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Tandukar B, Deivendran D, Chen L, Cruz-Pacheco N, Sharma H, Xu A, Bandari AK, Chen DB, George C, Marty A, Cho RJ, Cheng J, Saylor D, Gerami P, Arron ST, Bastian BC, Shain AH. Genetic evolution of keratinocytes to cutaneous squamous cell carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604673. [PMID: 39091884 PMCID: PMC11291049 DOI: 10.1101/2024.07.23.604673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
We performed multi-omic profiling of epidermal keratinocytes, precancerous actinic keratoses, and squamous cell carcinomas to understand the molecular transitions during skin carcinogenesis. Single-cell mutational analyses showed that most keratinocytes in normal skin had lower mutation burdens than melanocytes and fibroblasts, however keratinocytes with TP53 or NOTCH1 mutations had substantially higher mutation burdens, suggesting that these mutations prime keratinocytes for transformation by increasing their mutation rate. Mutational profiling and spatial transcriptomics on squamous cell carcinomas adjacent to actinic keratoses revealed TERT promoter and CDKN2A mutations emerging in actinic keratoses, whereas additional mutations inactivating ARID2 and activating the MAPK-pathway delineated the transition to squamous cell carcinomas. Spatial variation in gene expression patterns was common in both tumor and immune cells, with high expression of checkpoint molecules at the invasive front of tumors. In conclusion, this study documents key events during the evolution of cutaneous squamous cell carcinoma.
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Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2561-0. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
Abstract
Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome, proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field, offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.
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Affiliation(s)
- Fengying Sun
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China
| | - Haoyan Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dongqing Sun
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaliu Fu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Lei Gu
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China
| | - Qinqin Wang
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Dong
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Bin Duan
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Feiyang Xing
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jun Wu
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Minmin Xiao
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Qi Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China.
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China.
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Chen Li
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Chenfei Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Tieliu Shi
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University, Shanghai, 200062, China.
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3
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Bertrums EJM, de Kanter JK, Derks LLM, Verheul M, Trabut L, van Roosmalen MJ, Hasle H, Antoniou E, Reinhardt D, Dworzak MN, Mühlegger N, van den Heuvel-Eibrink MM, Zwaan CM, Goemans BF, van Boxtel R. Selective pressures of platinum compounds shape the evolution of therapy-related myeloid neoplasms. Nat Commun 2024; 15:6025. [PMID: 39019934 PMCID: PMC11255340 DOI: 10.1038/s41467-024-50384-z] [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: 06/12/2023] [Accepted: 07/08/2024] [Indexed: 07/19/2024] Open
Abstract
Therapy-related myeloid neoplasms (t-MN) arise as a complication of chemo- and/or radiotherapy. Although t-MN can occur both in adult and childhood cancer survivors, the mechanisms driving therapy-related leukemogenesis likely vary across different ages. Chemotherapy is thought to induce driver mutations in children, whereas in adults pre-existing mutant clones are selected by the exposure. However, selective pressures induced by chemotherapy early in life are less well studied. Here, we use single-cell whole genome sequencing and phylogenetic inference to show that the founding cell of t-MN in children starts expanding after cessation of platinum exposure. In patients with Li-Fraumeni syndrome, characterized by a germline TP53 mutation, we find that the t-MN already expands during treatment, suggesting that platinum-induced growth inhibition is TP53-dependent. Our results demonstrate that germline aberrations can interact with treatment exposures in inducing t-MN, which is important for the development of more targeted, patient-specific treatment regimens and follow-up.
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Affiliation(s)
- Eline J M Bertrums
- Princess Máxima Centrum for pediatric oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Jurrian K de Kanter
- Princess Máxima Centrum for pediatric oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Lucca L M Derks
- Princess Máxima Centrum for pediatric oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Mark Verheul
- Princess Máxima Centrum for pediatric oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Laurianne Trabut
- Princess Máxima Centrum for pediatric oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Markus J van Roosmalen
- Princess Máxima Centrum for pediatric oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Henrik Hasle
- Department of Pediatrics, Aarhus University Hospital, Aarhus, Denmark
| | - Evangelia Antoniou
- Clinic of Pediatrics III, University Hospital of Essen, Essen, Germany
- AML-BFM Study Group, Essen, Germany
| | - Dirk Reinhardt
- Clinic of Pediatrics III, University Hospital of Essen, Essen, Germany
- AML-BFM Study Group, Essen, Germany
| | - Michael N Dworzak
- St. Anna Children's Cancer Research Institute, Vienna, Austria
- St. Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Nora Mühlegger
- St. Anna Children's Cancer Research Institute, Vienna, Austria
| | | | - C Michel Zwaan
- Princess Máxima Centrum for pediatric oncology, Utrecht, the Netherlands
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Bianca F Goemans
- Princess Máxima Centrum for pediatric oncology, Utrecht, the Netherlands
| | - Ruben van Boxtel
- Princess Máxima Centrum for pediatric oncology, Utrecht, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
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4
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Qiao Y, Cheng T, Miao Z, Cui Y, Tu J. Recent Innovations and Technical Advances in High-Throughput Parallel Single-Cell Whole-Genome Sequencing Methods. SMALL METHODS 2024:e2400789. [PMID: 38979872 DOI: 10.1002/smtd.202400789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Indexed: 07/10/2024]
Abstract
Single-cell whole-genome sequencing (scWGS) detects cell heterogeneity at the aspect of genomic variations, which are inheritable and play an important role in life processes such as aging and cancer progression. The recent explosive development of high-throughput single-cell sequencing methods has enabled high-performance heterogeneity detection through a vast number of novel strategies. Despite the limitation on total cost, technical advances in high-throughput single-cell whole-genome sequencing methods are made for higher genome coverage, parallel throughput, and level of integration. This review highlights the technical advancements in high-throughput scWGS in the aspects of strategies design, data efficiency, parallel handling platforms, and their applications on human genome. The experimental innovations, remaining challenges, and perspectives are summarized and discussed.
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Affiliation(s)
- Yi Qiao
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Tianguang Cheng
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Zikun Miao
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Yue Cui
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Jing Tu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
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5
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Jia H, Tan S, Zhang YE. Chasing Sequencing Perfection: Marching Toward Higher Accuracy and Lower Costs. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae024. [PMID: 38991976 DOI: 10.1093/gpbjnl/qzae024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 07/13/2024]
Abstract
Next-generation sequencing (NGS), represented by Illumina platforms, has been an essential cornerstone of basic and applied research. However, the sequencing error rate of 1 per 1000 bp (10-3) represents a serious hurdle for research areas focusing on rare mutations, such as somatic mosaicism or microbe heterogeneity. By examining the high-fidelity sequencing methods developed in the past decade, we summarized three major factors underlying errors and the corresponding 12 strategies mitigating these errors. We then proposed a novel framework to classify 11 preexisting representative methods according to the corresponding combinatory strategies and identified three trends that emerged during methodological developments. We further extended this analysis to eight long-read sequencing methods, emphasizing error reduction strategies. Finally, we suggest two promising future directions that could achieve comparable or even higher accuracy with lower costs in both NGS and long-read sequencing.
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Affiliation(s)
- Hangxing Jia
- CAS Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shengjun Tan
- CAS Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong E Zhang
- CAS Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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6
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Pfeifer GP, Jin SG. Methods and applications of genome-wide profiling of DNA damage and rare mutations. Nat Rev Genet 2024:10.1038/s41576-024-00748-4. [PMID: 38918545 DOI: 10.1038/s41576-024-00748-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2024] [Indexed: 06/27/2024]
Abstract
DNA damage is a threat to genome integrity and can be a cause of many human diseases, owing to either changes in the chemical structure of DNA or conversion of the damage into a mutation, that is, a permanent change in DNA sequence. Determining the exact positions of DNA damage and ensuing mutations in the genome are important for identifying mechanisms of disease aetiology when characteristic mutations are prevalent and probably causative in a particular disease. However, this approach is challenging particularly when levels of DNA damage are low, for example, as a result of chronic exposure to environmental agents or certain endogenous processes, such as the generation of reactive oxygen species. Over the past few years, a comprehensive toolbox of genome-wide methods has been developed for the detection of DNA damage and rare mutations at single-nucleotide resolution in mammalian cells. Here, we review and compare these methods, describe their current applications and discuss future research questions that can now be addressed.
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Affiliation(s)
- Gerd P Pfeifer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
| | - Seung-Gi Jin
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
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7
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Gerami P, Tandukar B, Deivendran D, Olivares S, Chen L, Tang J, Tan T, Sharma H, Bandari AK, Cruz-Pacheco N, Chang D, Marty A, Olshen A, Murad NF, Song J, Lee J, Yeh I, Hunter Shain A. Molecular effects of indoor tanning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597225. [PMID: 38895302 PMCID: PMC11185634 DOI: 10.1101/2024.06.04.597225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Background Tanning bed users have a significantly increased risk of melanoma, but it remains unclear how indoor tanning drives melanomagenesis. Tanning bed radiation is often thought of as a substitute for natural UV radiation despite differences in the maximum doses, UV content, body sites exposed, and patterns of melanoma that arise. Methods To better understand the epidemiologic trends and etiology of melanoma associated with tanning bed use, we described the patterns of melanoma in patients with quantifiable tanning bed usage and performed exome sequencing of 182 melanocytes from normal skin of a subset of these patients. Results Tanning bed users were more likely than non-users to have melanoma on body sites with low cumulative levels of sun damage and were more likely to have multiple melanomas. The melanocytes in normal appearing skin from tanning bed users had higher mutation burdens, a higher proportion of melanocytes with pathogenic mutations, and distinct mutational signatures. These differences were most prominent over body sites that experience comparatively less exposure to natural sunlight. Conclusions We conclude that tanning bed radiation induces melanoma by increasing the mutation burden of melanocytes and by mutagenizing a broader field of melanocytes than are typically exposed to natural sunlight. The unique signatures of mutations in skin cells of tanning users may be attributable to the distinct spectra of radiation emitted from solariums.
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Affiliation(s)
- Pedram Gerami
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Bishal Tandukar
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Delahny Deivendran
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Shantel Olivares
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Limin Chen
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Jessica Tang
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Tuyet Tan
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- School of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Harsh Sharma
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Aravind K Bandari
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Noel Cruz-Pacheco
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Darwin Chang
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Department of Immunology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Annika Marty
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Adam Olshen
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Natalia Faraj Murad
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Jing Song
- Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jungwha Lee
- Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Iwei Yeh
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - A Hunter Shain
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
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8
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Klein KM, Mascarenhas R, Merrikh D, Khanbabaei M, Maroilley T, Kaur N, Liu Y, Soule T, Manalo M, Tamura G, Jacobs J, Hader W, Pfeffer G, Tarailo-Graovac M. Identification of a mosaic MTOR variant in purified neuronal DNA in a patient with focal cortical dysplasia using a novel depth electrode harvesting technique. Epilepsia 2024; 65:1768-1776. [PMID: 38587282 DOI: 10.1111/epi.17980] [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: 01/20/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/09/2024]
Abstract
OBJECTIVE Recent studies have identified brain somatic variants as a cause of focal epilepsy. These studies relied on resected tissue from epilepsy surgery, which is not available in most patients. The use of trace tissue adherent to depth electrodes used for stereo electroencephalography (EEG) has been proposed as an alternative but is hampered by the low cell quality and contamination by nonbrain cells. Here, we use our improved depth electrode harvesting technique that purifies neuronal nuclei to achieve molecular diagnosis in a patient with focal cortical dysplasia (FCD). METHODS Depth electrode tips were collected, pooled by brain region and seizure onset zone, and nuclei were isolated and sorted using fluorescence-activated nuclei sorting (FANS). Somatic DNA was amplified from neuronal and astrocyte nuclei using primary template amplification followed by exome sequencing of neuronal DNA from the affected pool, unaffected pool, and saliva. The identified variant was validated using droplet digital polymerase chain reaction (PCR). RESULTS An 11-year-old male with drug-resistant genetic-structural epilepsy due to left anterior insula FCD had seizures from age 3 years. Stereo EEG confirmed seizure onset in the left anterior insula. The two anterior insula electrodes were combined as the affected pool and three frontal electrodes as the unaffected pool. FANS isolated 140 neuronal nuclei from the affected and 245 neuronal nuclei from the unaffected pool. A novel somatic missense MTOR variant (p.Leu489Met, CADD score 23.7) was identified in the affected neuronal sample. Droplet digital PCR confirmed a mosaic gradient (variant allele frequency = .78% in affected neuronal sample; variant was absent in all other samples). SIGNIFICANCE Our findings confirm that harvesting neuronal DNA from depth electrodes followed by molecular analysis to identify brain somatic variants is feasible. Our novel method represents a significant improvement compared to the previous method by focusing the analysis on high-quality cells of the cell type of interest.
