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Vargas LN, Zhang Y, Wu C, Martin H, Alonso Goulart V, Plessis C, Sirard MA. Unraveling the role of sperm retained histones in bull fertility and daughter fertility. Theriogenology 2024; 230:299-304. [PMID: 39366208 DOI: 10.1016/j.theriogenology.2024.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 09/19/2024] [Accepted: 09/24/2024] [Indexed: 10/06/2024]
Abstract
During spermatogenesis, a substantial proportion of histones are substituted by protamine to condense the genome within the sperm head. Studies indicate that a minority of histones, typically ranging from 1 to 15 %, persist in mammalian sperm post-substitution. The persistence of histones in the zygote facilitates chromatin accessibility to transcription factors in regions crucial for early embryonic development. Nevertheless, the potential causal relationship between retained histones and fertility phenotypes remains uncertain. This study seeks to investigate this relationship. The results indicate that in mature bovine sperm, regions of DNA associated with fertility that bind to histones are primarily concentrated in promoters and transcription start sites, potentially impacting bull fertility and offspring fertility through the regulation of relevant genes. Furthermore, microRNAs and estradiol/ESR are suggested to be the main regulators of the canonical pathways identified, highlighting the need for additional research to investigate their potential utility as biomarkers.
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Affiliation(s)
- Luna Nascimento Vargas
- Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil; Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Brasília, Federal District, Brazil
| | - Ying Zhang
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des Sciences Animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Québec, Québec, Canada; State Key Laboratory of Reproductive Regulation & Breeding of Grassland livestock, College of Life Science, Inner Mongolia University, Hohhot, China
| | - Chongyang Wu
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des Sciences Animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Québec, Québec, Canada
| | - Hélène Martin
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des Sciences Animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Québec, Québec, Canada
| | - Vivian Alonso Goulart
- Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Clément Plessis
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des Sciences Animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Québec, Québec, Canada
| | - Marc-André Sirard
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des Sciences Animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Québec, Québec, Canada.
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2
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Pallarès-Albanell J, Ortega-Flores L, Senar-Serra T, Ruiz A, Abril JF, Rossello M, Almudi I. Gene regulatory dynamics during the development of a paleopteran insect, the mayfly Cloeon dipterum. Development 2024; 151:dev203017. [PMID: 39324209 DOI: 10.1242/dev.203017] [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: 05/01/2024] [Accepted: 09/13/2024] [Indexed: 09/27/2024]
Abstract
The evolution of insects has been marked by the appearance of key body plan innovations that promoted the outstanding ability of this lineage to adapt to new habitats, boosting the most successful radiation in animals. To understand the evolution of these new structures, it is essential to investigate which genes and gene regulatory networks participate during the embryonic development of insects. Great efforts have been made to fully understand gene expression and gene regulation during the development of holometabolous insects, in particular Drosophila melanogaster. Conversely, functional genomics resources and databases in other insect lineages are scarce. To provide a new platform to study gene regulation in insects, we generated ATAC-seq for the first time during the development of the mayfly Cloeon dipterum, which belongs to Paleoptera, the sister group to all other winged insects. With these comprehensive datasets along six developmental stages, we characterized pronounced changes in accessible chromatin between early and late embryogenesis. The application of ATAC-seq in mayflies provides a fundamental resource to understand the evolution of gene regulation in insects.
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Affiliation(s)
- Joan Pallarès-Albanell
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio) , Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Spain
| | - Laia Ortega-Flores
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Spain
| | - Tòt Senar-Serra
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio) , Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Spain
| | - Antoni Ruiz
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio) , Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Spain
| | - Josep F Abril
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Spain
- Institute of Biomedicine of Universitat de Barcelona (IBUB) , Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Spain
| | - Maria Rossello
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio) , Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Spain
| | - Isabel Almudi
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio) , Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Spain
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3
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Feng J, Dan X, Cui Y, Gong Y, Peng M, Sang Y, Ingvarsson PK, Wang J. Integrating evolutionary genomics of forest trees to inform future tree breeding amid rapid climate change. PLANT COMMUNICATIONS 2024; 5:101044. [PMID: 39095989 DOI: 10.1016/j.xplc.2024.101044] [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: 01/12/2024] [Revised: 06/03/2024] [Accepted: 07/31/2024] [Indexed: 08/04/2024]
Abstract
Global climate change is leading to rapid and drastic shifts in environmental conditions, posing threats to biodiversity and nearly all life forms worldwide. Forest trees serve as foundational components of terrestrial ecosystems and play a crucial and leading role in combating and mitigating the adverse effects of extreme climate events, despite their own vulnerability to these threats. Therefore, understanding and monitoring how natural forests respond to rapid climate change is a key priority for biodiversity conservation. Recent progress in evolutionary genomics, driven primarily by cutting-edge multi-omics technologies, offers powerful new tools to address several key issues. These include precise delineation of species and evolutionary units, inference of past evolutionary histories and demographic fluctuations, identification of environmentally adaptive variants, and measurement of genetic load levels. As the urgency to deal with more extreme environmental stresses grows, understanding the genomics of evolutionary history, local adaptation, future responses to climate change, and conservation and restoration of natural forest trees will be critical for research at the nexus of global change, population genomics, and conservation biology. In this review, we explore the application of evolutionary genomics to assess the effects of global climate change using multi-omics approaches and discuss the outlook for breeding of climate-adapted trees.
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Affiliation(s)
- Jiajun Feng
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xuming Dan
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yangkai Cui
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yi Gong
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Minyue Peng
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yupeng Sang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Pär K Ingvarsson
- Department of Plant Biology, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jing Wang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
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4
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Abassah-Oppong S, Zoia M, Mannion BJ, Rouco R, Tissières V, Spurrell CH, Roland V, Darbellay F, Itum A, Gamart J, Festa-Daroux TA, Sullivan CS, Kosicki M, Rodríguez-Carballo E, Fukuda-Yuzawa Y, Hunter RD, Novak CS, Plajzer-Frick I, Tran S, Akiyama JA, Dickel DE, Lopez-Rios J, Barozzi I, Andrey G, Visel A, Pennacchio LA, Cobb J, Osterwalder M. A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival. Nat Commun 2024; 15:8793. [PMID: 39389973 PMCID: PMC11467299 DOI: 10.1038/s41467-024-53009-7] [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: 10/06/2023] [Accepted: 09/26/2024] [Indexed: 10/12/2024] Open
Abstract
Approximately a quarter of the human genome consists of gene deserts, large regions devoid of genes often located adjacent to developmental genes and thought to contribute to their regulation. However, defining the regulatory functions embedded within these deserts is challenging due to their large size. Here, we explore the cis-regulatory architecture of a gene desert flanking the Shox2 gene, which encodes a transcription factor indispensable for proximal limb, craniofacial, and cardiac pacemaker development. We identify the gene desert as a regulatory hub containing more than 15 distinct enhancers recapitulating anatomical subdomains of Shox2 expression. Ablation of the gene desert leads to embryonic lethality due to Shox2 depletion in the cardiac sinus venosus, caused in part by the loss of a specific distal enhancer. The gene desert is also required for stylopod morphogenesis, mediated via distributed proximal limb enhancers. In summary, our study establishes a multi-layered role of the Shox2 gene desert in orchestrating pleiotropic developmental expression through modular arrangement and coordinated dynamics of tissue-specific enhancers.
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Affiliation(s)
- Samuel Abassah-Oppong
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, AB, T2N 1N4, Canada
- Department of Biological Sciences, Fort Hays State University, Hays, KS, 67601, USA
| | - Matteo Zoia
- Department for BioMedical Research (DBMR), University of Bern, 3008, Bern, Switzerland
| | - Brandon J Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, 94720, USA
| | - Raquel Rouco
- Department of Genetic Medicine and Development and iGE3, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Virginie Tissières
- Department for BioMedical Research (DBMR), University of Bern, 3008, Bern, Switzerland
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, 41013, Seville, Spain
- Department of Cardiology, Bern University Hospital, 3010, Bern, Switzerland
| | - Cailyn H Spurrell
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Virginia Roland
- Department for BioMedical Research (DBMR), University of Bern, 3008, Bern, Switzerland
| | - Fabrice Darbellay
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Genetic Medicine and Development and iGE3, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Anja Itum
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, AB, T2N 1N4, Canada
| | - Julie Gamart
- Department for BioMedical Research (DBMR), University of Bern, 3008, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, 3010, Bern, Switzerland
| | - Tabitha A Festa-Daroux
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, AB, T2N 1N4, Canada
| | - Carly S Sullivan
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, AB, T2N 1N4, Canada
| | - Michael Kosicki
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Eddie Rodríguez-Carballo
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - Yoko Fukuda-Yuzawa
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Riana D Hunter
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Catherine S Novak
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Stella Tran
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jennifer A Akiyama
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Javier Lopez-Rios
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, 41013, Seville, Spain
- School of Health Sciences, Universidad Loyola Andalucía, Seville, Spain
| | - Iros Barozzi
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Guillaume Andrey
- Department of Genetic Medicine and Development and iGE3, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- School of Natural Sciences, University of California, Merced, Merced, CA, 95343, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, 94720, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - John Cobb
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, AB, T2N 1N4, Canada.
| | - Marco Osterwalder
- Department for BioMedical Research (DBMR), University of Bern, 3008, Bern, Switzerland.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- Department of Cardiology, Bern University Hospital, 3010, Bern, Switzerland.
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5
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Li X, Lei W, You X, Kong X, Chen Z, Shan R, Zhang Y, Yu Y, Wang P, Chen C. The tea cultivar 'Chungui' with jasmine-like aroma: From genome and epigenome to quality. Int J Biol Macromol 2024; 281:136352. [PMID: 39374727 DOI: 10.1016/j.ijbiomac.2024.136352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2024] [Revised: 09/29/2024] [Accepted: 10/04/2024] [Indexed: 10/09/2024]
Abstract
'Chungui' is a newly promoted tea cultivar in China, renowned for producing oolong tea with a distinctive jasmine-like aroma. However, the genetic basis of this unique aroma remains unclear. In this study, the 'Chungui' genome, one of the most complete and well-annotated tea genomes, was assembled using PacBio HiFi reads and Hi-C sequencing. Through comparative analysis with typical jasmine flower volatiles, eight core compounds responsible for this aroma were identified. Further research revealed that the jasmine-like aroma in 'Chungui' is regulated by a coordinated mechanism involving a significant increase in chromatin accessibility and the demethylation of CHH and CHG in the promoter regions of key aroma-related genes during oolong tea processing. The study proposes that the formation of this unique aroma is driven by the synergistic effect of enhanced chromatin accessibility and reduced methylation, which together lead to the robust upregulation of genes involved in the biosynthesis of these core aroma components. These results provide a molecular foundation for understanding the unique jasmine-like aroma of 'Chungui' tea and sets the stage for future studies to explore the roles of these regulatory mechanisms in aroma formation.
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Affiliation(s)
- Xinlei Li
- Tea Research Institute, Fujian Academy of Agricultural Science, Fuzhou 350013, China
| | - Wenlong Lei
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Xiaomei You
- Tea Research Institute, Fujian Academy of Agricultural Science, Fuzhou 350013, China
| | - Xiangrui Kong
- Tea Research Institute, Fujian Academy of Agricultural Science, Fuzhou 350013, China
| | - Zhihui Chen
- Tea Research Institute, Fujian Academy of Agricultural Science, Fuzhou 350013, China
| | - Ruiyang Shan
- Tea Research Institute, Fujian Academy of Agricultural Science, Fuzhou 350013, China
| | - Yazhen Zhang
- Tea Research Institute, Fujian Academy of Agricultural Science, Fuzhou 350013, China
| | - Youben Yu
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Pengjie Wang
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Changsong Chen
- Tea Research Institute, Fujian Academy of Agricultural Science, Fuzhou 350013, China; Fujian Branch of National Center for Tea Improvement, Fuzhou 350013, China.
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6
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Bruner WS, Grant SFA. Translation of genome-wide association study: from genomic signals to biological insights. Front Genet 2024; 15:1375481. [PMID: 39421299 PMCID: PMC11484060 DOI: 10.3389/fgene.2024.1375481] [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: 01/23/2024] [Accepted: 09/24/2024] [Indexed: 10/19/2024] Open
Abstract
Since the turn of the 21st century, genome-wide association study (GWAS) have successfully identified genetic signals associated with a myriad of common complex traits and diseases. As we transition from establishing robust genetic associations with diverse phenotypes, the central challenge is now focused on characterizing the underlying functional mechanisms driving these signals. Previous GWAS efforts have revealed multiple variants, each conferring relatively subtle susceptibility, collectively contributing to the pathogenesis of various common diseases. Such variants can further exhibit associations with multiple other traits and differ across ancestries, plus disentangling causal variants from non-causal due to linkage disequilibrium complexities can lead to challenges in drawing direct biological conclusions. Combined with cellular context considerations, such challenges can reduce the capacity to definitively elucidate the biological significance of GWAS signals, limiting the potential to define mechanistic insights. This review will detail current and anticipated approaches for functional interpretation of GWAS signals, both in terms of characterizing the underlying causal variants and the corresponding effector genes.
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Affiliation(s)
- Winter S. Bruner
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Struan F. A. Grant
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
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7
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Barnada SM, Giner de Gracia A, Morenilla-Palao C, López-Cascales MT, Scopa C, Waltrich FJ, Mikkers HMM, Cicardi ME, Karlin J, Trotti D, Peterson KA, Brugmann SA, Santen GWE, McMahon SB, Herrera E, Trizzino M. ARID1A-BAF coordinates ZIC2 genomic occupancy for epithelial-to-mesenchymal transition in cranial neural crest specification. Am J Hum Genet 2024; 111:2232-2252. [PMID: 39226899 DOI: 10.1016/j.ajhg.2024.07.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/30/2024] [Accepted: 07/30/2024] [Indexed: 09/05/2024] Open
Abstract
The BAF chromatin remodeler regulates lineage commitment including cranial neural crest cell (CNCC) specification. Variants in BAF subunits cause Coffin-Siris syndrome (CSS), a congenital disorder characterized by coarse craniofacial features and intellectual disability. Approximately 50% of individuals with CSS harbor variants in one of the mutually exclusive BAF subunits, ARID1A/ARID1B. While Arid1a deletion in mouse neural crest causes severe craniofacial phenotypes, little is known about the role of ARID1A in CNCC specification. Using CSS-patient-derived ARID1A+/- induced pluripotent stem cells to model CNCC specification, we discovered that ARID1A-haploinsufficiency impairs epithelial-to-mesenchymal transition (EMT), a process necessary for CNCC delamination and migration from the neural tube. Furthermore, wild-type ARID1A-BAF regulates enhancers associated with EMT genes. ARID1A-BAF binding at these enhancers is impaired in heterozygotes while binding at promoters is unaffected. At the sequence level, these EMT enhancers contain binding motifs for ZIC2, and ZIC2 binding at these sites is ARID1A-dependent. When excluded from EMT enhancers, ZIC2 relocates to neuronal enhancers, triggering aberrant neuronal gene activation. In mice, deletion of Zic2 impairs NCC delamination, while ZIC2 overexpression in chick embryos at post-migratory neural crest stages elicits ectopic delamination from the neural tube. These findings reveal an essential ARID1A-ZIC2 axis essential for EMT and CNCC delamination.
