1
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Flynn A, Pattison AD, Balachander S, Boehm E, Bowen B, Dwight T, Rosello F, Hofmann O, Martelotto L, Zethoven M, Kirschner LS, Else T, Fishbein L, Gill AJ, Tischler AS, Giordano T, Prodanov T, Noble JR, Reddel RR, Trainer AH, Ghayee HK, Bourdeau I, Elston M, Ishak D, Ngeow Yuen Yie J, Hicks RJ, Crona J, Åkerström T, Stålberg P, Dahia P, Grimmond S, Clifton-Bligh R, Pacak K, Tothill RW. Multi-omic analysis of SDHB-deficient pheochromocytomas and paragangliomas identifies metastasis and treatment-related molecular profiles. RESEARCH SQUARE 2024:rs.3.rs-4410500. [PMID: 38978571 PMCID: PMC11230496 DOI: 10.21203/rs.3.rs-4410500/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Hereditary SDHB-mutant pheochromocytomas (PC) and paragangliomas (PG) are rare tumours with a high propensity to metastasize although their clinical behaviour is unpredictable. To characterize the genomic landscape of these tumours and identify metastasis biomarkers, we performed multi-omic analysis on 94 tumours from 79 patients using seven molecular methods. Sympathetic (chromaffin cell) and parasympathetic (non-chromaffin cell) PCPG had distinct molecular profiles reflecting their cell-of-origin and biochemical profile. TERT and ATRX-alterations were associated with metastatic PCPG and these tumours had an increased mutation load, and distinct transcriptional and telomeric features. Most PCPG had quiet genomes with some rare co-operative driver events observed, including EPAS1/HIF-2α mutations. Two mechanisms of acquired resistance to DNA alkylating chemotherapies were also detected - MGMT overexpression and mismatch repair-deficiency causing hypermutation. Our comprehensive multi-omic analysis of SDHB-mutant PCPG therefore identified features of metastatic disease and treatment response, expanding our understanding of these rare neuroendocrine tumours.
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Affiliation(s)
- Aidan Flynn
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, VIC, Australia
| | - Andrew D. Pattison
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, VIC, Australia
| | - Shiva Balachander
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, VIC, Australia
| | - Emma Boehm
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, VIC, Australia
| | - Blake Bowen
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, VIC, Australia
| | - Trisha Dwight
- Kolling Institute of Medical Research, Royal North Shore Hospital St Leonards NSW, Australia
| | | | - Oliver Hofmann
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, VIC, Australia
| | - Luciano Martelotto
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, VIC, Australia
| | | | - Lawrence S. Kirschner
- Division of Endocrinology, Diabetes and Metabolism, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | | | - Lauren Fishbein
- Department of Medicine, Division of Endocrinology, Metabolism, Diabetes, University of Colorado, Aurora, CO, USA
| | - Anthony J Gill
- Sydney Medical School, University of Sydney, Sydney NSW, Australia
- NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, St Leonards NSW, Australia
| | | | | | - Tamara Prodanov
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Jane R Noble
- Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Roger R Reddel
- Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Alison H. Trainer
- Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, VIC, Australia
| | - Hans Kumar Ghayee
- University of Florida and Malcom Randall VA Medical Center, Gainesville, FL, USA
| | | | - Marianne Elston
- Waikato Clinical Campus, University of Auckland, Hamilton, New Zealand
| | | | | | - Rodney J Hicks
- St Vincent’s Dept of Medicine, University of Melbourne, VIC, Australia
| | - Joakim Crona
- 18a Department of Medical Sciences, 18b Department of Surgical Sciences, Uppsala University, Sweden
| | - Tobias Åkerström
- 18a Department of Medical Sciences, 18b Department of Surgical Sciences, Uppsala University, Sweden
| | - Peter Stålberg
- 18a Department of Medical Sciences, 18b Department of Surgical Sciences, Uppsala University, Sweden
| | - Patricia Dahia
- Div. Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio (UTHSCSA), TX, USA
| | - Sean Grimmond
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, VIC, Australia
| | - Roderick Clifton-Bligh
- Kolling Institute of Medical Research, Royal North Shore Hospital St Leonards NSW, Australia
- Sydney Medical School, University of Sydney, Sydney NSW, Australia
| | - Karel Pacak
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Richard W Tothill
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, VIC, Australia
- Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
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2
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Chien JF, Liu H, Wang BA, Luo C, Bartlett A, Castanon R, Johnson ND, Nery JR, Osteen J, Li J, Altshul J, Kenworthy M, Valadon C, Liem M, Claffey N, O'Connor C, Seeker LA, Ecker JR, Behrens MM, Mukamel EA. Cell-type-specific effects of age and sex on human cortical neurons. Neuron 2024:S0896-6273(24)00360-X. [PMID: 38838671 DOI: 10.1016/j.neuron.2024.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/29/2024] [Accepted: 05/09/2024] [Indexed: 06/07/2024]
Abstract
Altered transcriptional and epigenetic regulation of brain cell types may contribute to cognitive changes with advanced age. Using single-nucleus multi-omic DNA methylation and transcriptome sequencing (snmCT-seq) in frontal cortex from young adult and aged donors, we found widespread age- and sex-related variation in specific neuron types. The proportion of inhibitory SST- and VIP-expressing neurons was reduced in aged donors. Excitatory neurons had more profound age-related changes in their gene expression and DNA methylation than inhibitory cells. Hundreds of genes involved in synaptic activity, including EGR1, were less expressed in aged adults. Genes located in subtelomeric regions increased their expression with age and correlated with reduced telomere length. We further mapped cell-type-specific sex differences in gene expression and X-inactivation escape genes. Multi-omic single-nucleus epigenomes and transcriptomes provide new insight into the effects of age and sex on human neurons.
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Affiliation(s)
- Jo-Fan Chien
- Department of Physics, University of California, San Diego, La Jolla, CA 92037, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Bang-An Wang
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Chongyuan Luo
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Rosa Castanon
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Nicholas D Johnson
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92037, USA; Computational Neurobiology Laboratory, Salk Institute, La Jolla, CA 92037, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Julia Osteen
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Junhao Li
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jordan Altshul
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Mia Kenworthy
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Cynthia Valadon
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Michelle Liem
- Flow Cytometry Core Facility, Salk Institute, La Jolla, CA 92037, USA
| | - Naomi Claffey
- Flow Cytometry Core Facility, Salk Institute, La Jolla, CA 92037, USA
| | - Carolyn O'Connor
- Flow Cytometry Core Facility, Salk Institute, La Jolla, CA 92037, USA
| | - Luise A Seeker
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA.
| | - M Margarita Behrens
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92037, USA; Computational Neurobiology Laboratory, Salk Institute, La Jolla, CA 92037, USA.
| | - Eran A Mukamel
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA.
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3
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Stephens Z, Kocher JP. Characterization of telomere variant repeats using long reads enables allele-specific telomere length estimation. BMC Bioinformatics 2024; 25:194. [PMID: 38755561 PMCID: PMC11100205 DOI: 10.1186/s12859-024-05807-5] [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: 11/27/2023] [Accepted: 05/09/2024] [Indexed: 05/18/2024] Open
Abstract
Telomeres are regions of repetitive DNA at the ends of linear chromosomes which protect chromosome ends from degradation. Telomere lengths have been extensively studied in the context of aging and disease, though most studies use average telomere lengths which are of limited utility. We present a method for identifying all 92 telomere alleles from long read sequencing data. Individual telomeres are identified using variant repeats proximal to telomere regions, which are unique across alleles. This high-throughput and high-resolution characterization of telomeres could be foundational to future studies investigating the roles of specific telomeres in aging and disease.
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4
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Hu X, Zhu B, Vokes N, Fujimoto J, Rojas Alvarez FR, Heeke S, Moreira AL, Solis LM, Haymaker C, Velcheti V, Sterman DH, Pass HI, Cheng C, Lee JJ, Zhang J, Wei Z, Wu J, Le X, Ostrin E, Toumazis I, Gibbons D, Su D, Fukuoka J, Antonoff MB, Gerber DE, Li C, Kadara H, Wang L, Davis M, Heymach JV, Hannash S, Wistuba I, Dubinett S, Alexandrov L, Lippman S, Spira A, Futreal AP, Reuben A, Zhang J. The evolution of lung adenocarcinoma precursors is associated with chromosomal instability and transition from innate to adaptive immune response/evasion. RESEARCH SQUARE 2024:rs.3.rs-4396272. [PMID: 38798564 PMCID: PMC11118701 DOI: 10.21203/rs.3.rs-4396272/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Studying lung adenocarcinoma (LUAD) early carcinogenesis is challenging, primarily due to the lack of LUAD precursors specimens. We amassed multi-omics data from 213 LUAD and LUAD precursors to identify molecular features underlying LUAD precancer evolution. We observed progressively increasing mutations, chromosomal aberrations, whole genome doubling and genomic instability from precancer to invasive LUAD, indicating aggravating chromosomal instability (CIN). Telomere shortening, a crucial genomic alteration linked to CIN, emerged at precancer stage. Moreover, later-stage lesions demonstrated increasing cancer stemness and decreasing alveolar identity, suggesting epithelial de-differentiation during early LUAD carcinogenesis. The innate immune cells progressively diminished from precancer to invasive LUAD, concomitant with a gradual recruitment of adaptive immune cells (except CD8+ and gamma-delta T cells that decreased in later stages) and upregulation of numerous immune checkpoints, suggesting LUAD precancer evolution is associated with a shift from innate to adaptive immune response and immune evasion mediated by various mechanisms.
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Affiliation(s)
- Xin Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Bo Zhu
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Natalie Vokes
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | | | - Frank R. Rojas Alvarez
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Simon Heeke
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Andre L. Moreira
- Department of Pathology, New York University Langone Medical Center, New York, 10012, USA
| | - Luisa M. Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Cara Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Vamsidhar Velcheti
- Department of Medical oncology, New York University, New York, 10012, USA
| | | | - Harvey I. Pass
- Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, 10016, USA
| | - Chao Cheng
- Department of Medicine, Epidemiology and Population Science, Baylor College of Medicine. Houston, TX, 77030, USA
| | - Jack J. Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Zhubo Wei
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jia Wu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xiuning Le
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Edwin Ostrin
- Department of General Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Iakovos Toumazis
- Department of Health Services Research, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Don Gibbons
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Dan Su
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
- Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Junya Fukuoka
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 8528523, Japan
| | - Mara B. Antonoff
- Department of Thoracic & Cardiovasc Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - David E. Gerber
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Chenyang Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mark Davis
- Moores Cancer Center, UC San Diego School of Medicine, San Diego, CA, 92037, USA
| | - John V. Heymach
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Samir Hannash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ignacio Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Steven Dubinett
- Departments of Medicine and Pathology, University of California Los Angeles and Greater Los Angeles Healthcare System, Los Angeles, CA, 90095, USA
| | - Ludmil Alexandrov
- Moores Cancer Center, UC San Diego School of Medicine, San Diego, CA, 92037, USA
| | - Scott Lippman
- Moores Cancer Center, UC San Diego School of Medicine, San Diego, CA, 92037, USA
| | - Avrum Spira
- Pathology & Laboratory Medicine, and Bioinformatics, Boston University, Boston, MA, 02215, USA
| | - Andrew P. Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Alexandre Reuben
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Lead contact
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5
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Meltzer WA, Gupta A, Lin PN, Brown RA, Benyamien-Roufaeil DS, Khatri R, Mahurkar AA, Song Y, Taylor RJ, Zalzman M. Reprogramming Chromosome Ends by Functional Histone Acetylation. Int J Mol Sci 2024; 25:3898. [PMID: 38612707 PMCID: PMC11011970 DOI: 10.3390/ijms25073898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Cancers harness embryonic programs to evade aging and promote survival. Normally, sequences at chromosome ends called telomeres shorten with cell division, serving as a countdown clock to limit cell replication. Therefore, a crucial aspect of cancerous transformation is avoiding replicative aging by activation of telomere repair programs. Mouse embryonic stem cells (mESCs) activate a transient expression of the gene Zscan4, which correlates with chromatin de-condensation and telomere extension. Head and neck squamous cell carcinoma (HNSCC) cancers reactivate ZSCAN4, which in turn regulates the phenotype of cancer stem cells (CSCs). Our study reveals a new role for human ZSCAN4 in facilitating functional histone H3 acetylation at telomere chromatin. Next-generation sequencing indicates ZSCAN4 enrichment at telomere chromatin. These changes correlate with ZSCAN4-induced histone H3 acetylation and telomere elongation, while CRISPR/Cas9 knockout of ZSCAN4 leads to reduced H3 acetylation and telomere shortening. Our study elucidates the intricate involvement of ZSCAN4 and its significant contribution to telomere chromatin remodeling. These findings suggest that ZSCAN4 induction serves as a novel link between 'stemness' and telomere maintenance. Targeting ZSCAN4 may offer new therapeutic approaches to effectively limit or enhance the replicative lifespan of stem cells and cancer cells.
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Affiliation(s)
- W. Alex Meltzer
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA (A.G.); (P.N.L.); (R.A.B.); (D.S.B.-R.); (R.K.)
| | - Aditi Gupta
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA (A.G.); (P.N.L.); (R.A.B.); (D.S.B.-R.); (R.K.)
| | - Phyo Nay Lin
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA (A.G.); (P.N.L.); (R.A.B.); (D.S.B.-R.); (R.K.)
| | - Robert A. Brown
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA (A.G.); (P.N.L.); (R.A.B.); (D.S.B.-R.); (R.K.)
| | - Daniel S. Benyamien-Roufaeil
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA (A.G.); (P.N.L.); (R.A.B.); (D.S.B.-R.); (R.K.)
| | - Raju Khatri
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA (A.G.); (P.N.L.); (R.A.B.); (D.S.B.-R.); (R.K.)
| | - Anup A. Mahurkar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (A.A.M.); (Y.S.)
| | - Yang Song
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (A.A.M.); (Y.S.)
| | - Rodney J. Taylor
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA;
- Marlene and Stewart Greenbaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Michal Zalzman
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA (A.G.); (P.N.L.); (R.A.B.); (D.S.B.-R.); (R.K.)
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA;
- Marlene and Stewart Greenbaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- The Center for Stem Cell Biology and Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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6
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Vaid R, Thombare K, Mendez A, Burgos-Panadero R, Djos A, Jachimowicz D, Lundberg K, Bartenhagen C, Kumar N, Tümmler C, Sihlbom C, Fransson S, Johnsen J, Kogner P, Martinsson T, Fischer M, Mondal T. METTL3 drives telomere targeting of TERRA lncRNA through m6A-dependent R-loop formation: a therapeutic target for ALT-positive neuroblastoma. Nucleic Acids Res 2024; 52:2648-2671. [PMID: 38180812 PMCID: PMC10954483 DOI: 10.1093/nar/gkad1242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/08/2023] [Accepted: 12/18/2023] [Indexed: 01/07/2024] Open
Abstract
Telomerase-negative tumors maintain telomere length by alternative lengthening of telomeres (ALT), but the underlying mechanism behind ALT remains poorly understood. A proportion of aggressive neuroblastoma (NB), particularly relapsed tumors, are positive for ALT (ALT+), suggesting that a better dissection of the ALT mechanism could lead to novel therapeutic opportunities. TERRA, a long non-coding RNA (lncRNA) derived from telomere ends, localizes to telomeres in a R-loop-dependent manner and plays a crucial role in telomere maintenance. Here we present evidence that RNA modification at the N6 position of internal adenosine (m6A) in TERRA by the methyltransferase METTL3 is essential for telomere maintenance in ALT+ cells, and the loss of TERRA m6A/METTL3 results in telomere damage. We observed that m6A modification is abundant in R-loop enriched TERRA, and the m6A-mediated recruitment of hnRNPA2B1 to TERRA is critical for R-loop formation. Our findings suggest that m6A drives telomere targeting of TERRA via R-loops, and this m6A-mediated R-loop formation could be a widespread mechanism employed by other chromatin-interacting lncRNAs. Furthermore, treatment of ALT+ NB cells with a METTL3 inhibitor resulted in compromised telomere targeting of TERRA and accumulation of DNA damage at telomeres, indicating that METTL3 inhibition may represent a therapeutic approach for ALT+ NB.