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Affiliation(s)
- Karl Martin Klein
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Rumika Mascarenhas
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Daria Merrikh
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Maryam Khanbabaei
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
| | - Tatiana Maroilley
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Navprabhjot Kaur
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
| | - Yiping Liu
- Flow Cytometry Core Facility, University of Calgary, Calgary, Alberta, Canada
| | - Tyler Soule
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Minette Manalo
- Department of Pediatrics, University of Calgary, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Goichiro Tamura
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
| | - Julia Jacobs
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
- Department of Pediatrics, University of Calgary, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Walter Hader
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
| | - Gerald Pfeffer
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Maja Tarailo-Graovac
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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9
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Graham JH, Schlachetzki JCM, Yang X, Breuss MW. Genomic Mosaicism of the Brain: Origin, Impact, and Utility. Neurosci Bull 2024; 40:759-776. [PMID: 37898991 PMCID: PMC11178748 DOI: 10.1007/s12264-023-01124-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/16/2023] [Indexed: 10/31/2023] Open
Abstract
Genomic mosaicism describes the phenomenon where some but not all cells within a tissue harbor unique genetic mutations. Traditionally, research focused on the impact of genomic mosaicism on clinical phenotype-motivated by its involvement in cancers and overgrowth syndromes. More recently, we increasingly shifted towards the plethora of neutral mosaic variants that can act as recorders of cellular lineage and environmental exposures. Here, we summarize the current state of the field of genomic mosaicism research with a special emphasis on our current understanding of this phenomenon in brain development and homeostasis. Although the field of genomic mosaicism has a rich history, technological advances in the last decade have changed our approaches and greatly improved our knowledge. We will provide current definitions and an overview of contemporary detection approaches for genomic mosaicism. Finally, we will discuss the impact and utility of genomic mosaicism.
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Affiliation(s)
- Jared H Graham
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, 92123, CA, USA
| | - Martin W Breuss
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA.
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10
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Yuan DJ, Zinno J, Botella T, Dhingra D, Wang S, Hawkins A, Swett A, Sotelo J, Raviram R, Hughes C, Potenski C, Yokoyama A, Kakiuchi N, Ogawa S, Landau DA. Genotype-to-phenotype mapping of somatic clonal mosaicism via single-cell co-capture of DNA mutations and mRNA transcripts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595241. [PMID: 38826366 PMCID: PMC11142212 DOI: 10.1101/2024.05.22.595241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Somatic mosaicism is a hallmark of malignancy that is also pervasively observed in human physiological aging, with clonal expansions of cells harboring mutations in recurrently mutated driver genes. Bulk sequencing of tissue microdissection captures mutation frequencies, but cannot distinguish which mutations co-occur in the same clones to reconstruct clonal architectures, nor phenotypically profile clonal populations to delineate how driver mutations impact cellular behavior. To address these challenges, we developed single-cell Genotype-to-Phenotype sequencing (scG2P) for high-throughput, highly-multiplexed, single-cell joint capture of recurrently mutated genomic regions and mRNA phenotypic markers in cells or nuclei isolated from solid tissues. We applied scG2P to aged esophagus samples from five individuals with high alcohol and tobacco exposure and observed a clonal landscape dominated by a large number of clones with a single driver event, but only rare clones with two driver mutations. NOTCH1 mutants dominate the clonal landscape and are linked to stunted epithelial differentiation, while TP53 mutants and double-driver mutants promote clonal expansion through both differentiation biases and increased cell cycling. Thus, joint single-cell highly multiplexed capture of somatic mutations and mRNA transcripts enables high resolution reconstruction of clonal architecture and associated phenotypes in solid tissue somatic mosaicism.
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Affiliation(s)
- Dennis J Yuan
- New York Genome Center, New York, NY
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - John Zinno
- New York Genome Center, New York, NY
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Theo Botella
- New York Genome Center, New York, NY
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | | | | | - Allegra Hawkins
- New York Genome Center, New York, NY
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Ariel Swett
- New York Genome Center, New York, NY
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Jesus Sotelo
- New York Genome Center, New York, NY
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Ramya Raviram
- New York Genome Center, New York, NY
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Clayton Hughes
- New York Genome Center, New York, NY
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Catherine Potenski
- New York Genome Center, New York, NY
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Akira Yokoyama
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Medical Oncology, Kyoto University, Kyoto, Japan
| | - Nobuyuki Kakiuchi
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- The Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Dan A Landau
- New York Genome Center, New York, NY
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY
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11
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Zhang X, Celic I, Mitchell H, Stuckert S, Vedula L, Han J. Comprehensive profiling of L1 retrotransposons in mouse. Nucleic Acids Res 2024; 52:5166-5178. [PMID: 38647072 PMCID: PMC11109951 DOI: 10.1093/nar/gkae273] [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: 11/13/2023] [Revised: 03/25/2024] [Accepted: 04/06/2024] [Indexed: 04/25/2024] Open
Abstract
L1 elements are retrotransposons currently active in mammals. Although L1s are typically silenced in most normal tissues, elevated L1 expression is associated with a variety of conditions, including cancer, aging, infertility and neurological disease. These associations have raised interest in the mapping of human endogenous de novo L1 insertions, and a variety of methods have been developed for this purpose. Adapting these methods to mouse genomes would allow us to monitor endogenous in vivo L1 activity in controlled, experimental conditions using mouse disease models. Here, we use a modified version of transposon insertion profiling, called nanoTIPseq, to selectively enrich young mouse L1s. By linking this amplification step with nanopore sequencing, we identified >95% annotated L1s from C57BL/6 genomic DNA using only 200 000 sequencing reads. In the process, we discovered 82 unannotated L1 insertions from a single C57BL/6 genome. Most of these unannotated L1s were near repetitive sequence and were not found with short-read TIPseq. We used nanoTIPseq on individual mouse breast cancer cells and were able to identify the annotated and unannotated L1s, as well as new insertions specific to individual cells, providing proof of principle for using nanoTIPseq to interrogate retrotransposition activity at the single-cell level in vivo.
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Affiliation(s)
- Xuanming Zhang
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Ivana Celic
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Hannah Mitchell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Sam Stuckert
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Lalitha Vedula
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jeffrey S Han
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
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12
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Cooper S, Obolenski S, Waters AJ, Bassett AR, Coelho MA. Analyzing the functional effects of DNA variants with gene editing. CELL REPORTS METHODS 2024; 4:100776. [PMID: 38744287 PMCID: PMC11133854 DOI: 10.1016/j.crmeth.2024.100776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/01/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Continual advancements in genomics have led to an ever-widening disparity between the rate of discovery of genetic variants and our current understanding of their functions and potential roles in disease. Systematic methods for phenotyping DNA variants are required to effectively translate genomics data into improved outcomes for patients with genetic diseases. To make the biggest impact, these approaches must be scalable and accurate, faithfully reflect disease biology, and define complex disease mechanisms. We compare current methods to analyze the function of variants in their endogenous DNA context using genome editing strategies, such as saturation genome editing, base editing and prime editing. We discuss how these technologies can be linked to high-content readouts to gain deep mechanistic insights into variant effects. Finally, we highlight key challenges that need to be addressed to bridge the genotype to phenotype gap, and ultimately improve the diagnosis and treatment of genetic diseases.
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Affiliation(s)
- Sarah Cooper
- Cellular and Gene Editing Research, Wellcome Sanger Institute, Hinxton, UK
| | - Sofia Obolenski
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK; Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Andrew J Waters
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Andrew R Bassett
- Cellular and Gene Editing Research, Wellcome Sanger Institute, Hinxton, UK.
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13
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Sun C, Kathuria K, Emery SB, Kim B, Burbulis IE, Shin JH, Weinberger DR, Moran JV, Kidd JM, Mills RE, McConnell MJ. Mapping recurrent mosaic copy number variation in human neurons. Nat Commun 2024; 15:4220. [PMID: 38760338 PMCID: PMC11101435 DOI: 10.1038/s41467-024-48392-0] [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: 03/03/2023] [Accepted: 04/29/2024] [Indexed: 05/19/2024] Open
Abstract
When somatic cells acquire complex karyotypes, they often are removed by the immune system. Mutant somatic cells that evade immune surveillance can lead to cancer. Neurons with complex karyotypes arise during neurotypical brain development, but neurons are almost never the origin of brain cancers. Instead, somatic mutations in neurons can bring about neurodevelopmental disorders, and contribute to the polygenic landscape of neuropsychiatric and neurodegenerative disease. A subset of human neurons harbors idiosyncratic copy number variants (CNVs, "CNV neurons"), but previous analyses of CNV neurons are limited by relatively small sample sizes. Here, we develop an allele-based validation approach, SCOVAL, to corroborate or reject read-depth based CNV calls in single human neurons. We apply this approach to 2,125 frontal cortical neurons from a neurotypical human brain. SCOVAL identifies 226 CNV neurons, which include a subclass of 65 CNV neurons with highly aberrant karyotypes containing whole or substantial losses on multiple chromosomes. Moreover, we find that CNV location appears to be nonrandom. Recurrent regions of neuronal genome rearrangement contain fewer, but longer, genes.
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Affiliation(s)
- Chen Sun
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Kunal Kathuria
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Sarah B Emery
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI, 48109, USA
| | - ByungJun Kim
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Ian E Burbulis
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, 22902, USA
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Sede de la Patagonia, Puerto Montt, Chile
| | - Joo Heon Shin
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences and Neuroscience, Johns Hopkins School of Medicine, 600 North Wolfe Street, Baltimore, MD, 21287, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, 733 North Broadway, Baltimore, MD, 21230, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine, University of Michigan Medical School, 1500 East Medical Center Drive, Ann Arbor, MI, 48109, USA
| | - Jeffrey M Kidd
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI, 48109, USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA.
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI, 48109, USA.
| | - Michael J McConnell
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD, 21205, USA.
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14
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Soloveva EV, Skleimova MM, Minaycheva LI, Garaeva AF, Zhigalina DI, Churkin EO, Okkel YV, Timofeeva OS, Petrov IA, Seitova GN, Lebedev IN, Stepanov VA. PGT-M for spinocerebellar ataxia type 1: development of a STR panel and a report of two clinical cases. J Assist Reprod Genet 2024; 41:1273-1283. [PMID: 38578603 PMCID: PMC11143087 DOI: 10.1007/s10815-024-03105-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/20/2024] [Indexed: 04/06/2024] Open
Abstract
PURPOSE To present the developed preimplantation genetic testing (PGT) for spinocerebellar ataxia type 1 (SCA1) and the outcomes of IVF with PGT. METHODS PGT was performed for two unrelated couples from the Republic of Sakha (Yakutia) with the risk of SCA1 in one spouse. We have developed a system for PGT of a monogenic disease (PGT-M) for SCA1, which includes the analysis of a panel of 11 polymorphic STR markers linked to the ATXN1 gene and a pathogenic variant of the ATXN1 gene using nested PCR and fragment analysis. IVF/ICSI programs were performed according to standard protocols. Multiple displacement amplification (MDA) was used for whole genome amplification (WGA) and array comparative genomic hybridization (aCGH) for aneuploidy testing (PGT-A). RESULTS Eight STRs were informative for the first couple and ten for the second. Similarity of the haplotypes carrying pathogenic variants of the ATXN1 gene was noted. In the first case, during IVF/ICSI-PGT, three embryos reached the blastocyst stage and were biopsied. One embryo was diagnosed as normal by maternal STR haplotype and the ATXN1 allele. PGT-A revealed euploidy. The embryo transfer resulted in a singleton pregnancy, and a healthy boy was born. Postnatal diagnosis confirmed normal ATXN1. In the second case, two blastocysts were biopsied. Both were diagnosed as normal by PGT-M, but PGT-A revealed aneuploidy. CONCLUSION Birth of a healthy child after PGT for SCA1 was the first case of successful preimplantation prevention of SCA1 for the Yakut couple and the first case of successful PGT for SCA1 in Russia.
