1
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Xia Y, Inoue K, Zheng T, Qin Y, Zhao B. Reciprocal suppression between TGFβ signaling and TNF stimulation finetunes the macrophage inflammatory response. FASEB J 2024; 38:e23704. [PMID: 38884155 DOI: 10.1096/fj.202302230r] [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: 10/30/2023] [Revised: 04/23/2024] [Accepted: 05/15/2024] [Indexed: 06/18/2024]
Abstract
Inflammation plays a crucial role in the development of various disease conditions or is closely associated with them. Inflammatory cytokines like TNF often engage in interactions with other cytokines and growth factors, including TGFβ, to orchestrate inflammatory process. Basal/endogenous TGFβ signaling is a universal presence, yet the precise way TNF communicates with TGFβ signaling to regulate inflammation and influence inflammatory levels in macrophages has remained elusive. To address this question, this study utilized genetic approaches and a combination of molecular and cellular methods, including conditional TGFβ receptor knockout mice, human cells, RNAseq, ATACseq and Cut & Run-seq. The results reveal that the TGFβ signaling functions as a vital homeostatic pathway, curtailing uncontrolled inflammation in macrophages in response to TNF. Conversely, TNF employs two previously unrecognized mechanisms to suppress the TGFβ signaling. These mechanisms encompass epigenetic inhibition and RBP-J-mediated inhibition of the TGFβ signaling pathway by TNF. These mechanisms empower TNF to diminish the antagonistic influence exerted by the TGFβ signaling pathway, ultimately enhancing TNF's capacity to induce heightened levels of inflammation. This reciprocal suppression dynamic between TNF and the TGFβ signaling pathway holds unique physiopathological significance, as it serves as a crucial "braking" mechanism. The balance between TNF levels and the activity of the endogenous TGFβ signaling pathway plays a pivotal role in determining the overall extent of inflammation. The potential for therapeutically augmenting the TGFβ signaling pathway presents an intriguing avenue for countering the impact of TNF and, consequently, developing innovative strategies for inflammation control.
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Affiliation(s)
- Yuhan Xia
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Kazuki Inoue
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Ting Zheng
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Yongli Qin
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Baohong Zhao
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
- Graduate Program in Cell and Development Biology, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
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2
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Yaacov O, Mathiyalagan P, Berk-Rauch HE, Ganesh SK, Zhu L, Hoffmann TJ, Iribarren C, Risch N, Lee D, Chakravarti A. Identification of the Molecular Components of Enhancer-Mediated Gene Expression Variation in Multiple Tissues Regulating Blood Pressure. Hypertension 2024; 81:1500-1510. [PMID: 38747164 PMCID: PMC11168860 DOI: 10.1161/hypertensionaha.123.22538] [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: 12/13/2023] [Accepted: 04/24/2024] [Indexed: 06/14/2024]
Abstract
BACKGROUND Inter-individual variation in blood pressure (BP) arises in part from sequence variants within enhancers modulating the expression of causal genes. We propose that these genes, active in tissues relevant to BP physiology, can be identified from tissue-level epigenomic data and genotypes of BP-phenotyped individuals. METHODS We used chromatin accessibility data from the heart, adrenal, kidney, and artery to identify cis-regulatory elements (CREs) in these tissues and estimate the impact of common human single-nucleotide variants within these CREs on gene expression, using machine learning methods. To identify causal genes, we performed a gene-wise association test. We conducted analyses in 2 separate large-scale cohorts: 77 822 individuals from the Genetic Epidemiology Research on Adult Health and Aging and 315 270 individuals from the UK Biobank. RESULTS We identified 309, 259, 331, and 367 genes (false discovery rate <0.05) for diastolic BP and 191, 184, 204, and 204 genes for systolic BP in the artery, kidney, heart, and adrenal, respectively, in Genetic Epidemiology Research on Adult Health and Aging; 50% to 70% of these genes were replicated in the UK Biobank, significantly higher than the 12% to 15% expected by chance (P<0.0001). These results enabled tissue expression prediction of these 988 to 2875 putative BP genes in individuals of both cohorts to construct an expression polygenic score. This score explained ≈27% of the reported single-nucleotide variant heritability, substantially higher than expected from prior studies. CONCLUSIONS Our work demonstrates the power of tissue-restricted comprehensive CRE analysis, followed by CRE-based expression prediction, for understanding BP regulation in relevant tissues and provides dual-modality supporting evidence, CRE and expression, for the causality genes.
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Affiliation(s)
- Or Yaacov
- Center for Human Genetics and Genomics, NYU Grossman School of Medicine, New York, NY, USA
| | - Prabhu Mathiyalagan
- Center for Human Genetics and Genomics, NYU Grossman School of Medicine, New York, NY, USA
- Benthos Prime Central, Houston, TX, USA
| | - Hanna E. Berk-Rauch
- Center for Human Genetics and Genomics, NYU Grossman School of Medicine, New York, NY, USA
| | - Santhi K. Ganesh
- Department of Internal Medicine & Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Luke Zhu
- Center for Human Genetics and Genomics, NYU Grossman School of Medicine, New York, NY, USA
| | - Thomas J. Hoffmann
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Carlos Iribarren
- Kaiser Permanente Northern California Division of Research, Oakland, CA, USA
| | - Neil Risch
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Kaiser Permanente Northern California Division of Research, Oakland, CA, USA
| | - Dongwon Lee
- Department of Pediatrics, Division of Nephrology, Boston Children’s Hospital, Boston & Harvard Medical School, Boston, MA, USA
| | - Aravinda Chakravarti
- Center for Human Genetics and Genomics, NYU Grossman School of Medicine, New York, NY, USA
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3
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Li M, Jin Y, Xu Y, Sun Y, Yuan R, Zhang X, Qu S, Lv M, Liao M, Liang W, Zhang L, Chen X. From degraded to deciphered: ATAC-seq's application potential in forensic diagnosis. Int J Legal Med 2024; 138:1273-1285. [PMID: 38491322 DOI: 10.1007/s00414-024-03206-2] [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: 10/25/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
In recent years, molecular biology-based diagnostic techniques have made remarkable strides and are now extensively utilized in clinical practice, providing invaluable insights for disease diagnosis and treatment. However, forensic medicine, especially forensic pathology, has witnessed relatively limited progress in the application of molecular biology technologies. A significant challenge in employing molecular techniques for forensic diagnoses lies in the quantitative and qualitative changes observed in diagnostic markers due to sample degradation-a recognized and formidable obstacle. Inspired by the success of DNA sequencing in forensic practices, which enables accurate individual identification even in cases involving degraded and deteriorated tissues and organs, we propose the application of the assay for transposase-accessible chromatin with sequencing (ATAC-seq) to identify targets at the transcriptional onset, exploring chromatin and DNA-level alterations for injury and disease inference in forensic samples. This study employs ATAC-seq to explore alterations in chromatin accessibility post-injury and their subsequent changes over a 2-h degradation period, employing traumatic brain injury (TBI) as a representative model. Our findings reveal high sensitivity of chromatin accessibility sites to injury, evidenced by shifts in thousands of peak positions post-TBI. Remarkably, these alterations remain largely unaffected by early degradation. Our results robustly endorse the notion that integrating and incorporating these specific loci for injury and disease diagnosis in forensic samples holds tremendous promise for practical application. We further validated the above results using human cortical tissue, which supported that early degradation did not significantly affect chromatin accessibility. This pioneering advancement in molecular diagnostic techniques may revolutionize the field of forensic science, especially forensic pathology.
