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Klapwijk JC, Del Rio Espinola A, Libertini S, Collin P, Fellows MD, Jobling S, Lynch AM, Martus H, Vickers C, Zeller A, Biasco L, Brugman MH, Bushmann FD, Cathomen T, Ertl HCJ, Gabriel R, Gao G, Jadlowsky JK, Kimber I, Lanz TA, Levine BL, Micklethwaite KP, Onodera M, Pizzurro DM, Reed S, Rothe M, Sabatino D, Salk JJ, Schambach A, Themis M, Yuan J. Improving the assessment of risk factors relevant to potential carcinogenicity of gene therapies: a consensus paper. Hum Gene Ther 2024. [PMID: 39049734 DOI: 10.1089/hum.2024.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024] Open
Abstract
Regulators and industry are actively seeking improvements and alternatives to current models and approaches to evaluate potential carcinogenicity of gene therapies (GTs). A meeting of invited experts was organised by NC3Rs/UKEMS (London, March 2023) to discuss this topic. This paper describes the consensus reached amongst delegates on the definition of vector genotoxicity, sources of uncertainty, suitable toxicological endpoints for genotoxic assessment of GTs, and future research needs. The collected recommendations should inform the further development of regulatory guidelines for the non-clinical toxicological assessment of GT products.
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Affiliation(s)
- Jan C Klapwijk
- Cornelis Consulting Ltd, Ware, United Kingdom of Great Britain and Northern Ireland;
| | | | - Silvana Libertini
- Novartis Institutes for BioMedical Research Basel, Basel, Basel-Stadt, Switzerland;
| | - Philippe Collin
- AstraZeneca R&D Cambridge, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, Cambridge, United Kingdom of Great Britain and Northern Ireland;
| | - Mick D Fellows
- AstraZeneca R&D Cambridge, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, Cambridge, United Kingdom of Great Britain and Northern Ireland;
| | - Susan Jobling
- TestaVec Ltd, Maidenhead, United Kingdom of Great Britain and Northern Ireland
- Brunel University London, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Uxbridge, Greater London, United Kingdom of Great Britain and Northern Ireland;
| | - Antohny M Lynch
- GlaxoSmithKline, Genetic Toxicology, Ware, United Kingdom of Great Britain and Northern Ireland;
| | - HansJoerg Martus
- Novartis Institutes for BioMedical Research Basel, Basel, Basel-Stadt, Switzerland;
| | - Catherine Vickers
- National Centre for the Replacement Refinement and Reduction of Animals in Research, London, United Kingdom of Great Britain and Northern Ireland;
| | - Andreas Zeller
- F Hoffmann-La Roche Ltd, pRED, Pharma Research & Early Development , Roche Innovation Center, Basel, Switzerland;
| | - Luca Biasco
- UCL, Zayed Centre for Research (ZCR), London, United Kingdom of Great Britain and Northern Ireland;
| | - Martijn H Brugman
- GlaxoSmithKline Research & Development Limited, Cell and Gene Therapy, GSK Medicine Research Centre, Stevenage, Hertfordshire, United Kingdom of Great Britain and Northern Ireland;
| | - Frederic D Bushmann
- University of Pennsylvania Perelman School of Medicine, Department of Microbiology, Philadelphia, Pennsylvania, United States;
| | - Toni Cathomen
- University Medical Center Freiburg, Institute for Transfusion Medicine and Gene Therapy, Hugstetter Str. 55, Freiburg, Germany, 79106;
| | - Hildegund C J Ertl
- Wistar Institute of Anatomy and Biology, Ertl Laboratory Vaccine & Immunotherapy Center, Philadelphia, Pennsylvania, United States;
| | | | - Guangping Gao
- University of Massachusetts Medical School, Horae Gene Therapy Center, Worcester, Massachusetts, United States;
| | - Julie K Jadlowsky
- University of Pennsylvania Perelman School of Medicine, Center for Cellular Immunotherapies and Department of Pathology and Laboratory Medicine, Philadelphia, Pennsylvania, United States;
| | - Ian Kimber
- The University of Manchester, Faculty of Biology, Medicine and Health, Manchester, United Kingdom of Great Britain and Northern Ireland;
| | - Thomas A Lanz
- Pfizer Global Research and Development, Drug Safety Research & Development, Groton, Connecticut, United States;
| | - Bruce L Levine
- University of Pennsylvania Perelman School of Medicine, Center for Cellular Immunotherapies and Department of Pathology and Laboratory Medicine, Philadelphia, Pennsylvania, United States;
| | - Kenneth P Micklethwaite
- Westmead Hospital, Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead, New South Wales, Australia
- Westmead Hospital ICPMR, NSW Health Pathology Blood Transplant and Cell Therapies Laboratory , Westmead, New South Wales, Australia
- Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- The University of Sydney Sydney Medical School, Sydney, New South Wales, Australia;
| | - Masafumi Onodera
- National Center for Child Health and Development, Gene & Cell Therapy Promotion Center, Setagaya-ku, Tokyo, Japan;
| | | | - Simon Reed
- Cardiff University School of Medicine, Division of Cancer and Genetics, Cardiff, Cardiff, United Kingdom of Great Britain and Northern Ireland;
| | - Michael Rothe
- Hannover Medical School, Institute of Experimental Hematology, Hannover, Niedersachsen, Germany;
| | - Denise Sabatino
- University of Pennsylvania School of Medicine, Pediatrics, The Children's Hospital of Philadelphia, 3501 Civic Center Blvd, Colket Translational Research Blg, Rm 5020, Philadelphia, Pennsylvania, United States, 19104
- The Children's Hospital of Philadelphia;
| | - Jesse J Salk
- TwinStrand Biosciences, Seattle, Washington, United States
- University of Washington School of Medicine, Department of Medicine, Divisions of Hematology and Medical Oncology, Seattle, Washington, United States;
| | - Axel Schambach
- Hannover Medical School, Institute of Experimental Hematology, Hannover, Germany
- Boston Children's Hospital, Division of Hematology/Oncology, Boston, Massachusetts, United States;
| | - Michael Themis
- TestaVec Ltd, London, Greater London, United Kingdom of Great Britain and Northern Ireland
- Brunel University London, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Uxbridge, United Kingdom of Great Britain and Northern Ireland;
| | - Jing Yuan
- Kymera Therapeutics Inc, Watertown, Massachusetts, United States;
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2
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Metanat Y, Viktor P, Amajd A, Kaur I, Hamed AM, Abed Al-Abadi NK, Alwan NH, Chaitanya MVNL, Lakshmaiya N, Ghildiyal P, Khalaf OM, Ciongradi CI, Sârbu I. The paths toward non-viral CAR-T cell manufacturing: A comprehensive review of state-of-the-art methods. Life Sci 2024; 348:122683. [PMID: 38702027 DOI: 10.1016/j.lfs.2024.122683] [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: 01/24/2024] [Revised: 04/11/2024] [Accepted: 04/28/2024] [Indexed: 05/06/2024]
Abstract
Although CAR-T cell therapy has emerged as a game-changer in cancer immunotherapy several bottlenecks limit its widespread use as a front-line therapy. Current protocols for the production of CAR-T cells rely mainly on the use of lentiviral/retroviral vectors. Nevertheless, according to the safety concerns around the use of viral vectors, there are several regulatory hurdles to their clinical use. Large-scale production of viral vectors under "Current Good Manufacturing Practice" (cGMP) involves rigorous quality control assessments and regulatory requirements that impose exorbitant costs on suppliers and as a result, lead to a significant increase in the cost of treatment. Pursuing an efficient non-viral method for genetic modification of immune cells is a hot topic in cell-based gene therapy. This study aims to investigate the current state-of-the-art in non-viral methods of CAR-T cell manufacturing. In the first part of this study, after reviewing the advantages and disadvantages of the clinical use of viral vectors, different non-viral vectors and the path of their clinical translation are discussed. These vectors include transposons (sleeping beauty, piggyBac, Tol2, and Tc Buster), programmable nucleases (ZFNs, TALENs, and CRISPR/Cas9), mRNA, plasmids, minicircles, and nanoplasmids. Afterward, various methods for efficient delivery of non-viral vectors into the cells are reviewed.
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Affiliation(s)
- Yekta Metanat
- Faculty of Medicine, Zahedan University of Medical Sciences, Sistan and Baluchestan Province, Iran
| | - Patrik Viktor
- Óbuda University, Karoly Keleti faculty, Tavaszmező u. 15-17, H-1084 Budapest, Hungary
| | - Ayesha Amajd
- Faculty of Transport and Aviation Engineering, Silesian University of Technology, Krasińskiego 8 Street, 40-019 Katowice, Poland
| | - Irwanjot Kaur
- Department of Biotechnology and Genetics, Jain (Deemed-to-be) University, Bangalore, Karnataka, India; Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan-303012, India
| | | | | | | | - M V N L Chaitanya
- School of pharmaceutical sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, Punjab - 144411, India
| | | | - Pallavi Ghildiyal
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | | | - Carmen Iulia Ciongradi
- 2nd Department of Surgery-Pediatric Surgery and Orthopedics, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iași, Romania.
| | - Ioan Sârbu
- 2nd Department of Surgery-Pediatric Surgery and Orthopedics, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iași, Romania.
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3
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Rossi M, Breman E. Engineering strategies to safely drive CAR T-cells into the future. Front Immunol 2024; 15:1411393. [PMID: 38962002 PMCID: PMC11219585 DOI: 10.3389/fimmu.2024.1411393] [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: 04/02/2024] [Accepted: 05/27/2024] [Indexed: 07/05/2024] Open
Abstract
Chimeric antigen receptor (CAR) T-cell therapy has proven a breakthrough in cancer treatment in the last decade, giving unprecedented results against hematological malignancies. All approved CAR T-cell products, as well as many being assessed in clinical trials, are generated using viral vectors to deploy the exogenous genetic material into T-cells. Viral vectors have a long-standing clinical history in gene delivery, and thus underwent iterations of optimization to improve their efficiency and safety. Nonetheless, their capacity to integrate semi-randomly into the host genome makes them potentially oncogenic via insertional mutagenesis and dysregulation of key cellular genes. Secondary cancers following CAR T-cell administration appear to be a rare adverse event. However several cases documented in the last few years put the spotlight on this issue, which might have been underestimated so far, given the relatively recent deployment of CAR T-cell therapies. Furthermore, the initial successes obtained in hematological malignancies have not yet been replicated in solid tumors. It is now clear that further enhancements are needed to allow CAR T-cells to increase long-term persistence, overcome exhaustion and cope with the immunosuppressive tumor microenvironment. To this aim, a variety of genomic engineering strategies are under evaluation, most relying on CRISPR/Cas9 or other gene editing technologies. These approaches are liable to introduce unintended, irreversible genomic alterations in the product cells. In the first part of this review, we will discuss the viral and non-viral approaches used for the generation of CAR T-cells, whereas in the second part we will focus on gene editing and non-gene editing T-cell engineering, with particular regard to advantages, limitations, and safety. Finally, we will critically analyze the different gene deployment and genomic engineering combinations, delineating strategies with a superior safety profile for the production of next-generation CAR T-cell.
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Luo P, Yang J, Jian L, Dong J, Yin S, Luo C, Zhou S. Knockdown of PGBD5 inhibits the malignant progression of glioma through upregulation of the PPAR pathway. Int J Oncol 2024; 64:55. [PMID: 38577941 PMCID: PMC11015917 DOI: 10.3892/ijo.2024.5643] [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: 11/01/2023] [Accepted: 02/05/2024] [Indexed: 04/06/2024] Open
Abstract
Glioma is the most common type of primary intracranial malignant tumor, and because of its high invasiveness and recurrence, its prognosis remains poor. The present study investigated the biological function of piggyBac transportable element derived 5 (PGBD5) in glioma. Glioma and para-cancerous tissues were obtained from five patients. Reverse transcription-quantitative PCR and western blotting were used to detect the expression levels of PGBD5. Transwell assay and flow cytometry were used to evaluate cell migration, invasion, apoptosis and cell cycle distribution. In addition, a nude mouse tumor transplantation model was established to study the downstream pathways of PGBD5 and the molecular mechanism was analyzed using transcriptome sequencing. The mRNA and protein expression levels of PGBD5 were increased in glioma tissues and cells. Notably, knockdown of PGBD5 in vitro could inhibit the migration and invasion of glioma cells. In addition, the knockdown of PGBD5 expression promoted apoptosis and caused cell cycle arrest in the G2/M phase, thus inhibiting cell proliferation. Furthermore, in vivo experiments revealed that knockdown of PGBD5 expression could inhibit Ki67 expression and slow tumor growth. Changes in PGBD5 expression were also shown to be closely related to the peroxisome proliferator-activated receptor (PPAR) signaling pathway. In conclusion, interference with PGBD5 could inhibit the malignant progression of glioma through the PPAR pathway, suggesting that PGBD5 may be a potential molecular target of glioma.