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Affiliation(s)
- Samantha M Barnada
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Aida Giner de Gracia
- Instituto de Neurociencias de Alicante (Consejo Superior de Investigaciones Científicas- Universidad Miguel Hernández, CSIC-UMH). Campus San Juan, Avd. Ramón y Cajal s/n, 03550 San Juan de Alicante, Spain
| | - Cruz Morenilla-Palao
- Instituto de Neurociencias de Alicante (Consejo Superior de Investigaciones Científicas- Universidad Miguel Hernández, CSIC-UMH). Campus San Juan, Avd. Ramón y Cajal s/n, 03550 San Juan de Alicante, Spain
| | - Maria Teresa López-Cascales
- Instituto de Neurociencias de Alicante (Consejo Superior de Investigaciones Científicas- Universidad Miguel Hernández, CSIC-UMH). Campus San Juan, Avd. Ramón y Cajal s/n, 03550 San Juan de Alicante, Spain
| | - Chiara Scopa
- Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - Francis J Waltrich
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Harald M M Mikkers
- Department of Cell & Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Maria Elena Cicardi
- Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jonathan Karlin
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Davide Trotti
- Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Samantha A Brugmann
- Division of Developmental Biology, Department of Pediatrics at Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Steven B McMahon
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Eloísa Herrera
- Instituto de Neurociencias de Alicante (Consejo Superior de Investigaciones Científicas- Universidad Miguel Hernández, CSIC-UMH). Campus San Juan, Avd. Ramón y Cajal s/n, 03550 San Juan de Alicante, Spain.
| | - Marco Trizzino
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA; Department of Life Sciences, Imperial College London, London, UK.
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8
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Stötzel M, Cheng CY, IIik IA, Kumar AS, Omgba PA, van der Weijden VA, Zhang Y, Vingron M, Meissner A, Aktaş T, Kretzmer H, Bulut-Karslioğlu A. TET activity safeguards pluripotency throughout embryonic dormancy. Nat Struct Mol Biol 2024; 31:1625-1639. [PMID: 38783076 PMCID: PMC11479945 DOI: 10.1038/s41594-024-01313-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/10/2024] [Indexed: 05/25/2024]
Abstract
Dormancy is an essential biological process for the propagation of many life forms through generations and stressful conditions. Early embryos of many mammals are preservable for weeks to months within the uterus in a dormant state called diapause, which can be induced in vitro through mTOR inhibition. Cellular strategies that safeguard original cell identity within the silent genomic landscape of dormancy are not known. Here we show that the protection of cis-regulatory elements from silencing is key to maintaining pluripotency in the dormant state. We reveal a TET-transcription factor axis, in which TET-mediated DNA demethylation and recruitment of methylation-sensitive transcription factor TFE3 drive transcriptionally inert chromatin adaptations during dormancy transition. Perturbation of TET activity compromises pluripotency and survival of mouse embryos under dormancy, whereas its enhancement improves survival rates. Our results reveal an essential mechanism for propagating the cellular identity of dormant cells, with implications for regeneration and disease.
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Affiliation(s)
- Maximilian Stötzel
- Stem Cell Chromatin Lab, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Chieh-Yu Cheng
- Stem Cell Chromatin Lab, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Ibrahim A IIik
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Abhishek Sampath Kumar
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Persia Akbari Omgba
- Stem Cell Chromatin Lab, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | | | - Yufei Zhang
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Tuğçe Aktaş
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
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9
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Tetik-Elsherbiny N, Elsherbiny A, Setya A, Gahn J, Tang Y, Gupta P, Dou Y, Serke H, Wieland T, Dubrac A, Heineke J, Potente M, Cordero J, Ola R, Dobreva G. RNF20-mediated transcriptional pausing and VEGFA splicing orchestrate vessel growth. NATURE CARDIOVASCULAR RESEARCH 2024; 3:1199-1216. [PMID: 39322771 PMCID: PMC11473366 DOI: 10.1038/s44161-024-00546-5] [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: 04/06/2023] [Accepted: 08/29/2024] [Indexed: 09/27/2024]
Abstract
Signal-responsive gene expression is essential for vascular development, yet the mechanisms integrating signaling inputs with transcriptional activities are largely unknown. Here we show that RNF20, the primary E3 ubiquitin ligase for histone H2B, plays a multifaceted role in sprouting angiogenesis. RNF20 mediates RNA polymerase (Pol II) promoter-proximal pausing at genes highly paused in endothelial cells, involved in VEGFA signaling, stress response, cell cycle control and mRNA splicing. It also orchestrates large-scale mRNA processing events that alter the bioavailability and function of critical pro-angiogenic factors, such as VEGFA. Mechanistically, RNF20 restricts ERG-dependent Pol II pause release at highly paused genes while binding to Notch1 to promote H2B monoubiquitination at Notch target genes and Notch-dependent gene expression. This balance is crucial, as loss of Rnf20 leads to uncontrolled tip cell specification. Our findings highlight the pivotal role of RNF20 in regulating VEGF-Notch signaling circuits during vessel growth, underscoring its potential for therapeutic modulation of angiogenesis.
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Affiliation(s)
- Nalan Tetik-Elsherbiny
- Department of Cardiovascular Genomics and Epigenomics, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Adel Elsherbiny
- Department of Cardiovascular Genomics and Epigenomics, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Aadhyaa Setya
- Department of Cardiovascular Genomics and Epigenomics, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Johannes Gahn
- Cardiovascular Pharmacology, European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Yongqin Tang
- Department of Cardiovascular Genomics and Epigenomics, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Purnima Gupta
- Cardiovascular Pharmacology, European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Yanliang Dou
- Department of Cardiovascular Genomics and Epigenomics, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Heike Serke
- Department of Cardiovascular Genomics and Epigenomics, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- German Centre for Cardiovascular Research (DZHK), Mannheim, Germany
| | - Thomas Wieland
- German Centre for Cardiovascular Research (DZHK), Mannheim, Germany
- Experimental Pharmacology, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | | | - Joerg Heineke
- German Centre for Cardiovascular Research (DZHK), Mannheim, Germany
- Department of Cardiovascular Physiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Michael Potente
- German Centre for Cardiovascular Research (DZHK), Mannheim, Germany
- Angiogenesis & Metabolism Laboratory, Center of Vascular Biomedicine, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Helmholtz-Institute for Translational AngioCardioScience (HI-TAC) of the Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) at Heidelberg University, Heidelberg, Germany
| | - Julio Cordero
- Department of Cardiovascular Genomics and Epigenomics, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- German Centre for Cardiovascular Research (DZHK), Mannheim, Germany.
| | - Roxana Ola
- Cardiovascular Pharmacology, European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- German Centre for Cardiovascular Research (DZHK), Mannheim, Germany.
| | - Gergana Dobreva
- Department of Cardiovascular Genomics and Epigenomics, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- German Centre for Cardiovascular Research (DZHK), Mannheim, Germany.
- Helmholtz-Institute for Translational AngioCardioScience (HI-TAC) of the Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) at Heidelberg University, Heidelberg, Germany.
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10
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Liu SX, Muelken P, Maxim ZL, Ramakrishnan A, Estill MS, LeSage MG, Smethells JR, Shen L, Tran PV, Harris AC, Gewirtz JC. Differential gene expression and chromatin accessibility in the medial prefrontal cortex associated with individual differences in rat behavioral models of opioid use disorder. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582799. [PMID: 38979145 PMCID: PMC11230220 DOI: 10.1101/2024.02.29.582799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Opioid use disorder (OUD) is a neuropsychological disease that has a devastating impact on public health. Substantial individual differences in vulnerability exist, the neurobiological substrates of which remain unclear. To address this question, we investigated genome-wide gene transcription (RNA-seq) and chromatin accessibility (ATAC-seq) in the medial prefrontal cortex (mPFC) of male and female rats exhibiting differential vulnerability in behavioral paradigms modeling different phases of OUD: Withdrawal-Induced Anhedonia (WIA), Demand, and Reinstatement. Ingenuity Pathway Analysis (IPA) of RNA-seq revealed greater changes in canonical pathways in Resilient (vs. Saline) rats in comparison to Vulnerable (vs. Saline) rats across 3 paradigms, suggesting brain adaptations that might contribute to resilience to OUD across its trajectory. Analyses of gene networks and upstream regulators implicated processes involved in oligodendrocyte maturation and myelination in WIA, neuroinflammation in Demand, and metabolism in Reinstatement. Motif analysis of ATAC-seq showed changes in chromatin accessibility to a small set of transcription factor (TF) binding sites as a function either of opioid exposure (i.e., morphine versus saline) generally or of individual vulnerability specifically. Some of these were shared across the 3 paradigms and others were unique to each. In conclusion, we have identified changes in biological pathways, TFs, and their binding motifs that vary with paradigm and OUD vulnerability. These findings point to the involvement of distinct transcriptional and epigenetic mechanisms in response to opioid exposure, vulnerability to OUD, and different stages of the disorder.
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11
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Gunn JC, Christensen BM, Bueno EM, Cohen ZP, Kissonergis AS, Chen YH. Agricultural insect pests as models for studying stress-induced evolutionary processes. INSECT MOLECULAR BIOLOGY 2024; 33:432-443. [PMID: 38655882 DOI: 10.1111/imb.12915] [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: 12/15/2023] [Accepted: 04/14/2024] [Indexed: 04/26/2024]
Abstract
Agricultural insect pests (AIPs) are widely successful in adapting to natural and anthropogenic stressors, repeatedly overcoming population bottlenecks and acquiring resistance to intensive management practices. Although they have been largely overlooked in evolutionary studies, AIPs are ideal systems for understanding rapid adaptation under novel environmental conditions. Researchers have identified several genomic mechanisms that likely contribute to adaptive stress responses, including positive selection on de novo mutations, polygenic selection on standing allelic variation and phenotypic plasticity (e.g., hormesis). However, new theory suggests that stress itself may induce epigenetic modifications, which may confer heritable physiological changes (i.e., stress-resistant phenotypes). In this perspective, we discuss how environmental stress from agricultural management generates the epigenetic and genetic modifications that are associated with rapid adaptation in AIPs. We summarise existing evidence for stress-induced evolutionary processes in the context of insecticide resistance. Ultimately, we propose that studying AIPs offers new opportunities and resources for advancing our knowledge of stress-induced evolution.
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Affiliation(s)
- Joe C Gunn
- Department of Plant and Soil Science, University of Vermont, Burlington, Vermont, USA
| | - Blair M Christensen
- Department of Plant and Soil Science, University of Vermont, Burlington, Vermont, USA
| | - Erika M Bueno
- Department of Plant and Soil Science, University of Vermont, Burlington, Vermont, USA
| | - Zachary P Cohen
- Insect Control and Cotton Disease Research, USDA ARS, College Station, Texas, USA
| | | | - Yolanda H Chen
- Department of Plant and Soil Science, University of Vermont, Burlington, Vermont, USA
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12
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Alfeghaly C, Castel G, Cazottes E, Moscatelli M, Moinard E, Casanova M, Boni J, Mahadik K, Lammers J, Freour T, Chauviere L, Piqueras C, Boers R, Boers J, Gribnau J, David L, Ouimette JF, Rougeulle C. XIST dampens X chromosome activity in a SPEN-dependent manner during early human development. Nat Struct Mol Biol 2024; 31:1589-1600. [PMID: 38834912 PMCID: PMC11479943 DOI: 10.1038/s41594-024-01325-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/25/2024] [Indexed: 06/06/2024]
Abstract
XIST (X-inactive specific transcript) long noncoding RNA (lncRNA) is responsible for X chromosome inactivation (XCI) in placental mammals, yet it accumulates on both X chromosomes in human female preimplantation embryos without triggering X chromosome silencing. The XACT (X-active coating transcript) lncRNA coaccumulates with XIST on active X chromosomes and may antagonize XIST function. Here, we used human embryonic stem cells in a naive state of pluripotency to assess the function of XIST and XACT in shaping the X chromosome chromatin and transcriptional landscapes during preimplantation development. We show that XIST triggers the deposition of polycomb-mediated repressive histone modifications and dampens the transcription of most X-linked genes in a SPEN-dependent manner, while XACT deficiency does not significantly affect XIST activity or X-linked gene expression. Our study demonstrates that XIST is functional before XCI, confirms the existence of a transient process of X chromosome dosage compensation and reveals that XCI and dampening rely on the same set of factors.
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Affiliation(s)
- Charbel Alfeghaly
- Epigenetics and Cell Fate, CNRS, Université Paris Cité, Paris, France
| | - Gaël Castel
- Epigenetics and Cell Fate, CNRS, Université Paris Cité, Paris, France
| | - Emmanuel Cazottes
- Epigenetics and Cell Fate, CNRS, Université Paris Cité, Paris, France
| | | | - Eva Moinard
- Center for Research in Transplantation and Translational Immunology (CR2TI), CHU Nantes, Inserm, Nantes Université, Nantes, France
| | - Miguel Casanova
- Epigenetics and Cell Fate, CNRS, Université Paris Cité, Paris, France
| | - Juliette Boni
- Epigenetics and Cell Fate, CNRS, Université Paris Cité, Paris, France
| | - Kasturi Mahadik
- Epigenetics and Cell Fate, CNRS, Université Paris Cité, Paris, France
| | - Jenna Lammers
- Service de Biologie de la Reproduction, CHU Nantes, Nantes Université, Nantes, France
| | - Thomas Freour
- Service de Biologie de la Reproduction, CHU Nantes, Nantes Université, Nantes, France
| | - Louis Chauviere
- Epigenetics and Cell Fate, CNRS, Université Paris Cité, Paris, France
| | - Carla Piqueras
- Epigenetics and Cell Fate, CNRS, Université Paris Cité, Paris, France
| | - Ruben Boers
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Joachim Boers
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Laurent David
- Center for Research in Transplantation and Translational Immunology (CR2TI), CHU Nantes, Inserm, Nantes Université, Nantes, France
- BioCore, CNRS, CHU Nantes, Inserm, Nantes Université, Nantes, France
| | | | - Claire Rougeulle
- Epigenetics and Cell Fate, CNRS, Université Paris Cité, Paris, France.
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13
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Hockemeyer K, Sakellaropoulos T, Chen X, Ivashkiv O, Sirenko M, Zhou H, Gambi G, Battistello E, Avrampou K, Sun Z, Guillamot M, Chiriboga L, Jour G, Dolgalev I, Corrigan K, Bhatt K, Osman I, Tsirigos A, Kourtis N, Aifantis I. The stress response regulator HSF1 modulates natural killer cell anti-tumour immunity. Nat Cell Biol 2024; 26:1734-1744. [PMID: 39223375 DOI: 10.1038/s41556-024-01490-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 07/18/2024] [Indexed: 09/04/2024]
Abstract
Diverse cellular insults converge on activation of the heat shock factor 1 (HSF1), which regulates the proteotoxic stress response to maintain protein homoeostasis. HSF1 regulates numerous gene programmes beyond the proteotoxic stress response in a cell-type- and context-specific manner to promote malignancy. However, the role(s) of HSF1 in immune populations of the tumour microenvironment remain elusive. Here, we leverage an in vivo model of HSF1 activation and single-cell transcriptomic tumour profiling to show that augmented HSF1 activity in natural killer (NK) cells impairs cytotoxicity, cytokine production and subsequent anti-tumour immunity. Mechanistically, HSF1 directly binds and regulates the expression of key mediators of NK cell effector function. This work demonstrates that HSF1 regulates the immune response under the stress conditions of the tumour microenvironment. These findings have important implications for enhancing the efficacy of adoptive NK cell therapies and for designing combinatorial strategies including modulators of NK cell-mediated tumour killing.
