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Zhang H, Liu B, Cheng J, Li Z, Jia M, Li M, Zhao L, Wang L, Xi Y. Characterization and integrated analysis of extrachromosomal DNA amplification in hematological malignancies. Neoplasia 2024; 56:101025. [PMID: 38996538 PMCID: PMC11301242 DOI: 10.1016/j.neo.2024.101025] [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: 02/27/2024] [Accepted: 07/03/2024] [Indexed: 07/14/2024]
Abstract
The study of extrachromosomal DNA (ecDNA), an element existing beyond classical chromosomes, contributes to creating a more comprehensive map of the cancer genome. In hematological malignancies, research on ecDNA has lacked comprehensive investigation into its frequency, structure, function, and mechanisms of formation. We re-analyzed WGS data from 208 hematological cancer samples across 11 types, focusing on ecDNA characteristics. Amplification of ecDNA was observed in 7 of these cancer types, with no instances found in normal blood cells. Patients with leukemia carrying ecDNA showed a low induction therapy remission rate (<30 %), a high relapse rate (75 %) among those who achieved complete remission, and a significantly lower survival rate compared to the general leukemia population, even those with complex chromosomal karyotypes. Among the 55 identified ecDNA amplicons, 268 genes were detected, of which 38 are known cancer-related genes exhibiting significantly increased copy numbers. By integrating RNA-Seq data, we discovered that the increased copy number, resulting in a higher amount of available DNA templates, indeed leads to the elevated expression of genes encoded on ecDNA. Additionally, through the integration of H3K4me3/H3K27ac chromatin immunoprecipitation sequencing, assay for transposase-accessible chromatin with sequencing, and high-throughput chromosome conformation capture data, we identified that ecDNA amplifications can also facilitate efficient, copy number-independent amplification of oncogenes. This process is linked to active histone modifications, improved chromatin accessibility, and enhancer hijacking, all of which are effects of ecDNA amplification. Mechanistically, chromothripsis and dysfunction of the DNA repair pathway can, to some extent, explain the origin of ecDNA.
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Affiliation(s)
- Hao Zhang
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Bei Liu
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Juan Cheng
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Zijian Li
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Mingfeng Jia
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Ming Li
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Long Zhao
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Lina Wang
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Yaming Xi
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China.
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Yang C, Trivedi V, Dyson K, Gu T, Candelario KM, Yegorov O, Mitchell DA. Identification of tumor rejection antigens and the immunologic landscape of medulloblastoma. Genome Med 2024; 16:102. [PMID: 39160595 PMCID: PMC11331754 DOI: 10.1186/s13073-024-01363-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/12/2024] [Indexed: 08/21/2024] Open
Abstract
BACKGROUND The current standard of care treatments for medulloblastoma are insufficient as these do not take tumor heterogeneity into account. Newer, safer, patient-specific treatment approaches are required to treat high-risk medulloblastoma patients who are not cured by the standard therapies. Immunotherapy is a promising treatment modality that could be key to improving survival and avoiding morbidity. For an effective immune response, appropriate tumor antigens must be targeted. While medulloblastoma patients with subgroup-specific genetic substitutions have been previously reported, the immunogenicity of these genetic alterations remains unknown. The aim of this study is to identify potential tumor rejection antigens for the development of antigen-directed cellular therapies for medulloblastoma. METHODS We developed a cancer immunogenomics pipeline and performed a comprehensive analysis of medulloblastoma subgroup-specific transcription profiles (n = 170, 18 WNT, 46 SHH, 41 Group 3, and 65 Group 4 patient tumors) available through International Cancer Genome Consortium (ICGC) and European Genome-Phenome Archive (EGA). We performed in silico antigen prediction across a broad array of antigen classes including neoantigens, tumor-associated antigens (TAAs), and fusion proteins. Furthermore, we evaluated the antigen processing and presentation pathway in tumor cells and the immune infiltrating cell landscape using the latest computational deconvolution methods. RESULTS Medulloblastoma patients were found to express multiple private and shared immunogenic antigens. The proportion of predicted TAAs was higher than neoantigens and gene fusions for all molecular subgroups, except for sonic hedgehog (SHH), which had a higher neoantigen burden. Importantly, cancer-testis antigens, as well as previously unappreciated neurodevelopmental antigens, were found to be expressed by most patients across all medulloblastoma subgroups. Despite being immunologically cold, medulloblastoma subgroups were found to have distinct immune cell gene signatures. CONCLUSIONS Using a custom antigen prediction pipeline, we identified potential tumor rejection antigens with important implications for the development of immunotherapy for medulloblastoma.
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Affiliation(s)
- Changlin Yang
- UF Brain Tumor Immunotherapy Program, Preston A. Wells Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, University of Florida, 1333 Center Drive, BSB B1-118, Gainesville, FL, 32610, USA
| | - Vrunda Trivedi
- UF Brain Tumor Immunotherapy Program, Preston A. Wells Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, University of Florida, 1333 Center Drive, BSB B1-118, Gainesville, FL, 32610, USA
| | - Kyle Dyson
- UF Brain Tumor Immunotherapy Program, Preston A. Wells Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, University of Florida, 1333 Center Drive, BSB B1-118, Gainesville, FL, 32610, USA
| | - Tongjun Gu
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Kate M Candelario
- UF Brain Tumor Immunotherapy Program, Preston A. Wells Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, University of Florida, 1333 Center Drive, BSB B1-118, Gainesville, FL, 32610, USA
| | - Oleg Yegorov
- UF Brain Tumor Immunotherapy Program, Preston A. Wells Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, University of Florida, 1333 Center Drive, BSB B1-118, Gainesville, FL, 32610, USA
| | - Duane A Mitchell
- UF Brain Tumor Immunotherapy Program, Preston A. Wells Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, University of Florida, 1333 Center Drive, BSB B1-118, Gainesville, FL, 32610, USA.
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Lu H, Wang Y, Chaudhary S, Balaga V, Ke H, Shi F, Liu J, Huo Y, Romanienko PJ, Xia B, De S, Chan CS, Shen Z. Medulloblastomas Initiated by Homologous Recombination Defects in Mice. THE AMERICAN JOURNAL OF PATHOLOGY 2024:S0002-9440(24)00294-3. [PMID: 39168365 DOI: 10.1016/j.ajpath.2024.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/08/2024] [Accepted: 07/31/2024] [Indexed: 08/23/2024]
Abstract
Germline mutations of homologous-recombination (HR) genes are among the top contributors to medulloblastomas. A significant portion of human medulloblastomas exhibited genomic signatures of HR defects. We asked whether ablation of Brca2, Palb2, and their related Brca1 and Bccip genes, in the mouse brain can differentially initiate medulloblastomas. We established conditional knockout mouse models of these HR-genes, and a conditional knockdown of Bccip (shBccip-KD). Deletion of any of these genes led to microcephaly and neurological defects, with Brca1- and Bccip- producing the worst. Trp53 co-deletion significantly rescued the microcephaly with Brca1, Palb2, and Brca2 deficiency, but it exhibited limited impact on Bccip- mice. For the first time, inactivation of either Brca1 or Palb2 with Trp53 was found to induce medulloblastomas. Bccip/Trp53 deletions failed, despite that shBccip-CKD was highly penetrative, to induce medulloblastomas. The tumors displayed diverse immunohistochemical features and chromosome copy number variation. While there were widespread upregulations of cell proliferative pathways, most of the tumors expressed biomarkers of the Sonic Hedgehog subgroup. The MBs developed from Brca1-, Palb2-, and Brca2- mice were highly sensitive to a PARP inhibitor, but not the ones from shBccip-CKD mice. Our models recapitulate the spontaneous medulloblastoma development with high penetrance and narrow time-window, providing ideal platforms to test therapeutic agents with the ability to differentiate HR defective and proficient tumors.
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Affiliation(s)
- Huimei Lu
- Rutgers Cancer Institute of New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School
| | - Yuan Wang
- Rutgers Cancer Institute of New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School
| | - Shipra Chaudhary
- Rutgers Cancer Institute of New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School
| | - Varshita Balaga
- Rutgers Cancer Institute of New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School
| | - Hua Ke
- Rutgers Cancer Institute of New Jersey
| | | | - Jingmei Liu
- Rutgers Cancer Institute of New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School
| | - Yangyin Huo
- Rutgers Cancer Institute of New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School
| | | | - Bing Xia
- Rutgers Cancer Institute of New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School
| | | | - Chang S Chan
- Rutgers Cancer Institute of New Jersey; Department of Medicine, Rutgers Robert Wood Johnson Medical School
| | - Zhiyuan Shen
- Rutgers Cancer Institute of New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School.
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4
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Li H, Xie L, Zhang J, Xu Y, Wu X, Chen Z, Mao R. Uterine tumors mimicking ovarian sex cord tumors with rhabdoid differentiation: a clinicopathologic study of 4 cases: A case series analysis. Medicine (Baltimore) 2024; 103:e39123. [PMID: 39151492 PMCID: PMC11332788 DOI: 10.1097/md.0000000000039123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 06/19/2024] [Accepted: 07/09/2024] [Indexed: 08/19/2024] Open
Abstract
RATIONALE Uterine tumors resembling ovarian sex cord tumors (UTROSCT) with rhabdoid features are uncommon mesenchymal neoplasms exhibiting diverse histological patterns, including significant rhabdoid morphology. A thorough comprehension of their clinicopathologic features is crucial for precise diagnosis and effective management. PATIENT CONCERNS This study presents 4 cases of UTROSCT with rhabdoid features, diagnosed in patients aged 31 to 58. Varied recurrence patterns were observed, including similar recurrent lesions to the primary tumors with subsequent mortality, initial invasion and lymph node metastasis, and presence of only primary tumor. DIAGNOSES Histopathological examination revealed diverse morphological patterns, prominently featuring rhabdoid differentiation. Immunohistochemical analysis showed expression of hormone receptors, sex cord, smooth muscle, and epithelial markers, notably WT1, CD56, and CD99. Molecular analysis identified ESR1-NCOA2 fusions and ESR1 and NCOA2/3 rearrangements, indicating a potential association between these genetic alterations and extensive rhabdoid differentiation. INTERVENTIONS Various treatments were administered post-recurrence, including chemotherapy and targeted therapies. However, poor clinical outcomes were observed in all cases. OUTCOMES Despite aggressive treatments, including chemotherapy and targeted therapies, poor clinical outcomes were observed, highlighting the aggressive nature of UTROSCT with significant rhabdoid differentiation. LESSONS This case series emphasizes the importance of detailed pathological reporting, comprehensive molecular testing, and thorough tumor staging in UTROSCT cases with rhabdoid features. Enhanced understanding of the clinicopathologic characteristics of UTROSCT with rhabdoid differentiation is crucial for accurate diagnosis, prognostication, and management strategies.
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Affiliation(s)
- Hongling Li
- Department of Pathology, Foshan Hospital of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Foshan, China
| | - Le Xie
- Department of Pathology, Foshan Hospital of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Foshan, China
| | - Jinhui Zhang
- Department of Pathology, Foshan Hospital of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Foshan, China
| | - Yuanyuan Xu
- Department of Pathology, Foshan Hospital of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Foshan, China
| | - Xingyan Wu
- Department of Pathology, Foshan Hospital of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Foshan, China
| | - Zengwei Chen
- Department of Pathology, Foshan Hospital of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Foshan, China
| | - Rongjun Mao
- Department of Pathology, Foshan Hospital of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Foshan, China
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5
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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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Nunes L, Li F, Wu M, Luo T, Hammarström K, Torell E, Ljuslinder I, Mezheyeuski A, Edqvist PH, Löfgren-Burström A, Zingmark C, Edin S, Larsson C, Mathot L, Osterman E, Osterlund E, Ljungström V, Neves I, Yacoub N, Guðnadóttir U, Birgisson H, Enblad M, Ponten F, Palmqvist R, Xu X, Uhlén M, Wu K, Glimelius B, Lin C, Sjöblom T. Prognostic genome and transcriptome signatures in colorectal cancers. Nature 2024:10.1038/s41586-024-07769-3. [PMID: 39112715 DOI: 10.1038/s41586-024-07769-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/01/2024] [Indexed: 08/17/2024]
Abstract
Colorectal cancer is caused by a sequence of somatic genomic alterations affecting driver genes in core cancer pathways1. Here, to understand the functional and prognostic impact of cancer-causing somatic mutations, we analysed the whole genomes and transcriptomes of 1,063 primary colorectal cancers in a population-based cohort with long-term follow-up. From the 96 mutated driver genes, 9 were not previously implicated in colorectal cancer and 24 had not been linked to any cancer. Two distinct patterns of pathway co-mutations were observed, timing analyses identified nine early and three late driver gene mutations, and several signatures of colorectal-cancer-specific mutational processes were identified. Mutations in WNT, EGFR and TGFβ pathway genes, the mitochondrial CYB gene and 3 regulatory elements along with 21 copy-number variations and the COSMIC SBS44 signature correlated with survival. Gene expression classification yielded five prognostic subtypes with distinct molecular features, in part explained by underlying genomic alterations. Microsatellite-instable tumours divided into two classes with different levels of hypoxia and infiltration of immune and stromal cells. To our knowledge, this study constitutes the largest integrated genome and transcriptome analysis of colorectal cancer, and interlinks mutations, gene expression and patient outcomes. The identification of prognostic mutations and expression subtypes can guide future efforts to individualize colorectal cancer therapy.
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Affiliation(s)
- Luís Nunes
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Fuqiang Li
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen, China
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China
| | - Meizhen Wu
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen, China
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China
| | - Tian Luo
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen, China
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China
| | - Klara Hammarström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Emma Torell
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ingrid Ljuslinder
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Artur Mezheyeuski
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Per-Henrik Edqvist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Carl Zingmark
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Sofia Edin
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Chatarina Larsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lucy Mathot
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Erik Osterman
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Emerik Osterlund
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Inês Neves
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Nicole Yacoub
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Unnur Guðnadóttir
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Helgi Birgisson
- Department of Surgical Sciences, Uppsala University, Akademiska sjukhuset, Uppsala, Sweden
| | - Malin Enblad
- Department of Surgical Sciences, Uppsala University, Akademiska sjukhuset, Uppsala, Sweden
| | - Fredrik Ponten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Richard Palmqvist
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Xun Xu
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China
| | - Mathias Uhlén
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Kui Wu
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China.
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen, China.
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China.
| | - Bengt Glimelius
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Cong Lin
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China.
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen, China.
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China.
| | - Tobias Sjöblom
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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7
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Masago K, Kuroda H, Sasaki E, Fujita Y, Fujita S, Horio Y, Endo M, Ishihara H, Hanai N, Matsushita H. Novel gene fusions in human oropharyngeal carcinoma. Cancer Genet 2024; 286-287:29-34. [PMID: 38971117 DOI: 10.1016/j.cancergen.2024.06.004] [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: 02/13/2024] [Revised: 05/13/2024] [Accepted: 06/30/2024] [Indexed: 07/08/2024]
Abstract
Few reports have analyzed the fusion genes involved in carcinogenesis in the oropharynx, where the incidence of human papillomavirus-associated tumors is relatively low. The aim of this study was to identify novel driver fusion genes in patients with oropharyngeal cancer. The study enrolled fifty-seven patients who were diagnosed with oropharyngeal carcinoma. RNA sequencing data from fresh-frozen specimens were used to identify candidate fusion genes via the JAFFA, arriba, and STAR-Fusion pipelines. Candidate fusion genes were confirmed by direct sequencing. The expression level of a candidate fusion gene was compared to that of tumors without fusion genes. Finally, filtering was performed for driver genes using the annoFuse pipeline. In addition, the VIRTUS pipeline was used to analyze the presence of human papillomavirus in the tumors. We identified 5 (8.8 %) novel potential driver in-frame fusion genes, MKNK2::MOB3A, ICMT::RPS6KA3, ATP1B3::GRK7, CSNK2A1::KIF16B, and FGFR3::MAEA, and 1 (1.8 %) known in-frame fusion gene, FGFR3::TACC3, in 57 patients with pharyngeal carcinoma. Our results suggest that sporadic fusion genes may contribute to tumorigenesis in oropharyngeal carcinomas.
