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Ulicevic J, Shao Z, Jasnovidova O, Bressin A, Gajos M, Ng AH, Annaldasula S, Meierhofer D, Church GM, Busskamp V, Mayer A. Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation. Mol Syst Biol 2024; 20:767-798. [PMID: 38755290 PMCID: PMC11219738 DOI: 10.1038/s44320-024-00039-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Static gene expression programs have been extensively characterized in stem cells and mature human cells. However, the dynamics of RNA isoform changes upon cell-state-transitions during cell differentiation, the determinants and functional consequences have largely remained unclear. Here, we established an improved model for human neurogenesis in vitro that is amenable for systems-wide analyses of gene expression. Our multi-omics analysis reveals that the pronounced alterations in cell morphology correlate strongly with widespread changes in RNA isoform expression. Our approach identifies thousands of new RNA isoforms that are expressed at distinct differentiation stages. RNA isoforms mainly arise from exon skipping and the alternative usage of transcription start and polyadenylation sites during human neurogenesis. The transcript isoform changes can remodel the identity and functions of protein isoforms. Finally, our study identifies a set of RNA binding proteins as a potential determinant of differentiation stage-specific global isoform changes. This work supports the view of regulated isoform changes that underlie state-transitions during neurogenesis.
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Affiliation(s)
- Jelena Ulicevic
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Zhihao Shao
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Olga Jasnovidova
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Annkatrin Bressin
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martyna Gajos
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Alex Hm Ng
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, USA
| | - Siddharth Annaldasula
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - David Meierhofer
- Mass Spectrometry Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - George M Church
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, USA
| | - Volker Busskamp
- Department of Ophthalmology, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - Andreas Mayer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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2
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Rydén M, Sjögren A, Önnerfjord P, Turkiewicz A, Tjörnstrand J, Englund M, Ali N. Exploring the Early Molecular Pathogenesis of Osteoarthritis Using Differential Network Analysis of Human Synovial Fluid. Mol Cell Proteomics 2024; 23:100785. [PMID: 38750696 DOI: 10.1016/j.mcpro.2024.100785] [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: 08/15/2023] [Revised: 04/17/2024] [Accepted: 05/11/2024] [Indexed: 06/23/2024] Open
Abstract
The molecular mechanisms that drive the onset and development of osteoarthritis (OA) remain largely unknown. In this exploratory study, we used a proteomic platform (SOMAscan assay) to measure the relative abundance of more than 6000 proteins in synovial fluid (SF) from knees of human donors with healthy or mildly degenerated tissues, and knees with late-stage OA from patients undergoing knee replacement surgery. Using a linear mixed effects model, we estimated the differential abundance of 6251 proteins between the three groups. We found 583 proteins upregulated in the late-stage OA, including MMP1, collagenase 3 and interleukin-6. Further, we selected 760 proteins (800 aptamers) based on absolute fold changes between the healthy and mild degeneration groups. To those, we applied Gaussian Graphical Models (GGMs) to analyze the conditional dependence of proteins and to identify key proteins and subnetworks involved in early OA pathogenesis. After regularization and stability selection, we identified 102 proteins involved in GGM networks. Notably, network complexity was lost in the protein graph for mild degeneration when compared to controls, suggesting a disruption in the regular protein interplay. Furthermore, among our main findings were several downregulated (in mild degeneration versus healthy) proteins with unique interactions in the healthy group, one of which, SLCO5A1, has not previously been associated with OA. Our results suggest that this protein is important for healthy joint function. Further, our data suggests that SF proteomics, combined with GGMs, can reveal novel insights into the molecular pathogenesis and identification of biomarker candidates for early-stage OA.
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Affiliation(s)
- Martin Rydén
- Clinical Epidemiology Unit, Department of Clinical Sciences Lund, Orthopedics, Faculty of Medicine, Lund University, Lund, Sweden
| | - Amanda Sjögren
- Clinical Epidemiology Unit, Department of Clinical Sciences Lund, Orthopedics, Faculty of Medicine, Lund University, Lund, Sweden.