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Affiliation(s)
- Roshan Vaid
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Ketan Thombare
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Akram Mendez
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Rebeca Burgos-Panadero
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Anna Djos
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Daniel Jachimowicz
- Translational Genomics, Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Kristina Ihrmark Lundberg
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institute, and Pediatric Oncology, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Christoph Bartenhagen
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Department of Pediatric Oncology and Hematology, University of Cologne, Cologne, Germany
| | - Navinder Kumar
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Conny Tümmler
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institute, and Pediatric Oncology, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Carina Sihlbom
- Proteomics Core Facility, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Susanne Fransson
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - John Inge Johnsen
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institute, and Pediatric Oncology, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Per Kogner
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institute, and Pediatric Oncology, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Tommy Martinsson
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Department of Pediatric Oncology and Hematology, University of Cologne, Cologne, Germany
| | - Tanmoy Mondal
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Chemistry, Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, 41345 Sweden
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7
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Chien CW, Tang YA, Jeng SL, Pan HA, Sun HS. Blastocyst telomere length predicts successful implantation after frozen-thawed embryo transfer. Hum Reprod Open 2024; 2024:hoae012. [PMID: 38515829 PMCID: PMC10955253 DOI: 10.1093/hropen/hoae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 02/04/2024] [Indexed: 03/23/2024] Open
Abstract
STUDY QUESTION Do embryos with longer telomere length (TL) at the blastocyst stage have a higher capacity to survive after frozen-thawed embryo transfer (FET)? SUMMARY ANSWER Digitally estimated TL using low-pass whole genome sequencing (WGS) data from the preimplantation genetic testing for aneuploidy (PGT-A) process demonstrates that blastocyst TL is the most essential factor associated with likelihood of implantation. WHAT IS KNOWN ALREADY The lifetime TL is established in the early cleavage cycles following fertilization through a recombination-based lengthening mechanism and starts erosion beyond the blastocyst stage. In addition, a telomerase-mediated slow erosion of TL in human fetuses has been observed from a gestational age of 6-11 weeks. Finally, an abnormal shortening of telomeres is likely involved in embryo loss during early development. STUDY DESIGN SIZE DURATION Blastocyst samples were obtained from patients who underwent PGT-A and FET in an IVF center from March 2015 to May 2018. Digitally estimated mitochondrial copy number (mtCN) and TL were used to study associations with the implantation potential of each embryo. PARTICIPANTS/MATERIALS SETTING AND METHODS In total, 965 blastocysts from 232 cycles (164 patients) were available to investigate the biological and clinical relevance of TL. A WGS-based workflow was applied to determine the ploidy of each embryo. Data from low-pass WGS-PGT-A were used to estimate the mtCN and TL for each embryo. Single-variant and multi-variant logistic regression, decision tree, and random forest models were applied to study various factors in association with the implantation potential of each embryo. MAIN RESULTS AND THE ROLE OF CHANCE Of the 965 blastocysts originally available, only 216 underwent FET. While mtCN from the transferred embryos is significantly associated with the ploidy call of each embryo, mtCN has no role in impacting IVF outcomes after an embryo transfer in these women. The results indicate that mtCN is a marker of embryo aneuploidy. On the other hand, digitally estimated TL is the most prominent univariant factor and showed a significant positive association with pregnancy outcomes (P < 0.01, odds ratio 79.1). We combined several maternal and embryo parameters to study the joint effects on successful implantation. The machine learning models, namely decision tree and random forest, were trained and yielded classification accuracy of 0.82 and 0.91, respectively. Taken together, these results support the vital role of TL in governing implantation potential, perhaps through the ability to control embryo survival after transfer. LIMITATIONS REASONS FOR CAUTION The small sample size limits our study as only 216 blastocysts were transferred. The number was further reduced to 153 blastocysts, where pregnancy outcomes could be accurately traced. The other limitation of this study is that all data were collected from a single IVF center. The uniform and controlled operation of IVF cycles in a single center may cause selection bias. WIDER IMPLICATIONS OF THE FINDINGS We present novel findings to show that digitally estimated TL at the blastocyst stage is a predictor of pregnancy capacity after a FET cycle. As elective single-embryo transfer has become the mainstream direction in reproductive medicine, prioritizing embryos based on their implantation potential is crucial for clinical infertility treatment in order to reduce twin pregnancy rate and the time to pregnancy in an IVF center. The AI-powered, random forest prediction model established in this study thus provides a way to improve clinical practice and optimize the chances for people with fertility problems to achieve parenthood. STUDY FUNDING/COMPETING INTERESTS This study was supported by a grant from the National Science and Technology Council, Taiwan (MOST 108-2321-B-006-013 -). There were no competing interests. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Chun-Wei Chien
- Center for Genomic Medicine, Innovation Headquarters, National Cheng Kung University, Tainan, Taiwan
| | - Yen-An Tang
- Center for Genomic Medicine, Innovation Headquarters, National Cheng Kung University, Tainan, Taiwan
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shuen-Lin Jeng
- Department of Statistics, Institute of Data Science, National Cheng Kung University, Tainan, Taiwan
- Center for Innovative FinTech Business Models, National Cheng Kung University, Tainan, Taiwan
| | - Hsien-An Pan
- IVF center, An-An Women and Children Clinic, Tainan, Taiwan
- Department of Obstetrics and Gynecology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - H Sunny Sun
- Center for Genomic Medicine, Innovation Headquarters, National Cheng Kung University, Tainan, Taiwan
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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8
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Chaisson MJP, Sulovari A, Valdmanis PN, Miller DE, Eichler EE. Advances in the discovery and analyses of human tandem repeats. Emerg Top Life Sci 2023; 7:361-381. [PMID: 37905568 PMCID: PMC10806765 DOI: 10.1042/etls20230074] [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: 06/12/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023]
Abstract
Long-read sequencing platforms provide unparalleled access to the structure and composition of all classes of tandemly repeated DNA from STRs to satellite arrays. This review summarizes our current understanding of their organization within the human genome, their importance with respect to disease, as well as the advances and challenges in understanding their genetic diversity and functional effects. Novel computational methods are being developed to visualize and associate these complex patterns of human variation with disease, expression, and epigenetic differences. We predict accurate characterization of this repeat-rich form of human variation will become increasingly relevant to both basic and clinical human genetics.
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Affiliation(s)
- Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, U.S.A
- The Genomic and Epigenomic Regulation Program, USC Norris Cancer Center, University of Southern California, Los Angeles, CA 90089, U.S.A
| | - Arvis Sulovari
- Computational Biology, Cajal Neuroscience Inc, Seattle, WA 98102, U.S.A
| | - Paul N Valdmanis
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, U.S.A
| | - Danny E Miller
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, U.S.A
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, U.S.A
- Department of Pediatrics, University of Washington, Seattle, WA 98195, U.S.A
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, U.S.A
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9
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Ferrer A, Stephens ZD, Kocher JPA. Experimental and Computational Approaches to Measure Telomere Length: Recent Advances and Future Directions. Curr Hematol Malig Rep 2023; 18:284-291. [PMID: 37947937 PMCID: PMC10709248 DOI: 10.1007/s11899-023-00717-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2023] [Indexed: 11/12/2023]
Abstract
PURPOSE OF REVIEW The length of telomeres, protective structures at the chromosome ends, is a well-established biomarker for pathological conditions including multisystemic syndromes called telomere biology disorders. Approaches to measure telomere length (TL) differ on whether they estimate average, distribution, or chromosome-specific TL, and each presents their own advantages and limitations. RECENT FINDINGS The development of long-read sequencing and publication of the telomere-to-telomere human genome reference has allowed for scalable and high-resolution TL estimation in pre-existing sequencing datasets but is still impractical as a dedicated TL test. As sequencing costs continue to fall and strategies for selectively enriching telomere regions prior to sequencing improve, these approaches may become a promising alternative to classic methods. Measurement methods rely on probe hybridization, qPCR or more recently, computational methods using sequencing data. Refinements of existing techniques and new approaches have been recently developed but a test that is accurate, simple, and scalable is still lacking.
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Affiliation(s)
- Alejandro Ferrer
- Division of Hematology, Mayo Clinic, Rochester, 200 First Street SW, Rochester, MN, USA.
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
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10
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Guo M, Songyang Z, Xiong Y. ChArmTelo Enables Large-Scale Chromosome Arm-Level Telomere Analysis across Human Populations and in Cancer Patients. SMALL METHODS 2023; 7:e2300385. [PMID: 37526331 DOI: 10.1002/smtd.202300385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/29/2023] [Indexed: 08/02/2023]
Abstract
Telomeres are structures protecting chromosome ends. However, a scalable and cost-effective method to investigate chromosome arm-level (ChArm) telomeres (Telos) in large-scale projects is still lacking, hindering intensive investigation of high-resolution telomeres across cancers and other diseases. Here, ChArmTelo, the first computational toolbox to analyze telomeres at chromosome arm level in human and other animal species, using 10X linked-read and similar technologies, is presented. ChArmTelo currently consists of two algorithms, TeloEM and TeloKnow, for arm-level telomere length (TL) analysis. The algorithms are demonstrated by comprehensive analysis of chromosome arm-level telomere lengths (chArmTLs) in nearly 400 whole genome sequencing samples (WGS) from human populations and animals, including healthy and cancer samples. Notably, considerable performance improvement contributed by using the latest complete telomere-to-telomere reference genome (CHM13v2), compared to hg38, is shown. ChArmTelo reveals population-specific chArmTL differences and liver cancer signatures of chArmTLs and that DNA replication origin disruption may contribute to cancer by affecting TLs. Importantly, ChArmTelo can be readily applied to tens of thousands of cancer and healthy samples with published WGS data.
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Affiliation(s)
- Mengbiao Guo
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhou Songyang
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yuanyan Xiong
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
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11
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Mock A, Teleanu MV, Kreutzfeldt S, Heilig CE, Hüllein J, Möhrmann L, Jahn A, Hanf D, Kerle IA, Singh HM, Hutter B, Uhrig S, Fröhlich M, Neumann O, Hartig A, Brückmann S, Hirsch S, Grund K, Dikow N, Lipka DB, Renner M, Bhatti IA, Apostolidis L, Schlenk RF, Schaaf CP, Stenzinger A, Schröck E, Hübschmann D, Heining C, Horak P, Glimm H, Fröhling S. NCT/DKFZ MASTER handbook of interpreting whole-genome, transcriptome, and methylome data for precision oncology. NPJ Precis Oncol 2023; 7:109. [PMID: 37884744 PMCID: PMC10603123 DOI: 10.1038/s41698-023-00458-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
Analysis of selected cancer genes has become an important tool in precision oncology but cannot fully capture the molecular features and, most importantly, vulnerabilities of individual tumors. Observational and interventional studies have shown that decision-making based on comprehensive molecular characterization adds significant clinical value. However, the complexity and heterogeneity of the resulting data are major challenges for disciplines involved in interpretation and recommendations for individualized care, and limited information exists on how to approach multilayered tumor profiles in clinical routine. We report our experience with the practical use of data from whole-genome or exome and RNA sequencing and DNA methylation profiling within the MASTER (Molecularly Aided Stratification for Tumor Eradication Research) program of the National Center for Tumor Diseases (NCT) Heidelberg and Dresden and the German Cancer Research Center (DKFZ). We cover all relevant steps of an end-to-end precision oncology workflow, from sample collection, molecular analysis, and variant prioritization to assigning treatment recommendations and discussion in the molecular tumor board. To provide insight into our approach to multidimensional tumor profiles and guidance on interpreting their biological impact and diagnostic and therapeutic implications, we present case studies from the NCT/DKFZ molecular tumor board that illustrate our daily practice. This manual is intended to be useful for physicians, biologists, and bioinformaticians involved in the clinical interpretation of genome-wide molecular information.
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Affiliation(s)
- Andreas Mock
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Pathology, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Maria-Veronica Teleanu
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Hematology, Oncology and Rheumatology, Heidelberg Unversity Hospital, Heidelberg, Germany
| | - Simon Kreutzfeldt
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph E Heilig
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jennifer Hüllein
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Lino Möhrmann
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases/University Cancer Center (NCT/UCC) Dresden, Dresden, Germany
- DKFZ, Heidelberg, Germany
| | - Arne Jahn
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus, Technische Universität Dresden and Hereditary Cancer Syndrome Center Dresden, Dresden, Germany
| | - Dorothea Hanf
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases/University Cancer Center (NCT/UCC) Dresden, Dresden, Germany
- DKFZ, Heidelberg, Germany
| | - Irina A Kerle
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases/University Cancer Center (NCT/UCC) Dresden, Dresden, Germany
- DKFZ, Heidelberg, Germany
| | - Hans Martin Singh
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology, NCT Heidelberg and Heidelberg University Hospital, Heidelberg, Germany
| | - Barbara Hutter
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Sebastian Uhrig
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Martina Fröhlich
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Olaf Neumann
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas Hartig
- Institute of Pathology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Sascha Brückmann
- Institute of Pathology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Steffen Hirsch
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Kerstin Grund
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Nicola Dikow
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel B Lipka
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Translational Cancer Epigenomics, Division of Translational Medical Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Marcus Renner
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Irfan Ahmed Bhatti
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology, NCT Heidelberg and Heidelberg University Hospital, Heidelberg, Germany
| | - Leonidas Apostolidis
- Department of Medical Oncology, NCT Heidelberg and Heidelberg University Hospital, Heidelberg, Germany
| | - Richard F Schlenk
- Department of Hematology, Oncology and Rheumatology, Heidelberg Unversity Hospital, Heidelberg, Germany
- Department of Medical Oncology, NCT Heidelberg and Heidelberg University Hospital, Heidelberg, Germany
- NCT Trial Center, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Christian P Schaaf
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Evelin Schröck
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus, Technische Universität Dresden and Hereditary Cancer Syndrome Center Dresden, Dresden, Germany
| | - Daniel Hübschmann
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Christoph Heining
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases/University Cancer Center (NCT/UCC) Dresden, Dresden, Germany
- DKFZ, Heidelberg, Germany
| | - Peter Horak
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hanno Glimm
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases/University Cancer Center (NCT/UCC) Dresden, Dresden, Germany
- DKFZ, Heidelberg, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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12
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Sung S, Kim E, Niida H, Kim C, Lee J. Distinct characteristics of two types of alternative lengthening of telomeres in mouse embryonic stem cells. Nucleic Acids Res 2023; 51:9122-9143. [PMID: 37496110 PMCID: PMC10516625 DOI: 10.1093/nar/gkad617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 06/27/2023] [Accepted: 07/13/2023] [Indexed: 07/28/2023] Open
Abstract
Telomere length must be maintained in actively dividing cells to avoid cellular arrest or death. In the absence of telomerase activity, activation of alternative lengthening of telomeres (ALT) allows the maintenance of telomeric length and prolongs the cellular lifespan. Our previous studies have established two types of ALT survivors from mouse embryonic stem cells. The key differences between these ALT survivors are telomere-constituting sequences: non-telomeric sequences and canonical telomeric repeats, with each type of ALT survivors being referred to as type I and type II, respectively. We explored how the characteristics of the two types of ALT lines reflect their fates using multi-omics approaches. The most notable gene expression signatures of type I and type II ALT cell lines were chromatin remodelling and DNA repair, respectively. Compared with type II cells, type I ALT cells accumulated more mutations and demonstrated persistent telomere instability. These findings indicate that cells of the same origin have separate routes for survival, thus providing insights into the plasticity of crisis-suffering cells and cancers.