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Affiliation(s)
- Katsuhiro Masago
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan; Division of Translational Oncoimmunology, Aichi Cancer Research Institute, Nagoya, Japan.
| | - Hiroaki Kuroda
- Department of Respiratory Surgery, Aichi Cancer Center Hospital, Nagoya, Japan; Division of Translational Oncoimmunology, Aichi Cancer Research Institute, Nagoya, Japan; Department of Thoracic Surgery, Teikyo University Mizonokuchi Hospital, Kawasaki, Japan
| | - Eiichi Sasaki
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan
| | - Yasuko Fujita
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan
| | - Shiro Fujita
- Department of Respiratory Medicine, Kobe Central Hospital, Kobe, Japan
| | - Yoshitsugu Horio
- Department of Respiratory Medicine, Aichi Cancer Center Hospital, Nagoya, Japan; Division of Translational Oncoimmunology, Aichi Cancer Research Institute, Nagoya, Japan
| | - Motoyoshi Endo
- Department of Molecular Biology, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Hiromasa Ishihara
- Division of Translational Oncoimmunology, Aichi Cancer Research Institute, Nagoya, Japan
| | - Nobuhiro Hanai
- Department of Head and Neck Surgery, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Hirokazu Matsushita
- Division of Translational Oncoimmunology, Aichi Cancer Research Institute, Nagoya, Japan
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8
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Kim JY, Park K, Park WY, Ahn JS, Im YH, Lee JE, Kim SW, Nam SJ, Yu J, Park YH. Prognostic value of structural variants in early breast cancer patients. NPJ Breast Cancer 2024; 10:64. [PMID: 39068172 PMCID: PMC11283467 DOI: 10.1038/s41523-024-00669-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 07/08/2024] [Indexed: 07/30/2024] Open
Abstract
Genomic analysis of structural variants(SVs) in breast cancer (BC) patients has been conducted, but the relationship between genomic alterations and BC prognosis remains unclear. We performed RNA sequencing of 297 early BC fresh-frozen tissues. We identified SVs using three tools (STAR.Arriba, STAR.fusion, and STAR.SEQR) with the COSMIC and Mitelman databases as guide references. We found a median of five to eight fusions per sample. In BC intrinsic subtypes, normal subtype had the fewest fusions (median: 1, interquartile range [IQR]: 0, 3) followed by luminal A (median: 5.5, IQR: 2.75, 10.25), luminal B (median: 9, IQR: 6, 16.5), HER2-enriched (median: 9, IQR: 6, 16.5) and basal (median 10, IQR: 6, 15.5) subtypes (p < 0.05). Intrachromosomal fusion was more frequent observed rather than interchromosomal fusion. In location, chromosome 17 had the most fusions followed by chromosome 1 and 11. When samples were divided into high and low fusion groups based on a cut-off value of 11 fusions, five-year event-free survival (5Y-EFS) was 68.1% in the high fusion group (n = 72) and 80.1% in the low fusion group (n = 125) (p = 0.024) while 75.6% among all patients (95% confidence interval: 0.699, 0.819). Among BC subtype, TNBCs with more fusions had shorter EFS compared to those with fewer fusions (5Y-EFS rate: 65.1% vs. 85.7%; p = 0.013) but no EFS differences were observed in other BC subtypes. ESTIMATE ImmuneScore was also associated with the number of fusions in TNBC (p < 0.005) and TNBCs with high ImmuneScore had better 5Y-EFS compared to those with low ImmuneScore (p = 0.041). In conclusion, diverse fusions were observed by BC subtype, and the number of fusions was associated with BC survival outcome and immune status in TNBC.
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Affiliation(s)
- Ji-Yeon Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyunghee Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Jin Seok Ahn
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young-Hyuck Im
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jeong Eon Lee
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seok Won Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seok Jin Nam
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jonghan Yu
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yeon Hee Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University School of Medicine, Seoul, Korea.
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9
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Zhou K, Zhang M, Zhai D, Wang Z, Liu T, Xie Y, Shi Y, Shi H, Chen Q, Li X, Xu J, Cai Z, Zhang Y, Shao N, Lin Y. Genomic and transcriptomic profiling of inflammatory breast cancer reveals distinct molecular characteristics to non-inflammatory breast cancers. Breast Cancer Res Treat 2024:10.1007/s10549-024-07437-0. [PMID: 39030466 DOI: 10.1007/s10549-024-07437-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024]
Abstract
PURPOSE Inflammatory breast cancer (IBC), a rare and highly aggressive form of breast cancer, accounts for 10% of breast cancer-related deaths. Previous omics studies of IBC have focused solely on one of genomics or transcriptomics and did not discover common differences that could distinguish IBC from non-IBC. METHODS Seventeen IBC patients and five non-IBC patients as well as additional thirty-three Asian breast cancer samples from TCGA-BRCA were included for the study. We performed whole-exon sequencing (WES) to investigate different somatic genomic alterations, copy number variants, and large structural variants between IBC and non-IBC. Bulk RNA sequencing (RNA-seq) was performed to examine the differentially expressed genes, pathway enrichment, and gene fusions. WES and RNA-seq data were further investigated in combination to discover genes that were dysregulated in both genomics and transcriptomics. RESULTS Copy number variation analysis identified 10 cytobands that showed higher frequency in IBC. Structural variation analysis showed more frequent deletions in IBC. Pathway enrichment and immune infiltration analysis indicated increased immune activation in IBC samples. Gene fusions including CTSC-RAB38 were found to be more common in IBC. We demonstrated more commonly dysregulated RAS pathway in IBC according to both WES and RNA-seq. Inhibitors targeting RAS signaling and its downstream pathways were predicted to possess promising effects in IBC treatment. CONCLUSION We discovered differences unique in Asian women that could potentially explain IBC etiology and presented RAS signaling pathway as a potential therapeutic target in IBC treatment.
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Affiliation(s)
- Kaiwen Zhou
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Mengmeng Zhang
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Duanyang Zhai
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Zilin Wang
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Ting Liu
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yubin Xie
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yawei Shi
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Huijuan Shi
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Qianjun Chen
- Department of Breast Oncology, Traditional Chinese Medicine Hospital of Guangdong Province, Guangzhou, Guangdong, China
| | - Xiaoping Li
- Department of Breast Oncology, Jiangmen Central Hospital, Jiangmen, Guangdong, China
| | - Juan Xu
- Department of Breast Oncology, Maternal and Child Health Care Hospital of Guangdong Province, Guangzhou, China
| | - Zhenhai Cai
- Department of Breast Oncology, Jieyang People's Hospital, Jieyang, Guangdong, China
| | - Yunjian Zhang
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Nan Shao
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Ying Lin
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.
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10
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Mulet-Lazaro R, van Herk S, Nuetzel M, Sijs-Szabo A, Díaz N, Kelly K, Erpelinck-Verschueren C, Schwarzfischer-Pfeilschifter L, Stanewsky H, Ackermann U, Glatz D, Raithel J, Fischer A, Pohl S, Rijneveld A, Vaquerizas JM, Thiede C, Plass C, Wouters BJ, Delwel R, Rehli M, Gebhard C. Epigenetic alterations affecting hematopoietic regulatory networks as drivers of mixed myeloid/lymphoid leukemia. Nat Commun 2024; 15:5693. [PMID: 38972954 PMCID: PMC11228033 DOI: 10.1038/s41467-024-49811-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 06/19/2024] [Indexed: 07/09/2024] Open
Abstract
Leukemias with ambiguous lineage comprise several loosely defined entities, often without a clear mechanistic basis. Here, we extensively profile the epigenome and transcriptome of a subgroup of such leukemias with CpG Island Methylator Phenotype. These leukemias exhibit comparable hybrid myeloid/lymphoid epigenetic landscapes, yet heterogeneous genetic alterations, suggesting they are defined by their shared epigenetic profile rather than common genetic lesions. Gene expression enrichment reveals similarity with early T-cell precursor acute lymphoblastic leukemia and a lymphoid progenitor cell of origin. In line with this, integration of differential DNA methylation and gene expression shows widespread silencing of myeloid transcription factors. Moreover, binding sites for hematopoietic transcription factors, including CEBPA, SPI1 and LEF1, are uniquely inaccessible in these leukemias. Hypermethylation also results in loss of CTCF binding, accompanied by changes in chromatin interactions involving key transcription factors. In conclusion, epigenetic dysregulation, and not genetic lesions, explains the mixed phenotype of this group of leukemias with ambiguous lineage. The data collected here constitute a useful and comprehensive epigenomic reference for subsequent studies of acute myeloid leukemias, T-cell acute lymphoblastic leukemias and mixed-phenotype leukemias.
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Affiliation(s)
- Roger Mulet-Lazaro
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Stanley van Herk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Margit Nuetzel
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Aniko Sijs-Szabo
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Noelia Díaz
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
- Renewable Marine Resources Department, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | - Katherine Kelly
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Claudia Erpelinck-Verschueren
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | | | - Hanna Stanewsky
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Ute Ackermann
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Dagmar Glatz
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Johanna Raithel
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Alexander Fischer
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Sandra Pohl
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany
| | - Anita Rijneveld
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital 8 Campus, London, United Kingdom
| | - Christian Thiede
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bas J Wouters
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
| | - Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
| | - Michael Rehli
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.
- Leibniz Institute for Immunotherapy (LIT), Regensburg, Germany.
| | - Claudia Gebhard
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.
- Leibniz Institute for Immunotherapy (LIT), Regensburg, Germany.
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11
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Kim SW, Kim N, Choi YJ, Lee ST, Choi JR, Shin S. Real-World Clinical Utility of Targeted RNA Sequencing in Leukemia Diagnosis and Management. Cancers (Basel) 2024; 16:2467. [PMID: 39001529 PMCID: PMC11240350 DOI: 10.3390/cancers16132467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/02/2024] [Accepted: 07/04/2024] [Indexed: 07/16/2024] Open
Abstract
Gene fusions are key drivers in acute leukemia, impacting diagnosis and treatment decisions. We analyzed 264 leukemia patients using targeted RNA sequencing with conventional karyotyping and reverse transcription polymerase chain reaction (RT-PCR). Leukemic fusions were detected in 127 patients (48.1%). The new guidelines introduced additional diagnostic criteria, expanding the spectrum of gene fusions. We discovered three novel fusions (RUNX1::DOPEY2, RUNX1::MACROD2, and ZCCHC7::LRP1B). We analyzed recurrent breakpoints for the KMT2A and NUP98 rearrangements. Targeted RNA sequencing showed consistent results with RT-PCR in all tested samples. However, when compared to conventional karyotyping, we observed an 83.3% concordance rate, with 29 cases found only in targeted RNA sequencing, 7 cases with discordant results, and 5 cases found only in conventional karyotyping. For the five cases where known leukemic gene rearrangements were suspected only in conventional karyotyping, we conducted additional messenger RNA sequencing in four cases and proved no pathogenic gene rearrangements. Targeted RNA sequencing proved advantageous for the rapid and accurate interpretation of gene rearrangements. The concurrent use of multiple methods was essential for a comprehensive evaluation. Comprehensive molecular analysis enhances our understanding of leukemia's genetic basis, aiding diagnosis and classification. Advanced molecular techniques improve clinical decision-making, offering potential benefits.
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Affiliation(s)
- Seo Wan Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea (J.R.C.)
| | - Namsoo Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea (J.R.C.)
| | - Yu Jeong Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea (J.R.C.)
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea (J.R.C.)
- Dxome Co., Ltd., Seongnam-si 13558, Republic of Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea (J.R.C.)
- Dxome Co., Ltd., Seongnam-si 13558, Republic of Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea (J.R.C.)
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12
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Xu H, Chen X, Sun Y, Hu X, Zhang X, Wang Y, Tang Q, Zhu Q, Song K, Chen H, Sheng X, Yao Y, Zhuang D, Chen L, Mao Y, Qin Z. Comprehensive molecular characterization of long-term glioblastoma survivors. Cancer Lett 2024; 593:216938. [PMID: 38734160 DOI: 10.1016/j.canlet.2024.216938] [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: 01/30/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024]
Abstract
Fewer than 5 % glioblastoma (GBM) patients survive over five years and are termed long-term survivors (LTS), yet their molecular background is unclear. The present cohort included 72 isocitrate dehydrogenase (IDH)-wildtype GBM patients, consisting of 35 LTS and 37 short-term survivors (STS), and we employed whole exome sequencing, RNA-seq and DNA methylation array to delineate this largest LTS cohort to date. Although LTS and STS demonstrated analogous clinical characters and classical GBM biomarkers, CASC5 (P = 0.002) and SPEN (P = 0.013) mutations were enriched in LTS, whereas gene-to-gene fusions were concentrated in STS (P = 0.007). Importantly, LTS exhibited higher tumor mutation burden (P < 0.001) and copy number (CN) increase (P = 0.013), but lower mutant-allele tumor heterogeneity score (P < 0.001) and CN decrease (P = 0.026). Additionally, LTS demonstrated hypermethylated genome (P < 0.001) relative to STS. Differentially expressed and methylated genes both enriched in olfactory transduction. Further, analysis of the tumor microenvironment revealed higher infiltration of M1 macrophages (P = 0.043), B cells (P = 0.016), class-switched memory B cells (P = 0.002), central memory CD4+ T cells (P = 0.031) and CD4+ Th1 cells (P = 0.005) in LTS. We also separately analyzed a subset of patients who were methylation class-defined GBM, contributing 70.8 % of the entire cohort, and obtained similar results relative to prior analyses. Finally, we demonstrated that LTS and STS could be distinguished using a subset of molecular features. Taken together, the present study delineated unique molecular attributes of LTS GBM.
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Affiliation(s)
- Hao Xu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Xinyu Chen
- Department of Breast and Urologic Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ying Sun
- GenomiCare Biotechnology (Shanghai) Co. Ltd., Shanghai, China; Department of Data Science, Shanghai CreateCured Biotechnology Co. Ltd., Shanghai, China
| | - Xiaomu Hu
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xuan Zhang
- GenomiCare Biotechnology (Shanghai) Co. Ltd., Shanghai, China
| | - Ye Wang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Qisheng Tang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Qiongji Zhu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Kun Song
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Hong Chen
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaofang Sheng
- Department of Radiation Oncology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yu Yao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Dongxiao Zhuang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Lingchao Chen
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China.
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China.
| | - Zhiyong Qin
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China.
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13
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Mochizuki A, Shiraishi K, Honda T, Higashiyama RI, Sunami K, Matsuda M, Shimada Y, Miyazaki Y, Yoshida Y, Watanabe SI, Yatabe Y, Hamamoto R, Kohno T. Passive Smoking-Induced Mutagenesis as a Promoter of Lung Carcinogenesis. J Thorac Oncol 2024; 19:984-994. [PMID: 38382595 DOI: 10.1016/j.jtho.2024.02.006] [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: 09/01/2023] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 02/23/2024]
Abstract
INTRODUCTION The International Agency for Research on Cancer has classified passive smoking (PS) or secondhand smoke exposure as a group 1 carcinogen linked to lung cancer. However, in contrast to active smoking, the mutagenic properties of PS remain unclear. METHODS A consecutive cohort of 564 lung adenocarcinoma samples from female never-smokers, who provided detailed information about their exposure to PS during adolescence and in their thirties through a questionnaire, was prepared. Of these, all 291 cases for whom frozen tumor tissues were available were subjected to whole exome sequencing to estimate tumor mutational burden, and the top 84 cases who were exposed daily, or not, to PS during adolescence, in their thirties or in both periods, were further subjected to whole genome sequencing. RESULTS A modest yet statistically significant increase in tumor mutational burden was observed in the group exposed to PS compared with the group not exposed to PS (median values = 1.44 versus 1.29 per megabase, respectively; p = 0.020). Instead of inducing driver oncogene mutations, PS-induced substantial subclonal mutations exhibiting APOBEC-type signatures, including SMAD4 and ADGRG6 hotspot mutations. A polymorphic APOBEC3A/3B allele-specific to the Asian population that leads to up-regulated expression of APOBEC3A accentuated the mutational load in individuals exposed daily to PS during adolescence. CONCLUSIONS This study reveals that PS-induced mutagenesis can promote lung carcinogenesis. The APOBEC3A/3B polymorphism may serve as a biomarker for identifying passive nonsmoking individuals at high risk of developing lung cancer.