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Affiliation(s)
- Pengren Luo
- Department of Neurosurgery, The First People's Hospital of Yunnan Province, Yunnan 650500, P.R. China
- Department of Neurosurgery, The Affiliated Hospital of Kunming University of Science and Technology, Yunnan 650500, P.R. China
- Medical School, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Jinhong Yang
- Medical School, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Lipeng Jian
- Department of Neurosurgery, The First People's Hospital of Yunnan Province, Yunnan 650500, P.R. China
| | - Jigen Dong
- Department of Neurosurgery, The First People's Hospital of Yunnan Province, Yunnan 650500, P.R. China
| | - Shi Yin
- Department of Neurosurgery, The First People's Hospital of Yunnan Province, Yunnan 650500, P.R. China
| | - Chao Luo
- Department of Neurosurgery, The First People's Hospital of Yunnan Province, Yunnan 650500, P.R. China
| | - Shuai Zhou
- Department of Neurosurgery, The First People's Hospital of Yunnan Province, Yunnan 650500, P.R. China
- Department of Neurosurgery, The Affiliated Hospital of Kunming University of Science and Technology, Yunnan 650500, P.R. China
- Medical School, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
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5
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Yamada M, Keller RR, Gutierrez RL, Cameron D, Suzuki H, Sanghrajka R, Vaynshteyn J, Gerwin J, Maura F, Hooper W, Shah M, Robine N, Demarest P, Bayin NS, Zapater LJ, Reed C, Hébert S, Masilionis I, Chaligne R, Socci ND, Taylor MD, Kleinman CL, Joyner AL, Raju GP, Kentsis A. Childhood cancer mutagenesis caused by transposase-derived PGBD5. SCIENCE ADVANCES 2024; 10:eadn4649. [PMID: 38517960 PMCID: PMC10959420 DOI: 10.1126/sciadv.adn4649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/16/2024] [Indexed: 03/24/2024]
Abstract
Genomic rearrangements are a hallmark of most childhood tumors, including medulloblastoma, one of the most common brain tumors in children, but their causes remain largely unknown. Here, we show that PiggyBac transposable element derived 5 (Pgbd5) promotes tumor development in multiple developmentally accurate mouse models of Sonic Hedgehog (SHH) medulloblastoma. Most Pgbd5-deficient mice do not develop tumors, while maintaining normal cerebellar development. Ectopic activation of SHH signaling is sufficient to enforce cerebellar granule cell progenitor-like cell states, which exhibit Pgbd5-dependent expression of distinct DNA repair and neurodevelopmental factors. Mouse medulloblastomas expressing Pgbd5 have increased numbers of somatic structural DNA rearrangements, some of which carry PGBD5-specific sequences at their breakpoints. Similar sequence breakpoints recurrently affect somatic DNA rearrangements of known tumor suppressors and oncogenes in medulloblastomas in 329 children. This identifies PGBD5 as a medulloblastoma mutator and provides a genetic mechanism for the generation of oncogenic DNA rearrangements in childhood cancer.
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Affiliation(s)
- Makiko Yamada
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - Ross R. Keller
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | | | - Daniel Cameron
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - Hiromichi Suzuki
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Reeti Sanghrajka
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Jake Vaynshteyn
- Departments of Neurology and Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey Gerwin
- Departments of Neurology and Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesco Maura
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - William Hooper
- Computational Biology, New York Genome Center, New York, NY, USA
| | - Minita Shah
- Computational Biology, New York Genome Center, New York, NY, USA
| | - Nicolas Robine
- Computational Biology, New York Genome Center, New York, NY, USA
| | - Phillip Demarest
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - N. Sumru Bayin
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge University, Cambridge, UK
| | - Luz Jubierre Zapater
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - Casie Reed
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - Steven Hébert
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Ignas Masilionis
- Single-Cell Analytics Innovation Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronan Chaligne
- Single-Cell Analytics Innovation Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas D. Socci
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael D. Taylor
- Department of Pediatrics—Hematology/Oncology and Neurosurgery, Baylor College of Medicine, Houston, TX, USA
- Hematology-Oncology Section, Texas Children’s Cancer Center, Houston, TX, USA
- The Arthur and Sonia Labatt Brain Tumour Research Centre and the Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Claudia L. Kleinman
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Alexandra L. Joyner
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
- Biochemistry, Cell and Molecular Biology Program and Neuroscience Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - G. Praveen Raju
- Departments of Neurology and Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alex Kentsis
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Medical College of Cornell University, New York, NY, USA
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Suo A, Yang J, Mao C, Li W, Wu X, Xie W, Yang Z, Guo S, Zheng B, Zheng Y. Phased secondary small interfering RNAs in Camellia sinensis var. assamica. NAR Genom Bioinform 2023; 5:lqad103. [PMID: 38025046 PMCID: PMC10673657 DOI: 10.1093/nargab/lqad103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023] Open
Abstract
Phased secondary small interfering RNAs (phasiRNAs) in plants play important roles in regulating genome stability, plant development and stress adaption. Camellia sinensis var. assamica has immense economic, medicinal and cultural significance. However, there are still no studies of phasiRNAs and their putative functions in this valuable plant. We identified 476 and 43 PHAS loci which generated 4290 twenty one nucleotide (nt) and 264 twenty four nt phasiRNAs, respectively. Moreover, the analysis of degradome revealed more than 35000 potential targets for these phasiRNAs. We identified several conserved 21 nt phasiRNA generation pathways in tea plant, including miR390 → TAS3, miR482/miR2118 → NB-LRR, miR393 → F-box, miR828 → MYB/TAS4, and miR7122 → PPR in this study. Furthermore, we found that some transposase and plant mobile domain genes could generate phasiRNAs. Our results show that phasiRNAs target genes in the same family in cis- or trans-manners, and different members of the same gene family may generate the same phasiRNAs. The phasiRNAs, generated by transposase and plant mobile domain genes, and their targets, suggest that phasiRNAs may be involved in the inhibition of transposable elements in tea plant. To summarize, these results provide a comprehensive view of phasiRNAs in Camellia sinensis var. assamica.
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Affiliation(s)
- Angbaji Suo
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
| | - Jun Yang
- School of Criminal Investigation, Yunnan Police College, No. 249 North Jiaochang Road, 650223 Yunnan, China
| | - Chunyi Mao
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
| | - Wanran Li
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
| | - Xingwang Wu
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
| | - Wenping Xie
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
| | - Zhengan Yang
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
| | - Shiyong Guo
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, No. 220 Handan Road, 200433 Shanghai, China
| | - Yun Zheng
- College of Landscape and Horticulture, Yunnan Agricultural University, No. 95 Jinhei Road, 650201 Yunnan, China
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7
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Han M, Perkins MH, Novaes LS, Xu T, Chang H. Advances in transposable elements: from mechanisms to applications in mammalian genomics. Front Genet 2023; 14:1290146. [PMID: 38098473 PMCID: PMC10719622 DOI: 10.3389/fgene.2023.1290146] [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: 09/07/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
It has been 70 years since Barbara McClintock discovered transposable elements (TE), and the mechanistic studies and functional applications of transposable elements have been at the forefront of life science research. As an essential part of the genome, TEs have been discovered in most species of prokaryotes and eukaryotes, and the relative proportion of the total genetic sequence they comprise gradually increases with the expansion of the genome. In humans, TEs account for about 40% of the genome and are deeply involved in gene regulation, chromosome structure maintenance, inflammatory response, and the etiology of genetic and non-genetic diseases. In-depth functional studies of TEs in mammalian cells and the human body have led to a greater understanding of these fundamental biological processes. At the same time, as a potent mutagen and efficient genome editing tool, TEs have been transformed into biological tools critical for developing new techniques. By controlling the random insertion of TEs into the genome to change the phenotype in cells and model organisms, critical proteins of many diseases have been systematically identified. Exploiting the TE's highly efficient in vitro insertion activity has driven the development of cutting-edge sequencing technologies. Recently, a new technology combining CRISPR with TEs was reported, which provides a novel targeted insertion system to both academia and industry. We suggest that interrogating biological processes that generally depend on the actions of TEs with TEs-derived genetic tools is a very efficient strategy. For example, excessive activation of TEs is an essential factor in the occurrence of cancer in humans. As potent mutagens, TEs have also been used to unravel the key regulatory elements and mechanisms of carcinogenesis. Through this review, we aim to effectively combine the traditional views of TEs with recent research progress, systematically link the mechanistic discoveries of TEs with the technological developments of TE-based tools, and provide a comprehensive approach and understanding for researchers in different fields.
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Affiliation(s)
- Mei Han
- Guangzhou National Laboratory, Guangzhou, China
| | - Matthew H. Perkins
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Leonardo Santana Novaes
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Tao Xu
- Guangzhou National Laboratory, Guangzhou, China
| | - Hao Chang
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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8
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Rodriguez-Fos E, Planas-Fèlix M, Burkert M, Puiggròs M, Toedling J, Thiessen N, Blanc E, Szymansky A, Hertwig F, Ishaque N, Beule D, Torrents D, Eggert A, Koche RP, Schwarz RF, Haase K, Schulte JH, Henssen AG. Mutational topography reflects clinical neuroblastoma heterogeneity. CELL GENOMICS 2023; 3:100402. [PMID: 37868040 PMCID: PMC10589636 DOI: 10.1016/j.xgen.2023.100402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/13/2023] [Accepted: 08/11/2023] [Indexed: 10/24/2023]
Abstract
Neuroblastoma is a pediatric solid tumor characterized by strong clinical heterogeneity. Although clinical risk-defining genomic alterations exist in neuroblastomas, the mutational processes involved in their generation remain largely unclear. By examining the topography and mutational signatures derived from all variant classes, we identified co-occurring mutational footprints, which we termed mutational scenarios. We demonstrate that clinical neuroblastoma heterogeneity is associated with differences in the mutational processes driving these scenarios, linking risk-defining pathognomonic variants to distinct molecular processes. Whereas high-risk MYCN-amplified neuroblastomas were characterized by signs of replication slippage and stress, homologous recombination-associated signatures defined high-risk non-MYCN-amplified patients. Non-high-risk neuroblastomas were marked by footprints of chromosome mis-segregation and TOP1 mutational activity. Furthermore, analysis of subclonal mutations uncovered differential activity of these processes through neuroblastoma evolution. Thus, clinical heterogeneity of neuroblastoma patients can be linked to differences in the mutational processes that are active in their tumors.
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Affiliation(s)
- Elias Rodriguez-Fos
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mercè Planas-Fèlix
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Burkert
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Montserrat Puiggròs
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center – Center for Genomic Regulation – Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Joern Toedling
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nina Thiessen
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Eric Blanc
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Annabell Szymansky
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Falk Hertwig
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Naveed Ishaque
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Dieter Beule
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - David Torrents
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center – Center for Genomic Regulation – Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Angelika Eggert
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Richard P. Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roland F. Schwarz
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- BIFOLD – Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
| | - Kerstin Haase
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johannes H. Schulte
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Anton G. Henssen
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
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9
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Geller JI, Hong AL, Vallance KL, Evageliou N, Aldrink JH, Cost NG, Treece AL, Renfro LA, Mullen EA. Children's Oncology Group's 2023 blueprint for research: Renal tumors. Pediatr Blood Cancer 2023; 70 Suppl 6:e30586. [PMID: 37477907 PMCID: PMC10529605 DOI: 10.1002/pbc.30586] [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: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/22/2023]
Abstract
Every year, approximately 600 infants, children, and adolescents are diagnosed with renal cancer in the United States. In addition to Wilms tumor (WT), which accounts for about 80% of all pediatric renal cancers, clear cell sarcoma of the kidney, renal cell carcinoma, malignant rhabdoid tumor, as well as more rare cancers (other sarcomas, rare carcinomas, lymphoma) and benign tumors can originate within the kidney. WT itself can be divided into favorable histology (FHWT), with a 5-year overall survival (OS) exceeding 90%, and anaplastic histology, with 4-year OS of 73.7%. Outcomes of the other pediatric renal cancers include clear cell sarcoma (5-year OS: 90%), malignant rhabdoid tumor (5-year OS: 10% for stages 3 and 4), and renal cell carcinoma (4-year OS: 84.8%). Recent clinical trials have identified novel biological prognostic markers for FHWT, and a series of Children's Oncology Group (COG) trials have demonstrated improving outcomes with therapy modification, and opportunities for further care refinement.
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Affiliation(s)
- James I Geller
- Division of Oncology, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, USA
| | - Andrew L Hong
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kelly L Vallance
- Hematology and Oncology, Cook Children's Medical Center, Fort Worth, Texas, USA
| | - Nick Evageliou
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jennifer H Aldrink
- Division of Pediatric Surgery, Department of Surgery, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Nicholas G Cost
- Department of Surgery, Division of Urology and the Surgical Oncology Program at Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Amy L Treece
- Department of Pathology and Laboratory Medicine, Children's of Alabama, Birmingham, Alabama, USA
| | | | - Elizabeth A Mullen
- Dana-Farber/Boston Children's Blood Disorders and Cancer Center, Boston, Massachusetts, USA
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10
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Pearson ADJ, Federico S, Gatz SA, Ortiz M, Lesa G, Scobie N, Gounaris I, Weiner SL, Weigel B, Unger TJ, Stewart E, Smith M, Slotkin EK, Reaman G, Pappo A, Nysom K, Norga K, McDonough J, Marshall LV, Ludwinski D, Ligas F, Karres D, Kool M, Horner TJ, Henssen A, Heenen D, Hawkins DS, Gore L, Bender JG, Galluzzo S, Fox E, de Rojas T, Davies BR, Chakrabarti J, Carmichael J, Bradford D, Blanc P, Bernardi R, Benchetrit S, Akindele K, Vassal G. Paediatric Strategy Forum for medicinal product development of DNA damage response pathway inhibitors in children and adolescents with cancer: ACCELERATE in collaboration with the European Medicines Agency with participation of the Food and Drug Administration. Eur J Cancer 2023; 190:112950. [PMID: 37441939 DOI: 10.1016/j.ejca.2023.112950] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/09/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023]
Abstract
DNA damage response inhibitors have a potentially important therapeutic role in paediatric cancers; however, their optimal use, including patient selection and combination strategy, remains unknown. Moreover, there is an imbalance between the number of drugs with diverse mechanisms of action and the limited number of paediatric patients available to be enrolled in early-phase trials, so prioritisation and a strategy are essential. While PARP inhibitors targeting homologous recombination-deficient tumours have been used primarily in the treatment of adult cancers with BRCA1/2 mutations, BRCA1/2 mutations occur infrequently in childhood tumours, and therefore, a specific response hypothesis is required. Combinations with targeted radiotherapy, ATR inhibitors, or antibody drug conjugates with DNA topoisomerase I inhibitor-related warheads warrant evaluation. Additional monotherapy trials of PARP inhibitors with the same mechanism of action are not recommended. PARP1-specific inhibitors and PARP inhibitors with very good central nervous system penetration also deserve evaluation. ATR, ATM, DNA-PK, CHK1, WEE1, DNA polymerase theta and PKMYT1 inhibitors are early in paediatric development. There should be an overall coordinated strategy for their development. Therefore, an academia/industry consensus of the relevant biomarkers will be established and a focused meeting on ATR inhibitors (as proof of principle) held. CHK1 inhibitors have demonstrated activity in desmoplastic small round cell tumours and have a potential role in the treatment of other paediatric malignancies, such as neuroblastoma and Ewing sarcoma. Access to CHK1 inhibitors for paediatric clinical trials is a high priority. The three key elements in evaluating these inhibitors in children are (1) innovative trial design (design driven by a clear hypothesis with the intent to further investigate responders and non-responders with detailed retrospective molecular analyses to generate a revised or new hypothesis); (2) biomarker selection and (3) rational combination therapy, which is limited by overlapping toxicity. To maximally benefit children with cancer, investigators should work collaboratively to learn the lessons from the past and apply them to future studies. Plans should be based on the relevant biology, with a focus on simultaneous and parallel research in preclinical and clinical settings, and an overall integrated and collaborative strategy.