| | - Patrik Önnerfjord
- Department of Clinical Sciences Lund, Rheumatology, Rheumatology and Molecular Skeletal Biology, Faculty of Medicine, Lund University, Lund, Sweden
| | - Aleksandra Turkiewicz
- Clinical Epidemiology Unit, Department of Clinical Sciences Lund, Orthopedics, Faculty of Medicine, Lund University, Lund, Sweden
| | - Jon Tjörnstrand
- Department of Orthopaedics, Skåne University Hospital, Lund, Sweden
| | - Martin Englund
- Clinical Epidemiology Unit, Department of Clinical Sciences Lund, Orthopedics, Faculty of Medicine, Lund University, Lund, Sweden
| | - Neserin Ali
- Clinical Epidemiology Unit, Department of Clinical Sciences Lund, Orthopedics, Faculty of Medicine, Lund University, Lund, Sweden
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3
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Viggiano M, Ceroni F, Visconti P, Posar A, Scaduto MC, Sandoni L, Baravelli I, Cameli C, Rochat MJ, Maresca A, Vaisfeld A, Gentilini D, Calzari L, Carelli V, Zody MC, Maestrini E, Bacchelli E. Genomic analysis of 116 autism families strengthens known risk genes and highlights promising candidates. NPJ Genom Med 2024; 9:21. [PMID: 38519481 PMCID: PMC10959942 DOI: 10.1038/s41525-024-00411-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a strong genetic component in which rare variants contribute significantly to risk. We performed whole genome and/or exome sequencing (WGS and WES) and SNP-array analysis to identify both rare sequence and copy number variants (SNVs and CNVs) in 435 individuals from 116 ASD families. We identified 37 rare potentially damaging de novo SNVs (pdSNVs) in the cases (n = 144). Interestingly, two of them (one stop-gain and one missense variant) occurred in the same gene, BRSK2. Moreover, the identification of 8 severe de novo pdSNVs in genes not previously implicated in ASD (AGPAT3, IRX5, MGAT5B, RAB8B, RAP1A, RASAL2, SLC9A1, YME1L1) highlighted promising candidates. Potentially damaging CNVs (pdCNVs) provided support to the involvement of inherited variants in PHF3, NEGR1, TIAM1 and HOMER1 in neurodevelopmental disorders (NDD), although mostly acting as susceptibility factors with incomplete penetrance. Interpretation of identified pdSNVs/pdCNVs according to the ACMG guidelines led to a molecular diagnosis in 19/144 cases, although this figure represents a lower limit and is expected to increase thanks to further clarification of the role of likely pathogenic variants in ASD/NDD candidate genes not yet established. In conclusion, our study highlights promising ASD candidate genes and contributes to characterize the allelic diversity, mode of inheritance and phenotypic impact of de novo and inherited risk variants in ASD/NDD genes.
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Affiliation(s)
- Marta Viggiano
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Fabiola Ceroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Paola Visconti
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
| | - Annio Posar
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Maria Cristina Scaduto
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
| | - Laura Sandoni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Irene Baravelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Cinzia Cameli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Magali J Rochat
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Functional and Molecular Neuroimaging Unit, Bologna, Italy
| | - Alessandra Maresca
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Alessandro Vaisfeld
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Davide Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Bioinformatics and Statistical Genomic Unit, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Luciano Calzari
- Bioinformatics and Statistical Genomic Unit, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Valerio Carelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | | | - Elena Maestrini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
| | - Elena Bacchelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
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4
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Zoch A, Konieczny G, Auchynnikava T, Stallmeyer B, Rotte N, Heep M, Berrens RV, Schito M, Kabayama Y, Schöpp T, Kliesch S, Houston B, Nagirnaja L, O'Bryan MK, Aston KI, Conrad DF, Rappsilber J, Allshire RC, Cook AG, Tüttelmann F, O'Carroll D. C19ORF84 connects piRNA and DNA methylation machineries to defend the mammalian germ line. Mol Cell 2024; 84:1021-1035.e11. [PMID: 38359823 PMCID: PMC10960678 DOI: 10.1016/j.molcel.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 12/01/2023] [Accepted: 01/17/2024] [Indexed: 02/17/2024]
Abstract
In the male mouse germ line, PIWI-interacting RNAs (piRNAs), bound by the PIWI protein MIWI2 (PIWIL4), guide DNA methylation of young active transposons through SPOCD1. However, the underlying mechanisms of SPOCD1-mediated piRNA-directed transposon methylation and whether this pathway functions to protect the human germ line remain unknown. We identified loss-of-function variants in human SPOCD1 that cause defective transposon silencing and male infertility. Through the analysis of these pathogenic alleles, we discovered that the uncharacterized protein C19ORF84 interacts with SPOCD1. DNMT3C, the DNA methyltransferase responsible for transposon methylation, associates with SPOCD1 and C19ORF84 in fetal gonocytes. Furthermore, C19ORF84 is essential for piRNA-directed DNA methylation and male mouse fertility. Finally, C19ORF84 mediates the in vivo association of SPOCD1 with the de novo methylation machinery. In summary, we have discovered a conserved role for the human piRNA pathway in transposon silencing and C19ORF84, an uncharacterized protein essential for orchestrating piRNA-directed DNA methylation.
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Affiliation(s)
- Ansgar Zoch
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute for Stem Cell Research, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK.
| | - Gabriela Konieczny
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute for Stem Cell Research, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Tania Auchynnikava
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Birgit Stallmeyer
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Nadja Rotte
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Madeleine Heep
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute for Stem Cell Research, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Rebecca V Berrens
- Institute for Developmental and Regenerative Medicine, University of Oxford, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Drive, Oxford OX37TY, UK
| | - Martina Schito
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute for Stem Cell Research, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Yuka Kabayama
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute for Stem Cell Research, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Theresa Schöpp
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute for Stem Cell Research, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital Münster, Münster, Germany
| | - Brendan Houston
- School of BioSciences and Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Liina Nagirnaja
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Moira K O'Bryan
- School of BioSciences and Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Kenneth I Aston
- Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Donald F Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA; Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland, OR, USA
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK; Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Robin C Allshire
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Atlanta G Cook
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Dónal O'Carroll
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute for Stem Cell Research, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK.