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Affiliation(s)
- Sanghyun Sung
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Seoul 08826, Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Gwanak-ro 1, Seoul 08826, Korea
| | - Eunkyeong Kim
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Seoul 08826, Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Gwanak-ro 1, Seoul 08826, Korea
| | - Hiroyuki Niida
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan
| | - Chuna Kim
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Gwahak-ro 125, Daejeon 34141, Korea
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Seoul 08826, Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Gwanak-ro 1, Seoul 08826, Korea
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13
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Sharaf R, Jin DX, Grady J, Napier C, Ebot E, Frampton GM, Albacker LA, Thomas DM, Montesion M. A pan-sarcoma landscape of telomeric content shows that alterations in RAD51B and GID4 are associated with higher telomeric content. NPJ Genom Med 2023; 8:26. [PMID: 37709802 PMCID: PMC10502097 DOI: 10.1038/s41525-023-00369-6] [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: 05/17/2023] [Accepted: 08/18/2023] [Indexed: 09/16/2023] Open
Abstract
Tumor cells need to activate a telomere maintenance mechanism, enabling limitless replication. The bulk of evidence supports that sarcomas predominantly use alternative lengthening of telomeres (ALT) mechanism, commonly associated with alterations in ATRX and DAXX. In our dataset, only 12.3% of sarcomas harbored alterations in these genes. Thus, we checked for the presence of other genomic determinants of high telomeric content in sarcomas. Our dataset consisted of 13555 sarcoma samples, sequenced as a part of routine clinical care on the FoundationOne®Heme platform. We observed a median telomeric content of 622.3 telomeric reads per GC-matched million reads (TRPM) across all samples. In agreement with previous studies, telomeric content was significantly higher in ATRX altered and POT1 altered sarcomas. We further observed that sarcomas with alterations in RAD51B or GID4 were enriched in samples with high telomeric content, specifically within uterus leiomyosarcoma for RAD51B and soft tissue sarcoma (not otherwise specified, nos) for GID4, Furthermore, RAD51B and POT1 alterations were mutually exclusive with ATRX and DAXX alterations, suggestive of functional redundancy. Our results propose a role played by RAD51B and GID4 in telomere elongation in sarcomas and open research opportunities for agents aimed at targeting this critical pathway in tumorigenesis.
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Affiliation(s)
| | | | - John Grady
- Omico Australian Genomic Cancer Medicine, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, Australia
| | - Christine Napier
- Omico Australian Genomic Cancer Medicine, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, Australia
| | - Ericka Ebot
- Foundation Medicine Inc., Cambridge, MA, USA
| | | | | | - David M Thomas
- Omico Australian Genomic Cancer Medicine, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, Australia
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14
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Abel HJ, Oetjen KA, Miller CA, Ramakrishnan SM, Day RB, Helton NM, Fronick CC, Fulton RS, Heath SE, Tarnawsky SP, Nonavinkere Srivatsan S, Duncavage EJ, Schroeder MC, Payton JE, Spencer DH, Walter MJ, Westervelt P, DiPersio JF, Ley TJ, Link DC. Genomic landscape of TP53-mutated myeloid malignancies. Blood Adv 2023; 7:4586-4598. [PMID: 37339484 PMCID: PMC10425686 DOI: 10.1182/bloodadvances.2023010156] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/19/2023] [Accepted: 06/07/2023] [Indexed: 06/22/2023] Open
Abstract
TP53-mutated myeloid malignancies are associated with complex cytogenetics and extensive structural variants, which complicates detailed genomic analysis by conventional clinical techniques. We performed whole-genome sequencing (WGS) of 42 acute myeloid leukemia (AML)/myelodysplastic syndromes (MDS) cases with paired normal tissue to better characterize the genomic landscape of TP53-mutated AML/MDS. WGS accurately determines TP53 allele status, a key prognostic factor, resulting in the reclassification of 12% of cases from monoallelic to multihit. Although aneuploidy and chromothripsis are shared with most TP53-mutated cancers, the specific chromosome abnormalities are distinct to each cancer type, suggesting a dependence on the tissue of origin. ETV6 expression is reduced in nearly all cases of TP53-mutated AML/MDS, either through gene deletion or presumed epigenetic silencing. Within the AML cohort, mutations of NF1 are highly enriched, with deletions of 1 copy of NF1 present in 45% of cases and biallelic mutations in 17%. Telomere content is increased in TP53-mutated AMLs compared with other AML subtypes, and abnormal telomeric sequences were detected in the interstitial regions of chromosomes. These data highlight the unique features of TP53-mutated myeloid malignancies, including the high frequency of chromothripsis and structural variation, the frequent involvement of unique genes (including NF1 and ETV6) as cooperating events, and evidence for altered telomere maintenance.
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Affiliation(s)
- Haley J. Abel
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Karolyn A. Oetjen
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Christopher A. Miller
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Sai M. Ramakrishnan
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Ryan B. Day
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Nichole M. Helton
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Catrina C. Fronick
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Robert S. Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Sharon E. Heath
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Stefan P. Tarnawsky
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | | | - Eric J. Duncavage
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO
| | - Molly C. Schroeder
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO
| | - Jacqueline E. Payton
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO
| | - David H. Spencer
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO
| | - Matthew J. Walter
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Peter Westervelt
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - John F. DiPersio
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Timothy J. Ley
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Daniel C. Link
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
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15
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Stundon JL, Ijaz H, Gaonkar KS, Kaufman RS, Jin R, Karras A, Vaksman Z, Kim J, Corbett RJ, Lueder MR, Miller DP, Guo Y, Santi M, Li M, Lopez G, Storm PB, Resnick AC, Waanders AJ, MacFarland SP, Stewart DR, Diskin SJ, Rokita JL, Cole KA. Alternative lengthening of telomeres (ALT) in pediatric high-grade gliomas can occur without ATRX mutation and is enriched in patients with pathogenic germline mismatch repair (MMR) variants. Neuro Oncol 2023; 25:1331-1342. [PMID: 36541551 PMCID: PMC10326481 DOI: 10.1093/neuonc/noac278] [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: 08/05/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND To achieve replicative immortality, most cancers develop a telomere maintenance mechanism, such as reactivation of telomerase or alternative lengthening of telomeres (ALT). There are limited data on the prevalence and clinical significance of ALT in pediatric brain tumors, and ALT-directed therapy is not available. METHODS We performed C-circle analysis (CCA) on 579 pediatric brain tumors that had corresponding tumor/normal whole genome sequencing through the Open Pediatric Brain Tumor Atlas (OpenPBTA). We detected ALT in 6.9% (n = 40/579) of these tumors and completed additional validation by ultrabright telomeric foci in situ on a subset of these tumors. We used CCA to validate TelomereHunter for computational prediction of ALT status and focus subsequent analyses on pediatric high-grade gliomas (pHGGs) Finally, we examined whether ALT is associated with recurrent somatic or germline alterations. RESULTS ALT is common in pHGGs (n = 24/63, 38.1%), but occurs infrequently in other pediatric brain tumors (<3%). Somatic ATRX mutations occur in 50% of ALT+ pHGGs and in 30% of ALT- pHGGs. Rare pathogenic germline variants in mismatch repair (MMR) genes are significantly associated with an increased occurrence of ALT. CONCLUSIONS We demonstrate that ATRX is mutated in only a subset of ALT+ pHGGs, suggesting other mechanisms of ATRX loss of function or alterations in other genes may be associated with the development of ALT in these patients. We show that germline variants in MMR are associated with the development of ALT in patients with pHGG.
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Affiliation(s)
- Jennifer L Stundon
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania,USA
| | - Heba Ijaz
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania,USA
| | - Krutika S Gaonkar
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Rebecca S Kaufman
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Run Jin
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Anastasios Karras
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Zalman Vaksman
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Jung Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland,USA
| | - Ryan J Corbett
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Matthew R Lueder
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Daniel P Miller
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Yiran Guo
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Marilyn Li
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Gonzalo Lopez
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Phillip B Storm
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Adam C Resnick
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Angela J Waanders
- Division of Hematology, Oncology, NeuroOncology, and Stem Cell Transplant, Ann & Robert H Lurie Children’s Hospital of Chicago, Illinois,USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,USA
| | - Suzanne P MacFarland
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania,USA
| | - Douglas R Stewart
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland,USA
| | - Sharon J Diskin
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania,USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania,USA
| | - Jo Lynne Rokita
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Kristina A Cole
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania,USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania,USA
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16
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Becher OJ. A new path to alternative lengthening of telomeres? Neuro Oncol 2023; 25:1343-1344. [PMID: 36883676 PMCID: PMC10326486 DOI: 10.1093/neuonc/noad054] [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: 02/28/2023] [Indexed: 03/09/2023] Open
Affiliation(s)
- Oren J Becher
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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17
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Cararo Lopes E, Sawant A, Moore D, Ke H, Shi F, Laddha S, Chen Y, Sharma A, Naumann J, Guo JY, Gomez M, Ibrahim M, Smith TL, Riedlinger GM, Lattime EC, Trooskin S, Ganesan S, Su X, Pasqualini R, Arap W, De S, Chan CS, White E. Integrated metabolic and genetic analysis reveals distinct features of human differentiated thyroid cancer. Clin Transl Med 2023; 13:e1298. [PMID: 37317665 PMCID: PMC10267429 DOI: 10.1002/ctm2.1298] [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: 03/10/2023] [Revised: 05/22/2023] [Accepted: 05/27/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND Differentiated thyroid cancer (DTC) affects thousands of lives worldwide each year. Typically, DTC is a treatable disease with a good prognosis. Yet, some patients are subjected to partial or total thyroidectomy and radioiodine therapy to prevent local disease recurrence and metastasis. Unfortunately, thyroidectomy and/or radioiodine therapy often worsen(s) quality of life and might be unnecessary in indolent DTC cases. On the other hand, the lack of biomarkers indicating a potential metastatic thyroid cancer imposes an additional challenge to managing and treating patients with this disease. AIM The presented clinical setting highlights the unmet need for a precise molecular diagnosis of DTC and potential metastatic disease, which should dictate appropriate therapy. MATERIALS AND METHODS In this article, we present a differential multi-omics model approach, including metabolomics, genomics, and bioinformatic models, to distinguish normal glands from thyroid tumours. Additionally, we are proposing biomarkers that could indicate potential metastatic diseases in papillary thyroid cancer (PTC), a sub-class of DTC. RESULTS Normal and tumour thyroid tissue from DTC patients had a distinct yet well-defined metabolic profile with high levels of anabolic metabolites and/or other metabolites associated with the energy maintenance of tumour cells. The consistency of the DTC metabolic profile allowed us to build a bioinformatic classification model capable of clearly distinguishing normal from tumor thyroid tissues, which might help diagnose thyroid cancer. Moreover, based on PTC patient samples, our data suggest that elevated nuclear and mitochondrial DNA mutational burden, intra-tumour heterogeneity, shortened telomere length, and altered metabolic profile reflect the potential for metastatic disease. DISCUSSION Altogether, this work indicates that a differential and integrated multi-omics approach might improve DTC management, perhaps preventing unnecessary thyroid gland removal and/or radioiodine therapy. CONCLUSIONS Well-designed, prospective translational clinical trials will ultimately show the value of this integrated multi-omics approach and early diagnosis of DTC and potential metastatic PTC.
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Affiliation(s)
- Eduardo Cararo Lopes
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
- Department of Molecular Biology and BiochemistryRutgers UniversityPiscatawayNew JerseyUSA
| | - Akshada Sawant
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
| | - Dirk Moore
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
- Department of Biostatistics and EpidemiologyRutgers School of Public HealthPiscatawayNew JerseyUSA
| | - Hua Ke
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
| | - Fuqian Shi
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
| | - Saurabh Laddha
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
| | - Ying Chen
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
| | - Anchal Sharma
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
| | - Jake Naumann
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
| | - Jessie Yanxiang Guo
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
- Department of MedicineRobert Wood Johnson Medical SchoolRutgers UniversityNew BrunswickNew JerseyUSA
- Department of Chemical BiologyRutgers Ernest Mario School of PharmacyPiscatawayNew JerseyUSA
| | - Maria Gomez
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
| | - Maria Ibrahim
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
| | - Tracey L. Smith
- Rutgers Cancer Institute of New JerseyNewarkNew JerseyUSA
- Division of Cancer BiologyDepartment of Radiation OncologyRutgers New Jersey Medical SchoolNewarkNew JerseyUSA
| | | | - Edmund C. Lattime
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
- Department of Surgery, Robert Wood Johnson Medical SchoolRutgers UniversityNew BrunswickNew JerseyUSA
| | - Stanley Trooskin
- Department of Surgery, Robert Wood Johnson Medical SchoolRutgers UniversityNew BrunswickNew JerseyUSA
| | - Shridar Ganesan
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
- Department of MedicineRobert Wood Johnson Medical SchoolRutgers UniversityNew BrunswickNew JerseyUSA
| | - Xiaoyang Su
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
- Department of MedicineRobert Wood Johnson Medical SchoolRutgers UniversityNew BrunswickNew JerseyUSA
| | - Renata Pasqualini
- Rutgers Cancer Institute of New JerseyNewarkNew JerseyUSA
- Division of Cancer BiologyDepartment of Radiation OncologyRutgers New Jersey Medical SchoolNewarkNew JerseyUSA
| | - Wadih Arap
- Rutgers Cancer Institute of New JerseyNewarkNew JerseyUSA
- Division of Hematology/OncologyDepartment of MedicineRutgers New Jersey Medical SchoolNewarkNew JerseyUSA
| | - Subhajyoti De
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
| | - Chang S. Chan
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
- Department of MedicineRobert Wood Johnson Medical SchoolRutgers UniversityNew BrunswickNew JerseyUSA
| | - Eileen White
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
- Department of Molecular Biology and BiochemistryRutgers UniversityPiscatawayNew JerseyUSA
- Ludwig Princeton Branch, Ludwig Institute for Cancer ResearchPrinceton UniversityPrincetonNew JerseyUSA
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18
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Telomere Length Changes in Cancer: Insights on Carcinogenesis and Potential for Non-Invasive Diagnostic Strategies. Genes (Basel) 2023; 14:genes14030715. [PMID: 36980987 PMCID: PMC10047978 DOI: 10.3390/genes14030715] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Telomere dynamics play a crucial role in the maintenance of chromosome integrity; changes in telomere length may thus contribute to the development of various diseases including cancer. Understanding the role of telomeric DNA in carcinogenesis and detecting the presence of cell-free telomeric DNA (cf-telDNA) in body fluids offer a potential biomarker for novel cancer screening and diagnostic strategies. Liquid biopsy is becoming increasingly popular due to its undeniable benefits over conventional invasive methods. However, the organization and function of cf-telDNA in the extracellular milieu are understudied. This paper provides a review based on 3,398,017 cancer patients, patients with other conditions, and control individuals with the aim to shed more light on the inconsistent nature of telomere lengthening/shortening in oncological contexts. To gain a better understanding of biological factors (e.g., telomerase activation, alternative lengthening of telomeres) affecting telomere homeostasis across different types of cancer, we summarize mechanisms responsible for telomere length maintenance. In conclusion, we compare tissue- and liquid biopsy-based approaches in cancer assessment and provide a brief outlook on the methodology used for telomere length evaluation, highlighting the advances of state-of-the-art approaches in the field.