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Affiliation(s)
- Akifumi Mochizuki
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan; Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Takayuki Honda
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Kuniko Sunami
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Maiko Matsuda
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Yoko Shimada
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasunari Miyazaki
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yukihiro Yoshida
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Shun-Ichi Watanabe
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Yasushi Yatabe
- Department of Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Ryuji Hamamoto
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan.
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14
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Zheng D, Elnegiry AA, Luo C, Bendahou MA, Xie L, Bell D, Takahashi Y, Hanna E, Mias GI, Tsoi MF, Gu B. Brd4::Nutm1 fusion gene initiates NUT carcinoma in vivo. Life Sci Alliance 2024; 7:e202402602. [PMID: 38724194 PMCID: PMC11082452 DOI: 10.26508/lsa.202402602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
NUT carcinoma (NC) is an aggressive cancer with no effective treatment. About 70% of NUT carcinoma is associated with chromosome translocation events that lead to the formation of a BRD4::NUTM1 fusion gene. Because the BRD4::NUTM1 gene is unequivocally cytotoxic when ectopically expressed in cell lines, questions remain on whether the fusion gene can initiate NC. Here, we report the first genetically engineered mouse model for NUT carcinoma that recapitulates the human t(15;19) chromosome translocation in mice. We demonstrated that the mouse t(2;17) syntenic chromosome translocation, forming the Brd4::Nutm1 fusion gene, could induce aggressive carcinomas in mice. The tumors present histopathological and molecular features similar to human NC, with enrichment of undifferentiated cells. Similar to the reports of human NC incidence, Brd4::Nutm1 can induce NC from a broad range of tissues with a strong phenotypical variability. The consistent induction of poorly differentiated carcinoma demonstrated a strong reprogramming activity of BRD4::NUTM1. The new mouse model provided a critical preclinical model for NC that will lead to better understanding and therapy development for NC.
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Affiliation(s)
- Dejin Zheng
- https://ror.org/05hs6h993 Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, East Lansing, MI, USA
- https://ror.org/05hs6h993 Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Ahmed A Elnegiry
- https://ror.org/05hs6h993 Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, East Lansing, MI, USA
- https://ror.org/05hs6h993 Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Home Institution: Department of Cytology and Histology, Faculty of Veterinary Medicine, Aswan University, Aswan, Egypt
| | - Chenxiang Luo
- https://ror.org/05hs6h993 Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, East Lansing, MI, USA
- https://ror.org/05hs6h993 Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Home Institution: Center for Reproductive Medicine and Department of Gynecology & Obstetrics, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Mohammed Amine Bendahou
- Infection Biology and Cancer Biology Program, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Liangqi Xie
- Infection Biology and Cancer Biology Program, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Diana Bell
- City of Hope Comprehensive Cancer Center, Pathology, Duarte, CA, USA
| | - Yoko Takahashi
- Department of Head and Neck Surgery, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ehab Hanna
- Department of Head and Neck Surgery, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George I Mias
- https://ror.org/05hs6h993 Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- https://ror.org/05hs6h993 Department of Biochemistry and Molecular Biology, College of Nature Science, Michigan State University, East Lansing, MI, USA
| | - Mayra F Tsoi
- https://ror.org/05hs6h993 Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Bin Gu
- https://ror.org/05hs6h993 Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, East Lansing, MI, USA
- https://ror.org/05hs6h993 Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
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15
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Meijer DM, Ruano D, Briaire-de Bruijn IH, Wijers-Koster PM, van de Sande MAJ, Gelderblom H, Cleton-Jansen AM, de Miranda NFCC, Kuijjer ML, Bovée JVMG. The Variable Genomic Landscape During Osteosarcoma Progression: Insights From a Longitudinal WGS Analysis. Genes Chromosomes Cancer 2024; 63:e23253. [PMID: 39023390 DOI: 10.1002/gcc.23253] [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: 05/14/2024] [Revised: 06/06/2024] [Accepted: 06/10/2024] [Indexed: 07/20/2024] Open
Abstract
Osteosarcoma is a primary bone tumor that exhibits a complex genomic landscape characterized by gross chromosomal abnormalities. Osteosarcoma patients often develop metastatic disease, resulting in limited therapeutic options and poor survival rates. To gain knowledge on the mechanisms underlying osteosarcoma heterogeneity and metastatic process, it is important to obtain a detailed profile of the genomic alterations that accompany osteosarcoma progression. We performed WGS on multiple tissue samples from six patients with osteosarcoma, including the treatment naïve biopsy of the primary tumor, resection of the primary tumor after neoadjuvant chemotherapy, local recurrence, and distant metastases. A comprehensive analysis of single-nucleotide variants (SNVs), structural variants, copy number alterations (CNAs), and chromothripsis events revealed the genomic heterogeneity during osteosarcoma progression. SNVs and structural variants were found to accumulate over time, contributing to an increased complexity of the genome of osteosarcoma during disease progression. Phylogenetic trees based on SNVs and structural variants reveal distinct evolutionary patterns between patients, including linear, neutral, and branched patterns. The majority of osteosarcomas showed variable copy number profiles or gained whole-genome doubling in later occurrences. Large proportions of the genome were affected by loss of heterozygosity (LOH), although these regions remain stable during progression. Additionally, chromothripsis is not confined to a single early event, as multiple other chromothripsis events may appear in later occurrences. Together, we provide a detailed analysis of the complex genome of osteosarcomas and show that five of six osteosarcoma genomes are highly dynamic and variable during progression.
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Affiliation(s)
- Debora M Meijer
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | | | - Hans Gelderblom
- Department of Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Noel F C C de Miranda
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marieke L Kuijjer
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, The Netherlands
- Centre for Molecular Medicine Norway (NCMM), Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Judith V M G Bovée
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, The Netherlands
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16
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Tlemsani C, Heske CM, Elloumi F, Pongor L, Khandagale P, Varma S, Luna A, Meltzer PS, Khan J, Reinhold WC, Pommier Y. Sarcoma_CellminerCDB: A tool to interrogate the genomic and functional characteristics of a comprehensive collection of sarcoma cell lines. iScience 2024; 27:109781. [PMID: 38868205 PMCID: PMC11167437 DOI: 10.1016/j.isci.2024.109781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/28/2023] [Accepted: 04/15/2024] [Indexed: 06/14/2024] Open
Abstract
Sarcomas are a diverse group of rare malignancies composed of multiple different clinical and molecular subtypes. Due to their rarity and heterogeneity, basic, translational, and clinical research in sarcoma has trailed behind that of other cancers. Outcomes for patients remain generally poor due to an incomplete understanding of disease biology and a lack of novel therapies. To address some of the limitations impeding preclinical sarcoma research, we have developed Sarcoma_CellMinerCDB, a publicly available interactive tool that merges publicly available sarcoma cell line data and newly generated omics data to create a comprehensive database of genomic, transcriptomic, methylomic, proteomic, metabolic, and pharmacologic data on 133 annotated sarcoma cell lines. The reproducibility, functionality, biological relevance, and therapeutic applications of Sarcoma_CellMinerCDB described herein are powerful tools to address and generate biological questions and test hypotheses for translational research. Sarcoma_CellMinerCDB (https://discover.nci.nih.gov/SarcomaCellMinerCDB) aims to contribute to advancing the preclinical study of sarcoma.
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Affiliation(s)
- Camille Tlemsani
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
- Department of Medical Oncology, Cochin Hospital, Paris Cancer Institute CARPEM, Université Paris Cité, APHP. Centre, Paris, France
- Institut Cochin, INSERM U1016, CNRS UMR8104, Paris Cancer Institute CARPEM, Université Paris Cité, Paris, France
| | - Christine M. Heske
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fathi Elloumi
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Lorinc Pongor
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
- Hungarian Centre of Excellence for Molecular Medicine, Cancer Genomics and Epigenetics Core Group, Szeged, Hungary
| | - Prashant Khandagale
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sudhir Varma
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Augustin Luna
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
- Computational Biology Branch, National Library of Medicine, NIH, Bethesda, Maryland 20892, USA
| | - Paul S. Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - William C. Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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17
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Huang CY, Jiang N, Shen M, Lai GG, Tan AC, Jain A, Saw SP, Ang MK, Ng QS, Lim DW, Kanesvaran R, Tan EH, Tan WL, Ong BH, Chua KL, Anantham D, Takano AM, Lim KH, Tam WL, Sim NL, Skanderup AJ, Tan DS, Rozen SG. Oncogene-Driven Non-Small Cell Lung Cancers in Patients with a History of Smoking Lack Smoking-Induced Mutations. Cancer Res 2024; 84:2009-2020. [PMID: 38587551 DOI: 10.1158/0008-5472.can-23-2551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/29/2023] [Accepted: 03/27/2024] [Indexed: 04/09/2024]
Abstract
Non-small cell lung cancers (NSCLC) in nonsmokers are mostly driven by mutations in the oncogenes EGFR, ERBB2, and MET and fusions involving ALK and RET. In addition to occurring in nonsmokers, alterations in these "nonsmoking-related oncogenes" (NSRO) also occur in smokers. To better understand the clonal architecture and genomic landscape of NSRO-driven tumors in smokers compared with typical-smoking NSCLCs, we investigated genomic and transcriptomic alterations in 173 tumor sectors from 48 NSCLC patients. NSRO-driven NSCLCs in smokers and nonsmokers had similar genomic landscapes. Surprisingly, even in patients with prominent smoking histories, the mutational signature caused by tobacco smoking was essentially absent in NSRO-driven NSCLCs, which was confirmed in two large NSCLC data sets from other geographic regions. However, NSRO-driven NSCLCs in smokers had higher transcriptomic activities related to the regulation of the cell cycle. These findings suggest that, whereas the genomic landscape is similar between NSRO-driven NSCLC in smokers and nonsmokers, smoking still affects the tumor phenotype independently of genomic alterations. SIGNIFICANCE Non-small cell lung cancers driven by nonsmoking-related oncogenes do not harbor genomic scars caused by smoking regardless of smoking history, indicating that the impact of smoking on these tumors is mainly nongenomic.
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Affiliation(s)
- Chen-Yang Huang
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Division of Hematology-Oncology, Department of Internal Medicine, Linkou Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan
| | - Nanhai Jiang
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Meixin Shen
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Gillianne G Lai
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Aaron C Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Amit Jain
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Stephanie P Saw
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Mei Kim Ang
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Quan Sing Ng
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Darren W Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Ravindran Kanesvaran
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Eng Huat Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Wan Ling Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Boon-Hean Ong
- Department of Cardiothoracic Surgery, National Heart Centre Singapore, Singapore, Singapore
| | - Kevin L Chua
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Devanand Anantham
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Angela M Takano
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Kiat Hon Lim
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Wai Leong Tam
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ngak Leng Sim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Anders J Skanderup
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Daniel S Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Duke-NUS Medical School Singapore, Singapore, Singapore
- Cancer Therapeutics Research Laboratory, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Steven G Rozen
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina
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18
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Suzuki K, Koyama D, Oka Y, Sato Y, Sekine R, Fukatsu M, Hayashi K, Takano M, Hashimoto Y, Ikezoe T. Myeloid sarcoma with plasmacytoid dendritic cell-like proliferation associated with IKZF1, ETV6 and DNMT3A mutations. Int J Hematol 2024:10.1007/s12185-024-03806-z. [PMID: 38861243 DOI: 10.1007/s12185-024-03806-z] [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: 01/14/2024] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
The classification of clonal plasmacytoid dendritic cell (pDC) proliferation associated with myeloid neoplasms remains a topic of ongoing debate. Although the fifth edition of the World Health Organization classification classifies clonal pDC proliferation into two categories, it is unclear whether this classification adequately captures the complexities of clonal pDC pathogenesis. We present a clinical case featuring myeloid sarcoma with pDC-like cells in cervical lymph nodes and bone marrow (BM). Analysis of biopsy specimens and BM aspirate revealed two distinct cellular populations expressing myeloid and pDC markers. One population exhibited myeloid leukemia and monocyte markers, including MPO, CD13, CD33, CD11b, and CD14, while the other manifested an immunophenotype reminiscent of pDCs, characterized by expression of CD56 and CD123. Additionally, whole exome sequencing and RNA sequencing of BM mononuclear cells were conducted to explore the pathophysiology of this rare malignancy, and unveiled pDC-like cell proliferation driven by IKZF1 and ETV6 mutations originating from clonal hematopoiesis initiated by a DNMT3A mutation. Notably, venetoclax-based therapy exhibited efficacy for achieving and sustaining complete remission. This case provides pivotal insights into the mechanistic aspects of pDC/pDC-like cell proliferation in myeloid sarcoma, offering valuable perspectives on therapeutic strategies.
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Affiliation(s)
- Kengo Suzuki
- Department of Hematology, Fukushima Medical University, Fukushima, 960-1295, Japan
| | - Daisuke Koyama
- Department of Hematology, Fukushima Medical University, Fukushima, 960-1295, Japan.
| | - Yuka Oka
- Department of Diagnostic Pathology, Fukushima Medical University, Fukushima, 960-1295, Japan
| | - Yuki Sato
- Department of Hematology, Fukushima Medical University, Fukushima, 960-1295, Japan
| | - Rei Sekine
- Department of Diagnostic Pathology, Fukushima Medical University, Fukushima, 960-1295, Japan
| | - Masahiko Fukatsu
- Department of Hematology, Fukushima Medical University, Fukushima, 960-1295, Japan
| | - Kiyohito Hayashi
- Department of Hematology, Fukushima Medical University, Fukushima, 960-1295, Japan
| | - Motoki Takano
- Department of Hematology, Fukushima Medical University, Fukushima, 960-1295, Japan
| | - Yuko Hashimoto
- Department of Diagnostic Pathology, Fukushima Medical University, Fukushima, 960-1295, Japan
| | - Takayuki Ikezoe
- Department of Hematology, Fukushima Medical University, Fukushima, 960-1295, Japan
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19
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Hamdi Y, Boujemaa M, Ben Aissa-Haj J, Radouani F, Khyatti M, Mighri N, Hannachi M, Ghedira K, Souiai O, Hkimi C, Kammoun MS, Mejri N, Bouaziz H, Beloufa MA, Charoute H, Barakat A, Najjar I, Taniguchi H, Pietrosemoli N, Dellagi K, Abdelhak S, Boubaker MS, Chica C, Rouleau E. A regionally based precision medicine implementation initiative in North Africa:The PerMediNA consortium. Transl Oncol 2024; 44:101940. [PMID: 38537326 DOI: 10.1016/j.tranon.2024.101940] [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: 12/06/2023] [Revised: 02/23/2024] [Accepted: 03/11/2024] [Indexed: 04/21/2024] Open
Abstract
Precision Medicine is being increasingly used in the developed world to improve health care. While several Precision Medicine (PM) initiatives have been launched worldwide, their implementations have proven to be more challenging particularly in low- and middle-income countries. To address this issue, the "Personalized Medicine in North Africa" initiative (PerMediNA) was launched in three North African countries namely Tunisia, Algeria and Morocco. PerMediNA is coordinated by Institut Pasteur de Tunis together with the French Ministry for Europe and Foreign Affairs, with the support of Institut Pasteur in France. The project is carried out along with Institut Pasteur d'Algérie and Institut Pasteur du Maroc in collaboration with national and international leading institutions in the field of PM including Institut Gustave Roussy in Paris. PerMediNA aims to assess the readiness level of PM implementation in North Africa, to strengthen PM infrastructure, to provide workforce training, to generate genomic data on North African populations, to implement cost effective, affordable and sustainable genetic testing for cancer patients and to inform policy makers on how to translate research knowledge into health products and services. Gender equity and involvement of young scientists in this implementation process are other key goals of the PerMediNA project. In this paper, we are describing PerMediNA as the first PM implementation initiative in North Africa. Such initiatives contribute significantly in shortening existing health disparities and inequities between developed and developing countries and accelerate access to innovative treatments for global health.