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Affiliation(s)
- Kathryn Hockemeyer
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Theodore Sakellaropoulos
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, NYU Langone Medical Center, New York, NY, USA
| | - Xufeng Chen
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Olha Ivashkiv
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Maria Sirenko
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Hua Zhou
- Applied Bioinformatics Laboratories, NYU Langone Medical Center, New York, NY, USA
| | - Giovanni Gambi
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Elena Battistello
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Kleopatra Avrampou
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Zhengxi Sun
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Maria Guillamot
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Luis Chiriboga
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - George Jour
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Ronald O. Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY, USA
| | - Igor Dolgalev
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, NYU Langone Medical Center, New York, NY, USA
| | - Kate Corrigan
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Kamala Bhatt
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Iman Osman
- Ronald O. Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY, USA
- Department of Urology, NYU Grossman School of Medicine, New York, NY, USA
- Interdisciplinary Melanoma Cooperative Group, NYU Langone Medical Center, New York, NY, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, NYU Langone Medical Center, New York, NY, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Nikos Kourtis
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA.
- Laura & Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA.
- Regeneron Pharmaceuticals, Tarrytown, NY, USA.
| | - Iannis Aifantis
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA.
- Laura & Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA.
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14
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Han Y, Shi L, Jiang N, Huang J, Jia X, Zhu B. Dissecting the Single-Cell Diversity and Heterogeneity Underlying Cervical Precancerous Lesions and Cancer Tissues. Reprod Sci 2024:10.1007/s43032-024-01695-5. [PMID: 39354287 DOI: 10.1007/s43032-024-01695-5] [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: 04/03/2024] [Accepted: 09/08/2024] [Indexed: 10/03/2024]
Abstract
The underlying cellular diversity and heterogeneity from cervix precancerous lesions to cervical squamous cell carcinoma (CSCC) is investigated. Four single-cell datasets including normal tissues, normal adjacent tissues, precancerous lesions, and cervical tumors were integrated to perform disease stage analysis. Single-cell compositional data analysis (scCODA) was utilized to reveal the compositional changes of each cell type. Differentially expressed genes (DEGs) among cell types were annotated using BioCarta. An assay for transposase-accessible chromatin sequencing (ATAC-seq) analysis was performed to correlate epigenetic alterations with gene expression profiles. Lastly, a logistic regression model was used to assess the similarity between the original and new cohort data (HRA001742). After global annotation, seven distinct cell types were categorized. Eight consensus-upregulated DEGs were identified in B cells among different disease statuses, which could be utilized to predict the overall survival of CSCC patients. Inferred copy number variation (CNV) analysis of epithelial cells guided disease progression classification. Trajectory and ATAC-seq integration analysis identified 95 key transcription factors (TF) and one immunohistochemistry (IHC) testified key-node TF (YY1) involved in epithelial cells from CSCC initiation to progression. The consistency of epithelial cell subpopulation markers was revealed with single-cell sequencing, bulk sequencing, and RT-qPCR detection. KRT8 and KRT15, markers of Epi6, showed progressively higher expression with disease progression as revealed by IHC detection. The logistic regression model testified the robustness of the resemblance of clusters among the various datasets utilized in this study. Valuable insights into CSCC cellular diversity and heterogeneity provide a foundation for future targeted therapy.
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Affiliation(s)
- Yanling Han
- Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
| | - Lu Shi
- CRE Life Institute, Beijing, 100000, China
| | - Nan Jiang
- Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
| | - Jiamin Huang
- Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
| | - Xiuzhi Jia
- Department of Immunology and Pathogen Biology, College of Medicine, Lishui University, Lishui, 323000, China.
- Center of Disease Immunity and Intervention, College of Medicine, Lishui University, Lishui, 323000, China.
| | - Bo Zhu
- Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China.
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15
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La'ah AS, Tsai P, Yarmishyn AA, Ching L, Chen C, Chien Y, Chen JC, Tsai M, Chen Y, Ma C, Hsu P, Luo Y, Chen Y, Chiou G, Lu K, Lin W, Chou Y, Wang M, Chiou S. Neutrophils Recruited by NKX2-1 Suppression via Activation of CXCLs/CXCR2 Axis Promote Lung Adenocarcinoma Progression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400370. [PMID: 39113226 PMCID: PMC11481344 DOI: 10.1002/advs.202400370] [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: 01/10/2024] [Revised: 06/14/2024] [Indexed: 10/17/2024]
Abstract
NK2 Homeobox 1 (NKX2-1) is a well-characterized pathological marker that delineates lung adenocarcinoma (LUAD) progression. The advancement of LUAD is influenced by the immune tumor microenvironment through paracrine signaling. However, the involvement of NKX2-1 in modeling the tumor immune microenvironment is still unclear. Here, the downregulation of NKX2-1 is observed in high-grade LUAD. Meanwhile, single-cell RNA sequencing and Visium in situ capturing profiling revealed the recruitment and infiltration of neutrophils in orthotopic syngeneic tumors exhibiting strong cell-cell communication through the activation of CXCLs/CXCR2 signaling. The depletion of NKX2-1 triggered the expression and secretion of CXCL1, CXCL2, CXCL3, and CXCL5 in LUAD cells. Chemokine secretion is analyzed by chemokine array and validated by qRT-PCR. ATAC-seq revealed the restrictive regulation of NKX2-1 on the promoters of CXCL1, CXCL2, and CXCL5 genes. This phenomenon led to increased tumor growth, and conversely, tumor growth decreased when inhibited by the CXCR2 antagonist SB225002. This study unveils how NKX2-1 modulates the infiltration of tumor-promoting neutrophils by inhibiting CXCLs/CXCR2-dependent mechanisms. Hence, targeting CXCR2 in NKX2-1-low tumors is a potential antitumor therapy that may improve LUAD patient outcomes.
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Affiliation(s)
- Anita S La'ah
- Taiwan International Graduate Program in Molecular MedicineNational Yang Ming Chiao Tung University and Academia SinicaTaipei115Taiwan
- Department of Medical ResearchTaipei Veterans General HospitalTaipei112Taiwan
| | - Ping‐Hsing Tsai
- Department of Medical ResearchTaipei Veterans General HospitalTaipei112Taiwan
- Institute of PharmacologySchool of MedicineNational Yang Ming Chiao Tung UniversityTaipei112Taiwan
| | | | - Lo‐Jei Ching
- Institute of Clinical MedicineNational Yang Ming Chiao Tung UniversityTaipei112Taiwan
| | - Chih‐Ying Chen
- Department of Medical ResearchTaipei Veterans General HospitalTaipei112Taiwan
| | - Yueh Chien
- Department of Medical ResearchTaipei Veterans General HospitalTaipei112Taiwan
- Institute of PharmacologySchool of MedicineNational Yang Ming Chiao Tung UniversityTaipei112Taiwan
| | - Jerry Chieh‐Yu Chen
- Taiwan International Graduate Program in Molecular MedicineNational Yang Ming Chiao Tung University and Academia SinicaTaipei115Taiwan
| | - Ming‐Long Tsai
- Department of Medical ResearchTaipei Veterans General HospitalTaipei112Taiwan
| | - Yi‐Chen Chen
- Department of Medical ResearchTaipei Veterans General HospitalTaipei112Taiwan
| | - Chun Ma
- Department of Medical ResearchTaipei Veterans General HospitalTaipei112Taiwan
| | - Po‐Kuei Hsu
- School of MedicineNational Yang Ming Chiao Tung UniversityTaipei112Taiwan
- Department of SurgeryTaipei Veterans General HospitalTaipei112Taiwan
| | - Yung‐Hung Luo
- Institute of Clinical MedicineNational Yang Ming Chiao Tung UniversityTaipei112Taiwan
- School of MedicineNational Yang Ming Chiao Tung UniversityTaipei112Taiwan
- Department of Chest MedicineTaipei Veterans General HospitalTaipei112Taiwan
| | - Yuh‐Min Chen
- Institute of Clinical MedicineNational Yang Ming Chiao Tung UniversityTaipei112Taiwan
- Department of Chest MedicineTaipei Veterans General HospitalTaipei112Taiwan
- Taipei Cancer CenterTaipei Medical UniversityTaipei110Taiwan
| | - Guang‐Yuh Chiou
- Department of Biological Science and TechnologyNational Yang Ming Chiao Tung UniversityHsinChu300093Taiwan
| | - Kai‐Hsi Lu
- Department of Medical Research and EducationCheng‐Hsin General HospitalTaipei112Taiwan
| | - Wen‐Chang Lin
- Institute of Biomedical SciencesAcademia SinicaTaipei115Taiwan
| | - Yu‐Ting Chou
- Institute of BiotechnologyNational Tsing Hua UniversityHsinchu300044Taiwan
| | - Mong‐Lien Wang
- Taiwan International Graduate Program in Molecular MedicineNational Yang Ming Chiao Tung University and Academia SinicaTaipei115Taiwan
- Department of Medical ResearchTaipei Veterans General HospitalTaipei112Taiwan
- Institute of Food Safety and Health Risk AssessmentSchool of Pharmaceutical SciencesNational Yang Ming Chiao Tung UniversityTaipei112Taiwan
| | - Shih‐Hwa Chiou
- Taiwan International Graduate Program in Molecular MedicineNational Yang Ming Chiao Tung University and Academia SinicaTaipei115Taiwan
- Department of Medical ResearchTaipei Veterans General HospitalTaipei112Taiwan
- Institute of PharmacologySchool of MedicineNational Yang Ming Chiao Tung UniversityTaipei112Taiwan
- Genomic Research CenterAcademia SinicaTaipei115Taiwan
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16
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Zhang Z, Chang L, Wang B, Wei Y, Li X, Li X, Zhang Y, Wang K, Qiao R, Yang F, Yu T, Han X. Differential chromatin accessibility and Gene Expression Associated with Backfat Deposition in pigs. BMC Genomics 2024; 25:902. [PMID: 39349998 PMCID: PMC11441165 DOI: 10.1186/s12864-024-10805-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Accepted: 09/17/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Backfat serves as a vital fat reservoir in pigs, and its excessive accumulation will adversely impact pig growth performance, farming efficiency, and pork quality. The aim of this research is to integrate assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and RNA sequencing (RNA-seq) to explore the molecular mechanisms underlying porcine backfat deposition. RESULTS ATAC-seq analysis identified 568 genes originating from 698 regions exhibiting differential accessibility, which were significantly enriched in pathways pertinent to adipocyte differentiation and lipid metabolism. Besides, a total of 283 transcription factors (TFs) were identified by motif analysis. RNA-seq analysis revealed 978 differentially expressed genes (DEGs), which were enriched in pathways related to energy metabolism, cell cycle and signal transduction. The integration of ATAC-seq and RNA-seq data indicates that DEG expression levels are associated with chromatin accessibility. This comprehensive study highlights the involvement of critical pathways, including the Wnt signaling pathway, Jak-STAT signaling pathway, and fatty acid degradation, in the regulation of backfat deposition. Through rigorous analysis, we identified several candidate genes (LEP, CTBP2, EHHADH, OSMR, TCF7L2, BCL2, FGF1, UCP2, CCND1, TIMP1, and VDR) as potentially significant contributors to backfat deposition. Additionally, we constructed TF-TF and TF-target gene regulatory networks and identified a series of potential TFs related to backfat deposition (FOS, STAT3, SMAD3, and ESR1). CONCLUSIONS This study represents the first application of ATAC-seq and RNA-seq, affording a novel perspective into the mechanisms underlying backfat deposition and providing invaluable resources for the enhancement of pig breeding programs.
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Affiliation(s)
- Zhe Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Lebin Chang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Bingjie Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yilin Wei
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
- Sanya Institute, Hainan Academy of Agricultural Science, Sanya, 572025, China
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yongqian Zhang
- Henan Yifa Animal Husbandry Co., Ltd, Hebi, 458000, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Feng Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Tong Yu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.
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17
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Lee AS, Ayers LJ, Kosicki M, Chan WM, Fozo LN, Pratt BM, Collins TE, Zhao B, Rose MF, Sanchis-Juan A, Fu JM, Wong I, Zhao X, Tenney AP, Lee C, Laricchia KM, Barry BJ, Bradford VR, Jurgens JA, England EM, Lek M, MacArthur DG, Lee EA, Talkowski ME, Brand H, Pennacchio LA, Engle EC. A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders. Nat Commun 2024; 15:8268. [PMID: 39333082 PMCID: PMC11436875 DOI: 10.1038/s41467-024-52463-7] [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: 12/12/2023] [Accepted: 09/04/2024] [Indexed: 09/29/2024] Open
Abstract
Unsolved Mendelian cases often lack obvious pathogenic coding variants, suggesting potential non-coding etiologies. Here, we present a single cell multi-omic framework integrating embryonic mouse chromatin accessibility, histone modification, and gene expression assays to discover cranial motor neuron (cMN) cis-regulatory elements and subsequently nominate candidate non-coding variants in the congenital cranial dysinnervation disorders (CCDDs), a set of Mendelian disorders altering cMN development. We generate single cell epigenomic profiles for ~86,000 cMNs and related cell types, identifying ~250,000 accessible regulatory elements with cognate gene predictions for ~145,000 putative enhancers. We evaluate enhancer activity for 59 elements using an in vivo transgenic assay and validate 44 (75%), demonstrating that single cell accessibility can be a strong predictor of enhancer activity. Applying our cMN atlas to 899 whole genome sequences from 270 genetically unsolved CCDD pedigrees, we achieve significant reduction in our variant search space and nominate candidate variants predicted to regulate known CCDD disease genes MAFB, PHOX2A, CHN1, and EBF3 - as well as candidates in recurrently mutated enhancers through peak- and gene-centric allelic aggregation. This work delivers non-coding variant discoveries of relevance to CCDDs and a generalizable framework for nominating non-coding variants of potentially high functional impact in other Mendelian disorders.
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Affiliation(s)
- Arthur S Lee
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA.
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Lauren J Ayers
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael Kosicki
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Wai-Man Chan
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Lydia N Fozo
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Brandon M Pratt
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Thomas E Collins
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Boxun Zhao
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Matthew F Rose
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Medical Genetics Training Program, Harvard Medical School, Boston, MA, USA
| | - Alba Sanchis-Juan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jack M Fu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Isaac Wong
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Xuefang Zhao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alan P Tenney
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cassia Lee
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Harvard College, Cambridge, MA, USA
| | - Kristen M Laricchia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brenda J Barry
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Victoria R Bradford
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Julie A Jurgens
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eleina M England
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, NSW, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Eunjung Alice Lee
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Michael E Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Harrison Brand
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Elizabeth C Engle
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA.
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- Medical Genetics Training Program, Harvard Medical School, Boston, MA, USA.
- Department of Ophthalmology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
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18
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Verma K, Croft W, Margielewska-Davies S, Pearce H, Stephens C, Diaconescu D, Bevington S, Craddock C, Amel-Kashipaz R, Zuo J, Kinsella FAM, Moss P. CD70 identifies alloreactive T cells and represents a potential target for prevention and treatment of acute GVHD. Blood Adv 2024; 8:4900-4912. [PMID: 39028952 PMCID: PMC11421336 DOI: 10.1182/bloodadvances.2024012909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 06/08/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024] Open
Abstract
ABSTRACT Graft-versus-host disease (GVHD) remains a major challenge after allogeneic hematopoietic stem cell transplantation (allo-HSCT), and further understanding of its immunopathology is crucial for developing new treatments. CD70 interacts with CD27 and is upregulated transiently on T cells after recent T-cell receptor (TCR) engagement. Here, we investigated the functional and clinical significance of CD70 expression on T cells during the early posttransplantation period. CD70 was expressed on a subset of highly activated memory T cells within the first 2 weeks after transplant, which then gradually declined in most patients. CD70+ T cells exhibited an open chromatin landscape and a transcriptional profile indicative of intense Myelocytomatosis oncogene (MYC)-driven glycolysis and proliferation. CD4+ and CD8+CD70+ T-cell numbers increased by ninefold and fourfold, respectively, during acute GVHD (aGVHD) and displayed an oligoclonal TCR repertoire. These cells expressed CCR4 and CCR6 chemokine receptors and were markedly increased in aGVHD tissue samples. Furthermore, CD70+ T cells demonstrated alloreactive specificity in vitro, and proliferative and inflammatory cytokine responses were markedly attenuated by CD70 blockade. These findings identify CD70 as a marker of highly activated alloreactive T cells and reveal the potential therapeutic importance of inhibiting CD27-CD70 costimulation in both the prophylaxis and treatment of aGVHD.