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19
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Sun Q, Wang H, Tao S, Xi X. Large-Scale Detection of Telomeric Motif Sequences in Genomic Data Using TelFinder. Microbiol Spectr 2023; 11:e0392822. [PMID: 36847562 PMCID: PMC10100673 DOI: 10.1128/spectrum.03928-22] [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: 09/26/2022] [Accepted: 02/04/2023] [Indexed: 03/01/2023] Open
Abstract
Telomeres are regions of tandem repeated sequences at the ends of linear chromosomes that protect against DNA damage and chromosome fusion. Telomeres are associated with senescence and cancers and have attracted the attention of an increasing number of researchers. However, few telomeric motif sequences are known. Given the mounting interest in telomeres, an efficient computational tool for the de novo detection of the telomeric motif sequence of new species is needed since experimental-based methods are costly in terms of time and effort. Here, we report the development of TelFinder, an easy-to-use and freely available tool for the de novo detection of telomeric motif sequences from genomic data. The vast quantity of readily available genomic data makes it possible to apply this tool to any species of interest, which will undoubtedly inspire studies requiring telomeric repeat information and improve the utilization of these genomic data sets. We have tested TelFinder on telomeric sequences available in the Telomerase Database, and the detection accuracy reaches 90%. In addition, variation analyses in telomere sequences can be performed by TelFinder for the first time. The telomere variation preference of different chromosomes and even at the ends of the chromosome can provide clues regarding the underlying mechanisms of telomeres. Overall, these results shed new light on the divergent evolution of telomeres. IMPORTANCE Telomeres are reported to be highly correlated with the cell cycle and aging. As a result, research on telomere composition and evolution has become more and more urgent. However, using experimental methods to detect telomeric motif sequences is slow and costly. To combat this challenge, we developed TelFinder, a computational tool for the de novo detection of the telomere composition only using genomic data. In this study, we showed that a lot of complicated telomeric motifs could be identified by TelFinder only using genomic data. In addition, TelFinder can be used to check variation analyses in telomere sequences, which could lead to a deeper understanding of telomere sequences.
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Affiliation(s)
- Qing Sun
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
- Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Hao Wang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
- Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Shiheng Tao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
- Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Xuguang Xi
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
- Université Paris-Saclay, ENS Paris-Saclay, CNRS, LBPA, Gif-sur-Yvette, France
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20
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Falcinelli M, Dell'Omo G, Grassi E, Mariella E, Leto SM, Scardellato S, Lorenzato A, Arena S, Bertotti A, Trusolino L, Bardelli A, d'Adda di Fagagna F. Colorectal cancer patient-derived organoids and cell lines harboring ATRX and/or DAXX mutations lack Alternative Lengthening of Telomeres (ALT). Cell Death Dis 2023; 14:96. [PMID: 36759506 PMCID: PMC9911751 DOI: 10.1038/s41419-023-05640-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/19/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023]
Abstract
Telomere maintenance is necessary to maintain cancer cell unlimited viability. However, the mechanisms maintaining telomere length in colorectal cancer (CRC) have not been extensively investigated. Telomere maintenance mechanisms (TMM) include the re-expression of telomerase or alternative lengthening of telomeres (ALT). ALT is genetically associated with somatic alterations in alpha-thalassemia/mental retardation X-linked (ATRX) and death domain-associated protein (DAXX) genes. Cells displaying ALT present distinctive features including C-circles made of telomeric DNA, long and heterogenous telomeric tracts, and telomeric DNA co-localized with promyelocytic leukemia (PML) bodies forming so-called ALT-associated PML bodies (APBs). Here, we identified mutations in ATRX and/or DAXX genes in an extensive collection of CRC samples including 119 patient-derived organoids (PDOs) and 232 established CRC cell lines. C-circles measured in CRC PDOs and cell lines showed low levels overall. We also observed that CRC PDOs and cell lines did not display a significant accumulation of APBs or long telomeres with no appreciable differences between wild-type and mutated ATRX/DAXX samples. Overall, our extensive analyses indicate that CRC is not prone to engage ALT, even when carrying genetic lesions in ATRX and/or DAXX, and support the notion that ATRX/DAXX genomic footprints are not reliable predictors of ALT.
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Affiliation(s)
- Marta Falcinelli
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Giulia Dell'Omo
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Elena Grassi
- Department of Oncology, University of Torino, 1060 Candiolo, Torino, Italy
- Candiolo Cancer Institute - FPO IRCCs, 10060 Candiolo, Torino, Italy
| | - Elisa Mariella
- Department of Oncology, University of Torino, 1060 Candiolo, Torino, Italy
- Candiolo Cancer Institute - FPO IRCCs, 10060 Candiolo, Torino, Italy
| | | | | | - Annalisa Lorenzato
- Department of Oncology, University of Torino, 1060 Candiolo, Torino, Italy
- Candiolo Cancer Institute - FPO IRCCs, 10060 Candiolo, Torino, Italy
| | - Sabrina Arena
- Department of Oncology, University of Torino, 1060 Candiolo, Torino, Italy
- Candiolo Cancer Institute - FPO IRCCs, 10060 Candiolo, Torino, Italy
| | - Andrea Bertotti
- Department of Oncology, University of Torino, 1060 Candiolo, Torino, Italy
- Candiolo Cancer Institute - FPO IRCCs, 10060 Candiolo, Torino, Italy
| | - Livio Trusolino
- Department of Oncology, University of Torino, 1060 Candiolo, Torino, Italy
- Candiolo Cancer Institute - FPO IRCCs, 10060 Candiolo, Torino, Italy
| | - Alberto Bardelli
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
- Department of Oncology, University of Torino, 1060 Candiolo, Torino, Italy
- Candiolo Cancer Institute - FPO IRCCs, 10060 Candiolo, Torino, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy.
- Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza", Pavia, Italy.
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21
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Heaphy CM, Singhi AD. Reprint of: The Diagnostic and Prognostic Utility of Incorporating DAXX, ATRX, and Alternative Lengthening of Telomeres (ALT) to the Evaluation of Pancreatic Neuroendocrine Tumors (PanNETs). Hum Pathol 2023; 132:1-11. [PMID: 36702689 DOI: 10.1016/j.humpath.2023.01.004] [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: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 01/26/2023]
Abstract
Pancreatic neuroendocrine tumors (PanNETs) are a heterogeneous group of neoplasms with increasing incidence and an ill-defined pathobiology. Although many PanNETs are indolent and remain stable for years, a subset may behave aggressively and metastasize widely. Thus, the increasing and frequent detection of PanNETs presents a treatment dilemma. Current prognostic systems are susceptible to interpretation errors, sampling issues, and do not accurately reflect the clinical behavior of these neoplasms. Hence, additional biomarkers are needed to improve the prognostic stratification of patients diagnosed with a PanNET. Recent studies have identified alterations in death domain-associated protein 6 (DAXX) and alpha-thalassemia/mental retardation X-linked (ATRX), as well as alternative lengthening of telomeres (ALT), as promising prognostic biomarkers. This review summarizes the identification, clinical utility, and specific nuances in testing for DAXX/ATRX by immunohistochemistry and ALT by telomere-specific fluorescence in situ hybridization in PanNETs. Furthermore, a discussion on diagnostic indications for DAXX, ATRX, and ALT status is provided to include the distinction between PanNETs and pancreatic neuroendocrine carcinomas (PanNECs), and determining pancreatic origin for metastatic neuroendocrine tumors in the setting of an unknown primary.
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Affiliation(s)
- Christopher M Heaphy
- Department of Medicine, Boston University, School of Medicine, Boston, MA, 02118, USA
| | - Aatur D Singhi
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA.
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22
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Abel HJ, Oetjen KA, Miller CA, Ramakrishnan SM, Day RB, Helton NM, Fronick CC, Fulton RS, Heath SE, Tarnawsky SP, Srivatsan SN, Duncavage EJ, Schroeder MC, Payton JE, Spencer DH, Walter MJ, Westervelt P, DiPersio JF, Ley TJ, Link DC. Genomic landscape of TP53 -mutated myeloid malignancies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.10.23284322. [PMID: 36711871 PMCID: PMC9882519 DOI: 10.1101/2023.01.10.23284322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
TP53 -mutated myeloid malignancies are most frequently associated with complex cytogenetics. The presence of complex and extensive structural variants complicates detailed genomic analysis by conventional clinical techniques. We performed whole genome sequencing of 42 AML/MDS cases with paired normal tissue to characterize the genomic landscape of TP53 -mutated myeloid malignancies. The vast majority of cases had multi-hit involvement at the TP53 genetic locus (94%), as well as aneuploidy and chromothripsis. Chromosomal patterns of aneuploidy differed significantly from TP53 -mutated cancers arising in other tissues. Recurrent structural variants affected regions that include ETV6 on chr12p, RUNX1 on chr21, and NF1 on chr17q. Most notably for ETV6 , transcript expression was low in cases of TP53 -mutated myeloid malignancies both with and without structural rearrangements involving chromosome 12p. Telomeric content is increased in TP53 -mutated AML/MDS compared other AML subtypes, and telomeric content was detected adjacent to interstitial regions of chromosomes. The genomic landscape of TP53 -mutated myeloid malignancies reveals recurrent structural variants affecting key hematopoietic transcription factors and telomeric repeats that are generally not detected by panel sequencing or conventional cytogenetic analyses. Key Points WGS comprehensively determines TP53 mutation status, resulting in the reclassification of 12% of cases from mono-allelic to multi-hit Chromothripsis is more frequent than previously appreciated, with a preference for specific chromosomes ETV6 is deleted in 45% of cases, with evidence for epigenetic suppression in non-deleted cases NF1 is mutated in 48% of cases, with multi-hit mutations in 17% of these cases TP53 -mutated AML/MDS is associated with altered telomere content compared with other AMLs.
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Affiliation(s)
- Haley J. Abel
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | - Karolyn A. Oetjen
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | - Christopher A. Miller
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | - Sai M. Ramakrishnan
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | - Ryan B. Day
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | - Nichole M. Helton
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | | | - Robert S. Fulton
- McDonnell Genome Institute, Washington University School of Medicine
| | - Sharon E. Heath
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | - Stefan P. Tarnawsky
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | | | - Eric J. Duncavage
- Department of Pathology & Immunology, Washington University School of Medicine
| | - Molly C. Schroeder
- Department of Pathology & Immunology, Washington University School of Medicine
| | | | - David H. Spencer
- Division of Oncology, Department of Medicine, Washington University School of Medicine
- McDonnell Genome Institute, Washington University School of Medicine
- Department of Pathology & Immunology, Washington University School of Medicine
| | - Matthew J. Walter
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | - Peter Westervelt
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | - John F. DiPersio
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | - Timothy J. Ley
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | - Daniel C. Link
- Division of Oncology, Department of Medicine, Washington University School of Medicine
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23
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Robbe P, Ridout KE, Vavoulis DV, Dréau H, Kinnersley B, Denny N, Chubb D, Appleby N, Cutts A, Cornish AJ, Lopez-Pascua L, Clifford R, Burns A, Stamatopoulos B, Cabes M, Alsolami R, Antoniou P, Oates M, Cavalieri D, Gibson J, Prabhu AV, Schwessinger R, Jennings D, James T, Maheswari U, Duran-Ferrer M, Carninci P, Knight SJL, Månsson R, Hughes J, Davies J, Ross M, Bentley D, Strefford JC, Devereux S, Pettitt AR, Hillmen P, Caulfield MJ, Houlston RS, Martín-Subero JI, Schuh A. Whole-genome sequencing of chronic lymphocytic leukemia identifies subgroups with distinct biological and clinical features. Nat Genet 2022; 54:1675-1689. [PMID: 36333502 PMCID: PMC9649442 DOI: 10.1038/s41588-022-01211-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/16/2022] [Indexed: 11/06/2022]
Abstract
The value of genome-wide over targeted driver analyses for predicting clinical outcomes of cancer patients is debated. Here, we report the whole-genome sequencing of 485 chronic lymphocytic leukemia patients enrolled in clinical trials as part of the United Kingdom's 100,000 Genomes Project. We identify an extended catalog of recurrent coding and noncoding genetic mutations that represents a source for future studies and provide the most complete high-resolution map of structural variants, copy number changes and global genome features including telomere length, mutational signatures and genomic complexity. We demonstrate the relationship of these features with clinical outcome and show that integration of 186 distinct recurrent genomic alterations defines five genomic subgroups that associate with response to therapy, refining conventional outcome prediction. While requiring independent validation, our findings highlight the potential of whole-genome sequencing to inform future risk stratification in chronic lymphocytic leukemia.