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5
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Long Q, Sebesta M, Sedova K, Haluza V, Alagia A, Liu Z, Stefl R, Gullerova M. The phosphorylated trimeric SOSS1 complex and RNA polymerase II trigger liquid-liquid phase separation at double-strand breaks. Cell Rep 2023; 42:113489. [PMID: 38039132 DOI: 10.1016/j.celrep.2023.113489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/17/2023] [Accepted: 11/09/2023] [Indexed: 12/03/2023] Open
Abstract
Double-strand breaks (DSBs) are the most severe type of DNA damage. Previously, we demonstrated that RNA polymerase II (RNAPII) phosphorylated at the tyrosine 1 (Y1P) residue of its C-terminal domain (CTD) generates RNAs at DSBs. However, the regulation of transcription at DSBs remains enigmatic. Here, we show that the damage-activated tyrosine kinase c-Abl phosphorylates hSSB1, enabling its interaction with Y1P RNAPII at DSBs. Furthermore, the trimeric SOSS1 complex, consisting of hSSB1, INTS3, and c9orf80, binds to Y1P RNAPII in response to DNA damage in an R-loop-dependent manner. Specifically, hSSB1, as a part of the trimeric SOSS1 complex, exhibits a strong affinity for R-loops, even in the presence of replication protein A (RPA). Our in vitro and in vivo data reveal that the SOSS1 complex and RNAPII form dynamic liquid-like repair compartments at DSBs. Depletion of the SOSS1 complex impairs DNA repair, underscoring its biological role in the R-loop-dependent DNA damage response.
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Affiliation(s)
- Qilin Long
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Marek Sebesta
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic.
| | - Katerina Sedova
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Vojtech Haluza
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Adele Alagia
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Zhichao Liu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Richard Stefl
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic; National Center for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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6
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Benedum J, Franke V, Appel LM, Walch L, Bruno M, Schneeweiss R, Gruber J, Oberndorfer H, Frank E, Strobl X, Polyansky A, Zagrovic B, Akalin A, Slade D. The SPOC proteins DIDO3 and PHF3 co-regulate gene expression and neuronal differentiation. Nat Commun 2023; 14:7912. [PMID: 38036524 PMCID: PMC10689479 DOI: 10.1038/s41467-023-43724-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 11/17/2023] [Indexed: 12/02/2023] Open
Abstract
Transcription is regulated by a multitude of activators and repressors, which bind to the RNA polymerase II (Pol II) machinery and modulate its progression. Death-inducer obliterator 3 (DIDO3) and PHD finger protein 3 (PHF3) are paralogue proteins that regulate transcription elongation by docking onto phosphorylated serine-2 in the C-terminal domain (CTD) of Pol II through their SPOC domains. Here, we show that DIDO3 and PHF3 form a complex that bridges the Pol II elongation machinery with chromatin and RNA processing factors and tethers Pol II in a phase-separated microenvironment. Their SPOC domains and C-terminal intrinsically disordered regions are critical for transcription regulation. PHF3 and DIDO exert cooperative and antagonistic effects on the expression of neuronal genes and are both essential for neuronal differentiation. In the absence of PHF3, DIDO3 is upregulated as a compensatory mechanism. In addition to shared gene targets, DIDO specifically regulates genes required for lipid metabolism. Collectively, our work reveals multiple layers of gene expression regulation by the DIDO3 and PHF3 paralogues, which have specific, co-regulatory and redundant functions in transcription.
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Affiliation(s)
- Johannes Benedum
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Vedran Franke
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany
| | - Lisa-Marie Appel
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Lena Walch
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Melania Bruno
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Rebecca Schneeweiss
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Juliane Gruber
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Helena Oberndorfer
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Emma Frank
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Xué Strobl
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Anton Polyansky
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Altuna Akalin
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany
| | - Dea Slade
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria.
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria.
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.
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7
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Bacchelli E, Viggiano M, Ceroni F, Visconti P, Posar A, Scaduto M, Sandoni L, Baravelli I, Cameli C, Rochat M, Maresca A, Vaisfeld A, Gentilini D, Calzari L, Carelli V, Zody M, Maestrini E. Whole genome analysis of rare deleterious variants adds further evidence to BRSK2 and other risk genes in Autism Spectrum Disorder. RESEARCH SQUARE 2023:rs.3.rs-3468592. [PMID: 37961520 PMCID: PMC10635364 DOI: 10.21203/rs.3.rs-3468592/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a strong genetic component in which rare variants contribute significantly to risk. We have performed whole genome and/or exome sequencing (WGS and WES) and SNP-array analysis to identify both rare sequence and copy number variants (SNVs and CNVs) in 435 individuals from 116 ASD families. We identified 37 rare potentially damaging de novo SNVs (pdSNVs) in cases (n = 144). Interestingly, two of them (one stop-gain and one missense variant) occurred in the same gene, BRSK2. Moreover, the identification of 9 severe de novo pdSNVs in genes not previously implicated in ASD (RASAL2, RAP1A, IRX5, SLC9A1, AGPAT3, MGAT3, RAB8B, MGAT5B, YME1L1), highlighted novel candidates. Potentially damaging CNVs (pdCNVs) provided support to the involvement of inherited variants in PHF3, NEGR1, TIAM1 and HOMER1 in neurodevelopmental disorders (NDD), although mostly acting as susceptibility factors with incomplete penetrance. Interpretation of identified pdSNVs/pdCNVs according to the ACMG guidelines led to a molecular diagnosis in 19/144 cases, but this figure represents a lower limit and is expected to increase thanks to further clarification of the role of likely pathogenic variants in new ASD/NDD candidates. In conclusion, our study strengthens the role of BRSK2 and other neurodevelopmental genes in ASD risk, highlights novel candidates and contributes to characterize the allelic diversity, mode of inheritance and phenotypic impact of de novo and inherited risk variants in ASD/NDD genes.
