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Vanderstichele T, Burnham KL, de Klein N, Tardaguila M, Howell B, Walter K, Kundu K, Koeppel J, Lee W, Tokolyi A, Persyn E, Nath AP, Marten J, Petrovski S, Roberts DJ, Di Angelantonio E, Danesh J, Berton A, Platt A, Butterworth AS, Soranzo N, Parts L, Inouye M, Paul DS, Davenport EE. Misexpression of inactive genes in whole blood is associated with nearby rare structural variants. Am J Hum Genet 2024; 111:1524-1543. [PMID: 39053458 DOI: 10.1016/j.ajhg.2024.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024] Open
Abstract
Gene misexpression is the aberrant transcription of a gene in a context where it is usually inactive. Despite its known pathological consequences in specific rare diseases, we have a limited understanding of its wider prevalence and mechanisms in humans. To address this, we analyzed gene misexpression in 4,568 whole-blood bulk RNA sequencing samples from INTERVAL study blood donors. We found that while individual misexpression events occur rarely, in aggregate they were found in almost all samples and a third of inactive protein-coding genes. Using 2,821 paired whole-genome and RNA sequencing samples, we identified that misexpression events are enriched in cis for rare structural variants. We established putative mechanisms through which a subset of SVs lead to gene misexpression, including transcriptional readthrough, transcript fusions, and gene inversion. Overall, we develop misexpression as a type of transcriptomic outlier analysis and extend our understanding of the variety of mechanisms by which genetic variants can influence gene expression.
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Affiliation(s)
| | - Katie L Burnham
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Niek de Klein
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Brittany Howell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Klaudia Walter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Kousik Kundu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge, UK
| | - Jonas Koeppel
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Wanseon Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Alex Tokolyi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Elodie Persyn
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Artika P Nath
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Jonathan Marten
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK; Department of Medicine, University of Melbourne, Austin Health, Melbourne, VIC, Australia
| | - David J Roberts
- Radcliffe Department of Medicine, John Radcliffe Hospital, Oxford, UK; Clinical Services, NHS Blood and Transplant, Oxford Centre, John Radcliffe Hospital, Oxford, UK
| | - Emanuele Di Angelantonio
- Human Technopole, Fondazione Human Technopole, Milan, Italy; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK; National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - John Danesh
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK; National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Alix Berton
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Molndal, Sweden
| | - Adam Platt
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK; National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Nicole Soranzo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; Human Technopole, Fondazione Human Technopole, Milan, Italy; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK; National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
| | - Leopold Parts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Michael Inouye
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Dirk S Paul
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
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Walker M, Mayr EM, Koppermann ML, Terron A, Wagner Y, Kling C, Pfarr N. [Molecular pathological analysis through the ages]. PATHOLOGIE (HEIDELBERG, GERMANY) 2024; 45:173-179. [PMID: 38619582 PMCID: PMC11045621 DOI: 10.1007/s00292-024-01326-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
BACKGROUND Molecular pathological examinations of tumor samples encompass a wide range of diagnostic analyses. Especially in recent years, numerous new biomarkers have come to the forefront-the analysis of which is crucial for therapy decisions. OBJECTIVES Within the field of molecular pathology, the demands of next generation sequencing (NGS)-based requirements have experienced massive growth in recent years. To meet this demand, methods are constantly being adapted and further developed. The following sections aim to illuminate how this trend arises and which analyses are gaining importance. METHODS The article provides an overview of the essential nucleic acid-based analysis techniques in the field of massive parallel sequencing. Terms such as DNA- and RNA-based techniques, as well as the associated analysis methods, are described, particularly with regard to their use in routine molecular pathological diagnostics. RESULTS The breadth of genomic sequencing has been steadily growing in recent years, particularly due to the increasing relevance of personalized medicine, along with the rising approvals of targeted therapeutics. This necessitates, among other things, the analysis of new biomarkers. The diagnostics as part of interdisciplinary molecular tumor boards (MTB) are now based on large gene panels (> 1 megabase). Furthermore, through the "Modellvorhaben Genomsequenzierung" § 64e, whole exome or whole genome sequencing has been made available for oncological patients. Given these developments, it is evident that future analyses will require the integration of additional omics fields, such as whole transcriptome analysis, epigenomics, and proteomics. CONCLUSION The challenges of personalized medicine along with the necessity of simultaneously assessing numerous new biomarkers require the implementation and execution of new techniques in molecular pathology whose complexity is steadily increasing.
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Affiliation(s)
- Maria Walker
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Eva-Maria Mayr
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Mai-Lan Koppermann
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Ana Terron
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Yoko Wagner
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Charlotte Kling
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
- Deutsches Konsortium für Translationale Krebsforschung (DKTK), Heidelberg, Deutschland
| | - Nicole Pfarr
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland.
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Jama M, Zhang M, Poile C, Nakas A, Sharkey A, Dzialo J, Dawson A, Kutywayo K, Fennell DA, Hollox EJ. Gene fusions during the early evolution of mesothelioma correlate with impaired DNA repair and Hippo pathways. Genes Chromosomes Cancer 2024; 63:e23189. [PMID: 37421230 DOI: 10.1002/gcc.23189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/10/2023] Open
Abstract
Malignant pleural mesothelioma (MPM), a rare cancer a long latency period (up to 40 years) between asbestos exposure and disease presentation. The mechanisms coupling asbestos to recurrent somatic alterations are poorly defined. Gene fusions arising through genomic instability may create novel drivers during early MPM evolution. We explored the gene fusions that occurred early in the evolutionary history of the tumor. We conducted multiregional whole exome sequencing (WES) of 106 samples from 20 patients undergoing pleurectomy decortication and identified 24 clonal nonrecurrent gene fusions, three of which were novel (FMO9P-OR2W5, GBA3, and SP9). The number of early gene fusion events detected varied from zero to eight per tumor, and presence of gene fusions was associated with clonal losses involving the Hippo pathway genes and homologous recombination DNA repair genes. Fusions involved known tumor suppressors BAP1, MTAP, and LRP1B, and a clonal oncogenic fusion involving CACNA1D-ERC2, PARD3B-NT5DC2, and STAB2-NT5DC2 fusions were also identified as clonal fusions. Gene fusions events occur early during MPM evolution. Individual fusions are rare as no recurrent truncal fusions event were found. This suggests the importance of early disruption of these pathways in generating genomic rearrangements resulting in potentially oncogenic gene fusions.