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Affiliation(s)
- Andrew D J Pearson
- ACCELERATE, c/o BLSI, Clos Chapelle-aux-Champs 30, Bte 1.30.30 BE-1200 Brussels, Belgium.
| | - Sara Federico
- St Jude Children's Research Hospital, Memphis, TN, USA
| | - Susanne A Gatz
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Michael Ortiz
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Giovanni Lesa
- Paediatric Medicines Office, Scientific Evidence Generation Department, Human Division, European Medicines Agency (EMA), Amsterdam, the Netherlands
| | | | - Ioannis Gounaris
- Merck Serono Ltd (an affiliate of Merck KGaA, Darmstadt, Germany), Feltham, UK
| | | | | | - T J Unger
- Repare Therapeutics, Cambridge, MA, USA
| | | | | | | | - Gregory Reaman
- US Food and Drug Administration, Silver Springs, MD, USA
| | - Alberto Pappo
- St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Koen Norga
- Antwerp University Hospital, Antwerp, Belgium; Paediatric Committee of the European Medicines Agency (EMA), Amsterdam, the Netherlands; Federal Agency for Medicines and Health Products, Brussels, Belgium
| | - Joe McDonough
- The Andrew McDonough B+ Foundation, Wilmington, DE, USA
| | - Lynley V Marshall
- The Royal Marsden NHS Foundation Hospital, The Institute of Cancer Research, Sutton, Surrey, UK
| | | | - Franca Ligas
- Paediatric Medicines Office, Scientific Evidence Generation Department, Human Division, European Medicines Agency (EMA), Amsterdam, the Netherlands
| | - Dominik Karres
- Paediatric Medicines Office, Scientific Evidence Generation Department, Human Division, European Medicines Agency (EMA), Amsterdam, the Netherlands
| | - Marcel Kool
- Hopp Children's Cancer Center, Heidelberg, Germany
| | | | | | | | - Douglas S Hawkins
- Seattle Children's Hospital, Seattle, WA, USA; Children's Oncology Group, Seattle, WA, USA
| | - Lia Gore
- Children's Hospital Colorado, Aurora, CO, USA; University of Colorado School of Medicine, Aurora, CO, USA
| | | | | | - Elizabeth Fox
- St Jude Children's Research Hospital, Memphis, TN, USA
| | - Teresa de Rojas
- ACCELERATE, c/o BLSI, Clos Chapelle-aux-Champs 30, Bte 1.30.30 BE-1200 Brussels, Belgium
| | | | | | - Juliet Carmichael
- The Royal Marsden NHS Foundation Hospital, The Institute of Cancer Research, Sutton, Surrey, UK
| | - Diana Bradford
- US Food and Drug Administration, Silver Springs, MD, USA
| | | | - Ronald Bernardi
- Genentech, a Member of the Roche Group, South San Francisco, CA, USA
| | - Sylvie Benchetrit
- National Agency for the Safety of Medicine and Health Products, Paris, France
| | | | - Gilles Vassal
- ACCELERATE, c/o BLSI, Clos Chapelle-aux-Champs 30, Bte 1.30.30 BE-1200 Brussels, Belgium; Gustave Roussy Cancer Centre, Paris, France
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11
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Mendoza-Castrejon J, Magee JA. Layered immunity and layered leukemogenicity: Developmentally restricted mechanisms of pediatric leukemia initiation. Immunol Rev 2023; 315:197-215. [PMID: 36588481 PMCID: PMC10301262 DOI: 10.1111/imr.13180] [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] [Indexed: 01/03/2023]
Abstract
Hematopoietic stem cells (HSCs) and multipotent progenitor cells (MPPs) arise in successive waves during ontogeny, and their properties change significantly throughout life. Ontological changes in HSCs/MPPs underlie corresponding changes in mechanisms of pediatric leukemia initiation. As HSCs and MPPs progress from fetal to neonatal, juvenile and adult stages of life, they undergo transcriptional and epigenetic reprogramming that modifies immune output to meet age-specific pathogenic challenges. Some immune cells arise exclusively from fetal HSCs/MPPs. We propose that this layered immunity instructs cell fates that underlie a parallel layered leukemogenicity. Indeed, some pediatric leukemias, such as juvenile myelomonocytic leukemia, myeloid leukemia of Down syndrome, and infant pre-B-cell acute lymphoblastic leukemia, are age-restricted. They only present during infancy or early childhood. These leukemias likely arise from fetal progenitors that lose competence for transformation as they age. Other childhood leukemias, such as non-infant pre-B-cell acute lymphoblastic leukemia and acute myeloid leukemia, have mutation profiles that are common in childhood but rare in morphologically similar adult leukemias. These differences could reflect temporal changes in mechanisms of mutagenesis or changes in how progenitors respond to a given mutation at different ages. Interactions between leukemogenic mutations and normal developmental switches offer potential targets for therapy.
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Affiliation(s)
- Jonny Mendoza-Castrejon
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO 63110
| | - Jeffrey A. Magee
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO 63110
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO 63110
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12
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Bushman FD. DNA transposon mechanisms and pathways of genotoxicity. Mol Ther 2023; 31:613-615. [PMID: 36754054 PMCID: PMC10014265 DOI: 10.1016/j.ymthe.2023.01.023] [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: 01/13/2023] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 02/10/2023] Open
Affiliation(s)
- Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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13
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Wang S, Gao B, Miskey C, Guan Z, Sang Y, Chen C, Wang X, Ivics Z, Song C. Passer, a highly active transposon from a fish genome, as a potential new robust genetic manipulation tool. Nucleic Acids Res 2023; 51:1843-1858. [PMID: 36688327 PMCID: PMC9976928 DOI: 10.1093/nar/gkad005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 12/26/2022] [Accepted: 01/03/2023] [Indexed: 01/24/2023] Open
Abstract
The discovery of new, active DNA transposons can expand the range of genetic tools and provide more options for genomic manipulation. In this study, a bioinformatics analysis suggested that Passer (PS) transposons, which are members of the pogo superfamily, show signs of recent and current activity in animals and may be active in some species. Cell-based transposition assays revealed that the native PS transposases from Gasterosteus aculeatus and Danio rerio displayed very high activity in human cells relative to the Sleeping Beauty transposon. A typical overproduction inhibition phenomenon was observed for PS, and transposition capacity was decreased by ∼12% with each kilobase increase in the insertion size. Furthermore, PS exhibited a pronounced integration preference for genes and their transcriptional regulatory regions. We further show that two domesticated human proteins derived from PS transposases have lost their transposition activity. Overall, PS may represent an alternative with a potentially efficient genetic manipulation tool for transgenesis and mutagenesis applications.
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Affiliation(s)
- Saisai Wang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Bo Gao
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, D-63225 Langen, Germany
| | - Zhongxia Guan
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Yatong Sang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Xiaoyan Wang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, D-63225 Langen, Germany
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
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14
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Akhouayri L, Ostano P, Mello-Grand M, Gregnanin I, Crivelli F, Laurora S, Liscia D, Leone F, Santoro A, Mulè A, Guarino D, Maggiore C, Carlino A, Magno S, Scatolini M, Di Leone A, Masetti R, Chiorino G. Identification of a minimum number of genes to predict triple-negative breast cancer subgroups from gene expression profiles. Hum Genomics 2022; 16:70. [PMID: 36536459 PMCID: PMC9764480 DOI: 10.1186/s40246-022-00436-6] [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: 09/20/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is a very heterogeneous disease. Several gene expression and mutation profiling approaches were used to classify it, and all converged to the identification of distinct molecular subtypes, with some overlapping across different approaches. However, a standardised tool to routinely classify TNBC in the clinics and guide personalised treatment is lacking. We aimed at defining a specific gene signature for each of the six TNBC subtypes proposed by Lehman et al. in 2011 (basal-like 1 (BL1); basal-like 2 (BL2); mesenchymal (M); immunomodulatory (IM); mesenchymal stem-like (MSL); and luminal androgen receptor (LAR)), to be able to accurately predict them. METHODS Lehman's TNBCtype subtyping tool was applied to RNA-sequencing data from 482 TNBC (GSE164458), and a minimal subtype-specific gene signature was defined by combining two class comparison techniques with seven attribute selection methods. Several machine learning algorithms for subtype prediction were used, and the best classifier was applied on microarray data from 72 Italian TNBC and on the TNBC subset of the BRCA-TCGA data set. RESULTS We identified two signatures with the 120 and 81 top up- and downregulated genes that define the six TNBC subtypes, with prediction accuracy ranging from 88.6 to 89.4%, and even improving after removal of the least important genes. Network analysis was used to identify highly interconnected genes within each subgroup. Two druggable matrix metalloproteinases were found in the BL1 and BL2 subsets, and several druggable targets were complementary to androgen receptor or aromatase in the LAR subset. Several secondary drug-target interactions were found among the upregulated genes in the M, IM and MSL subsets. CONCLUSIONS Our study took full advantage of available TNBC data sets to stratify samples and genes into distinct subtypes, according to gene expression profiles. The development of a data mining approach to acquire a large amount of information from several data sets has allowed us to identify a well-determined minimal number of genes that may help in the recognition of TNBC subtypes. These genes, most of which have been previously found to be associated with breast cancer, have the potential to become novel diagnostic markers and/or therapeutic targets for specific TNBC subsets.
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Affiliation(s)
- Laila Akhouayri
- grid.412148.a0000 0001 2180 2473Department of Biomedical Sciences, Genetics and Molecular Biology Laboratory, Faculty of Medicine and Pharmacy, Hassan II-Casablanca University, Casablanca, Morocco ,grid.7605.40000 0001 2336 6580Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Paola Ostano
- grid.452265.2Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Biella, Italy
| | | | - Ilaria Gregnanin
- grid.452265.2Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Biella, Italy
| | - Francesca Crivelli
- grid.452265.2Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Biella, Italy ,Clinical Research Division, “Degli Infermi” Hospital, Ponderano, BI Italy
| | - Sara Laurora
- grid.452265.2Molecular Oncology Lab, Fondazione Edo ed Elvo Tempia, Biella, Italy
| | - Daniele Liscia
- Pathology Department, “Degli Infermi” Hospital, Ponderano, BI Italy
| | - Francesco Leone
- Oncology Department, “Degli Infermi” Hospital, Ponderano, BI Italy
| | - Angela Santoro
- grid.414603.4Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Antonino Mulè
- grid.414603.4Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Donatella Guarino
- grid.414603.4Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Claudia Maggiore
- grid.414603.4Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Angela Carlino
- grid.414603.4Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Stefano Magno
- grid.414603.4Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Maria Scatolini
- grid.452265.2Molecular Oncology Lab, Fondazione Edo ed Elvo Tempia, Biella, Italy
| | - Alba Di Leone
- grid.414603.4Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Riccardo Masetti
- grid.414603.4Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giovanna Chiorino
- grid.452265.2Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Biella, Italy
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15
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Hont AB, Dumont B, Sutton KS, Anderson J, Kentsis A, Drost J, Hong AL, Verschuur A. The tumor microenvironment and immune targeting therapy in pediatric renal tumors. Pediatr Blood Cancer 2022; 70 Suppl 2:e30110. [PMID: 36451260 DOI: 10.1002/pbc.30110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 12/04/2022]
Abstract
This review highlights the role of several immunomodulating elements contributing to the tumor microenvironment of various pediatric renal tumors including Wilms tumor. The roles of innate and adaptive immune cells in renal tumors are summarized as well as immunomodulatory cytokines and other proteins. The expression and the predictive role of checkpoint modulators like PD-L1 and immunomodulating proteins like glypican-3, B7-H3, COX-2 are highlighted with a translational view toward potential therapeutic innovations. We further discuss the current state of preclinical models in advancing this field of study. Finally, examples of clinical trials of immunomodulating strategies such as monoclonal antibodies and chimeric antigen receptor T (CAR-T) cells for relapsed/refractory/progressive pediatric renal tumors are described.