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Affiliation(s)
- Elena V Soloveva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia.
| | - Maria M Skleimova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Larisa I Minaycheva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Anna F Garaeva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Daria I Zhigalina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Egor O Churkin
- ART Center of the Siberian State Medical University of the Ministry of Health of Russia, Tomsk, Russia
| | - Yulia V Okkel
- ART Center of the Siberian State Medical University of the Ministry of Health of Russia, Tomsk, Russia
| | - Oksana S Timofeeva
- ART Center of the Siberian State Medical University of the Ministry of Health of Russia, Tomsk, Russia
- Department of Obstetrics and Gynecology of the Siberian State Medical University of the Ministry of Health of Russia, Tomsk, Russia
| | - Ilya A Petrov
- ART Center of the Siberian State Medical University of the Ministry of Health of Russia, Tomsk, Russia
- Department of Obstetrics and Gynecology of the Siberian State Medical University of the Ministry of Health of Russia, Tomsk, Russia
| | - Gulnara N Seitova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Igor N Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Vadim A Stepanov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
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15
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Chung C, Yang X, Hevner RF, Kennedy K, Vong KI, Liu Y, Patel A, Nedunuri R, Barton ST, Noel G, Barrows C, Stanley V, Mittal S, Breuss MW, Schlachetzki JCM, Kingsmore SF, Gleeson JG. Cell-type-resolved mosaicism reveals clonal dynamics of the human forebrain. Nature 2024; 629:384-392. [PMID: 38600385 PMCID: PMC11194162 DOI: 10.1038/s41586-024-07292-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 03/11/2024] [Indexed: 04/12/2024]
Abstract
Debate remains around the anatomical origins of specific brain cell subtypes and lineage relationships within the human forebrain1-7. Thus, direct observation in the mature human brain is critical for a complete understanding of its structural organization and cellular origins. Here we utilize brain mosaic variation within specific cell types as distinct indicators for clonal dynamics, denoted as cell-type-specific mosaic variant barcode analysis. From four hemispheres and two different human neurotypical donors, we identified 287 and 780 mosaic variants, respectively, that were used to deconvolve clonal dynamics. Clonal spread and allele fractions within the brain reveal that local hippocampal excitatory neurons are more lineage-restricted than resident neocortical excitatory neurons or resident basal ganglia GABAergic inhibitory neurons. Furthermore, simultaneous genome transcriptome analysis at both a cell-type-specific and a single-cell level suggests a dorsal neocortical origin for a subgroup of DLX1+ inhibitory neurons that disperse radially from an origin shared with excitatory neurons. Finally, the distribution of mosaic variants across 17 locations within one parietal lobe reveals that restriction of clonal spread in the anterior-posterior axis precedes restriction in the dorsal-ventral axis for both excitatory and inhibitory neurons. Thus, cell-type-resolved somatic mosaicism can uncover lineage relationships governing the development of the human forebrain.
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Affiliation(s)
- Changuk Chung
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Robert F Hevner
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
- Department of Pathology, UC San Diego School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Keng Ioi Vong
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Yang Liu
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Arzoo Patel
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Rahul Nedunuri
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Scott T Barton
- Division of Medical Education, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Geoffroy Noel
- Division of Anatomy, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Chelsea Barrows
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Valentina Stanley
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Swapnil Mittal
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Martin W Breuss
- Department of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO, USA
| | - Johannes C M Schlachetzki
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Joseph G Gleeson
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
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16
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Ganz J, Luquette LJ, Bizzotto S, Miller MB, Zhou Z, Bohrson CL, Jin H, Tran AV, Viswanadham VV, McDonough G, Brown K, Chahine Y, Chhouk B, Galor A, Park PJ, Walsh CA. Contrasting somatic mutation patterns in aging human neurons and oligodendrocytes. Cell 2024; 187:1955-1970.e23. [PMID: 38503282 PMCID: PMC11062076 DOI: 10.1016/j.cell.2024.02.025] [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: 01/09/2023] [Revised: 12/06/2023] [Accepted: 02/21/2024] [Indexed: 03/21/2024]
Abstract
Characterizing somatic mutations in the brain is important for disentangling the complex mechanisms of aging, yet little is known about mutational patterns in different brain cell types. Here, we performed whole-genome sequencing (WGS) of 86 single oligodendrocytes, 20 mixed glia, and 56 single neurons from neurotypical individuals spanning 0.4-104 years of age and identified >92,000 somatic single-nucleotide variants (sSNVs) and small insertions/deletions (indels). Although both cell types accumulate somatic mutations linearly with age, oligodendrocytes accumulated sSNVs 81% faster than neurons and indels 28% slower than neurons. Correlation of mutations with single-nucleus RNA profiles and chromatin accessibility from the same brains revealed that oligodendrocyte mutations are enriched in inactive genomic regions and are distributed across the genome similarly to mutations in brain cancers. In contrast, neuronal mutations are enriched in open, transcriptionally active chromatin. These stark differences suggest an assortment of active mutagenic processes in oligodendrocytes and neurons.
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Affiliation(s)
- Javier Ganz
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lovelace J Luquette
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Sara Bizzotto
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Sorbonne Université, Institut du Cerveau (Paris Brain Institute) ICM, Inserm, CNRS, Hôpital de la Pitié Salpêtrière, 75013 Paris, France
| | - Michael B Miller
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Zinan Zhou
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Craig L Bohrson
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Hu Jin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Antuan V Tran
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Gannon McDonough
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine Brown
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yasmine Chahine
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Brian Chhouk
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Alon Galor
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA.
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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17
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Awotoye W, Mossey PA, Hetmanski JB, Gowans LJ, Eshete MA, Adeyemo WL, Alade A, Zeng E, Adamson O, James O, Fashina A, Ogunlewe MO, Naicker T, Adeleke C, Busch T, Li M, Petrin A, Oladayo A, Kayali S, Olotu J, Sule V, Hassan M, Pape J, Aladenika ET, Donkor P, Arthur FK, Obiri-Yeboah S, Sabbah DK, Agbenorku P, Ray D, Plange-Rhule G, Oti AA, Albokhari D, Sobreira N, Dunnwald M, Beaty TH, Taub M, Marazita ML, Adeyemo AA, Murray JC, Butali A. Damaging Mutations in AFDN Contribute to Risk of Nonsyndromic Cleft Lip With or Without Cleft Palate. Cleft Palate Craniofac J 2024; 61:697-705. [PMID: 36384317 PMCID: PMC10185709 DOI: 10.1177/10556656221135926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Novel or rare damaging mutations have been implicated in the developmental pathogenesis of nonsyndromic cleft lip with or without cleft palate (nsCL ± P). Thus, we investigated the human genome for high-impact mutations that could explain the risk of nsCL ± P in our cohorts. We conducted next-generation sequencing (NGS) analysis of 130 nsCL ± P case-parent African trios to identify pathogenic variants that contribute to the risk of clefting. We replicated this analysis using whole-exome sequence data from a Brazilian nsCL ± P cohort. Computational analyses were then used to predict the mechanism by which these variants could result in increased risks for nsCL ± P. We discovered damaging mutations within the AFDN gene, a cell adhesion molecule (CAMs) that was previously shown to contribute to cleft palate in mice. These mutations include p.Met1164Ile, p.Thr453Asn, p.Pro1638Ala, p.Arg669Gln, p.Ala1717Val, and p.Arg1596His. We also discovered a novel splicing p.Leu1588Leu mutation in this protein. Computational analysis suggests that these amino acid changes affect the interactions with other cleft-associated genes including nectins (PVRL1, PVRL2, PVRL3, and PVRL4) CDH1, CTNNA1, and CTNND1. This is the first report on the contribution of AFDN to the risk for nsCL ± P in humans. AFDN encodes AFADIN, an important CAM that forms calcium-independent complexes with nectins 1 and 4 (encoded by the genes PVRL1 and PVRL4). This discovery shows the power of NGS analysis of multiethnic cleft samples in combination with a computational approach in the understanding of the pathogenesis of nsCL ± P.
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Affiliation(s)
- Waheed Awotoye
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Peter A. Mossey
- Department of Orthodontics, University of Dundee, Dundee, UK
| | - Jacqueline B. Hetmanski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Lord J.J Gowans
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Mekonen A. Eshete
- Addis Ababa University, School Medicine, Surgical Department, Addis Ababa, Ethiopia
| | - Wasiu L. Adeyemo
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos Nigeria
| | - Azeez Alade
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
- Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - Erliang Zeng
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Olawale Adamson
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos Nigeria
| | - Olutayo James
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos Nigeria
| | - Azeez Fashina
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos Nigeria
| | - Modupe O Ogunlewe
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos Nigeria
| | - Thirona Naicker
- Department of Pediatrics, University of KwaZulu-Natal, South Africa
| | - Chinyere Adeleke
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Tamara Busch
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Mary Li
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Aline Petrin
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - Abimbola Oladayo
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Sami Kayali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Joy Olotu
- Department of Anatomy, University of Port Harcourt
| | - Veronica Sule
- Department of Operative Dentistry, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Mohaned Hassan
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - John Pape
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Emmanuel T. Aladenika
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Peter Donkor
- Department of Surgery, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Fareed K.N. Arthur
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Solomon Obiri-Yeboah
- Department of Maxillofacial Sciences, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Daniel K. Sabbah
- Department of Child Oral Health and Orthodontics, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Pius Agbenorku
- Department of Surgery, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Debashree Ray
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Gyikua Plange-Rhule
- Department of Child Health, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Alexander Acheampong Oti
- Department of Maxillofacial Sciences, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Daniah Albokhari
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University
| | | | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Margaret Taub
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, and Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | - Azeez Butali
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
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18
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Ren P, Zhang J, Vijg J. Somatic mutations in aging and disease. GeroScience 2024:10.1007/s11357-024-01113-3. [PMID: 38488948 DOI: 10.1007/s11357-024-01113-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
Time always leaves its mark, and our genome is no exception. Mutations in the genome of somatic cells were first hypothesized to be the cause of aging in the 1950s, shortly after the molecular structure of DNA had been described. Somatic mutation theories of aging are based on the fact that mutations in DNA as the ultimate template for all cellular functions are irreversible. However, it took until the 1990s to develop the methods to test if DNA mutations accumulate with age in different organs and tissues and estimate the severity of the problem. By now, numerous studies have documented the accumulation of somatic mutations with age in normal cells and tissues of mice, humans, and other animals, showing clock-like mutational signatures that provide information on the underlying causes of the mutations. In this review, we will first briefly discuss the recent advances in next-generation sequencing that now allow quantitative analysis of somatic mutations. Second, we will provide evidence that the mutation rate differs between cell types, with a focus on differences between germline and somatic mutation rate. Third, we will discuss somatic mutational signatures as measures of aging, environmental exposure, and activities of DNA repair processes. Fourth, we will explain the concept of clonally amplified somatic mutations, with a focus on clonal hematopoiesis. Fifth, we will briefly discuss somatic mutations in the transcriptome and in our other genome, i.e., the genome of mitochondria. We will end with a brief discussion of a possible causal contribution of somatic mutations to the aging process.
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Affiliation(s)
- Peijun Ren
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jie Zhang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jan Vijg
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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19
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Rosendahl Huber A, Pleguezuelos-Manzano C, Puschhof J, Ubels J, Boot C, Saftien A, Verheul M, Trabut LT, Groenen N, van Roosmalen M, Ouyang KS, Wood H, Quirke P, Meijer G, Cuppen E, Clevers H, van Boxtel R. Improved detection of colibactin-induced mutations by genotoxic E. coli in organoids and colorectal cancer. Cancer Cell 2024; 42:487-496.e6. [PMID: 38471458 DOI: 10.1016/j.ccell.2024.02.009] [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: 09/21/2022] [Revised: 01/26/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024]
Abstract
Co-culture of intestinal organoids with a colibactin-producing pks+E. coli strain (EcC) revealed mutational signatures also found in colorectal cancer (CRC). E. coli Nissle 1917 (EcN) remains a commonly used probiotic, despite harboring the pks operon and inducing double strand DNA breaks. We determine the mutagenicity of EcN and three CRC-derived pks+E. coli strains with an analytical framework based on sequence characteristic of colibactin-induced mutations. All strains, including EcN, display varying levels of mutagenic activity. Furthermore, a machine learning approach attributing individual mutations to colibactin reveals that patients with colibactin-induced mutations are diagnosed at a younger age and that colibactin can induce a specific APC mutation. These approaches allow the sensitive detection of colibactin-induced mutations in ∼12% of CRC genomes and even in whole exome sequencing data, representing a crucial step toward pinpointing the mutagenic activity of distinct pks+E. coli strains.