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Affiliation(s)
- Pauline Robbe
- Department of Oncology, University of Oxford, Oxford, UK
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kate E Ridout
- Department of Oncology, University of Oxford, Oxford, UK
| | | | - Helene Dréau
- Department of Oncology, University of Oxford, Oxford, UK
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - Nicholas Denny
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Daniel Chubb
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - Niamh Appleby
- Department of Oncology, University of Oxford, Oxford, UK
| | - Anthony Cutts
- Department of Oncology, University of Oxford, Oxford, UK
| | - Alex J Cornish
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | | | - Ruth Clifford
- Department of Haematology, University Hospital Limerick, Limerick, Ireland
- Limerick Digital Cancer Research Centre, School of Medicine,University of Limerick, Limerick, Ireland
| | - Adam Burns
- Department of Oncology, University of Oxford, Oxford, UK
| | - Basile Stamatopoulos
- Laboratory of Clinical Cell Therapy, Jules Bordet Institute, ULB Cancer Research Center (U-CRC)- Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Maite Cabes
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Reem Alsolami
- Department of Medical Laboratory Technology, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | | | - Doriane Cavalieri
- Department of Haematology, CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | - Jane Gibson
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Anika V Prabhu
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ron Schwessinger
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Daisy Jennings
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | | | - Martí Duran-Ferrer
- Biomedical Epigenomics Group, Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Samantha J L Knight
- Oxford University Clinical Academic Graduate School, University of Oxford Medical Sciences Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Robert Månsson
- Center for Hematology and Regenerative Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Jim Hughes
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - James Davies
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Mark Ross
- Illumina Cambridge Ltd., Cambridge, UK
| | | | - Jonathan C Strefford
- Cancer Genomics, Cancer Sciences, Faculty of Medicine, Group University of Southampton, Southampton, UK
| | - Stephen Devereux
- King's College Hospital, NHS Foundation Trust, London, UK
- Kings College London, London, UK
| | - Andrew R Pettitt
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
- Clatterbridge Cancer Centre NHS Foundation Trust, Liverpool, UK
| | | | - Mark J Caulfield
- Genomics England, London, UK
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - José I Martín-Subero
- Human Technopole, Milan, Italy
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Anna Schuh
- Department of Oncology, University of Oxford, Oxford, UK.
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24
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Heaphy CM, Singhi AD. The diagnostic and prognostic utility of incorporating DAXX, ATRX, and alternative lengthening of telomeres to the evaluation of pancreatic neuroendocrine tumors. Hum Pathol 2022; 129:11-20. [PMID: 35872157 DOI: 10.1016/j.humpath.2022.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 12/14/2022]
Abstract
Pancreatic neuroendocrine tumors (PanNETs) are a heterogeneous group of neoplasms with increasing incidence and an ill-defined pathobiology. Although many PanNETs are indolent and remain stable for years, a subset may behave aggressively and metastasize widely. Thus, the increasing and frequent detection of PanNETs presents a treatment dilemma. Current prognostic systems are susceptible to interpretation errors, sampling issues, and do not accurately reflect the clinical behavior of these neoplasms. Hence, additional biomarkers are needed to improve the prognostic stratification of patients diagnosed with a PanNET. Recent studies have identified alterations in death domain-associated protein 6 (DAXX) and alpha-thalassemia/mental retardation X-linked (ATRX), as well as alternative lengthening of telomeres (ALT), as promising prognostic biomarkers. This review summarizes the identification, clinical utility, and specific nuances in testing for DAXX/ATRX by immunohistochemistry and ALT by telomere-specific fluorescence in situ hybridization in PanNETs. Furthermore, a discussion on diagnostic indications for DAXX, ATRX, and ALT status is provided to include the distinction between PanNETs and pancreatic neuroendocrine carcinomas (PanNECs), and determining pancreatic origin for metastatic neuroendocrine tumors in the setting of an unknown primary.
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Affiliation(s)
- Christopher M Heaphy
- Department of Medicine, Boston University, School of Medicine, Boston, MA, 02118, USA
| | - Aatur D Singhi
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA.
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25
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Meeser A, Bartenhagen C, Werr L, Hellmann AM, Kahlert Y, Hemstedt N, Nürnberg P, Altmüller J, Ackermann S, Hero B, Simon T, Peifer M, Fischer M, Rosswog C. Reliable assessment of telomere maintenance mechanisms in neuroblastoma. Cell Biosci 2022; 12:160. [PMID: 36153564 PMCID: PMC9508734 DOI: 10.1186/s13578-022-00896-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 09/03/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Telomere maintenance mechanisms (TMM) are a hallmark of high-risk neuroblastoma, and are conferred by activation of telomerase or alternative lengthening of telomeres (ALT). However, detection of TMM is not yet part of the clinical routine, and consensus on TMM detection, especially on ALT assessment, remains to be achieved. METHODS Whole genome sequencing (WGS) data of 68 primary neuroblastoma samples were analyzed. Telomere length was calculated from WGS data or by telomere restriction fragment analysis (n = 39). ALT was assessed by C-circle assay (CCA, n = 67) and detection of ALT-associated PML nuclear bodies (APB) by combined fluorescence in situ hybridization and immunofluorescence staining (n = 68). RNA sequencing was performed (n = 64) to determine expression of TERT and telomeric long non-coding RNA (TERRA). Telomerase activity was examined by telomerase repeat amplification protocol (TRAP, n = 15). RESULTS Tumors were considered as telomerase-positive if they harbored a TERT rearrangement, MYCN amplification or high TERT expression (45.6%, 31/68), and ALT-positive if they were positive for APB and CCA (19.1%, 13/68). If all these markers were absent, tumors were considered TMM-negative (25.0%, 17/68). According to these criteria, the majority of samples were classified unambiguously (89.7%, 61/68). Assessment of additional ALT-associated parameters clarified the TMM status of the remaining seven cases with high likelihood: ALT-positive tumors had higher TERRA expression, longer telomeres, more telomere insertions, a characteristic pattern of telomere variant repeats, and were associated with ATRX mutations. CONCLUSIONS We here propose a workflow to reliably detect TMM in neuroblastoma. We show that unambiguous classification is feasible following a stepwise approach that determines both, activation of telomerase and ALT. The workflow proposed in this study can be used in clinical routine and provides a framework to systematically and reliably determine telomere maintenance mechanisms for risk stratification and treatment allocation of neuroblastoma patients.
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Affiliation(s)
- Alina Meeser
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany
| | - Christoph Bartenhagen
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany
| | - Lisa Werr
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany
| | - Anna-Maria Hellmann
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany
| | - Yvonne Kahlert
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany
| | - Nadine Hemstedt
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
- Core Facility Genomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Sandra Ackermann
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany
| | - Barbara Hero
- Department of Pediatric Oncology and Hematology, University of Cologne, Cologne, Germany
| | - Thorsten Simon
- Department of Pediatric Oncology and Hematology, University of Cologne, Cologne, Germany
| | - Martin Peifer
- Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
- Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany.
| | - Carolina Rosswog
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
- Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany.
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26
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Tan KT, Slevin MK, Meyerson M, Li H. Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres. Genome Biol 2022; 23:180. [PMID: 36028900 PMCID: PMC9414165 DOI: 10.1186/s13059-022-02751-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 08/16/2022] [Indexed: 12/27/2022] Open
Abstract
Nanopore long-read sequencing is an emerging approach for studying genomes, including long repetitive elements like telomeres. Here, we report extensive basecalling induced errors at telomere repeats across nanopore datasets, sequencing platforms, basecallers, and basecalling models. We find that telomeres in many organisms are frequently miscalled. We demonstrate that tuning of nanopore basecalling models leads to improved recovery and analysis of telomeric regions, with minimal negative impact on other genomic regions. We highlight the importance of verifying nanopore basecalls in long, repetitive, and poorly defined regions, and showcase how artefacts can be resolved by improvements in nanopore basecalling models.
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Affiliation(s)
- Kar-Tong Tan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Michael K Slevin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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27
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Robinson PS, Thomas LE, Abascal F, Jung H, Harvey LMR, West HD, Olafsson S, Lee BCH, Coorens THH, Lee-Six H, Butlin L, Lander N, Truscott R, Sanders MA, Lensing SV, Buczacki SJA, Ten Hoopen R, Coleman N, Brunton-Sim R, Rushbrook S, Saeb-Parsy K, Lalloo F, Campbell PJ, Martincorena I, Sampson JR, Stratton MR. Inherited MUTYH mutations cause elevated somatic mutation rates and distinctive mutational signatures in normal human cells. Nat Commun 2022; 13:3949. [PMID: 35803914 PMCID: PMC9270427 DOI: 10.1038/s41467-022-31341-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 06/14/2022] [Indexed: 12/21/2022] Open
Abstract
Cellular DNA damage caused by reactive oxygen species is repaired by the base excision repair (BER) pathway which includes the DNA glycosylase MUTYH. Inherited biallelic MUTYH mutations cause predisposition to colorectal adenomas and carcinoma. However, the mechanistic progression from germline MUTYH mutations to MUTYH-Associated Polyposis (MAP) is incompletely understood. Here, we sequence normal tissue DNAs from 10 individuals with MAP. Somatic base substitution mutation rates in intestinal epithelial cells were elevated 2 to 4-fold in all individuals, except for one showing a 31-fold increase, and were also increased in other tissues. The increased mutation burdens were of multiple mutational signatures characterised by C > A changes. Different mutation rates and signatures between individuals are likely due to different MUTYH mutations or additional inherited mutations in other BER pathway genes. The elevated base substitution rate in normal cells likely accounts for the predisposition to neoplasia in MAP. Despite ubiquitously elevated mutation rates, individuals with MAP do not display overt evidence of premature ageing. Thus, accumulation of somatic mutations may not be sufficient to cause the global organismal functional decline of ageing.
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Affiliation(s)
- Philip S Robinson
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Laura E Thomas
- Institute of Life Science, Swansea University, Swansea, SA28PP, UK
| | - Federico Abascal
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Hyunchul Jung
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Luke M R Harvey
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Hannah D West
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Sigurgeir Olafsson
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Bernard C H Lee
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Tim H H Coorens
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Henry Lee-Six
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Laura Butlin
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Nicola Lander
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Rebekah Truscott
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Mathijs A Sanders
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Haematology, Erasmus University Medical Centre, 3015 CN, Rotterdam, The Netherlands
| | - Stefanie V Lensing
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Simon J A Buczacki
- Nuffield Department of Surgical Sciences, Medical Sciences Division, University of Oxford, Oxford, UK
| | | | - Nicholas Coleman
- Department of Pathology, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Simon Rushbrook
- Norfolk and Norwich University Hospital, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge NIHR Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Oxford Road, Manchester, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Julian R Sampson
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK.
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28
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The genomic and transcriptional landscape of primary central nervous system lymphoma. Nat Commun 2022; 13:2558. [PMID: 35538064 PMCID: PMC9091224 DOI: 10.1038/s41467-022-30050-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 04/12/2022] [Indexed: 02/07/2023] Open
Abstract
Primary lymphomas of the central nervous system (PCNSL) are mainly diffuse large B-cell lymphomas (DLBCLs) confined to the central nervous system (CNS). Molecular drivers of PCNSL have not been fully elucidated. Here, we profile and compare the whole-genome and transcriptome landscape of 51 CNS lymphomas (CNSL) to 39 follicular lymphoma and 36 DLBCL cases outside the CNS. We find recurrent mutations in JAK-STAT, NFkB, and B-cell receptor signaling pathways, including hallmark mutations in MYD88 L265P (67%) and CD79B (63%), and CDKN2A deletions (83%). PCNSLs exhibit significantly more focal deletions of HLA-D (6p21) locus as a potential mechanism of immune evasion. Mutational signatures correlating with DNA replication and mitosis are significantly enriched in PCNSL. TERT gene expression is significantly higher in PCNSL compared to activated B-cell (ABC)-DLBCL. Transcriptome analysis clearly distinguishes PCNSL and systemic DLBCL into distinct molecular subtypes. Epstein-Barr virus (EBV)+ CNSL cases lack recurrent mutational hotspots apart from IG and HLA-DRB loci. We show that PCNSL can be clearly distinguished from DLBCL, having distinct expression profiles, IG expression and translocation patterns, as well as specific combinations of genetic alterations.
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29
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Wei L, Zou C, Chen L, Lin Y, Liang L, Hu B, Mao Y, Zou D. Molecular Insights and Prognosis Associated With RBM8A in Glioblastoma. Front Mol Biosci 2022; 9:876603. [PMID: 35573726 PMCID: PMC9098818 DOI: 10.3389/fmolb.2022.876603] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/04/2022] [Indexed: 12/31/2022] Open
Abstract
Background: Glioblastoma (GBM) is the most invasive brain tumors, and it is associated with high rates of recurrence and mortality. The purpose of this study was to investigate the expression of RBM8A in GBM and the potential influence of its expression on the disease. Methods: Levels of RBM8A mRNA in GBM patients and controls were examined in The Cancer Genome Atlas (TCGA), GSE16011 and GSE90604 databases. GBM samples in TCGA were divided into RBM8Ahigh and RBM8Alow groups. Differentially expressed genes (DEGs) between GBM patients and controls were identified, as were DEGs between RBM8Ahigh and RBM8Alow groups. DEGs common to both of these comparisons were analyzed for coexpression and regression analyses. In addition, we identified potential effects of RBM8A on competing endogenous RNAs, immune cell infiltration, methylation modifications, and somatic mutations. Results: RBM8A is expressed at significantly higher levels in GBM than control samples, and its level correlates with tumor purity. We identified a total of 488 mRNAs that differed between GBM and controls as well as between RBM8Ahigh and RBM8Alow groups, which enrichment analysis revealed to be associated mainly with neuroblast proliferation, and T cell immune responses. We identified 174 mRNAs that gave areas under the receiver operating characteristic curve >0.7 among coexpression module genes, of which 13 were significantly associated with overall survival of GBM patients. We integrated 11 candidate mRNAs through LASSO algorithm, then nomogram, risk score, and decision curve analyses were analyzed. We found that RBM8A may compete with DLEU1 for binding to miR-128-1-5p, and aberrant RBM8A expression was associations with tumor infiltration by immune cells. Some mRNAs associated with GBM prognosis also appear to be methylated or mutated. Conclusions: Our study strongly links RBM8A expression to GBM pathobiology and patient prognosis. The candidate mRNAs identified here may lead to therapeutic targets against the disease.
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Affiliation(s)
- Lei Wei
- Department of Neurology, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chun Zou
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Liechun Chen
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yan Lin
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Lucong Liang
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Beiquan Hu
- Department of Neurosurgery, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yingwei Mao
- Department of Biology, Pennsylvania State University, University Park, PA, United States
- *Correspondence: Donghua Zou, ; Yingwei Mao,
| | - Donghua Zou
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- *Correspondence: Donghua Zou, ; Yingwei Mao,
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30
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Zhou Y, Wang Y, Xiong X, Appel AG, Zhang C, Wang X. Profiles of telomeric repeats in Insecta reveal diverse forms of telomeric motifs in Hymenopterans. Life Sci Alliance 2022; 5:5/7/e202101163. [PMID: 35365574 PMCID: PMC8977481 DOI: 10.26508/lsa.202101163] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 12/23/2022] Open
Abstract
Telomeres consist of highly conserved simple tandem telomeric repeat motif (TRM): (TTAGG)n in arthropods, (TTAGGG)n in vertebrates, and (TTTAGGG)n in most plants. TRM can be detected from chromosome-level assembly, which typically requires long-read sequencing data. To take advantage of short-read data, we developed an ultra-fast Telomeric Repeats Identification Pipeline and evaluated its performance on 91 species. With proven accuracy, we applied Telomeric Repeats Identification Pipeline in 129 insect species, using 7 Tbp of short-read sequences. We confirmed (TTAGG)n as the TRM in 19 orders, suggesting it is the ancestral form in insects. Systematic profiling in Hymenopterans revealed a diverse range of TRMs, including the canonical 5-bp TTAGG (bees, ants, and basal sawflies), three independent losses of tandem repeat form TRM (Ichneumonoids, hunting wasps, and gall-forming wasps), and most interestingly, a common 8-bp (TTATTGGG)n in Chalcid wasps with two 9-bp variants in the miniature wasp (TTACTTGGG) and fig wasps (TTATTGGGG). Our results identified extraordinary evolutionary fluidity of Hymenopteran TRMs, and rapid evolution of TRM and repeat abundance at all evolutionary scales, providing novel insights into telomere evolution.