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Affiliation(s)
- Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia.
| | - Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Jihenne Ben Aissa-Haj
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia; Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Fouzia Radouani
- Chlamydiae and Mycoplasmas Laboratory, Research Department, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Meriem Khyatti
- Laboratory of Viral Oncology, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Najah Mighri
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Mariem Hannachi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics LR20IPT09, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics LR20IPT09, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Oussema Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics LR20IPT09, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Chaima Hkimi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics LR20IPT09, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Mohamed Selim Kammoun
- Laboratory of Bioinformatics, Biomathematics and Biostatistics LR20IPT09, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Nesrine Mejri
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia; Medical Oncology Department, Abderrahmane Mami Hospital, Faculty of Medicine, University Tunis El Manar, Tunis, Tunisia
| | - Hanen Bouaziz
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia; Department of Carcinological Surgery, Salah Azaiez Institute, Tunis, Tunisia
| | | | - Hicham Charoute
- Research unit of Epidemiology, Biostatistics and Bioinformatics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Abdelhamid Barakat
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc 20360, Casablanca, Morocco
| | - Imène Najjar
- Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Paris 75015, France
| | - Hiroaki Taniguchi
- The Polish Academy of Sciences, Poland; University Mohamed VI, Morocco
| | - Natalia Pietrosemoli
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub F-75015, Paris, France
| | - Koussay Dellagi
- Pasteur Network Association, Institut Pasteur, Paris, France
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Mohamed Samir Boubaker
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia; Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Claudia Chica
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub F-75015, Paris, France
| | - Etienne Rouleau
- Department of Biology and Pathology-Cancer Genetics Laboratory-Gustave Roussy 94805, Villejuif, France
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20
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Mariella E, Grasso G, Miotto M, Buzo K, Reilly NM, Andrei P, Vitiello PP, Crisafulli G, Arena S, Rospo G, Corti G, Lorenzato A, Cancelliere C, Barault L, Gionfriddo G, Linnebacher M, Russo M, Di Nicolantonio F, Bardelli A. Transcriptome-wide gene expression outlier analysis pinpoints therapeutic vulnerabilities in colorectal cancer. Mol Oncol 2024; 18:1460-1485. [PMID: 38468448 PMCID: PMC11161737 DOI: 10.1002/1878-0261.13622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
Multiple strategies are continuously being explored to expand the drug target repertoire in solid tumors. We devised a novel computational workflow for transcriptome-wide gene expression outlier analysis that allows the systematic identification of both overexpression and underexpression events in cancer cells. Here, it was applied to expression values obtained through RNA sequencing in 226 colorectal cancer (CRC) cell lines that were also characterized by whole-exome sequencing and microarray-based DNA methylation profiling. We found cell models displaying an abnormally high or low expression level for 3533 and 965 genes, respectively. Gene expression abnormalities that have been previously associated with clinically relevant features of CRC cell lines were confirmed. Moreover, by integrating multi-omics data, we identified both genetic and epigenetic alternations underlying outlier expression values. Importantly, our atlas of CRC gene expression outliers can guide the discovery of novel drug targets and biomarkers. As a proof of concept, we found that CRC cell lines lacking expression of the MTAP gene are sensitive to treatment with a PRMT5-MTA inhibitor (MRTX1719). Finally, other tumor types may also benefit from this approach.
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Affiliation(s)
- Elisa Mariella
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
- IFOM ETS, The AIRC Institute of Molecular OncologyMilanItaly
| | - Gaia Grasso
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
- IFOM ETS, The AIRC Institute of Molecular OncologyMilanItaly
| | - Martina Miotto
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
- IFOM ETS, The AIRC Institute of Molecular OncologyMilanItaly
| | - Kristi Buzo
- Department of OncologyUniversity of TorinoCandiolo (TO)Italy
- Candiolo Cancer InstituteFPO‐IRCCSCandiolo (TO)Italy
| | | | - Pietro Andrei
- Department of OncologyUniversity of TorinoCandiolo (TO)Italy
| | - Pietro Paolo Vitiello
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
- IFOM ETS, The AIRC Institute of Molecular OncologyMilanItaly
| | | | - Sabrina Arena
- Department of OncologyUniversity of TorinoCandiolo (TO)Italy
- Candiolo Cancer InstituteFPO‐IRCCSCandiolo (TO)Italy
| | - Giuseppe Rospo
- Department of OncologyUniversity of TorinoCandiolo (TO)Italy
- Present address:
Boehringer Ingelheim RCV GmbH & Co KGViennaAustria
| | - Giorgio Corti
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
| | - Annalisa Lorenzato
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
| | | | - Ludovic Barault
- Department of OncologyUniversity of TorinoCandiolo (TO)Italy
| | | | - Michael Linnebacher
- Clinic of General Surgery, Molecular Oncology and ImmunotherapyUniversity of RostockGermany
| | - Mariangela Russo
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
- IFOM ETS, The AIRC Institute of Molecular OncologyMilanItaly
| | - Federica Di Nicolantonio
- Department of OncologyUniversity of TorinoCandiolo (TO)Italy
- Candiolo Cancer InstituteFPO‐IRCCSCandiolo (TO)Italy
| | - Alberto Bardelli
- Department of Oncology, Molecular Biotechnology CenterUniversity of TorinoItaly
- IFOM ETS, The AIRC Institute of Molecular OncologyMilanItaly
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21
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Poscente M, Tolomeo D, Arshadi A, Agostini A, L'Abbate A, Solimando AG, Palumbo O, Carella M, Palumbo P, González T, Hernández-Rivas JM, Bassi L, Isidori R, Dell'Aquila M, Trapè G, Latagliata R, Pessina G, Natoni F, Storlazzi CT. Aggressive systemic mastocytosis with the co-occurrence of PRKG2::PDGFRB, KAT6A::NCOA2, and RXRA::NOTCH1 fusion transcripts and a heterozygous RUNX1 frameshift mutation. Cancer Genet 2024; 284-285:5-11. [PMID: 38471404 DOI: 10.1016/j.cancergen.2024.03.002] [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: 07/11/2023] [Revised: 01/05/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024]
Abstract
Systemic mastocytosis (SM) is a myeloproliferative neoplasm displaying abnormal mast cell proliferation. It is subdivided into different forms, including aggressive systemic mastocytosis (ASM) and systemic mastocytosis with an associated hematologic neoplasm (SM-AHN). Oncogenic genetic alterations include point mutations, mainly the KIT D816V, conferring poor prognosis and therapy resistance, and fusion genes, with those involving PDGFRA/PDGFRB as the most recurrent events. We here describe an ASM case negative to the KIT D816V and JAK2 V617F alterations but showing a RUNX1 frameshift heterozygous mutation and the co-occurrence of three fusion transcripts. The first one, PRKG2::PDGFRB, was generated by a balanced t(4;5)(q24;q32) translocation as the sole abnormality. Other two novel chimeras, KAT6A::NCOA2 and RXRA::NOTCH1, originated from cryptic intra-chromosomal abnormalities. The patient rapidly evolved towards SM-AHN, characterized by the persistence of the PRKG2::PDGFRB chimera, due to the presence of an extra copy of the der(5)t(4;5)(q24;q34) chromosome and an increase in the RUNX1 mutation allelic frequency. The results indicated that the transcriptional landscape and the mutational profile of SM deserve attention to predict the evolution and prognosis of this complex disease, whose classification criteria are still a matter of debate.
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Affiliation(s)
- M Poscente
- UOSD Laboratorio di Genetica Medica, Ospedale Belcolle, Viterbo, Italy
| | - D Tolomeo
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - A Arshadi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - A Agostini
- Department of Precision and Regenerative Medicine and Ionian Area, Unit of Internal Medicine and Clinical Oncology, University of Bari Aldo Moro, Bari, Italy
| | - A L'Abbate
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari (IBIOM), Consiglio Nazionale delle Ricerche, Bari, Italy
| | - A G Solimando
- Department of Precision and Regenerative Medicine and Ionian Area, Unit of Internal Medicine and Clinical Oncology, University of Bari Aldo Moro, Bari, Italy; IRCCS Istituto Tumori "Giovanni Paolo II", Bari, Italy
| | - O Palumbo
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo Foggia, Italy
| | - M Carella
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo Foggia, Italy
| | - P Palumbo
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo Foggia, Italy
| | - T González
- Department of Medicine, Universidad de Salamanca, Department of Hematology, Hospital Universitario de Salamanca, IBSAL, IBMCC-Centro de Investigación del Cáncer (USAL-CSIC), Salamanca, Spain
| | - J M Hernández-Rivas
- Department of Medicine, Universidad de Salamanca, Department of Hematology, Hospital Universitario de Salamanca, IBSAL, IBMCC-Centro de Investigación del Cáncer (USAL-CSIC), Salamanca, Spain
| | - L Bassi
- UOSD Laboratorio di Genetica Medica, Ospedale Belcolle, Viterbo, Italy
| | - R Isidori
- UOSD Laboratorio di Genetica Medica, Ospedale Belcolle, Viterbo, Italy
| | - M Dell'Aquila
- UOC Anatomia Patologica, Ospedale Belcolle, Viterbo, Italy
| | - G Trapè
- UOC Ematologia, Ospedale Belcolle, Viterbo, Italy
| | - R Latagliata
- UOC Ematologia, Ospedale Belcolle, Viterbo, Italy
| | - G Pessina
- UOSD Laboratorio di Genetica Medica, Ospedale Belcolle, Viterbo, Italy
| | - F Natoni
- UOSD Laboratorio di Genetica Medica, Ospedale Belcolle, Viterbo, Italy
| | - C T Storlazzi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy.
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22
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Lang F, Sorn P, Suchan M, Henrich A, Albrecht C, Köhl N, Beicht A, Riesgo-Ferreiro P, Holtsträter C, Schrörs B, Weber D, Löwer M, Sahin U, Ibn-Salem J. Prediction of tumor-specific splicing from somatic mutations as a source of neoantigen candidates. BIOINFORMATICS ADVANCES 2024; 4:vbae080. [PMID: 38863673 PMCID: PMC11165244 DOI: 10.1093/bioadv/vbae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/26/2024] [Accepted: 05/28/2024] [Indexed: 06/13/2024]
Abstract
Motivation Neoantigens are promising targets for cancer immunotherapies and might arise from alternative splicing. However, detecting tumor-specific splicing is challenging because many non-canonical splice junctions identified in tumors also appear in healthy tissues. To increase tumor-specificity, we focused on splicing caused by somatic mutations as a source for neoantigen candidates in individual patients. Results We developed the tool splice2neo with multiple functionalities to integrate predicted splice effects from somatic mutations with splice junctions detected in tumor RNA-seq and to annotate the resulting transcript and peptide sequences. Additionally, we provide the tool EasyQuant for targeted RNA-seq read mapping to candidate splice junctions. Using a stringent detection rule, we predicted 1.7 splice junctions per patient as splice targets with a false discovery rate below 5% in a melanoma cohort. We confirmed tumor-specificity using independent, healthy tissue samples. Furthermore, using tumor-derived RNA, we confirmed individual exon-skipping events experimentally. Most target splice junctions encoded neoepitope candidates with predicted major histocompatibility complex (MHC)-I or MHC-II binding. Compared to neoepitope candidates from non-synonymous point mutations, the splicing-derived MHC-I neoepitope candidates had lower self-similarity to corresponding wild-type peptides. In conclusion, we demonstrate that identifying mutation-derived, tumor-specific splice junctions can lead to additional neoantigen candidates to expand the target repertoire for cancer immunotherapies. Availability and implementation The R package splice2neo and the python package EasyQuant are available at https://github.com/TRON-Bioinformatics/splice2neo and https://github.com/TRON-Bioinformatics/easyquant, respectively.
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Affiliation(s)
- Franziska Lang
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
- Faculty of Biology, Johannes Gutenberg University Mainz, Mainz 55128, Germany
| | - Patrick Sorn
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Martin Suchan
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Alina Henrich
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Christian Albrecht
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Nina Köhl
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Aline Beicht
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Pablo Riesgo-Ferreiro
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Christoph Holtsträter
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Barbara Schrörs
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - David Weber
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Martin Löwer
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
| | - Ugur Sahin
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
- BioNTech SE, Mainz 55131, Germany
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz 55131, Germany
| | - Jonas Ibn-Salem
- TRON—Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz 55131, Germany
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23
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Hofvander J, Qiu A, Lee K, Bilenky M, Carles A, Cao Q, Moksa M, Steif J, Su E, Sotiriou A, Goytain A, Hill LA, Singer S, Andrulis IL, Wunder JS, Mertens F, Banito A, Jones KB, Underhill TM, Nielsen TO, Hirst M. Synovial Sarcoma Chromatin Dynamics Reveal a Continuum in SS18:SSX Reprograming. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594262. [PMID: 38798672 PMCID: PMC11118320 DOI: 10.1101/2024.05.14.594262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Synovial sarcoma (SyS) is an aggressive soft-tissue malignancy characterized by a pathognomonic chromosomal translocation leading to the formation of the SS18::SSX fusion oncoprotein. SS18::SSX associates with mammalian BAF complexes suggesting deregulation of chromatin architecture as the oncogenic driver in this tumour type. To examine the epigenomic state of SyS we performed comprehensive multi-omics analysis on 52 primary pre-treatment human SyS tumours. Our analysis revealed a continuum of epigenomic states across the cohort at fusion target genes independent of rare somatic genetic lesions. We identify cell-of-origin signatures defined by enhancer states and reveal unexpected relationships between H2AK119Ub1 and active marks. The number of bivalent promoters, dually marked by the repressive H3K27me3 and activating H3K4me3 marks, has strong prognostic value and outperforms tumor grade in predicting patient outcome. Finally, we identify SyS defining epigenomic features including H3K4me3 expansion associated with striking promoter DNA hypomethylation in which SyS displays the lowest mean methylation level of any sarcoma subtype. We explore these distinctive features as potential vulnerabilities in SyS and identify H3K4me3 inhibition as a promising therapeutic strategy.
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Affiliation(s)
- Jakob Hofvander
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Alvin Qiu
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, UBC, Vancouver, Canada
| | - Kiera Lee
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, UBC, Vancouver, Canada
| | - Misha Bilenky
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Annaïck Carles
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
| | - Qi Cao
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
| | - Michelle Moksa
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
| | - Jonathan Steif
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
| | - Edmund Su
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
| | - Afroditi Sotiriou
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, Germany
- Soft-Tissue Sarcoma Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Germany
| | - Angela Goytain
- Department of Pathology and Laboratory Medicine, UBC, Vancouver, Canada
| | - Lesley A Hill
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sam Singer
- Sarcoma Biology Laboratory, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Irene L Andrulis
- University Musculoskeletal Oncology Unit, Mount Sinai Hospital, Toronto, Canada
| | - Jay S Wunder
- Lunefeld-Tanenbaum Research Institute, Sinai Health System and Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Fredrik Mertens
- Division of Clinical Genetics, Lund University and Skåne University Hospital, Lund, Sweden
| | - Ana Banito
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, Germany
- Soft-Tissue Sarcoma Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kevin B Jones
- Department of Orthopaedics, University of Utah, Salt Lake City, Utah, United States of America
- Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
| | - T Michael Underhill
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Torsten O Nielsen
- Department of Pathology and Laboratory Medicine, UBC, Vancouver, Canada
| | - Martin Hirst
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
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24
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Park SJ, Ju S, Goh SH, Yoon BH, Park JL, Kim JH, Lee S, Lee SJ, Kwon Y, Lee W, Park KC, Lee GK, Park SY, Kim S, Kim SY, Han JY, Lee C. Proteogenomic Characterization Reveals Estrogen Signaling as a Target for Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations. Cancer Res 2024; 84:1491-1503. [PMID: 38607364 DOI: 10.1158/0008-5472.can-23-1551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 10/24/2023] [Accepted: 01/18/2024] [Indexed: 04/13/2024]
Abstract
Never-smoker lung adenocarcinoma (NSLA) is prevalent in Asian populations, particularly in women. EGFR mutations and anaplastic lymphoma kinase (ALK) fusions are major genetic alterations observed in NSLA, and NSLA with these alterations have been well studied and can be treated with targeted therapies. To provide insights into the molecular profile of NSLA without EGFR and ALK alterations (NENA), we selected 141 NSLA tissues and performed proteogenomic characterization, including whole genome sequencing (WGS), transcriptomic, methylation EPIC array, total proteomic, and phosphoproteomic analyses. Forty patients with NSLA harboring EGFR and ALK alterations and seven patients with NENA with microsatellite instability were excluded. Genome analysis revealed that TP53 (25%), KRAS (22%), and SETD2 (11%) mutations and ROS1 fusions (14%) were the most frequent genetic alterations in NENA patients. Proteogenomic impact analysis revealed that STK11 and ERBB2 somatic mutations had broad effects on cancer-associated genes in NENA. DNA copy number alteration analysis identified 22 prognostic proteins that influenced transcriptomic and proteomic changes. Gene set enrichment analysis revealed estrogen signaling as the key pathway activated in NENA. Increased estrogen signaling was associated with proteogenomic alterations, such as copy number deletions in chromosomes 14 and 21, STK11 mutation, and DNA hypomethylation of LLGL2 and ST14. Finally, saracatinib, an Src inhibitor, was identified as a potential drug for targeting activated estrogen signaling in NENA and was experimentally validated in vitro. Collectively, this study enhanced our understanding of NENA NSLA by elucidating the proteogenomic landscape and proposed saracatinib as a potential treatment for this patient population that lacks effective targeted therapies. SIGNIFICANCE The proteogenomic landscape in never-smoker lung cancer without known driver mutations reveals prognostic proteins and enhanced estrogen signaling that can be targeted as a potential therapeutic strategy to improve patient outcomes.