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Affiliation(s)
| | | | | | | | - Annio Posar
- IRCCS Istituto delle Scienze Neurologiche di Bologna
| | - Maria Scaduto
- IRCCS Istituto delle Scienze Neurologiche di Bologna
| | | | | | | | - Magali Rochat
- IRCCS Istituto delle Scienze Neurologiche di Bologna
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8
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Moreno RY, Juetten KJ, Panina SB, Butalewicz JP, Floyd BM, Venkat Ramani MK, Marcotte EM, Brodbelt JS, Zhang YJ. Distinctive interactomes of RNA polymerase II phosphorylation during different stages of transcription. iScience 2023; 26:107581. [PMID: 37664589 PMCID: PMC10470302 DOI: 10.1016/j.isci.2023.107581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/28/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023] Open
Abstract
During eukaryotic transcription, RNA polymerase II undergoes dynamic post-translational modifications on the C-terminal domain (CTD) of the largest subunit, generating an information-rich PTM landscape that transcriptional regulators bind. The phosphorylation of Ser5 and Ser2 of CTD heptad occurs spatiotemporally with the transcriptional stages, recruiting different transcriptional regulators to Pol II. To delineate the protein interactomes at different transcriptional stages, we reconstructed phosphorylation patterns of the CTD at Ser5 and Ser2 in vitro. Our results showed that distinct protein interactomes are recruited to RNA polymerase II at different stages of transcription by the phosphorylation of Ser2 and Ser5 of the CTD heptads. In particular, we characterized calcium homeostasis endoplasmic reticulum protein (CHERP) as a regulator bound by phospho-Ser2 heptad. Pol II association with CHERP recruits an accessory splicing complex whose loss results in broad changes in alternative splicing events. Our results shed light on the PTM-coded recruitment process that coordinates transcription.
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Affiliation(s)
| | - Kyle J. Juetten
- Department of Chemistry, University of Texas, Austin, TX, USA
| | - Svetlana B. Panina
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | | | - Brendan M. Floyd
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | | | - Edward M. Marcotte
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | | | - Y. Jessie Zhang
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
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9
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Collombet S, Rall I, Dugast-Darzacq C, Heckert A, Halavatyi A, Le Saux A, Dailey G, Darzacq X, Heard E. RNA polymerase II depletion from the inactive X chromosome territory is not mediated by physical compartmentalization. Nat Struct Mol Biol 2023; 30:1216-1223. [PMID: 37291424 PMCID: PMC10442225 DOI: 10.1038/s41594-023-01008-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 04/28/2023] [Indexed: 06/10/2023]
Abstract
Subnuclear compartmentalization has been proposed to play an important role in gene regulation by segregating active and inactive parts of the genome in distinct physical and biochemical environments. During X chromosome inactivation (XCI), the noncoding Xist RNA coats the X chromosome, triggers gene silencing and forms a dense body of heterochromatin from which the transcription machinery appears to be excluded. Phase separation has been proposed to be involved in XCI, and might explain the exclusion of the transcription machinery by preventing its diffusion into the Xist-coated territory. Here, using quantitative fluorescence microscopy and single-particle tracking, we show that RNA polymerase II (RNAPII) freely accesses the Xist territory during the initiation of XCI. Instead, the apparent depletion of RNAPII is due to the loss of its chromatin stably bound fraction. These findings indicate that initial exclusion of RNAPII from the inactive X reflects the absence of actively transcribing RNAPII, rather than a consequence of putative physical compartmentalization of the inactive X heterochromatin domain.
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Affiliation(s)
| | - Isabell Rall
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Claire Dugast-Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA
| | - Alec Heckert
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA
| | | | - Agnes Le Saux
- Curie Institute, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, Paris, France
| | - Gina Dailey
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA.
| | - Edith Heard
- European Molecular Biology Laboratory, Heidelberg, Germany.
- Curie Institute, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, Paris, France.
- College de France, Paris, France.
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10
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Zeng JH, Li HJ, Liu K, Liang CQ, Wu HY, Chen WY, Tang MH, Zhao WL, Cai DQ, Qi XF. Loss of circIGF1R Suppresses Cardiomyocytes Proliferation by Sponging miR-362-5p. DNA Cell Biol 2023. [PMID: 37347924 DOI: 10.1089/dna.2022.0590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2023] Open
Abstract
Circular RNAs (circRNAs) are generally formed by the back-splicing of precursor mRNA. Increasing evidence implicates the important role of circRNAs in cardiovascular diseases. However, the role of circ-insulin-like growth factor 1 receptor (circIGF1R) in cardiomyocyte (CM) proliferation remains unclear. Here, we investigated the potential role of the circIGF1R in the proliferation of CMs. We found that circIGF1R expression in heart tissues and primary CMs from adult mice was significantly lower than that in neonatal mice at postnatal 1 day (p1). Increased circIGF1R expression was detected in the injured neonatal heart at 0.5 and 1 days post-resection. circIGF1R knockdown significantly decreased the proliferation of primary CMs. Combined prediction software, luciferase reporter gene analysis, and quantitative real time-PCR (qPCR) revealed that circIGF1R interacted with miR-362-5p. A significant increase in miR-362-5p expression was detected in the adult heart compared with that in the neonatal heart. Further, heart injury significantly decreased the expression of miR-362-5p in neonatal mice. Treatment with miR-362-5p mimics significantly suppressed the proliferation of primary CMs, whereas knockdown of miR-362-5p promoted the CMs proliferation. Meanwhile, miR-362-5p silencing can rescue the proliferation inhibition of CMs induced by circIGF1R knockdown. Target prediction and qPCR validation revealed that miR-362-5p significantly inhibited the expression of Phf3 in primary CMs. In addition, decreased Phf3 expression was detected in adult hearts compared with neonatal hearts. Consistently, increased Phf3 expression was detected in injured neonatal hearts compared with that in sham hearts. Knockdown of Phf3 markedly repressed CMs proliferation. Taken together, these findings suggest that circIGF1R might contribute to cardiomyocyte proliferation by promoting Pfh3 expression by sponging miR-362-5p and provide an important experimental basis for the regulation of heart regeneration.