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Affiliation(s)
- Manrui Li
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Yuntian Jin
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Yang Xu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Yihan Sun
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Ruixuan Yuan
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Xiao Zhang
- Department of Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China.
| | - Lin Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China.
| | - Xiameng Chen
- Department of Forensic Pathology and Forensic Clinical Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China.
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4
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Liao X, Scheidereit E, Kuppe C. New tools to study renal fibrogenesis. Curr Opin Nephrol Hypertens 2024; 33:420-426. [PMID: 38587103 PMCID: PMC11139246 DOI: 10.1097/mnh.0000000000000988] [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] [Indexed: 04/09/2024]
Abstract
PURPOSE OF REVIEW Kidney fibrosis is a key pathological aspect and outcome of chronic kidney disease (CKD). The advent of multiomic analyses using human kidney tissue, enabled by technological advances, marks a new chapter of discovery in fibrosis research of the kidney. This review highlights the rapid advancements of single-cell and spatial multiomic techniques that offer new avenues for exploring research questions related to human kidney fibrosis development. RECENT FINDINGS We recently focused on understanding the origin and transition of myofibroblasts in kidney fibrosis using single-cell RNA sequencing (scRNA-seq) [1] . We analysed cells from healthy human kidneys and compared them to patient samples with CKD. We identified PDGFRα+/PDGFRβ+ mesenchymal cells as the primary cellular source of extracellular matrix (ECM) in human kidney fibrosis. We found several commonly shared cell states of fibroblasts and myofibroblasts and provided insights into molecular regulators. Novel single-cell and spatial multiomics tools are now available to shed light on cell lineages, the plasticity of kidney cells and cell-cell communication in fibrosis. SUMMARY As further single-cell and spatial multiomic approaches are being developed, opportunities to apply these methods to human kidney tissues expand similarly. Careful design and optimisation of the multiomic experiments are needed to answer questions related to cell lineages, plasticity and cell-cell communication in kidney fibrosis.
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Affiliation(s)
- Xian Liao
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
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5
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Salignon J, Millan-Ariño L, Garcia MU, Riedel CG. Cactus: A user-friendly and reproducible ATAC-Seq and mRNA-Seq analysis pipeline for data preprocessing, differential analysis, and enrichment analysis. Genomics 2024; 116:110858. [PMID: 38735595 DOI: 10.1016/j.ygeno.2024.110858] [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: 02/09/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/14/2024]
Abstract
The ever decreasing cost of Next-Generation Sequencing coupled with the emergence of efficient and reproducible analysis pipelines has rendered genomic methods more accessible. However, downstream analyses are basic or missing in most workflows, creating a significant barrier for non-bioinformaticians. To help close this gap, we developed Cactus, an end-to-end pipeline for analyzing ATAC-Seq and mRNA-Seq data, either separately or jointly. Its Nextflow-, container-, and virtual environment-based architecture ensures efficient and reproducible analyses. Cactus preprocesses raw reads, conducts differential analyses between conditions, and performs enrichment analyses in various databases, including DNA-binding motifs, ChIP-Seq binding sites, chromatin states, and ontologies. We demonstrate the utility of Cactus in a multi-modal and multi-species case study as well as by showcasing its unique capabilities as compared to other ATAC-Seq pipelines. In conclusion, Cactus can assist researchers in gaining comprehensive insights from chromatin accessibility and gene expression data in a quick, user-friendly, and reproducible manner.
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Affiliation(s)
- Jérôme Salignon
- Department of Bioscience and Nutrition, Karolinska Institute, Blickagången 16, Huddinge SE-141 83, Sweden.
| | - Lluís Millan-Ariño
- Department of Bioscience and Nutrition, Karolinska Institute, Blickagången 16, Huddinge SE-141 83, Sweden
| | - Maxime U Garcia
- National Genomics Infrastructure, Science for Life Laboratory, Tomtebodavägen 23A, Solna SE-171 65, Sweden; Department of Oncology-Pathology, Karolinska Institute, Visionsgatan 4, Solna SE-171 64, Sweden
| | - Christian G Riedel
- Department of Bioscience and Nutrition, Karolinska Institute, Blickagången 16, Huddinge SE-141 83, Sweden.
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6
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Jackson DJ, Cerveau N, Posnien N. De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms - a brief guide. Front Zool 2024; 21:17. [PMID: 38902827 DOI: 10.1186/s12983-024-00538-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
Many questions in biology benefit greatly from the use of a variety of model systems. High-throughput sequencing methods have been a triumph in the democratization of diverse model systems. They allow for the economical sequencing of an entire genome or transcriptome of interest, and with technical variations can even provide insight into genome organization and the expression and regulation of genes. The analysis and biological interpretation of such large datasets can present significant challenges that depend on the 'scientific status' of the model system. While high-quality genome and transcriptome references are readily available for well-established model systems, the establishment of such references for an emerging model system often requires extensive resources such as finances, expertise and computation capabilities. The de novo assembly of a transcriptome represents an excellent entry point for genetic and molecular studies in emerging model systems as it can efficiently assess gene content while also serving as a reference for differential gene expression studies. However, the process of de novo transcriptome assembly is non-trivial, and as a rule must be empirically optimized for every dataset. For the researcher working with an emerging model system, and with little to no experience with assembling and quantifying short-read data from the Illumina platform, these processes can be daunting. In this guide we outline the major challenges faced when establishing a reference transcriptome de novo and we provide advice on how to approach such an endeavor. We describe the major experimental and bioinformatic steps, provide some broad recommendations and cautions for the newcomer to de novo transcriptome assembly and differential gene expression analyses. Moreover, we provide an initial selection of tools that can assist in the journey from raw short-read data to assembled transcriptome and lists of differentially expressed genes.
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Affiliation(s)
- Daniel J Jackson
- University of Göttingen, Department of Geobiology, Goldschmidtstr.3, Göttingen, 37077, Germany.
| | - Nicolas Cerveau
- University of Göttingen, Department of Geobiology, Goldschmidtstr.3, Göttingen, 37077, Germany
| | - Nico Posnien
- University of Göttingen, Department of Developmental Biology, GZMB, Justus-Von-Liebig-Weg 11, Göttingen, 37077, Germany.