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Affiliation(s)
- Kriti Verma
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Wayne Croft
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | | | - Hayden Pearce
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Christine Stephens
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Diana Diaconescu
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Sarah Bevington
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Charles Craddock
- Centre for Clinical Haematology, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom
- Warwick Clinical Trials Unit, Warwick University, Coventry, United Kingdom
| | | | - Jianmin Zuo
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Francesca A M Kinsella
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
- Centre for Clinical Haematology, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom
| | - Paul Moss
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
- Centre for Clinical Haematology, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom
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19
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Xia L, Lu J, Qin Y, Huang R, Kong F, Deng Y. Analysis of chromatin accessibility in peripheral blood mononuclear cells from patients with early-stage breast cancer. Front Pharmacol 2024; 15:1465586. [PMID: 39376611 PMCID: PMC11456436 DOI: 10.3389/fphar.2024.1465586] [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: 07/16/2024] [Accepted: 08/27/2024] [Indexed: 10/09/2024] Open
Abstract
Objective: This study was aimed at exploring a specific open region of chromatin in the peripheral blood mononuclear cells (PBMCs) of patients with breast cancer and evaluating its feasibility as a biomarker for diagnosing and predicting breast cancer prognosis. Methods: We obtained PBMCs from breast cancer patients and healthy people for the assay for transposase-accessible chromatin (ATAC) sequencing (n = 3) and obtained the GSE27562 chip sequencing data for secondary analyses. Through bioinformatics analysis, we mined the pattern changes for chromatin accessibility in the PBMCs of breast cancer patients. Results: A total of 1,906 differentially accessible regions (DARs) and 1,632 differentially expressed genes (DEGs) were identified via ATAC sequencing. The upregulated DEGs in the disease group were mainly distributed in the cells, organelles, and cell-intima-related structures and were mainly responsible for biological functions such as cell nitrogen complex metabolism, macromolecular metabolism, and cell communication, in addition to functions such as nucleic acid binding, enzyme binding, hydrolase reaction, and transferase activity. Combined with microarray data analysis, the following set of nine DEGs showed intersection between the ATAC and microarray data: JUN, MSL2, CDC42, TRIB1, SERTAD3, RAB14, RHOB, RAB40B, and PRKDC. HOMER predicted and identified five transcription factors that could potentially bind to these peak sites, namely NFY, Sp 2, GFY, NRF, and ELK 1. Conclusion: Chromatin accessibility analysis of the PBMCs from patients with early-stage breast cancer underscores its potential as a significant avenue for biomarker discovery in breast cancer diagnostics and treatment. By screening the transcription factors and DEGs related to breast cancer, this study provides a comprehensive theoretical foundation that is expected to guide future clinical applications and therapeutic developments.
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Affiliation(s)
- Longjie Xia
- Department of Cosmetology and Plastic Surgery Center, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, China
- Department of General Surgery, Guangzhou First People’s Hospital, Guangzhou, China
| | - Jiamin Lu
- Department of Plastic Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Yixuan Qin
- Department of Cosmetology and Plastic Surgery Center, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, China
| | - Runchun Huang
- Department of Cosmetology and Plastic Surgery Center, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, China
| | - Fanbiao Kong
- Department of Colorectal and Anal Surgery, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, China
| | - Yu Deng
- Department of Plastic Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
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20
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Adams NM, Galitsyna A, Tiniakou I, Esteva E, Lau CM, Reyes J, Abdennur N, Shkolikov A, Yap GS, Khodadadi-Jamayran A, Mirny LA, Reizis B. Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.18.613709. [PMID: 39345451 PMCID: PMC11430140 DOI: 10.1101/2024.09.18.613709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
The cohesin protein complex extrudes chromatin loops, stopping at CTCF-bound sites, to organize chromosomes into topologically associated domains, yet the biological implications of this process are poorly understood. We show that cohesin is required for the post-mitotic differentiation and function of antigen-presenting dendritic cells (DCs), particularly for antigen cross-presentation and IL-12 secretion by type 1 conventional DCs (cDC1s) in vivo. The chromatin organization of DCs was shaped by cohesin and the DC-specifying transcription factor IRF8, which controlled chromatin looping and chromosome compartmentalization, respectively. Notably, optimal expression of IRF8 itself required CTCF/cohesin-binding sites demarcating the Irf8 gene. During DC activation, cohesin was required for the induction of a subset of genes with distal enhancers. Accordingly, the deletion of CTCF sites flanking the Il12b gene reduced IL-12 production by cDC1s. Our data reveal an essential role of cohesin-mediated chromatin regulation in cell differentiation and function in vivo, and its bi-directional crosstalk with lineage-specifying transcription factors.
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Affiliation(s)
- Nicholas M. Adams
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Aleksandra Galitsyna
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ioanna Tiniakou
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Eduardo Esteva
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Colleen M. Lau
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY 14853, USA
| | - Jojo Reyes
- Center for Immunity and Inflammation, Department of Medicine, New Jersey Medical School, Rutgers University, Newark NJ 07101, USA
| | - Nezar Abdennur
- Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | | | - George S. Yap
- Center for Immunity and Inflammation, Department of Medicine, New Jersey Medical School, Rutgers University, Newark NJ 07101, USA
| | - Alireza Khodadadi-Jamayran
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Leonid A. Mirny
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
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21
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Zhang Y, Chen K, Tang SC, Cai Y, Nambu A, See YX, Fu C, Raju A, Lebeau B, Ling Z, Chan JJ, Tay Y, Mutwil M, Lakshmanan M, Tucker-Kellogg G, Chng WJ, Tenen DG, Osato M, Tergaonkar V, Fullwood MJ. Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth. Nat Struct Mol Biol 2024:10.1038/s41594-024-01391-7. [PMID: 39304765 DOI: 10.1038/s41594-024-01391-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 06/28/2024] [Indexed: 09/22/2024]
Abstract
Human silencers have been shown to regulate developmental gene expression. However, the functional importance of human silencers needs to be elucidated, such as whether they can form 'super-silencers' and whether they are linked to cancer progression. Here, we show two silencer components of the FGF18 gene can cooperate through compensatory chromatin interactions to form a super-silencer. Double knockout of two silencers exhibited synergistic upregulation of FGF18 expression and changes in cell identity. To perturb the super-silencers, we applied combinational treatment of an enhancer of zeste homolog 2 inhibitor GSK343, and a repressor element 1-silencing transcription factor inhibitor, X5050 ('GR'). Interestingly, GR led to severe loss of topologically associated domains and loops, which were associated with reduced CTCF and TOP2A mRNA levels. Moreover, GR synergistically upregulated super-silencer-controlled genes related to cell cycle, apoptosis and DNA damage, leading to anticancer effects in vivo. Overall, our data demonstrated a super-silencer example and showed that GR can disrupt super-silencers, potentially leading to cancer ablation.
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Affiliation(s)
- Ying Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Kaijing Chen
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Seng Chuan Tang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yichao Cai
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Akiko Nambu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yi Xiang See
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chaoyu Fu
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Anandhkumar Raju
- Laboratory of NF-κB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Benjamin Lebeau
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Zixun Ling
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jia Jia Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yvonne Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Manikandan Lakshmanan
- Laboratory of NF-κB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Greg Tucker-Kellogg
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Computational Biology Programme, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research (N2CR), Centre for Translational Medicine, Singapore, Singapore
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), National University Health System (NUHS), Singapore, Singapore
| | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Harvard Stem Cells Institute, Harvard Medical School, Boston, MA, USA
| | - Motomi Osato
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Vinay Tergaonkar
- Laboratory of NF-κB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
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22
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Ivanković M, Brand JN, Pandolfini L, Brown T, Pippel M, Rozanski A, Schubert T, Grohme MA, Winkler S, Robledillo L, Zhang M, Codino A, Gustincich S, Vila-Farré M, Zhang S, Papantonis A, Marques A, Rink JC. A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence. Nat Commun 2024; 15:8215. [PMID: 39294119 PMCID: PMC11410931 DOI: 10.1038/s41467-024-52380-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 08/30/2024] [Indexed: 09/20/2024] Open
Abstract
The planarian Schmidtea mediterranea is being studied as a model species for regeneration, but the assembly of planarian genomes remains challenging. Here, we report a high-quality haplotype-phased, chromosome-scale genome assembly of the sexual S2 strain of S. mediterranea and high-quality chromosome-scale assemblies of its three close relatives, S. polychroa, S. nova, and S. lugubris. Using hybrid gene annotations and optimized ATAC-seq and ChIP-seq protocols for regulatory element annotation, we provide valuable genome resources for the planarian research community and a first comparative perspective on planarian genome evolution. Our analyses reveal substantial divergence in protein-coding sequences and regulatory regions but considerable conservation within promoter and enhancer annotations. We also find frequent retrotransposon-associated chromosomal inversions and interchromosomal translocations within the genus Schmidtea and, remarkably, independent and nearly complete losses of ancestral metazoan synteny in Schmidtea and two other flatworm groups. Overall, our results suggest that platyhelminth genomes can evolve without syntenic constraints.
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Affiliation(s)
- Mario Ivanković
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Jeremias N Brand
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Luca Pandolfini
- Center for Human Technologies, Non-coding RNA and RNA-based therapeutics, Istituto Italiano di Tecnologia, Genova, Italy
| | - Thomas Brown
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Andrei Rozanski
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Til Schubert
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Markus A Grohme
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Laura Robledillo
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Meng Zhang
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Azzurra Codino
- Center for Human Technologies, Non-coding RNA and RNA-based therapeutics, Istituto Italiano di Tecnologia, Genova, Italy
| | - Stefano Gustincich
- Center for Human Technologies, Non-coding RNA and RNA-based therapeutics, Istituto Italiano di Tecnologia, Genova, Italy
| | - Miquel Vila-Farré
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Shu Zhang
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jochen C Rink
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
- Faculty of Biology und Psychology, Georg-August-University Göttingen, Göttingen, Germany.
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23
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Hoffman JA, Trotter KW, Archer TK. RNA Polymerase II coordinates histone deacetylation at active promoters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.17.613553. [PMID: 39345547 PMCID: PMC11429789 DOI: 10.1101/2024.09.17.613553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Nucleosomes at actively transcribed promoters have specific histone post-transcriptional modifications and histone variants. These features are thought to contribute to the formation and maintenance of a permissive chromatin environment. Recent reports have drawn conflicting conclusions about whether these histone modifications depend on transcription. We used triptolide to inhibit transcription initiation and degrade RNA Polymerase II and interrogated the effect on histone modifications. Transcription initiation was dispensable for de novo and steady-state histone acetylation at transcription start sites (TSSs) and enhancers. However, at steady state, blocking transcription initiation increased the levels of histone acetylation and H2AZ incorporation at active TSSs. These results demonstrate that deposition of specific histone modifications at TSSs is not dependent on transcription and that transcription limits the maintenance of these marks.
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Affiliation(s)
- Jackson A. Hoffman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health; Research Triangle Park, 27709, NC, USA
| | - Kevin W. Trotter
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health; Research Triangle Park, 27709, NC, USA
| | - Trevor K. Archer
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health; Research Triangle Park, 27709, NC, USA
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He H, Bell SM, Davis AK, Zhao S, Sridharan A, Na CL, Guo M, Xu Y, Snowball J, Swarr DT, Zacharias WJ, Whitsett JA. PRDM3/16 regulate chromatin accessibility required for NKX2-1 mediated alveolar epithelial differentiation and function. Nat Commun 2024; 15:8112. [PMID: 39284798 PMCID: PMC11405758 DOI: 10.1038/s41467-024-52154-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 08/27/2024] [Indexed: 09/20/2024] Open
Abstract
While the critical role of NKX2-1 and its transcriptional targets in lung morphogenesis and pulmonary epithelial cell differentiation is increasingly known, mechanisms by which chromatin accessibility alters the epigenetic landscape and how NKX2-1 interacts with other co-activators required for alveolar epithelial cell differentiation and function are not well understood. Combined deletion of the histone methyl transferases Prdm3 and Prdm16 in early lung endoderm causes perinatal lethality due to respiratory failure from loss of AT2 cells and the accumulation of partially differentiated AT1 cells. Combination of single-cell RNA-seq, bulk ATAC-seq, and CUT&RUN data demonstrate that PRDM3 and PRDM16 regulate chromatin accessibility at NKX2-1 transcriptional targets critical for perinatal AT2 cell differentiation and surfactant homeostasis. Lineage specific deletion of PRDM3/16 in AT2 cells leads to lineage infidelity, with PRDM3/16 null cells acquiring partial AT1 fate. Together, these data demonstrate that NKX2-1-dependent regulation of alveolar epithelial cell differentiation is mediated by epigenomic modulation via PRDM3/16.
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Affiliation(s)
- Hua He
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.
- NHC Key Laboratory of Chronobiology, Sichuan University, Chengdu, Sichuan, China.
| | - Sheila M Bell
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ashley Kuenzi Davis
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Shuyang Zhao
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Anusha Sridharan
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Cheng-Lun Na
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Minzhe Guo
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yan Xu
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - John Snowball
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Daniel T Swarr
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - William J Zacharias
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jeffrey A Whitsett
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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Cheng S, Miao B, Li T, Zhao G, Zhang B. Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae054. [PMID: 39255248 PMCID: PMC11464419 DOI: 10.1093/gpbjnl/qzae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/28/2024] [Accepted: 07/18/2024] [Indexed: 09/12/2024]
Abstract
Efficient and reliable profiling methods are essential to study epigenetics. Tn5, one of the first identified prokaryotic transposases with high DNA-binding and tagmentation efficiency, is widely adopted in different genomic and epigenomic protocols for high-throughputly exploring the genome and epigenome. Based on Tn5, the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and the Cleavage Under Targets and Tagmentation (CUT&Tag) were developed to measure chromatin accessibility and detect DNA-protein interactions. These methodologies can be applied to large amounts of biological samples with low-input levels, such as rare tissues, embryos, and sorted single cells. However, fast and proper processing of these epigenomic data has become a bottleneck because massive data production continues to increase quickly. Furthermore, inappropriate data analysis can generate biased or misleading conclusions. Therefore, it is essential to evaluate the performance of Tn5-based ATAC-seq and CUT&Tag data processing bioinformatics tools, many of which were developed mostly for analyzing chromatin immunoprecipitation followed by sequencing (ChIP-seq) data. Here, we conducted a comprehensive benchmarking analysis to evaluate the performance of eight popular software for processing ATAC-seq and CUT&Tag data. We compared the sensitivity, specificity, and peak width distribution for both narrow-type and broad-type peak calling. We also tested the influence of the availability of control IgG input in CUT&Tag data analysis. Finally, we evaluated the differential analysis strategies commonly used for analyzing the CUT&Tag data. Our study provided comprehensive guidance for selecting bioinformatics tools and recommended analysis strategies, which were implemented into Docker/Singularity images for streamlined data analysis.
