas
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Matthew Moscou
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ksenia V Krasileva
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.
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27
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Chang TC, Carter RA, Li Y, Li Y, Wang H, Edmonson MN, Chen X, Arnold P, Geiger TL, Wu G, Peng J, Dyer M, Downing JR, Green DR, Thomas PG, Zhang J. The neoepitope landscape in pediatric cancers. Genome Med 2017; 9:78. [PMID: 28854978 PMCID: PMC5577668 DOI: 10.1186/s13073-017-0468-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/10/2017] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Neoepitopes derived from tumor-specific somatic mutations are promising targets for immunotherapy in childhood cancers. However, the potential for such therapies in targeting these epitopes remains uncertain due to a lack of knowledge of the neoepitope landscape in childhood cancer. Studies to date have focused primarily on missense mutations without exploring gene fusions, which are a major class of oncogenic drivers in pediatric cancer. METHODS We developed an analytical workflow for identification of putative neoepitopes based on somatic missense mutations and gene fusions using whole-genome sequencing data. Transcriptome sequencing data were incorporated to interrogate the expression status of the neoepitopes. RESULTS We present the neoepitope landscape of somatic alterations including missense mutations and oncogenic gene fusions identified in 540 childhood cancer genomes and transcriptomes representing 23 cancer subtypes. We found that 88% of leukemias, 78% of central nervous system tumors, and 90% of solid tumors had at least one predicted neoepitope. Mutation hotspots in KRAS and histone H3 genes encode potential epitopes in multiple patients. Additionally, the ETV6-RUNX1 fusion was found to encode putative neoepitopes in a high proportion (69.6%) of the pediatric leukemia harboring this fusion. CONCLUSIONS Our study presents a comprehensive repertoire of potential neoepitopes in childhood cancers, and will facilitate the development of immunotherapeutic approaches designed to exploit them. The source code of the workflow is available at GitHub ( https://github.com/zhanglabstjude/neoepitope ).
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Affiliation(s)
- Ti-Cheng Chang
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee, 38105, USA
| | - Robert A Carter
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee, 38105, USA
| | - Yongjin Li
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee, 38105, USA
| | - Yuxin Li
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, 38105, USA.,St Jude Proteomics Facility, St Jude Children's Research Hospital, Memphis, Tennessee, 38105, USA
| | - Hong Wang
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, 38105, USA
| | - Michael N Edmonson
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee, 38105, USA
| | - Xiang Chen
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee, 38105, USA
| | - Paula Arnold
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee, 38105, USA
| | - Terrence L Geiger
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee, 38105, USA
| | - Gang Wu
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee, 38105, USA
| | - Junmin Peng
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, 38105, USA.,St Jude Proteomics Facility, St Jude Children's Research Hospital, Memphis, Tennessee, 38105, USA
| | - Michael Dyer
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, 38105, USA
| | - James R Downing
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee, 38105, USA
| | - Douglas R Green
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee, 38105, USA
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee, 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee, 38105, USA.
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28
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Paciello G, Ficarra E. FuGePrior: A novel gene fusion prioritization algorithm based on accurate fusion structure analysis in cancer RNA-seq samples. BMC Bioinformatics 2017; 18:58. [PMID: 28114882 PMCID: PMC5260008 DOI: 10.1186/s12859-016-1450-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 12/22/2016] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Latest Next Generation Sequencing technologies opened the way to a novel era of genomic studies, allowing to gain novel insights into multifactorial pathologies as cancer. In particular gene fusion detection and comprehension have been deeply enhanced by these methods. However, state of the art algorithms for gene fusion identification are still challenging. Indeed, they identify huge amounts of poorly overlapping candidates and all the reported fusions should be considered for in lab validation clearly overwhelming wet lab capabilities. RESULTS In this work we propose a novel methodological approach and tool named FuGePrior for the prioritization of gene fusions from paired-end RNA-Seq data. The proposed pipeline combines state of the art tools for chimeric transcript discovery and prioritization, a series of filtering and processing steps designed by considering modern literature on gene fusions and an analysis on functional reliability of gene fusion structure. CONCLUSIONS FuGePrior performance has been assessed on two publicly available paired-end RNA-Seq datasets: The first by Edgren and colleagues includes four breast cancer cell lines and a normal breast sample, whereas the second by Ren and colleagues comprises fourteen primary prostate cancer samples and their paired normal counterparts. FuGePrior results accounted for a reduction in the number of fusions output of chimeric transcript discovery tools that ranges from 65 to 75% depending on the considered breast cancer cell line and from 37 to 65% according to the prostate cancer sample under examination. Furthermore, since both datasets come with a partial validation we were able to assess the performance of FuGePrior in correctly prioritizing real gene fusions. Specifically, 25 out of 26 validated fusions in breast cancer dataset have been correctly labelled as reliable and biologically significant. Similarly, 2 out of 5 validated fusions in prostate dataset have been recognized as priority by FuGePrior tool.