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7
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Singh PP, Reeves GA, Contrepois K, Papsdorf K, Miklas JW, Ellenberger M, Hu CK, Snyder MP, Brunet A. Evolution of diapause in the African turquoise killifish by remodeling the ancient gene regulatory landscape. Cell 2024; 187:3338-3356.e30. [PMID: 38810644 DOI: 10.1016/j.cell.2024.04.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 11/30/2023] [Accepted: 04/30/2024] [Indexed: 05/31/2024]
Abstract
Suspended animation states allow organisms to survive extreme environments. The African turquoise killifish has evolved diapause as a form of suspended development to survive a complete drought. However, the mechanisms underlying the evolution of extreme survival states are unknown. To understand diapause evolution, we performed integrative multi-omics (gene expression, chromatin accessibility, and lipidomics) in the embryos of multiple killifish species. We find that diapause evolved by a recent remodeling of regulatory elements at very ancient gene duplicates (paralogs) present in all vertebrates. CRISPR-Cas9-based perturbations identify the transcription factors REST/NRSF and FOXOs as critical for the diapause gene expression program, including genes involved in lipid metabolism. Indeed, diapause shows a distinct lipid profile, with an increase in triglycerides with very-long-chain fatty acids. Our work suggests a mechanism for the evolution of complex adaptations and offers strategies to promote long-term survival by activating suspended animation programs in other species.
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Affiliation(s)
| | - G Adam Reeves
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University, Stanford, CA, USA; Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | | | - Jason W Miklas
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Chi-Kuo Hu
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, CA, USA; Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA; Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA, USA; Glenn Center for the Biology of Aging, Stanford University, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
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8
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Chu SY, Lai YW, Hsu TC, Lu TM, Yu HH. Isoforms of Terminal Selector Mamo Control Axon Guidance during Adult Drosophila Memory Center Construction via Semaphorin-1a. Dev Biol 2024:S0012-1606(24)00160-X. [PMID: 38906235 DOI: 10.1016/j.ydbio.2024.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/16/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
In animals undergoing metamorphosis, the appearance of the nervous system is coincidently transformed by the morphogenesis of neurons. Such morphogenic alterations are exemplified in three types of intrinsic neurons in the Drosophila memory center. In contrast to the well-characterized remodeling of γ neurons, the morphogenesis of α/β and α'/β' neurons has not been adequately explored. Here, we show that mamo, a BTB-zinc finger transcription factor that acts as a terminal selector for α'/β' neurons, controls the formation of the correct axonal pattern of α'/β' neurons. Intriguingly, specific Mamo isoforms are preferentially expressed in α'/β' neurons to regulate the expression of axon guidance molecule Semaphorin-1a. This action directs proper axon guidance in α'/β' neurons, which is also crucial for wiring of α'/β' neurons with downstream neurons. Taken together, our results provide molecular insights into how neurons establish correct axonal patterns in circuitry assembly during adult memory center construction.
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Affiliation(s)
- Sao-Yu Chu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Yen-Wei Lai
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Tsai-Chi Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Tsai-Ming Lu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Hung-Hsiang Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.
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9
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Aguirre S, Pappa S, Serna-Pujol N, Padilla N, Iacobucci S, Nacht AS, Vicent GP, Jordan A, de la Cruz X, Martínez-Balbás MA. PHF2-mediated H3K9me balance orchestrates heterochromatin stability and neural progenitor proliferation. EMBO Rep 2024:10.1038/s44319-024-00178-7. [PMID: 38890452 DOI: 10.1038/s44319-024-00178-7] [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: 11/30/2023] [Revised: 05/18/2024] [Accepted: 06/04/2024] [Indexed: 06/20/2024] Open
Abstract
Heterochromatin stability is crucial for progenitor proliferation during early neurogenesis. It relays on the maintenance of local hubs of H3K9me. However, understanding the formation of efficient localized levels of H3K9me remains limited. To address this question, we used neural stem cells to analyze the function of the H3K9me2 demethylase PHF2, which is crucial for progenitor proliferation. Through mass-spectroscopy and genome-wide assays, we show that PHF2 interacts with heterochromatin components and is enriched at pericentromeric heterochromatin (PcH) boundaries where it maintains transcriptional activity. This binding is essential for silencing the satellite repeats, preventing DNA damage and genome instability. PHF2's depletion increases the transcription of heterochromatic repeats, accompanied by a decrease in H3K9me3 levels and alterations in PcH organization. We further show that PHF2's PHD and catalytic domains are crucial for maintaining PcH stability, thereby safeguarding genome integrity. These results highlight the multifaceted nature of PHF2's functions in maintaining heterochromatin stability and regulating gene expression during neural development. Our study unravels the intricate relationship between heterochromatin stability and progenitor proliferation during mammalian neurogenesis.
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Affiliation(s)
- Samuel Aguirre
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08028, Spain
| | - Stella Pappa
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08028, Spain
| | - Núria Serna-Pujol
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08028, Spain
| | - Natalia Padilla
- Vall d'Hebron Institute of Research (VHIR), Passeig de la Vall d'Hebron, 119, E-08035, Barcelona, Spain
| | - Simona Iacobucci
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08028, Spain
| | - A Silvina Nacht
- Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Guillermo P Vicent
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08028, Spain
| | - Albert Jordan
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08028, Spain
| | - Xavier de la Cruz
- Vall d'Hebron Institute of Research (VHIR), Passeig de la Vall d'Hebron, 119, E-08035, Barcelona, Spain
- Institut Català per la Recerca i Estudis Avançats (ICREA), Barcelona, 08018, Spain
| | - Marian A Martínez-Balbás
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08028, Spain.
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10
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Li H, Humphreys BD. Protocol for multimodal profiling of human kidneys with simultaneous high-throughput ATAC and RNA expression with sequencing. STAR Protoc 2024; 5:103049. [PMID: 38900631 DOI: 10.1016/j.xpro.2024.103049] [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: 03/05/2024] [Revised: 03/31/2024] [Accepted: 04/15/2024] [Indexed: 06/22/2024] Open
Abstract
Simultaneous high-throughput ATAC and RNA expression with sequencing (SHARE-seq) profiles transcriptomics and chromatin accessibility in the same cells at high throughput. Here, we present a protocol for multimodal profiling of human kidneys with SHARE-seq. We describe steps for processing fixed nuclei for SHARE-seq split-pool barcoding and library preparation. We also detail how to determine the optimal working concentration of Tn5 transposase for transposition and tagmentation. This protocol allows researchers to generate large-scale single-cell multiomics data at low reagent cost. For complete details on the use and execution of this protocol, please refer to Li et al.1.
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Affiliation(s)
- Haikuo Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63105, USA.
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63105, USA; Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO 63105, USA.