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Affiliation(s)
- Maymun Jama
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Min Zhang
- Mesothelioma Research Programme, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
- Novogene Corpotation Ltd., Building 301, Beijing, China
| | - Charlotte Poile
- Mesothelioma Research Programme, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Apostolos Nakas
- Thoracic Medical Oncology, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Annabel Sharkey
- Department of Cardio-Thoracic Surgery, Sheffield Teaching Hospital NHS Trust, Sheffield, UK
| | - Joanna Dzialo
- Mesothelioma Research Programme, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Alan Dawson
- Thoracic Medical Oncology, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Kudazyi Kutywayo
- Mesothelioma Research Programme, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
- Department of Cardio-Thoracic Surgery, Sheffield Teaching Hospital NHS Trust, Sheffield, UK
| | - Dean A Fennell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Mesothelioma Research Programme, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
- Thoracic Medical Oncology, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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Hafstað V, Häkkinen J, Persson H. Fast and sensitive validation of fusion transcripts in whole-genome sequencing data. BMC Bioinformatics 2023; 24:359. [PMID: 37741966 PMCID: PMC10518092 DOI: 10.1186/s12859-023-05489-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023] Open
Abstract
BACKGROUND In cancer, genomic rearrangements can create fusion genes that either combine protein-coding sequences from two different partner genes or place one gene under the control of the promoter of another gene. These fusion genes can act as oncogenic drivers in tumor development and several fusions involving kinases have been successfully exploited as drug targets. Expressed fusions can be identified in RNA sequencing (RNA-Seq) data, but fusion prediction software often has a high fraction of false positive fusion transcript predictions. This is problematic for both research and clinical applications. RESULTS We describe a method for validation of fusion transcripts detected by RNA-Seq in matched whole-genome sequencing (WGS) data. Our pipeline uses discordant read pairs to identify supported fusion events and analyzes soft-clipped read alignments to determine genomic breakpoints. We have tested it on matched RNA-Seq and WGS data for both tumors and cancer cell lines and show that it can be used to validate both new predicted gene fusions and experimentally validated fusion events. It was considerably faster and more sensitive than using BreakDancer and Manta, software that is instead designed to detect many different types of structural variants on a genome-wide scale. CONCLUSIONS We have developed a fast and very sensitive pipeline for validation of gene fusions detected by RNA-Seq in matched WGS data. It can be used to identify high-quality gene fusions for further bioinformatic and experimental studies, including validation of genomic breakpoints and studies of the mechanisms that generate fusions. In a clinical setting, it could help find expressed gene fusions for personalized therapy.
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Affiliation(s)
- Völundur Hafstað
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University Cancer Centre, Lund, Sweden
| | - Jari Häkkinen
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University Cancer Centre, Lund, Sweden
| | - Helena Persson
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University Cancer Centre, Lund, Sweden.
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Kim TW, Ji H, Yun NH, Shin CH, Kim HH, Cho YB. Two antisense RNAs-AFAP1-AS1 and MLK7-AS1-promote colorectal cancer progression by sponging miR-149-5p and miR-485-5p. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:305-320. [PMID: 37547289 PMCID: PMC10400868 DOI: 10.1016/j.omtn.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 07/11/2023] [Indexed: 08/08/2023]
Abstract
Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths. Antisense RNAs (asRNAs) are closely associated with cancer malignancy. This study aimed to identify the action mechanism of asRNAs in controlling CRC malignancy. Analysis of the RNA sequencing data revealed that AFAP1-AS1 and MLK7-AS1 were upregulated in CRC patients and cell lines. High levels of both asRNAs were associated with poor prognosis in patients with CRC. Both in vitro and in vivo experiments revealed that the knockdown of the two asRNAs decreased the proliferative and metastatic abilities of CRC cells. Mechanistically, AFAP1-AS1 and MLK7-AS1 decreased the levels of miR-149-5p and miR-485-5p by functioning as ceRNAs. Overexpression of miRNAs by introducing miRNA mimics suppressed the expression of SHMT2 and IGFBP5 by directly binding to the 3' UTR of their mRNA. Knockdown of both asRNAs decreased the expression of SHMT2 and IGFBP5, which was reversed by inhibition of both miRNAs by miRNA inhibitors. In vivo pharmacological targeting of both asRNAs by small interfering RNA-loaded nanoparticles showed that knockdown of asRNAs significantly reduced tumor growth and metastasis. Our findings demonstrate that AFAP1-AS1 and MLK7-AS1 promote CRC progression by sponging the tumor-suppressing miRNAs miR-149-5p and miR-485-5p, thus upregulating SHMT2 and IGFBP5.
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Affiliation(s)
- Tae Won Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, Republic of Korea
| | - Haein Ji
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, Republic of Korea
| | - Nak Hyeon Yun
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, Republic of Korea
| | - Chang Hoon Shin
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, Republic of Korea
| | - Hyeon Ho Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, Republic of Korea
- Institute for Future Medicine, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Yong Beom Cho
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, Republic of Korea
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Gyeonggi-do 16419, Republic of Korea
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Mistretta B, Rankothgedera S, Castillo M, Rao M, Holloway K, Bhardwaj A, El Noafal M, Albarracin C, El-Zein R, Rezaei H, Su X, Akbani R, Shao XM, Czerniecki BJ, Karchin R, Bedrosian I, Gunaratne PH. Chimeric RNAs reveal putative neoantigen peptides for developing tumor vaccines for breast cancer. Front Immunol 2023; 14:1188831. [PMID: 37744342 PMCID: PMC10512078 DOI: 10.3389/fimmu.2023.1188831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/27/2023] [Indexed: 09/26/2023] Open
Abstract
Introduction We present here a strategy to identify immunogenic neoantigen candidates from unique amino acid sequences at the junctions of fusion proteins which can serve as targets in the development of tumor vaccines for the treatment of breastcancer. Method We mined the sequence reads of breast tumor tissue that are usually discarded as discordant paired-end reads and discovered cancer specific fusion transcripts using tissue from cancer free controls as reference. Binding affinity predictions of novel peptide sequences crossing the fusion junction were analyzed by the MHC Class I binding predictor, MHCnuggets. CD8+ T cell responses against the 15 peptides were assessed through in vitro Enzyme Linked Immunospot (ELISpot). Results We uncovered 20 novel fusion transcripts from 75 breast tumors of 3 subtypes: TNBC, HER2+, and HR+. Of these, the NSFP1-LRRC37A2 fusion transcript was selected for further study. The 3833 bp chimeric RNA predicted by the consensus fusion junction sequence is consistent with a read-through transcription of the 5'-gene NSFP1-Pseudo gene NSFP1 (NSFtruncation at exon 12/13) followed by trans-splicing to connect withLRRC37A2 located immediately 3' through exon 1/2. A total of 15 different 8-mer neoantigen peptides discovered from the NSFP1 and LRRC37A2 truncations were predicted to bind to a total of 35 unique MHC class I alleles with a binding affinity of IC50<500nM.); 1 of which elicited a robust immune response. Conclusion Our data provides a framework to identify immunogenic neoantigen candidates from fusion transcripts and suggests a potential vaccine strategy to target the immunogenic neopeptides in patients with tumors carrying the NSFP1-LRRC37A2 fusion.