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Affiliation(s)
- Giulia Paciello
- Department of Control and Computer Engineering DAUIN, Politecnico di Torino, C.so Duca degli Abruzzi 24, Turin, 10129, Italy.
| | - Elisa Ficarra
- Department of Control and Computer Engineering DAUIN, Politecnico di Torino, C.so Duca degli Abruzzi 24, Turin, 10129, Italy
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Abstract
Plant cell walls are composed of complex polysaccharides such as cellulose and hemicellulose. In order to efficiently hydrolyze cellulose, the synergistic action of several cellulases is required. Some anaerobic cellulolytic bacteria form multienzyme complexes, namely cellulosomes, while other microorganisms produce a portfolio of diverse enzymes that work in synergistic fashion. Molecular biological methods can mimic such effects through the generation of artificial bi- or multifunctional fusion enzymes. Endoglucanase and β-glucosidase from extremely thermophilic anaerobic bacteria Fervidobacterium gondwanense and Fervidobacterium islandicum, respectively, were fused end-to-end in an approach to optimize polysaccharide degradation. Both enzymes are optimally active at 90 °C and pH 6.0-7.0 representing excellent candidates for fusion experiments. The direct linkage of both enzymes led to an increased activity toward the substrate specific for β-glucosidase, but to a decreased activity of endoglucanase. However, these enzyme chimeras were superior over 1:1 mixtures of individual enzymes, because combined activities resulted in a higher final product yield. Therefore, such fusion enzymes exhibit promising features for application in industrial bioethanol production processes.
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Affiliation(s)
- Mazen Rizk
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, 21073, Hamburg, Germany
| | - Garabed Antranikian
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, 21073, Hamburg, Germany
| | - Skander Elleuche
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, 21073, Hamburg, Germany.
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Lekomtsev S, Aligianni S, Lapao A, Bürckstümmer T. Efficient generation and reversion of chromosomal translocations using CRISPR/Cas technology. BMC Genomics 2016; 17:739. [PMID: 27640184 PMCID: PMC5027121 DOI: 10.1186/s12864-016-3084-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 09/14/2016] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Chromosomal translocations are a hallmark of cancer cells and give rise to fusion oncogenes. To gain insight into the mechanisms governing tumorigenesis, adequate model cell lines are required. RESULTS We employ the versatile CRISPR/Cas system to engineer cell lines in which chromosomal translocations are either generated de novo (CD74-ROS1) or existing translocations are reverted back to the original configuration (BCR-ABL1). To this end, we co-apply two guide RNAs to artificially generate two breakpoints and screen for spontaneous fusion events by PCR. CONCLUSIONS The approach we use is efficient and delivers clones bearing translocationsin a predictable fashion. Detailed analysis suggests that the clones display no additional undesired alterations, implying that the approach is robust and precise.
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Affiliation(s)
- Sergey Lekomtsev
- Horizon Discovery Ltd, Cambridge Research Park, Waterbeach, Cambridge, United Kingdom
| | - Sofia Aligianni
- Horizon Genomics GmbH, Campus Vienna Biocenter, Vienna, Austria
| | - Ana Lapao
- Horizon Genomics GmbH, Campus Vienna Biocenter, Vienna, Austria
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Henry CS, Lerma-Ortiz C, Gerdes SY, Mullen JD, Colasanti R, Zhukov A, Frelin O, Thiaville JJ, Zallot R, Niehaus TD, Hasnain G, Conrad N, Hanson AD, de Crécy-Lagard V. Systematic identification and analysis of frequent gene fusion events in metabolic pathways. BMC Genomics 2016; 17:473. [PMID: 27342196 PMCID: PMC4921024 DOI: 10.1186/s12864-016-2782-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 05/26/2016] [Indexed: 11/19/2022] Open
Abstract
Background Gene fusions are the most powerful type of in silico-derived functional associations. However, many fusion compilations were made when <100 genomes were available, and algorithms for identifying fusions need updating to handle the current avalanche of sequenced genomes. The availability of a large fusion dataset would help probe functional associations and enable systematic analysis of where and why fusion events occur. Results Here we present a systematic analysis of fusions in prokaryotes. We manually generated two training sets: (i) 121 fusions in the model organism Escherichia coli; (ii) 131 fusions found in B vitamin metabolism. These sets were used to develop a fusion prediction algorithm that captured the training set fusions with only 7 % false negatives and 50 % false positives, a substantial improvement over existing approaches. This algorithm was then applied to identify 3.8 million potential fusions across 11,473 genomes. The results of the analysis are available in a searchable database at http://modelseed.org/projects/fusions/. A functional analysis identified 3,000 reactions associated with frequent fusion events and revealed areas of metabolism where fusions are particularly prevalent. Conclusions Customary definitions of fusions were shown to be ambiguous, and a stricter one was proposed. Exploring the genes participating in fusion events showed that they most commonly encode transporters, regulators, and metabolic enzymes. The major rationales for fusions between metabolic genes appear to be overcoming pathway bottlenecks, avoiding toxicity, controlling competing pathways, and facilitating expression and assembly of protein complexes. Finally, our fusion dataset provides powerful clues to decipher the biological activities of domains of unknown function. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2782-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA. .,Computation Institute, The University of Chicago, Chicago, IL, 60637, USA.