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11
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Liu J, Ma J, Wen J, Zhou X. A Cell Cycle-Aware Network for Data Integration and Label Transferring of Single-Cell RNA-Seq and ATAC-Seq. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401815. [PMID: 38887194 DOI: 10.1002/advs.202401815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/22/2024] [Indexed: 06/20/2024]
Abstract
In recent years, the integration of single-cell multi-omics data has provided a more comprehensive understanding of cell functions and internal regulatory mechanisms from a non-single omics perspective, but it still suffers many challenges, such as omics-variance, sparsity, cell heterogeneity, and confounding factors. As it is known, the cell cycle is regarded as a confounder when analyzing other factors in single-cell RNA-seq data, but it is not clear how it will work on the integrated single-cell multi-omics data. Here, a cell cycle-aware network (CCAN) is developed to remove cell cycle effects from the integrated single-cell multi-omics data while keeping the cell type-specific variations. This is the first computational model to study the cell-cycle effects in the integration of single-cell multi-omics data. Validations on several benchmark datasets show the outstanding performance of CCAN in a variety of downstream analyses and applications, including removing cell cycle effects and batch effects of scRNA-seq datasets from different protocols, integrating paired and unpaired scRNA-seq and scATAC-seq data, accurately transferring cell type labels from scRNA-seq to scATAC-seq data, and characterizing the differentiation process from hematopoietic stem cells to different lineages in the integration of differentiation data.
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Affiliation(s)
- Jiajia Liu
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Jian Ma
- Department of Electronic Information and Computer Engineering, The Engineering & Technical College of Chengdu University of Technology, Leshan, Sichuan, 614000, China
| | - Jianguo Wen
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
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12
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Lee HM, Muhammad N, Lieu EL, Cai F, Mu J, Ha YS, Cao G, Suchors C, Joves K, Chronis C, Li K, Ducker GS, Olszewski K, Cai L, Allison DB, Bachert SE, Ewing WR, Wong H, Seo H, Kim IY, Faubert B, Kim J, Kim J. Concurrent loss of LKB1 and KEAP1 enhances SHMT-mediated antioxidant defence in KRAS-mutant lung cancer. Nat Metab 2024:10.1038/s42255-024-01066-z. [PMID: 38877143 DOI: 10.1038/s42255-024-01066-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 05/16/2024] [Indexed: 06/16/2024]
Abstract
Non-small-cell lung cancer (NSCLC) with concurrent mutations in KRAS and the tumour suppressor LKB1 (KL NSCLC) is refractory to most therapies and has one of the worst predicted outcomes. Here we describe a KL-induced metabolic vulnerability associated with serine-glycine-one-carbon (SGOC) metabolism. Using RNA-seq and metabolomics data from human NSCLC, we uncovered that LKB1 loss enhanced SGOC metabolism via serine hydroxymethyltransferase (SHMT). LKB1 loss, in collaboration with KEAP1 loss, activated SHMT through inactivation of the salt-induced kinase (SIK)-NRF2 axis and satisfied the increased demand for one-carbon units necessary for antioxidant defence. Chemical and genetic SHMT suppression increased cellular sensitivity to oxidative stress and cell death. Further, the SHMT inhibitor enhanced the in vivo therapeutic efficacy of paclitaxel (first-line NSCLC therapy inducing oxidative stress) in KEAP1-mutant KL tumours. The data reveal how this highly aggressive molecular subtype of NSCLC fulfills their metabolic requirements and provides insight into therapeutic strategies.
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Affiliation(s)
- Hyun Min Lee
- Department of Urology, Yale School of Medicine, New Haven, CT, USA
| | - Nefertiti Muhammad
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Elizabeth L Lieu
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Feng Cai
- Children's Medical Center Research Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jiawei Mu
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yun-Sok Ha
- Department of Urology, School of Medicine, Kyungpook National University, Kyungpook National University Chilgok Hospital, Daegu, Korea
| | - Guoshen Cao
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Chamey Suchors
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Kenneth Joves
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Constantinos Chronis
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Kailong Li
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Gregory S Ducker
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | | | - Ling Cai
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA
| | - Derek B Allison
- Department of Pathology and Laboratory Medicine, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Sara E Bachert
- Department of Pathology and Laboratory Medicine, University of Kentucky College of Medicine, Lexington, KY, USA
| | | | - Harvey Wong
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Hyosun Seo
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Isaac Y Kim
- Department of Urology, Yale School of Medicine, New Haven, CT, USA
| | - Brandon Faubert
- Department of Medicine-Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | - James Kim
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jiyeon Kim
- Department of Urology, Yale School of Medicine, New Haven, CT, USA.
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA.
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13
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Roy Chowdhury N, Gurevich V, Shamay M. KSHV genome harbors both constitutive and lytically induced enhancers. J Virol 2024; 98:e0017924. [PMID: 38695538 DOI: 10.1128/jvi.00179-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/03/2024] [Indexed: 06/14/2024] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) belongs to the gamma-herpesvirus family and is a well-known human oncogenic virus. In infected cells, the viral genome of 165 kbp is circular DNA wrapped in chromatin. The tight control of gene expression is critical for latency, the transition into the lytic phase, and the development of viral-associated malignancies. Distal cis-regulatory elements, such as enhancers and silencers, can regulate gene expression in a position- and orientation-independent manner. Open chromatin is another characteristic feature of enhancers. To systematically search for enhancers, we cloned all the open chromatin regions in the KSHV genome downstream of the luciferase gene and tested their enhancer activity in infected and uninfected cells. A silencer was detected upstream of the latency-associated nuclear antigen promoter. Two constitutive enhancers were identified in the K12p-OriLyt-R and ORF29 Intron regions, where ORF29 Intron is a tissue-specific enhancer. The following promoters: OriLyt-L, PANp, ALTp, and the terminal repeats (TRs) acted as lytically induced enhancers. The expression of the replication and transcription activator (RTA), the master regulator of the lytic cycle, was sufficient to induce the activity of lytic enhancers in uninfected cells. We propose that the TRs that span about 24 kbp region serve as a "viral super-enhancer" that integrates the repressive effect of the latency-associated nuclear antigen (LANA) with the activating effect of RTA. Utilizing CRISPR activation and interference techniques, we determined the connections between these enhancers and their regulated genes. The silencer and enhancers described here provide an additional layer to the complex gene regulation of herpesviruses.IMPORTANCEIn this study, we performed a systematic functional assay to identify cis-regulatory elements within the genome of the oncogenic herpesvirus, Kaposi's sarcoma-associated herpesvirus (KSHV). Similar to other herpesviruses, KSHV presents both latent and lytic phases. Therefore, our assays were performed in uninfected cells, during latent infection, and under lytic conditions. We identified two constitutive enhancers, one of which seems to be a tissue-specific enhancer. In addition, four lytically induced enhancers, which are all responsive to the replication and transcription activator (RTA), were identified. Furthermore, a silencer was identified between the major latency promoter and the lytic gene locus. Utilizing CRISPR activation and interference techniques, we determined the connections between these enhancers and their regulated genes. The terminal repeats, spanning a region of about 24 kbp, seem like a "viral super-enhancer" that integrates the repressive effect of the latency-associated nuclear antigen (LANA) with the activating effect of RTA to regulate latency to lytic transition.