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Affiliation(s)
- Axel Rosendahl Huber
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Cayetano Pleguezuelos-Manzano
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Jens Puschhof
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands; Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Joske Ubels
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Charelle Boot
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Aurelia Saftien
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands; Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Mark Verheul
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Laurianne T Trabut
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Niels Groenen
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Markus van Roosmalen
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Kyanna S Ouyang
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Henry Wood
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Phil Quirke
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Gerrit Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Edwin Cuppen
- University Medical Center Utrecht, Utrecht, the Netherlands; Hartwig Medical Foundation, Amsterdam, the Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands; Roche Pharmaceutical Research and Early Development, 4058 Basel, Switzerland.
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands.
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20
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Wang Y, Chen Y, Gao J, Xie H, Guo Y, Yang J, Liu J, Chen Z, Li Q, Li M, Ren J, Wen L, Tang F. Mapping crossover events of mouse meiotic recombination by restriction fragment ligation-based Refresh-seq. Cell Discov 2024; 10:26. [PMID: 38443370 PMCID: PMC10915157 DOI: 10.1038/s41421-023-00638-9] [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: 06/02/2023] [Accepted: 12/11/2023] [Indexed: 03/07/2024] Open
Abstract
Single-cell whole-genome sequencing methods have undergone great improvements over the past decade. However, allele dropout, which means the inability to detect both alleles simultaneously in an individual diploid cell, largely restricts the application of these methods particularly for medical applications. Here, we develop a new single-cell whole-genome sequencing method based on third-generation sequencing (TGS) platform named Refresh-seq (restriction fragment ligation-based genome amplification and TGS). It is based on restriction endonuclease cutting and ligation strategy in which two alleles in an individual cell can be cut into equal fragments and tend to be amplified simultaneously. As a new single-cell long-read genome sequencing method, Refresh-seq features much lower allele dropout rate compared with SMOOTH-seq. Furthermore, we apply Refresh-seq to 688 sperm cells and 272 female haploid cells (secondary polar bodies and parthenogenetic oocytes) from F1 hybrid mice. We acquire high-resolution genetic map of mouse meiosis recombination at low sequencing depth and reveal the sexual dimorphism in meiotic crossovers. We also phase the structure variations (deletions and insertions) in sperm cells and female haploid cells with high precision. Refresh-seq shows great performance in screening aneuploid sperm cells and oocytes due to the low allele dropout rate and has great potential for medical applications such as preimplantation genetic diagnosis.
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Affiliation(s)
- Yan Wang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Yijun Chen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Junpeng Gao
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Emergency Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Haoling Xie
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Yuqing Guo
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Jingwei Yang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Jun'e Liu
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Zonggui Chen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Changping Laboratory, Beijing, China
| | - Qingqing Li
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Mengyao Li
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Jie Ren
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Lu Wen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Fuchou Tang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China.
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- Changping Laboratory, Beijing, China.
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21
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Lim J, Park C, Kim M, Kim H, Kim J, Lee DS. Advances in single-cell omics and multiomics for high-resolution molecular profiling. Exp Mol Med 2024; 56:515-526. [PMID: 38443594 PMCID: PMC10984936 DOI: 10.1038/s12276-024-01186-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/05/2023] [Accepted: 12/13/2023] [Indexed: 03/07/2024] Open
Abstract
Single-cell omics technologies have revolutionized molecular profiling by providing high-resolution insights into cellular heterogeneity and complexity. Traditional bulk omics approaches average signals from heterogeneous cell populations, thereby obscuring important cellular nuances. Single-cell omics studies enable the analysis of individual cells and reveal diverse cell types, dynamic cellular states, and rare cell populations. These techniques offer unprecedented resolution and sensitivity, enabling researchers to unravel the molecular landscape of individual cells. Furthermore, the integration of multimodal omics data within a single cell provides a comprehensive and holistic view of cellular processes. By combining multiple omics dimensions, multimodal omics approaches can facilitate the elucidation of complex cellular interactions, regulatory networks, and molecular mechanisms. This integrative approach enhances our understanding of cellular systems, from development to disease. This review provides an overview of the recent advances in single-cell and multimodal omics for high-resolution molecular profiling. We discuss the principles and methodologies for representatives of each omics method, highlighting the strengths and limitations of the different techniques. In addition, we present case studies demonstrating the applications of single-cell and multimodal omics in various fields, including developmental biology, neurobiology, cancer research, immunology, and precision medicine.
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Affiliation(s)
- Jongsu Lim
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Chanho Park
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Minjae Kim
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Hyukhee Kim
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Junil Kim
- School of Systems Biomedical Science, Soongsil University, Seoul, 06978, Republic of Korea
| | - Dong-Sung Lee
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea.
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22
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Li R, Su P, Shi Y, Shi H, Ding S, Su X, Chen P, Wu D. Gene doping detection in the era of genomics. Drug Test Anal 2024. [PMID: 38403949 DOI: 10.1002/dta.3664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/27/2024]
Abstract
Recent progress in gene editing has enabled development of gene therapies for many genetic diseases, but also made gene doping an emerging risk in sports and competitions. By delivery of exogenous transgenes into human body, gene doping not only challenges competition fairness but also places health risk on athletes. World Anti-Doping Agency (WADA) has clearly inhibited the use of gene and cell doping in sports, and many techniques have been developed for gene doping detection. In this review, we will summarize the main tools for gene doping detection at present, highlight the main challenges for current tools, and elaborate future utilizations of high-throughput sequencing for unbiased, sensitive, economic and large-scale gene doping detections. Quantitative real-time PCR assays are the widely used detection methods at present, which are useful for detection of known targets but are vulnerable to codon optimization at exon-exon junction sites of the transgenes. High-throughput sequencing has become a powerful tool for various applications in life and health research, and the era of genomics has made it possible for sensitive and large-scale gene doping detections. Non-biased genomic profiling could efficiently detect new doping targets, and low-input genomics amplification and long-read third-generation sequencing also have application potentials for more efficient and straightforward gene doping detection. By closely monitoring scientific advancements in gene editing and sport genetics, high-throughput sequencing could play a more and more important role in gene detection and hopefully contribute to doping-free sports in the future.
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Affiliation(s)
- Ruihong Li
- eHealth Program of Shanghai Anti-doping Laboratory, Shanghai University of Sport, Shanghai, China
- Shanghai Center of Agri-Products Quality and Safety, Shanghai, China
| | - Peipei Su
- Innovative Program of Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Shi
- eHealth Program of Shanghai Anti-doping Laboratory, Shanghai University of Sport, Shanghai, China
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, Shanghai, China
| | - Hui Shi
- eHealth Program of Shanghai Anti-doping Laboratory, Shanghai University of Sport, Shanghai, China
- Department of Rheumatology and Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shengqian Ding
- eHealth Program of Shanghai Anti-doping Laboratory, Shanghai University of Sport, Shanghai, China
| | - Xianbin Su
- eHealth Program of Shanghai Anti-doping Laboratory, Shanghai University of Sport, Shanghai, China
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Peijie Chen
- School of Exercise and Health, Shanghai University of Sport, Shanghai, China
| | - Die Wu
- eHealth Program of Shanghai Anti-doping Laboratory, Shanghai University of Sport, Shanghai, China
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23
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Youk J, Kwon HW, Lim J, Kim E, Kim T, Kim R, Park S, Yi K, Nam CH, Jeon S, An Y, Choi J, Na H, Lee ES, Cho Y, Min DW, Kim H, Kang YR, Choi SH, Bae MJ, Lee CG, Kim JG, Kim YS, Yu T, Lee WC, Shin JY, Lee DS, Kim TY, Ku T, Kim SY, Lee JH, Koo BK, Lee H, Yi OV, Han EC, Chang JH, Kim KS, Son TG, Ju YS. Quantitative and qualitative mutational impact of ionizing radiation on normal cells. CELL GENOMICS 2024; 4:100499. [PMID: 38359788 PMCID: PMC10879144 DOI: 10.1016/j.xgen.2024.100499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 10/23/2023] [Accepted: 01/09/2024] [Indexed: 02/17/2024]
Abstract
The comprehensive genomic impact of ionizing radiation (IR), a carcinogen, on healthy somatic cells remains unclear. Using large-scale whole-genome sequencing (WGS) of clones expanded from irradiated murine and human single cells, we revealed that IR induces a characteristic spectrum of short insertions or deletions (indels) and structural variations (SVs), including balanced inversions, translocations, composite SVs (deletion-insertion, deletion-inversion, and deletion-translocation composites), and complex genomic rearrangements (CGRs), including chromoplexy, chromothripsis, and SV by breakage-fusion-bridge cycles. Our findings suggest that 1 Gy IR exposure causes an average of 2.33 mutational events per Gb genome, comprising 2.15 indels, 0.17 SVs, and 0.01 CGRs, despite a high level of inter-cellular stochasticity. The mutational burden was dependent on total irradiation dose, regardless of dose rate or cell type. The findings were further validated in IR-induced secondary cancers and single cells without clonalization. Overall, our study highlights a comprehensive and clear picture of IR effects on normal mammalian genomes.
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Affiliation(s)
- Jeonghwan Youk
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hyun Woo Kwon
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Department of Nuclear Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Joonoh Lim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Eunji Kim
- Department of Radiation Oncology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, 20, Boramae-ro 5 Gil, Dongjak-gu, Seoul 07061, Republic of Korea; Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Taewoo Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Ryul Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Seongyeol Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Kijong Yi
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Chang Hyun Nam
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sara Jeon
- Department of Biological Sciences & IMBG, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Yohan An
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Jinwook Choi
- Wellcome - MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW Cambridge, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, CB2 3EL Cambridge, UK
| | - Hyelin Na
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Eon-Seok Lee
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Youngwon Cho
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Dong-Wook Min
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - HyoJin Kim
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Yeong-Rok Kang
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Si Ho Choi
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Min Ji Bae
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Chang Geun Lee
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Joon-Goon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KI for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Young Seo Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KI for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Tosol Yu
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Radiation Oncology, Dongnam Institute of Radiological and Medical Science, Busan 46033, Republic of Korea
| | | | | | - Dong Soo Lee
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Tae-You Kim
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Cancer Research Institute, Seoul National University, Seoul, Republic of Korea; Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Taeyun Ku
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KI for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Su Yeon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Joo-Hyeon Lee
- Wellcome - MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW Cambridge, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, CB2 3EL Cambridge, UK
| | - Bon-Kyoung Koo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Hyunsook Lee
- Department of Biological Sciences & IMBG, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - On Vox Yi
- Department of Breast Surgery, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Eon Chul Han
- Department of Surgery, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Ji Hyun Chang
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Radiation Oncology, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Kyung Su Kim
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Radiation Oncology, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Tae Gen Son
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea.
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA.
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24
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Hosokawa M, Nishikawa Y. Tools for microbial single-cell genomics for obtaining uncultured microbial genomes. Biophys Rev 2024; 16:69-77. [PMID: 38495448 PMCID: PMC10937852 DOI: 10.1007/s12551-023-01124-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 08/23/2023] [Indexed: 03/19/2024] Open
Abstract
The advent of next-generation sequencing technologies has facilitated the acquisition of large amounts of DNA sequence data at a relatively low cost, leading to numerous breakthroughs in decoding microbial genomes. Among the various genome sequencing activities, metagenomic analysis, which entails the direct analysis of uncultured microbial DNA, has had a profound impact on microbiome research and has emerged as an indispensable technology in this field. Despite its valuable contributions, metagenomic analysis is a "bulk analysis" technique that analyzes samples containing a wide diversity of microbes, such as bacteria, yielding information that is averaged across the entire microbial population. In order to gain a deeper understanding of the heterogeneous nature of the microbial world, there is a growing need for single-cell analysis, similar to its use in human cell biology. With this paradigm shift in mind, comprehensive single-cell genomics technology has become a much-anticipated innovation that is now poised to revolutionize microbiome research. It has the potential to enable the discovery of differences at the strain level and to facilitate a more comprehensive examination of microbial ecosystems. In this review, we summarize the current state-of-the-art in microbial single-cell genomics, highlighting the potential impact of this technology on our understanding of the microbial world. The successful implementation of this technology is expected to have a profound impact in the field, leading to new discoveries and insights into the diversity and evolution of microbes.