| | - Claudia Lerma-Ortiz
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Svetlana Y Gerdes
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA.,Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Jeffrey D Mullen
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Ric Colasanti
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Aleksey Zhukov
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Océane Frelin
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Jennifer J Thiaville
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Rémi Zallot
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Thomas D Niehaus
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Ghulam Hasnain
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Neal Conrad
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Valérie de Crécy-Lagard
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA.
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Andersson MK, Stenman G. The landscape of gene fusions and somatic mutations in salivary gland neoplasms - Implications for diagnosis and therapy. Oral Oncol 2016; 57:63-9. [PMID: 27101980 DOI: 10.1016/j.oraloncology.2016.04.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 04/01/2016] [Indexed: 12/15/2022]
Abstract
Recent studies of the genomic landscape of salivary gland tumors have provided important insights into the molecular pathogenesis of these tumors. The most consistent alterations identified include a translocation-generated gene fusion network involving transcription factors, transcriptional coactivators, tyrosine kinase receptors, and other kinases. In addition, next-generation sequencing studies of a few subtypes of salivary neoplasms have revealed hotspot mutations in individual genes and mutations clustering to specific pathways frequently altered in cancer. Although limited, these studies have opened up new avenues for improved classification and targeted therapies of salivary gland cancers. In this review, we summarize the latest developments in this field, focusing on tumor types for which clinically important molecular data are available.
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Affiliation(s)
- Mattias K Andersson
- Sahlgrenska Cancer Center, Department of Pathology, Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, Sweden
| | - Göran Stenman
- Sahlgrenska Cancer Center, Department of Pathology, Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, Sweden
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Tomlins SA, Day JR, Lonigro RJ, Hovelson DH, Siddiqui J, Kunju LP, Dunn RL, Meyer S, Hodge P, Groskopf J, Wei JT, Chinnaiyan AM. Urine TMPRSS2:ERG Plus PCA3 for Individualized Prostate Cancer Risk Assessment. Eur Urol 2015; 70:45-53. [PMID: 25985884 DOI: 10.1016/j.eururo.2015.04.039] [Citation(s) in RCA: 258] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/29/2015] [Indexed: 01/08/2023]
Abstract
BACKGROUND TMPRSS2:ERG (T2:ERG) and prostate cancer antigen 3 (PCA3) are the most advanced urine-based prostate cancer (PCa) early detection biomarkers. OBJECTIVE Validate logistic regression models, termed Mi-Prostate Score (MiPS), that incorporate serum prostate-specific antigen (PSA; or the multivariate Prostate Cancer Prevention Trial risk calculator version 1.0 [PCPTrc]) and urine T2:ERG and PCA3 scores for predicting PCa and high-grade PCa on biopsy. DESIGN, SETTING, AND PARTICIPANTS T2:ERG and PCA3 scores were generated using clinical-grade transcription-mediated amplification assays. Pretrained MiPS models were applied to a validation cohort of whole urine samples prospectively collected after digital rectal examination from 1244 men presenting for biopsy. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Area under the curve (AUC) was used to compare the performance of serum PSA (or the PCPTrc) alone and MiPS models. Decision curve analysis (DCA) was used to assess clinical benefit. RESULTS AND LIMITATIONS Among informative validation cohort samples (n=1225 [98%], 80% from patients presenting for initial biopsy), models incorporating T2:ERG had significantly greater AUC than PSA (or PCPTrc) for predicting PCa (PSA: 0.693 vs 0.585; PCPTrc: 0.718 vs 0.639; both p<0.001) or high-grade (Gleason score >6) PCa on biopsy (PSA: 0.729 vs 0.651, p<0.001; PCPTrc: 0.754 vs 0.707, p=0.006). MiPS models incorporating T2:ERG score had significantly greater AUC (all p<0.001) than models incorporating only PCA3 plus PSA (or PCPTrc or high-grade cancer PCPTrc [PCPThg]). DCA demonstrated net benefit of the MiPS_PCPTrc (or MiPS_PCPThg) model compared with the PCPTrc (or PCPThg) across relevant threshold probabilities. CONCLUSIONS Incorporating urine T2:ERG and PCA3 scores improves the performance of serum PSA (or PCPTrc) for predicting PCa and high-grade PCa on biopsy. PATIENT SUMMARY Incorporation of two prostate cancer (PCa)-specific biomarkers (TMPRSS2:ERG and PCA3) measured in the urine improved on serum prostate-specific antigen (or a multivariate risk calculator) for predicting the presence of PCa and high-grade PCa on biopsy. A combined test, Mi-Prostate Score, uses models validated in this study and is clinically available to provide individualized risk estimates.