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Affiliation(s)
- Jun-Hui Zeng
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University, Guangzhou, China
| | - Hong-Ji Li
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University, Guangzhou, China
| | - Kun Liu
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University, Guangzhou, China
| | - Chi-Qian Liang
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University, Guangzhou, China
| | - Hai-Yan Wu
- Department of Hematology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Wu-Yun Chen
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University, Guangzhou, China
| | - Ming-Hui Tang
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University, Guangzhou, China
| | - Wan-Ling Zhao
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University, Guangzhou, China
| | - Dong-Qing Cai
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University, Guangzhou, China
| | - Xu-Feng Qi
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University, Guangzhou, China
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11
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Brown RB. Dysregulated phosphate metabolism in autism spectrum disorder: associations and insights for future research. Expert Rev Mol Med 2023; 25:e20. [PMID: 37309057 PMCID: PMC10407224 DOI: 10.1017/erm.2023.15] [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: 11/07/2022] [Revised: 03/27/2023] [Accepted: 05/09/2023] [Indexed: 06/14/2023]
Abstract
Studies of autism spectrum disorder (ASD) related to exposure to toxic levels of dietary phosphate are lacking. Phosphate toxicity from dysregulated phosphate metabolism can negatively impact almost every major organ system of the body, including the central nervous system. The present paper used a grounded theory-literature review method to synthesise associations of dysregulated phosphate metabolism with the aetiology of ASD. Cell signalling in autism has been linked to an altered balance between phosphoinositide kinases, which phosphorylate proteins, and the counteracting effect of phosphatases in neuronal membranes. Glial cell overgrowth in the developing ASD brain can lead to disturbances in neuro-circuitry, neuroinflammation and immune responses which are potentially related to excessive inorganic phosphate. The rise in ASD prevalence has been suggested to originate in changes to the gut microbiome from increasing consumption of additives in processed food, including phosphate additives. Ketogenic diets and dietary patterns that eliminate casein also reduce phosphate intake, which may account for many of the suggested benefits of these diets in children with ASD. Dysregulated phosphate metabolism is causatively linked to comorbid conditions associated with ASD such as cancer, tuberous sclerosis, mitochondrial dysfunction, diabetes, epilepsy, obesity, chronic kidney disease, tauopathy, cardiovascular disease and bone mineral disorders. Associations and proposals presented in this paper offer novel insights and directions for future research linking the aetiology of ASD with dysregulated phosphate metabolism and phosphate toxicity from excessive dietary phosphorus intake.
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Affiliation(s)
- Ronald B. Brown
- University of Waterloo, School of Public Health Sciences, Waterloo, ON N2L 3G1, Canada
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12
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Spain L, Coulton A, Lobon I, Rowan A, Schnidrig D, Shepherd ST, Shum B, Byrne F, Goicoechea M, Piperni E, Au L, Edmonds K, Carlyle E, Hunter N, Renn A, Messiou C, Hughes P, Nobbs J, Foijer F, van den Bos H, Wardenaar R, Spierings DC, Spencer C, Schmitt AM, Tippu Z, Lingard K, Grostate L, Peat K, Kelly K, Sarker S, Vaughan S, Mangwende M, Terry L, Kelly D, Biano J, Murra A, Korteweg J, Lewis C, O'Flaherty M, Cattin AL, Emmerich M, Gerard CL, Pallikonda HA, Lynch J, Mason R, Rogiers A, Xu H, Huebner A, McGranahan N, Al Bakir M, Murai J, Naceur-Lombardelli C, Borg E, Mitchison M, Moore DA, Falzon M, Proctor I, Stamp GW, Nye EL, Young K, Furness AJ, Pickering L, Stewart R, Mahadeva U, Green A, Larkin J, Litchfield K, Swanton C, Jamal-Hanjani M, Turajlic S. Late-Stage Metastatic Melanoma Emerges through a Diversity of Evolutionary Pathways. Cancer Discov 2023; 13:1364-1385. [PMID: 36977461 PMCID: PMC10236155 DOI: 10.1158/2159-8290.cd-22-1427] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/06/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023]
Abstract
Understanding the evolutionary pathways to metastasis and resistance to immune-checkpoint inhibitors (ICI) in melanoma is critical for improving outcomes. Here, we present the most comprehensive intrapatient metastatic melanoma dataset assembled to date as part of the Posthumous Evaluation of Advanced Cancer Environment (PEACE) research autopsy program, including 222 exome sequencing, 493 panel-sequenced, 161 RNA sequencing, and 22 single-cell whole-genome sequencing samples from 14 ICI-treated patients. We observed frequent whole-genome doubling and widespread loss of heterozygosity, often involving antigen-presentation machinery. We found KIT extrachromosomal DNA may have contributed to the lack of response to KIT inhibitors of a KIT-driven melanoma. At the lesion-level, MYC amplifications were enriched in ICI nonresponders. Single-cell sequencing revealed polyclonal seeding of metastases originating from clones with different ploidy in one patient. Finally, we observed that brain metastases that diverged early in molecular evolution emerge late in disease. Overall, our study illustrates the diverse evolutionary landscape of advanced melanoma. SIGNIFICANCE Despite treatment advances, melanoma remains a deadly disease at stage IV. Through research autopsy and dense sampling of metastases combined with extensive multiomic profiling, our study elucidates the many mechanisms that melanomas use to evade treatment and the immune system, whether through mutations, widespread copy-number alterations, or extrachromosomal DNA. See related commentary by Shain, p. 1294. This article is highlighted in the In This Issue feature, p. 1275.