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Affiliation(s)
- Nilabja Roy Chowdhury
- Daniella Lee Casper Laboratory in Viral Oncology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Vyacheslav Gurevich
- Daniella Lee Casper Laboratory in Viral Oncology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Meir Shamay
- Daniella Lee Casper Laboratory in Viral Oncology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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14
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Inoue SI, Emmett MJ, Lim HW, Midha M, Richter HJ, Celwyn IJ, Mehmood R, Chondronikola M, Klein S, Hauck AK, Lazar MA. Short-term cold exposure induces persistent epigenomic memory in brown fat. Cell Metab 2024:S1550-4131(24)00187-6. [PMID: 38889724 DOI: 10.1016/j.cmet.2024.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 04/01/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024]
Abstract
Deficiency of the epigenome modulator histone deacetylase 3 (HDAC3) in brown adipose tissue (BAT) impairs the ability of mice to survive in near-freezing temperatures. Here, we report that short-term exposure to mild cold temperature (STEMCT: 15°C for 24 h) averted lethal hypothermia of mice lacking HDAC3 in BAT (HDAC3 BAT KO) exposed to 4°C. STEMCT restored the induction of the thermogenic coactivator PGC-1α along with UCP1 at 22°C, which is greatly impaired in HDAC3-deficient BAT, and deletion of either UCP1 or PGC-1α prevented the protective effect of STEMCT. Remarkably, this protection lasted for up to 7 days. Transcriptional activator C/EBPβ was induced by short-term cold exposure in mouse and human BAT and, uniquely, remained high for 7 days following STEMCT. Adeno-associated virus-mediated knockdown of BAT C/EBPβ in HDAC3 BAT KO mice erased the persistent memory of STEMCT, revealing the existence of a C/EBPβ-dependent and HDAC3-independent cold-adaptive epigenomic memory.
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Affiliation(s)
- Shin-Ichi Inoue
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Matthew J Emmett
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Hee-Woong Lim
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Mohit Midha
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Hannah J Richter
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Isaac J Celwyn
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Rashid Mehmood
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Maria Chondronikola
- Institute of Metabolic Science-Metabolic Research Laboratories and Medical Research Council Metabolic Diseases Unit, University of Cambridge, Cambridge, UK; Department of Nutrition and Dietetics, Harokopio University of Athens, Athens, Greece
| | - Samuel Klein
- Division of Geriatrics and Nutritional Science, Washington University School of Medicine, St. Louis, MO, USA
| | - Amy K Hauck
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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15
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Battaglia C, Michieletto D. Loops are geometric catalysts for DNA integration. Nucleic Acids Res 2024:gkae484. [PMID: 38864388 DOI: 10.1093/nar/gkae484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 05/21/2024] [Accepted: 06/11/2024] [Indexed: 06/13/2024] Open
Abstract
The insertion of DNA elements within genomes underpins both genetic diversity and disease when unregulated. Most of DNA insertions are not random and the physical mechanisms underlying the integration site selection are poorly understood. Here, we perform Molecular Dynamics simulations to study the insertion of DNA elements, such as viral DNA or transposons, into naked DNA or chromatin substrates. More specifically, we explore the role of loops within the polymeric substrate and discover that they act as 'geometric catalysts' for DNA integration by reducing the energy barrier for substrate deformation. Additionally, we discover that the 1D pattern and 3D conformation of loops have a marked effect on the distribution of integration sites. Finally, we show that loops may compete with nucleosomes to attract DNA integrations. These results may be tested in vitro and they may help to understand patterns of DNA insertions with implications in genome evolution and engineering.
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Affiliation(s)
- Cleis Battaglia
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
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16
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Shoaran M, Sabaie H, Mostafavi M, Rezazadeh M. A comprehensive review of the applications of RNA sequencing in celiac disease research. Gene 2024; 927:148681. [PMID: 38871036 DOI: 10.1016/j.gene.2024.148681] [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: 02/02/2024] [Revised: 06/06/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024]
Abstract
RNA sequencing (RNA-seq) has undergone substantial advancements in recent decades and has emerged as a vital technique for profiling the transcriptome. The transition from bulk sequencing to single-cell and spatial approaches has facilitated the achievement of higher precision at cell resolution. It provides valuable biological knowledge about individual immune cells and aids in the discovery of the molecular mechanisms that contribute to the development of autoimmune diseases. Celiac disease (CeD) is an autoimmune disorder characterized by a strong immune response to gluten consumption. RNA-seq has led to significantly advanced research in multiple fields, particularly in CeD research. It has been instrumental in studies involving comparative transcriptomics, nutritional genomics and wheat research, cancer research in the context of CeD, genetic and noncoding RNA-mediated epigenetic insights, disease monitoring and biomarker discovery, regulation of mitochondrial functions, therapeutic target identification and drug mechanism of action, dietary factors, immune cell profiling and the immune landscape. This review offers a comprehensive examination of recent RNA-seq technology research in the field of CeD, highlighting future challenges and opportunities for its application.
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Affiliation(s)
- Maryam Shoaran
- Pediatric Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hani Sabaie
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehrnaz Mostafavi
- Faculty of Allied Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Rezazadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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17
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Van Der Byl W, Nüssing S, Peters TJ, Ahn A, Li H, Ledergor G, David E, Koh AS, Wagle MV, Deguit CDT, de Menezes MN, Travers A, Sampurno S, Ramsbottom KM, Li R, Kallies A, Beavis PA, Jungmann R, Bastings MMC, Belz GT, Goel S, Trapani JA, Crabtree GR, Chang HY, Amit I, Goodnow CC, Luciani F, Parish IA. The CD8 + T cell tolerance checkpoint triggers a distinct differentiation state defined by protein translation defects. Immunity 2024; 57:1324-1344.e8. [PMID: 38776918 DOI: 10.1016/j.immuni.2024.04.026] [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: 05/15/2023] [Revised: 02/01/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
Peripheral CD8+ T cell tolerance is a checkpoint in both autoimmune disease and anti-cancer immunity. Despite its importance, the relationship between tolerance-induced states and other CD8+ T cell differentiation states remains unclear. Using flow cytometric phenotyping, single-cell RNA sequencing (scRNA-seq), and chromatin accessibility profiling, we demonstrated that in vivo peripheral tolerance to a self-antigen triggered a fundamentally distinct differentiation state separate from exhaustion, memory, and functional effector cells but analogous to cells defectively primed against tumors. Tolerant cells diverged early and progressively from effector cells, adopting a transcriptionally and epigenetically distinct state within 60 h of antigen encounter. Breaching tolerance required the synergistic actions of strong T cell receptor (TCR) signaling and inflammation, which cooperatively induced gene modules that enhanced protein translation. Weak TCR signaling during bystander infection failed to breach tolerance due to the uncoupling of effector gene expression from protein translation. Thus, tolerance engages a distinct differentiation trajectory enforced by protein translation defects.