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Affiliation(s)
- Brandon Mistretta
- Department of Biology & Biochemistry, University of Houston, Houston, TX, United States
| | - Sakuni Rankothgedera
- Department of Biology & Biochemistry, University of Houston, Houston, TX, United States
| | - Micah Castillo
- Department of Biology & Biochemistry, University of Houston, Houston, TX, United States
| | - Mitchell Rao
- Department of Biology & Biochemistry, University of Houston, Houston, TX, United States
| | - Kimberly Holloway
- Department of Biology & Biochemistry, University of Houston, Houston, TX, United States
| | - Anjana Bhardwaj
- Department of Breast Surgical Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Maha El Noafal
- Department of Medicine, Houston Methodist Research Institute, Houston, TX, United States
| | - Constance Albarracin
- Department of Pathology, The UT MD Anderson Cancer Center, Houston, TX, United States
| | - Randa El-Zein
- Department of Medicine, Houston Methodist Research Institute, Houston, TX, United States
| | - Hengameh Rezaei
- Department of Biology & Biochemistry, University of Houston, Houston, TX, United States
| | - Xiaoping Su
- Department of Bioinformatics & Computational Biology, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Rehan Akbani
- Department of Bioinformatics & Computational Biology, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Xiaoshan M. Shao
- Biomedical Engineering Department, Institute for Computational Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Brian J. Czerniecki
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Rachel Karchin
- Biomedical Engineering Department, Institute for Computational Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Isabelle Bedrosian
- Department of Breast Surgical Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Preethi H. Gunaratne
- Department of Biology & Biochemistry, University of Houston, Houston, TX, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
- Department of Breast Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, United States
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Ilnytskyy Y, Petersen L, McIntyre JB, Konno M, D'Silva A, Dean M, Elegbede A, Golubov A, Kovalchuk O, Kovalchuk I, Bebb G. Genome-wide Detection of Chimeric Transcripts in Early-stage Non-small Cell Lung Cancer. Cancer Genomics Proteomics 2023; 20:417-432. [PMID: 37643782 PMCID: PMC10464939 DOI: 10.21873/cgp.20394] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/23/2023] [Accepted: 07/06/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND/AIM Lung cancer remains the main culprit in cancer-related mortality worldwide. Transcript fusions play a critical role in the initiation and progression of multiple cancers. Treatment approaches based on specific targeting of discovered driver events, such as mutations in EGFR, and fusions in NTRK, ROS1, and ALK genes led to profound improvements in clinical outcomes. The formation of chimeric proteins due to genomic rearrangements or at the post-transcriptional level is widespread and plays a critical role in tumor initiation and progression. Yet, the fusion landscape of lung cancer remains underexplored. MATERIALS AND METHODS We used the JAFFA pipeline to discover transcript fusions in early-stage non-small cell lung cancer (NSCLC). The set of detected fusions was further analyzed to identify recurrent events, genes with multiple partners and fusions with high predicted oncogenic potential. Finally, we used a generalized linear model (GLM) to establish statistical associations between fusion occurrences and clinicopathological variables. RNA sequencing was used to discover and characterize transcript fusions in 270 NSCLC samples selected from the Glans-Look specimen repository. The samples were obtained during the early stages of disease prior to the initiation of chemo- or radiotherapy. RESULTS We identified a set of 792 fusions where 751 were novel, and 33 were recurrent. Four of the 33 recurrent fusions were significantly associated with clinicopathological variables. Several of the fusion partners were represented by well-established oncogenes ERBB4, BRAF, FGFR2, and MET. CONCLUSION The data presented in this study allow researchers to identify, select, and validate promising candidates for targeted clinical interventions.
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Affiliation(s)
| | | | | | - Mie Konno
- Alberta Health Services, Calgary, Alberta, Canada
| | | | | | | | | | | | | | - Gwyn Bebb
- University of Calgary, Calgary, Alberta, Canada
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Knott T, Creeden J, Horbach B, Rauch‐Zumbrägel M, Vat L, Harnik H, Maravic Z. Stakeholders' expectations of precision medicine: A qualitative study to identify areas of (mis)alignment. Health Sci Rep 2023; 6:e1428. [PMID: 37599652 PMCID: PMC10435831 DOI: 10.1002/hsr2.1428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 06/08/2023] [Accepted: 07/04/2023] [Indexed: 08/22/2023] Open
Abstract
Background and Aims To sustainably address challenges in implementing precision medicine (PM), coordinated efforts of different stakeholders are required. Understanding their expectations represents a first key step toward aligning on future actions and strategies. Here, we aimed to explore the expectations of different stakeholders from themselves and each other regarding PM. Methods This collaborative qualitative study was initiated by the global multistakeholder consortium From Testing to Targeted Treatments (FT3). Structured interviews were conducted with participants from five stakeholder groups: patients/patient advocates, healthcare providers (HCPs), researchers, policymakers/regulators/payers and industry representatives. A broad reach across geography, roles, experiences, and disease areas was sought. Results were analyzed by grounded theory methodology. Results All stakeholders stated that optimal implementation of PM can only be achieved through collaboration; industry representatives were the biggest promoters of collaboration. Stakeholders agreed that PM should be implemented focusing on the patient's best interest; HCPs were seen as important gatekeepers for PM by interacting directly with patients, and policymakers/payers were perceived as the most important drivers of access to PM. Areas of misalignment included the role of industry in clinical trial design and in access to PM (perceived as important by patients, HCPs and policymakers but not by industry representatives), and the stakeholders responsible for elaborating guidelines on PM use (patients indicated policymakers, while researchers indicated themselves). Priorities for optimal PM implementation and suggested actions included the need for enhancing high-level policy focus, improving genomic literacy, optimizing the health technology assessment for PM, advocating for equitable access, promoting collaboration between industry and other stakeholder groups and development of reliable research standards. Conclusion Stakeholder expectations revealed in this study suggested that no stakeholder group can drive change on its own; a global, multistakeholder collaborative approach that brings together current programs and best practices to support universal access to PM is needed.