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Affiliation(s)
- Lavinia Spain
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Alexander Coulton
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, United Kingdom
| | - Irene Lobon
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Desiree Schnidrig
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Scott T.C. Shepherd
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Benjamin Shum
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Fiona Byrne
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Maria Goicoechea
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Elisa Piperni
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Lewis Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Kim Edmonds
- The Royal Marsden Hospital, London, United Kingdom
| | | | - Nikki Hunter
- The Royal Marsden Hospital, London, United Kingdom
| | | | - Christina Messiou
- The Royal Marsden Hospital, London, United Kingdom
- The Institute of Cancer Research, Kensington and Chelsea, United Kingdom
| | - Peta Hughes
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Jaime Nobbs
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Hilda van den Bos
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Rene Wardenaar
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Diana C.J. Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Charlotte Spencer
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | | | - Zayd Tippu
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | | | | | - Kema Peat
- The Royal Marsden Hospital, London, United Kingdom
| | | | - Sarah Sarker
- The Royal Marsden Hospital, London, United Kingdom
| | | | | | - Lauren Terry
- The Royal Marsden Hospital, London, United Kingdom
| | - Denise Kelly
- The Royal Marsden Hospital, London, United Kingdom
| | | | - Aida Murra
- The Royal Marsden Hospital, London, United Kingdom
| | | | | | | | - Anne-Laure Cattin
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Max Emmerich
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- St. John's Institute of Dermatology, Guy's and St Thomas’ Hospital NHS Foundation Trust, London, United Kingdom
| | - Camille L. Gerard
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Precision Oncology Center, Oncology Department, Lausanne University Hospital, Lausanne, Switzerland
| | | | - Joanna Lynch
- The Royal Marsden Hospital, London, United Kingdom
| | - Robert Mason
- Gold Coast University Hospital, Queensland, Australia
| | - Aljosja Rogiers
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- The Royal Marsden Hospital, London, United Kingdom
| | - Hang Xu
- The Francis Crick Institute, London, United Kingdom
| | - Ariana Huebner
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, United Kingdom
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, United Kingdom
| | - Nicholas McGranahan
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, United Kingdom
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, United Kingdom
| | - Jun Murai
- Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, United Kingdom
- Drug Discovery Technology Laboratories, Ono Pharmaceutical Co., Ltd. Osaka, Japan
| | | | - Elaine Borg
- University College London Hospital, London, United Kingdom
| | | | - David A. Moore
- Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Mary Falzon
- University College London Hospital, London, United Kingdom
| | - Ian Proctor
- University College London Hospital, London, United Kingdom
| | | | - Emma L. Nye
- The Francis Crick Institute, London, United Kingdom
| | - Kate Young
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Andrew J.S. Furness
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
- The Institute of Cancer Research, Kensington and Chelsea, United Kingdom
| | | | - Ruby Stewart
- Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Ula Mahadeva
- Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Anna Green
- Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - James Larkin
- Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Kevin Litchfield
- Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, United Kingdom
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, United Kingdom
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, United Kingdom
- Department of Medical Oncology, University College London Hospitals, London, United Kingdom
| | | | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
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13
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Stoltze UK, Foss-Skiftesvik J, van Overeem Hansen T, Byrjalsen A, Sehested A, Scheie D, Stamm Mikkelsen T, Rasmussen S, Bak M, Okkels H, Thude Callesen M, Skjøth-Rasmussen J, Gerdes AM, Schmiegelow K, Mathiasen R, Wadt K. Genetic predisposition and evolutionary traces of pediatric cancer risk: a prospective 5-year population-based genome sequencing study of children with CNS tumors. Neuro Oncol 2023; 25:761-773. [PMID: 35902210 PMCID: PMC10076945 DOI: 10.1093/neuonc/noac187] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The etiology of central nervous system (CNS) tumors in children is largely unknown and population-based studies of genetic predisposition are lacking. METHODS In this prospective, population-based study, we performed germline whole-genome sequencing in 128 children with CNS tumors, supplemented by a systematic pedigree analysis covering 3543 close relatives. RESULTS Thirteen children (10%) harbored pathogenic variants in known cancer genes. These children were more likely to have medulloblastoma (OR 5.9, CI 1.6-21.2) and develop metasynchronous CNS tumors (P = 0.01). Similar carrier frequencies were seen among children with low-grade glioma (12.8%) and high-grade tumors (12.2%). Next, considering the high mortality of childhood CNS tumors throughout most of human evolution, we explored known pediatric-onset cancer genes, showing that they are more evolutionarily constrained than genes associated with risk of adult-onset malignancies (P = 5e-4) and all other genes (P = 5e-17). Based on this observation, we expanded our analysis to 2986 genes exhibiting high evolutionary constraint in 141,456 humans. This analysis identified eight directly causative loss-of-functions variants, and showed a dose-response association between degree of constraint and likelihood of pathogenicity-raising the question of the role of other highly constrained gene alterations detected. CONCLUSIONS Approximately 10% of pediatric CNS tumors can be attributed to rare variants in known cancer genes. Genes associated with high risk of childhood cancer show evolutionary evidence of constraint.