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Affiliation(s)
- Siyuan Cheng
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Benpeng Miao
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63108, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Tiandao Li
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Guoyan Zhao
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63108, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Bo Zhang
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63108, USA
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Wang L, Baek S, Prasad G, Wildenthal J, Guo K, Sturgill D, Truongvo T, Char E, Pegoraro G, McKinnon K, Hoskins JW, Amundadottir LT, Arda HE. Predictive Prioritization of Enhancers Associated with Pancreas Disease Risk. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.07.611794. [PMID: 39314336 PMCID: PMC11418953 DOI: 10.1101/2024.09.07.611794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Genetic and epigenetic variations in regulatory enhancer elements increase susceptibility to a range of pathologies. Despite recent advances, linking enhancer elements to target genes and predicting transcriptional outcomes of enhancer dysfunction remain significant challenges. Using 3D chromatin conformation assays, we generated an extensive enhancer interaction dataset for the human pancreas, encompassing more than 20 donors and five major cell types, including both exocrine and endocrine compartments. We employed a network approach to parse chromatin interactions into enhancer-promoter tree models, facilitating a quantitative, genome-wide analysis of enhancer connectivity. With these tree models, we developed a machine learning algorithm to estimate the impact of enhancer perturbations on cell type-specific gene expression in the human pancreas. Orthogonal to our computational approach, we perturbed enhancer function in primary human pancreas cells using CRISPR interference and quantified the effects at the single-cell level through RNA FISH coupled with high-throughput imaging. Our enhancer tree models enabled the annotation of common germline risk variants associated with pancreas diseases, linking them to putative target genes in specific cell types. For pancreatic ductal adenocarcinoma, we found a stronger enrichment of disease susceptibility variants within acinar cell regulatory elements, despite ductal cells historically being assumed as the primary cell-of-origin. Our integrative approach-combining cell type-specific enhancer-promoter interaction mapping, computational models, and single-cell enhancer perturbation assays-produced a robust resource for studying the genetic basis of pancreas disorders.
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Affiliation(s)
- Li Wang
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gauri Prasad
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of Translational Genomics, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - John Wildenthal
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Konnie Guo
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thucnhi Truongvo
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erin Char
- Laboratory of Translational Genomics, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gianluca Pegoraro
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katherine McKinnon
- Vaccine Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | - Jason W. Hoskins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laufey T. Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - H. Efsun Arda
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Xue Y, Yin T, Yuan S, Wang L, Lin H, Jin T, Xu R, Gu J, Shen S, Chen X, Chen Z, Sima N, Chen L, Lu W, Li X, Cheng X, Wang H. CYP1B1 promotes PARPi-resistance via histone H1.4 interaction and increased chromatin accessibility in ovarian cancer. Drug Resist Updat 2024; 77:101151. [PMID: 39395328 DOI: 10.1016/j.drup.2024.101151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 09/05/2024] [Accepted: 09/06/2024] [Indexed: 10/14/2024]
Abstract
INTRODUCTION Ovarian cancer is the most lethal gynecological cancer and presents significant therapeutic challenges. The discovery of synthetic lethality between PARP inhibitors (PARPi) and homologous recombination deficiency marked a new era in treating BRCA1/2-mutated tumors. However, PARPi resistance remains a major clinical challenge. METHODS RNA sequencing was used to identify genes altered by PARPi treatment and LC-MS was used to detect proteins interacting with CYP1B1. Resistance mechanisms were explored through ATAC-seq and gene expression manipulation. Additional techniques, including micrococcal nuclease digestion assays, DAPI staining, and fluorescence microscopy, were used to assess changes in nuclear morphology and chromatin accessibility. RESULTS The gradual exposure of Olaparib has developed a PARPi-resistant cell line, A2780-OlaR, which exhibits significant upregulation of CYP1B1 at both RNA and protein levels. Down-regulating CYP1B1 expression or using specific inhibitors decreased the cellular response to Olaparib. Linker histone H1.4 was identified as associated with CYP1B1. ATAC-seq showed differential chromatin accessibility between A2780-OlaR and parental cells, indicating that the downregulation of H1.4 was associated with increased chromatin accessibility and higher cell viability after Olaparib treatment. CONCLUSION Our findings reveal a novel role for CYP1B1 in driving PARPi resistance through distinct molecular mechanisms in A2780-OlaR. This study highlights the importance of chromatin accessibility in PARPi efficacy and suggests the CYP1B1/H1.4 axis as a promising therapeutic target for overcoming drug resistance in ovarian cancer, offering potentially therapeutic benefits.
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Affiliation(s)
- Yite Xue
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China; Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, Hangzhou, China
| | - Taotao Yin
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China; Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, Hangzhou, China
| | - Shuo Yuan
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China; Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, Hangzhou, China
| | - Lingfang Wang
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China; Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, Hangzhou, China
| | - Hui Lin
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China; Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, Hangzhou, China
| | - Tianzhe Jin
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China; Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, Hangzhou, China
| | - Ruiyi Xu
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China; Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, Hangzhou, China
| | - Jiaxin Gu
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China; Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, Hangzhou, China
| | - Shizhen Shen
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China; Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, Hangzhou, China
| | - Xiaojing Chen
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China; Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, Hangzhou, China
| | - Zhuoye Chen
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China; Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, Hangzhou, China
| | - Ni Sima
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China; Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, Hangzhou, China
| | - Lifeng Chen
- Department of Gynecology, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Weiguo Lu
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China; Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, Hangzhou, China; Cancer Center, Zhejiang University, Hangzhou, China
| | - Xiao Li
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China; Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, Hangzhou, China.
| | - Xiaodong Cheng
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China; Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, Hangzhou, China.
| | - Hui Wang
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China; Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, Hangzhou, China.
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28
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Sun Z, Wang Z, Zhang Y, Li X, Zhou H, Shao S, Cao H, Liu H, Zhang D. SMARCC2 silencing suppresses oncogenic activation through modulation of chromatin accessibility in breast cancer. Biochem Biophys Res Commun 2024; 724:150223. [PMID: 38852505 DOI: 10.1016/j.bbrc.2024.150223] [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: 05/28/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024]
Abstract
SWI/SNF chromatin remodeling complexes play a key role in gene transcription as epigenetic regulators and are typically considered to act as tumor suppressors in cancers. Compared to other cancer-related components of the SWI/SNF complex, research on SMARCC2, a component of the initial BAF core, has been relatively limited. This study aimed to elucidate the role of SMARCC2 in breast cancer by employing various in vitro and in vivo methods including cell proliferation assays, mammosphere formation, and xenograft models, complemented by RNA-seq, ATAC-seq, and ChIP analyses. The results showed that SMARCC2 silencing surprisingly led to the suppression of breast tumorigenesis, indicating a pro-tumorigenic function for SMARCC2 in breast cancer, which contrasts with the roles of other SWI/SNF subunits. In addition, SMARCC2 depletion reduces cancer stem cell features of breast cancer cells. Mechanistic study showed that SMARCC2 silencing downregulated the oncogenic Ras-PI3K signaling pathway, likely by directly regulating the chromatin accessibility of the enhancers of the key genes such as PIK3CB. Together, these results expand our understanding of the SWI/SNF complex's role in cancer development and identify SMARCC2 as a promising new target for breast cancer therapies.
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Affiliation(s)
- Zhaoran Sun
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Xuzhou Medical University, Xuzhou, China
| | - Zhongkun Wang
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Xuzhou Medical University, Xuzhou, China; School of Pharmacy, Bengbu Medical University, Bengbu, Anhui, China
| | - Yirao Zhang
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Xuzhou Medical University, Xuzhou, China
| | - Xue Li
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Xuzhou Medical University, Xuzhou, China
| | - Hanchi Zhou
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Xuzhou Medical University, Xuzhou, China
| | - Simin Shao
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Xuzhou Medical University, Xuzhou, China
| | - Haowei Cao
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Xuzhou Medical University, Xuzhou, China
| | - Hao Liu
- School of Pharmacy, Bengbu Medical University, Bengbu, Anhui, China.
| | - Daoyong Zhang
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Xuzhou Medical University, Xuzhou, China.
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29
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Sharp JA, Sparago E, Thomas R, Alimenti K, Wang W, Blower MD. Role of the SAF-A SAP domain in X inactivation, transcription, splicing, and cell proliferation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.09.612041. [PMID: 39314300 PMCID: PMC11419091 DOI: 10.1101/2024.09.09.612041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
SAF-A is conserved throughout vertebrates and has emerged as an important factor regulating a multitude of nuclear functions, including lncRNA localization, gene expression, and splicing. SAF-A has several functional domains, including an N-terminal SAP domain that binds directly to DNA. Phosphorylation of SAP domain serines S14 and S26 are important for SAF-A localization and function during mitosis, however whether these serines are involved in interphase functions of SAF-A is not known. In this study we tested for the role of the SAP domain, and SAP domain serines S14 and S26 in X chromosome inactivation, protein dynamics, gene expression, splicing, and cell proliferation. Here we show that the SAP domain serines S14 and S26 are required to maintain XIST RNA localization and polycomb-dependent histone modifications on the inactive X chromosome in female cells. In addition, we present evidence that an Xi localization signal resides in the SAP domain. We found that that the SAP domain is not required to maintain gene expression and plays only a minor role in mRNA splicing. In contrast, the SAF-A SAP domain, in particular serines S14 and S26, are required for normal protein dynamics, and to maintain normal cell proliferation. We propose a model whereby dynamic phosphorylation of SAF-A serines S14 and S26 mediates rapid turnover of SAF-A interactions with DNA during interphase.
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Affiliation(s)
- Judith A Sharp
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, 72 E. Concord St, K112, Boston, MA 02118
| | - Emily Sparago
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, 72 E. Concord St, K112, Boston, MA 02118
| | - Rachael Thomas
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, 72 E. Concord St, K112, Boston, MA 02118
| | - Kaitlyn Alimenti
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, 72 E. Concord St, K112, Boston, MA 02118
| | - Wei Wang
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, 72 E. Concord St, K112, Boston, MA 02118
| | - Michael D Blower
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, 72 E. Concord St, K112, Boston, MA 02118
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30
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Khoroshkin M, Buyan A, Dodel M, Navickas A, Yu J, Trejo F, Doty A, Baratam R, Zhou S, Lee SB, Joshi T, Garcia K, Choi B, Miglani S, Subramanyam V, Modi H, Carpenter C, Markett D, Corces MR, Mardakheh FK, Kulakovskiy IV, Goodarzi H. Systematic identification of post-transcriptional regulatory modules. Nat Commun 2024; 15:7872. [PMID: 39251607 PMCID: PMC11385195 DOI: 10.1038/s41467-024-52215-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 08/27/2024] [Indexed: 09/11/2024] Open
Abstract
In our cells, a limited number of RNA binding proteins (RBPs) are responsible for all aspects of RNA metabolism across the entire transcriptome. To accomplish this, RBPs form regulatory units that act on specific target regulons. However, the landscape of RBP combinatorial interactions remains poorly explored. Here, we perform a systematic annotation of RBP combinatorial interactions via multimodal data integration. We build a large-scale map of RBP protein neighborhoods by generating in vivo proximity-dependent biotinylation datasets of 50 human RBPs. In parallel, we use CRISPR interference with single-cell readout to capture transcriptomic changes upon RBP knockdowns. By combining these physical and functional interaction readouts, along with the atlas of RBP mRNA targets from eCLIP assays, we generate an integrated map of functional RBP interactions. We then use this map to match RBPs to their context-specific functions and validate the predicted functions biochemically for four RBPs. This study provides a detailed map of RBP interactions and deconvolves them into distinct regulatory modules with annotated functions and target regulons. This multimodal and integrative framework provides a principled approach for studying post-transcriptional regulatory processes and enriches our understanding of their underlying mechanisms.
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Affiliation(s)
- Matvei Khoroshkin
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Andrey Buyan
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - Martin Dodel
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Albertas Navickas
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Institut Curie, UMR3348 CNRS, Inserm, Orsay, France
| | - Johnny Yu
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Fathima Trejo
- College of Arts and Sciences, University of San Francisco, San Francisco, CA, USA
| | - Anthony Doty
- College of Arts and Sciences, University of San Francisco, San Francisco, CA, USA
| | - Rithvik Baratam
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Shaopu Zhou
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Sean B Lee
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Tanvi Joshi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Kristle Garcia
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Benedict Choi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Sohit Miglani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Vishvak Subramanyam
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Hailey Modi
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Christopher Carpenter
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel Markett
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - M Ryan Corces
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Faraz K Mardakheh
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Ivan V Kulakovskiy
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia.
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
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31
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Assa G, Kalter N, Rosenberg M, Beck A, Markovich O, Gontmakher T, Hendel A, Yakhini Z. Quantifying allele-specific CRISPR editing activity with CRISPECTOR2.0. Nucleic Acids Res 2024; 52:e78. [PMID: 39077930 PMCID: PMC11381363 DOI: 10.1093/nar/gkae651] [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: 10/17/2023] [Revised: 06/24/2024] [Accepted: 07/18/2024] [Indexed: 07/31/2024] Open
Abstract
Off-target effects present a significant impediment to the safe and efficient use of CRISPR-Cas genome editing. Since off-target activity is influenced by the genomic sequence, the presence of sequence variants leads to varying on- and off-target profiles among different alleles or individuals. However, a reliable tool that quantifies genome editing activity in an allelic context is not available. Here, we introduce CRISPECTOR2.0, an extended version of our previously published software tool CRISPECTOR, with an allele-specific editing activity quantification option. CRISPECTOR2.0 enables reference-free, allele-aware, precise quantification of on- and off-target activity, by using de novo sample-specific single nucleotide variant (SNV) detection and statistical-based allele-calling algorithms. We demonstrate CRISPECTOR2.0 efficacy in analyzing samples containing multiple alleles and quantifying allele-specific editing activity, using data from diverse cell types, including primary human cells, plants, and an original extensive human cell line database. We identified instances where an SNV induced changes in the protospacer adjacent motif sequence, resulting in allele-specific editing. Intriguingly, differential allelic editing was also observed in regions carrying distal SNVs, hinting at the involvement of additional epigenetic factors. Our findings highlight the importance of allele-specific editing measurement as a milestone in the adaptation of efficient, accurate, and safe personalized genome editing.