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Affiliation(s)
- Yihang Zhou
- Fundamental Research Center, Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Life Sciences and Technology, Tongji University, Shanghai, China.,Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA.,Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL, USA
| | - Yi Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Xiao Xiong
- Fundamental Research Center, Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Life Sciences and Technology, Tongji University, Shanghai, China.,Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA.,Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL, USA
| | - Arthur G Appel
- Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL, USA.,Department of Entomology and Plant Pathology, Auburn University, AL, USA
| | - Chao Zhang
- Fundamental Research Center, Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA.,Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL, USA.,Department of Entomology and Plant Pathology, Auburn University, AL, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
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31
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Wong KM, King DA, Schwartz EK, Herrera RE, Morrison AJ. Retinoblastoma protein regulates carcinogen susceptibility at heterochromatic cancer driver loci. Life Sci Alliance 2022; 5:e202101134. [PMID: 34983823 PMCID: PMC8739494 DOI: 10.26508/lsa.202101134] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 12/11/2022] Open
Abstract
Carcinogenic insult, such as UV light exposure, creates DNA lesions that evolve into mutations if left unrepaired. These resulting mutations can contribute to carcinogenesis and drive malignant phenotypes. Susceptibility to carcinogens (i.e., the propensity to form a carcinogen-induced DNA lesion) is regulated by both genetic and epigenetic factors. Importantly, carcinogen susceptibility is a critical contributor to cancer mutagenesis. It is known that mutations can be prevented by tumor suppressor regulation of DNA damage response pathways; however, their roles carcinogen susceptibility have not yet been reported. In this study, we reveal that the retinoblastoma (RB1) tumor suppressor regulates UV susceptibility across broad regions of the genome. In particular, centromere and telomere-proximal regions exhibit significant increases in UV lesion susceptibility when RB1 is deleted. Several cancer-related genes are located within genomic regions of increased susceptibility, including telomerase reverse transcriptase, TERT, thereby accelerating mutagenic potential in cancers with RB1 pathway alterations. These findings reveal novel genome stability mechanisms of a tumor suppressor and uncover new pathways to accumulate mutations during cancer evolution.
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Affiliation(s)
- Ka Man Wong
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Devin A King
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Erin K Schwartz
- Department of Biology, Stanford University, Stanford, CA, USA
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32
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Sharaf R, Montesion M, Hopkins JF, Song J, Frampton GM, Albacker LA. A pan-cancer landscape of telomeric content shows that RAD21 and HGF alterations are associated with longer telomeres. Genome Med 2022; 14:25. [PMID: 35227290 PMCID: PMC8883689 DOI: 10.1186/s13073-022-01029-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 02/11/2022] [Indexed: 01/02/2023] Open
Abstract
Background Cancer cells can proliferate indefinitely through telomere maintenance mechanisms. These mechanisms include telomerase-dependent elongation, mediated by TERT activation, and alternative lengthening of telomeres (ALT), linked to loss of ATRX or DAXX. Methods We analyzed the telomeric content of 89,959 tumor samples within the Foundation Medicine dataset and investigated the genomic determinants of high telomeric content, linking them to clinical outcomes, when available. Results Telomeric content varied widely by disease type with leiomyosarcoma having the highest and Merkel cell carcinoma having the lowest telomeric content. In agreement with previous studies, telomeric content was significantly higher in samples with alterations in TERC, ATRX, and DAXX. We further identified that amplifications in two genes, RAD21 and HGF, were enriched in samples with high telomeric content, which was confirmed using the PCAWG/ICGC dataset. We identified the minimal amplified region associated with high telomeric content for RAD21 (8q23.1–8q24.12), which excludes MYC, and for HGF (7q21.11). Our results demonstrated that RAD21 and HGF exerted an additive telomere lengthening effect on samples with existing alterations in canonical genes previously associated with telomere elongation. Furthermore, patients with breast cancer who harbor RAD21 alterations had poor median overall survival and trended towards higher levels of Ki-67 staining. Conclusions This study highlights the importance of the role played by RAD21 (8q23.1–8q24.12) and HGF (7q21.11) in the lengthening of telomeres, supporting unlimited replication in tumors. These findings open avenues for work aimed at targeting this crucial pathway in tumorigenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01029-7.
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Affiliation(s)
- Radwa Sharaf
- Foundation Medicine Inc, 150 Second Street, Cambridge, MA, 02141, USA
| | - Meagan Montesion
- Foundation Medicine Inc, 150 Second Street, Cambridge, MA, 02141, USA
| | - Julia F Hopkins
- Foundation Medicine Inc, 150 Second Street, Cambridge, MA, 02141, USA
| | - Jiarong Song
- Foundation Medicine Inc, 150 Second Street, Cambridge, MA, 02141, USA
| | | | - Lee A Albacker
- Foundation Medicine Inc, 150 Second Street, Cambridge, MA, 02141, USA.
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33
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Holmes O, Nones K, Tang YH, Loffler KA, Lee M, Patch AM, Dagg RA, Lau LMS, Leonard C, Wood S, Xu Q, Pickett HA, Reddel RR, Barbour AP, Grimmond SM, Waddell N, Pearson JV. qmotif: determination of telomere content from whole-genome sequence data. BIOINFORMATICS ADVANCES 2022; 2:vbac005. [PMID: 36699384 PMCID: PMC9710677 DOI: 10.1093/bioadv/vbac005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/15/2021] [Indexed: 01/28/2023]
Abstract
Motivation Changes in telomere length have been observed in cancer and can be indicative of mechanisms involved in carcinogenesis. Most methods used to estimate telomere length require laboratory analysis of DNA samples. Here, we present qmotif, a fast and easy tool that determines telomeric repeat sequences content as an estimate of telomere length directly from whole-genome sequencing. Results qmotif shows similar results to quantitative PCR, the standard method for high-throughput clinical telomere length quantification. qmotif output correlates strongly with the output of other tools for determining telomere sequence content, TelSeq and TelomereHunter, but can run in a fraction of the time-usually under a minute. Availability and implementation qmotif is implemented in Java and source code is available at https://github.com/AdamaJava/adamajava, with instructions on how to build and use the application available from https://adamajava.readthedocs.io/en/latest/. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Oliver Holmes
- QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, QLD, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane 4072, QLD, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, QLD, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane 4072, QLD, Australia
| | - Yue Hang Tang
- Surgical Oncology Group, Diamantina Institute, The University of Queensland, Translational Research Institute at the Princess Alexandra Hospital, Woolloongabba, Brisbane 4102, QLD, Australia
| | - Kelly A Loffler
- Surgical Oncology Group, Diamantina Institute, The University of Queensland, Translational Research Institute at the Princess Alexandra Hospital, Woolloongabba, Brisbane 4102, QLD, Australia,Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia
| | - Michael Lee
- Children’s Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Ann-Marie Patch
- QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, QLD, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane 4072, QLD, Australia
| | - Rebecca A Dagg
- Children’s Hospital at Westmead, University of Sydney, Westmead, NSW 2145, Australia
| | - Loretta M S Lau
- Children’s Hospital at Westmead, University of Sydney, Westmead, NSW 2145, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, QLD, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane 4072, QLD, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, QLD, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane 4072, QLD, Australia
| | - Qinying Xu
- QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, QLD, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane 4072, QLD, Australia
| | - Hilda A Pickett
- Children’s Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Roger R Reddel
- Children’s Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Andrew P Barbour
- Surgical Oncology Group, Diamantina Institute, The University of Queensland, Translational Research Institute at the Princess Alexandra Hospital, Woolloongabba, Brisbane 4102, QLD, Australia
| | - Sean M Grimmond
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane 4072, QLD, Australia,University of Melbourne, Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, QLD, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane 4072, QLD, Australia,To whom correspondence should be addressed. or
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, QLD, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane 4072, QLD, Australia,To whom correspondence should be addressed. or
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34
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Stephens Z, Ferrer A, Boardman L, Iyer RK, Kocher JPA. Telogator: a method for reporting chromosome-specific telomere lengths from long reads. Bioinformatics 2022; 38:1788-1793. [PMID: 35022670 PMCID: PMC8963315 DOI: 10.1093/bioinformatics/btac005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/17/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Telomeres are the repetitive sequences found at the ends of eukaryotic chromosomes and are often thought of as a 'biological clock,' with their average length shortening during division in most cells. In addition to their association with senescence, abnormal telomere lengths are well known to be associated with multiple cancers, short telomere syndromes and as risk factors for a broad range of diseases. While a majority of methods for measuring telomere length will report average lengths across all chromosomes, it is known that aberrations in specific chromosome arms are biomarkers for certain diseases. Due to their repetitive nature, characterizing telomeres at this resolution is prohibitive for short read sequencing approaches, and is challenging still even with longer reads. RESULTS We present Telogator: a method for reporting chromosome-specific telomere length from long read sequencing data. We demonstrate Telogator's sensitivity in detecting chromosome-specific telomere length in simulated data across a range of read lengths and error rates. Telogator is then applied to 10 germline samples, yielding a high correlation with short read methods in reporting average telomere length. In addition, we investigate common subtelomere rearrangements and identify the minimum read length required to anchor telomere/subtelomere boundaries in samples with these haplotypes. AVAILABILITY AND IMPLEMENTATION Telogator is written in Python3 and is available at github.com/zstephens/telogator. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zachary Stephens
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | | | - Lisa Boardman
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55902, USA
| | - Ravishankar K Iyer
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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35
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Hames-Fathi S, Nottley SWG, Pillay N. Unravelling undifferentiated soft tissue sarcomas: insights from genomics. Histopathology 2021; 80:109-121. [DOI: 10.1111/his.14446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Shadi Hames-Fathi
- Research Department of Pathology University College London UCL Cancer Institute LondonUK
| | - Steven W G Nottley
- Research Department of Pathology University College London UCL Cancer Institute LondonUK
| | - Nischalan Pillay
- Research Department of Pathology University College London UCL Cancer Institute LondonUK
- Department of Cellular and Molecular Pathology Royal National Orthopaedic Hospital NHS Trust Stanmore UK
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36
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Fang W, Wu CH, Sun QL, Gu ZT, Zhu L, Mao T, Zhang XF, Xu N, Lu TP, Tsai MH, Chen LH, Lai LC, Chuang EY. Novel Tumor-Specific Antigens for Immunotherapy Identified From Multi-omics Profiling in Thymic Carcinomas. Front Immunol 2021; 12:748820. [PMID: 34867976 PMCID: PMC8635231 DOI: 10.3389/fimmu.2021.748820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/28/2021] [Indexed: 12/30/2022] Open
Abstract
Thymic carcinoma (TC) is the most aggressive thymic epithelial neoplasm. TC patients with microsatellite instability, whole-genome doubling, or alternative tumor-specific antigens from gene fusion are most likely to benefit from immunotherapies. However, due to the rarity of this disease, how to prioritize the putative biomarkers and what constitutes an optimal treatment regimen remains largely unknown. Therefore, we integrated genomic and transcriptomic analyses from TC patients and revealed that frameshift indels in KMT2C and CYLD frequently produce neoantigens. Moreover, a median of 3 fusion-derived neoantigens was predicted across affected patients, especially the CATSPERB-TC2N neoantigens that were recurrently predicted in TC patients. Lastly, potentially actionable alterations with early levels of evidence were uncovered and could be used for designing clinical trials. In summary, this study shed light on our understanding of tumorigenesis and presented new avenues for molecular characterization and immunotherapy in TC.
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Affiliation(s)
- Wentao Fang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Chia-Hsin Wu
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Qiang-Ling Sun
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai JiaoTong University, Shanghai, China.,Thoracic Cancer institute, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhi-Tao Gu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Lei Zhu
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Teng Mao
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Xue-Fei Zhang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Ning Xu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Tzu-Pin Lu
- Bioinformatics and Biostatistics Core, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan.,Department of Public Health, National Taiwan University, Taipei, Taiwan
| | - Mong-Hsun Tsai
- Bioinformatics and Biostatistics Core, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan.,Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Li-Han Chen
- Institute of Fisheries Science, National Taiwan University, Taipei, Taiwan
| | - Liang-Chuan Lai
- Bioinformatics and Biostatistics Core, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Eric Y Chuang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan.,Bioinformatics and Biostatistics Core, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan.,Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan.,Master Program for Biomedical Engineering, China Medical University, Taichung, Taiwan
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37
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Abstract
Replicative immortality is a hallmark of cancer, and can be achieved through telomere lengthening and maintenance. Although the role of telomere length in cancer has been well studied, its association to genomic features is less well known. Here, we report the telomere lengths of 392 localized prostate cancer tumours and characterize their relationship to genomic, transcriptomic and proteomic features. Shorter tumour telomere lengths are associated with elevated genomic instability, including single-nucleotide variants, indels and structural variants. Genes involved in cell proliferation and signaling are correlated with tumour telomere length at all levels of the central dogma. Telomere length is also associated with multiple clinical features of a tumour. Longer telomere lengths in non-tumour samples are associated with a lower rate of biochemical relapse. In summary, we describe the multi-level integration of telomere length, genomics, transcriptomics and proteomics in localized prostate cancer.
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38
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Stainczyk SA, Westermann F. Neuroblastoma-Telomere maintenance, deregulated signaling transduction and beyond. Int J Cancer 2021; 150:903-915. [PMID: 34636058 DOI: 10.1002/ijc.33839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 09/06/2021] [Accepted: 09/27/2021] [Indexed: 11/11/2022]
Abstract
The childhood malignancy neuroblastoma belongs to the group of embryonal tumors and originates from progenitor cells of the sympathoadrenal lineage. Treatment options for children with high-risk and relapsed disease are still very limited. In recent years, an ever-growing molecular diversity was identified using (epi)-genetic profiling of neuroblastoma tumors, indicating that molecularly targeted therapies could be a promising therapeutic option. In this review article, we summarize the various molecular subtypes and genetic events associated with neuroblastoma and describe recent advances in targeted therapies. We lay a strong emphasis on the importance of telomere maintenance mechanisms for understanding tumor progression and risk classification of neuroblastoma.
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Affiliation(s)
- Sabine A Stainczyk
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Westermann
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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39
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Robinson PS, Coorens THH, Palles C, Mitchell E, Abascal F, Olafsson S, Lee BCH, Lawson ARJ, Lee-Six H, Moore L, Sanders MA, Hewinson J, Martin L, Pinna CMA, Galavotti S, Rahbari R, Campbell PJ, Martincorena I, Tomlinson I, Stratton MR. Increased somatic mutation burdens in normal human cells due to defective DNA polymerases. Nat Genet 2021; 53:1434-1442. [PMID: 34594041 PMCID: PMC8492474 DOI: 10.1038/s41588-021-00930-y] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/28/2021] [Indexed: 02/08/2023]
Abstract
Mutation accumulation in somatic cells contributes to cancer development and is proposed as a cause of aging. DNA polymerases Pol ε and Pol δ replicate DNA during cell division. However, in some cancers, defective proofreading due to acquired POLE/POLD1 exonuclease domain mutations causes markedly elevated somatic mutation burdens with distinctive mutational signatures. Germline POLE/POLD1 mutations cause familial cancer predisposition. Here, we sequenced normal tissue and tumor DNA from individuals with germline POLE/POLD1 mutations. Increased mutation burdens with characteristic mutational signatures were found in normal adult somatic cell types, during early embryogenesis and in sperm. Thus human physiology can tolerate ubiquitously elevated mutation burdens. Except for increased cancer risk, individuals with germline POLE/POLD1 mutations do not exhibit overt features of premature aging. These results do not support a model in which all features of aging are attributable to widespread cell malfunction directly resulting from somatic mutation burdens accrued during life.