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Affiliation(s)
- Seung-Jin Park
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Shinyeong Ju
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Sung-Ho Goh
- National Cancer Center, Goyang, Republic of Korea
| | - Byoung-Ha Yoon
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jong-Lyul Park
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jeong-Hwan Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Seonjeong Lee
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology, Seoul, Republic of Korea
| | - Sang-Jin Lee
- National Cancer Center, Goyang, Republic of Korea
| | - Yumi Kwon
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Wonyeop Lee
- National Cancer Center, Goyang, Republic of Korea
| | - Kyung Chan Park
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | | | | | - Sunshin Kim
- National Cancer Center, Goyang, Republic of Korea
| | - Seon-Young Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Ji-Youn Han
- National Cancer Center, Goyang, Republic of Korea
| | - Cheolju Lee
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology, Seoul, Republic of Korea
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25
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Priesterbach-Ackley LP, van Kuik J, Tops BBJ, Lasorella A, Iavarone A, van Hecke W, Robe PA, Wesseling P, de Leng WWJ. RT-PCR assay to detect FGFR3::TACC3 fusions in formalin-fixed, paraffin-embedded glioblastoma samples. Neurooncol Pract 2024; 11:142-149. [PMID: 38496910 PMCID: PMC10940835 DOI: 10.1093/nop/npad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024] Open
Abstract
Background One targeted treatment option for isocitrate dehydrogenase (IDH)-wild-type glioblastoma focuses on tumors with fibroblast growth factor receptor 3::transforming acidic coiled-coil-containing protein 3 (FGFR3::TACC3) fusions. FGFR3::TACC3 fusion detection can be challenging, as targeted RNA next-generation sequencing (NGS) is not routinely performed, and immunohistochemistry is an imperfect surrogate marker. Fusion status can be determined using reverse transcription polymerase chain reaction (RT-PCR) on fresh frozen (FF) material, but sometimes only formalin-fixed, paraffin-embedded (FFPE) tissue is available. Aim To develop an RT-PCR assay to determine FGFR3::TACC3 status in FFPE glioblastoma samples. Methods Twelve tissue microarrays with 353 historical glioblastoma samples were immunohistochemically stained for FGFR3. Samples with overexpression of FGFR3 (n = 13) were subjected to FGFR3::TACC3 RT-PCR on FFPE, using 5 primer sets for the detection of 5 common fusion variants. Fusion-negative samples were additionally analyzed with NGS (n = 6), FGFR3 Fluorescence In Situ Hybridization (n = 6), and RNA sequencing (n = 5). Results Using RT-PCR on FFPE material of the 13 samples with FGFR3 overexpression, we detected an FGFR3::TACC3 fusion in 7 samples, covering 3 different fusion variants. For 5 of these FF was available, and the presence of the fusion was confirmed through RT-PCR on FF. With RNA sequencing, 1 additional sample was found to harbor an FGFR3::TACC3 fusion (variant not covered by current RT-PCR for FFPE). The frequency of FGFR3::TACC3 fusion in this cohort was 9/353 (2.5%). Conclusions RT-PCR for FGFR3::TACC3 fusions can successfully be performed on FFPE material, with a specificity of 100% and (due to limited primer sets) a sensitivity of 83.3%. This assay allows for the identification of potential targeted treatment options when only formalin-fixed tissue is available.
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Affiliation(s)
| | - Joyce van Kuik
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bastiaan B J Tops
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Anna Lasorella
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Antonio Iavarone
- Department of Neurological Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Wim van Hecke
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Pierre A Robe
- Department of Neurosurgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Pieter Wesseling
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pathology, Amsterdam University Medical Centers/VUmc & Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
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26
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Lee Y, Chowdhury T, Kim S, Yu HJ, Kim KM, Kang H, Kim MS, Kim JW, Kim YH, Ji SY, Hwang K, Han JH, Hwang J, Yoo SK, Lee KS, Choe G, Won JK, Park SH, Lee YK, Shin JH, Park CK, Kim CY, Kim JI. Central neurocytoma exhibits radial glial cell signatures with FGFR3 hypomethylation and overexpression. Exp Mol Med 2024; 56:975-986. [PMID: 38609519 PMCID: PMC11059271 DOI: 10.1038/s12276-024-01204-3] [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: 07/12/2023] [Revised: 12/01/2023] [Accepted: 01/30/2024] [Indexed: 04/14/2024] Open
Abstract
We explored the genomic events underlying central neurocytoma (CN), a rare neoplasm of the central nervous system, via multiomics approaches, including whole-exome sequencing, bulk and single-nuclei RNA sequencing, and methylation sequencing. We identified FGFR3 hypomethylation leading to FGFR3 overexpression as a major event in the ontogeny of CN that affects crucial downstream events, such as aberrant PI3K-AKT activity and neuronal development pathways. Furthermore, we found similarities between CN and radial glial cells based on analyses of gene markers and CN tumor cells and postulate that CN tumorigenesis is due to dysregulation of radial glial cell differentiation into neurons. Our data demonstrate the potential role of FGFR3 as one of the leading drivers of tumorigenesis in CN.
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Affiliation(s)
- Yeajina Lee
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Tamrin Chowdhury
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sojin Kim
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hyeon Jong Yu
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Kyung-Min Kim
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Ho Kang
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Min-Sung Kim
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jin Wook Kim
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Yong-Hwy Kim
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - So Young Ji
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Kihwan Hwang
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Jung Ho Han
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Jinha Hwang
- Department of Laboratory Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - Seong-Keun Yoo
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kyu Sang Lee
- Department of Pathology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Gheeyoung Choe
- Department of Pathology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Jae-Kyung Won
- Department of Pathology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Yong Kyu Lee
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Chul-Kee Park
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea.
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Chae-Yong Kim
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, Republic of Korea.
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea.
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea.
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27
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Jiang YZ, Ma D, Jin X, Xiao Y, Yu Y, Shi J, Zhou YF, Fu T, Lin CJ, Dai LJ, Liu CL, Zhao S, Su GH, Hou W, Liu Y, Chen Q, Yang J, Zhang N, Zhang WJ, Liu W, Ge W, Yang WT, You C, Gu Y, Kaklamani V, Bertucci F, Verschraegen C, Daemen A, Shah NM, Wang T, Guo T, Shi L, Perou CM, Zheng Y, Huang W, Shao ZM. Integrated multiomic profiling of breast cancer in the Chinese population reveals patient stratification and therapeutic vulnerabilities. NATURE CANCER 2024; 5:673-690. [PMID: 38347143 DOI: 10.1038/s43018-024-00725-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/04/2024] [Indexed: 04/30/2024]
Abstract
Molecular profiling guides precision treatment of breast cancer; however, Asian patients are underrepresented in publicly available large-scale studies. We established a comprehensive multiomics cohort of 773 Chinese patients with breast cancer and systematically analyzed their genomic, transcriptomic, proteomic, metabolomic, radiomic and digital pathology characteristics. Here we show that compared to breast cancers in white individuals, Asian individuals had more targetable AKT1 mutations. Integrated analysis revealed a higher proportion of HER2-enriched subtype and correspondingly more frequent ERBB2 amplification and higher HER2 protein abundance in the Chinese HR+HER2+ cohort, stressing anti-HER2 therapy for these individuals. Furthermore, comprehensive metabolomic and proteomic analyses revealed ferroptosis as a potential therapeutic target for basal-like tumors. The integration of clinical, transcriptomic, metabolomic, radiomic and pathological features allowed for efficient stratification of patients into groups with varying recurrence risks. Our study provides a public resource and new insights into the biology and ancestry specificity of breast cancer in the Asian population, offering potential for further precision treatment approaches.
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Affiliation(s)
- Yi-Zhou Jiang
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Ding Ma
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xi Jin
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi Xiao
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jinxiu Shi
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies (SIBPT), Shanghai, China
| | - Yi-Fan Zhou
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Tong Fu
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Cai-Jin Lin
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lei-Jie Dai
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Cheng-Lin Liu
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shen Zhao
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Guan-Hua Su
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yaqing Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qingwang Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jingcheng Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
- Greater Bay Area Institute of Precision Medicine, Guangzhou, China
| | - Naixin Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Wen-Juan Zhang
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei Liu
- Westlake Omics (Hangzhou) Biotechnology, Hangzhou, China
| | - Weigang Ge
- Westlake Omics (Hangzhou) Biotechnology, Hangzhou, China
| | - Wen-Tao Yang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Chao You
- Department of Radiology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yajia Gu
- Department of Radiology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Virginia Kaklamani
- Division Haematology/Oncology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - François Bertucci
- Predictive Oncology Laboratory and Department of Medical Oncology, CRCM, Institut Paoli-Calmettes, Inserm UMR1068, CNRS UMR7258, Aix-Marseille Université, Marseille, France
| | | | - Anneleen Daemen
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, USA
| | - Nakul M Shah
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Tiannan Guo
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
- International Human Phenome Institutes (Shanghai), Shanghai, China
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
| | - Wei Huang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies (SIBPT), Shanghai, China.
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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28
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Acanda De La Rocha AM, Berlow NE, Fader M, Coats ER, Saghira C, Espinal PS, Galano J, Khatib Z, Abdella H, Maher OM, Vorontsova Y, Andrade-Feraud CM, Daccache A, Jacome A, Reis V, Holcomb B, Ghurani Y, Rimblas L, Guilarte TR, Hu N, Salyakina D, Azzam DJ. Feasibility of functional precision medicine for guiding treatment of relapsed or refractory pediatric cancers. Nat Med 2024; 30:990-1000. [PMID: 38605166 PMCID: PMC11031400 DOI: 10.1038/s41591-024-02848-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 01/31/2024] [Indexed: 04/13/2024]
Abstract
Children with rare, relapsed or refractory cancers often face limited treatment options, and few predictive biomarkers are available that can enable personalized treatment recommendations. The implementation of functional precision medicine (FPM), which combines genomic profiling with drug sensitivity testing (DST) of patient-derived tumor cells, has potential to identify treatment options when standard-of-care is exhausted. The goal of this prospective observational study was to generate FPM data for pediatric patients with relapsed or refractory cancer. The primary objective was to determine the feasibility of returning FPM-based treatment recommendations in real time to the FPM tumor board (FPMTB) within a clinically actionable timeframe (<4 weeks). The secondary objective was to assess clinical outcomes from patients enrolled in the study. Twenty-five patients with relapsed or refractory solid and hematological cancers were enrolled; 21 patients underwent DST and 20 also completed genomic profiling. Median turnaround times for DST and genomics were within 10 days and 27 days, respectively. Treatment recommendations were made for 19 patients (76%), of whom 14 received therapeutic interventions. Six patients received subsequent FPM-guided treatments. Among these patients, five (83%) experienced a greater than 1.3-fold improvement in progression-free survival associated with their FPM-guided therapy relative to their previous therapy, and demonstrated a significant increase in progression-free survival and objective response rate compared to those of eight non-guided patients. The findings from our proof-of-principle study illustrate the potential for FPM to positively impact clinical care for pediatric and adolescent patients with relapsed or refractory cancers and warrant further validation in large prospective studies. ClinicalTrials.gov registration: NCT03860376 .
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Affiliation(s)
- Arlet M Acanda De La Rocha
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | | | - Maggie Fader
- Division of Pediatric Hematology Oncology, Department of Pediatrics, Nicklaus Children's Hospital, Miami, FL, USA
| | - Ebony R Coats
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Cima Saghira
- Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Paula S Espinal
- Center for Precision Medicine, Nicklaus Children's Hospital, Miami, FL, USA
| | - Jeanette Galano
- Center for Precision Medicine, Nicklaus Children's Hospital, Miami, FL, USA
| | - Ziad Khatib
- Division of Pediatric Hematology Oncology, Department of Pediatrics, Nicklaus Children's Hospital, Miami, FL, USA
| | - Haneen Abdella
- Division of Pediatric Hematology Oncology, Department of Pediatrics, Nicklaus Children's Hospital, Miami, FL, USA
| | - Ossama M Maher
- Division of Pediatric Hematology Oncology, Department of Pediatrics, Nicklaus Children's Hospital, Miami, FL, USA
| | - Yana Vorontsova
- Center for Precision Medicine, Nicklaus Children's Hospital, Miami, FL, USA
| | - Cristina M Andrade-Feraud
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Aimee Daccache
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Alexa Jacome
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Victoria Reis
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Baylee Holcomb
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Yasmin Ghurani
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Lilliam Rimblas
- Division of Pediatric Hematology Oncology, Department of Pediatrics, Nicklaus Children's Hospital, Miami, FL, USA
| | - Tomás R Guilarte
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Nan Hu
- Department of Biostatistics, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Daria Salyakina
- Center for Precision Medicine, Nicklaus Children's Hospital, Miami, FL, USA
| | - Diana J Azzam
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA.
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29
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Liu XD, Zhang Y, He HY. Targeted next-generation sequencing of 491 lung cancers in clinical practice: Implications for future detection strategy and targeted therapy. Heliyon 2024; 10:e27591. [PMID: 38496837 PMCID: PMC10944278 DOI: 10.1016/j.heliyon.2024.e27591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/03/2024] [Accepted: 03/04/2024] [Indexed: 03/19/2024] Open
Abstract
Although lung cancer remains the most common cause of global cancer-related mortality, the identification of oncogenic driver alterations and the development of targeted drugs has dramatically altered the therapeutic landscape. In this retrospective study, we found that 97.7% samples carried at least one mutation in the 25 genes tested in our cohort. 53.6% samples were positive for EGFR mutations, followed by TP53 (41.1%), KRAS (11.8%), ERBB2 (4.3%). EGFR mutations were mainly found in female adenocarcinomas, while TP53 was mainly found in male non-adenocarcinomas. Significant differences can be found in the mutation rate of EGFR (60.9% vs 11.9%), KRAS (12.2% vs 25.0%), STK11 (1.5% vs 11.9%), FGFR3 (2.4% vs 0.0%) and ERBB4 (1.2% vs 6.1%) between adenocarcinoma in our cohort and TCGA-LUAD data (all p < 0.001). What's more, we found that the mutation of EGFR increased significantly from adenocarcinomas in situ (AIS, 21.4%) to microinvasive adenocarcinomas (MIA, 52.4%) and invasive adenocarcinomas (IA, 61.1%), while the mutation of ERBB2 dropped markedly from AIS (21.4%) to MIA (9.5%) and IA (4.1%). At last, comparations between targeted NGS and ARMS-based single gene test in the detection of EGFR showed a 94.6% consistence. In conclusion, targeted NGS can provide a comprehensive mutational profile of lung cancer. Considering the high mutation rate of EGFR in NSCLC of Asian populations, a specialized detection strategy should be conducted.