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Affiliation(s)
- Willem Van Der Byl
- The Kirby Institute for Infection and Immunity, UNSW, Sydney, NSW, Australia; School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, NSW, Australia
| | - Simone Nüssing
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Timothy J Peters
- Garvan Institute of Medical Research, Sydney, NSW, Australia; University of New South Wales Sydney, Sydney, NSW, Australia
| | - Antonio Ahn
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Hanjie Li
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Guy Ledergor
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Andrew S Koh
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Mayura V Wagle
- Garvan Institute of Medical Research, Sydney, NSW, Australia; John Curtin School of Medical Research, ANU, Canberra, ACT, Australia
| | | | - Maria N de Menezes
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Avraham Travers
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Shienny Sampurno
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Kelly M Ramsbottom
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Axel Kallies
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC, Australia
| | - Paul A Beavis
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany; Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maartje M C Bastings
- Institute of Materials, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Interfaculty Bioengineering Institute, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Gabrielle T Belz
- The Frazer Institute, The University of Queensland, Brisbane, QLD, Australia; Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Shom Goel
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Joseph A Trapani
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Gerald R Crabtree
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA; Departments of Pathology and Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Chris C Goodnow
- School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, NSW, Australia; Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Fabio Luciani
- The Kirby Institute for Infection and Immunity, UNSW, Sydney, NSW, Australia; School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, NSW, Australia.
| | - Ian A Parish
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia; John Curtin School of Medical Research, ANU, Canberra, ACT, Australia.
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18
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Curion F, Theis FJ. Machine learning integrative approaches to advance computational immunology. Genome Med 2024; 16:80. [PMID: 38862979 PMCID: PMC11165829 DOI: 10.1186/s13073-024-01350-3] [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: 06/29/2023] [Accepted: 05/23/2024] [Indexed: 06/13/2024] Open
Abstract
The study of immunology, traditionally reliant on proteomics to evaluate individual immune cells, has been revolutionized by single-cell RNA sequencing. Computational immunologists play a crucial role in analysing these datasets, moving beyond traditional protein marker identification to encompass a more detailed view of cellular phenotypes and their functional roles. Recent technological advancements allow the simultaneous measurements of multiple cellular components-transcriptome, proteome, chromatin, epigenetic modifications and metabolites-within single cells, including in spatial contexts within tissues. This has led to the generation of complex multiscale datasets that can include multimodal measurements from the same cells or a mix of paired and unpaired modalities. Modern machine learning (ML) techniques allow for the integration of multiple "omics" data without the need for extensive independent modelling of each modality. This review focuses on recent advancements in ML integrative approaches applied to immunological studies. We highlight the importance of these methods in creating a unified representation of multiscale data collections, particularly for single-cell and spatial profiling technologies. Finally, we discuss the challenges of these holistic approaches and how they will be instrumental in the development of a common coordinate framework for multiscale studies, thereby accelerating research and enabling discoveries in the computational immunology field.
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Affiliation(s)
- Fabiola Curion
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Munich, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Munich, Germany.
- School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
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19
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Humphreys JL, Beveridge CA, Tanurdžić M. Strigolactone induces D14-dependent large-scale changes in gene expression requiring SWI/SNF chromatin remodellers. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38858857 DOI: 10.1111/tpj.16873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 06/12/2024]
Abstract
Strigolactones (SL) function as plant hormones in control of multiple aspects of plant development, mostly via the regulation of gene expression. Immediate early-gene regulation by SL remains unexplored due to difficulty in dissecting early from late gene expression responses to SL. We used synthetic SL, rac-GR24 treatment of protoplasts and RNA-seq to explore early SL-induced changes in gene expression over time (5-180 minutes) and discovered rapid, dynamic and SL receptor D14-dependent regulation of gene expression in response to rac-GR24. Importantly, we discovered a significant dependence of SL signalling on chromatin remodelling processes, as the induction of a key SL-induced transcription factor BRANCHED1 requires the SWI/SNF chromatin remodelling ATPase SPLAYED (SYD) and leads to upregulation of a homologue SWI/SNF ATPase BRAHMA. ATAC-seq profiling of genome-wide changes in chromatin accessibility in response to rac-GR24 identified large-scale changes, with over 1400 differentially accessible regions. These changes in chromatin accessibility often precede transcriptional changes and are likely to harbour SL cis-regulatory elements. Importantly, we discovered that this early and extensive modification of the chromatin landscape also requires SYD. This study, therefore, provides evidence that SL signalling requires regulation of chromatin accessibility, and it identifies genomic locations harbouring likely SL cis-regulatory sequences.
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Affiliation(s)
- Jazmine L Humphreys
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
- ARC Centre for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Christine A Beveridge
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
- ARC Centre for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Miloš Tanurdžić
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
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20
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Ichiyama-Kobayashi S, Hata K, Wakamori K, Takahata Y, Murakami T, Yamanaka H, Takano H, Yao R, Uzawa N, Nishimura R. Chromatin profiling identifies chondrocyte-specific Sox9 enhancers important for skeletal development. JCI Insight 2024; 9:e175486. [PMID: 38855864 DOI: 10.1172/jci.insight.175486] [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: 09/06/2023] [Accepted: 05/01/2024] [Indexed: 06/11/2024] Open
Abstract
The transcription factor SRY-related HMG box 9 (Sox9) is essential for chondrogenesis. Mutations in and around SOX9 cause campomelic dysplasia (CD) characterized by skeletal malformations. Although the function of Sox9 in this context is well studied, the mechanisms that regulate Sox9 expression in chondrocytes remain to be elucidated. Here, we have used genome-wide profiling to identify 2 Sox9 enhancers located in a proximal breakpoint cluster responsible for CD. Enhancer activity of E308 (located 308 kb 5' upstream) and E160 (located 160 kb 5' upstream) correlated with Sox9 expression levels, and both enhancers showed a synergistic effect in vitro. While single deletions in mice had no apparent effect, simultaneous deletion of both E308 and E160 caused a dwarf phenotype, concomitant with a reduction of Sox9 expression in chondrocytes. Moreover, bone morphogenetic protein 2-dependent chondrocyte differentiation of limb bud mesenchymal cells was severely attenuated in E308/E160 deletion mice. Finally, we found that an open chromatin region upstream of the Sox9 gene was reorganized in the E308/E160 deletion mice to partially compensate for the loss of E308 and E160. In conclusion, our findings reveal a mechanism of Sox9 gene regulation in chondrocytes that might aid in our understanding of the pathophysiology of skeletal disorders.