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Affiliation(s)
- Amy B Hont
- Department of Hematology/Oncology, Children's National Hospital, George Washington University, Washington, District of Columbia, USA
| | - Benoit Dumont
- Pediatric Hematology and Oncology Institute, Léon Bérard Cancer Center, Lyon, France
| | - Kathryn S Sutton
- Department of Pediatrics, Children's Healthcare of Atlanta, Emory University, Atlanta, Georgia, USA
| | - John Anderson
- Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Alex Kentsis
- Tow Center for Developmental Oncology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center and Weill Medical College of Cornell University, New York, New York, USA
| | - Jarno Drost
- Princess Máxima Center and Oncode Institute, Utrecht, The Netherlands
| | - Andrew L Hong
- Department of Pediatrics, Children's Healthcare of Atlanta, Emory University, Atlanta, Georgia, USA
| | - Arnauld Verschuur
- Department of Pediatric Hematology and Oncology, Hôpital d'Enfants de la Timone, APHM, Marseille, France
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16
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Xie W, Zeng Y, Hu L, Hao J, Chen Y, Yun X, Lin Q, Li H. Based on different immune responses under the glucose metabolizing type of papillary thyroid cancer and the response to anti-PD-1 therapy. Front Immunol 2022; 13:991656. [PMID: 36211409 PMCID: PMC9536150 DOI: 10.3389/fimmu.2022.991656] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/19/2022] [Indexed: 12/28/2022] Open
Abstract
Glucose metabolism-related genes play an important role in the development and immunotherapy of many tumours, but their role in thyroid cancer is ambiguous. To investigate the role of glucose metabolism-related genes in the development of papillary thyroid cancer (PTC) and their correlation with the clinical outcome of PTC, we collected transcriptomic data from 501 PTC patients in the Cancer Genome Atlas (TCGA). We performed nonnegative matrix decomposition clustering of 2752 glucose metabolism-related genes from transcriptome data and classified PTC patients into three subgroups (C1 for high activation of glucose metabolism, C2 for low activation of glucose metabolism and C3 for moderate activation of glucose metabolism) based on the activation of different glucose metabolism-related genes in 10 glucose metabolism-related pathways. We found a positive correlation between the activation level of glucose metabolism and the tumour mutation burden (TMB), neoantigen number, mRNA stemness index (mRNAsi), age, and tumour stage in PTC patients. Next, we constructed a prognostic prediction model for PTC using six glucose metabolism-related genes (PGBD5, TPO, IGFBPL1, TMEM171, SOD3, TDRD9) and constructed a nomogram based on the risk score and clinical parameters of PTC patients. Both the prognostic risk prediction model and nomogram had high stability and accuracy for predicting the progression-free interval (PFI) in PTC patients. Patients were then divided into high-risk and low-risk groups by risk score. The high-risk group was sensitive to paclitaxel and anti-PD-1 treatment, and the low-risk group was sensitive to sorafenib treatment. We found that the high-risk group was enriched in inflammatory response pathways and associated with high level of immune cell infiltration. To verify the accuracy of the prognostic prediction model, we knocked down PGBD5 in PTC cells and found that the proliferation ability of PTC cells was significantly reduced. This suggests that PGBD5 may be a relatively important oncogene in PTC. Our study constructed a prognostic prediction model and classification of PTC by glucose metabolism-related genes, which provides a new perspective on the role of glucose metabolism in the development and immune microenvironment of PTC and in guiding chemotherapy, targeted therapy and immune checkpoint blockade therapy of PTC.
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Affiliation(s)
- Wenjun Xie
- Department of General Surgery, Shengli Clinical Medical College, Fujian Provincial Hospital, Fuzhou, China
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, China
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Yu Zeng
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Linfei Hu
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Jiaru Hao
- Department of Gastrointestinal Cancer Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Yuzheng Chen
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, China
- Department of Endocrinology, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Xinwei Yun
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- *Correspondence: Xinwei Yun, ; Qiang Lin, ; Huashui Li,
| | - Qiang Lin
- Department of General Surgery, Shengli Clinical Medical College, Fujian Provincial Hospital, Fuzhou, China
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, China
- *Correspondence: Xinwei Yun, ; Qiang Lin, ; Huashui Li,
| | - Huashui Li
- Department of General Surgery, Shengli Clinical Medical College, Fujian Provincial Hospital, Fuzhou, China
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, China
- *Correspondence: Xinwei Yun, ; Qiang Lin, ; Huashui Li,
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17
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Kolacsek O, Wachtl G, Fóthi Á, Schamberger A, Sándor S, Pergel E, Varga N, Raskó T, Izsvák Z, Apáti Á, Orbán TI. Functional indications for transposase domestications - Characterization of the human piggyBac transposase derived (PGBD) activities. Gene 2022; 834:146609. [PMID: 35609796 DOI: 10.1016/j.gene.2022.146609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 12/13/2022]
Abstract
Transposable elements are widespread in all living organisms. In addition to self-reproduction, they are a major source of genetic variation that drives genome evolution but our knowledge of the functions of human genes derived from transposases is limited. There are examples of transposon-derived, domesticated human genes that lost (SETMAR) or retained (THAP9) their transposase activity, however, several remnants in the human genome have not been thoroughly investigated yet. These include the five human piggyBac-derived sequences (PGBD1-5) which share ancestry with the Trichoplusia ni originated piggyBac (PB) transposase. Since PB is widely used in gene delivery applications, the potential activities of endogenous PGBDs are important to address. However, previous data is controversial, especially with the claimed transposition activity of PGBD5, it awaits further investigations. Here, we aimed to systematically analyze all five human PGBD proteins from several aspects, including phylogenetic conservation, potential transposase activity, expression pattern and their regulation in different stress conditions. Among PGBDs, PGBD5 is under the highest purifying selection, and exhibits the most cell type specific expression pattern. In a two-component vector system, none of the human PGBDs could mobilize either the insect PB transposon or the endogenous human PB-like MER75 and MER85 elements with intact terminal sequences. When cells were exposed to various stress conditions, including hypoxia, oxidative or UV stress, the expression profiles of all PGBDs showed different, often cell type specific responses; however, the pattern of PGBD5 in most cases had the opposite tendency than that of the other piggyBac-derived elements. Taken together, our results indicate that human PGBD elements did not retain their mobilizing activity, but their cell type specific, and cellular stress related expression profiles point toward distinct domesticated functions that require further characterization.
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Affiliation(s)
- Orsolya Kolacsek
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Gerda Wachtl
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary; Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Ábel Fóthi
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Anita Schamberger
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Sára Sándor
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Enikő Pergel
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Nóra Varga
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Tamás Raskó
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Ágota Apáti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Tamás I Orbán
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.
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18
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Bhat A, Ghatage T, Bhan S, Lahane GP, Dhar A, Kumar R, Pandita RK, Bhat KM, Ramos KS, Pandita TK. Role of Transposable Elements in Genome Stability: Implications for Health and Disease. Int J Mol Sci 2022; 23:7802. [PMID: 35887150 PMCID: PMC9319628 DOI: 10.3390/ijms23147802] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 12/11/2022] Open
Abstract
Most living organisms have in their genome a sizable proportion of DNA sequences capable of mobilization; these sequences are commonly referred to as transposons, transposable elements (TEs), or jumping genes. Although long thought to have no biological significance, advances in DNA sequencing and analytical technologies have enabled precise characterization of TEs and confirmed their ubiquitous presence across all forms of life. These findings have ignited intense debates over their biological significance. The available evidence now supports the notion that TEs exert major influence over many biological aspects of organismal life. Transposable elements contribute significantly to the evolution of the genome by giving rise to genetic variations in both active and passive modes. Due to their intrinsic nature of mobility within the genome, TEs primarily cause gene disruption and large-scale genomic alterations including inversions, deletions, and duplications. Besides genomic instability, growing evidence also points to many physiologically important functions of TEs, such as gene regulation through cis-acting control elements and modulation of the transcriptome through epigenetic control. In this review, we discuss the latest evidence demonstrating the impact of TEs on genome stability and the underling mechanisms, including those developed to mitigate the deleterious impact of TEs on genomic stability and human health. We have also highlighted the potential therapeutic application of TEs.
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Affiliation(s)
- Audesh Bhat
- Centre for Molecular Biology, Central University of Jammu, Jammu 181143, India;
| | - Trupti Ghatage
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Sonali Bhan
- Centre for Molecular Biology, Central University of Jammu, Jammu 181143, India;
| | - Ganesh P. Lahane
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Arti Dhar
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Rakesh Kumar
- Department of Biotechnology, Shri Mata Vaishnav Devi University, Katra 182320, India;
| | - Raj K. Pandita
- Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA;
| | - Krishna M. Bhat
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Kenneth S. Ramos
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX 77030, USA;
| | - Tej K. Pandita
- Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA;
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX 77030, USA;
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19
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Moretti A, Ponzo M, Nicolette CA, Tcherepanova IY, Biondi A, Magnani CF. The Past, Present, and Future of Non-Viral CAR T Cells. Front Immunol 2022; 13:867013. [PMID: 35757746 PMCID: PMC9218214 DOI: 10.3389/fimmu.2022.867013] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/28/2022] [Indexed: 12/14/2022] Open
Abstract
Adoptive transfer of chimeric antigen receptor (CAR) T lymphocytes is a powerful technology that has revolutionized the way we conceive immunotherapy. The impressive clinical results of complete and prolonged response in refractory and relapsed diseases have shifted the landscape of treatment for hematological malignancies, particularly those of lymphoid origin, and opens up new possibilities for the treatment of solid neoplasms. However, the widening use of cell therapy is hampered by the accessibility to viral vectors that are commonly used for T cell transfection. In the era of messenger RNA (mRNA) vaccines and CRISPR/Cas (clustered regularly interspaced short palindromic repeat-CRISPR-associated) precise genome editing, novel and virus-free methods for T cell engineering are emerging as a more versatile, flexible, and sustainable alternative for next-generation CAR T cell manufacturing. Here, we discuss how the use of non-viral vectors can address some of the limitations of the viral methods of gene transfer and allow us to deliver genetic information in a stable, effective and straightforward manner. In particular, we address the main transposon systems such as Sleeping Beauty (SB) and piggyBac (PB), the utilization of mRNA, and innovative approaches of nanotechnology like Lipid-based and Polymer-based DNA nanocarriers and nanovectors. We also describe the most relevant preclinical data that have recently led to the use of non-viral gene therapy in emerging clinical trials, and the related safety and efficacy aspects. We will also provide practical considerations for future trials to enable successful and safe cell therapy with non-viral methods for CAR T cell generation.
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Affiliation(s)
- Alex Moretti
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione Monza e Brianza per il Bambino e la sua Mamma (MBBM), Monza, Italy
| | - Marianna Ponzo
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione Monza e Brianza per il Bambino e la sua Mamma (MBBM), Monza, Italy
| | | | | | - Andrea Biondi
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione Monza e Brianza per il Bambino e la sua Mamma (MBBM), Monza, Italy
- Department of Pediatrics, University of Milano - Bicocca, Milan, Italy
- Clinica Pediatrica, University of Milano - Bicocca/Fondazione MBBM, Monza, Italy
| | - Chiara F. Magnani
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione Monza e Brianza per il Bambino e la sua Mamma (MBBM), Monza, Italy
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
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20
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Cosenza MR, Rodriguez-Martin B, Korbel JO. Structural Variation in Cancer: Role, Prevalence, and Mechanisms. Annu Rev Genomics Hum Genet 2022; 23:123-152. [DOI: 10.1146/annurev-genom-120121-101149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Somatic rearrangements resulting in genomic structural variation drive malignant phenotypes by altering the expression or function of cancer genes. Pan-cancer studies have revealed that structural variants (SVs) are the predominant class of driver mutation in most cancer types, but because they are difficult to discover, they remain understudied when compared with point mutations. This review provides an overview of the current knowledge of somatic SVs, discussing their primary roles, prevalence in different contexts, and mutational mechanisms. SVs arise throughout the life history of cancer, and 55% of driver mutations uncovered by the Pan-Cancer Analysis of Whole Genomes project represent SVs. Leveraging the convergence of cell biology and genomics, we propose a mechanistic classification of somatic SVs, from simple to highly complex DNA rearrangement classes. The actions of DNA repair and DNA replication processes together with mitotic errors result in a rich spectrum of SV formation processes, with cascading effects mediating extensive structural diversity after an initiating DNA lesion has formed. Thanks to new sequencing technologies, including the sequencing of single-cell genomes, open questions about the molecular triggers and the biomolecules involved in SV formation as well as their mutational rates can now be addressed. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
| | | | - Jan O. Korbel
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
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21
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Jia B, Jin J, Han M, Li B, Yuan Y. Directed yeast genome evolution by controlled introduction of trans-chromosomic structural variations. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1703-1717. [PMID: 35633480 DOI: 10.1007/s11427-021-2084-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/07/2022] [Indexed: 12/17/2022]
Abstract
Naturally occurring structural variations (SVs) are a considerable source of genomic variation that can reshape the 3D architecture of chromosomes. Controllable methods aimed at introducing the complex SVs and their related molecular mechanisms have remained farfetched. In this study, an SV-prone yeast strain was developed using Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) technology with two synthetic chromosomes, namely synV and synX. The biosynthesis of astaxanthin is used as a readout and a proof of concept for the application of SVs in industries. Our findings showed that complex SVs, including a pericentric inversion and a trans-chromosome translocation between synV and synX, resulted in two neo-chromosomes and a 2.7-fold yield of astaxanthin. Also, genetic targets were mapped, which resulted in a higher astaxanthin yield, thus demonstrating the SVs' ability to reorganize genetic information along the chromosomes. The rational design of trans-chromosome translocation and pericentric inversion enabled precise induction of these phenomena. Collectively, this study provides an effective tool to not only accelerate the directed genome evolution but also to reveal the mechanistic insight of complex SVs for altering phenotypes.