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Affiliation(s)
- Masahito Hosokawa
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-Cho, Shinjuku-Ku, Tokyo, 162-8480 Japan
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-Ku, Tokyo, 169-8555 Japan
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-Cho, Shinjuku-Ku, Tokyo, 162-0041 Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, 3-4-1 Okubo, Shinjuku-Ku, Tokyo, 169-8555 Japan
- bitBiome, Inc., 513 Wasedatsurumaki-Cho, Shinjuku-Ku, Tokyo, 162-0041 Japan
| | - Yohei Nishikawa
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-Ku, Tokyo, 169-8555 Japan
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-Cho, Shinjuku-Ku, Tokyo, 162-0041 Japan
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25
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Bowers RM, Gonzalez-Pena V, Wardhani K, Goudeau D, Blow MJ, Udwary D, Klein D, Vill AC, Brito IL, Woyke T, Malmstrom R, Gawad C. scMicrobe PTA: Near Complete Genomes from Single Bacterial Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.30.577819. [PMID: 38352480 PMCID: PMC10862798 DOI: 10.1101/2024.01.30.577819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Microbial genomes produced by single-cell amplification are largely incomplete. Here, we show that primary template amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard amplification approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.
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Affiliation(s)
- Robert M Bowers
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Kartika Wardhani
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Danielle Goudeau
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew James Blow
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Daniel Udwary
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Klein
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rex Malmstrom
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Charles Gawad
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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26
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Cooper SE, Coelho MA, Strauss ME, Gontarczyk AM, Wu Q, Garnett MJ, Marioni JC, Bassett AR. scSNV-seq: high-throughput phenotyping of single nucleotide variants by coupled single-cell genotyping and transcriptomics. Genome Biol 2024; 25:20. [PMID: 38225637 PMCID: PMC10789043 DOI: 10.1186/s13059-024-03169-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/09/2024] [Indexed: 01/17/2024] Open
Abstract
CRISPR screens with single-cell transcriptomic readouts are a valuable tool to understand the effect of genetic perturbations including single nucleotide variants (SNVs) associated with diseases. Interpretation of these data is currently limited as genotypes cannot be accurately inferred from guide RNA identity alone. scSNV-seq overcomes this limitation by coupling single-cell genotyping and transcriptomics of the same cells enabling accurate and high-throughput screening of SNVs. Analysis of variants across the JAK1 gene with scSNV-seq demonstrates the importance of determining the precise genetic perturbation and accurately classifies clinically observed missense variants into three functional categories: benign, loss of function, and separation of function.
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Affiliation(s)
- Sarah E Cooper
- Cellular and Gene Editing Research, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Matthew A Coelho
- Translational Cancer Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Magdalena E Strauss
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Aleksander M Gontarczyk
- Cellular and Gene Editing Research, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Qianxin Wu
- Cellular and Gene Editing Research, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Mathew J Garnett
- Translational Cancer Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - John C Marioni
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Cellular Genetics, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- Present Address: Genentech, South San Francisco, CA, USA
| | - Andrew R Bassett
- Cellular and Gene Editing Research, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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27
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Nishikawa Y, Wagatsuma R, Tsukada Y, Chia-ling L, Chijiiwa R, Hosokawa M, Takeyama H. Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles. THE ISME JOURNAL 2024; 18:wrae124. [PMID: 38976038 PMCID: PMC11283719 DOI: 10.1093/ismejo/wrae124] [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: 12/28/2023] [Revised: 04/18/2024] [Accepted: 07/03/2024] [Indexed: 07/09/2024]
Abstract
Environmental viruses (primarily bacteriophages) are widely recognized as playing an important role in ecosystem homeostasis through the infection of host cells. However, the majority of environmental viruses are still unknown as their mosaic structure and frequent mutations in their sequences hinder genome construction in current metagenomics. To enable the large-scale acquisition of environmental viral genomes, we developed a new single-viral genome sequencing platform with microfluidic-generated gel beads. Amplification of individual DNA viral genomes in mass-produced gel beads allows high-throughput genome sequencing compared to conventional single-virus genomics. The sequencing analysis of river water samples yielded 1431 diverse viral single-amplified genomes, whereas viral metagenomics recovered 100 viral metagenome-assembled genomes at the comparable sequence depth. The 99.5% of viral single-amplified genomes were determined novel at the species level, most of which could not be recovered by a metagenomic assembly. The large-scale acquisition of diverse viral genomes identified protein clusters commonly detected in different viral strains, allowing the gene transfer to be tracked. Moreover, comparative genomics within the same viral species revealed that the profiles of various methyltransferase subtypes were diverse, suggesting an enhanced escape from host bacterial internal defense mechanisms. Our use of gel bead-based single-virus genomics will contribute to exploring the nature of viruses by accelerating the accumulation of draft genomes of environmental DNA viruses.
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Affiliation(s)
- Yohei Nishikawa
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST-Waseda University, 3-4-1 Okubo, Tokyo 169-0082, Japan
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda Tsurumaki-cho, Tokyo 162–0041, Japan
| | - Ryota Wagatsuma
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST-Waseda University, 3-4-1 Okubo, Tokyo 169-0082, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yuko Tsukada
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Lin Chia-ling
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Rieka Chijiiwa
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda Tsurumaki-cho, Tokyo 162–0041, Japan
| | - Masahito Hosokawa
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST-Waseda University, 3-4-1 Okubo, Tokyo 169-0082, Japan
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda Tsurumaki-cho, Tokyo 162–0041, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Haruko Takeyama
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST-Waseda University, 3-4-1 Okubo, Tokyo 169-0082, Japan
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda Tsurumaki-cho, Tokyo 162–0041, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
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28
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Bowers RM, Gonzalez-Pena V, Wardhani K, Goudeau D, Blow MJ, Udwary D, Klein D, Vill AC, Brito IL, Woyke T, Malmstrom RR, Gawad C. scMicrobe PTA: near complete genomes from single bacterial cells. ISME COMMUNICATIONS 2024; 4:ycae085. [PMID: 39021442 PMCID: PMC11253033 DOI: 10.1093/ismeco/ycae085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 06/05/2024] [Indexed: 07/20/2024]
Abstract
Microbial genomes produced by standard single-cell amplification methods are largely incomplete. Here, we show that primary template-directed amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard multiple displacement amplification-based approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.
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Affiliation(s)
- Robert M Bowers
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | | | - Kartika Wardhani
- Department of Pediatrics, Stanford University, Stanford, CA, United States
| | - Danielle Goudeau
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Matthew James Blow
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Daniel Udwary
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - David Klein
- Department of Pediatrics, Stanford University, Stanford, CA, United States
| | - Albert C Vill
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Ilana L Brito
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Rex R Malmstrom
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Charles Gawad
- Department of Pediatrics, Stanford University, Stanford, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
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29
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Ospino MC, Engel K, Ruiz-Navas S, Binns WJ, Doxey AC, Neufeld JD. Evaluation of multiple displacement amplification for metagenomic analysis of low biomass samples. ISME COMMUNICATIONS 2024; 4:ycae024. [PMID: 38500705 PMCID: PMC10945365 DOI: 10.1093/ismeco/ycae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 03/20/2024]
Abstract
Combining multiple displacement amplification (MDA) with metagenomics enables the analysis of samples with extremely low DNA concentrations, making them suitable for high-throughput sequencing. Although amplification bias and nonspecific amplification have been reported from MDA-amplified samples, the impact of MDA on metagenomic datasets is not well understood. We compared three MDA methods (i.e. bulk MDA, emulsion MDA, and primase MDA) for metagenomic analysis of two DNA template concentrations (approx. 1 and 100 pg) derived from a microbial community standard "mock community" and two low biomass environmental samples (i.e. borehole fluid and groundwater). We assessed the impact of MDA on metagenome-based community composition, assembly quality, functional profiles, and binning. We found amplification bias against high GC content genomes but relatively low nonspecific amplification such as chimeras, artifacts, or contamination for all MDA methods. We observed MDA-associated representational bias for microbial community profiles, especially for low-input DNA and with the primase MDA method. Nevertheless, similar taxa were represented in MDA-amplified libraries to those of unamplified samples. The MDA libraries were highly fragmented, but similar functional profiles to the unamplified libraries were obtained for bulk MDA and emulsion MDA at higher DNA input and across these MDA libraries for the groundwater sample. Medium to low-quality bins were possible for the high input bulk MDA metagenomes for the most simple microbial communities, borehole fluid, and mock community. Although MDA-based amplification should be avoided, it can still reveal meaningful taxonomic and functional information from samples with extremely low DNA concentration where direct metagenomics is otherwise impossible.
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Affiliation(s)
| | - Katja Engel
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Santiago Ruiz-Navas
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - W Jeffrey Binns
- Safety and Technical Research, Nuclear Waste Management Organization of Canada, Toronto, Ontario M4T 2S3, Canada
| | - Andrew C Doxey
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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30
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Russell AJC, Weir JA, Nadaf NM, Shabet M, Kumar V, Kambhampati S, Raichur R, Marrero GJ, Liu S, Balderrama KS, Vanderburg CR, Shanmugam V, Tian L, Iorgulescu JB, Yoon CH, Wu CJ, Macosko EZ, Chen F. Slide-tags enables single-nucleus barcoding for multimodal spatial genomics. Nature 2024; 625:101-109. [PMID: 38093010 PMCID: PMC10764288 DOI: 10.1038/s41586-023-06837-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 11/06/2023] [Indexed: 12/17/2023]
Abstract
Recent technological innovations have enabled the high-throughput quantification of gene expression and epigenetic regulation within individual cells, transforming our understanding of how complex tissues are constructed1-6. However, missing from these measurements is the ability to routinely and easily spatially localize these profiled cells. We developed a strategy, Slide-tags, in which single nuclei within an intact tissue section are tagged with spatial barcode oligonucleotides derived from DNA-barcoded beads with known positions. These tagged nuclei can then be used as an input into a wide variety of single-nucleus profiling assays. Application of Slide-tags to the mouse hippocampus positioned nuclei at less than 10 μm spatial resolution and delivered whole-transcriptome data that are indistinguishable in quality from ordinary single-nucleus RNA-sequencing data. To demonstrate that Slide-tags can be applied to a wide variety of human tissues, we performed the assay on brain, tonsil and melanoma. We revealed cell-type-specific spatially varying gene expression across cortical layers and spatially contextualized receptor-ligand interactions driving B cell maturation in lymphoid tissue. A major benefit of Slide-tags is that it is easily adaptable to almost any single-cell measurement technology. As a proof of principle, we performed multiomic measurements of open chromatin, RNA and T cell receptor (TCR) sequences in the same cells from metastatic melanoma, identifying transcription factor motifs driving cancer cell state transitions in spatially distinct microenvironments. Slide-tags offers a universal platform for importing the compendium of established single-cell measurements into the spatial genomics repertoire.
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Affiliation(s)
- Andrew J C Russell
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Jackson A Weir
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Cambridge, MA, USA
| | - Naeem M Nadaf
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Vipin Kumar
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sandeep Kambhampati
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard University, Boston, MA, USA
| | - Ruth Raichur
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Sophia Liu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Biophysics Program, Harvard University, Boston, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - Vignesh Shanmugam
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Luyi Tian
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Guangzhou Laboratory, Guangdong, China
| | - J Bryan Iorgulescu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Stem Cell Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Boston, MA, USA
- Molecular Diagnostics Laboratory, Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charles H Yoon
- Department of Surgical Oncology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Catherine J Wu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Stem Cell Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Evan Z Macosko
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA.