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Affiliation(s)
- Sachi Ichiyama-Kobayashi
- Department of Molecular and Cellular Biochemistry
- Department of Oral and Maxillofacial Oncology and Surgery, and
| | - Kenji Hata
- Department of Molecular and Cellular Biochemistry
| | - Kanta Wakamori
- Department of Molecular and Cellular Biochemistry
- Department of Oral and Maxillofacial Oncology and Surgery, and
| | - Yoshifumi Takahata
- Department of Molecular and Cellular Biochemistry
- Genome Editing Research and Development Unit, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
| | | | - Hitomi Yamanaka
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo, Japan
| | - Hiroshi Takano
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo, Japan
| | - Ryoji Yao
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo, Japan
| | - Narikazu Uzawa
- Department of Oral and Maxillofacial Oncology and Surgery, and
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21
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Paul SK, Oshima M, Patil A, Sone M, Kato H, Maezawa Y, Kaneko H, Fukuyo M, Rahmutulla B, Ouchi Y, Tsujimura K, Nakanishi M, Kaneda A, Iwama A, Yokote K, Eto K, Takayama N. Retrotransposons in Werner syndrome-derived macrophages trigger type I interferon-dependent inflammation in an atherosclerosis model. Nat Commun 2024; 15:4772. [PMID: 38858384 PMCID: PMC11164933 DOI: 10.1038/s41467-024-48663-w] [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: 05/07/2022] [Accepted: 05/07/2024] [Indexed: 06/12/2024] Open
Abstract
The underlying mechanisms of atherosclerosis, the second leading cause of death among Werner syndrome (WS) patients, are not fully understood. Here, we establish an in vitro co-culture system using macrophages (iMφs), vascular endothelial cells (iVECs), and vascular smooth muscle cells (iVSMCs) derived from induced pluripotent stem cells. In co-culture, WS-iMφs induces endothelial dysfunction in WS-iVECs and characteristics of the synthetic phenotype in WS-iVSMCs. Transcriptomics and open chromatin analysis reveal accelerated activation of type I interferon signaling and reduced chromatin accessibility of several transcriptional binding sites required for cellular homeostasis in WS-iMφs. Furthermore, the H3K9me3 levels show an inverse correlation with retrotransposable elements, and retrotransposable element-derived double-stranded RNA activates the DExH-box helicase 58 (DHX58)-dependent cytoplasmic RNA sensing pathway in WS-iMφs. Conversely, silencing type I interferon signaling in WS-iMφs rescues cell proliferation and suppresses cellular senescence and inflammation. These findings suggest that Mφ-specific inhibition of type I interferon signaling could be targeted to treat atherosclerosis in WS patients.
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Affiliation(s)
- Sudip Kumar Paul
- Department of Regenerative Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Motohiko Oshima
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | - Masamitsu Sone
- Department of Regenerative Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Hibernation Metabolism, Physiology and Development Group, Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Hisaya Kato
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yoshiro Maezawa
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiyori Kaneko
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yasuo Ouchi
- Department of Regenerative Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Kyoko Tsujimura
- Department of Regenerative Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | | | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Iwama
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Koutaro Yokote
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba, Japan.
| | - Koji Eto
- Department of Regenerative Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan.
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan.
| | - Naoya Takayama
- Department of Regenerative Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan.
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22
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Lim LQJ, Adler L, Hajaj E, Soria LR, Perry RBT, Darzi N, Brody R, Furth N, Lichtenstein M, Bab-Dinitz E, Porat Z, Melman T, Brandis A, Aylon Y, Ben-Dor S, Orr I, Pri-Or A, Seger R, Shaul Y, Ruppin E, Oren M, Perez M, Meier J, Brunetti-Pierri N, Shema E, Ulitsky I, Erez A, Malitsky S, Itkin M. ASS1 metabolically contributes to the nuclear and cytosolic p53-mediated DNA damage response. Nat Metab 2024:10.1038/s42255-024-01060-5. [PMID: 38858597 DOI: 10.1038/s42255-024-01060-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 04/30/2024] [Indexed: 06/12/2024]
Abstract
Downregulation of the urea cycle enzyme argininosuccinate synthase (ASS1) in multiple tumors is associated with a poor prognosis partly because of the metabolic diversion of cytosolic aspartate for pyrimidine synthesis, supporting proliferation and mutagenesis owing to nucleotide imbalance. Here, we find that prolonged loss of ASS1 promotes DNA damage in colon cancer cells and fibroblasts from subjects with citrullinemia type I. Following acute induction of DNA damage with doxorubicin, ASS1 expression is elevated in the cytosol and the nucleus with at least a partial dependency on p53; ASS1 metabolically restrains cell cycle progression in the cytosol by restricting nucleotide synthesis. In the nucleus, ASS1 and ASL generate fumarate for the succination of SMARCC1, destabilizing the chromatin-remodeling complex SMARCC1-SNF5 to decrease gene transcription, specifically in a subset of the p53-regulated cell cycle genes. Thus, following DNA damage, ASS1 is part of the p53 network that pauses cell cycle progression, enabling genome maintenance and survival. Loss of ASS1 contributes to DNA damage and promotes cell cycle progression, likely contributing to cancer mutagenesis and, hence, adaptability potential.
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Affiliation(s)
- Lisha Qiu Jin Lim
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Lital Adler
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Emma Hajaj
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Medicine D, Beilinson Hospital, Petah Tikva, Israel
| | - Leandro R Soria
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Rotem Ben-Tov Perry
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Naama Darzi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ruchama Brody
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Furth
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Lichtenstein
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Elizabeta Bab-Dinitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ziv Porat
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Tevie Melman
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Brandis
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Yael Aylon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Irit Orr
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Amir Pri-Or
- The De Botton Protein Profiling Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Rony Seger
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yoav Shaul
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eytan Ruppin
- Cancer Data Science Lab, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Moshe Oren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Minervo Perez
- Cancer Data Science Lab, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Jordan Meier
- Cancer Data Science Lab, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Department of Translational Medicine, Medical Genetics, University of Naples Federico II, Naples, Italy
- Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomics and Experimental Medicine Program, University of Naples Federico II, Naples, Italy
| | - Efrat Shema
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Ayelet Erez
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Sergey Malitsky
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Maxim Itkin
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
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23
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Robertson AL, Yue L, Choudhuri A, Kubaczka C, Wattrus SJ, Mandelbaum J, Avagyan S, Yang S, Freeman RJ, Chan V, Blair MC, Daley GQ, Zon LI. Hematopoietic stem cell division is governed by distinct RUNX1 binding partners. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.07.596542. [PMID: 38895208 PMCID: PMC11185638 DOI: 10.1101/2024.06.07.596542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
A defined number of hematopoietic stem cell (HSC) clones are born during development and expand to form the pool of adult stem cells. An intricate balance between self-renewal and differentiation of these HSCs supports hematopoiesis for life. HSC fate is determined by complex transcription factor networks that drive cell-type specific gene programs. The transcription factor RUNX1 is required for definitive hematopoiesis, and mutations in Runx1 have been shown to reduce clonal diversity. The RUNX1 cofactor, CBFý, stabilizes RUNX1 binding to DNA, and disruption of their interaction alters downstream gene expression. Chemical screening for modulators of Runx1 and HSC expansion in zebrafish led us to identify a new mechanism for the RUNX1 inhibitor, Ro5-3335. We found that Ro5-3335 increased HSC divisions in zebrafish, and animals transplanted with Ro5-3335 treated cells had enhanced chimerism compared to untreated cells. Using human CD34+ cells, we show that Ro5-3335 remodels the RUNX1 transcription complex by binding to ELF1, independent of CBFý. This allows specific expression of cell cycle and hematopoietic genes that enhance HSC self-renewal and prevent differentiation. Furthermore, we provide the first evidence to show that it is possible to pharmacologically increase the number of stem cell clones in vivo , revealing a previously unknown mechanism for enhancing clonal diversity. Our studies have revealed a mechanism by which binding partners of RUNX1 determine cell fate, with ELF transcription factors guiding cell division. This information could lead to treatments that enhance clonal diversity for blood diseases.