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Affiliation(s)
- Bin Jia
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Jin Jin
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Mingzhe Han
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Bingzhi Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Yingjin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
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22
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Almeida MV, Vernaz G, Putman AL, Miska EA. Taming transposable elements in vertebrates: from epigenetic silencing to domestication. Trends Genet 2022; 38:529-553. [DOI: 10.1016/j.tig.2022.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/20/2022]
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23
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Yu Z, Du M, Lu L. A Novel 16-Genes Signature Scoring System as Prognostic Model to Evaluate Survival Risk in Patients with Glioblastoma. Biomedicines 2022; 10:biomedicines10020317. [PMID: 35203526 PMCID: PMC8869708 DOI: 10.3390/biomedicines10020317] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/15/2022] Open
Abstract
Previous studies have found that gene expression levels are associated with prognosis and some genes can be used to predict the survival risk of glioblastoma (GBM) patients. However, most of them just built the survival-related gene signature, and personal survival risk can be evaluated only in group. This study aimed to find the prognostic survival related genes of GBM, and construct survival risk prediction model, which can be used to evaluate survival risk by individual. We collected gene expression data and clinical information from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Cox regression analysis and LASSO-cox regression analysis were performed to get survival-related genes and establish the overall survival prediction model. The ROC curve and Kaplan Meier analysis were used to evaluate the prediction ability of the model in training set and two independent cohorts. We also analyzed the biological functions of survival-related genes by GO and KEGG enrichment analysis. We identified 99 genes associated with overall survival and selected 16 genes (IGFBP2, GPRASP1, C1R, CHRM3, CLSTN2, NELL1, SEZ6L2, NMB, ICAM5, HPCAL4, SNAP91, PCSK1N, PGBD5, INA, UCHL1 and LHX6) to establish the survival risk prediction model. Multivariate Cox regression analysis indicted that the risk score could predict overall survival independent of age and gender. ROC analyses showed that our model was more robust than four existing signatures. The sixteen genes can also be potential transcriptional biomarkers and the model can assist doctors on clinical decision-making and personalized treatment of GBM patients.
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24
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Abstract
Ciliate genomes are replete with "junk" DNA insertions that require DNA splicing for their removal. What is the evolutionary source of these insertions? This Primer explores a new study in PLOS Biology that supports a classic model of transposon origins.
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Affiliation(s)
- Yi Feng
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, New York, United States of America
| | - Laura F. Landweber
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, New York, United States of America
- * E-mail:
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25
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Sabatella M, Mantere T, Waanders E, Neveling K, Mensenkamp AR, van Dijk F, Hehir‐Kwa JY, Derks R, Kwint M, O'Gorman L, Tropa Martins M, Gidding CEM, Lequin MH, Küsters B, Wesseling P, Nelen M, Biegel JA, Hoischen A, Jongmans MC, Kuiper RP. Optical genome mapping identifies a germline retrotransposon insertion in SMARCB1 in two siblings with atypical teratoid rhabdoid tumors. J Pathol 2021; 255:202-211. [PMID: 34231212 PMCID: PMC8519051 DOI: 10.1002/path.5755] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/28/2021] [Accepted: 07/04/2021] [Indexed: 11/29/2022]
Abstract
In a subset of pediatric cancers, a germline cancer predisposition is highly suspected based on clinical and pathological findings, but genetic evidence is lacking, which hampers genetic counseling and predictive testing in the families involved. We describe a family with two siblings born from healthy parents who were both neonatally diagnosed with atypical teratoid rhabdoid tumor (ATRT). This rare and aggressive pediatric tumor is associated with biallelic inactivation of SMARCB1, and in 30% of the cases, a predisposing germline mutation is involved. Whereas the tumors of both siblings showed loss of expression of SMARCB1 and acquired homozygosity of the locus, whole exome and whole genome sequencing failed to identify germline or somatic SMARCB1 pathogenic mutations. We therefore hypothesized that the insertion of a pathogenic repeat‐rich structure might hamper its detection, and we performed optical genome mapping (OGM) as an alternative strategy to identify structural variation in this locus. Using this approach, an insertion of ~2.8 kb within intron 2 of SMARCB1 was detected. Long‐range PCR covering this region remained unsuccessful, but PacBio HiFi genome sequencing identified this insertion to be a SINE‐VNTR‐Alu, subfamily E (SVA‐E) retrotransposon element, which was present in a mosaic state in the mother. This SVA‐E insertion disrupts correct splicing of the gene, resulting in loss of a functional allele. This case demonstrates the power of OGM and long‐read sequencing to identify genomic variations in high‐risk cancer‐predisposing genes that are refractory to detection with standard techniques, thereby completing the clinical and molecular diagnosis of such complex cases and greatly improving counseling and surveillance of the families involved. © 2021 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)
| | - Tuomo Mantere
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter OuluUniversity of OuluOuluFinland
| | - Esmé Waanders
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Kornelia Neveling
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
| | - Arjen R Mensenkamp
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Freerk van Dijk
- Princess Máxima Centre for Pediatric OncologyUtrechtThe Netherlands
| | | | - Ronnie Derks
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Michael Kwint
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Luke O'Gorman
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | | | | | - Maarten H Lequin
- Department of RadiologyUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Benno Küsters
- Department of PathologyRadboud University Medical CenterNijmegenThe Netherlands
| | - Pieter Wesseling
- Princess Máxima Centre for Pediatric OncologyUtrechtThe Netherlands
- Department of PathologyAmsterdam University Medical Centers, Location VUmc and Brain Tumor Center AmsterdamAmsterdamThe Netherlands
| | - Marcel Nelen
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Jacklyn A Biegel
- Department of Pathology and Laboratory MedicineChildren's Hospital, Los AngelesLos AngelesCAUSA
- Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Alexander Hoischen
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI)Radboud University Medical CenterNijmegenThe Netherlands
| | - Marjolijn C Jongmans
- Princess Máxima Centre for Pediatric OncologyUtrechtThe Netherlands
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Roland P Kuiper
- Princess Máxima Centre for Pediatric OncologyUtrechtThe Netherlands
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
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26
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Genomic Mosaicism Formed by Somatic Variation in the Aging and Diseased Brain. Genes (Basel) 2021; 12:genes12071071. [PMID: 34356087 PMCID: PMC8305509 DOI: 10.3390/genes12071071] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 12/22/2022] Open
Abstract
Over the past 20 years, analyses of single brain cell genomes have revealed that the brain is composed of cells with myriad distinct genomes: the brain is a genomic mosaic, generated by a host of DNA sequence-altering processes that occur somatically and do not affect the germline. As such, these sequence changes are not heritable. Some processes appear to occur during neurogenesis, when cells are mitotic, whereas others may also function in post-mitotic cells. Here, we review multiple forms of DNA sequence alterations that have now been documented: aneuploidies and aneusomies, smaller copy number variations (CNVs), somatic repeat expansions, retrotransposons, genomic cDNAs (gencDNAs) associated with somatic gene recombination (SGR), and single nucleotide variations (SNVs). A catch-all term of DNA content variation (DCV) has also been used to describe the overall phenomenon, which can include multiple forms within a single cell’s genome. A requisite step in the analyses of genomic mosaicism is ongoing technology development, which is also discussed. Genomic mosaicism alters one of the most stable biological molecules, DNA, which may have many repercussions, ranging from normal functions including effects of aging, to creating dysfunction that occurs in neurodegenerative and other brain diseases, most of which show sporadic presentation, unlinked to causal, heritable genes.
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27
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Beckermann TM, Luo W, Wilson CM, Veach RA, Wilson MH. Cognate restriction of transposition by piggyBac-like proteins. Nucleic Acids Res 2021; 49:8135-8144. [PMID: 34232995 DOI: 10.1093/nar/gkab578] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 06/16/2021] [Accepted: 06/26/2021] [Indexed: 11/14/2022] Open
Abstract
Mobile genetic elements have been harnessed for gene transfer for a wide variety of applications including generation of stable cell lines, recombinant protein production, creation of transgenic animals, and engineering cell and gene therapy products. The piggyBac transposon family includes transposase or transposase-like proteins from a variety of species including insect, bat and human. Recently, human piggyBac transposable element derived 5 (PGBD5) protein was reported to be able to transpose piggyBac transposons in human cells raising possible safety concerns for piggyBac-mediated gene transfer applications. We evaluated three piggyBac-like proteins across species including piggyBac (insect), piggyBat (bat) and PGBD5 (human) for their ability to mobilize piggyBac transposons in human cells. We observed a lack of cross-species transposition activity. piggyBac and piggyBat activity was restricted to their cognate transposons. PGBD5 was unable to mobilize piggyBac transposons based on excision, colony count and plasmid rescue analysis, and it was unable to bind piggyBac terminal repeats. Within the piggyBac family, we observed a lack of cross-species activity and found that PGBD5 was unable to bind, excise or integrate piggyBac transposons in human cells. Transposition activity appears restricted within species within the piggyBac family of mobile genetic elements.
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Affiliation(s)
- Thomas M Beckermann
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Veterans Affairs, Tennessee Valley Health Services, Nashville, TN 37212, USA
| | - Wentian Luo
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Veterans Affairs, Tennessee Valley Health Services, Nashville, TN 37212, USA
| | - Catherine M Wilson
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ruth Ann Veach
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Veterans Affairs, Tennessee Valley Health Services, Nashville, TN 37212, USA
| | - Matthew H Wilson
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Veterans Affairs, Tennessee Valley Health Services, Nashville, TN 37212, USA.,Departments of Pharmacology and Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
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28
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Guérineau M, Bessa L, Moriau S, Lescop E, Bontems F, Mathy N, Guittet E, Bischerour J, Bétermier M, Morellet N. The unusual structure of the PiggyMac cysteine-rich domain reveals zinc finger diversity in PiggyBac-related transposases. Mob DNA 2021; 12:12. [PMID: 33926516 PMCID: PMC8086355 DOI: 10.1186/s13100-021-00240-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/09/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Transposons are mobile genetic elements that colonize genomes and drive their plasticity in all organisms. DNA transposon-encoded transposases bind to the ends of their cognate transposons and catalyze their movement. In some cases, exaptation of transposon genes has allowed novel cellular functions to emerge. The PiggyMac (Pgm) endonuclease of the ciliate Paramecium tetraurelia is a domesticated transposase from the PiggyBac family. It carries a core catalytic domain typical of PiggyBac-related transposases and a short cysteine-rich domain (CRD), flanked by N- and C-terminal extensions. During sexual processes Pgm catalyzes programmed genome rearrangements (PGR) that eliminate ~ 30% of germline DNA from the somatic genome at each generation. How Pgm recognizes its DNA cleavage sites in chromatin is unclear and the structure-function relationships of its different domains have remained elusive. RESULTS We provide insight into Pgm structure by determining the fold adopted by its CRD, an essential domain required for PGR. Using Nuclear Magnetic Resonance, we show that the Pgm CRD binds two Zn2+ ions and forms an unusual binuclear cross-brace zinc finger, with a circularly permutated treble-clef fold flanked by two flexible arms. The Pgm CRD structure clearly differs from that of several other PiggyBac-related transposases, among which is the well-studied PB transposase from Trichoplusia ni. Instead, the arrangement of cysteines and histidines in the primary sequence of the Pgm CRD resembles that of active transposases from piggyBac-like elements found in other species and of human PiggyBac-derived domesticated transposases. We show that, unlike the PB CRD, the Pgm CRD does not bind DNA. Instead, it interacts weakly with the N-terminus of histone H3, whatever its lysine methylation state. CONCLUSIONS The present study points to the structural diversity of the CRD among transposases from the PiggyBac family and their domesticated derivatives, and highlights the diverse interactions this domain may establish with chromatin, from sequence-specific DNA binding to contacts with histone tails. Our data suggest that the Pgm CRD fold, whose unusual arrangement of cysteines and histidines is found in all PiggyBac-related domesticated transposases from Paramecium and Tetrahymena, was already present in the ancestral active transposase that gave rise to ciliate domesticated proteins.
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Affiliation(s)
- Marc Guérineau
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
| | - Luiza Bessa
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
- Present addresses: Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Séverine Moriau
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
| | - Ewen Lescop
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
| | - François Bontems
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
| | - Nathalie Mathy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
- Reproduction et Développement des Plantes UMR 5667, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon Cedex 07, France
| | - Eric Guittet
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
| | - Julien Bischerour
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
| | - Mireille Bétermier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France.
| | - Nelly Morellet
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France.
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Hoffman LM, Richardson EA, Ho B, Margol A, Reddy A, Lafay-Cousin L, Chi S, Slavc I, Judkins A, Hasselblatt M, Bourdeaut F, Frühwald MC, Vibhakar R, Bouffet E, Huang A. Advancing biology-based therapeutic approaches for atypical teratoid rhabdoid tumors. Neuro Oncol 2021; 22:944-954. [PMID: 32129445 DOI: 10.1093/neuonc/noaa046] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Atypical teratoid rhabdoid tumor (ATRT) is a rare, highly malignant central nervous system cancer arising in infants and younger children, historically considered to be homogeneous, monogenic, and incurable. Recent use of intensified therapies has modestly improved survival for ATRT; however, a majority of patients will still succumb to their disease. While ATRTs almost universally exhibit loss of SMARCB1 (BAF47/INI1/SNF5), recent whole genome, transcriptome, and epigenomic analyses of large cohorts reveal previously underappreciated molecular heterogeneity. These discoveries provide novel insights into how SMARCB1 loss drives oncogenesis and confer specific therapeutic vulnerabilities, raising exciting prospects for molecularly stratified treatment for patients with ATRT.