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Affiliation(s)
- Tanya Knott
- Sarah Jennifer Knott FoundationDublinIreland
- From Testing to Targeted Treatments (FT3) Board Member, The SynergistBrusselsBelgium
| | - James Creeden
- From Testing to Targeted Treatments (FT3) Board Member, The SynergistBrusselsBelgium
- Creeden ConsultingBaselSwitzerland
| | - Benjamin Horbach
- F. Hoffmann‐La Roche Ltd.BaselSwitzerland
- From Testing to Targeted Treatments (FT3) Member, The SynergistBrusselsBelgium
| | | | - Lidewij Vat
- From Testing to Targeted Treatments (FT3) Program Team, The SynergistBrusselsBelgium
| | - Helena Harnik
- From Testing to Targeted Treatments (FT3) Program Team, The SynergistBrusselsBelgium
| | - Zorana Maravic
- From Testing to Targeted Treatments (FT3) Member, The SynergistBrusselsBelgium
- Digestive Cancers EuropeBrusselsBelgium
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Maximizing Small Biopsy Patient Samples: Unified RNA-Seq Platform Assessment of over 120,000 Patient Biopsies. J Pers Med 2022; 13:jpm13010024. [PMID: 36675685 PMCID: PMC9866839 DOI: 10.3390/jpm13010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/06/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Despite its wide-ranging benefits, whole-transcriptome or RNA exome profiling is challenging to implement in a clinical diagnostic setting. The Unified Assay is a comprehensive workflow wherein exome-enriched RNA-sequencing (RNA-Seq) assays are performed on clinical samples and analyzed by a series of advanced machine learning-based classifiers. Gene expression signatures and rare and/or novel genomic events, including fusions, mitochondrial variants, and loss of heterozygosity were assessed using RNA-Seq data generated from 120,313 clinical samples across three clinical indications (thyroid cancer, lung cancer, and interstitial lung disease). Since its implementation, the data derived from the Unified Assay have allowed significantly more patients to avoid unnecessary diagnostic surgery and have played an important role in guiding follow-up decisions regarding treatment. Collectively, data from the Unified Assay show the utility of RNA-Seq and RNA expression signatures in the clinical laboratory, and their importance to the future of precision medicine.
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10
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Dorney R, Dhungel BP, Rasko JEJ, Hebbard L, Schmitz U. Recent advances in cancer fusion transcript detection. Brief Bioinform 2022; 24:6918739. [PMID: 36527429 PMCID: PMC9851307 DOI: 10.1093/bib/bbac519] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/11/2022] [Accepted: 10/31/2022] [Indexed: 12/23/2022] Open
Abstract
Extensive investigation of gene fusions in cancer has led to the discovery of novel biomarkers and therapeutic targets. To date, most studies have neglected chromosomal rearrangement-independent fusion transcripts and complex fusion structures such as double or triple-hop fusions, and fusion-circRNAs. In this review, we untangle fusion-related terminology and propose a classification system involving both gene and transcript fusions. We highlight the importance of RNA-level fusions and how long-read sequencing approaches can improve detection and characterization. Moreover, we discuss novel bioinformatic tools to identify fusions in long-read sequencing data and strategies to experimentally validate and functionally characterize fusion transcripts.
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Affiliation(s)
- Ryley Dorney
- epartment of Molecular & Cell Biology, College of Public Health, Medical & Vet Sciences, James Cook University, Douglas, QLD 4811, Australia,Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns 4878, Australia
| | - Bijay P Dhungel
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia,Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2006, Australia,Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns 4878, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia,Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Lionel Hebbard
- epartment of Molecular & Cell Biology, College of Public Health, Medical & Vet Sciences, James Cook University, Douglas, QLD 4811, Australia,Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, Sydney, New South Wales, Australia
| | - Ulf Schmitz
- Corresponding author. Ulf Schmitz, Department of Molecular and Cell Biology, College of Public Health, Medical and Vet Sciences, James Cook University, Douglas, QLD 4811, Australia. E-mail:
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11
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Fonseca-Montaño MA, Blancas S, Herrera-Montalvo LA, Hidalgo-Miranda A. Cancer Genomics. Arch Med Res 2022; 53:723-731. [PMID: 36460546 DOI: 10.1016/j.arcmed.2022.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 12/04/2022]
Abstract
In the past decade, genomics has fundamentally changed our view of cancer biology, allowing comprehensive analyses of mutations, copy number alterations, structural variants, gene expression and DNA methylation profiles in large-scale studies across different cancer types. Efforts like The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) have fostered international collaborations for cancer genomic analyses and have generated public databases that give scientists around the world access to thoroughly curated data, which have been extensively used as a tool for further hypothesis driven research on several aspects of cancer biology. In parallel, some of these findings are being translated into specific clinical benefits for cancer patients. In this review, we provide a brief historical description of the evolution of international public cancer genome projects and related databases, as well as we discuss about their impact on general cancer research.
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Affiliation(s)
- Marco A Fonseca-Montaño
- Instituto Nacional de Medicina Genómica, Ciudad de México, México; Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Ciudad de México, México
| | - Susana Blancas
- Instituto Nacional de Medicina Genómica, Ciudad de México, México; Cátedras Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México; Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Ciudad de México, México
| | | | - Alfredo Hidalgo-Miranda
- Instituto Nacional de Medicina Genómica, Ciudad de México, México; Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Ciudad de México, México.
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12
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PANAGOPOULOS IOANNIS, HEIM SVERRE. Neoplasia-associated Chromosome Translocations Resulting in Gene Truncation. Cancer Genomics Proteomics 2022; 19:647-672. [PMID: 36316036 PMCID: PMC9620447 DOI: 10.21873/cgp.20349] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/27/2022] Open
Abstract
Chromosomal translocations in cancer as well as benign neoplasias typically lead to the formation of fusion genes. Such genes may encode chimeric proteins when two protein-coding regions fuse in-frame, or they may result in deregulation of genes via promoter swapping or translocation of the gene into the vicinity of a highly active regulatory element. A less studied consequence of chromosomal translocations is the fusion of two breakpoint genes resulting in an out-of-frame chimera. The breaks then occur in one or both protein-coding regions forming a stop codon in the chimeric transcript shortly after the fusion point. Though the latter genetic events and mechanisms at first awoke little research interest, careful investigations have established them as neither rare nor inconsequential. In the present work, we review and discuss the truncation of genes in neoplastic cells resulting from chromosomal rearrangements, especially from seemingly balanced translocations.