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Affiliation(s)
- Scott A Tomlins
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - John R Day
- Hologic/Gen-Probe Inc., San Diego, CA, USA
| | - Robert J Lonigro
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Daniel H Hovelson
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Javed Siddiqui
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - L Priya Kunju
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Rodney L Dunn
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | | | | | - John T Wei
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA; Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, USA.
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Abstract
Intrahepatic cholangiocarcinomas (iCCA) are primary intrahepatic malignancies originating from biliary epithelia. While both hepatocellular cancer and iCCA can present as mass lesions within the liver, these cancers are distinct in their morphology, etiology, pathology, natural history and response to therapy. There is a need for accurate and sensitive molecular markers for the diagnosis of iCCA. Recent advances in elucidating molecular and genetic characteristics of iCCA offer the potential of molecular-based diagnosis of iCCA. Specific genetic mutations of IDH1/2, BAP1, p53, and KRAS, FGFR gene fusions and alterations in microRNA have all been described in iCCA. Although there are no accurate serum or biliary biomarkers currently available for diagnosis of iCCA, several potential candidates have been identified. Knowledge of specific genetic or molecular abnormalities offers potential for individualized approaches for the treatment of patients with iCCA in the future.
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Affiliation(s)
- Hiroaki Haga
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.
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35
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Caria P, Vanni R. FISH molecular testing in cytological preparations from solid tumors. Mol Cytogenet 2014; 7:56. [PMID: 25478010 PMCID: PMC4255722 DOI: 10.1186/s13039-014-0056-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 07/30/2014] [Indexed: 11/10/2022] Open
Abstract
Many of the exciting new developments in solid tumor molecular cytogenetics impact classical and molecular pathology. Fluorescence in situ hybridization to identify specific DNA target sequences in nuclei of non-dividing cells in solid neoplasms has contributed to the integration of molecular cytogenetics into cytology in spite of the remarkable promiscuity of cancer genes. Indeed, although it is a low-throughput assay, fluorescence in situ hybridization enables the direct disclosure and localization of genetic markers in single nuclei. Gene fusions are among the most prominent genetic alterations in cancer, providing markers that may be determinant in needle biopsies that are negative or suspicious for malignancy, and may contribute to the correct classification of the tumors. In view of the expanding use of fluorescence in situ hybridization in cytology, future challenges include automated sample evaluation and the specification of common criteria for interpreting and reporting results.