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Affiliation(s)
- Philip S Robinson
- Wellcome Sanger Institute, Hinxton, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | | | - Claire Palles
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | | | | | - Bernard C H Lee
- Wellcome Sanger Institute, Hinxton, UK
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | | | | | | | - Mathijs A Sanders
- Wellcome Sanger Institute, Hinxton, UK
- Department of Haematology, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | | | - Lynn Martin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Claudia M A Pinna
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sara Galavotti
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | | | | | - Ian Tomlinson
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Edinburgh, UK.
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40
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Hu K, Ghandi M, Huang FW. Integrated evaluation of telomerase activation and telomere maintenance across cancer cell lines. eLife 2021; 10:e66198. [PMID: 34486523 PMCID: PMC8530513 DOI: 10.7554/elife.66198] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
In cancer, telomere maintenance is critical for the development of replicative immortality. Using genome sequences from the Cancer Cell Line Encyclopedia and Genomics of Drug Sensitivity in Cancer Project, we calculated telomere content across 1299 cancer cell lines. We find that telomerase reverse transcriptase (TERT) expression correlates with telomere content in lung, central nervous system, and leukemia cell lines. Using CRISPR/Cas9 screening data, we show that lower telomeric content is associated with dependency of CST telomere maintenance genes. Increased dependencies of shelterin members are associated with wild-type TP53 status. Investigating the epigenetic regulation of TERT, we find widespread allele-specific expression in promoter-wildtype contexts. TERT promoter-mutant cell lines exhibit hypomethylation at PRC2-repressed regions, suggesting a cooperative global epigenetic state in the reactivation of telomerase. By incorporating telomere content with genomic features across comprehensively characterized cell lines, we provide further insights into the role of telomere regulation in cancer immortality.
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Affiliation(s)
- Kevin Hu
- Broad Institute of MIT and HarvardCambridgeUnited States
- Division of Hematology/Oncology, Department of Medicine; Bakar Computational Health Sciences Institute; Institute for Human Genetics; University of California, San FranciscoSan FranciscoUnited States
- Helen Diller Family Comprehensive Cancer CenterSan FranciscoUnited States
| | - Mahmoud Ghandi
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Franklin W Huang
- Broad Institute of MIT and HarvardCambridgeUnited States
- Division of Hematology/Oncology, Department of Medicine; Bakar Computational Health Sciences Institute; Institute for Human Genetics; University of California, San FranciscoSan FranciscoUnited States
- Helen Diller Family Comprehensive Cancer CenterSan FranciscoUnited States
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41
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Zhang T, Joubert P, Ansari-Pour N, Zhao W, Hoang PH, Lokanga R, Moye AL, Rosenbaum J, Gonzalez-Perez A, Martínez-Jiménez F, Castro A, Muscarella LA, Hofman P, Consonni D, Pesatori AC, Kebede M, Li M, Gould Rothberg BE, Peneva I, Schabath MB, Poeta ML, Costantini M, Hirsch D, Heselmeyer-Haddad K, Hutchinson A, Olanich M, Lawrence SM, Lenz P, Duggan M, Bhawsar PMS, Sang J, Kim J, Mendoza L, Saini N, Klimczak LJ, Islam SMA, Otlu B, Khandekar A, Cole N, Stewart DR, Choi J, Brown KM, Caporaso NE, Wilson SH, Pommier Y, Lan Q, Rothman N, Almeida JS, Carter H, Ried T, Kim CF, Lopez-Bigas N, Garcia-Closas M, Shi J, Bossé Y, Zhu B, Gordenin DA, Alexandrov LB, Chanock SJ, Wedge DC, Landi MT. Genomic and evolutionary classification of lung cancer in never smokers. Nat Genet 2021; 53:1348-1359. [PMID: 34493867 PMCID: PMC8432745 DOI: 10.1038/s41588-021-00920-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 07/15/2021] [Indexed: 12/26/2022]
Abstract
Lung cancer in never smokers (LCINS) is a common cause of cancer mortality but its genomic landscape is poorly characterized. Here high-coverage whole-genome sequencing of 232 LCINS showed 3 subtypes defined by copy number aberrations. The dominant subtype (piano), which is rare in lung cancer in smokers, features somatic UBA1 mutations, germline AR variants and stem cell-like properties, including low mutational burden, high intratumor heterogeneity, long telomeres, frequent KRAS mutations and slow growth, as suggested by the occurrence of cancer drivers' progenitor cells many years before tumor diagnosis. The other subtypes are characterized by specific amplifications and EGFR mutations (mezzo-forte) and whole-genome doubling (forte). No strong tobacco smoking signatures were detected, even in cases with exposure to secondhand tobacco smoke. Genes within the receptor tyrosine kinase-Ras pathway had distinct impacts on survival; five genomic alterations independently doubled mortality. These findings create avenues for personalized treatment in LCINS.
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Affiliation(s)
- Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Quebec City, Quebec, Canada
| | - Naser Ansari-Pour
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Phuc H Hoang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Rachel Lokanga
- Cancer Genomics Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Aaron L Moye
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA
| | | | - Abel Gonzalez-Perez
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Francisco Martínez-Jiménez
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Andrea Castro
- Department of Medicine, Division of Medical Genetics, University of California San Diego, San Diego, CA, USA
| | - Lucia Anna Muscarella
- Laboratory of Oncology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, University Hospital Federation OncoAge, Nice Hospital, University Côte d'Azur, Nice, France
| | - Dario Consonni
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela C Pesatori
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Michael Kebede
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Mengying Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Bonnie E Gould Rothberg
- Smilow Cancer Hospital, Yale-New Haven Health, New Haven, CT, USA
- Yale Comprehensive Cancer Center, New Haven, CT, USA
| | - Iliana Peneva
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Maria Luana Poeta
- Department of Bioscience, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy
| | - Manuela Costantini
- Department of Urology, Istituto di Ricovero e Cura a Carattere Scientifico Regina Elena National Cancer Institute, Rome, Italy
| | - Daniela Hirsch
- Cancer Genomics Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mary Olanich
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Scott M Lawrence
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Petra Lenz
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Maire Duggan
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Praphulla M S Bhawsar
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jian Sang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jung Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Laura Mendoza
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Natalie Saini
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle, NC, USA
| | - Leszek J Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle, NC, USA
| | - S M Ashiqul Islam
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Burcak Otlu
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Nathan Cole
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Douglas R Stewart
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle, NC, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jonas S Almeida
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Hannah Carter
- Department of Medicine, Division of Medical Genetics, University of California San Diego, San Diego, CA, USA
| | - Thomas Ried
- Cancer Genomics Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Carla F Kim
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | | | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Quebec City, Quebec, Canada
- Department of Molecular Medicine, Laval University, Quebec City, Quebec, Canada
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Dmitry A Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle, NC, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - David C Wedge
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
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42
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Stefos GC, Szantai E, Konstantopoulos D, Samiotaki M, Fousteri M. aniFOUND: analysing the associated proteome and genomic landscape of the repaired nascent non-replicative chromatin. Nucleic Acids Res 2021; 49:e64. [PMID: 33693861 DOI: 10.1093/nar/gkab144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 02/01/2021] [Accepted: 02/22/2021] [Indexed: 12/13/2022] Open
Abstract
Specific capture of chromatin fractions with distinct and well-defined features has emerged as both challenging and a key strategy towards a comprehensive understanding of genome biology. In this context, we developed aniFOUND (accelerated native isolation of factors on unscheduled nascent DNA), an antibody-free method, which can label, capture, map and characterise nascent chromatin fragments that are synthesized in response to specific cues outside S-phase. We used the 'unscheduled' DNA synthesis (UDS) that takes place during the repair of UV-induced DNA lesions and coupled the captured chromatin to high-throughput analytical technologies. By mass-spectrometry we identified several factors with no previously known role in UVC-DNA damage response (DDR) as well as known DDR proteins. We experimentally validated the repair-dependent recruitment of the chromatin remodeller RSF1 and the cohesin-loader NIPBL at sites of UVC-induced photolesions. Developing aniFOUND-seq, a protocol for mapping UDS activity with high resolution, allowed us to monitor the landscape of UVC repair-synthesis events genome wide. We further resolved repair efficacy of the rather unexplored repeated genome, in particular rDNA and telomeres. In summary, aniFOUND delineates the proteome composition and genomic landscape of chromatin loci with specific features by integrating state-of-the-art 'omics' technologies to promote a comprehensive view of their function.
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Affiliation(s)
- Georgios C Stefos
- Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari 16672, Greece
| | - Eszter Szantai
- Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari 16672, Greece
| | | | | | - Maria Fousteri
- Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari 16672, Greece
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43
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Feuerbach L. Formal reply to "Alternative lengthening of telomeres is not synonymous with mutations in ATRX/DAXX". Nat Commun 2021; 12:1551. [PMID: 33692348 PMCID: PMC7946925 DOI: 10.1038/s41467-021-21796-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 02/11/2021] [Indexed: 11/26/2022] Open
Affiliation(s)
- Lars Feuerbach
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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44
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Mariani M, Zimmerman C, Rodriguez P, Hasenohr E, Aimola G, Gerrard DL, Richman A, Dest A, Flamand L, Kaufer B, Frietze S. Higher-Order Chromatin Structures of Chromosomally Integrated HHV-6A Predict Integration Sites. Front Cell Infect Microbiol 2021; 11:612656. [PMID: 33718266 PMCID: PMC7953476 DOI: 10.3389/fcimb.2021.612656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/20/2021] [Indexed: 12/31/2022] Open
Abstract
Human herpesvirus -6A and 6B (HHV-6A/B) can integrate their genomes into the telomeres of human chromosomes. Viral integration can occur in several cell types, including germinal cells, resulting in individuals that harbor the viral genome in every cell of their body. The integrated genome is efficiently silenced but can sporadically reactivate resulting in various clinical symptoms. To date, the integration mechanism and the subsequent silencing of HHV-6A/B genes remains poorly understood. Here we investigate the genome-wide chromatin contacts of the integrated HHV-6A in latently-infected cells. We show that HHV-6A becomes transcriptionally silent upon infection of these cells over the course of seven days. In addition, we established an HHV-6-specific 4C-seq approach, revealing that the HHV-6A 3D interactome is associated with quiescent chromatin states in cells harboring integrated virus. Furthermore, we observed that the majority of virus chromatin interactions occur toward the distal ends of specific human chromosomes. Exploiting this finding, we established a 4C-seq method that accurately detects the chromosomal integration sites. We further implement long-read minION sequencing in the 4C-seq assay and developed a method to identify HHV-6A/B integration sites in clinical samples.
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Affiliation(s)
- Michael Mariani
- Department of Biomedical and Health Sciences, College of Nursing and Health Sciences, University of Vermont, Burlington, VT, United States
| | - Cosima Zimmerman
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | - Princess Rodriguez
- Department of Biomedical and Health Sciences, College of Nursing and Health Sciences, University of Vermont, Burlington, VT, United States
| | - Ellie Hasenohr
- Department of Biomedical and Health Sciences, College of Nursing and Health Sciences, University of Vermont, Burlington, VT, United States
| | - Giulia Aimola
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | - Diana Lea Gerrard
- Department of Biomedical and Health Sciences, College of Nursing and Health Sciences, University of Vermont, Burlington, VT, United States
| | - Alyssa Richman
- Department of Biomedical and Health Sciences, College of Nursing and Health Sciences, University of Vermont, Burlington, VT, United States
| | - Andrea Dest
- Department of Biomedical and Health Sciences, College of Nursing and Health Sciences, University of Vermont, Burlington, VT, United States
| | - Louis Flamand
- Division of Infectious Disease and Immunity, CHU de Québec Research Center-Université Laval, Quebec City, QC, Canada
| | - Benedikt Kaufer
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | - Seth Frietze
- Department of Biomedical and Health Sciences, College of Nursing and Health Sciences, University of Vermont, Burlington, VT, United States.,University of Vermont Cancer Center, Burlington, VT, United States
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45
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Hartlieb SA, Sieverling L, Nadler-Holly M, Ziehm M, Toprak UH, Herrmann C, Ishaque N, Okonechnikov K, Gartlgruber M, Park YG, Wecht EM, Savelyeva L, Henrich KO, Rosswog C, Fischer M, Hero B, Jones DTW, Pfaff E, Witt O, Pfister SM, Volckmann R, Koster J, Kiesel K, Rippe K, Taschner-Mandl S, Ambros P, Brors B, Selbach M, Feuerbach L, Westermann F. Alternative lengthening of telomeres in childhood neuroblastoma from genome to proteome. Nat Commun 2021; 12:1269. [PMID: 33627664 PMCID: PMC7904810 DOI: 10.1038/s41467-021-21247-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 01/13/2021] [Indexed: 02/08/2023] Open
Abstract
Telomere maintenance by telomerase activation or alternative lengthening of telomeres (ALT) is a major determinant of poor outcome in neuroblastoma. Here, we screen for ALT in primary and relapsed neuroblastomas (n = 760) and characterize its features using multi-omics profiling. ALT-positive tumors are molecularly distinct from other neuroblastoma subtypes and enriched in a population-based clinical sequencing study cohort for relapsed cases. They display reduced ATRX/DAXX complex abundance, due to either ATRX mutations (55%) or low protein expression. The heterochromatic histone mark H3K9me3 recognized by ATRX is enriched at the telomeres of ALT-positive tumors. Notably, we find a high frequency of telomeric repeat loci with a neuroblastoma ALT-specific hotspot on chr1q42.2 and loss of the adjacent chromosomal segment forming a neo-telomere. ALT-positive neuroblastomas proliferate slowly, which is reflected by a protracted clinical course of disease. Nevertheless, children with an ALT-positive neuroblastoma have dismal outcome.