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Affiliation(s)
- Lindsey M Hoffman
- Center for Cancer and Blood Disorders, Phoenix Children's Hospital, Phoenix, Arizona, USA
| | - Elizabeth Anne Richardson
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ben Ho
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ashley Margol
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, California, USA.,Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Alyssa Reddy
- Departments of Neurology and Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Lucie Lafay-Cousin
- Department of Pediatric Hematology Oncology and Blood and Marrow Transplantation, Alberta Children's Hospital, Calgary, Alberta, Canada.,Department of Paediatrics and Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Susan Chi
- Pediatric Medical Neuro-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts, USA.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Irene Slavc
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria.,Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Alexander Judkins
- Center for Personalized Medicine, Children's Hospital of Los Angeles.,Pathology and Laboratory Medicine, Children's Hospital of Los Angeles.,Department of Pathology, Keck School of Medicine University of Southern California, Los Angeles, California, USA
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Franck Bourdeaut
- Curie Institute, Integrated Cancer Research Site, Paris, France.,Departments of Genetics and of Oncopediatry and Young Adults, Curie Institute, Paris, France.,INSERM U830, Laboratory of Translational Research in Pediatric Oncology, SIREDO Pediatric Oncology Center, Curie Institute, Paris, France
| | - Michael C Frühwald
- Swabian Children's Cancer Center, University Children's Hospital, University Hospital Augsburg, Augsburg, Germany.,Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, University of Münster, Münster, Germany.,EU-RHAB Registry Working Group, Augsburg, Germany
| | - Rajeev Vibhakar
- Department of Pediatrics, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA.,Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, Colorado, USA.,Department of Neurosurgery, University of Colorado Denver, Aurora, Colorado, USA
| | - Eric Bouffet
- Child Health Evaluative Sciences, SickKids Research Institute, Toronto, Ontario, Canada.,Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada.,Division of Hematology/Oncology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Annie Huang
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada.,Division of Hematology/Oncology, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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30
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Helou L, Beauclair L, Dardente H, Piégu B, Tsakou-Ngouafo L, Lecomte T, Kentsis A, Pontarotti P, Bigot Y. The piggyBac-derived protein 5 (PGBD5) transposes both the closely and the distantly related piggyBac-like elements Tcr-pble and Ifp2. J Mol Biol 2021; 433:166839. [PMID: 33539889 DOI: 10.1016/j.jmb.2021.166839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 12/21/2020] [Accepted: 01/14/2021] [Indexed: 12/16/2022]
Abstract
The vertebrate piggyBac derived transposase 5 (PGBD5) encodes a domesticated transposase, which is active and able to transpose its distantly related piggyBac-like element (pble), Ifp2. This raised the question whether PGBD5 would be more effective at mobilizing a phylogenetically closely related pble element. We aimed to identify the pble most closely related to the pgbd5 gene. We updated the landscape of vertebrate pgbd genes to develop efficient filters and identify the most closely related pble to each of these genes. We found that Tcr-pble is phylogenetically the closest pble to the pgbd5 gene. Furthermore, we evaluated the capacity of two murine and human PGBD5 isoforms, Mm523 and Hs524, to transpose both Tcr-pble and Ifp2 elements. We found that both pbles could be transposed by Mm523 with similar efficiency. However, integrations of both pbles occurred through both proper transposition and improper PGBD5-dependent recombination. This suggested that the ability of PGBD5 to bind both pbles may not be based on the primary sequence of element ends, but may involve recognition of inner DNA motifs, possibly related to palindromic repeats. In agreement with this hypothesis, we identified internal palindromic repeats near the end of 24 pble sequences, which display distinct sequences.
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Affiliation(s)
- Laura Helou
- UMR INRAE 0085, CNRS 7247, Physiologie de la Reproduction et des Comportements, Centre INRA Val de Loire, 37380 Nouzilly, France
| | - Linda Beauclair
- UMR INRAE 0085, CNRS 7247, Physiologie de la Reproduction et des Comportements, Centre INRA Val de Loire, 37380 Nouzilly, France
| | - Hugues Dardente
- UMR INRAE 0085, CNRS 7247, Physiologie de la Reproduction et des Comportements, Centre INRA Val de Loire, 37380 Nouzilly, France
| | - Benoît Piégu
- UMR INRAE 0085, CNRS 7247, Physiologie de la Reproduction et des Comportements, Centre INRA Val de Loire, 37380 Nouzilly, France
| | - Louis Tsakou-Ngouafo
- UMR MEPHI D-258, I, IRD, Aix Marseille Université, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; CNRS SNC 5039, 13005 Marseille, France
| | | | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, Cornell University, New York, NY, USA; Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pierre Pontarotti
- UMR INRAE 0085, CNRS 7247, Physiologie de la Reproduction et des Comportements, Centre INRA Val de Loire, 37380 Nouzilly, France; CNRS SNC 5039, 13005 Marseille, France
| | - Yves Bigot
- UMR INRAE 0085, CNRS 7247, Physiologie de la Reproduction et des Comportements, Centre INRA Val de Loire, 37380 Nouzilly, France.
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31
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Helou L, Beauclair L, Dardente H, Arensburger P, Buisine N, Jaszczyszyn Y, Guillou F, Lecomte T, Kentsis A, Bigot Y. The C-terminal Domain of piggyBac Transposase Is Not Required for DNA Transposition. J Mol Biol 2021; 433:166805. [PMID: 33450253 DOI: 10.1016/j.jmb.2020.166805] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 12/29/2020] [Indexed: 12/21/2022]
Abstract
PiggyBac(PB)-like elements (pble) are members of a eukaryotic DNA transposon family. This family is of interest to evolutionary genomics because pble transposases have been domesticated at least 9 times in vertebrates. The amino acid sequence of pble transposases can be split into three regions: an acidic N-terminal domain (~100 aa), a central domain (~400 aa) containing a DD[D/E] catalytic triad, and a cysteine-rich domain (CRD; ~90 aa). Two recent reports suggested that a functional CRD is required for pble transposase activity. Here we found that two CRD-deficient pble transposases, a PB variant and an isoform encoded by the domesticated PB-derived vertebrate transposase gene 5 (pgbd5) trigger transposition of the Ifp2 pble. When overexpressed in HeLa cells, these CRD-deficient transposases can insert Ifp2 elements with proper and improper transposon ends, associated with deleterious effects on cells. Finally, we found that mouse CRD-deficient transposase Pgbd5, as well as PB, do not insert pbles at random into chromosomes. Transposition events occurred more often in genic regions, in the neighbourhood of the transcription start sites and were often found in genes predominantly expressed in the human central nervous system.
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Affiliation(s)
- Laura Helou
- PRC, UMR INRAE 0085, CNRS 7247, Centre INRAE Val de Loire, 37380 Nouzilly, France
| | - Linda Beauclair
- PRC, UMR INRAE 0085, CNRS 7247, Centre INRAE Val de Loire, 37380 Nouzilly, France
| | - Hugues Dardente
- PRC, UMR INRAE 0085, CNRS 7247, Centre INRAE Val de Loire, 37380 Nouzilly, France
| | - Peter Arensburger
- Biological Sciences Department, California State Polytechnic University, Pomona, CA 91768, USA
| | - Nicolas Buisine
- UMR CNRS 7221, Muséum National d'Histoire Naturelle, 75005 Paris, France
| | - Yan Jaszczyszyn
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Florian Guillou
- PRC, UMR INRAE 0085, CNRS 7247, Centre INRAE Val de Loire, 37380 Nouzilly, France
| | | | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, Cornell University, New York, NY, USA; Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yves Bigot
- PRC, UMR INRAE 0085, CNRS 7247, Centre INRAE Val de Loire, 37380 Nouzilly, France.
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32
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Ahmadi A, De Toma I, Vilor-Tejedor N, Eftekhariyan Ghamsari MR, Sadeghi I. Transposable elements in brain health and disease. Ageing Res Rev 2020; 64:101153. [PMID: 32977057 DOI: 10.1016/j.arr.2020.101153] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 07/22/2020] [Accepted: 08/19/2020] [Indexed: 12/17/2022]
Abstract
Transposable elements (TEs) occupy a large fraction of the human genome but only a small proportion of these elements are still active today. Recent works have suggested that TEs are expressed and active in the brain, challenging the dogma that neuronal genomes are static and revealing that they are susceptible to somatic genomic alterations. These new findings have major implications for understanding the neuroplasticity of the brain, which could hypothetically have a role in behavior and cognition, and contribute to vulnerability to disease. As active TEs could induce genetic diversity and mutagenesis, their influences on human brain development and diseases are of great interest. In this review, we will focus on the active TEs in the human genome and discuss in detail their impacts on human brain development. Furthermore, the association between TEs and brain-related diseases is discussed.
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Abstract
INTRODUCTION Ependymoma is the third most common malignant pediatric brain tumor. Although the biology that drives ependymoma is slowly being unraveled, the ability to translate these findings to clinical care remains an ongoing challenge. Epigenetic alterations appear to play a central role in the development of molecular classification of ependymoma. METHODS We reviewed the published literature available describing genetic and epigenetic underpinnings of ependymoma that have been reported to date and have summarized the information regarding genetic drivers of ependymoma that may point us toward therapeutic strategies. RESULTS Ependymoma is a molecularly heterogeneous disease which has now been divided into at least nine distinct molecular subtypes based on DNA methylation and gene expression profiling. DNA methylation has emerged as an effective tool for classification of brain tumors alongside histopathology and other molecular diagnostics. There have been large retrospective cohorts describing molecular subgroup identity as a powerful independent predictor of outcome. There is limited published data on prospective trials to date however this is forthcoming which will lead to molecular stratification in the next generation of clinical studies. CONCLUSION This is a review of recent advancements in our understanding of the epigenetic basis of ependymoma and discussion of how these findings reveal potential therapeutic opportunities.
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34
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Structural basis of seamless excision and specific targeting by piggyBac transposase. Nat Commun 2020; 11:3446. [PMID: 32651359 PMCID: PMC7351741 DOI: 10.1038/s41467-020-17128-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/02/2020] [Indexed: 12/16/2022] Open
Abstract
The piggyBac DNA transposon is used widely in genome engineering applications. Unlike other transposons, its excision site can be precisely repaired without leaving footprints and it integrates specifically at TTAA tetranucleotides. We present cryo-EM structures of piggyBac transpososomes: a synaptic complex with hairpin DNA intermediates and a strand transfer complex capturing the integration step. The results show that the excised TTAA hairpin intermediate and the TTAA target adopt essentially identical conformations, providing a mechanistic link connecting the two unique properties of piggyBac. The transposase forms an asymmetric dimer in which the two central domains synapse the ends while two C-terminal domains form a separate dimer that contacts only one transposon end. In the strand transfer structure, target DNA is severely bent and the TTAA target is unpaired. In-cell data suggest that asymmetry promotes synaptic complex formation, and modifying ends with additional transposase binding sites stimulates activity.
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35
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Kentsis A. Why do young people get cancer? Pediatr Blood Cancer 2020; 67:e28335. [PMID: 32391946 PMCID: PMC7582786 DOI: 10.1002/pbc.28335] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 12/12/2022]
Abstract
Oncologists and cancer biologists are frequently confronted by the question of what causes cancer? This is particularly vexing for cancers affecting children and young adults who have had limited exposure to environmental mutagens and the effects of aging. Here, I focus on a general framework of the causes of early-onset cancer development in children and young adults by relating inherited and constitutional cancer predisposition, oncogenic pathogens, and developmental mutations. This framework has implications not only for mechanistic investigation of young cancers, but should also clarify improved strategies for their treatment, screening, and potential prevention.
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Affiliation(s)
- Alex Kentsis
- Sloan Kettering Institute and Department of Pediatrics, Weill Medical College of Cornell University and Memorial Sloan Kettering Cancer Center, New York, New York
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36
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Abstract
A new hypothesis suggests that somatic genome remodeling during normal development can cause mutations that explain many early onset cancers in children and adults.
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Affiliation(s)
- Alex Kentsis
- Sloan Kettering Institute and Department of Pediatrics, Weill Medical College of Cornell University and Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Steven A. Frank
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, United States
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37
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Colaprico A, Olsen C, Bailey MH, Odom GJ, Terkelsen T, Silva TC, Olsen AV, Cantini L, Zinovyev A, Barillot E, Noushmehr H, Bertoli G, Castiglioni I, Cava C, Bontempi G, Chen XS, Papaleo E. Interpreting pathways to discover cancer driver genes with Moonlight. Nat Commun 2020; 11:69. [PMID: 31900418 PMCID: PMC6941958 DOI: 10.1038/s41467-019-13803-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 11/22/2019] [Indexed: 12/28/2022] Open
Abstract
Cancer driver gene alterations influence cancer development, occurring in oncogenes, tumor suppressors, and dual role genes. Discovering dual role cancer genes is difficult because of their elusive context-dependent behavior. We define oncogenic mediators as genes controlling biological processes. With them, we classify cancer driver genes, unveiling their roles in cancer mechanisms. To this end, we present Moonlight, a tool that incorporates multiple -omics data to identify critical cancer driver genes. With Moonlight, we analyze 8000+ tumor samples from 18 cancer types, discovering 3310 oncogenic mediators, 151 having dual roles. By incorporating additional data (amplification, mutation, DNA methylation, chromatin accessibility), we reveal 1000+ cancer driver genes, corroborating known molecular mechanisms. Additionally, we confirm critical cancer driver genes by analysing cell-line datasets. We discover inactivation of tumor suppressors in intron regions and that tissue type and subtype indicate dual role status. These findings help explain tumor heterogeneity and could guide therapeutic decisions.