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Affiliation(s)
- IOANNIS PANAGOPOULOS
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - SVERRE HEIM
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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13
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Kiyose H, Nakagawa H, Ono A, Aikata H, Ueno M, Hayami S, Yamaue H, Chayama K, Shimada M, Wong JH, Fujimoto A. Comprehensive analysis of full-length transcripts reveals novel splicing abnormalities and oncogenic transcripts in liver cancer. PLoS Genet 2022; 18:e1010342. [PMID: 35926060 PMCID: PMC9380957 DOI: 10.1371/journal.pgen.1010342] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/16/2022] [Accepted: 07/14/2022] [Indexed: 12/24/2022] Open
Abstract
Genes generate transcripts of various functions by alternative splicing. However, in most transcriptome studies, short-reads sequencing technologies (next-generation sequencers) have been used, leaving full-length transcripts unobserved directly. Although long-reads sequencing technologies would enable the sequencing of full-length transcripts, the data analysis is difficult. In this study, we developed an analysis pipeline named SPLICE and analyzed cDNA sequences from 42 pairs of hepatocellular carcinoma (HCC) and matched non-cancerous livers with an Oxford Nanopore sequencer. Our analysis detected 46,663 transcripts from the protein-coding genes in the HCCs and the matched non-cancerous livers, of which 5,366 (11.5%) were novel. A comparison of expression levels identified 9,933 differentially expressed transcripts (DETs) in 4,744 genes. Interestingly, 746 genes with DETs, including the LINE1-MET transcript, were not found by a gene-level analysis. We also found that fusion transcripts of transposable elements and hepatitis B virus (HBV) were overexpressed in HCCs. In vitro experiments on DETs showed that LINE1-MET and HBV-human transposable elements promoted cell growth. Furthermore, fusion gene detection showed novel recurrent fusion events that were not detected in the short-reads. These results suggest the efficiency of full-length transcriptome studies and the importance of splicing variants in carcinogenesis. Genes generate transcripts of various functions by alternative splicing. However, in most transcriptome studies, short-reads sequencing technologies (next-generation sequencers) have been used, leaving full-length transcripts unobserved directly. In this study, we developed an analysis pipeline named SPLICE for long-read transcriptome sequencing and analyzed cDNA sequences from 42 pairs of hepatocellular carcinoma (HCC), and matched non-cancerous livers with an Oxford Nanopore sequencer. Our analysis detected 5,366 novel transcripts and 9,933 differentially expressed transcripts in 4,744 genes between HCCs and non-cancerous livers. An analysis of hepatitis B virus (HBV) transcripts showed that fusion transcripts of the HBV gene and human transposable elements were overexpressed in HBV-infected HCCs. We also identified fusion genes that were not found in the short-reads. These results suggest that long-reads sequencing technologies provide a fuller understanding of cancer transcripts and that our method contributes to the analysis of transcriptome sequences by such technologies.
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Affiliation(s)
- Hiroki Kiyose
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Atsushi Ono
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hiroshi Aikata
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Masaki Ueno
- Department of Surgery II, Wakayama Medical University, Wakayama, Japan
| | - Shinya Hayami
- Department of Surgery II, Wakayama Medical University, Wakayama, Japan
| | - Hiroki Yamaue
- Department of Surgery II, Wakayama Medical University, Wakayama, Japan
| | - Kazuaki Chayama
- Collaborative Research Laboratory of Medical Innovation, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Research Center for Hepatology and Gastroenterology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Mihoko Shimada
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jing Hao Wong
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akihiro Fujimoto
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- * E-mail:
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14
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Karaoglanoglu F, Chauve C, Hach F. Genion, an accurate tool to detect gene fusion from long transcriptomics reads. BMC Genomics 2022; 23:129. [PMID: 35164688 PMCID: PMC8842519 DOI: 10.1186/s12864-022-08339-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 01/27/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The advent of next-generation sequencing technologies empowered a wide variety of transcriptomics studies. A widely studied topic is gene fusion which is observed in many cancer types and suspected of having oncogenic properties. Gene fusions are the result of structural genomic events that bring two genes closely located and result in a fused transcript. This is different from fusion transcripts created during or after the transcription process. These chimeric transcripts are also known as read-through and trans-splicing transcripts. Gene fusion discovery with short reads is a well-studied problem, and many methods have been developed. But the sensitivity of these methods is limited by the technology, especially the short read length. Advances in long-read sequencing technologies allow the generation of long transcriptomics reads at a low cost. Transcriptomic long-read sequencing presents unique opportunities to overcome the shortcomings of short-read technologies for gene fusion detection while introducing new challenges. RESULTS We present Genion, a sensitive and fast gene fusion detection method that can also detect read-through events. We compare Genion against a recently introduced long-read gene fusion discovery method, LongGF, both on simulated and real datasets. On simulated data, Genion accurately identifies the gene fusions and its clustering accuracy for detecting fusion reads is better than LongGF. Furthermore, our results on the breast cancer cell line MCF-7 show that Genion correctly identifies all the experimentally validated gene fusions. CONCLUSIONS Genion is an accurate gene fusion caller. Genion is implemented in C++ and is available at https://github.com/vpc-ccg/genion .
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Affiliation(s)
- Fatih Karaoglanoglu
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada.,Vancouver Prostate Centre, Vancouver, BC, Canada
| | - Cedric Chauve
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada.
| | - Faraz Hach
- Vancouver Prostate Centre, Vancouver, BC, Canada. .,Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada.