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Affiliation(s)
- Guy Assa
- Arazi School of Computer Science, Reichman University, Herzliya 4610101, Israel
| | - Nechama Kalter
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Michael Rosenberg
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Avigail Beck
- Arazi School of Computer Science, Reichman University, Herzliya 4610101, Israel
| | - Oshry Markovich
- Rahan Meristem (1998) Ltd. Kibbutz Rosh-Hanikra, Western Galilee 2282500, Israel
| | - Tanya Gontmakher
- Rahan Meristem (1998) Ltd. Kibbutz Rosh-Hanikra, Western Galilee 2282500, Israel
| | - Ayal Hendel
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Zohar Yakhini
- Arazi School of Computer Science, Reichman University, Herzliya 4610101, Israel
- The Henry & Marilyn Taub Faculty of Computer Science, Technion - Israel Institute of Technology, Haifa 3200003, Israel
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32
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Launonen KM, Varis V, Aaltonen N, Niskanen EA, Varjosalo M, Paakinaho V, Palvimo JJ. Central role of SUMOylation in the regulation of chromatin interactions and transcriptional outputs of the androgen receptor in prostate cancer cells. Nucleic Acids Res 2024; 52:9519-9535. [PMID: 39106160 PMCID: PMC11381344 DOI: 10.1093/nar/gkae653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 06/17/2024] [Accepted: 07/17/2024] [Indexed: 08/09/2024] Open
Abstract
The androgen receptor (AR) is pivotal in prostate cancer (PCa) progression and represents a critical therapeutic target. AR-mediated gene regulation involves intricate interactions with nuclear proteins, with many mediating and undergoing post-translational modifications that present alternative therapeutic avenues. Through chromatin proteomics in PCa cells, we identified SUMO ligases together with nuclear receptor coregulators and pioneer transcription factors within the AR's protein network. Intriguingly, this network displayed a significant association with SUMO2/3. To elucidate the influence of SUMOylation on AR chromatin interactions and subsequent gene regulation, we inhibited SUMOylation using ML-792 (SUMOi). While androgens generally facilitated the co-occupancy of SUMO2/3 and AR on chromatin, SUMOi induced divergent effects dependent on the type of AR-binding site (ARB). SUMOi augmented AR's pioneer-like binding on inaccessible chromatin regions abundant in androgen response elements (AREs) and diminished its interaction with accessible chromatin regions sparse in AREs yet rich in pioneer transcription factor motifs. The SUMOi-impacted ARBs divergently influenced AR-regulated genes; those associated with AR-mediated activation played roles in negative regulation of cell proliferation, while those with AR-mediated repression were involved in pattern formation. In conclusion, our findings underscore the pervasive influence of SUMOylation in shaping AR's role in PCa cells, potentially unveiling new therapeutic strategies.
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Affiliation(s)
- Kaisa-Mari Launonen
- Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Vera Varis
- Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Niina Aaltonen
- Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Einari A Niskanen
- Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- HiLIFE-Proteomics Unit, University of Helsinki, Helsinki, Finland
| | - Ville Paakinaho
- Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Jorma J Palvimo
- Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
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33
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Protti G, Spreafico R. A primer on single-cell RNA-seq analysis using dendritic cells as a case study. FEBS Lett 2024. [PMID: 39245787 DOI: 10.1002/1873-3468.15009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/18/2024] [Accepted: 08/12/2024] [Indexed: 09/10/2024]
Abstract
Recent advances in single-cell (sc) transcriptomics have revolutionized our understanding of dendritic cells (DCs), pivotal players of the immune system. ScRNA-sequencing (scRNA-seq) has unraveled a previously unrecognized complexity and heterogeneity of DC subsets, shedding light on their ontogeny and specialized roles. However, navigating the rapid technological progress and computational methods can be daunting for researchers unfamiliar with the field. This review aims to provide immunologists with a comprehensive introduction to sc transcriptomic analysis, offering insights into recent developments in DC biology. Addressing common analytical queries, we guide readers through popular tools and methodologies, supplemented with references to benchmarks and tutorials for in-depth understanding. By examining findings from pioneering studies, we illustrate how computational techniques have expanded our knowledge of DC biology. Through this synthesis, we aim to equip researchers with the necessary tools and knowledge to navigate and leverage scRNA-seq for unraveling the intricacies of DC biology and advancing immunological research.
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Affiliation(s)
- Giulia Protti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Roberto Spreafico
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA
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34
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Chai C, Gibson J, Li P, Pampari A, Patel A, Kundaje A, Wang B. Flexible use of conserved motif vocabularies constrains genome access in cell type evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.03.611027. [PMID: 39282369 PMCID: PMC11398382 DOI: 10.1101/2024.09.03.611027] [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: 09/25/2024]
Abstract
Cell types evolve into a hierarchy with related types grouped into families. How cell type diversification is constrained by the stable separation between families over vast evolutionary times remains unknown. Here, integrating single-nucleus multiomic sequencing and deep learning, we show that hundreds of sequence features (motifs) divide into distinct sets associated with accessible genomes of specific cell type families. This division is conserved across highly divergent, early-branching animals including flatworms and cnidarians. While specific interactions between motifs delineate cell type relationships within families, surprisingly, these interactions are not conserved between species. Consistently, while deep learning models trained on one species can predict accessibility of other species' sequences, their predictions frequently rely on distinct, but synonymous, motif combinations. We propose that long-term stability of cell type families is maintained through genome access specified by conserved motif sets, or 'vocabularies', whereas cell types diversify through flexible use of motifs within each set.
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Affiliation(s)
- Chew Chai
- Department of Bioengineering, Stanford University, Stanford, USA
| | - Jesse Gibson
- Department of Bioengineering, Stanford University, Stanford, USA
| | - Pengyang Li
- Department of Bioengineering, Stanford University, Stanford, USA
| | - Anusri Pampari
- Department of Computer Science, Stanford University, Stanford, USA
| | - Aman Patel
- Department of Computer Science, Stanford University, Stanford, USA
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, USA
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, USA
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35
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Wenz BM, He Y, Chen NC, Pickrell JK, Li JH, Dudek MF, Li T, Keener R, Voight BF, Brown CD, Battle A. Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.04.610850. [PMID: 39282458 PMCID: PMC11398312 DOI: 10.1101/2024.09.04.610850] [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: 09/21/2024]
Abstract
Background Understanding the genetic causes for variability in chromatin accessibility can shed light on the molecular mechanisms through which genetic variants may affect complex traits. Thousands of ATAC-seq samples have been collected that hold information about chromatin accessibility across diverse cell types and contexts, but most of these are not paired with genetic information and come from diverse distinct projects and laboratories. Results We report here joint genotyping, chromatin accessibility peak calling, and discovery of quantitative trait loci which influence chromatin accessibility (caQTLs), demonstrating the capability of performing caQTL analysis on a large scale in a diverse sample set without pre-existing genotype information. Using 10,293 profiling samples representing 1,454 unique donor individuals across 653 studies from public databases, we catalog 23,381 caQTLs in total. After joint discovery analysis, we cluster samples based on accessible chromatin profiles to identify context-specific caQTLs. We find that caQTLs are strongly enriched for annotations of gene regulatory elements across diverse cell types and tissues and are often strongly linked with genetic variation associated with changes in expression (eQTLs), indicating that caQTLs can mediate genetic effects on gene expression. We demonstrate sharing of causal variants for chromatin accessibility and diverse complex human traits, enabling a more complete picture of the genetic mechanisms underlying complex human phenotypes. Conclusions Our work provides a proof of principle for caQTL calling from previously ungenotyped samples, and represents one of the largest, most diverse caQTL resources currently available, informing mechanisms of genetic regulation of gene expression and contribution to disease.
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Affiliation(s)
- Brandon M Wenz
- Genetics and Epigenetics Program, Cell and Molecular Biology Graduate Group, Biomedical Graduate Studies, University of Pennsylvania - Perelman School of Medicine, Philadelphia PA 19104
| | - Yuan He
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, 21218
| | - Nae-Chyun Chen
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, 21218
| | | | | | - Max F Dudek
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Taibo Li
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, 21218
| | - Rebecca Keener
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, 21218
| | - Benjamin F Voight
- Department of Genetics, University of Pennsylvania - Perelman School of Medicine, Philadelphia, PA, 19104
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania - Perelman School of Medicine, Philadelphia PA, 19104
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania - Perelman School of Medicine, Philadelphia, PA, 19104
| | - Christopher D Brown
- Department of Genetics, University of Pennsylvania - Perelman School of Medicine, Philadelphia, PA, 19104
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, 21218
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, 21218
- Department of Genetic Medicine, Johns Hopkins University; Baltimore, MD, 21218
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, 21218
- Data Science and AI Institute, Johns Hopkins University, Baltimore, MD, 21218
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36
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Califano J, Nakagawa T, Luebeck J, Zhu K, Lange J, Sasik R, Phillips C, Sadat S, Javadzadeh S, Yang Q, Wang A, Pestonjamasp K, Rosenthal S, Fisch K, Mischel P, Bafna V. Inhibition of novel human-HPV hybrid ecDNA enhancers reduces oncogene expression and tumor growth in oropharyngeal cancer. RESEARCH SQUARE 2024:rs.3.rs-4636308. [PMID: 39281879 PMCID: PMC11398563 DOI: 10.21203/rs.3.rs-4636308/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/18/2024]
Abstract
Extrachromosomal circular DNA (ecDNA) have been found in most types of human cancers, and ecDNA incorporating viral genomes has recently been described, specifically in human papillomavirus (HPV)-mediated oropharyngeal cancer (OPC). However, the molecular mechanisms of human-viral hybrid ecDNA (hybrid ecDNA) for carcinogenesis remains elusive. We characterized the epigenetic status of hybrid ecDNA using HPVOPC cell lines and patient-derived tumor xenografts, identifying HPV oncogenes E6/E7 in hybrid ecDNA were flanked by novel somatic DNA enhancers and HPV L1 enhancers, with strong cis-interaction. Targeting of these enhancers by clustered regularly interspaced short palindromic repeats interference or hybrid ecDNA by bromodomain and extra-terminal inhibitor reduced E6/E7 expression, and significantly inhibited in vitro and/or in vivo growth only in ecDNA(+) models. HPV DNA in hybrid ecDNA structures are associated with novel somatic and HPV enhancers in hybrid ecDNA that drive HPV ongogene expression and carcinogenesis, and can be targeted with ecDNA disrupting therapeutics.
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37
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Jena SG, Verma A, Engelhardt BE. Answering open questions in biology using spatial genomics and structured methods. BMC Bioinformatics 2024; 25:291. [PMID: 39232666 PMCID: PMC11375982 DOI: 10.1186/s12859-024-05912-5] [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: 10/10/2023] [Accepted: 08/22/2024] [Indexed: 09/06/2024] Open
Abstract
Genomics methods have uncovered patterns in a range of biological systems, but obscure important aspects of cell behavior: the shapes, relative locations, movement, and interactions of cells in space. Spatial technologies that collect genomic or epigenomic data while preserving spatial information have begun to overcome these limitations. These new data promise a deeper understanding of the factors that affect cellular behavior, and in particular the ability to directly test existing theories about cell state and variation in the context of morphology, location, motility, and signaling that could not be tested before. Rapid advancements in resolution, ease-of-use, and scale of spatial genomics technologies to address these questions also require an updated toolkit of statistical methods with which to interrogate these data. We present a framework to respond to this new avenue of research: four open biological questions that can now be answered using spatial genomics data paired with methods for analysis. We outline spatial data modalities for each open question that may yield specific insights, discuss how conflicting theories may be tested by comparing the data to conceptual models of biological behavior, and highlight statistical and machine learning-based tools that may prove particularly helpful to recover biological understanding.
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Affiliation(s)
- Siddhartha G Jena
- Department of Stem Cell and Regenerative Biology, Harvard, 7 Divinity Ave, Cambridge, MA, USA
| | - Archit Verma
- Gladstone Institutes, 1650 Owens Street, San Francisco, CA, 94158, USA
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38
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Saeki N, Inui-Yamamoto C, Ikeda Y, Kanai R, Hata K, Itoh S, Inubushi T, Akiyama S, Ohba S, Abe M. Deletion of Trps1 regulatory elements recapitulates postnatal hip joint abnormalities and growth retardation of Trichorhinophalangeal syndrome in mice. Hum Mol Genet 2024; 33:1618-1629. [PMID: 38899779 DOI: 10.1093/hmg/ddae102] [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: 02/27/2024] [Revised: 05/09/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024] Open
Abstract
Trichorhinophalangeal syndrome (TRPS) is a genetic disorder caused by point mutations or deletions in the gene-encoding transcription factor TRPS1. TRPS patients display a range of skeletal dysplasias, including reduced jaw size, short stature, and a cone-shaped digit epiphysis. Certain TRPS patients experience early onset coxarthrosis that leads to a devastating drop in their daily activities. The etiologies of congenital skeletal abnormalities of TRPS were revealed through the analysis of Trps1 mutant mouse strains. However, early postnatal lethality in Trps1 knockout mice has hampered the study of postnatal TRPS pathology. Here, through epigenomic analysis we identified two previously uncharacterized candidate gene regulatory regions in the first intron of Trps1. We deleted these regions, either individually or simultaneously, and examined their effects on skeletal morphogenesis. Animals that were deleted individually for either region displayed only modest phenotypes. In contrast, the Trps1Δint/Δint mouse strain with simultaneous deletion of both genomic regions exhibit postnatal growth retardation. This strain displayed delayed secondary ossification center formation in the long bones and misshaped hip joint development that resulted in acetabular dysplasia. Reducing one allele of the Trps1 gene in Trps1Δint mice resulted in medial patellar dislocation that has been observed in some patients with TRPS. Our novel Trps1 hypomorphic strain recapitulates many postnatal pathologies observed in human TRPS patients, thus positioning this strain as a useful animal model to study postnatal TRPS pathogenesis. Our observations also suggest that Trps1 gene expression is regulated through several regulatory elements, thus guaranteeing robust expression maintenance in skeletal cells.
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Affiliation(s)
- Naoya Saeki
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
- Department of Special Needs Dentistry, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Chizuko Inui-Yamamoto
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Yuki Ikeda
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Rinna Kanai
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
- Department of Fixed Prosthodontics and Orofacial Function, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Kenji Hata
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Shousaku Itoh
- Department of Restorative Dentistry and Endodontology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Toshihiro Inubushi
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Shigehisa Akiyama
- Department of Special Needs Dentistry, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Shinsuke Ohba
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Makoto Abe
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
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39
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El Zarif T, Meador CB, Qiu X, Seo JH, Davidsohn MP, Savignano H, Lakshminarayanan G, McClure HM, Canniff J, Fortunato B, Li R, Banwait MK, Semaan K, Eid M, Long H, Hung YP, Mahadevan NR, Barbie DA, Oser MG, Piotrowska Z, Choueiri TK, Baca SC, Hata AN, Freedman ML, Berchuck JE. Detecting Small Cell Transformation in Patients with Advanced EGFR Mutant Lung Adenocarcinoma through Epigenomic cfDNA Profiling. Clin Cancer Res 2024; 30:3798-3811. [PMID: 38912901 PMCID: PMC11369616 DOI: 10.1158/1078-0432.ccr-24-0466] [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: 02/09/2024] [Revised: 04/04/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024]
Abstract
PURPOSE Histologic transformation to small cell lung cancer (SCLC) is a mechanism of treatment resistance in patients with advanced oncogene-driven lung adenocarcinoma (LUAD) that currently requires histologic review for diagnosis. Herein, we sought to develop an epigenomic cell-free DNA (cfDNA)-based approach to noninvasively detect small cell transformation in patients with EGFR mutant (EGFRm) LUAD. EXPERIMENTAL DESIGN To characterize the epigenomic landscape of transformed (t)SCLC relative to LUAD and de novo SCLC, we performed chromatin immunoprecipitation sequencing (ChIP-seq) to profile the histone modifications H3K27ac, H3K4me3, and H3K27me3; methylated DNA immunoprecipitation sequencing (MeDIP-seq); assay for transposase-accessible chromatin sequencing; and RNA sequencing on 26 lung cancer patient-derived xenograft (PDX) tumors. We then generated and analyzed H3K27ac ChIP-seq, MeDIP-seq, and whole genome sequencing cfDNA data from 1 mL aliquots of plasma from patients with EGFRm LUAD with or without tSCLC. RESULTS Analysis of 126 epigenomic libraries from the lung cancer PDXs revealed widespread epigenomic reprogramming between LUAD and tSCLC, with a large number of differential H3K27ac (n = 24,424), DNA methylation (n = 3,298), and chromatin accessibility (n = 16,352) sites between the two histologies. Tumor-informed analysis of each of these three epigenomic features in cfDNA resulted in accurate noninvasive discrimination between patients with EGFRm LUAD versus tSCLC [area under the receiver operating characteristic curve (AUROC) = 0.82-0.87]. A multianalyte cfDNA-based classifier integrating these three epigenomic features discriminated between EGFRm LUAD versus tSCLC with an AUROC of 0.94. CONCLUSIONS These data demonstrate the feasibility of detecting small cell transformation in patients with EGFRm LUAD through epigenomic cfDNA profiling of 1 mL of patient plasma.