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Affiliation(s)
- Ulrik Kristoffer Stoltze
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Genetics, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - Jon Foss-Skiftesvik
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
- Department of Neurosurgery, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - Anna Byrjalsen
- Department of Clinical Genetics, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - Astrid Sehested
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - David Scheie
- Department of Pathology, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - Torben Stamm Mikkelsen
- Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Copenhagen University, Copenhagen, Denmark
| | - Mads Bak
- Department of Clinical Genetics, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - Henrik Okkels
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
| | - Michael Thude Callesen
- Department of Pediatrics and Adolescent Medicine, Odense University Hospital, Odense, Denmark
| | - Jane Skjøth-Rasmussen
- Department of Neurosurgery, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - René Mathiasen
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - Karin Wadt
- Department of Clinical Genetics, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
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14
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Appel LM, Benedum J, Engl M, Platzer S, Schleiffer A, Strobl X, Slade D. SPOC domain proteins in health and disease. Genes Dev 2023; 37:140-170. [PMID: 36927757 PMCID: PMC10111866 DOI: 10.1101/gad.350314.122] [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: 03/18/2023]
Abstract
Since it was first described >20 yr ago, the SPOC domain (Spen paralog and ortholog C-terminal domain) has been identified in many proteins all across eukaryotic species. SPOC-containing proteins regulate gene expression on various levels ranging from transcription to RNA processing, modification, export, and stability, as well as X-chromosome inactivation. Their manifold roles in controlling transcriptional output implicate them in a plethora of developmental processes, and their misregulation is often associated with cancer. Here, we provide an overview of the biophysical properties of the SPOC domain and its interaction with phosphorylated binding partners, the phylogenetic origin of SPOC domain proteins, the diverse functions of mammalian SPOC proteins and their homologs, the mechanisms by which they regulate differentiation and development, and their roles in cancer.
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Affiliation(s)
- Lisa-Marie Appel
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
| | - Johannes Benedum
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Magdalena Engl
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Sebastian Platzer
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), 1030 Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Xué Strobl
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Dea Slade
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria;
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
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15
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Appel LM, Franke V, Benedum J, Grishkovskaya I, Strobl X, Polyansky A, Ammann G, Platzer S, Neudolt A, Wunder A, Walch L, Kaiser S, Zagrovic B, Djinovic-Carugo K, Akalin A, Slade D. The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators. Nat Commun 2023; 14:166. [PMID: 36631525 PMCID: PMC9834408 DOI: 10.1038/s41467-023-35853-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
The heptad repeats of the C-terminal domain (CTD) of RNA polymerase II (Pol II) are extensively modified throughout the transcription cycle. The CTD coordinates RNA synthesis and processing by recruiting transcription regulators as well as RNA capping, splicing and 3'end processing factors. The SPOC domain of PHF3 was recently identified as a CTD reader domain specifically binding to phosphorylated serine-2 residues in adjacent CTD repeats. Here, we establish the SPOC domains of the human proteins DIDO, SHARP (also known as SPEN) and RBM15 as phosphoserine binding modules that can act as CTD readers but also recognize other phosphorylated binding partners. We report the crystal structure of SHARP SPOC in complex with CTD and identify the molecular determinants for its specific binding to phosphorylated serine-5. PHF3 and DIDO SPOC domains preferentially interact with the Pol II elongation complex, while RBM15 and SHARP SPOC domains engage with writers and readers of m6A, the most abundant RNA modification. RBM15 positively regulates m6A levels and mRNA stability in a SPOC-dependent manner, while SHARP SPOC is essential for its localization to inactive X-chromosomes. Our findings suggest that the SPOC domain is a major interface between the transcription machinery and regulators of transcription and co-transcriptional processes.
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Affiliation(s)
- Lisa-Marie Appel
- Department of Radiation Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Vedran Franke
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Johannes Benedum
- Department of Radiation Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030, Vienna, Austria
| | - Irina Grishkovskaya
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Xué Strobl
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030, Vienna, Austria
| | - Anton Polyansky
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Gregor Ammann
- Department of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Sebastian Platzer
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Andrea Neudolt
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Anna Wunder
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Lena Walch
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Stefanie Kaiser
- Department of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Kristina Djinovic-Carugo
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter, Campus Vienna Biocenter 5, 1030, Vienna, Austria
- Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecčna Pot 113, 1000, Ljubljana, Slovenia
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, Cedex 9, France
| | - Altuna Akalin
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Dea Slade
- Department of Radiation Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria.
- Comprehensive Cancer Center, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria.
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria.