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15
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Loo SK, Yates ME, Yang S, Oesterreich S, Lee AV, Wang X. Fusion-Associated Carcinomas of the Breast: Diagnostic, Prognostic, and Therapeutic Significance. Genes Chromosomes Cancer 2022; 61:261-273. [PMID: 35106856 DOI: 10.1002/gcc.23029] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 11/11/2022] Open
Abstract
Recurrent gene fusions comprise a class of viable genetic targets in solid tumors that have culminated several recent break-through cancer therapies. Their role in breast cancer, however, remains largely underappreciated due to the complexity of genomic rearrangements in breast malignancy. Just recently, we and others have identified several recurrent gene fusions in breast cancer with important clinical and biological implications. Examples of the most significant recurrent gene fusions to date include 1) ESR1-CCDC170 gene fusions in luminal B and endocrine resistant breast cancer that exert oncogenic function via modulating the HER2/HER3/SRC complex, 2) ESR1 exon 6 fusions in metastatic disease that drive estrogen-independent ER transcriptional activity, 3) BCL2L14-ETV6 fusions in a more aggressive form of the triple negative subtype that prime epithelial-mesenchymal transition and endow paclitaxel resistance, 4) the ETV6-NTRK3 fusion in secretory breast carcinoma that constitutively activates NTRK3 kinase, 5) the oncogenic MYB-NFIB fusion as a genetic driver underpinning adenoid cystic carcinomas of the breast that activates MYB pathway, and 6) the NOTCH/MAST kinase gene fusions that activate NOTCH and MAST signaling. Importantly, these fusions are enriched in more aggressive and lethal breast cancer presentations and appear to confer therapeutic resistance. Thus, these gene fusions could be utilized as genetic biomarkers to identify patients that require more intensive treatment and surveillance. In addition, kinase fusions are currently being evaluated in breast cancer clinical trials and on-going mechanistic investigation is exposing therapeutic vulnerabilities in patients with fusion positive disease. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Suet Kee Loo
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Megan E Yates
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA, USA.,Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sichun Yang
- Center for Proteomics and Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| | - Steffi Oesterreich
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adrian V Lee
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xiaosong Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
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16
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Davidson NM, Chen Y, Sadras T, Ryland GL, Blombery P, Ekert PG, Göke J, Oshlack A. JAFFAL: detecting fusion genes with long-read transcriptome sequencing. Genome Biol 2022; 23:10. [PMID: 34991664 PMCID: PMC8739696 DOI: 10.1186/s13059-021-02588-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 12/22/2021] [Indexed: 12/26/2022] Open
Abstract
In cancer, fusions are important diagnostic markers and targets for therapy. Long-read transcriptome sequencing allows the discovery of fusions with their full-length isoform structure. However, due to higher sequencing error rates, fusion finding algorithms designed for short reads do not work. Here we present JAFFAL, to identify fusions from long-read transcriptome sequencing. We validate JAFFAL using simulations, cell lines, and patient data from Nanopore and PacBio. We apply JAFFAL to single-cell data and find fusions spanning three genes demonstrating transcripts detected from complex rearrangements. JAFFAL is available at https://github.com/Oshlack/JAFFA/wiki .
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Affiliation(s)
- Nadia M Davidson
- Peter MacCallum Cancer Centre, Victoria, Australia.
- School of BioSciences, University of Melbourne, Victoria, Australia.
- The Walter and Eliza Hall Institute, Victoria, Australia.
| | - Ying Chen
- Genome Institute of Singapore, Singapore, Singapore
| | - Teresa Sadras
- Peter MacCallum Cancer Centre, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Georgina L Ryland
- Peter MacCallum Cancer Centre, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
- Centre for Cancer Research, University of Melbourne, Victoria, Australia
| | - Piers Blombery
- Peter MacCallum Cancer Centre, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Paul G Ekert
- Peter MacCallum Cancer Centre, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
- Children's Cancer Institute, Lowy Cancer Centre, UNSW, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW, Sydney, NSW, Australia
- Murdoch Children's Research Institute, Victoria, Australia
| | - Jonathan Göke
- Genome Institute of Singapore, Singapore, Singapore
- National Cancer Centre Singapore, Singapore, Singapore
| | - Alicia Oshlack
- Peter MacCallum Cancer Centre, Victoria, Australia.
- School of BioSciences, University of Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia.
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17
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Palande V, Siegal T, Detroja R, Gorohovski A, Glass R, Flueh C, Kanner AA, Laviv Y, Har-Nof S, Levy-Barda A, Viviana Karpuj M, Kurtz M, Perez S, Raviv Shay D, Frenkel-Morgenstern M. Detection of gene mutations and gene-gene fusions in circulating cell-free DNA of glioblastoma patients: an avenue for clinically relevant diagnostic analysis. Mol Oncol 2021; 16:2098-2114. [PMID: 34875133 PMCID: PMC9120899 DOI: 10.1002/1878-0261.13157] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 09/04/2021] [Accepted: 12/06/2021] [Indexed: 11/20/2022] Open
Abstract
Glioblastoma (GBM) is the most common type of glioma and is uniformly fatal. Currently, tumour heterogeneity and mutation acquisition are major impedances for tailoring personalized therapy. We collected blood and tumour tissue samples from 25 GBM patients and 25 blood samples from healthy controls. Cell‐free DNA (cfDNA) was extracted from the plasma of GBM patients and from healthy controls. Tumour DNA was extracted from fresh tumour samples. Extracted DNA was sequenced using a whole‐genome sequencing procedure. We also collected 180 tumour DNA datasets from GBM patients publicly available at the TCGA/PANCANCER project. These data were analysed for mutations and gene–gene fusions that could be potential druggable targets. We found that plasma cfDNA concentrations in GBM patients were significantly elevated (22.6 ± 5 ng·mL−1), as compared to healthy controls (1.4 ± 0.4 ng·mL−1) of the same average age. We identified unique mutations in the cfDNA and tumour DNA of each GBM patient, including some of the most frequently mutated genes in GBM according to the COSMIC database (TP53, 18.75%; EGFR, 37.5%; NF1, 12.5%; LRP1B, 25%; IRS4, 25%). Using our gene–gene fusion database, ChiTaRS 5.0, we identified gene–gene fusions in cfDNA and tumour DNA, such as KDR–PDGFRA and NCDN–PDGFRA, which correspond to previously reported alterations of PDGFRA in GBM (44% of all samples). Interestingly, the PDGFRA protein fusions can be targeted by tyrosine kinase inhibitors such as imatinib, sunitinib, and sorafenib. Moreover, we identified BCR–ABL1 (in 8% of patients), COL1A1–PDGFB (8%), NIN–PDGFRB (8%), and FGFR1–BCR (4%) in cfDNA of patients, which can be targeted by analogues of imatinib. ROS1 fusions (CEP85L–ROS1 and GOPC–ROS1), identified in 8% of patient cfDNA, might be targeted by crizotinib, entrectinib, or larotrectinib. Thus, our study suggests that integrated analysis of cfDNA plasma concentration, gene mutations, and gene–gene fusions can serve as a diagnostic modality for distinguishing GBM patients who may benefit from targeted therapy. These results open new avenues for precision medicine in GBM, using noninvasive liquid biopsy diagnostics to assess personalized patient profiles. Moreover, repeated detection of druggable targets over the course of the disease may provide real‐time information on the evolving molecular landscape of the tumour.