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Affiliation(s)
- Xiao-dan Liu
- Department of Pathology, School of Basic Medical Sciences, Peking University Third Hospital, Peking University Health Science Center, Beijing, 100191, China
| | - Yan Zhang
- Department of Pathology, School of Basic Medical Sciences, Peking University Third Hospital, Peking University Health Science Center, Beijing, 100191, China
| | - Hui-ying He
- Department of Pathology, School of Basic Medical Sciences, Peking University Third Hospital, Peking University Health Science Center, Beijing, 100191, China
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30
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Yuan X, Wang H, Sun Z, Zhou C, Chu SC, Bu J, Shen N. Anchored-fusion enables targeted fusion search in bulk and single-cell RNA sequencing data. CELL REPORTS METHODS 2024; 4:100733. [PMID: 38503288 PMCID: PMC10985232 DOI: 10.1016/j.crmeth.2024.100733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/15/2024] [Accepted: 02/23/2024] [Indexed: 03/21/2024]
Abstract
Here, we present Anchored-fusion, a highly sensitive fusion gene detection tool. It anchors a gene of interest, which often involves driver fusion events, and recovers non-unique matches of short-read sequences that are typically filtered out by conventional algorithms. In addition, Anchored-fusion contains a module based on a deep learning hierarchical structure that incorporates self-distillation learning (hierarchical view learning and distillation [HVLD]), which effectively filters out false positive chimeric fragments generated during sequencing while maintaining true fusion genes. Anchored-fusion enables highly sensitive detection of fusion genes, thus allowing for application in cases with low sequencing depths. We benchmark Anchored-fusion under various conditions and found it outperformed other tools in detecting fusion events in simulated data, bulk RNA sequencing (bRNA-seq) data, and single-cell RNA sequencing (scRNA-seq) data. Our results demonstrate that Anchored-fusion can be a useful tool for fusion detection tasks in clinically relevant RNA-seq data and can be applied to investigate intratumor heterogeneity in scRNA-seq data.
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Affiliation(s)
- Xilu Yuan
- Zhejiang Provincial Key Laboratory of Service Robot, College of Computer Science, Zhejiang University, Hangzhou, China
| | - Haishuai Wang
- Zhejiang Provincial Key Laboratory of Service Robot, College of Computer Science, Zhejiang University, Hangzhou, China; Shanghai Artificial Intelligence Laboratory, Shanghai, China.
| | - Zhongquan Sun
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chunpeng Zhou
- Zhejiang Provincial Key Laboratory of Service Robot, College of Computer Science, Zhejiang University, Hangzhou, China
| | - Simon Chong Chu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jiajun Bu
- Zhejiang Provincial Key Laboratory of Service Robot, College of Computer Science, Zhejiang University, Hangzhou, China
| | - Ning Shen
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
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31
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Zakimi N, Nguyen MP, Raleigh DR. Gene transcript fusions are associated with clinical outcomes and molecular groups of meningiomas. Acta Neuropathol 2024; 147:57. [PMID: 38509407 PMCID: PMC10954959 DOI: 10.1007/s00401-024-02708-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Affiliation(s)
- Naomi Zakimi
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Minh P Nguyen
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - David R Raleigh
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
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32
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Fiflis DN, Rey NA, Venugopal-Lavanya H, Sewell B, Mitchell-Dick A, Clements KN, Milo S, Benkert AR, Rosales A, Fergione S, Asokan A. Repurposing CRISPR-Cas13 systems for robust mRNA trans-splicing. Nat Commun 2024; 15:2325. [PMID: 38485709 PMCID: PMC10940283 DOI: 10.1038/s41467-024-46172-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/16/2024] [Indexed: 03/18/2024] Open
Abstract
Type VI CRISPR enzymes have been developed as programmable RNA-guided Cas proteins for eukaryotic RNA editing. Notably, Cas13 has been utilized for site-targeted single base edits, demethylation, RNA cleavage or knockdown and alternative splicing. However, the ability to edit large stretches of mRNA transcripts remains a significant challenge. Here, we demonstrate that CRISPR-Cas13 systems can be repurposed to assist trans-splicing of exogenous RNA fragments into an endogenous pre-mRNA transcript, a method termed CRISPR Assisted mRNA Fragment Trans-splicing (CRAFT). Using split reporter-based assays, we evaluate orthogonal Cas13 systems, optimize guide RNA length and screen for optimal trans-splicing site(s) across a range of intronic targets. We achieve markedly improved editing of large 5' and 3' segments in different endogenous mRNAs across various mammalian cell types compared to other spliceosome-mediated trans-splicing methods. CRAFT can serve as a versatile platform for attachment of protein tags, studying the impact of multiple mutations/single nucleotide polymorphisms, modification of untranslated regions (UTRs) or replacing large segments of mRNA transcripts.
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Affiliation(s)
- David N Fiflis
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Nicolas A Rey
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | | | - Beatrice Sewell
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | | | - Katie N Clements
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Sydney Milo
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Abigail R Benkert
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Alan Rosales
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Sophia Fergione
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Aravind Asokan
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA.
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC, USA.
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33
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Budurlean L, Tukaramrao DB, Zhang L, Dovat S, Broach J. Integrating Optical Genome Mapping and Whole Genome Sequencing in Somatic Structural Variant Detection. J Pers Med 2024; 14:291. [PMID: 38541033 PMCID: PMC10971281 DOI: 10.3390/jpm14030291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/01/2024] [Accepted: 03/07/2024] [Indexed: 04/10/2024] Open
Abstract
Structural variants drive tumorigenesis by disrupting normal gene function through insertions, inversions, translocations, and copy number changes, including deletions and duplications. Detecting structural variants is crucial for revealing their roles in tumor development, clinical outcomes, and personalized therapy. Presently, most studies rely on short-read data from next-generation sequencing that aligns back to a reference genome to determine if and, if so, where a structural variant occurs. However, structural variant discovery by short-read sequencing is challenging, primarily because of the difficulty in mapping regions of repetitive sequences. Optical genome mapping (OGM) is a recent technology used for imaging and assembling long DNA strands to detect structural variations. To capture the structural variant landscape more thoroughly in the human genome, we developed an integrated pipeline that combines Bionano OGM and Illumina whole-genome sequencing and applied it to samples from 29 pediatric B-ALL patients. The addition of OGM allowed us to identify 511 deletions, 506 insertions, 93 duplications/gains, and 145 translocations that were otherwise missed in the short-read data. Moreover, we identified several novel gene fusions, the expression of which was confirmed by RNA sequencing. Our results highlight the benefit of integrating OGM and short-read detection methods to obtain a comprehensive analysis of genetic variation that can aid in clinical diagnosis, provide new therapeutic targets, and improve personalized medicine in cancers driven by structural variation.
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Affiliation(s)
- Laura Budurlean
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
| | | | - Lijun Zhang
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sinisa Dovat
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
- Department of Pediatrics, Penn State Cancer Institute, Hershey, PA 17033, USA
| | - James Broach
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
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34
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Chen L, Zhang C, Xue R, Liu M, Bai J, Bao J, Wang Y, Jiang N, Li Z, Wang W, Wang R, Zheng B, Yang A, Hu J, Liu K, Shen S, Zhang Y, Bai M, Wang Y, Zhu Y, Yang S, Gao Q, Gu J, Gao D, Wang XW, Nakagawa H, Zhang N, Wu L, Rozen SG, Bai F, Wang H. Deep whole-genome analysis of 494 hepatocellular carcinomas. Nature 2024; 627:586-593. [PMID: 38355797 DOI: 10.1038/s41586-024-07054-3] [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: 06/13/2022] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
Over half of hepatocellular carcinoma (HCC) cases diagnosed worldwide are in China1-3. However, whole-genome analysis of hepatitis B virus (HBV)-associated HCC in Chinese individuals is limited4-8, with current analyses of HCC mainly from non-HBV-enriched populations9,10. Here we initiated the Chinese Liver Cancer Atlas (CLCA) project and performed deep whole-genome sequencing (average depth, 120×) of 494 HCC tumours. We identified 6 coding and 28 non-coding previously undescribed driver candidates. Five previously undescribed mutational signatures were found, including aristolochic-acid-associated indel and doublet base signatures, and a single-base-substitution signature that we termed SBS_H8. Pentanucleotide context analysis and experimental validation confirmed that SBS_H8 was distinct to the aristolochic-acid-associated SBS22. Notably, HBV integrations could take the form of extrachromosomal circular DNA, resulting in elevated copy numbers and gene expression. Our high-depth data also enabled us to characterize subclonal clustered alterations, including chromothripsis, chromoplexy and kataegis, suggesting that these catastrophic events could also occur in late stages of hepatocarcinogenesis. Pathway analysis of all classes of alterations further linked non-coding mutations to dysregulation of liver metabolism. Finally, we performed in vitro and in vivo assays to show that fibrinogen alpha chain (FGA), determined as both a candidate coding and non-coding driver, regulates HCC progression and metastasis. Our CLCA study depicts a detailed genomic landscape and evolutionary history of HCC in Chinese individuals, providing important clinical implications.
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Affiliation(s)
- Lei Chen
- National Center for Liver Cancer/Eastern Hepatobiliary Surgery Hospital, Shanghai, China.
| | - Chong Zhang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking University, Beijing, China
| | - Ruidong Xue
- Peking University-Yunnan Baiyao International Medical Research Center, International Cancer Institute, Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Translational Cancer Research Center, Peking University First Hospital, Beijing, China
| | - Mo Liu
- Centre for Computational Biology and Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Jian Bai
- Berry Oncology Corporation, Beijing, China
| | - Jinxia Bao
- Model Animal Research Center, Medical School, Nanjing University, Nanjing, China
| | - Yin Wang
- Berry Oncology Corporation, Beijing, China
| | - Nanhai Jiang
- Centre for Computational Biology and Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Zhixuan Li
- National Center for Liver Cancer/Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Wenwen Wang
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Ruiru Wang
- Berry Oncology Corporation, Beijing, China
| | - Bo Zheng
- National Center for Liver Cancer/Eastern Hepatobiliary Surgery Hospital, Shanghai, China
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | | | - Ji Hu
- National Center for Liver Cancer/Eastern Hepatobiliary Surgery Hospital, Shanghai, China
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Ke Liu
- Berry Oncology Corporation, Beijing, China
| | - Siyun Shen
- National Center for Liver Cancer/Eastern Hepatobiliary Surgery Hospital, Shanghai, China
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Yangqianwen Zhang
- National Center for Liver Cancer/Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Mixue Bai
- National Center for Liver Cancer/Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Yan Wang
- Berry Oncology Corporation, Beijing, China
| | - Yanjing Zhu
- National Center for Liver Cancer/Eastern Hepatobiliary Surgery Hospital, Shanghai, China
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Shuai Yang
- National Center for Liver Cancer/Eastern Hepatobiliary Surgery Hospital, Shanghai, China
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jin Gu
- MOE Key Laboratory for Bioinformatics, Department of Automation, Tsinghua University, Beijing, China
| | - Dong Gao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, CAS, Shanghai, China
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ning Zhang
- Peking University-Yunnan Baiyao International Medical Research Center, International Cancer Institute, Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Translational Cancer Research Center, Peking University First Hospital, Beijing, China
| | - Lin Wu
- Berry Oncology Corporation, Beijing, China.
| | - Steven G Rozen
- Centre for Computational Biology and Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore.
| | - Fan Bai
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking University, Beijing, China.
| | - Hongyang Wang
- National Center for Liver Cancer/Eastern Hepatobiliary Surgery Hospital, Shanghai, China.
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35
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Martin SB, Polubothu S, Bruzos AL, Kelly G, Horswell S, Sauvadet A, Bryant D, Zecchin D, Riachi M, Michailidis F, Sadri A, Muwanga-Nanyonjo N, Lopez-Balboa P, Knöpfel N, Bulstrode N, Pittman A, Yeh I, Kinsler VA. Mosaic BRAF Fusions Are a Recurrent Cause of Congenital Melanocytic Nevi Targetable by MAPK Pathway Inhibition. J Invest Dermatol 2024; 144:593-600.e7. [PMID: 37716647 DOI: 10.1016/j.jid.2023.06.213] [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: 02/01/2023] [Revised: 05/16/2023] [Accepted: 06/06/2023] [Indexed: 09/18/2023]
Abstract
Among children with multiple congenital melanocytic nevi, 25% have no established genetic cause, of whom many develop a hyperproliferative and severely pruritic phenotype resistant to treatment. Gene fusions have been reported in individual cases of congenital melanocytic nevi. We studied 169 patients with congenital melanocytic nevi in this study, 38 of whom were double wild type for pathogenic NRAS/BRAF variants. Nineteen of these 38 patients had sufficient tissue to undergo RNA sequencing, which revealed mosaic BRAF fusions in 11 of 19 patients and mosaic RAF1 fusions in 1 of 19. Recurrently, fusions involved the loss of the 5´ regulatory domain of BRAF or RAF1 but preserved the kinase domain. We validated all cases and detected the fusions in two separate nevi in 5 of 12 patients, confirming clonality. The absence of the fusion in blood in 8 of 12 patients indicated mosaicism. Primary culture of BRAF-fusion nevus cells from 3 of 12 patients demonstrated highly increased MAPK activation, despite only mildly increased BRAF expression, suggesting additional mechanisms of kinase activation. Trametinib quenched MAPK hyperactivation in vitro, and treatment of two patients caused rapid improvement in bulk tissue, improving bodily movement and reducing inflammation and severe pruritus. These findings offer a genetic diagnosis to an additional group of patients and trametinib as a treatment option for the severe associated phenotypes.
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Affiliation(s)
- Sara Barberan Martin
- Mosaicism and Precision Medicine laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Osmond Street Institute of Child Health, London, United Kingdom
| | - Satyamaanasa Polubothu
- Genetics and Genomic Medicine, UCL Great Osmond Street Institute of Child Health, London, United Kingdom; Paediatric Dermatology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Alicia Lopez Bruzos
- Mosaicism and Precision Medicine laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Osmond Street Institute of Child Health, London, United Kingdom
| | - Gavin Kelly
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, United Kingdom
| | - Stuart Horswell
- Open Targets, Welcome Sanger Institute, Cambridge, United Kingdom
| | - Aimie Sauvadet
- Mosaicism and Precision Medicine laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Osmond Street Institute of Child Health, London, United Kingdom
| | - Dale Bryant
- Mosaicism and Precision Medicine laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Osmond Street Institute of Child Health, London, United Kingdom
| | - Davide Zecchin
- Mosaicism and Precision Medicine laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Osmond Street Institute of Child Health, London, United Kingdom
| | - Melissa Riachi
- Mosaicism and Precision Medicine laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Osmond Street Institute of Child Health, London, United Kingdom
| | - Fanourios Michailidis
- Mosaicism and Precision Medicine laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Osmond Street Institute of Child Health, London, United Kingdom
| | - Amir Sadri
- Plastic and Reconstructive Surgery, Great Ormond Street Hospital for Children and UCL Great Osmond Street Institute of Child Health, London, United Kingdom
| | - Noreen Muwanga-Nanyonjo
- Mosaicism and Precision Medicine laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Osmond Street Institute of Child Health, London, United Kingdom
| | - Pablo Lopez-Balboa
- Paediatric Dermatology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Nicole Knöpfel
- Mosaicism and Precision Medicine laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Osmond Street Institute of Child Health, London, United Kingdom; Paediatric Dermatology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Neil Bulstrode
- Paediatric Dermatology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Alan Pittman
- Genetics Research Centre (A.P.), St George's University of London, London, United Kingdom
| | - Iwei Yeh
- Dermatology and Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Veronica A Kinsler
- Mosaicism and Precision Medicine laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Osmond Street Institute of Child Health, London, United Kingdom; Paediatric Dermatology, Great Ormond Street Hospital for Children, London, United Kingdom.