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
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31
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Dungan AM, Tandon K, Jameson V, Gotze CR, Blackall LL, van Oppen MJH. A targeted approach to enrich host-associated bacteria for metagenomic sequencing. FEMS MICROBES 2023; 5:xtad021. [PMID: 38264162 PMCID: PMC10804224 DOI: 10.1093/femsmc/xtad021] [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: 08/29/2023] [Revised: 11/02/2023] [Accepted: 11/27/2023] [Indexed: 01/25/2024] Open
Abstract
Multicellular eukaryotic organisms are hosts to communities of bacteria that reside on or inside their tissues. Often the eukaryotic members of the system contribute to high proportions of metagenomic sequencing reads, making it challenging to achieve sufficient sequencing depth to evaluate bacterial ecology. Stony corals are one such complex community; however, separation of bacterial from eukaryotic (primarily coral and algal symbiont) cells has so far not been successful. Using a combination of hybridization chain reaction fluorescence in situ hybridization and fluorescence activated cell sorting (HCR-FISH + FACS), we sorted two populations of bacteria from five genotypes of the coral Acropora loripes, targeting (i) Endozoicomonas spp, and (ii) all other bacteria. NovaSeq sequencing resulted in 67-91 M reads per sample, 55%-90% of which were identified as bacterial. Most reads were taxonomically assigned to the key coral-associated family, Endozoicomonadaceae, with Vibrionaceae also abundant. Endozoicomonadaceae were 5x more abundant in the 'Endozoicomonas' population, highlighting the success of the dual-labelling approach. This method effectively enriched coral samples for bacteria with <1% contamination from host and algal symbionts. The application of this method will allow researchers to decipher the functional potential of coral-associated bacteria. This method can also be adapted to accommodate other host-associated communities.
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Affiliation(s)
- Ashley M Dungan
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kshitij Tandon
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Vanta Jameson
- Melbourne Cytometry Platform, Department of Microbiology and Immunology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Cecilie Ravn Gotze
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
- Reef Recovery, Restoration and Adaptation Program, Australian Institute of Marine Science, Townsville, QLD 4810, Australia
| | - Linda L Blackall
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Madeleine J H van Oppen
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
- Reef Recovery, Restoration and Adaptation Program, Australian Institute of Marine Science, Townsville, QLD 4810, Australia
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32
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Kalef-Ezra E, Turan ZG, Perez-Rodriguez D, Bomann I, Behera S, Morley C, Scholz SW, Jaunmuktane Z, Demeulemeester J, Sedlazeck FJ, Proukakis C. Single-cell somatic copy number variants in brain using different amplification methods and reference genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.07.552289. [PMID: 37609320 PMCID: PMC10441336 DOI: 10.1101/2023.08.07.552289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The presence of somatic mutations, including copy number variants (CNVs), in the brain is well recognized. Comprehensive study requires single-cell whole genome amplification, with several methods available, prior to sequencing. We compared PicoPLEX with two recent adaptations of multiple displacement amplification (MDA): primary template-directed amplification (PTA) and droplet MDA, across 93 human brain cortical nuclei. We demonstrated different properties for each, with PTA providing the broadest amplification, PicoPLEX the most even, and distinct chimeric profiles. Furthermore, we performed CNV calling on two brains with multiple system atrophy and one control brain using different reference genomes. We found that 38% of brain cells have at least one Mb-scale CNV, with some supported by bulk sequencing or single-cells from other brain regions. Our study highlights the importance of selecting whole genome amplification method and reference genome for CNV calling, while supporting the existence of somatic CNVs in healthy and diseased human brain.
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Zhang X, Celic I, Mitchell H, Stuckert S, Vedula L, Han JS. Comprehensive profiling of L1 retrotransposons in mouse. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566638. [PMID: 38014156 PMCID: PMC10680791 DOI: 10.1101/2023.11.13.566638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
L1 elements are retrotransposons currently active in mammals. Although L1s are typically silenced in most normal tissues, elevated L1 expression is associated with a variety of conditions, including cancer, aging, infertility, and neurological disease. These associations have raised interest in the mapping of human endogenous de novo L1 insertions, and a variety of methods have been developed for this purpose. Adapting these methods to mouse genomes would allow us to monitor endogenous in vivo L1 activity in controlled, experimental conditions using mouse disease models. Here we use a modified version of transposon insertion profiling, called nanoTIPseq, to selectively enrich young mouse L1s. By linking this amplification step with nanopore sequencing, we identified >95% annotated L1s from C57BL/6 genomic DNA using only 200,000 sequencing reads. In the process, we discovered 82 unannotated L1 insertions from a single C57BL/6 genome. Most of these unannotated L1s were near repetitive sequence and were not found with short-read TIPseq. We used nanoTIPseq on individual mouse breast cancer cells and were able to identify the annotated and unannotated L1s, as well as new insertions specific to individual cells, providing proof of principle for using nanoTIPseq to interrogate retrotransposition activity at the single cell level in vivo .
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34
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Derks LLM, van Boxtel R. Stem cell mutations, associated cancer risk, and consequences for regenerative medicine. Cell Stem Cell 2023; 30:1421-1433. [PMID: 37832550 PMCID: PMC10624213 DOI: 10.1016/j.stem.2023.09.008] [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: 07/17/2023] [Revised: 09/05/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
Mutation accumulation in stem cells has been associated with cancer risk. However, the presence of numerous mutant clones in healthy tissues has raised the question of what limits cancer initiation. Here, we review recent developments in characterizing mutation accumulation in healthy tissues and compare mutation rates in stem cells during development and adult life with corresponding cancer risk. A certain level of mutagenesis within the stem cell pool might be beneficial to limit the size of malignant clones through competition. This knowledge impacts our understanding of carcinogenesis with potential consequences for the use of stem cells in regenerative medicine.
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Affiliation(s)
- Lucca L M Derks
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands.
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35
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Chung C, Yang X, Hevner RF, Kennedy K, Vong KI, Liu Y, Patel A, Nedunuri R, Barton ST, Barrows C, Stanley V, Mittal S, Breuss MW, Schlachetzki JCM, Gleeson JG. Cell-type-resolved somatic mosaicism reveals clonal dynamics of the human forebrain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563814. [PMID: 37961480 PMCID: PMC10634852 DOI: 10.1101/2023.10.24.563814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Debate remains around anatomic origins of specific brain cell subtypes and lineage relationships within the human forebrain. Thus, direct observation in the mature human brain is critical for a complete understanding of the structural organization and cellular origins. Here, we utilize brain mosaic variation within specific cell types as distinct indicators for clonal dynamics, denoted as cell-type-specific Mosaic Variant Barcode Analysis. From four hemispheres from two different human neurotypical donors, we identified 287 and 780 mosaic variants (MVs), respectively that were used to deconvolve clonal dynamics. Clonal spread and allelic fractions within the brain reveal that local hippocampal excitatory neurons are more lineage-restricted compared with resident neocortical excitatory neurons or resident basal ganglia GABAergic inhibitory neurons. Furthermore, simultaneous genome-transcriptome analysis at both a cell-type-specific and single-cell level suggests a dorsal neocortical origin for a subgroup of DLX1+ inhibitory neurons that disperse radially from an origin shared with excitatory neurons. Finally, the distribution of MVs across 17 locations within one parietal lobe reveals restrictions of clonal spread in the anterior-posterior axis precedes that of the dorsal-ventral axis for both excitatory and inhibitory neurons. Thus cell-type resolved somatic mosaicism can uncover lineage relationships governing the development of the human forebrain.
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Affiliation(s)
- Changuk Chung
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, USA
| | - Robert F. Hevner
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92037, USA
- Department of Pathology, UC San Diego School of Medicine, University of California, San Diego, La Jolla, CA, 92037, USA
| | | | - Keng Ioi Vong
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Yang Liu
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Arzoo Patel
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Rahul Nedunuri
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Scott T. Barton
- Division of Medical Education, School of Medicine, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Chelsea Barrows
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Valentina Stanley
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Swapnil Mittal
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Martin W. Breuss
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado Aurora, CO, 80045, USA
| | | | - Joseph G. Gleeson
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, 92123, USA
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36
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Jeong D, Lee AC, Shin K, Kim J, Ham MH, Lee C, Lee S, Choi A, Ryu T, Kim O, Jung Y, Kwon S, Lee DS. Hema-seq reveals genomic aberrations in a rare simultaneous occurrence of hematological malignancies. CELL REPORTS METHODS 2023; 3:100617. [PMID: 37852254 PMCID: PMC10626221 DOI: 10.1016/j.crmeth.2023.100617] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/24/2023] [Accepted: 09/21/2023] [Indexed: 10/20/2023]
Abstract
Co-occurrence of multiple myeloma and acute myelogenous leukemia is rare, with both malignancies often tracing back to multipotent hematopoietic stem cells. Cytogenetic techniques are the established baseline for diagnosis and characterization of complex hematological malignancies. In this study, we develop a workflow called Hema-seq to delineate clonal changes across various hematopoietic lineages through the integration of whole-genome sequencing, copy-number variations, cell morphology, and cytogenetic aberrations. In Hema-seq, cells are selected from Wright-stained slides and fluorescent probe-stained slides for sequencing. This technique therefore enables direct linking of whole-genome sequences to cytogenetic profiles. Through this method, we mapped sequential clonal alterations within the hematopoietic lineage, identifying critical shifts leading to myeloma and acute myeloid leukemia (AML) cell formations. By synthesizing data from each cell lineage, we provided insights into the hematopoietic tree's clonal evolution. Overall, this study highlights Hema-seq's capability in deciphering genomic heterogeneity in complex hematological malignancies, which can enable better diagnosis and treatment strategies.
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Affiliation(s)
- Dajeong Jeong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Amos C Lee
- Bio-MAX Institute, Seoul National University, Seoul 08826, Republic of Korea; Meteor Biotech Co., Ltd., Seoul 08826, Republic of Korea
| | - Kyoungseob Shin
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Jinhyun Kim
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Myoung Hee Ham
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Changhee Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Sumin Lee
- Meteor Biotech Co., Ltd., Seoul 08826, Republic of Korea; Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Ahyoun Choi
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Taehoon Ryu
- ATG Lifetech, Inc., Seoul 08507, Republic of Korea
| | - Okju Kim
- ATG Lifetech, Inc., Seoul 08507, Republic of Korea
| | - Yushin Jung
- ATG Lifetech, Inc., Seoul 08507, Republic of Korea
| | - Sunghoon Kwon
- Bio-MAX Institute, Seoul National University, Seoul 08826, Republic of Korea; Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea; Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea; Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul 08826, Republic of Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.
| | - Dong Soon Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.
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37
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Zhou Y, Li T, Choppavarapu L, Jin VX. Integration of scHi-C and scRNA-seq data defines distinct 3D-regulated and biological-context dependent cell subpopulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560193. [PMID: 37873257 PMCID: PMC10592853 DOI: 10.1101/2023.09.29.560193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
An integration of 3D chromatin structure and gene expression at single-cell resolution has yet been demonstrated. Here, we develop a computational method, a multiomic data integration (MUDI) algorithm, which integrates scHi-C and scRNA-seq data to precisely define the 3D-regulated and biological-context dependent cell subpopulations or topologically integrated subpopulations (TISPs). We demonstrate its algorithmic utility on the publicly available and newly generated scHi-C and scRNA-seq data. We then test and apply MUDI in a breast cancer cell model system to demonstrate its biological-context dependent utility. We found the newly defined topologically conserved associating domain (CAD) is the characteristic single-cell 3D chromatin structure and better characterizes chromatin domains in single-cell resolution. We further identify 20 TISPs uniquely characterizing 3D-regulated breast cancer cellular states. We reveal two of TISPs are remarkably resemble to high cycling breast cancer persister cells and chromatin modifying enzymes might be functional regulators to drive the alteration of the 3D chromatin structures. Our comprehensive integration of scHi-C and scRNA-seq data in cancer cells at single-cell resolution provides mechanistic insights into 3D-regulated heterogeneity of developing drug-tolerant cancer cells.