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Affiliation(s)
- Talal El Zarif
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Department of Medicine, Yale School of Medicine, New Haven, Connecticut.
| | - Catherine B. Meador
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.
| | - Xintao Qiu
- Department of Medicine, Yale School of Medicine, New Haven, Connecticut.
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.
| | - Matthew P. Davidsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.
| | - Hunter Savignano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.
| | - Gitanjali Lakshminarayanan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.
| | - Heather M. McClure
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.
| | - John Canniff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.
| | - Brad Fortunato
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.
| | - Rong Li
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.
| | - Mandeep K. Banwait
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.
| | - Karl Semaan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Eli and Edythe L. Broad Institute, Cambridge, Massachusetts.
| | - Marc Eid
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.
| | - Henry Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.
| | - Yin P. Hung
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.
| | - Navin R. Mahadevan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts.
| | - David A. Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
| | - Matthew G. Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
| | - Zofia Piotrowska
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.
| | - Toni K. Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
| | - Sylvan C. Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Eli and Edythe L. Broad Institute, Cambridge, Massachusetts.
| | - Aaron N. Hata
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.
| | - Matthew L. Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Eli and Edythe L. Broad Institute, Cambridge, Massachusetts.
| | - Jacob E. Berchuck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
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40
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Safi R, Wardell SE, Watkinson P, Qin X, Lee M, Park S, Krebs T, Dolan EL, Blattler A, Tsuji T, Nayak S, Khater M, Fontanillo C, Newlin MA, Kirkland ML, Xie Y, Long H, Fink EC, Fanning SW, Runyon S, Brown M, Xu S, Owzar K, Norris JD, McDonnell DP. Androgen receptor monomers and dimers regulate opposing biological processes in prostate cancer cells. Nat Commun 2024; 15:7675. [PMID: 39227594 PMCID: PMC11371910 DOI: 10.1038/s41467-024-52032-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: 11/04/2023] [Accepted: 08/23/2024] [Indexed: 09/05/2024] Open
Abstract
Most prostate cancers express the androgen receptor (AR), and tumor growth and progression are facilitated by exceptionally low levels of systemic or intratumorally produced androgens. Thus, absolute inhibition of the androgen signaling axis remains the goal of current therapeutic approaches to treat prostate cancer (PCa). Paradoxically, high dose androgens also exhibit considerable efficacy as a treatment modality in patients with late-stage metastatic PCa. Here we show that low levels of androgens, functioning through an AR monomer, facilitate a non-genomic activation of the mTOR signaling pathway to drive proliferation. Conversely, high dose androgens facilitate the formation of AR dimers/oligomers to suppress c-MYC expression, inhibit proliferation and drive a transcriptional program associated with a differentiated phenotype. These findings highlight the inherent liabilities in current approaches used to inhibit AR action in PCa and are instructive as to strategies that can be used to develop new therapeutics for this disease and other androgenopathies.
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Affiliation(s)
- Rachid Safi
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Suzanne E Wardell
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Paige Watkinson
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Xiaodi Qin
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA
| | - Marissa Lee
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA
| | - Sunghee Park
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Taylor Krebs
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Emma L Dolan
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Adam Blattler
- Oncogenesis Thematic Research Center, Bristol Myers Squibb, San Diego, CA, USA
| | - Toshiya Tsuji
- Oncogenesis Thematic Research Center, Bristol Myers Squibb, San Diego, CA, USA
| | - Surendra Nayak
- Oncogenesis Thematic Research Center, Bristol Myers Squibb, San Diego, CA, USA
| | - Marwa Khater
- Informatics and Predictive Sciences, Bristol Myers Squibb, San Diego, CA, USA
| | - Celia Fontanillo
- Informatics and Predictive Sciences, Bristol Myers Squibb, San Diego, CA, USA
| | - Madeline A Newlin
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Megan L Kirkland
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | | | - Henry Long
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Emma C Fink
- Department of Cancer Biology, Loyola University, Maywood, IL, USA
| | - Sean W Fanning
- Department of Cancer Biology, Loyola University, Maywood, IL, USA
| | - Scott Runyon
- RTI International, Research Triangle Park, NC, USA
| | - Myles Brown
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shuichan Xu
- Oncogenesis Thematic Research Center, Bristol Myers Squibb, San Diego, CA, USA
| | - Kouros Owzar
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - John D Norris
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Donald P McDonnell
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA.
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41
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He M, Zong X, Xu B, Qi W, Huang W, Djekidel MN, Zhang Y, Pagala VR, Li J, Hao X, Guy C, Bai L, Cross R, Li C, Peng J, Feng Y. Dynamic Foxp3-chromatin interaction controls tunable Treg cell function. J Exp Med 2024; 221:e20232068. [PMID: 38935023 PMCID: PMC11211070 DOI: 10.1084/jem.20232068] [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: 11/10/2023] [Revised: 04/11/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Nuclear factor Foxp3 determines regulatory T (Treg) cell fate and function via mechanisms that remain unclear. Here, we investigate the nature of Foxp3-mediated gene regulation in suppressing autoimmunity and antitumor immune response. Contrasting with previous models, we find that Foxp3-chromatin binding is regulated by Treg activation states, tumor microenvironment, and antigen and cytokine stimulations. Proteomics studies uncover dynamic proteins within Foxp3 proximity upon TCR or IL-2 receptor signaling in vitro, reflecting intricate interactions among Foxp3, signal transducers, and chromatin. Pharmacological inhibition and genetic knockdown experiments indicate that NFAT and AP-1 protein Batf are required for enhanced Foxp3-chromatin binding in activated Treg cells and tumor-infiltrating Treg cells to modulate target gene expression. Furthermore, mutations at the Foxp3 DNA-binding domain destabilize the Foxp3-chromatin association. These representative settings delineate context-dependent Foxp3-chromatin interaction, suggesting that Foxp3 associates with chromatin by hijacking DNA-binding proteins resulting from Treg activation or differentiation, which is stabilized by direct Foxp3-DNA binding, to dynamically regulate Treg cell function according to immunological contexts.
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Affiliation(s)
- Minghong He
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Xinying Zong
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Wenjie Qi
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Wenjun Huang
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | | | - Yang Zhang
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Vishwajeeth R. Pagala
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jun Li
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Xiaolei Hao
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Clifford Guy
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Lu Bai
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Richard Cross
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Junmin Peng
- Department of Structure Biology and Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Yongqiang Feng
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
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42
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Stewart KS, Abdusselamoglu MD, Tierney MT, Gola A, Hur YH, Gonzales KAU, Yuan S, Bonny AR, Yang Y, Infarinato NR, Cowley CJ, Levorse JM, Pasolli HA, Ghosh S, Rothlin CV, Fuchs E. Stem cells tightly regulate dead cell clearance to maintain tissue fitness. Nature 2024; 633:407-416. [PMID: 39169186 PMCID: PMC11390485 DOI: 10.1038/s41586-024-07855-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/19/2024] [Indexed: 08/23/2024]
Abstract
Billions of cells are eliminated daily from our bodies1-4. Although macrophages and dendritic cells are dedicated to migrating and engulfing dying cells and debris, many epithelial and mesenchymal tissue cells can digest nearby apoptotic corpses1-4. How these non-motile, non-professional phagocytes sense and eliminate dying cells while maintaining their normal tissue functions is unclear. Here we explore the mechanisms that underlie their multifunctionality by exploiting the cyclical bouts of tissue regeneration and degeneration during hair cycling. We show that hair follicle stem cells transiently unleash phagocytosis at the correct time and place through local molecular triggers that depend on both lipids released by neighbouring apoptotic corpses and retinoids released by healthy counterparts. We trace the heart of this dual ligand requirement to RARγ-RXRα, whose activation enables tight regulation of apoptotic cell clearance genes and provides an effective, tunable mechanism to offset phagocytic duties against the primary stem cell function of preserving tissue integrity during homeostasis. Finally, we provide functional evidence that hair follicle stem cell-mediated phagocytosis is not simply redundant with professional phagocytes but rather has clear benefits to tissue fitness. Our findings have broad implications for other non-motile tissue stem or progenitor cells that encounter cell death in an immune-privileged niche.
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Affiliation(s)
- Katherine S Stewart
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA.
| | - Merve Deniz Abdusselamoglu
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Matthew T Tierney
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Anita Gola
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Yun Ha Hur
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Kevin A U Gonzales
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Department of Discovery Technology and Genomics, Novo Nordisk Research Centre Oxford, Oxford, UK
| | - Shaopeng Yuan
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Altos Labs, Cambridge Institute of Science, Granta Park, Cambridge, UK
| | - Alain R Bonny
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Yihao Yang
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Altos Labs, San Diego, CA, USA
| | - Nicole R Infarinato
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- PrecisionScienta, Yardley, PA, USA
| | - Christopher J Cowley
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John M Levorse
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Cardiovascular Research Group, Temple University, Philadelphia, PA, USA
| | - Hilda Amalia Pasolli
- Electron Microscopy Resource Center, The Rockefeller University, New York, NY, USA
| | - Sourav Ghosh
- Departments of Neurology and Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Carla V Rothlin
- Departments of Immunobiology and Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Elaine Fuchs
- Howard Hughes Medical Institute, Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA.
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Li F, Tian J, Zhang L, He H, Song D. A multi-omics approach to reveal critical mechanisms of activator protein 1 (AP-1). Biomed Pharmacother 2024; 178:117225. [PMID: 39084078 DOI: 10.1016/j.biopha.2024.117225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 08/02/2024] Open
Abstract
The Activator Protein 1 (AP-1) transcription factor complex plays a pivotal role in the regulation of cancer-related genes, influencing cancer cell proliferation, invasion, migration, angiogenesis, and apoptosis. Composed of multiple subunits, AP-1 has diverse roles across different cancer types and environmental contexts, but its specific mechanisms remain unclear. The advent of multi-omics approaches has shed light on a more comprehensive understanding of AP-1's role and mechanism in gene regulation. This review collates recent genome-wide data on AP-1 and provides an overview of its expression, structure, function, and interaction across different diseases. An examination of these findings can illuminate the intricate nature of AP-1 regulation and its significant involvement in the progression of different diseases. Moreover, we discuss the potential use of AP-1 as a target for individual therapy and explore the various challenges associated with such an approach. Ultimately, this review provides valuable insights into the biology of AP-1 and its potential as a therapeutic target for cancer and disease treatments.
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Affiliation(s)
- Fei Li
- Clinical Medical Research Center for Women and Children Diseases, Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan 250014, China; School of Public Health, North China University of Science and Technology, Tangshan 063000, China
| | - Jiaqi Tian
- Clinical Medical Research Center for Women and Children Diseases, Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan 250014, China
| | - Lin Zhang
- Clinical Medical Research Center for Women and Children Diseases, Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan 250014, China
| | - Huan He
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun 130021, China
| | - Dandan Song
- Clinical Medical Research Center for Women and Children Diseases, Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan 250014, China.
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44
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German B, Alaiwi SA, Ho KL, Nanda JS, Fonseca MA, Burkhart DL, Sheahan AV, Bergom HE, Morel KL, Beltran H, Hwang JH, Freedman ML, Lawrenson K, Ellis L. MYBL2 Drives Prostate Cancer Plasticity: Inhibiting Its Transcriptional Target CDK2 for RB1-Deficient Neuroendocrine Prostate Cancer. CANCER RESEARCH COMMUNICATIONS 2024; 4:2295-2307. [PMID: 39113611 PMCID: PMC11368174 DOI: 10.1158/2767-9764.crc-24-0069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 07/05/2024] [Accepted: 08/06/2024] [Indexed: 09/03/2024]
Abstract
Phenotypic plasticity is a recognized mechanism driving therapeutic resistance in patients with prostate cancer. Although underlying molecular causations driving phenotypic plasticity have been identified, therapeutic success is yet to be achieved. To identify putative master regulator transcription factors (MR-TF) driving phenotypic plasticity in prostate cancer, this work utilized a multiomic approach using genetically engineered mouse models of prostate cancer combined with patient data to identify MYB proto-oncogene like 2 (MYBL2) as a significantly enriched transcription factor in prostate cancer exhibiting phenotypic plasticity. Genetic inhibition of Mybl2 using independent murine prostate cancer cell lines representing phenotypic plasticity demonstrated Mybl2 loss significantly decreased in vivo growth as well as cell fitness and repressed gene expression signatures involved in pluripotency and stemness. Because MYBL2 is currently not druggable, a MYBL2 gene signature was employed to identify cyclin-dependent kinase-2 (CDK2) as a potential therapeutic target. CDK2 inhibition phenocopied genetic loss of Mybl2 and significantly decreased in vivo tumor growth associated with enrichment of DNA damage. Together, this work demonstrates MYBL2 as an important MR-TF driving phenotypic plasticity in prostate cancer. Furthermore, high MYBL2 activity identifies prostate cancer that would be responsive to CDK2 inhibition. SIGNIFICANCE Prostate cancers that escape therapy targeting the androgen receptor signaling pathways via phenotypic plasticity are currently untreatable. Our study identifies MYBL2 as a MR-TF in phenotypic plastic prostate cancer and implicates CDK2 inhibition as a novel therapeutic target for this most lethal subtype of prostate cancer.
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Affiliation(s)
- Beatriz German
- Department of Surgery, Center for Prostate Disease Research, Murtha Cancer Center Research Program, Uniformed Services University of the Health Sciences, Bethesda, Maryland.
- Walter Reed National Military Medical Center, Bethesda, Maryland.
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland.
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland.
| | - Sarah A. Alaiwi
- Section of Cardiovascular Medicine, Yale University School of Medicine, New Haven, Connecticut.
| | - Kun-Lin Ho
- Department of Surgery, Center for Prostate Disease Research, Murtha Cancer Center Research Program, Uniformed Services University of the Health Sciences, Bethesda, Maryland.
- Walter Reed National Military Medical Center, Bethesda, Maryland.
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland.
| | - Jagpreet S. Nanda
- Department of Urology, Cedars-Sinai Medical Center, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, California.
| | - Marcos A. Fonseca
- Department of Obstetrics and Gynecology and the Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California.
| | - Deborah L. Burkhart
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
| | - Anjali V. Sheahan
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
| | - Hannah E. Bergom
- Department of Medicine, University of Minnesota-Twin Cities, Minneapolis, Minnesota.
| | - Katherine L. Morel
- South Australian Immunogenomics Cancer Institute, University of Adelaide, Adelaide, Australia.
| | - Himisha Beltran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
| | - Justin H. Hwang
- Department of Medicine, University of Minnesota-Twin Cities, Minneapolis, Minnesota.
| | - Matthew L. Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
| | - Kate Lawrenson
- Department of Obstetrics and Gynecology and the Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California.
- Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California.
| | - Leigh Ellis
- Department of Surgery, Center for Prostate Disease Research, Murtha Cancer Center Research Program, Uniformed Services University of the Health Sciences, Bethesda, Maryland.
- Walter Reed National Military Medical Center, Bethesda, Maryland.
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland.
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland.