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Affiliation(s)
- Antonio Colaprico
- Interuniversity Institute of Bioinformatics in Brussels (IB)2, Brussels, Belgium.
- Machine Learning Group, Université Libre de Bruxelles (ULB), Brussels, Belgium.
- Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA.
| | - Catharina Olsen
- Interuniversity Institute of Bioinformatics in Brussels (IB)2, Brussels, Belgium
- Machine Learning Group, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Center for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, UZ Brussel, Laarbeeklaan 101, 1090, Brussels, Belgium
- Brussels Interuniversity Genomics High Throughput core (BRIGHTcore), VUB-ULB, Laarbeeklaan 101, 1090, Brussels, Belgium
| | - Matthew H Bailey
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
- McDonnell Genome Institute, Washington University, St. Louis, MO, 63108, USA
| | - Gabriel J Odom
- Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
- Department of Biostatistics, Stempel College of Public Health, Florida International University, Miami, FL, 33199, USA
| | - Thilde Terkelsen
- Computational Biology Laboratory, and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Tiago C Silva
- Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
- Department of Genetics, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
| | - André V Olsen
- Computational Biology Laboratory, and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Laura Cantini
- Institut Curie, 26 rue d'Ulm, F-75248, Paris, France
- INSERM, U900, Paris, F-75248, France
- Mines ParisTech, Fontainebleau, F-77300, France
- Computational Systems Biology Team, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, Ecole Normale Supérieure, Paris Sciences et Lettres Research University, 75005, Paris, France
| | - Andrei Zinovyev
- Institut Curie, 26 rue d'Ulm, F-75248, Paris, France
- INSERM, U900, Paris, F-75248, France
- Mines ParisTech, Fontainebleau, F-77300, France
| | - Emmanuel Barillot
- Institut Curie, 26 rue d'Ulm, F-75248, Paris, France
- INSERM, U900, Paris, F-75248, France
- Mines ParisTech, Fontainebleau, F-77300, France
| | - Houtan Noushmehr
- Department of Genetics, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
- Department of Neurosurgery, Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Gloria Bertoli
- Institute of Molecular Bioimaging and Physiology of the National Research Council (IBFM-CNR), Milan, Italy
| | - Isabella Castiglioni
- Institute of Molecular Bioimaging and Physiology of the National Research Council (IBFM-CNR), Milan, Italy
| | - Claudia Cava
- Institute of Molecular Bioimaging and Physiology of the National Research Council (IBFM-CNR), Milan, Italy
| | - Gianluca Bontempi
- Interuniversity Institute of Bioinformatics in Brussels (IB)2, Brussels, Belgium
- Machine Learning Group, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Xi Steven Chen
- Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA.
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
| | - Elena Papaleo
- Computational Biology Laboratory, and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark.
- Translational Disease System Biology, Faculty of Health and Medical Science, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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Zhang J, Guo S, Ji G, Zhao H, Sun H, Ren Y, Tian S, Li M, Gong G, Zhang H, Xu Y. A unique chromosome translocation disrupting ClWIP1 leads to gynoecy in watermelon. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:265-277. [PMID: 31529543 DOI: 10.1111/tpj.14537] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/27/2019] [Accepted: 09/02/2019] [Indexed: 05/20/2023]
Abstract
To understand sex determination in watermelon (Citrullus lanatus), a spontaneous gynoecious watermelon mutant, XHBGM, was selected from the monoecious wild type XHB. Using map-based cloning, resequencing and fluorescence in situ hybridization analysis, a unique chromosome translocation between chromosome 2 and chromosome 3 was found in XHBGM. Based on the breakpoint location in chromosome 2, a putative C2H2 zinc finger transcription factor gene, ClWIP1 (gene ID Cla008537), an orthologue of the melon gynoecy gene CmWIP1, was disrupted. Using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated system 9 to edit ClWIP1, we obtained gynoecious watermelon lines. Functional studies showed that ClWIP1 is expressed specifically in carpel primordia and is related to the abortion of carpel primordia in early floral development. To identify the cellular and metabolic processes associated with ClWIP1, we compared the shoot apex transcriptomes of two gynoecious mutants and their corresponding wild types. Transcriptome analysis showed that differentially expressed genes related to the ethylene and cytokinin pathways were upregulated in the gynoecious mutants. This study explores the molecular mechanism of sex determination in watermelon and provides a theoretical and technical basis for breeding elite gynoecious watermelon lines.
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Affiliation(s)
- Jie Zhang
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Shaogui Guo
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Gaojie Ji
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
- Chinese Academy of Agricultural Engineering Planning and Design, Beijing, 100125, China
| | - Hong Zhao
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Honghe Sun
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Yi Ren
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Shouwei Tian
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Maoying Li
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Guoyi Gong
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Haiying Zhang
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Yong Xu
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
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39
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Koche RP, Rodriguez-Fos E, Helmsauer K, Burkert M, MacArthur IC, Maag J, Chamorro R, Munoz-Perez N, Puiggròs M, Dorado Garcia H, Bei Y, Röefzaad C, Bardinet V, Szymansky A, Winkler A, Thole T, Timme N, Kasack K, Fuchs S, Klironomos F, Thiessen N, Blanc E, Schmelz K, Künkele A, Hundsdörfer P, Rosswog C, Theissen J, Beule D, Deubzer H, Sauer S, Toedling J, Fischer M, Hertwig F, Schwarz RF, Eggert A, Torrents D, Schulte JH, Henssen AG. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma. Nat Genet 2019; 52:29-34. [PMID: 31844324 DOI: 10.1038/s41588-019-0547-z] [Citation(s) in RCA: 159] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/12/2019] [Indexed: 01/25/2023]
Abstract
Extrachromosomal circularization of DNA is an important genomic feature in cancer. However, the structure, composition and genome-wide frequency of extrachromosomal circular DNA have not yet been profiled extensively. Here, we combine genomic and transcriptomic approaches to describe the landscape of extrachromosomal circular DNA in neuroblastoma, a tumor arising in childhood from primitive cells of the sympathetic nervous system. Our analysis identifies and characterizes a wide catalog of somatically acquired and undescribed extrachromosomal circular DNAs. Moreover, we find that extrachromosomal circular DNAs are an unanticipated major source of somatic rearrangements, contributing to oncogenic remodeling through chimeric circularization and reintegration of circular DNA into the linear genome. Cancer-causing lesions can emerge out of circle-derived rearrangements and are associated with adverse clinical outcome. It is highly probable that circle-derived rearrangements represent an ongoing mutagenic process. Thus, extrachromosomal circular DNAs represent a multihit mutagenic process, with important functional and clinical implications for the origins of genomic remodeling in cancer.
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Affiliation(s)
- Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Elias Rodriguez-Fos
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Konstantin Helmsauer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Martin Burkert
- Department of Biology, Humboldt University, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ian C MacArthur
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jesper Maag
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rocio Chamorro
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Natalia Munoz-Perez
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Montserrat Puiggròs
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Heathcliff Dorado Garcia
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Yi Bei
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Claudia Röefzaad
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Victor Bardinet
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annabell Szymansky
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annika Winkler
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Theresa Thole
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Natalie Timme
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Katharina Kasack
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steffen Fuchs
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Filippos Klironomos
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Eric Blanc
- Berlin Institute of Health, Berlin, Germany
| | - Karin Schmelz
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annette Künkele
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Hundsdörfer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carolina Rosswog
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jessica Theissen
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Hedwig Deubzer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Joern Toedling
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany
| | - Falk Hertwig
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland F Schwarz
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Torrents
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Johannes H Schulte
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anton G Henssen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany. .,Berlin Institute of Health, Berlin, Germany. .,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany.
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40
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Bétermier M, Borde V, de Villartay JP. Coupling DNA Damage and Repair: an Essential Safeguard during Programmed DNA Double-Strand Breaks? Trends Cell Biol 2019; 30:87-96. [PMID: 31818700 DOI: 10.1016/j.tcb.2019.11.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 12/31/2022]
Abstract
DNA double-strand breaks (DSBs) are the most toxic DNA lesions given their oncogenic potential. Nevertheless, programmed DSBs (prDSBs) contribute to several biological processes. Formation of prDSBs is the 'price to pay' to achieve these essential biological functions. Generated by domesticated PiggyBac transposases, prDSBs have been integrated in the life cycle of ciliates. Created by Spo11 during meiotic recombination, they constitute a driving force of evolution and ensure balanced chromosome content for successful reproduction. Produced by the RAG1/2 recombinase, they are required for the development of the adaptive immune system in many species. The coevolution of processes that couple introduction of prDSBs to their accurate repair may constitute an effective safeguard against genomic instability.
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Affiliation(s)
- Mireille Bétermier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.
| | - Valérie Borde
- Institut Curie, CNRS UMR3244, Sorbonne Université, Paris, France.
| | - Jean-Pierre de Villartay
- Laboratory of Genome Dynamics in the Immune System, INSERM UMR1163, Université Paris Descartes Sorbonne Paris Cité, Institut Imagine, Paris, France.
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41
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42
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Ortiz MV, Ahmed S, Burns M, Henssen AG, Hollmann TJ, MacArthur I, Gunasekera S, Gaewsky L, Bradwin G, Ryan J, Letai A, He Y, Naranjo A, Chi YY, LaQuaglia M, Heaton T, Cifani P, Dome JS, Gadd S, Perlman E, Mullen E, Steen H, Kentsis A. Prohibitin is a prognostic marker and therapeutic target to block chemotherapy resistance in Wilms' tumor. JCI Insight 2019; 4:127098. [PMID: 31391345 DOI: 10.1172/jci.insight.127098] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 07/09/2019] [Indexed: 01/05/2023] Open
Abstract
Wilms' tumor is the most common type of childhood kidney cancer. To improve risk stratification and identify novel therapeutic targets for patients with Wilms' tumor, we used high-resolution mass spectrometry proteomics to identify urine tumor markers associated with Wilms' tumor relapse. We determined the urine proteomes at diagnosis of 49 patients with Wilms' tumor, non-Wilms' tumor renal tumors, and age-matched controls, leading to the quantitation of 6520 urine proteins. Supervised analysis revealed specific urine markers of renal rhabdoid tumors, kidney clear cell sarcomas, renal cell carcinomas as well as those detected in patients with cured and relapsed Wilms' tumor. In particular, urine prohibitin was significantly elevated at diagnosis in patients with relapsed as compared with cured Wilms' tumor. In a validation cohort of 139 patients, a specific urine prohibitin ELISA demonstrated that prohibitin concentrations greater than 998 ng/mL at diagnosis were significantly associated with ultimate Wilms' tumor relapse. Immunohistochemical analysis revealed that prohibitin was highly expressed in primary Wilms' tumor specimens and associated with disease stage. Using functional genetic experiments, we found that prohibitin was required for the growth and survival of Wilms' tumor cells. Overexpression of prohibitin was sufficient to block intrinsic mitochondrial apoptosis and to cause resistance to diverse chemotherapy drugs, at least in part by dysregulating factors that control apoptotic cytochrome c release from mitochondrial cristae. Thus, urine prohibitin may improve therapy stratification, noninvasive monitoring of treatment response, and early disease detection. In addition, therapeutic targeting of chemotherapy resistance induced by prohibitin dysregulation may offer improved therapies for patients with Wilms' and other relapsed or refractory tumors.
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Affiliation(s)
- Michael V Ortiz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Saima Ahmed
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Melissa Burns
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Anton G Henssen
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Travis J Hollmann
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ian MacArthur
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Shehana Gunasekera
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Lyvia Gaewsky
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Gary Bradwin
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Jeremy Ryan
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Anthony Letai
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Ying He
- Children's Oncology Group Statistics and Data Center, Department of Biostatistics, University of Florida, Gainesville, Florida, USA
| | - Arlene Naranjo
- Children's Oncology Group Statistics and Data Center, Department of Biostatistics, University of Florida, Gainesville, Florida, USA
| | - Yueh-Yun Chi
- Children's Oncology Group Statistics and Data Center, Department of Biostatistics, University of Florida, Gainesville, Florida, USA
| | - Michael LaQuaglia
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Todd Heaton
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jeffrey S Dome
- Center for Cancer and Blood Disorders, Children's National Health System, Washington, DC, USA
| | - Samantha Gadd
- Department of Pathology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Elizabeth Perlman
- Department of Pathology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | | | - Hanno Steen
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Alex Kentsis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Cornell Medical College, Cornell University, New York, New York, USA
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43
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Schleicher EM, Galvan AM, Imamura-Kawasawa Y, Moldovan GL, Nicolae CM. PARP10 promotes cellular proliferation and tumorigenesis by alleviating replication stress. Nucleic Acids Res 2019; 46:8908-8916. [PMID: 30032250 PMCID: PMC6158756 DOI: 10.1093/nar/gky658] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/10/2018] [Indexed: 12/18/2022] Open
Abstract
During carcinogenesis, cells are exposed to increased replication stress due to replication fork arrest at sites of DNA lesions and difficult to replicate genomic regions. Efficient fork restart and DNA repair are important for cancer cell proliferation. We previously showed that the ADP-ribosyltransferase PARP10 interacts with the replication protein proliferating cell nuclear antigen and promotes lesion bypass by recruiting specialized, non-replicative DNA polymerases. Here, we show that PARP10 is overexpressed in a large proportion of human tumors. To understand the role of PARP10 in cellular transformation, we inactivated PARP10 in HeLa cancer cells by CRISPR/Cas9-mediated gene knockout, and overexpressed it in non-transformed RPE-1 cells. We found that PARP10 promotes cellular proliferation, and its overexpression alleviates cellular sensitivity to replication stress and fosters the restart of stalled replication forks. Importantly, mouse xenograft studies showed that loss of PARP10 reduces the tumorigenesis activity of HeLa cells, while its overexpression results in tumor formation by non-transformed RPE-1 cells. Our findings indicate that PARP10 promotes cellular transformation, potentially by alleviating replication stress and suggest that targeting PARP10 may represent a novel therapeutic approach.