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Affiliation(s)
- Sabine A Hartlieb
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Lina Sieverling
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Applied Bioinformatics, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Michal Nadler-Holly
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Matthias Ziehm
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Umut H Toprak
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carl Herrmann
- Health Data Science Unit, Medical Faculty Heidelberg and BioQuant, Heidelberg, Germany
| | - Naveed Ishaque
- Digital Health Centre, Berlin Institute of Health (BIH), Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Moritz Gartlgruber
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Young-Gyu Park
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elisa Maria Wecht
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Larissa Savelyeva
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kai-Oliver Henrich
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carolina Rosswog
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Department of Pediatric Oncology and Hematology, University of Cologne, Cologne, Germany
| | - Barbara Hero
- Department of Pediatric Oncology and Hematology, University of Cologne, Cologne, Germany
| | - David T W Jones
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elke Pfaff
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, University Hospital, Heidelberg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, University Hospital, Heidelberg, Germany
| | - Richard Volckmann
- Department of Oncogenomics Amsterdam University Medical Centers (AUMC), Amsterdam, the Netherlands
| | - Jan Koster
- Department of Oncogenomics Amsterdam University Medical Centers (AUMC), Amsterdam, the Netherlands
| | - Katharina Kiesel
- Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Karsten Rippe
- Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | | | - Peter Ambros
- CCRI, St Anna Children's Cancer Research Institute, Vienna, Austria
| | - Benedikt Brors
- Applied Bioinformatics, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Lars Feuerbach
- Applied Bioinformatics, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Frank Westermann
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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46
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Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells. Nat Commun 2021; 12:1097. [PMID: 33597549 PMCID: PMC7889907 DOI: 10.1038/s41467-021-21341-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 01/14/2021] [Indexed: 12/30/2022] Open
Abstract
Telomeres are part of a highly refined system for maintaining the stability of linear chromosomes. Most telomeres rely on simple repetitive sequences and telomerase enzymes to protect chromosomal ends; however, in some species or telomerase-defective situations, an alternative lengthening of telomeres (ALT) mechanism is used. ALT mainly utilises recombination-based replication mechanisms and the constituents of ALT-based telomeres vary depending on models. Here we show that mouse telomeres can exploit non-telomeric, unique sequences in addition to telomeric repeats. We establish that a specific subtelomeric element, the mouse template for ALT (mTALT), is used for repairing telomeric DNA damage as well as for composing portions of telomeres in ALT-dependent mouse embryonic stem cells. Epigenomic and proteomic analyses before and after ALT activation reveal a high level of non-coding mTALT transcripts despite the heterochromatic nature of mTALT-based telomeres. After ALT activation, the increased HMGN1, a non-histone chromosomal protein, contributes to the maintenance of telomere stability by regulating telomeric transcription. These findings provide a molecular basis to study the evolution of new structures in telomeres. Telomeres can be maintained by a telomerase-independent mechanism called an alternative lengthening of telomeres (ALT). Here the authors use mouse Terc (telomerase RNA) knockout embryonic cells and provide longitudinal analysis of ALT telomeres maintained with non-telomeric sequences.
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47
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Lindrose AR, McLester-Davis LWY, Tristano RI, Kataria L, Gadalla SM, Eisenberg DTA, Verhulst S, Drury S. Method comparison studies of telomere length measurement using qPCR approaches: A critical appraisal of the literature. PLoS One 2021; 16:e0245582. [PMID: 33471860 PMCID: PMC7817045 DOI: 10.1371/journal.pone.0245582] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/05/2021] [Indexed: 12/16/2022] Open
Abstract
Use of telomere length (TL) as a biomarker for various environmental exposures and diseases has increased in recent years. Various methods have been developed to measure telomere length. Polymerase chain reaction (PCR)-based methods remain wide-spread for population-based studies due to the high-throughput capability. While several studies have evaluated the repeatability and reproducibility of different TL measurement methods, the results have been variable. We conducted a literature review of TL measurement cross-method comparison studies that included a PCR-based method published between January 1, 2002 and May 25, 2020. A total of 25 articles were found that matched the inclusion criteria. Papers were reviewed for quality of methodologic reporting of sample and DNA quality, PCR assay characteristics, sample blinding, and analytic approaches to determine final TL. Overall, methodologic reporting was low as assessed by two different reporting guidelines for qPCR-based TL measurement. There was a wide range in the reported correlation between methods (as assessed by Pearson’s r) and few studies utilized the recommended intra-class correlation coefficient (ICC) for assessment of assay repeatability and methodologic comparisons. The sample size for nearly all studies was less than 100, raising concerns about statistical power. Overall, this review found that the current literature on the relation between TL measurement methods is lacking in validity and scientific rigor. In light of these findings, we present reporting guidelines for PCR-based TL measurement methods and results of analyses of the effect of assay repeatability (ICC) on statistical power of cross-sectional and longitudinal studies. Additional cross-laboratory studies with rigorous methodologic and statistical reporting, adequate sample size, and blinding are essential to accurately determine assay repeatability and replicability as well as the relation between TL measurement methods.
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Affiliation(s)
- Alyssa R. Lindrose
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
- * E-mail: (ARL); (SD)
| | | | - Renee I. Tristano
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Leila Kataria
- School of Science and Engineering, Tulane University, New Orleans, Louisiana, United States of America
| | - Shahinaz M. Gadalla
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Dan T. A. Eisenberg
- Department of Anthropology, Department of Biology, Center for Studies in Demography and Ecology, University of Washington, Seattle, Washington, United States of America
| | - Simon Verhulst
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Stacy Drury
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
- Tulane Brain Institute, Tulane University, New Orleans, Louisiana, United States of America
- Department of Pediatrics, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
- * E-mail: (ARL); (SD)
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48
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Jäger N. Bioinformatics workflows for clinical applications in precision oncology. Semin Cancer Biol 2021; 84:103-112. [PMID: 33476720 DOI: 10.1016/j.semcancer.2020.12.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/15/2020] [Accepted: 12/28/2020] [Indexed: 12/23/2022]
Abstract
High-throughput molecular profiling of tumors is a fundamental aspect of precision oncology, enabling the identification of genomic alterations that can be targeted therapeutically. In this context, a patient is matched to a specific drug or therapy based on the tumor's underlying genetic driver events rather than the histologic classification. This approach requires extensive bioinformatics methodology and workflows, including raw sequencing data processing and quality control, variant calling and annotation, integration of different molecular data types, visualization and finally reporting the data to physicians, cancer researchers and pharmacologists in a format that is readily interpretable for clinical decision making. This review comprises a broad overview of these bioinformatics aspects and discusses the multiple analytical, technical and interpretational challenges that remain to efficiently translate molecular findings into personalized treatment recommendations.
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Affiliation(s)
- Natalie Jäger
- Hopp Children's Cancer Center Heidelberg (KiTZ) & Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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49
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Voronina N, Wong JKL, Hübschmann D, Hlevnjak M, Uhrig S, Heilig CE, Horak P, Kreutzfeldt S, Mock A, Stenzinger A, Hutter B, Fröhlich M, Brors B, Jahn A, Klink B, Gieldon L, Sieverling L, Feuerbach L, Chudasama P, Beck K, Kroiss M, Heining C, Möhrmann L, Fischer A, Schröck E, Glimm H, Zapatka M, Lichter P, Fröhling S, Ernst A. The landscape of chromothripsis across adult cancer types. Nat Commun 2020; 11:2320. [PMID: 32385320 PMCID: PMC7210959 DOI: 10.1038/s41467-020-16134-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 03/17/2020] [Indexed: 02/07/2023] Open
Abstract
Chromothripsis is a recently identified mutational phenomenon, by which a presumably single catastrophic event generates extensive genomic rearrangements of one or a few chromosome(s). Considered as an early event in tumour development, this form of genome instability plays a prominent role in tumour onset. Chromothripsis prevalence might have been underestimated when using low-resolution methods, and pan-cancer studies based on sequencing are rare. Here we analyse chromothripsis in 28 tumour types covering all major adult cancers (634 tumours, 316 whole-genome and 318 whole-exome sequences). We show that chromothripsis affects a substantial proportion of human cancers, with a prevalence of 49% across all cases. Chromothripsis generates entity-specific genomic alterations driving tumour development, including clinically relevant druggable fusions. Chromothripsis is linked with specific telomere patterns and univocal mutational signatures in distinct tumour entities. Longitudinal analysis of chromothriptic patterns in 24 matched tumour pairs reveals insights in the clonal evolution of tumours with chromothripsis. The shattering of chromosomes is a dramatic early event in tumourigenesis and is termed chromothripsis. Here, the authors examine chromothripsis across 28 tumour types and show that 49% of cancers exhibit features of chromothripsis.
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Affiliation(s)
- Natalia Voronina
- Group Genome Instability in Tumors, DKFZ, Heidelberg, Germany.,Division of Molecular Genetics, DKFZ, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - John K L Wong
- Division of Molecular Genetics, DKFZ, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Daniel Hübschmann
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Computational Oncology, Molecular Diagnostics Program, National Center for Tumor Diseases, DKFZ, Heidelberg, Germany.,Heidelberg Institute for Stem cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany.,Department of Pediatric Immunology, Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Mario Hlevnjak
- Division of Molecular Genetics, DKFZ, Heidelberg, Germany.,Computational Oncology, Molecular Diagnostics Program, National Center for Tumor Diseases, DKFZ, Heidelberg, Germany
| | - Sebastian Uhrig
- Computational Oncology, Molecular Diagnostics Program, National Center for Tumor Diseases, DKFZ, Heidelberg, Germany.,Division of Applied Bioinformatics, DKFZ and NCT Heidelberg, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Christoph E Heilig
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and DKFZ, Heidelberg, Germany.,DKFZ-Heidelberg Center for Personalized Oncology (HIPO), Heidelberg, Germany
| | - Peter Horak
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and DKFZ, Heidelberg, Germany.,DKFZ-Heidelberg Center for Personalized Oncology (HIPO), Heidelberg, Germany
| | - Simon Kreutzfeldt
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and DKFZ, Heidelberg, Germany.,DKFZ-Heidelberg Center for Personalized Oncology (HIPO), Heidelberg, Germany
| | - Andreas Mock
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and DKFZ, Heidelberg, Germany.,DKFZ-Heidelberg Center for Personalized Oncology (HIPO), Heidelberg, Germany
| | | | - Barbara Hutter
- Computational Oncology, Molecular Diagnostics Program, National Center for Tumor Diseases, DKFZ, Heidelberg, Germany.,Division of Applied Bioinformatics, DKFZ and NCT Heidelberg, Heidelberg, Germany
| | - Martina Fröhlich
- Computational Oncology, Molecular Diagnostics Program, National Center for Tumor Diseases, DKFZ, Heidelberg, Germany.,Division of Applied Bioinformatics, DKFZ and NCT Heidelberg, Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, DKFZ and NCT Heidelberg, Heidelberg, Germany
| | - Arne Jahn
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, ERN-GENTURIS, Hereditary Cancer Syndrome Center Dresden, German Cancer Consortium (DKTK), Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany.,Department of Translational Medical Oncology, NCT Dresden, Dresden, and DKFZ, Dresden, Germany.,Center for Personalized Oncology, University Hospital Carl Gustav Carus Dresden, Technical University of Dresden, Dresden, Germany.,German Cancer Consortium (DKTK), Dresden, Germany
| | - Barbara Klink
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, ERN-GENTURIS, Hereditary Cancer Syndrome Center Dresden, German Cancer Consortium (DKTK), Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany.,National Center of Genetics (NCG), Laboratoire national de santé (LNS), Dudelange, Luxembourg
| | - Laura Gieldon
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and DKFZ, Heidelberg, Germany.,DKFZ-Heidelberg Center for Personalized Oncology (HIPO), Heidelberg, Germany
| | - Lina Sieverling
- Division of Applied Bioinformatics, DKFZ and NCT Heidelberg, Heidelberg, Germany
| | - Lars Feuerbach
- Division of Applied Bioinformatics, DKFZ and NCT Heidelberg, Heidelberg, Germany
| | - Priya Chudasama
- Precision Sarcoma Research Group, DKFZ, National Center for Tumor (NCT) Diseases, Heidelberg, Germany
| | - Katja Beck
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and DKFZ, Heidelberg, Germany.,DKFZ-Heidelberg Center for Personalized Oncology (HIPO), Heidelberg, Germany
| | - Matthias Kroiss
- Department of Internal Medicine I, Division of Endocrinology and Diabetology, University Hospital Würzburg, Würzburg, Germany
| | - Christoph Heining
- Department of Translational Medical Oncology, NCT Dresden, Dresden, and DKFZ, Dresden, Germany.,Center for Personalized Oncology, University Hospital Carl Gustav Carus Dresden, Technical University of Dresden, Dresden, Germany.,German Cancer Consortium (DKTK), Dresden, Germany
| | - Lino Möhrmann
- Department of Translational Medical Oncology, NCT Dresden, Dresden, and DKFZ, Dresden, Germany.,Center for Personalized Oncology, University Hospital Carl Gustav Carus Dresden, Technical University of Dresden, Dresden, Germany.,German Cancer Consortium (DKTK), Dresden, Germany
| | - Andrea Fischer
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, ERN-GENTURIS, Hereditary Cancer Syndrome Center Dresden, German Cancer Consortium (DKTK), Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Evelin Schröck
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, ERN-GENTURIS, Hereditary Cancer Syndrome Center Dresden, German Cancer Consortium (DKTK), Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Hanno Glimm
- Department of Translational Medical Oncology, NCT Dresden, Dresden, and DKFZ, Dresden, Germany.,Center for Personalized Oncology, University Hospital Carl Gustav Carus Dresden, Technical University of Dresden, Dresden, Germany.,German Cancer Consortium (DKTK), Dresden, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, DKFZ, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, DKFZ, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and DKFZ, Heidelberg, Germany.,DKFZ-Heidelberg Center for Personalized Oncology (HIPO), Heidelberg, Germany
| | - Aurélie Ernst
- Group Genome Instability in Tumors, DKFZ, Heidelberg, Germany. .,Division of Molecular Genetics, DKFZ, Heidelberg, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany.
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50
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Sieverling L, Hong C, Koser SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortés-Ciriano I, Xi R, Kabbe R, Park PJ, Eils R, Schlesner M, Brors B, Rippe K, Jones DTW, Feuerbach L. Genomic footprints of activated telomere maintenance mechanisms in cancer. Nat Commun 2020; 11:733. [PMID: 32024817 PMCID: PMC7002710 DOI: 10.1038/s41467-019-13824-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 11/26/2019] [Indexed: 12/14/2022] Open
Abstract
Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the telomere content of tumors with ATRX or DAXX mutations (ATRX/DAXXtrunc) is increased, tumors with TERT modifications show a moderate decrease of telomere content. One quarter of all tumor samples contain somatic integrations of telomeric sequences into non-telomeric DNA. This fraction is increased to 80% prevalence in ATRX/DAXXtrunc tumors, which carry an aberrant telomere variant repeat (TVR) distribution as another genomic marker. The latter feature includes enrichment or depletion of the previously undescribed singleton TVRs TTCGGG and TTTGGG, respectively. Our systematic analysis provides new insight into the recurrent genomic alterations associated with telomere maintenance mechanisms in cancer.
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Affiliation(s)
- Lina Sieverling
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Chen Hong
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Sandra D Koser
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Philip Ginsbach
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Kortine Kleinheinz
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, 69120, Heidelberg, Germany
| | - Barbara Hutter
- German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Delia M Braun
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, 69120, Heidelberg, Germany
| | - Isidro Cortés-Ciriano
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Department of Chemistry, Centre for Molecular Science Informatics, University of Cambridge, Cambridge, CB2 1EW, UK
- Ludwig Center at Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Ruibin Xi
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing, 100871, China
| | - Rolf Kabbe
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Ludwig Center at Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, 69120, Heidelberg, Germany
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, 69120, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lars Feuerbach
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
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