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38
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Yi D, Nam JW, Jeong H. Toward the functional interpretation of somatic structural variations: bulk- and single-cell approaches. Brief Bioinform 2023; 24:bbad297. [PMID: 37587831 PMCID: PMC10516374 DOI: 10.1093/bib/bbad297] [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: 05/10/2023] [Revised: 07/05/2023] [Accepted: 07/23/2023] [Indexed: 08/18/2023] Open
Abstract
Structural variants (SVs) are genomic rearrangements that can take many different forms such as copy number alterations, inversions and translocations. During cell development and aging, somatic SVs accumulate in the genome with potentially neutral, deleterious or pathological effects. Generation of somatic SVs is a key mutational process in cancer development and progression. Despite their importance, the detection of somatic SVs is challenging, making them less studied than somatic single-nucleotide variants. In this review, we summarize recent advances in whole-genome sequencing (WGS)-based approaches for detecting somatic SVs at the tissue and single-cell levels and discuss their advantages and limitations. First, we describe the state-of-the-art computational algorithms for somatic SV calling using bulk WGS data and compare the performance of somatic SV detectors in the presence or absence of a matched-normal control. We then discuss the unique features of cutting-edge single-cell-based techniques for analyzing somatic SVs. The advantages and disadvantages of bulk and single-cell approaches are highlighted, along with a discussion of their sensitivity to copy-neutral SVs, usefulness for functional inferences and experimental and computational costs. Finally, computational approaches for linking somatic SVs to their functional readouts, such as those obtained from single-cell transcriptome and epigenome analyses, are illustrated, with a discussion of the promise of these approaches in health and diseases.
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Affiliation(s)
- Dohun Yi
- Department of Life Science, College of Natural Sciences, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul 04763, Republic of Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul 04763, Republic of Korea
- Bio-BigData Center, Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul 04763, Republic of Korea
- Hanyang Institute of Advanced BioConvergence, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Hyobin Jeong
- Department of Life Science, College of Natural Sciences, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul 04763, Republic of Korea
- Bio-BigData Center, Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul 04763, Republic of Korea
- Hanyang Institute of Advanced BioConvergence, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul 04763, Republic of Korea
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39
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Middelkamp S, Manders F, Peci F, van Roosmalen MJ, González DM, Bertrums EJ, van der Werf I, Derks LL, Groenen NM, Verheul M, Trabut L, Pleguezuelos-Manzano C, Brandsma AM, Antoniou E, Reinhardt D, Bierings M, Belderbos ME, van Boxtel R. Comprehensive single-cell genome analysis at nucleotide resolution using the PTA Analysis Toolbox. CELL GENOMICS 2023; 3:100389. [PMID: 37719152 PMCID: PMC10504672 DOI: 10.1016/j.xgen.2023.100389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/30/2023] [Accepted: 08/02/2023] [Indexed: 09/19/2023]
Abstract
Detection of somatic mutations in single cells has been severely hampered by technical limitations of whole-genome amplification. Novel technologies including primary template-directed amplification (PTA) significantly improved the accuracy of single-cell whole-genome sequencing (WGS) but still generate hundreds of artifacts per amplification reaction. We developed a comprehensive bioinformatic workflow, called the PTA Analysis Toolbox (PTATO), to accurately detect single base substitutions, insertions-deletions (indels), and structural variants in PTA-based WGS data. PTATO includes a machine learning approach and filtering based on recurrence to distinguish PTA artifacts from true mutations with high sensitivity (up to 90%), outperforming existing bioinformatic approaches. Using PTATO, we demonstrate that hematopoietic stem cells of patients with Fanconi anemia, which cannot be analyzed using regular WGS, have normal somatic single base substitution burdens but increased numbers of deletions. Our results show that PTATO enables studying somatic mutagenesis in the genomes of single cells with unprecedented sensitivity and accuracy.
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Affiliation(s)
- Sjors Middelkamp
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Freek Manders
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Flavia Peci
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Markus J. van Roosmalen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Diego Montiel González
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Eline J.M. Bertrums
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
- Department of Pediatric Oncology, Erasmus Medical Center – Sophia Children’s Hospital, Rotterdam, the Netherlands
| | - Inge van der Werf
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Lucca L.M. Derks
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Niels M. Groenen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Mark Verheul
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Laurianne Trabut
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Cayetano Pleguezuelos-Manzano
- Oncode Institute, Utrecht, the Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, the Netherlands
| | - Arianne M. Brandsma
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Evangelia Antoniou
- Department of Pediatric Hematology and Oncology, University Hospital Essen, Essen, Germany
| | - Dirk Reinhardt
- Department of Pediatric Hematology and Oncology, University Hospital Essen, Essen, Germany
| | - Marc Bierings
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
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40
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Kim J, Kim S, Yeom H, Song SW, Shin K, Bae S, Ryu HS, Kim JY, Choi A, Lee S, Ryu T, Choi Y, Kim H, Kim O, Jung Y, Kim N, Han W, Lee HB, Lee AC, Kwon S. Barcoded multiple displacement amplification for high coverage sequencing in spatial genomics. Nat Commun 2023; 14:5261. [PMID: 37644058 PMCID: PMC10465490 DOI: 10.1038/s41467-023-41019-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
Determining mutational landscapes in a spatial context is essential for understanding genetically heterogeneous cell microniches. Current approaches, such as Multiple Displacement Amplification (MDA), offer high genome coverage but limited multiplexing, which hinders large-scale spatial genomic studies. Here, we introduce barcoded MDA (bMDA), a technique that achieves high-coverage genomic analysis of low-input DNA while enhancing the multiplexing capabilities. By incorporating cell barcodes during MDA, bMDA streamlines library preparation in one pot, thereby overcoming a key bottleneck in spatial genomics. We apply bMDA to the integrative spatial analysis of triple-negative breast cancer tissues by examining copy number alterations, single nucleotide variations, structural variations, and kataegis signatures for each spatial microniche. This enables the assessment of subclonal evolutionary relationships within a spatial context. Therefore, bMDA has emerged as a scalable technology with the potential to advance the field of spatial genomics significantly.
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Affiliation(s)
- Jinhyun Kim
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sungsik Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Huiran Yeom
- Division of Data Science, College of Information and Communication Technology, The University of Suwon, Hwaseong, 18323, Republic of Korea
| | - Seo Woo Song
- Basic Science and Engineering Initiative, Children's Heart Center, Stanford University, Stanford, CA, USA
| | - Kyoungseob Shin
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sangwook Bae
- Renal Division and Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Han Suk Ryu
- Cancer Research Institute, Seoul National University, Seoul, 03080, Republic of Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Ji Young Kim
- Biomedical Research Institute, Seoul National University Hospital, Seoul, 03080, Republic of Korea
| | - Ahyoun Choi
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sumin Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Meteor Biotech, Co. Ltd., Seoul, 08826, Republic of Korea
| | - Taehoon Ryu
- ATG Lifetech Inc., Seoul, 08507, Republic of Korea
| | - Yeongjae Choi
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Hamin Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Okju Kim
- ATG Lifetech Inc., Seoul, 08507, Republic of Korea
| | - Yushin Jung
- ATG Lifetech Inc., Seoul, 08507, Republic of Korea
| | - Namphil Kim
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Wonshik Han
- Cancer Research Institute, Seoul National University, Seoul, 03080, Republic of Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, 03080, Republic of Korea
- Department of Surgery, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Han-Byoel Lee
- Cancer Research Institute, Seoul National University, Seoul, 03080, Republic of Korea.
- Biomedical Research Institute, Seoul National University Hospital, Seoul, 03080, Republic of Korea.
- Department of Surgery, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
| | - Amos C Lee
- Bio-MAX Institute, Seoul National University, Seoul, 08826, Republic of Korea.
- Meteor Biotech, Co. Ltd., Seoul, 08826, Republic of Korea.
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Biomedical Research Institute, Seoul National University Hospital, Seoul, 03080, Republic of Korea.
- Bio-MAX Institute, Seoul National University, Seoul, 08826, Republic of Korea.
- Inter-University Semiconductor Research Center, Seoul National University, Seoul, 08826, Republic of Korea.
- Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul, 08826, Republic of Korea.
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41
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Hård J, Mold JE, Eisfeldt J, Tellgren-Roth C, Häggqvist S, Bunikis I, Contreras-Lopez O, Chin CS, Nordlund J, Rubin CJ, Feuk L, Michaëlsson J, Ameur A. Long-read whole-genome analysis of human single cells. Nat Commun 2023; 14:5164. [PMID: 37620373 PMCID: PMC10449900 DOI: 10.1038/s41467-023-40898-3] [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: 02/06/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023] Open
Abstract
Long-read sequencing has dramatically increased our understanding of human genome variation. Here, we demonstrate that long-read technology can give new insights into the genomic architecture of individual cells. Clonally expanded CD8+ T-cells from a human donor were subjected to droplet-based multiple displacement amplification (dMDA) to generate long molecules with reduced bias. PacBio sequencing generated up to 40% genome coverage per single-cell, enabling detection of single nucleotide variants (SNVs), structural variants (SVs), and tandem repeats, also in regions inaccessible by short reads. 28 somatic SNVs were detected, including one case of mitochondrial heteroplasmy. 5473 high-confidence SVs/cell were discovered, a sixteen-fold increase compared to Illumina-based results from clonally related cells. Single-cell de novo assembly generated a genome size of up to 598 Mb and 1762 (12.8%) complete gene models. In summary, our work shows the promise of long-read sequencing toward characterization of the full spectrum of genetic variation in single cells.
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Affiliation(s)
- Joanna Hård
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- ETH AI Center, ETH Zurich, Zurich, Switzerland.
| | - Jeff E Mold
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Christian Tellgren-Roth
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Susana Häggqvist
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | | | - Jessica Nordlund
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Lars Feuk
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jakob Michaëlsson
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Adam Ameur
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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42
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Laufer VA, Glover TW, Wilson TE. Applications of advanced technologies for detecting genomic structural variation. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108475. [PMID: 37931775 PMCID: PMC10792551 DOI: 10.1016/j.mrrev.2023.108475] [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: 04/26/2023] [Revised: 09/07/2023] [Accepted: 11/02/2023] [Indexed: 11/08/2023]
Abstract
Chromosomal structural variation (SV) encompasses a heterogenous class of genetic variants that exerts strong influences on human health and disease. Despite their importance, many structural variants (SVs) have remained poorly characterized at even a basic level, a discrepancy predicated upon the technical limitations of prior genomic assays. However, recent advances in genomic technology can identify and localize SVs accurately, opening new questions regarding SV risk factors and their impacts in humans. Here, we first define and classify human SVs and their generative mechanisms, highlighting characteristics leveraged by various SV assays. We next examine the first-ever gapless assembly of the human genome and the technical process of assembling it, which required third-generation sequencing technologies to resolve structurally complex loci. The new portions of that "telomere-to-telomere" and subsequent pangenome assemblies highlight aspects of SV biology likely to develop in the near-term. We consider the strengths and limitations of the most promising new SV technologies and when they or longstanding approaches are best suited to meeting salient goals in the study of human SV in population-scale genomics research, clinical, and public health contexts. It is a watershed time in our understanding of human SV when new approaches are expected to fundamentally change genomic applications.
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Affiliation(s)
- Vincent A Laufer
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas W Glover
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas E Wilson
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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43
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Araten S, Mathieu R, Jetly A, Shin H, Hilal N, Zhang B, Morillo K, Nandan D, Sivankutty I, Chen MH, Choudhury S. High-quality nuclei isolation from postmortem human heart muscle tissues for single-cell studies. J Mol Cell Cardiol 2023; 179:7-17. [PMID: 36977444 PMCID: PMC10192033 DOI: 10.1016/j.yjmcc.2023.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/15/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023]
Abstract
Single-cell approaches have become an increasingly popular way of understanding the genetic factors behind disease. Isolation of DNA and RNA from human tissues is necessary to analyze multi-omic data sets, providing information on the single-cell genome, transcriptome, and epigenome. Here, we isolated high-quality single-nuclei from postmortem human heart tissues for DNA and RNA analysis. Postmortem human tissues were obtained from 106 individuals, 33 with a history of myocardial disease, diabetes, or smoking, and 73 controls without heart disease. We demonstrated that the Qiagen EZ1 instrument and kit consistently isolated genomic DNA of high yield, which can be used for checking DNA quality before conducting single-cell experiments. Here, we provide a method for single-nuclei isolation from cardiac tissue, otherwise known as the SoNIC method, which allows for the isolation of single cardiomyocyte nuclei from postmortem tissue by nuclear ploidy status. We also provide a detailed quality control measure for single-nuclei whole genome amplification and a pre-amplification method for confirming genomic integrity.