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Affiliation(s)
- Vikrant Palande
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
| | - Tali Siegal
- Neuro-Oncology Center, Rabin Medical Center, Petach Tikva, Israel and Hebrew University, 4941492, Jerusalem, Israel
| | - Rajesh Detroja
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
| | | | - Rainer Glass
- Department of Neurosurgery, Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Charlotte Flueh
- Department of Neurosurgery, University Hospital of Schleswig-Holstein, Campus Kiel, 24105, Kiel, Germany
| | - Andrew A Kanner
- Department of Neurosurgery, Rabin Medical Center, Petach Tikva, 4941492, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yoseph Laviv
- Department of Neurosurgery, Rabin Medical Center, Petach Tikva, 4941492, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sagi Har-Nof
- Department of Neurosurgery, Rabin Medical Center, Petach Tikva, 4941492, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Adva Levy-Barda
- Department of Pathology, Rabin Medical Center, Petach Tikva, 4941492, Israel
| | | | - Marina Kurtz
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
| | - Shira Perez
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
| | - Dorith Raviv Shay
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
| | - Milana Frenkel-Morgenstern
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel.,The Dangoor Centre For Personalized Medicine, Bar-Ilan University, Ramat Gan, 5290002, Israel
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18
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Bhakat KK, Ray S. The FAcilitates Chromatin Transcription (FACT) complex: Its roles in DNA repair and implications for cancer therapy. DNA Repair (Amst) 2021; 109:103246. [PMID: 34847380 DOI: 10.1016/j.dnarep.2021.103246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/07/2021] [Accepted: 11/03/2021] [Indexed: 12/17/2022]
Abstract
Genomic DNA in the nucleus is wrapped around nucleosomes, a repeating unit of chromatin. The nucleosome, consisting of octamer of core histones, is a barrier for several cellular processes that require access to the naked DNA. The FAcilitates Chromatin Transcription (FACT), a histone chaperone complex, is involved in nucleosome remodeling via eviction or assembly of histones during transcription, replication, and DNA repair. Increasing evidence suggests that FACT plays an important role in multiple DNA repair pathways including transcription-coupled nucleotide excision repair (TC-NER) of UV-induced damage, DNA single- and double-strand breaks (DSBs) repair, and base excision repair (BER) of oxidized or alkylated damaged bases. Further, studies have shown overexpression of FACT in multiple types of cancer and its association with drug resistance and patients' poor prognosis. In this review, we discuss how FACT is accumulated at the damage site and what functions it performs. We describe the known mechanisms by which FACT facilitates repair of different types of DNA damage. Further, we highlight the recent advances in a class of FACT inhibitors, called curaxins, which show promise as a new adjuvant therapy to sensitize multiple types of cancer to chemotherapy and radiation.
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Affiliation(s)
- Kishor K Bhakat
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA 68198; Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA 68198.
| | - Sutapa Ray
- Department of Pediatric, Division of Hematology/oncology, University of Nebraska Medical Center, Omaha, NE, USA 68198; Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA 68198
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19
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Drenner K, Basu GD, Goodman LJ, Ozols AA, LoBello JR, Royce T, Gordon MS, Borazanci EH, Steinbach MA, Trent J, Sharma S. The value of comprehensive genomic sequencing to maximize the identification of clinically actionable alterations in advanced cancer patients: a case series. Oncotarget 2021; 12:1836-1847. [PMID: 34504655 PMCID: PMC8416559 DOI: 10.18632/oncotarget.28046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/27/2021] [Indexed: 01/10/2023] Open
Abstract
PURPOSE We present seven cases of advanced cancer patients who initially underwent tumor testing utilizing smaller, panel-based tests, followed by a variety of therapeutic treatments which ultimately resulted in progression of their disease. These cases demonstrate the value of utilizing WES/RNA seq and characterization following disease progression in these patients and the determination of clinically targetable alterations as well as acquired resistance mutations. MATERIALS AND METHODS All patients are part of an IRB approved observational study. WES and RNA sequencing were performed, using GEM ExTra® on tumor and blood samples obtained during routine clinical care. To accurately determine somatic versus germline alterations the test was performed with paired normal testing from peripheral blood. RESULTS The presented cases demonstrate the clinical impact of actionable findings uncovered using GEM ExTra® in patients with advanced disease who failed many rounds of treatment. Unique alterations were identified resulting in newly identified potential targeted therapies, mechanisms of resistance, and variation in the genomic characterization of the primary versus the metastatic tumor. CONCLUSIONS Taken together our results demonstrate that GEM ExTra® maximizes detection of actionable mutations, thus allowing for appropriate treatment selection for patients harboring both common and rare genomic alterations.
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Affiliation(s)
- Kevin Drenner
- Translational Genomic Research Institute (Tgen), Phoenix, AZ 85004, USA
- These authors contributed equally to this work
| | - Gargi D. Basu
- Ashion Analytics, LLC, Phoenix, AZ 85004, USA
- These authors contributed equally to this work
| | | | | | | | | | | | | | | | - Jeffrey Trent
- Translational Genomic Research Institute (Tgen), Phoenix, AZ 85004, USA
| | - Sunil Sharma
- Translational Genomic Research Institute (Tgen), Phoenix, AZ 85004, USA
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20
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An Alternative Pipeline for Glioblastoma Therapeutics: A Systematic Review of Drug Repurposing in Glioblastoma. Cancers (Basel) 2021; 13:cancers13081953. [PMID: 33919596 PMCID: PMC8073966 DOI: 10.3390/cancers13081953] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Glioblastoma is a devastating malignancy that has continued to prove resistant to a variety of therapeutics. No new systemic therapy has been approved for use against glioblastoma in almost two decades. This observation is particularly disturbing given the amount of money invested in identifying novel therapies for this disease. A relatively rapid and economical pipeline for identification of novel agents is drug repurposing. Here, a comprehensive review detailing the state of drug repurposing in glioblastoma is provided. We reveal details on studies that have examined agents in vitro, in animal models and in patients. While most agents have not progressed beyond the initial stages, several drugs, from a variety of classes, have demonstrated promising results in early phase clinical trials. Abstract The treatment of glioblastoma (GBM) remains a significant challenge, with outcome for most pa-tients remaining poor. Although novel therapies have been developed, several obstacles restrict the incentive of drug developers to continue these efforts including the exorbitant cost, high failure rate and relatively small patient population. Repositioning drugs that have well-characterized mechanistic and safety profiles is an attractive alternative for drug development in GBM. In ad-dition, the relative ease with which repurposed agents can be transitioned to the clinic further supports their potential for examination in patients. Here, a systematic analysis of the literature and clinical trials provides a comprehensive review of primary articles and unpublished trials that use repurposed drugs for the treatment of GBM. The findings demonstrate that numerous drug classes that have a range of initial indications have efficacy against preclinical GBM models and that certain agents have shown significant potential for clinical benefit. With examination in randomized, placebo-controlled trials and the targeting of particular GBM subgroups, it is pos-sible that repurposing can be a cost-effective approach to identify agents for use in multimodal anti-GBM strategies.