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Affiliation(s)
- Emily M Schleicher
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Adri M Galvan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Yuka Imamura-Kawasawa
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.,Department of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.,Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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44
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MacArthur IC, Bei Y, Garcia HD, Ortiz MV, Toedling J, Klironomos F, Rolff J, Eggert A, Schulte JH, Kentsis A, Henssen AG. Prohibitin promotes de-differentiation and is a potential therapeutic target in neuroblastoma. JCI Insight 2019; 5:127130. [PMID: 30998507 DOI: 10.1172/jci.insight.127130] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Gain of the long arm of chromosome 17 (17q) is a cytogenetic hallmark of high-risk neuroblastoma, yet its contribution to neuroblastoma pathogenesis remains incompletely understood. Combining whole-genome and RNA sequencing of neuroblastomas, we identified the prohibitin (PHB) gene as highly expressed in tumors with 17q gain. High PHB expression correlated with poor prognosis and was associated with loss of gene expression programs promoting neuronal development and differentiation. PHB depletion induced differentiation and apoptosis and slowed cell cycle progression of neuroblastoma cells, at least in part through impaired ERK1/2 activation. Conversely, ectopic expression of PHB was sufficient to increase proliferation of neuroblastoma cells and was associated with suppression of markers associated with neuronal differentiation and favorable neuroblastoma outcome. Thus, PHB is a 17q oncogene in neuroblastoma that promotes tumor cell proliferation, and de-differentiation.
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Affiliation(s)
- Ian C MacArthur
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Medical Scientist Training Program, Albert Einstein College of Medicine, New York, New York, USA
| | - Yi Bei
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Heathcliff Dorado Garcia
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Michael V Ortiz
- Department of Pediatrics and Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Joern Toedling
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Filippos Klironomos
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jana Rolff
- Experimental Pharmacology and Oncology, Berlin, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium, Heidelberg, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Johannes H Schulte
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium, Heidelberg, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Alex Kentsis
- Department of Pediatrics and Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Departments of Pharmacology, Pediatrics, and Physiology and Biophysics, Weill Medical College of Cornell University, New York, New York, USA
| | - Anton G Henssen
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium, Heidelberg, Germany.,Berlin Institute of Health, Berlin, Germany.,Experimental and Clinical Research Center of the Max Delbrück Center and Charité Berlin, Berlin, Germany
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45
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Ly P, Brunner SF, Shoshani O, Kim DH, Lan W, Pyntikova T, Flanagan AM, Behjati S, Page DC, Campbell PJ, Cleveland DW. Chromosome segregation errors generate a diverse spectrum of simple and complex genomic rearrangements. Nat Genet 2019; 51:705-715. [PMID: 30833795 PMCID: PMC6441390 DOI: 10.1038/s41588-019-0360-8] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 01/23/2019] [Indexed: 01/05/2023]
Abstract
Cancer genomes are frequently characterized by numerical and structural chromosomal abnormalities. Here we integrated a centromere-specific inactivation approach with selection for a conditionally essential gene, a strategy termed CEN-SELECT, to systematically interrogate the structural landscape of mis-segregated chromosomes. We show that single-chromosome mis-segregation into a micronucleus can directly trigger a broad spectrum of genomic rearrangement types. Cytogenetic profiling revealed that mis-segregated chromosomes exhibit 120-fold-higher susceptibility to developing seven major categories of structural aberrations, including translocations, insertions, deletions, and complex reassembly through chromothripsis coupled to classical non-homologous end joining. Whole-genome sequencing of clonally propagated rearrangements identified random patterns of clustered breakpoints with copy-number alterations resulting in interspersed gene deletions and extrachromosomal DNA amplification events. We conclude that individual chromosome segregation errors during mitotic cell division are sufficient to drive extensive structural variations that recapitulate genomic features commonly associated with human disease.
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Affiliation(s)
- Peter Ly
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | | | - Ofer Shoshani
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Dong Hyun Kim
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Weijie Lan
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | | | - Adrienne M Flanagan
- University College London Cancer Institute, London, UK
- Department of Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - David C Page
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Don W Cleveland
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.
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46
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Slotkin EK, Diolaiti D, Shukla NN, Dela Cruz FS, Clark JJ, Gundem G, Yellapantula VD, Levine MF, You D, Ma P, Pachhal S, Ibanez Sanchez G, Benayed R, Jungbluth AA, Smyth LM, Mauguen A, Gushterova I, Ding H, Spraggon L, Darnell R, Califano A, Ladanyi M, Papaemmanuil E, Kung AL, Hyman DM, Roberts SS. Patient-Driven Discovery, Therapeutic Targeting, and Post-Clinical Validation of a Novel AKT1 Fusion-Driven Cancer. Cancer Discov 2019; 9:605-616. [PMID: 30877085 DOI: 10.1158/2159-8290.cd-18-0953] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 01/18/2019] [Accepted: 03/12/2019] [Indexed: 11/16/2022]
Abstract
Despite the important role of the PI3K/AKT/mTOR axis in the pathogenesis of cancer, to date there have been few functional oncogenic fusions identified involving the AKT genes. A 12-year-old female with a histopathologically indeterminate epithelioid neoplasm was found to harbor a novel fusion between the LAMTOR1 and AKT1 genes. Through expanded use access, she became the first pediatric patient to be treated with the oral ATP-competitive pan-AKT inhibitor ipatasertib. Treatment resulted in dramatic tumor regression, demonstrating through patient-driven discovery that the fusion resulted in activation of AKT1, was an oncogenic driver, and could be therapeutically targeted with clinical benefit. Post-clinical validation using patient-derived model systems corroborated these findings, confirmed a membrane-bound and constitutively active fusion protein, and identified potential mechanisms of resistance to single-agent treatment with ipatasertib. SIGNIFICANCE: This study describes the patient-driven discovery of the first AKT1 fusion-driven cancer and its treatment with the AKT inhibitor ipatasertib. Patient-derived in vitro and in vivo model systems are used to confirm the LAMTOR1-AKT1 fusion as a tumorigenic driver and identify potential mechanisms of resistance to AKT inhibition.This article is highlighted in the In This Issue feature, p. 565.
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Affiliation(s)
- Emily K Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Daniel Diolaiti
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neerav N Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Filemon S Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Gunes Gundem
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Venkata D Yellapantula
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Max F Levine
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daoqi You
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Peilin Ma
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sagarika Pachhal
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Achim A Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lillian M Smyth
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Audrey Mauguen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Hongxu Ding
- Columbia University Medical Center, New York, New York
| | | | | | | | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elli Papaemmanuil
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew L Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Stephen S Roberts
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
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47
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Goldman SL, MacKay M, Afshinnekoo E, Melnick AM, Wu S, Mason CE. The Impact of Heterogeneity on Single-Cell Sequencing. Front Genet 2019; 10:8. [PMID: 30881372 PMCID: PMC6405636 DOI: 10.3389/fgene.2019.00008] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 01/09/2019] [Indexed: 12/28/2022] Open
Abstract
The importance of diversity and cellular specialization is clear for many reasons, from population-level diversification, to improved resiliency to unforeseen stresses, to unique functions within metazoan organisms during development and differentiation. However, the level of cellular heterogeneity is just now becoming clear through the integration of genome-wide analyses and more cost effective Next Generation Sequencing (NGS). With easy access to single-cell NGS (scNGS), new opportunities exist to examine different levels of gene expression and somatic mutational heterogeneity, but these assays can generate yottabyte scale data. Here, we model the importance of heterogeneity for large-scale analysis of scNGS data, with a focus on the utilization in oncology and other diseases, providing a guide to aid in sample size and experimental design.
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Affiliation(s)
- Samantha L Goldman
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, United States.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
| | - Matthew MacKay
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, United States.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, United States.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States.,WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
| | - Ari M Melnick
- Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Shuxiu Wu
- Hangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, China.,Department of Radiation Oncology, Hangzhou Cancer Hospital, Hangzhou, China
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, United States.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States.,WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States.,The Feil Family Brain and Mind Research Institute, New York, NY, United States
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48
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Dna2 nuclease deficiency results in large and complex DNA insertions at chromosomal breaks. Nature 2018; 564:287-290. [PMID: 30518856 PMCID: PMC6346745 DOI: 10.1038/s41586-018-0769-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 10/23/2018] [Indexed: 11/22/2022]
Abstract
Insertions of mobile elements1-4, mitochondrial
DNA5 and fragments of
nuclear chromosomes6 at DNA
double strand breaks (DSBs) threaten genome integrity and are common in
cancer7-9. Insertions of chromosome fragments at
V(D)J loci can stimulate antibody diversification10. The origin of insertions of chromosomal
fragments and the mechanisms that prevent such insertions remain unknown. Here
we found the first mutant, lacking evolutionarily conserved Dna2 nuclease, that
shows frequent insertions of ~0.1-1.5 kb long sequences into DSBs with
many events carrying multiple DNA fragments joined together. Sequencing of
~500 DNA inserts revealed that they originate from Ty retrotransposons
(~8%), rDNA (~15%) and from throughout the genome with preference
for fragile regions such as origins of replication, R-loops, centromeres,
telomeres or replication fork barriers. Inserted fragments are not lost from
their original loci and therefore represent duplications. These duplications
depend on nonhomologous end-joining (NHEJ) and Pol4. We propose a model in which
alternative processing of DNA structures arising in Dna2-deficient cells can
result in the release of DNA fragments and their capture at DSBs.Similar DNA
insertions at DSBs are expected in any cells with linear extrachromosomal DNA
fragments.
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49
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Colombo AR, Triche T, Ramsingh G. Transposable Element Expression in Acute Myeloid Leukemia Transcriptome and Prognosis. Sci Rep 2018; 8:16449. [PMID: 30401833 PMCID: PMC6219593 DOI: 10.1038/s41598-018-34189-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/26/2018] [Indexed: 12/22/2022] Open
Abstract
Over half of the human genome is comprised of transposable elements (TE). Despite large-scale studies of the transcriptome in cancer, a comprehensive look at TE expression and its relationship to various mutations or prognosis has not been performed. We characterized the expression of TE in 178 adult acute myeloid leukemia (AML) patients using transcriptome data from The Cancer Genome Atlas. We characterized mutation specific dysregulation of TE expression using a multivariate linear model. We identified distinct patterns of TE expression associated with specific mutations and transcriptional networks. Genes regulating methylation was not associated with significant change in TE expression. Using an unpenalized cox regression analysis we identified a TE expression signature that predicted prognosis in AML. We identified 14 candidate prognostic TE transcripts (TEP) that classified AML as high/low-risk and this was independent of mutation-based and coding-gene expression based risk-stratification. TEP was able to predict prognosis in independent cohorts of 284 pediatric AML patients and 19 relapsed adult AML patients. This first comprehensive study of TE expression in AML demonstrates that TE expression can serve as a biomarker for prognosis in AML, and provides novel insights into the biology of AML. Studies characterizing its role in other cancers are warranted.
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Affiliation(s)
- Anthony R Colombo
- Jane Anne Nohl Division of Division of Hematology and Center for the Study of Blood Diseases, Keck School of Medicine of University of Southern California, Los Angeles, California, 90033, USA
| | - Timothy Triche
- Center for Epigenetics, Van Andel Research Institute, 333 Bostwick Ave NE, Grand Rapids, MI, 49503, USA.
| | - Giridharan Ramsingh
- Jane Anne Nohl Division of Division of Hematology and Center for the Study of Blood Diseases, Keck School of Medicine of University of Southern California, Los Angeles, California, 90033, USA.
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50
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Henssen AG, Kentsis A. Emerging functions of DNA transposases and oncogenic mutators in childhood cancer development. JCI Insight 2018; 3:123172. [PMID: 30333322 DOI: 10.1172/jci.insight.123172] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Our understanding of the molecular pathogenesis of childhood cancers has advanced substantially, but their fundamental causes remain poorly understood. Recently, multiple mechanisms of DNA damage and repair have been associated with mutations observed in human cancers. Here, we review the physiologic functions and oncogenic activities of transposable genetic elements. In particular, we focus on the recent studies implicating DNA transposases RAG1/2 and PGBD5 as oncogenic mutators that promote genomic rearrangements in childhood leukemias and solid tumors. We outline future studies that will be needed to define the contributions of transposons to mutational processes that become dysregulated in cancer cells. In addition, we discuss translational approaches, including synthetic lethal strategies, for identifying and developing improved clinical therapies to target oncogenic transposons and transposases.
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Affiliation(s)
- Anton G Henssen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin, Berlin, Germany.,German Cancer Consortium, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Alex Kentsis
- Departments of Pediatrics, Pharmacology, and Physiology and Biophysics, Weill Medical College of Cornell University, New York, New York, USA.,Sloan Kettering Institute, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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