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36
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Xu SM, Cheng Y, Fisher H, Janitz M. Recent advances in the investigation of fusion RNAs and their role in molecular pathology of cancer. Int J Biochem Cell Biol 2024; 168:106529. [PMID: 38246262 DOI: 10.1016/j.biocel.2024.106529] [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: 09/23/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 01/23/2024]
Abstract
Gene fusions have had a significant role in the development of various types of cancer, oftentimes involved in oncogenic activities through dysregulation of gene expression or signalling pathways. Some cancer-associated chromosomal translocations can undergo backsplicing, resulting in fusion-circular RNAs, a more stable isoform immune to RNase degradation. This stability makes fusion circular RNAs a promising diagnostic biomarker for cancer. While the detection of linear fusion RNAs and their function in certain cancers have been described in literature, fusion circular RNAs lag behind due to their low abundance in cancer cells. This review highlights current literature on the role of linear and circular fusion transcripts in cancer, tools currently available for detecting of these chimeric RNAs and their function and how they play a role in tumorigenesis.
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Affiliation(s)
- Si-Mei Xu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Yuning Cheng
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Harry Fisher
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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Yeung MC, Dermawan JK, Liu AP, Lam AY, Antonescu CR, Shek TW. Spindle cell neoplasms with novel LTK fusion - Expanding the spectrum of kinase fusion-positive soft tissue tumors. Genes Chromosomes Cancer 2024; 63:e23227. [PMID: 38517106 PMCID: PMC10963038 DOI: 10.1002/gcc.23227] [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: 11/13/2023] [Revised: 01/09/2024] [Accepted: 01/24/2024] [Indexed: 03/23/2024] Open
Abstract
AIMS Kinase fusion-positive soft tissue tumors represent an emerging, molecularly defined group of mesenchymal tumors with a wide morphologic spectrum and diverse activating kinases. Here, we present two cases of soft tissue tumors with novel LTK fusions. METHODS AND RESULTS Both cases presented as acral skin nodules (big toe and middle finger) in pediatric patients (17-year-old girl and 2-year-old boy). The tumors measured 2 and 3 cm in greatest dimension. Histologically, both cases exhibited bland-looking spindle cells infiltrating adipose tissue and accompanied by collagenous stroma. One case additionally displayed perivascular hyalinization and band-like stromal collagen. Both cases exhibited focal S100 staining, and one case had patchy coexpression of CD34. Targeted RNA-seq revealed the presence of novel in-frame MYH9::LTK and MYH10::LTK fusions, resulting in upregulation of LTK expression. Of interest, DNA methylation-based unsupervised clustering analysis in one case showed that the tumor clustered with dermatofibrosarcoma protuberans (DFSP). One tumor was excised with amputation with no local recurrence or distant metastasis at 18-month follow-up. The other case was initially marginally excised with local recurrence after one year, followed by wide local excision, with no evidence of disease at 10 years of follow-up. CONCLUSIONS This is the first reported case series of soft tissue tumors harboring LTK fusion, expanding the molecular landscape of soft tissue tumors driven by activating kinase fusions. Furthermore, studies involving a larger number of cases and integrated genomic analyses will be warranted to fully elucidate the pathogenesis and classification of these tumors.
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Affiliation(s)
- Maximus C.F. Yeung
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Hong Kong
| | - Josephine K Dermawan
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Anthony P.Y. Liu
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children’s Hospital, Hong Kong
| | - Albert Y.L. Lam
- Division of General Orthopaedics and Oncology, Department of Orthopedics and Traumatology, School of Clinical Medicine, The University of Hong Kong, Hong Kong
| | - Cristina R Antonescu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tony W.H. Shek
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Hong Kong
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Qin Q, Popic V, Yu H, White E, Khorgade A, Shin A, Wienand K, Dondi A, Beerenwinkel N, Vazquez F, Al’Khafaji AM, Haas BJ. CTAT-LR-fusion: accurate fusion transcript identification from long and short read isoform sequencing at bulk or single cell resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.24.581862. [PMID: 38464114 PMCID: PMC10925146 DOI: 10.1101/2024.02.24.581862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Gene fusions are found as cancer drivers in diverse adult and pediatric cancers. Accurate detection of fusion transcripts is essential in cancer clinical diagnostics, prognostics, and for guiding therapeutic development. Most currently available methods for fusion transcript detection are compatible with Illumina RNA-seq involving highly accurate short read sequences. Recent advances in long read isoform sequencing enable the detection of fusion transcripts at unprecedented resolution in bulk and single cell samples. Here we developed a new computational tool CTAT-LR-fusion to detect fusion transcripts from long read RNA-seq with or without companion short reads, with applications to bulk or single cell transcriptomes. We demonstrate that CTAT-LR-fusion exceeds fusion detection accuracy of alternative methods as benchmarked with simulated and real long read RNA-seq. Using short and long read RNA-seq, we further apply CTAT-LR-fusion to bulk transcriptomes of nine tumor cell lines, and to tumor single cells derived from a melanoma sample and three metastatic high grade serous ovarian carcinoma samples. In both bulk and in single cell RNA-seq, long isoform reads yielded higher sensitivity for fusion detection than short reads with notable exceptions. By combining short and long reads in CTAT-LR-fusion, we are able to further maximize detection of fusion splicing isoforms and fusion-expressing tumor cells. CTAT-LR-fusion is available at https://github.com/TrinityCTAT/CTAT-LR-fusion/wiki.
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Affiliation(s)
- Qian Qin
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Victoria Popic
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Houlin Yu
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Emily White
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Akanksha Khorgade
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Asa Shin
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Kirsty Wienand
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Arthur Dondi
- ETH Zurich, Department of Biosystems Science and Engineering, Schanzenstrasse 44, 4056 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Schanzenstrasse 44, 4056 Basel, Switzerland
| | - Niko Beerenwinkel
- ETH Zurich, Department of Biosystems Science and Engineering, Schanzenstrasse 44, 4056 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Schanzenstrasse 44, 4056 Basel, Switzerland
| | - Francisca Vazquez
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Aziz M. Al’Khafaji
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Brian J. Haas
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
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Zhang W, Schmitz AA, Kallionpää RE, Perälä M, Pitkänen N, Tukiainen M, Alanne E, Jöhrens K, Schulze-Rath R, Farahmand B, Zong J. Neurotrophic-tyrosine receptor kinase gene fusion in papillary thyroid cancer: A clinicogenomic biobank and record linkage study from Finland. Oncotarget 2024; 15:106-116. [PMID: 38329731 PMCID: PMC10852057 DOI: 10.18632/oncotarget.28555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 12/28/2023] [Indexed: 02/09/2024] Open
Abstract
Selective tropomyosin receptor kinase (TRK) inhibitors are approved targeted therapies for patients with solid tumors harboring a neurotrophic tyrosine receptor kinase (NTRK) gene fusion. Country-specific estimates of NTRK gene fusion frequency, and knowledge on the characteristics of affected patients, are limited. We identified patients with histologically-confirmed papillary thyroid cancer (PTC) from Finland's Auria Biobank. TRK protein expression was determined by pan-TRK immunohistochemistry. Immuno-stained tumor samples were scored by a certified pathologist. Gene fusions and other co-occurring gene alterations were identified by next generation sequencing. Patient characteristics and vital status were determined from linked hospital electronic health records (EHRs). Patients were followed from 1 year before PTC diagnosis until death. 6/389 (1.5%) PTC patients had an NTRK gene fusion (all NTRK3); mean age 43.8 years (and none had comorbidities) at PTC diagnosis. Gene fusion partners were EML4 (n = 3), ETV6 (n = 2), and RBPMS (n = 1). Of 3/6 patients with complete EHRs, all received radioactive iodine ablation only and were alive at end of follow-up (median observation, 9.12 years). In conclusion, NTRK gene fusion is infrequent in patients with PTC. Linkage of biobank samples to EHRs is feasible in describing the characteristics and outcomes of patients with PTC and potentially other cancer types.
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Affiliation(s)
- Wei Zhang
- Bayer HealthCare Pharmaceuticals Inc, Whippany, NJ 07981, USA
| | | | - Roosa E. Kallionpää
- Auria Biobank, Turku University Hospital, University of Turku, Turku, Finland
| | - Merja Perälä
- Auria Biobank, Turku University Hospital, University of Turku, Turku, Finland
| | - Niina Pitkänen
- Auria Biobank, Turku University Hospital, University of Turku, Turku, Finland
| | - Mikko Tukiainen
- Auria Biobank, Turku University Hospital, University of Turku, Turku, Finland
| | - Erika Alanne
- Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
- Western Finland Cancer Centre, Turku, Finland
| | - Korinna Jöhrens
- Dresden University Hospital, Technical University Dresden, Dresden, Germany
| | | | | | - Jihong Zong
- Bayer HealthCare Pharmaceuticals Inc, Whippany, NJ 07981, USA
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40
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Saba KH, Difilippo V, Kovac M, Cornmark L, Magnusson L, Nilsson J, van den Bos H, Spierings DC, Bidgoli M, Jonson T, Sumathi VP, Brosjö O, Staaf J, Foijer F, Styring E, Nathrath M, Baumhoer D, Nord KH. Disruption of the TP53 locus in osteosarcoma leads to TP53 promoter gene fusions and restoration of parts of the TP53 signalling pathway. J Pathol 2024; 262:147-160. [PMID: 38010733 DOI: 10.1002/path.6219] [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: 04/24/2023] [Revised: 08/24/2023] [Accepted: 09/19/2023] [Indexed: 11/29/2023]
Abstract
TP53 is the most frequently mutated gene in human cancer. This gene shows not only loss-of-function mutations but also recurrent missense mutations with gain-of-function activity. We have studied the primary bone malignancy osteosarcoma, which harbours one of the most rearranged genomes of all cancers. This is odd since it primarily affects children and adolescents who have not lived the long life thought necessary to accumulate massive numbers of mutations. In osteosarcoma, TP53 is often disrupted by structural variants. Here, we show through combined whole-genome and transcriptome analyses of 148 osteosarcomas that TP53 structural variants commonly result in loss of coding parts of the gene while simultaneously preserving and relocating the promoter region. The transferred TP53 promoter region is fused to genes previously implicated in cancer development. Paradoxically, these erroneously upregulated genes are significantly associated with the TP53 signalling pathway itself. This suggests that while the classical tumour suppressor activities of TP53 are lost, certain parts of the TP53 signalling pathway that are necessary for cancer cell survival and proliferation are retained. In line with this, our data suggest that transposition of the TP53 promoter is an early event that allows for a new normal state of genome-wide rearrangements in osteosarcoma. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Karim H Saba
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Valeria Difilippo
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Michal Kovac
- Bone Tumour Reference Centre at the Institute of Pathology, University Hospital and University of Basel, Basel, Switzerland
- Faculty of Informatics and Information Technologies, Slovak University of Technology, Bratislava, Slovakia
| | - Louise Cornmark
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Linda Magnusson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Jenny Nilsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Hilda van den Bos
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Diana Cj Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Mahtab Bidgoli
- Department of Clinical Genetics and Pathology, Laboratory Medicine, Medical Services, Skåne University Hospital, Lund, Sweden
| | - Tord Jonson
- Department of Clinical Genetics and Pathology, Laboratory Medicine, Medical Services, Skåne University Hospital, Lund, Sweden
| | - Vaiyapuri P Sumathi
- Department of Musculoskeletal Pathology, Royal Orthopaedic Hospital, Birmingham, UK
| | - Otte Brosjö
- Department of Orthopedics, Karolinska University Hospital, Stockholm, Sweden
| | - Johan Staaf
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Emelie Styring
- Department of Orthopedics, Lund University, Skåne University Hospital, Lund, Sweden
| | - Michaela Nathrath
- Children's Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Department of Pediatric Oncology, Klinikum Kassel, Kassel, Germany
| | - Daniel Baumhoer
- Bone Tumour Reference Centre at the Institute of Pathology, University Hospital and University of Basel, Basel, Switzerland
| | - Karolin H Nord
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
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41
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Bagger FO, Borgwardt L, Jespersen AS, Hansen AR, Bertelsen B, Kodama M, Nielsen FC. Whole genome sequencing in clinical practice. BMC Med Genomics 2024; 17:39. [PMID: 38287327 PMCID: PMC10823711 DOI: 10.1186/s12920-024-01795-w] [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: 08/14/2023] [Accepted: 01/01/2024] [Indexed: 01/31/2024] Open
Abstract
Whole genome sequencing (WGS) is becoming the preferred method for molecular genetic diagnosis of rare and unknown diseases and for identification of actionable cancer drivers. Compared to other molecular genetic methods, WGS captures most genomic variation and eliminates the need for sequential genetic testing. Whereas, the laboratory requirements are similar to conventional molecular genetics, the amount of data is large and WGS requires a comprehensive computational and storage infrastructure in order to facilitate data processing within a clinically relevant timeframe. The output of a single WGS analyses is roughly 5 MIO variants and data interpretation involves specialized staff collaborating with the clinical specialists in order to provide standard of care reports. Although the field is continuously refining the standards for variant classification, there are still unresolved issues associated with the clinical application. The review provides an overview of WGS in clinical practice - describing the technology and current applications as well as challenges connected with data processing, interpretation and clinical reporting.
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Affiliation(s)
- Frederik Otzen Bagger
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Line Borgwardt
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Sand Jespersen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Anna Reimer Hansen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Birgitte Bertelsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Miyako Kodama
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Finn Cilius Nielsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.
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42
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Güllülü Ö, Mayer BE, Toplek FB. Linking Gene Fusions to Bone Marrow Failure and Malignant Transformation in Dyskeratosis Congenita. Int J Mol Sci 2024; 25:1606. [PMID: 38338888 PMCID: PMC10855549 DOI: 10.3390/ijms25031606] [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: 12/14/2023] [Revised: 01/26/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
Dyskeratosis Congenita (DC) is a multisystem disorder intrinsically associated with telomere dysfunction, leading to bone marrow failure (BMF). Although the pathology of DC is largely driven by mutations in telomere-associated genes, the implications of gene fusions, which emerge due to telomere-induced genomic instability, remain unexplored. We meticulously analyzed gene fusions in RNA-Seq data from DC patients to provide deeper insights into DC's progression. The most significant DC-specific gene fusions were subsequently put through in silico assessments to ascertain biophysical and structural attributes, including charge patterning, inherent disorder, and propensity for self-association. Selected candidates were then analyzed using deep learning-powered structural predictions and molecular dynamics simulations to gauge their potential for forming higher-order oligomers. Our exploration revealed that genes participating in fusion events play crucial roles in upholding genomic stability, facilitating hematopoiesis, and suppressing tumors. Notably, our analysis spotlighted a particularly disordered polyampholyte fusion protein that exhibits robust higher-order oligomerization dynamics. To conclude, this research underscores the potential significance of several high-confidence gene fusions in the progression of BMF in DC, particularly through the dysregulation of genomic stability, hematopoiesis, and tumor suppression. Additionally, we propose that these fusion proteins might hold a detrimental role, specifically in inducing proteotoxicity-driven hematopoietic disruptions.
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Affiliation(s)
- Ömer Güllülü
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Benjamin E. Mayer
- Computational Biology & Simulation, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Fran Bačić Toplek
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
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43
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Balle CM, Kassentoft CG, van Heusden JI, Knudsen M, Raaby L, Gravholt CH. Rare Case of a Turner Syndrome Patient with Metastatic Dysgerminoma and No Y-Chromosomal Material with Pathogenic Variants Found in KIT and MTOR. Sex Dev 2024; 17:203-210. [PMID: 38281483 DOI: 10.1159/000536236] [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: 05/10/2023] [Accepted: 01/10/2024] [Indexed: 01/30/2024] Open
Abstract
INTRODUCTION The presence of Y-chromosomal material in females with Turner syndrome (TS) is a well-established risk factor for developing gonadoblastoma and malignant transformations thereof. However, these events are rarely seen in TS patients with no Y-chromosomal material. Thus, it is the current understanding that parts of the Y-chromosome are essential for the malignant transformation of gonadoblastoma in the dysgenetic gonad. METHODS We report a case of a TS female with an apparent 46,X,idic(Xq) karyotype, who was diagnosed with a metastatic dysgerminoma. Whole exome sequencing of the tumor and blood, along with RNA sequencing of the tumor, was performed to comprehensively search for cryptic Y-chromosomal material and pathogenic variants. RESULTS No Y-chromosomal material was detected in either tumor or blood. Whole exome-sequencing of DNA and RNA revealed a pathogenic somatic gain-of-function mutation in KIT and a pathogenic missense mutation in MTOR. The patient underwent total hysterectomy with bilateral salpingo-oophorectomy, followed by adjuvant chemotherapy. Unfortunately, she died due to chemotherapy-induced pneumonitis 7 months after the initial diagnosis. CONCLUSION Females with TS can develop metastatic dysgerminoma even in the absence of Y-chromosomal material. This questions the current understanding of Y-chromosomal material being essential for the malignant transformation of a gonadoblastoma in the dysgenetic gonad.