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Castillo H, Hanna P, Sachs LM, Buisine N, Godoy F, Gilbert C, Aguilera F, Muñoz D, Boisvert C, Debiais-Thibaud M, Wan J, Spicuglia S, Marcellini S. Xenopus tropicalis osteoblast-specific open chromatin regions reveal promoters and enhancers involved in human skeletal phenotypes and shed light on early vertebrate evolution. Cells Dev 2024; 179:203924. [PMID: 38692409 DOI: 10.1016/j.cdev.2024.203924] [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: 03/09/2024] [Revised: 04/18/2024] [Accepted: 04/26/2024] [Indexed: 05/03/2024]
Abstract
While understanding the genetic underpinnings of osteogenesis has far-reaching implications for skeletal diseases and evolution, a comprehensive characterization of the osteoblastic regulatory landscape in non-mammalian vertebrates is still lacking. Here, we compared the ATAC-Seq profile of Xenopus tropicalis (Xt) osteoblasts to a variety of non mineralizing control tissues, and identified osteoblast-specific nucleosome free regions (NFRs) at 527 promoters and 6747 distal regions. Sequence analyses, Gene Ontology, RNA-Seq and ChIP-Seq against four key histone marks confirmed that the distal regions correspond to bona fide osteogenic transcriptional enhancers exhibiting a shared regulatory logic with mammals. We report 425 regulatory regions conserved with human and globally associated to skeletogenic genes. Of these, 35 regions have been shown to impact human skeletal phenotypes by GWAS, including one trps1 enhancer and the runx2 promoter, two genes which are respectively involved in trichorhinophalangeal syndrome type I and cleidocranial dysplasia. Intriguingly, 60 osteoblastic NFRs also align to the genome of the elephant shark, a species lacking osteoblasts and bone tissue. To tackle this paradox, we chose to focus on dlx5 because its conserved promoter, known to integrate regulatory inputs during mammalian osteogenesis, harbours an osteoblast-specific NFR in both frog and human. Hence, we show that dlx5 is expressed in Xt and elephant shark odontoblasts, supporting a common cellular and genetic origin of bone and dentine. Taken together, our work (i) unravels the Xt osteogenic regulatory landscape, (ii) illustrates how cross-species comparisons harvest data relevant to human biology and (iii) reveals that a set of genes including bnc2, dlx5, ebf3, mir199a, nfia, runx2 and zfhx4 drove the development of a primitive form of mineralized skeletal tissue deep in the vertebrate lineage.
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Affiliation(s)
- Héctor Castillo
- Group for the Study of Developmental Processes (GDeP), School of Biological Sciences, University of Concepción, Chile.
| | - Patricia Hanna
- Group for the Study of Developmental Processes (GDeP), School of Biological Sciences, University of Concepción, Chile
| | - Laurent M Sachs
- UMR7221, Physiologie Moléculaire et Adaptation, CNRS, MNHN, Paris Cedex 05, France
| | - Nicolas Buisine
- UMR7221, Physiologie Moléculaire et Adaptation, CNRS, MNHN, Paris Cedex 05, France
| | - Francisco Godoy
- Group for the Study of Developmental Processes (GDeP), School of Biological Sciences, University of Concepción, Chile
| | - Clément Gilbert
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 12 route 128, 91190 Gif-sur-Yvette, France
| | - Felipe Aguilera
- Group for the Study of Developmental Processes (GDeP), School of Biological Sciences, University of Concepción, Chile
| | - David Muñoz
- Group for the Study of Developmental Processes (GDeP), School of Biological Sciences, University of Concepción, Chile
| | - Catherine Boisvert
- School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Mélanie Debiais-Thibaud
- Institut des Sciences de l'Evolution de Montpellier, ISEM, Univ Montpellier, CNRS, IRD, Montpellier, France
| | - Jing Wan
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France; Equipe Labelisée LIGUE contre le Cancer, Marseille, France
| | - Salvatore Spicuglia
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France; Equipe Labelisée LIGUE contre le Cancer, Marseille, France
| | - Sylvain Marcellini
- Group for the Study of Developmental Processes (GDeP), School of Biological Sciences, University of Concepción, Chile.
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46
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Francia M, Bot M, Boltz T, De la Hoz JF, Boks M, Kahn RS, Ophoff RA. Fibroblasts as an in vitro model of circadian genetic and genomic studies. Mamm Genome 2024; 35:432-444. [PMID: 38960898 PMCID: PMC11329553 DOI: 10.1007/s00335-024-10050-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024]
Abstract
Bipolar disorder (BD) is a heritable disorder characterized by shifts in mood that manifest in manic or depressive episodes. Clinical studies have identified abnormalities of the circadian system in BD patients as a hallmark of underlying pathophysiology. Fibroblasts are a well-established in vitro model for measuring circadian patterns. We set out to examine the underlying genetic architecture of circadian rhythm in fibroblasts, with the goal to assess its contribution to the polygenic nature of BD disease risk. We collected, from primary cell lines of 6 healthy individuals, temporal genomic features over a 48 h period from transcriptomic data (RNA-seq) and open chromatin data (ATAC-seq). The RNA-seq data showed that only a limited number of genes, primarily the known core clock genes such as ARNTL, CRY1, PER3, NR1D2 and TEF display circadian patterns of expression consistently across cell cultures. The ATAC-seq data identified that distinct transcription factor families, like those with the basic helix-loop-helix motif, were associated with regions that were increasing in accessibility over time. Whereas known glucocorticoid receptor target motifs were identified in those regions that were decreasing in accessibility. Further evaluation of these regions using stratified linkage disequilibrium score regression analysis failed to identify a significant presence of them in the known genetic architecture of BD, and other psychiatric disorders or neurobehavioral traits in which the circadian rhythm is affected. In this study, we characterize the biological pathways that are activated in this in vitro circadian model, evaluating the relevance of these processes in the context of the genetic architecture of BD and other disorders, highlighting its limitations and future applications for circadian genomic studies.
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Affiliation(s)
- Marcelo Francia
- Interdepartmental Program for Neuroscience, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
| | - Merel Bot
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Toni Boltz
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Juan F De la Hoz
- Bioinformatics Interdepartamental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Marco Boks
- Department Psychiatry, Brain Center University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - René S Kahn
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roel A Ophoff
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
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47
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Simmons AD, Baumann C, Zhang X, Kamp TJ, De La Fuente R, Palecek SP. Integrated multi-omics analysis identifies features that predict human pluripotent stem cell-derived progenitor differentiation to cardiomyocytes. J Mol Cell Cardiol 2024; 196:52-70. [PMID: 39222876 DOI: 10.1016/j.yjmcc.2024.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 07/30/2024] [Accepted: 08/30/2024] [Indexed: 09/04/2024]
Abstract
Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) are advancing cardiovascular development and disease modeling, drug testing, and regenerative therapies. However, hPSC-CM production is hindered by significant variability in the differentiation process. Establishment of early quality markers to monitor lineage progression and predict terminal differentiation outcomes would address this robustness and reproducibility roadblock in hPSC-CM production. An integrated transcriptomic and epigenomic analysis assesses how attributes of the cardiac progenitor cell (CPC) affect CM differentiation outcome. Resulting analysis identifies predictive markers of CPCs that give rise to high purity CM batches, including TTN, TRIM55, DGKI, MEF2C, MAB21L2, MYL7, LDB3, SLC7A11, and CALD1. Predictive models developed from these genes provide high accuracy in determining terminal CM purities at the CPC stage. Further, insights into mechanisms of batch failure and dominant non-CM cell types generated in failed batches are elucidated. Namely EMT, MAPK, and WNT signaling emerge as significant drivers of batch divergence, giving rise to off-target populations of fibroblasts/mural cells, skeletal myocytes, epicardial cells, and a non-CPC SLC7A11+ subpopulation. This study demonstrates how integrated multi-omic analysis of progenitor cells can identify quality attributes of that progenitor and predict differentiation outcomes, thereby improving differentiation protocols and increasing process robustness.
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Affiliation(s)
- Aaron D Simmons
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Claudia Baumann
- Department of Physiology and Pharmacology, and Regenerative Bioscience Center, University of Georgia, Athens, GA 30602, USA
| | - Xiangyu Zhang
- Department of Physiology and Pharmacology, and Regenerative Bioscience Center, University of Georgia, Athens, GA 30602, USA
| | - Timothy J Kamp
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Rabindranath De La Fuente
- Department of Physiology and Pharmacology, and Regenerative Bioscience Center, University of Georgia, Athens, GA 30602, USA
| | - Sean P Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Haberman N, Cheung R, Pizza G, Cvetesic N, Nagy D, Maude H, Blazquez L, Lenhard B, Cebola I, Rutter GA, Martinez-Sanchez A. Liver kinase B1 (LKB1) regulates the epigenetic landscape of mouse pancreatic beta cells. FASEB J 2024; 38:e23885. [PMID: 39139039 PMCID: PMC11378476 DOI: 10.1096/fj.202401078r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/26/2024] [Accepted: 08/02/2024] [Indexed: 08/15/2024]
Abstract
Liver kinase B1 (LKB1/STK11) is an important regulator of pancreatic β-cell identity and function. Elimination of Lkb1 from the β-cell results in improved glucose-stimulated insulin secretion and is accompanied by profound changes in gene expression, including the upregulation of several neuronal genes. The mechanisms through which LKB1 controls gene expression are, at present, poorly understood. Here, we explore the impact of β cell-selective deletion of Lkb1 on chromatin accessibility in mouse pancreatic islets. To characterize the role of LKB1 in the regulation of gene expression at the transcriptional level, we combine these data with a map of islet active transcription start sites and histone marks. We demonstrate that LKB1 elimination from β-cells results in widespread changes in chromatin accessibility, correlating with changes in transcript levels. Changes occurred in hundreds of promoter and enhancer regions, many of which were close to neuronal genes. We reveal that dysregulated enhancers are enriched in binding motifs for transcription factors (TFs) important for β-cell identity, such as FOXA, MAFA or RFX6, and we identify microRNAs (miRNAs) that are regulated by LKB1 at the transcriptional level. Overall, our study provides important new insights into the epigenetic mechanisms by which LKB1 regulates β-cell identity and function.
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Affiliation(s)
- Nejc Haberman
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Division of Neuroscience, Department of Brain Sciences, Imperial College London, London, UK
| | - Rebecca Cheung
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, UK
| | - Grazia Pizza
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, UK
| | - Nevena Cvetesic
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Dorka Nagy
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Hannah Maude
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Lorea Blazquez
- Department of Neurosciences, Biogipuzkoa Health Research Institute, San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), Madrid, Spain
| | - Boris Lenhard
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, UK
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Faculté de Médecine, Université de Montréal, Montréal, Quebec, Canada
- Lee Kong Chian Medical School, Nanyang Technological University, Singapore, Singapore
| | - Aida Martinez-Sanchez
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, UK
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49
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Sumida TS, Lincoln MR, He L, Park Y, Ota M, Oguchi A, Son R, Yi A, Stillwell HA, Leissa GA, Fujio K, Murakawa Y, Kulminski AM, Epstein CB, Bernstein BE, Kellis M, Hafler DA. An autoimmune transcriptional circuit drives FOXP3 + regulatory T cell dysfunction. Sci Transl Med 2024; 16:eadp1720. [PMID: 39196959 DOI: 10.1126/scitranslmed.adp1720] [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: 03/11/2024] [Accepted: 08/02/2024] [Indexed: 08/30/2024]
Abstract
Autoimmune diseases, among the most common disorders of young adults, are mediated by genetic and environmental factors. Although CD4+FOXP3+ regulatory T cells (Tregs) play a central role in preventing autoimmunity, the molecular mechanism underlying their dysfunction is unknown. Here, we performed comprehensive transcriptomic and epigenomic profiling of Tregs in the autoimmune disease multiple sclerosis (MS) to identify critical transcriptional programs regulating human autoimmunity. We found that up-regulation of a primate-specific short isoform of PR domain zinc finger protein 1 (PRDM1-S) induces expression of serum and glucocorticoid-regulated kinase 1 (SGK1) independent from the evolutionarily conserved long PRDM1, which led to destabilization of forkhead box P3 (FOXP3) and Treg dysfunction. This aberrant PRDM1-S/SGK1 axis is shared among other autoimmune diseases. Furthermore, the chromatin landscape profiling in Tregs from individuals with MS revealed enriched activating protein-1 (AP-1)/interferon regulatory factor (IRF) transcription factor binding as candidate upstream regulators of PRDM1-S expression and Treg dysfunction. Our study uncovers a mechanistic model where the evolutionary emergence of PRDM1-S and epigenetic priming of AP-1/IRF may be key drivers of dysfunctional Tregs in autoimmune diseases.
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Affiliation(s)
- Tomokazu S Sumida
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew R Lincoln
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON M6R 1B5, Canada
- Keenan Research Centre for Biomedical Science of St. Michael's Hospital, Toronto, ON M6R 1B5, Canada
| | - Liang He
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC 27705, USA
| | - Yongjin Park
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo 113-8655, Japan
| | - Akiko Oguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8303, Japan
| | - Raku Son
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8303, Japan
| | - Alice Yi
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Helen A Stillwell
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Greta A Leissa
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo 113-8655, Japan
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8303, Japan
| | - Alexander M Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC 27705, USA
| | | | - Bradley E Bernstein
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
| | - David A Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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50
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Narang S, Ghebrechristos Y, Evensen NA, Murrell N, Jasinski S, Ostrow TH, Teachey DT, Raetz EA, Lionnet T, Witkowski M, Aifantis I, Tsirigos A, Carroll WL. Clonal evolution of the 3D chromatin landscape in patients with relapsed pediatric B-cell acute lymphoblastic leukemia. Nat Commun 2024; 15:7425. [PMID: 39198446 PMCID: PMC11358475 DOI: 10.1038/s41467-024-51492-6] [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: 06/28/2023] [Accepted: 08/09/2024] [Indexed: 09/01/2024] Open
Abstract
Relapsed pediatric B-cell acute lymphoblastic leukemia (B-ALL) remains one of the leading causes of cancer mortality in children. We performed Hi-C, ATAC-seq, and RNA-seq on 12 matched diagnosis/relapse pediatric leukemia specimens to uncover dynamic structural variants (SVs) and 3D chromatin rewiring that may contribute to relapse. While translocations are assumed to occur early in leukemogenesis and be maintained throughout progression, we discovered novel, dynamic translocations and confirmed several fusion transcripts, suggesting functional and therapeutic relevance. Genome-wide chromatin remodeling was observed at all organizational levels: A/B compartments, TAD interactivity, and chromatin loops, including some loci shared by 25% of patients. Shared changes were found to drive the expression of genes/pathways previously implicated in resistance as well as novel therapeutic candidates, two of which (ATXN1 and MN1) we functionally validated. Overall, these results demonstrate chromatin reorganization under the selective pressure of therapy and offer the potential for discovery of novel therapeutic interventions.
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Affiliation(s)
- Sonali Narang
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Yohana Ghebrechristos
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Pathology, NYU Langone Health, New York, NY, USA
| | - Nikki A Evensen
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Nina Murrell
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Pathology, NYU Langone Health, New York, NY, USA
| | - Sylwia Jasinski
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, NYU Langone Health, New York, NY, USA
| | - Talia H Ostrow
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - David T Teachey
- Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elizabeth A Raetz
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, NYU Langone Health, New York, NY, USA
| | - Timothee Lionnet
- Institute for Systems Genetics and Department of Cell Biology, NYU Langone Health, New York, NY, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA
| | - Matthew Witkowski
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Iannis Aifantis
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
- Department of Pathology, NYU Langone Health, New York, NY, USA.
| | - Aristotelis Tsirigos
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
- Department of Pathology, NYU Langone Health, New York, NY, USA.
| | - William L Carroll
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, NYU Langone Health, New York, NY, USA.
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