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Affiliation(s)
- Sarah Araten
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Ronald Mathieu
- Flow Cytometry Core Facility, Boston Children's Hospital, Boston, MA, USA
| | - Anushka Jetly
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA; Harvard College, Cambridge, MA, USA
| | - Hoon Shin
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA; Harvard College, Cambridge, MA, USA
| | - Nazia Hilal
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Bo Zhang
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Biostatistics and Research Design Center, Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Katherine Morillo
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Deepa Nandan
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Indu Sivankutty
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Ming Hui Chen
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA; Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Sangita Choudhury
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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44
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Bizzotto S. The human brain through the lens of somatic mosaicism. Front Neurosci 2023; 17:1172469. [PMID: 37250426 PMCID: PMC10213359 DOI: 10.3389/fnins.2023.1172469] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/25/2023] [Indexed: 05/31/2023] Open
Abstract
Every cell in the human brain possesses a unique genome that is the product of the accumulation of somatic mutations starting from the first postzygotic cell division and continuing throughout life. Somatic mosaicism in the human brain has been the focus of several recent efforts that took advantage of key technological innovations to start elucidating brain development, aging and disease directly in human tissue. On one side, somatic mutation occurring in progenitor cells has been used as a natural barcoding system to address cell phylogenies of clone formation and cell segregation in the brain lineage. On the other side, analyses of mutation rates and patterns in the genome of brain cells have revealed mechanisms of brain aging and disorder predisposition. In addition to the study of somatic mosaicism in the normal human brain, the contribution of somatic mutation has been investigated in both developmental neuropsychiatric and neurodegenerative disorders. This review starts with a methodological perspective on the study of somatic mosaicism to then cover the most recent findings in brain development and aging, and ends with the role of somatic mutations in brain disease. Thus, this review underlies what we have learned and what is still possible to discover by looking at somatic mosaicism in the brain genome.
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45
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Manojlovic Z, Wlodarczyk J, Okitsu C, Jin Y, Van Den Berg D, Lieber MR, Hsieh CL. Construction of high coverage whole-genome sequencing libraries from single colon crypts without DNA extraction or whole-genome amplification. BMC Res Notes 2023; 16:66. [PMID: 37106434 PMCID: PMC10142246 DOI: 10.1186/s13104-023-06333-y] [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: 12/10/2022] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
OBJECTIVE Comprehensive and reliable genome-wide variant analysis of a small number of cells has been challenging due to genome coverage bias, PCR over-cycling, and the requirement of expensive technologies. To comprehensively identify genome alterations in single colon crypts that reflect genome heterogeneity of stem cells, we developed a method to construct whole-genome sequencing libraries from single colon crypts without DNA extraction, whole-genome amplification, or increased PCR enrichment cycles. RESULTS We present post-alignment statistics of 81 single-crypts (each contains four- to eight-fold less DNA than the requirement of conventional methods) and 16 bulk-tissue libraries to demonstrate the consistent success in obtaining reliable coverage, both in depth (≥ 30X) and breadth (≥ 92% of the genome covered at ≥ 10X depth), of the human genome. These single-crypt libraries are of comparable quality as libraries generated with the conventional method using high quality and quantities of purified DNA. Conceivably, our method can be applied to small biopsy samples from many tissues and can be combined with single cell targeted sequencing to comprehensively profile cancer genomes and their evolution. The broad potential application of this method offers expanded possibilities in cost-effectively examining genome heterogeneity in small numbers of cells at high resolution.
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Affiliation(s)
- Zarko Manojlovic
- Department of Urology, University of Southern California, 1441 Eastlake Ave., NTT5420, Los Angeles, CA, USA
| | - Jordan Wlodarczyk
- Department of Surgery, University of Southern California, Los Angeles, CA, USA
| | - Cindy Okitsu
- Department of Pathology, University of Southern California, Los Angeles, CA, USA
| | - Yuxin Jin
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - David Van Den Berg
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Michael R Lieber
- Department of Pathology, University of Southern California, Los Angeles, CA, USA
| | - Chih-Lin Hsieh
- Department of Urology, University of Southern California, 1441 Eastlake Ave., NTT5420, Los Angeles, CA, USA.
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Russell AJC, Weir JA, Nadaf NM, Shabet M, Kumar V, Kambhampati S, Raichur R, Marrero GJ, Liu S, Balderrama KS, Vanderburg CR, Shanmugam V, Tian L, Wu CJ, Yoon CH, Macosko EZ, Chen F. Slide-tags: scalable, single-nucleus barcoding for multi-modal spatial genomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.01.535228. [PMID: 37066158 PMCID: PMC10103946 DOI: 10.1101/2023.04.01.535228] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Recent technological innovations have enabled the high-throughput quantification of gene expression and epigenetic regulation within individual cells, transforming our understanding of how complex tissues are constructed. Missing from these measurements, however, is the ability to routinely and easily spatially localise these profiled cells. We developed a strategy, Slide-tags, in which single nuclei within an intact tissue section are 'tagged' with spatial barcode oligonucleotides derived from DNA-barcoded beads with known positions. These tagged nuclei can then be used as input into a wide variety of single-nucleus profiling assays. Application of Slide-tags to the mouse hippocampus positioned nuclei at less than 10 micron spatial resolution, and delivered whole-transcriptome data that was indistinguishable in quality from ordinary snRNA-seq. To demonstrate that Slide-tags can be applied to a wide variety of human tissues, we performed the assay on brain, tonsil, and melanoma. We revealed cell-type-specific spatially varying gene expression across cortical layers and spatially contextualised receptor-ligand interactions driving B-cell maturation in lymphoid tissue. A major benefit of Slide-tags is that it is easily adaptable to virtually any single-cell measurement technology. As proof of principle, we performed multiomic measurements of open chromatin, RNA, and T-cell receptor sequences in the same cells from metastatic melanoma. We identified spatially distinct tumour subpopulations to be differentially infiltrated by an expanded T-cell clone and undergoing cell state transition driven by spatially clustered accessible transcription factor motifs. Slide-tags offers a universal platform for importing the compendium of established single-cell measurements into the spatial genomics repertoire.
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47
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Li Z, Min S, Alliey-Rodriguez N, Giase G, Cheng L, Craig DW, Faulkner GJ, Asif H, Liu C, Gershon ES. Single-neuron whole genome sequencing identifies increased somatic mutation burden in Alzheimer's disease related genes. Neurobiol Aging 2023; 123:222-232. [PMID: 36599749 DOI: 10.1016/j.neurobiolaging.2022.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 12/15/2022]
Abstract
Accumulation of somatic mutations in human neurons is associated with aging and neurodegeneration. To shed light on the somatic mutational burden in Alzheimer's disease (AD) neurons and get more insight into the role of somatic mutations in AD pathogenesis, we performed single-neuron whole genome sequencing to detect genome-wide somatic mutations (single nucleotide variants (SNVs) and Indels) in 96 single prefrontal cortex neurons from 8 AD patients and 8 elderly controls. We found that the mutational burden is ∼3000 somatic mutations per neuron genome in elderly subjects. AD patients have increased somatic mutation burden in AD-related annotation categories, including AD risk genes and differentially expressed genes in AD neurons. Mutational signature analysis showed somatic SNVs (sSNVs) primarily caused by aging and oxidative DNA damage processes but no significant difference was detected between AD and controls. Additionally, functional somatic mutations identified in AD patients showed significant enrichment in several AD-related pathways, including AD pathway, Notch-signaling pathway and Calcium-signaling pathway. These findings provide genetic insights into how somatic mutations may alter the function of single neurons and exert their potential roles in the pathogenesis of AD.
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Affiliation(s)
- Zongchang Li
- Department of Psychiatry, The Second Xiangya Hospital; Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China; Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL, USA
| | - Shishi Min
- Department of Psychiatry, The Second Xiangya Hospital; Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China; Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA; Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Ney Alliey-Rodriguez
- Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL, USA
| | - Gina Giase
- School of Public Health, University of Illinois at Chicago, Chicago, IL, USA
| | - Lijun Cheng
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - David Wesley Craig
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Geoffrey J Faulkner
- Mater Research Institute - University of Queensland, Woolloongabba, Queensland, Australia; Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Huma Asif
- Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL, USA.
| | - Chunyu Liu
- Department of Psychiatry, The Second Xiangya Hospital; Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China; Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA; School of Psychology, Shaanxi Normal University, Xi'an, China.
| | - Elliot S Gershon
- Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL, USA; Department of Human Genetics, University of Chicago, Chicago, IL, USA.
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48
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Back to Basics: A Simplified Improvement to Multiple Displacement Amplification for Microbial Single-Cell Genomics. Int J Mol Sci 2023; 24:ijms24054270. [PMID: 36901710 PMCID: PMC10002425 DOI: 10.3390/ijms24054270] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/23/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
Microbial single-cell genomics (SCG) provides access to the genomes of rare and uncultured microorganisms and is a complementary method to metagenomics. Due to the femtogram-levels of DNA in a single microbial cell, sequencing the genome requires whole genome amplification (WGA) as a preliminary step. However, the most common WGA method, multiple displacement amplification (MDA), is known to be costly and biased against specific genomic regions, preventing high-throughput applications and resulting in uneven genome coverage. Thus, obtaining high-quality genomes from many taxa, especially minority members of microbial communities, becomes difficult. Here, we present a volume reduction approach that significantly reduces costs while improving genome coverage and uniformity of DNA amplification products in standard 384-well plates. Our results demonstrate that further volume reduction in specialized and complex setups (e.g., microfluidic chips) is likely unnecessary to obtain higher-quality microbial genomes. This volume reduction method makes SCG more feasible for future studies, thus helping to broaden our knowledge on the diversity and function of understudied and uncharacterized microorganisms in the environment.
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Recent Advances in Methods for Circulating Tumor Cell Detection. Int J Mol Sci 2023; 24:ijms24043902. [PMID: 36835311 PMCID: PMC9959336 DOI: 10.3390/ijms24043902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/06/2023] [Accepted: 02/12/2023] [Indexed: 02/17/2023] Open
Abstract
Circulating tumor cells (CTCs) are released from primary tumors and transported through the body via blood or lymphatic vessels before settling to form micrometastases under suitable conditions. Accordingly, several studies have identified CTCs as a negative prognostic factor for survival in many types of cancer. CTCs also reflect the current heterogeneity and genetic and biological state of tumors; so, their study can provide valuable insights into tumor progression, cell senescence, and cancer dormancy. Diverse methods with differing specificity, utility, costs, and sensitivity have been developed for isolating and characterizing CTCs. Additionally, novel techniques with the potential to overcome the limitations of existing ones are being developed. This primary literature review describes the current and emerging methods for enriching, detecting, isolating, and characterizing CTCs.
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50
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Olsen TR, Talla P, Furnari J, Bruce JN, Canoll P, Zha S, Sims PA. Scalable co-sequencing of RNA and DNA from individual nuclei. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527940. [PMID: 36798358 PMCID: PMC9934633 DOI: 10.1101/2023.02.09.527940] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The ideal technology for directly investigating the relationship between genotype and phenotype would analyze both RNA and DNA genome-wide and with single-cell resolution. However, existing tools lack the throughput required for comprehensive analysis of complex tumors and tissues. We introduce a highly scalable method for jointly profiling DNA and expression following nucleosome depletion (DEFND-seq). In DEFND-seq, nuclei are nucleosome-depleted, tagmented, and separated into individual droplets for mRNA and genomic DNA barcoding. Once nuclei have been depleted of nucleosomes, subsequent steps can be performed using the widely available 10x Genomics droplet microfluidic technology and commercial kits without experimental modification. We demonstrate the production of high-complexity mRNA and gDNA sequencing libraries from thousands of individual nuclei from both cell lines and archived surgical specimens for associating gene expression phenotypes with both copy number and single nucleotide variants.
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Affiliation(s)
- Timothy R Olsen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032
| | - Pranay Talla
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032
| | - Julia Furnari
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032
| | - Jeffrey N Bruce
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032
| | - Peter Canoll
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032
| | - Shan Zha
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032
- Institute for Cancer Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, 10032
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032
- Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, 10032
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032
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