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Affiliation(s)
- Camilla Mains Balle
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Michael Knudsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Line Raaby
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Claus Højbjerg Gravholt
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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44
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Kumar H, Luo R, Wen J, Yang C, Zhou X, Kim P. FusionNeoAntigen: a resource of fusion gene-specific neoantigens. Nucleic Acids Res 2024; 52:D1276-D1288. [PMID: 37870454 PMCID: PMC10767944 DOI: 10.1093/nar/gkad922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/02/2023] [Accepted: 10/09/2023] [Indexed: 10/24/2023] Open
Abstract
Among the diverse sources of neoantigens (i.e. single-nucleotide variants (SNVs), insertions or deletions (Indels) and fusion genes), fusion gene-derived neoantigens are generally more immunogenic, have multiple targets per mutation and are more widely distributed across various cancer types. Therefore, fusion gene-derived neoantigens are a potential source of highly immunogenic neoantigens and hold great promise for cancer immunotherapy. However, the lack of fusion protein sequence resources and knowledge prevents this application. We introduce 'FusionNeoAntigen', a dedicated resource for fusion-specific neoantigens, accessible at https://compbio.uth.edu/FusionNeoAntigen. In this resource, we provide fusion gene breakpoint crossing neoantigens focused on ∼43K fusion proteins of ∼16K in-frame fusion genes from FusionGDB2.0. FusionNeoAntigen provides fusion gene information, corresponding fusion protein sequences, fusion breakpoint peptide sequences, fusion gene-derived neoantigen prediction, virtual screening between fusion breakpoint peptides having potential fusion neoantigens and human leucocyte antigens (HLAs), fusion breakpoint RNA/protein sequences for developing vaccines, information on samples with fusion-specific neoantigen, potential CAR-T targetable cell-surface fusion proteins and literature curation. FusionNeoAntigen will help to develop fusion gene-based immunotherapies. We will report all potential fusion-specific neoantigens from all possible open reading frames of ∼120K human fusion genes in future versions.
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Affiliation(s)
- Himansu Kumar
- Department of Bioinformatics and Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ruihan Luo
- Department of Bioinformatics and Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jianguo Wen
- Department of Bioinformatics and Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Chengyuan Yang
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Department of Bioinformatics and Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Pora Kim
- Department of Bioinformatics and Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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45
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Itoh T, Omori Y, Seino M, Hirose K, Date F, Ono Y, Mizukami Y, Aoki S, Ishida M, Mizuma M, Morikawa T, Higuchi R, Honda G, Okamura Y, Kinoshita K, Unno M, Furukawa T. Gene Rearrangement and Expression of PRKACA and PRKACB Govern Morphobiology of Pancreatobiliary Oncocytic Neoplasms. Mod Pathol 2024; 37:100358. [PMID: 37871652 DOI: 10.1016/j.modpat.2023.100358] [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: 04/27/2023] [Revised: 09/29/2023] [Accepted: 10/15/2023] [Indexed: 10/25/2023]
Abstract
Intraductal oncocytic papillary neoplasms (IOPNs) are distinct from intraductal papillary mucinous neoplasms based on characteristic morphologic and genetic features represented by fusion genes involving PRKACA or PRKACB (PRKACA/B). However, pancreatic and biliary tumors with partial oncocytic features are often encountered clinically, and their molecular features are yet to be clarified. This study included 80 intraductal papillary neoplasms: 32 tumors with mature IOPN morphology (typical), 28 with partial or subclonal oncocytic features (atypical), and 20 without oncocytic features (control). We analyzed PRKACA/B fusion genes, including ATP1B1::PRKACA, DNAJB1::PRKACA, and ATP1B1::PRKACB, by reverse-transcription PCR; mRNA expression of fusion genes and nonrearranged PRKACA/B genes by quantitative reverse-transcription PCR; mutations in KRAS, BRAF, and GNAS by targeted sequencing or droplet digital PCR; and the expression of cyclic adenosine monophosphate (cAMP)-dependent protein kinase catalytic subunits α (PRKACA) and β (PRKACB), phosphorylated cAMP response element-binding protein, and aberrations of p16, p53, SMAD4, STK11, and β-catenin by immunohistochemistry. PRKACA/B fusion genes were detected in 100% (32/32) of typical, 46% (13/28) of atypical, and 0% (0/20) of control (P < .05). Expression of PRKACA, PRKACB, and phosphorylated cAMP response element-binding protein was upregulated in neoplasms with PRKACA/B fusion genes (P < .05). mRNA expression of the PRKACA/B fusion genes and protein expression of PRKACA or PRKACB tended to be higher in typical than in atypical cases (mRNA, P = .002; protein expression, P = .054). In some atypical neoplasms with mixed subtypes, PRKACA/B fusion genes were superimposed exclusively on oncocytic components. Typical IOPNs harbored fewer KRAS and GNAS mutations than control samples and fewer alterations in p53 and STK11 than atypical samples (P < .05). In conclusion, PRKACA/B fusion genes not only are the characteristic drivers of IOPNs but also play a crucial role in the development of subclonal oncocytic neoplasms. Moreover, oncocytic morphology is strongly associated with upregulation of PRKACA/B, which may provide clues for potential therapeutic options.
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Affiliation(s)
- Taito Itoh
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yuko Omori
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan; Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
| | - Mitsuru Seino
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Katsuya Hirose
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Fumiko Date
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan; Division of Gastroenterology, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Yusuke Mizukami
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan; Division of Gastroenterology, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Shuichi Aoki
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masaharu Ishida
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masamichi Mizuma
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takanori Morikawa
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ryota Higuchi
- Department of Surgery, Institute of Gastroenterology, Tokyo Women's Medical University, Tokyo, Japan
| | - Goro Honda
- Department of Surgery, Institute of Gastroenterology, Tokyo Women's Medical University, Tokyo, Japan
| | - Yasunobu Okamura
- Tohoku University Advanced Research Center for Innovations in Next-Generation Medicine, Sendai, Japan; Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku University Advanced Research Center for Innovations in Next-Generation Medicine, Sendai, Japan; Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan; Tohoku University Graduate School of Information Sciences, Sendai, Japan
| | - Michiaki Unno
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Toru Furukawa
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan.
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Koduru P, Chen W, Fuda F, Kaur G, Awan F, John S, Garcia R, Gagan J. RNASeq Analysis for Accurate Identification of Fusion Partners in Tumor Specific Translocations Detected by Standard FISH Probes in Hematologic Malignancies. CLINICAL PATHOLOGY (THOUSAND OAKS, VENTURA COUNTY, CALIF.) 2024; 17:2632010X241230262. [PMID: 38371338 PMCID: PMC10874141 DOI: 10.1177/2632010x241230262] [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: 04/18/2023] [Accepted: 01/17/2024] [Indexed: 02/20/2024]
Abstract
Background Fluorescence labeled DNA probes and in situ hybridization methods had shorter turn round time for results revolutionized their clinical application. Signals obtained from these probes are highly specific, yet they can produce fusion signals not necessarily representing fusion of actual genes due to other genes included in the probe design. In this study we evaluated discordance between cytogenetic, FISH and RNAseq results in 3 different patients with hematologic malignancies and illustrated the need to perform next generation sequencing (NGS) or RNASeq to accurately interpret FISH results. Methods Bone marrow or peripheral blood karyotypes and FISH were performed to detect recurring translocations associated with hematologic malignancies in clinical samples routinely referred to our clinical cytogenetics laboratory. When required, NGS was performed on DNA and RNA libraries to detect somatic alterations and gene fusions in some of these specimens. Discordance in results between these methods is further evaluated. Results For a patient with plasma cell leukemia standard FGFR3 / IGH dual fusion FISH assay detected fusion that was interpreted as FGFR3-positive leukemia, whereas NGS/RNASeq detected NSD2::IGH. For a pediatric acute lymphoblastic leukemia patient, a genetic diagnosis of PDGFRB-positive ALL was rendered because the PDGFRB break-apart probe detected clonal rearrangement, whereas NGS detected MEF2D::CSF1R. A MYC-positive B-prolymphocytic leukemia was rendered for another patient with a cytogenetically identified t(8;14) and MYC::IGH by FISH, whereas NGS detected a novel PVT1::RCOR1 not previously reported. Conclusions These are 3 cases in a series of several other concordant results, nevertheless, elucidate limitations when interpreting FISH results in clinical applications, particularly when other genes are included in probe design. In addition, when the observed FISH signals are atypical, this study illustrates the necessity to perform complementary laboratory assays, such as NGS and/or RNASeq, to accurately identify fusion genes in tumorigenic translocations.
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Affiliation(s)
- Prasad Koduru
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Weina Chen
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Franklin Fuda
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Gurbakhash Kaur
- Internal Medicine (Division of Oncology), UT Southwestern Medical Center, Dallas, TX, USA
| | - Farrukh Awan
- Internal Medicine (Division of Oncology), UT Southwestern Medical Center, Dallas, TX, USA
| | - Samuel John
- Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Rolando Garcia
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jeffrey Gagan
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
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Hamid F, Arora S, Chitkara P, Kumar S. A Protocol for the Detection of Fusion Transcripts Using RNA-Sequencing Data. Methods Mol Biol 2024; 2812:243-258. [PMID: 39068367 DOI: 10.1007/978-1-0716-3886-6_14] [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] [Indexed: 07/30/2024]
Abstract
Fusion transcripts are formed when two genes or their mRNAs fuse to produce a novel gene or chimeric transcript. Fusion genes are well-known cancer biomarkers used for cancer diagnosis and as therapeutic targets. Gene fusions are also found in normal physiology and lead to the evolution of novel genes that contribute to better survival and adaptation for an organism. Various in vitro approaches, such as FISH, PCR, RT-PCR, and chromosome banding techniques, have been used to detect gene fusion. However, all these approaches have low resolution and throughput. Due to the development of high-throughput next-generation sequencing technologies, the detection of fusion transcript becomes feasible using whole genome sequencing, RNA-Seq data, and bioinformatics tools. This chapter will overview the general computational protocol for fusion transcript detection from RNA-sequencing datasets.
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Affiliation(s)
- Fiza Hamid
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Simran Arora
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Pragya Chitkara
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Shailesh Kumar
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India.
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48
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Pei X, Yan X, Ding C. Proteogenomic Workflow for Characterization of Microphthalmia Transcription Factor (MiT) Family Translocation Renal Cell Carcinoma. Methods Mol Biol 2024; 2823:109-127. [PMID: 39052217 DOI: 10.1007/978-1-0716-3922-1_8] [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] [Indexed: 07/27/2024]
Abstract
Microphthalmia transcription factor (MiT) family translocation renal cell carcinoma (tRCC) is a rare, aggressive, and heterogeneous subtype of kidney cancer, which is not well characterized. Since genetic alterations are always associated with carcinogenesis, and proteins are the major executors of biological features, multi-omics studies can reveal the systematic tRCC biological process comprehensively. Here, we describe the proteogenomic workflow for characterization of tRCC in detail to provide the knowledge foundation for integrated proteogenomic analysis of tRCC and other malignant tumors in the future.
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Affiliation(s)
- Xiaoru Pei
- Center for Cell and Gene Therapy, Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute , Fudan University, Shanghai, China
| | - Xin Yan
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan center for outstanding overseas scientists of pulmonary fibrosis, College of Life Science, Institute of Biomedical Science, Henan Normal University, Xinxiang, Henan, China
| | - Chen Ding
- Center for Cell and Gene Therapy, Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute , Fudan University, Shanghai, China.
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49
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Khan S, Baligar P, Tandon C, Nayyar J, Tandon S. Molecular heterogeneity in prostate cancer and the role of targeted therapy. Life Sci 2024; 336:122270. [PMID: 37979833 DOI: 10.1016/j.lfs.2023.122270] [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: 07/31/2023] [Revised: 11/03/2023] [Accepted: 11/12/2023] [Indexed: 11/20/2023]
Abstract
Data collected from large-scale studies has shown that the incidence of prostate cancer globally is on the rise, which could be attributed to an overall increase in lifespan. So, the question is how has modern science with all its new technologies and clinical breakthroughs mitigated or managed this disease? The answer is not a simple one as prostate cancer exhibits various subtypes, each with its unique characteristics or signatures which creates challenges in treatment. To understand the complexity of prostate cancer these signatures must be deciphered. Molecular studies of prostate cancer samples have identified certain genetic and epigenetic alterations, which are instrumental in tumorigenesis. Some of these candidates include the androgen receptor (AR), various oncogenes, tumor suppressor genes, and the tumor microenvironment, which serve as major drivers that lead to cancer progression. These aberrant genes and their products can give an insight into prostate cancer development and progression by acting as potent markers to guide future therapeutic approaches. Thus, understanding the complexity of prostate cancer is crucial for targeting specific markers and tailoring treatments accordingly.
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Affiliation(s)
- Sabiha Khan
- Amity Institute of Molecular Medicine, Amity University Uttar Pradesh, India
| | - Prakash Baligar
- Amity Institute of Molecular Medicine, Amity University Uttar Pradesh, India
| | - Chanderdeep Tandon
- Amity School of Biological Sciences, Amity University Punjab, Mohali, India
| | - Jasamrit Nayyar
- Department of Chemistry, Goswami Ganesh Dutt Sanatan Dharam College, Chandigarh, India
| | - Simran Tandon
- Amity School of Health Sciences, Amity University Punjab, Mohali, India.
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50
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Difilippo V, Saba KH, Styring E, Magnusson L, Nilsson J, Nathrath M, Baumhoer D, Nord KH. Osteosarcomas With Few Chromosomal Alterations or Adult Onset Are Genetically Heterogeneous. J Transl Med 2024; 104:100283. [PMID: 37931683 DOI: 10.1016/j.labinv.2023.100283] [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: 06/22/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/08/2023] Open
Abstract
Osteosarcoma is the most common primary bone malignancy, often detected in children and adolescents and commonly associated with TP53 alterations along with a high number of chromosomal rearrangements. However, osteosarcoma can affect patients of any age, and some tumors display less genetic complexity. Besides TP53 variants, data on key driving mutations are lacking for many osteosarcomas, particularly those affecting adults. To detect osteosarcoma-specific alterations, we screened transcriptomic and genomic sequencing and copy number data from 150 bone tumors originally diagnosed as osteosarcomas. To increase the precision in gene fusion detection, we developed a bioinformatic tool denoted as NAFuse, which extracts gene fusions that are verified at both the genomic and transcriptomic levels. Apart from the already reported genetic subgroups of osteosarcoma with TP53 structural variants, or MDM2 and/or CDK4 amplification, we did not identify any recurrent genetic driver that signifies the remaining cases. Among the plethora of mutations identified, we found genetic alterations characteristic of, or similar to, those of other bone and soft tissue tumors in 8 cases. These mutations were found in tumors with relatively few other genetic alterations or in adults. Due to the lack of clinical context and available tissue, we can question the diagnosis only on a genetic basis. However, our findings support the notion that osteosarcomas with few chromosomal alterations or adult onset seem genetically distinct from conventional osteosarcomas of children and adolescents.
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Affiliation(s)
- Valeria Difilippo
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Karim H Saba
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Emelie Styring
- Department of Orthopedics, Lund University, Skåne University Hospital, Lund, Sweden
| | - Linda Magnusson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Jenny Nilsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Michaela Nathrath
- Children's Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany; Department of Pediatric Oncology, Klinikum Kassel, Kassel, Germany
| | - Daniel Baumhoer
- Bone Tumour Reference Centre at the Institute of Pathology, University Hospital and University of Basel, Basel, Switzerland
| | - Karolin H Nord
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden.
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