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21
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Jeck WR, Iafrate AJ, Nardi V. Nanopore Flongle Sequencing as a Rapid, Single-Specimen Clinical Test for Fusion Detection. J Mol Diagn 2021; 23:630-636. [PMID: 33618057 DOI: 10.1016/j.jmoldx.2021.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/18/2020] [Accepted: 02/04/2021] [Indexed: 12/23/2022] Open
Abstract
The identification of gene fusions is a cornerstone of diagnosis and treatment decision making for tumors of many forms and primary sites. Diverse molecular approaches are currently used for the molecular diagnosis of fusions, but few permit broad, partner agnostic detection of fusions over multiple potential targets. We previously described the combination of nanopore sequencing with the anchored multiplex PCR technique to permit a rapid testing paradigm. Recently, a new platform for nanopore sequencing has become publicly available, the Flongle flow cell from Oxford Nanopore Technologies, which offers lower throughput, but lower price testing. Here, we describe the results of retesting of 15 specimens previously tested with both Illumina and Oxford Nanopore Technologies MinION sequencing. Furthermore, we additionally blindly tested 13 specimens that had undergone clinical Illumina-based sequencing. The Flongle sequencing pipeline removed key complexities of a multiplexed nanopore sequencing protocol, reduced sequencing turnaround time, and showed excellent concordance with Illumina results. It was particularly strong in identifying notoriously difficult to detect CIC-DUX4 translocations. The Flongle sequencing pipeline may be the assay of choice for deployment in small- to medium-sized molecular laboratories.
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Affiliation(s)
- William R Jeck
- Department of Pathology, Duke University Medical Center, Durham, North Carolina
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22
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Scaravilli M, Koivukoski S, Latonen L. Androgen-Driven Fusion Genes and Chimeric Transcripts in Prostate Cancer. Front Cell Dev Biol 2021; 9:623809. [PMID: 33634124 PMCID: PMC7900491 DOI: 10.3389/fcell.2021.623809] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/14/2021] [Indexed: 12/15/2022] Open
Abstract
Androgens are steroid hormones governing the male reproductive development and function. As such, androgens and the key mediator of their effects, androgen receptor (AR), have a leading role in many diseases. Prostate cancer is a major disease where AR and its transcription factor function affect a significant number of patients worldwide. While disease-related AR-driven transcriptional programs are connected to the presence and activity of the receptor itself, also novel modes of transcriptional regulation by androgens are exploited by cancer cells. One of the most intriguing and ingenious mechanisms is to bring previously unconnected genes under the control of AR. Most often this occurs through genetic rearrangements resulting in fusion genes where an androgen-regulated promoter area is combined to a protein-coding area of a previously androgen-unaffected gene. These gene fusions are distinctly frequent in prostate cancer compared to other common solid tumors, a phenomenon still requiring an explanation. Interestingly, also another mode of connecting androgen regulation to a previously unaffected gene product exists via transcriptional read-through mechanisms. Furthermore, androgen regulation of fusion genes and transcripts is not linked to only protein-coding genes. Pseudogenes and non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs) can also be affected by androgens and de novo functions produced. In this review, we discuss the prevalence, molecular mechanisms, and functional evidence for androgen-regulated prostate cancer fusion genes and transcripts. We also discuss the clinical relevance of especially the most common prostate cancer fusion gene TMPRSS2-ERG, as well as present open questions of prostate cancer fusions requiring further investigation.
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Affiliation(s)
- Mauro Scaravilli
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Sonja Koivukoski
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Leena Latonen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
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23
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Minati R, Perreault C, Thibault P. A Roadmap Toward the Definition of Actionable Tumor-Specific Antigens. Front Immunol 2020; 11:583287. [PMID: 33424836 PMCID: PMC7793940 DOI: 10.3389/fimmu.2020.583287] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/30/2020] [Indexed: 12/15/2022] Open
Abstract
The search for tumor-specific antigens (TSAs) has considerably accelerated during the past decade due to the improvement of proteogenomic detection methods. This provides new opportunities for the development of novel antitumoral immunotherapies to mount an efficient T cell response against one or multiple types of tumors. While the identification of mutated antigens originating from coding exons has provided relatively few TSA candidates, the possibility of enlarging the repertoire of targetable TSAs by looking at antigens arising from non-canonical open reading frames opens up interesting avenues for cancer immunotherapy. In this review, we outline the potential sources of TSAs and the mechanisms responsible for their expression strictly in cancer cells. In line with the heterogeneity of cancer, we propose that discrete families of TSAs may be enriched in specific cancer types.
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Affiliation(s)
- Robin Minati
- École Normale Supérieure de Lyon, Université Claude Bernard Lyon I, Université de Lyon, Lyon, France
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Department of Chemistry, Université de Montréal, Montréal, QC, Canada
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24
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Fusion genes as biomarkers in pediatric cancers: A review of the current state and applicability in diagnostics and personalized therapy. Cancer Lett 2020; 499:24-38. [PMID: 33248210 DOI: 10.1016/j.canlet.2020.11.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 12/13/2022]
Abstract
The incidence of pediatric cancers is rising steadily across the world, along with the challenges in understanding the molecular mechanisms and devising effective therapeutic strategies. Pediatric cancers are presented with diverse molecular characteristics and more distinct subtypes when compared to adult cancers. Recent studies on the genomic landscape of pediatric cancers using next-generation sequencing (NGS) approaches have redefined this field by providing better subtype characterization and novel actionable targets. Since early identification and personalized treatment strategies influence therapeutic outcomes, survival, and quality of life in pediatric cancer patients, the quest for actionable biomarkers is of great value in this field. Fusion genes that are prevalent and recurrent in several pediatric cancers are ideally suited in this context due to their disease-specific occurrence. In this review, we explore the current status of fusion genes in pediatric cancer subtypes and their use as biomarkers for diagnosis and personalized therapy. We discuss the technological advancements made in recent years in NGS sequencing and their impact on fusion detection algorithms that have revolutionized this field. Finally, we also discuss the advantages of pairing liquid biopsy protocols for fusion detection and their eventual use in diagnosis and treatment monitoring.
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