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Affiliation(s)
- Paola Caria
- Department of Biomedical Sciences, University of Cagliari – Cittadella Universitaria, 09042 Monserrato (CA), Cagliari, Italy
| | - Roberta Vanni
- Department of Biomedical Sciences, University of Cagliari – Cittadella Universitaria, 09042 Monserrato (CA), Cagliari, Italy
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de Souza RR, Oliveira ID, del Giúdice Paniago M, Yaoita FHK, Caran EMM, Macedo CRPD, Petrilli AS, Abib SDCV, de Seixas Alves MT, de Toledo SRC. Investigation of IGF2, Hedgehog and fusion gene expression profiles in pediatric sarcomas. Growth Horm IGF Res 2014; 24:130-136. [PMID: 24846856 DOI: 10.1016/j.ghir.2014.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 04/04/2014] [Accepted: 04/08/2014] [Indexed: 11/28/2022]
Abstract
UNLABELLED The childhood sarcomas are malignant tumors with high mortality rates. They are divided into two genetic categories: a category without distinct pattern karyotypic changes and the other category showing unique translocations that originate gene rearrangements. This category includes rhabdomyosarcoma (RMS), Ewing's sarcoma (ES) and synovial sarcoma (SS). Diverse studies have related development genes, such as; IGF2, IHH, PTCH1 and GLI1 and sarcomatogenesis. OBJECTIVE To characterize the RMS, ES and SS rearrangements, we quantify the expression of IGF2 IHH, PTCH1 and GLI1 genes and correlate molecular data with clinical parameters of patients. DESIGN We analyzed 29 RMS, 10 SS and 60 ES tumor samples by RT-PCR (polymerase chain reaction-reverse transcription) and qPCR (quantitative PCR). RESULTS Among the samples of ARMS, 50% had rearrangements of PAX3/7-FOXO1, 60% of ES samples were EWS-FLI1 positive and 90% of SS samples were positive for SS18-SSX1/2. In relation to the control reference samples (QPCR Human Reference Total RNA-Stratagene, Human Skeletal Muscle Total RNA-Ambion, Universal RNA Human Normal Tissues-Ambion), RMS samples showed a high IGF2 gene expression (p<0.0001). Moreover, ES samples showed a low IGF2 gene expression (p<0.0001) and high IHH (p<0.0001), PTCH1 (p=0.0173) and GLI1 (p=0.0113) gene expressions. CONCLUSIONS The molecular characterization of IGF and Hedgehog pathway in these pediatric sarcomas may collaborate to enable a better understanding of the biological behavior of these neoplasms.
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Affiliation(s)
- Robson Ramos de Souza
- Pediatric Oncology Institute (GRAACC), Department of Pediatrics, Federal University of São Paulo, São Paulo, SP, Brazil; Department of Structural and Functional Biology, Federal University of São Paulo, São Paulo, SP, Brazil.
| | - Indhira Dias Oliveira
- Pediatric Oncology Institute (GRAACC), Department of Pediatrics, Federal University of São Paulo, São Paulo, SP, Brazil; Department of Structural and Functional Biology, Federal University of São Paulo, São Paulo, SP, Brazil.
| | - Mario del Giúdice Paniago
- Pediatric Oncology Institute (GRAACC), Department of Pediatrics, Federal University of São Paulo, São Paulo, SP, Brazil.
| | - Fernando Hideki Kato Yaoita
- Pediatric Oncology Institute (GRAACC), Department of Pediatrics, Federal University of São Paulo, São Paulo, SP, Brazil; Department of Structural and Functional Biology, Federal University of São Paulo, São Paulo, SP, Brazil.
| | - Eliana Maria Monteiro Caran
- Pediatric Oncology Institute (GRAACC), Department of Pediatrics, Federal University of São Paulo, São Paulo, SP, Brazil.
| | | | - Antonio Sergio Petrilli
- Pediatric Oncology Institute (GRAACC), Department of Pediatrics, Federal University of São Paulo, São Paulo, SP, Brazil.
| | - Simone de Campos Vieira Abib
- Pediatric Oncology Institute (GRAACC), Department of Pediatrics, Federal University of São Paulo, São Paulo, SP, Brazil; Division of Pediatric Surgery, Federal University of São Paulo, São Paulo, SP, Brazil.
| | - Maria Teresa de Seixas Alves
- Pediatric Oncology Institute (GRAACC), Department of Pediatrics, Federal University of São Paulo, São Paulo, SP, Brazil; Department of Pathology, Federal University of São Paulo, São Paulo, SP, Brazil.
| | - Silvia Regina Caminada de Toledo
- Pediatric Oncology Institute (GRAACC), Department of Pediatrics, Federal University of São Paulo, São Paulo, SP, Brazil; Department of Structural and Functional Biology, Federal University of São Paulo, São Paulo, SP, Brazil.
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Abstract
The Sec pathway for export of proteins across the cytoplasmic membrane to the bacterial periplasm and outer membrane was the first secretion pathway to be discovered in bacteria. A combination of bacterial genetics, development of an in vitro membrane vesicle system and the concurrent elaboration of the signal hypothesis from studies on eukaryotes led to the identification and characterization of two pathways leading to protein export through the SecYEG cytoplasmic membrane translocon. The Sec pathway is also required for assembly of proteins into the cytoplasmic membrane. Since the membrane translocon for Sec pathways is conserved across the three domains of life, the history of research progress in eukaryotes and bacteria was facilitated by the close interaction between those studying both classes of organisms.
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Affiliation(s)
- Jon Beckwith
- Department of Microbiology and Immunobiology, Harvard Medical School, HIM Building, Room 1047,77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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