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16
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Tirtakusuma R, Szoltysek K, Milne P, Grinev VV, Ptasinska A, Chin PS, Meyer C, Nakjang S, Hehir-Kwa JY, Williamson D, Cauchy P, Keane P, Assi SA, Ashtiani M, Kellaway SG, Imperato MR, Vogiatzi F, Schweighart EK, Lin S, Wunderlich M, Stutterheim J, Komkov A, Zerkalenkova E, Evans P, McNeill H, Elder A, Martinez-Soria N, Fordham SE, Shi Y, Russell LJ, Pal D, Smith A, Kingsbury Z, Becq J, Eckert C, Haas OA, Carey P, Bailey S, Skinner R, Miakova N, Collin M, Bigley V, Haniffa M, Marschalek R, Harrison CJ, Cargo CA, Schewe D, Olshanskaya Y, Thirman MJ, Cockerill PN, Mulloy JC, Blair HJ, Vormoor J, Allan JM, Bonifer C, Heidenreich O, Bomken S. Epigenetic regulator genes direct lineage switching in MLL/AF4 leukemia. Blood 2022; 140:1875-1890. [PMID: 35839448 PMCID: PMC10488321 DOI: 10.1182/blood.2021015036] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/30/2022] [Indexed: 11/20/2022] Open
Abstract
The fusion gene MLL/AF4 defines a high-risk subtype of pro-B acute lymphoblastic leukemia. Relapse can be associated with a lineage switch from acute lymphoblastic to acute myeloid leukemia, resulting in poor clinical outcomes caused by resistance to chemotherapies and immunotherapies. In this study, the myeloid relapses shared oncogene fusion breakpoints with their matched lymphoid presentations and originated from various differentiation stages from immature progenitors through to committed B-cell precursors. Lineage switching is linked to substantial changes in chromatin accessibility and rewiring of transcriptional programs, including alternative splicing. These findings indicate that the execution and maintenance of lymphoid lineage differentiation is impaired. The relapsed myeloid phenotype is recurrently associated with the altered expression, splicing, or mutation of chromatin modifiers, including CHD4 coding for the ATPase/helicase of the nucleosome remodelling and deacetylation complex. Perturbation of CHD4 alone or in combination with other mutated epigenetic modifiers induces myeloid gene expression in MLL/AF4+ cell models, indicating that lineage switching in MLL/AF4 leukemia is driven and maintained by disrupted epigenetic regulation.
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Affiliation(s)
- Ricky Tirtakusuma
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Katarzyna Szoltysek
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Maria Sklodowska-Curie Institute, Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Paul Milne
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Vasily V. Grinev
- Department of Genetics, the Faculty of Biology, Belarusian State University, Minsk, Republic of Belarus
| | - Anetta Ptasinska
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Paulynn S. Chin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Claus Meyer
- Institute of Pharmaceutical Biology/DCAL, Goethe-University, Frankfurt/Main, Germany
| | - Sirintra Nakjang
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Daniel Williamson
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Pierre Cauchy
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Peter Keane
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Salam A. Assi
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Minoo Ashtiani
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Sophie G. Kellaway
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Maria R. Imperato
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Fotini Vogiatzi
- ALL-BFM Study Group, Pediatric Hematology/Oncology, Christian Albrechts University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Germany
| | | | - Shan Lin
- Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Mark Wunderlich
- Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | | | - Alexander Komkov
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology, and Immunology, Moscow, Russia
| | - Elena Zerkalenkova
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology, and Immunology, Moscow, Russia
| | - Paul Evans
- Haematological Malignancy Diagnostic Service, St James’s University Hospital, Leeds, United Kingdom
| | - Hesta McNeill
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Alex Elder
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Natalia Martinez-Soria
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sarah E. Fordham
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Yuzhe Shi
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lisa J. Russell
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Deepali Pal
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Alex Smith
- Epidemiology and Cancer Statistics Group, University of York, York, United Kingdom
| | | | - Jennifer Becq
- Illumina Cambridge Ltd., Great Abington, United Kingdom
| | - Cornelia Eckert
- Department of Pediatric Oncology/Hematology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Oskar A. Haas
- St Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
| | - Peter Carey
- Department of Paediatric Haematology and Oncology, The Great North Children’s Hospital, Newcastle upon Tyne, United Kingdom
| | - Simon Bailey
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Department of Paediatric Haematology and Oncology, The Great North Children’s Hospital, Newcastle upon Tyne, United Kingdom
| | - Roderick Skinner
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Department of Paediatric Haematology and Oncology, The Great North Children’s Hospital, Newcastle upon Tyne, United Kingdom
| | - Natalia Miakova
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology, and Immunology, Moscow, Russia
| | - Matthew Collin
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Venetia Bigley
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Dermatology and Newcastle National Institute of Health Research (NIHR), Newcastle Biomedical Research Centre, Newcastle Hospitals National Health Service (NHS) Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology/DCAL, Goethe-University, Frankfurt/Main, Germany
| | - Christine J. Harrison
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Catherine A. Cargo
- Haematological Malignancy Diagnostic Service, St James’s University Hospital, Leeds, United Kingdom
| | - Denis Schewe
- Department of Pediatrics, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Yulia Olshanskaya
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology, and Immunology, Moscow, Russia
| | - Michael J. Thirman
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL
| | - Peter N. Cockerill
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - James C. Mulloy
- Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Helen J. Blair
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Josef Vormoor
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - James M. Allan
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Olaf Heidenreich
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Simon Bomken
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Department of Paediatric Haematology and Oncology, The Great North Children’s Hospital, Newcastle upon Tyne, United Kingdom
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