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24
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Ando T, Takazawa I, Spencer ZT, Ito R, Tomimori Y, Mikulski Z, Matsumoto K, Ishitani T, Denson LA, Kawakami Y, Kawakami Y, Kitaura J, Ahmed Y, Kawakami T. Ileal Crohn's Disease Exhibits Reduced Activity of Phospholipase C-β3-Dependent Wnt/β-Catenin Signaling Pathway. Cells 2024; 13:986. [PMID: 38891118 PMCID: PMC11171731 DOI: 10.3390/cells13110986] [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: 05/06/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Crohn's disease is a chronic, debilitating, inflammatory bowel disease. Here, we report a critical role of phospholipase C-β3 (PLC-β3) in intestinal homeostasis. In PLC-β3-deficient mice, exposure to oral dextran sodium sulfate induced lethality and severe inflammation in the small intestine. The lethality was due to PLC-β3 deficiency in multiple non-hematopoietic cell types. PLC-β3 deficiency resulted in reduced Wnt/β-catenin signaling, which is essential for homeostasis and the regeneration of the intestinal epithelium. PLC-β3 regulated the Wnt/β-catenin pathway in small intestinal epithelial cells (IECs) at transcriptional, epigenetic, and, potentially, protein-protein interaction levels. PLC-β3-deficient IECs were unable to respond to stimulation by R-spondin 1, an enhancer of Wnt/β-catenin signaling. Reduced expression of PLC-β3 and its signature genes was found in biopsies of patients with ileal Crohn's disease. PLC-β regulation of Wnt signaling was evolutionally conserved in Drosophila. Our data indicate that a reduction in PLC-β3-mediated Wnt/β-catenin signaling contributes to the pathogenesis of ileal Crohn's disease.
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Affiliation(s)
- Tomoaki Ando
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
- Atopy Research Center, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Ikuo Takazawa
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
| | - Zachary T. Spencer
- Department of Molecular and Systems Biology and the Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA; (Z.T.S.)
| | - Ryoji Ito
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
- Central Institute for Experimental Animals, Kawasaki 210-0821, Kanagawa, Japan
| | - Yoshiaki Tomimori
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
| | - Zbigniew Mikulski
- Imaging Facility, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Kenji Matsumoto
- Department of Allergy and Clinical Immunology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Tohru Ishitani
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi 371-0044, Gunma, Japan
| | - Lee A. Denson
- Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Yu Kawakami
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
| | - Yuko Kawakami
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
| | - Jiro Kitaura
- Atopy Research Center, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Yashi Ahmed
- Department of Molecular and Systems Biology and the Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA; (Z.T.S.)
| | - Toshiaki Kawakami
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
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25
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Sasaki M, Kato D, Murakami K, Yoshida H, Takase S, Otsubo T, Ogiwara H. Targeting dependency on a paralog pair of CBP/p300 against de-repression of KREMEN2 in SMARCB1-deficient cancers. Nat Commun 2024; 15:4770. [PMID: 38839769 PMCID: PMC11153594 DOI: 10.1038/s41467-024-49063-w] [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: 06/19/2023] [Accepted: 05/22/2024] [Indexed: 06/07/2024] Open
Abstract
SMARCB1, a subunit of the SWI/SNF chromatin remodeling complex, is the causative gene of rhabdoid tumors and epithelioid sarcomas. Here, we identify a paralog pair of CBP and p300 as a synthetic lethal target in SMARCB1-deficient cancers by using a dual siRNA screening method based on the "simultaneous inhibition of a paralog pair" concept. Treatment with CBP/p300 dual inhibitors suppresses growth of cell lines and tumor xenografts derived from SMARCB1-deficient cells but not from SMARCB1-proficient cells. SMARCB1-containing SWI/SNF complexes localize with H3K27me3 and its methyltransferase EZH2 at the promotor region of the KREMEN2 locus, resulting in transcriptional downregulation of KREMEN2. By contrast, SMARCB1 deficiency leads to localization of H3K27ac, and recruitment of its acetyltransferases CBP and p300, at the KREMEN2 locus, resulting in transcriptional upregulation of KREMEN2, which cooperates with the SMARCA1 chromatin remodeling complex. Simultaneous inhibition of CBP/p300 leads to transcriptional downregulation of KREMEN2, followed by apoptosis induction via monomerization of KREMEN1 due to a failure to interact with KREMEN2, which suppresses anti-apoptotic signaling pathways. Taken together, our findings indicate that simultaneous inhibitors of CBP/p300 could be promising therapeutic agents for SMARCB1-deficient cancers.
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Affiliation(s)
- Mariko Sasaki
- Division of Cancer Therapeutics, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Daiki Kato
- Cancer Research Unit, Sumitomo Pharma Co., Ltd, 3-1-98 Kasugade-naka, Konohana-ku, Osaka, 554-0022, Japan
| | - Karin Murakami
- Cancer Research Unit, Sumitomo Pharma Co., Ltd, 3-1-98 Kasugade-naka, Konohana-ku, Osaka, 554-0022, Japan
| | - Hiroshi Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Shohei Takase
- Division of Cancer Therapeutics, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Tsuguteru Otsubo
- Cancer Research Unit, Sumitomo Pharma Co., Ltd, 3-1-98 Kasugade-naka, Konohana-ku, Osaka, 554-0022, Japan
| | - Hideaki Ogiwara
- Division of Cancer Therapeutics, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
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26
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Huo Q, Song R, Ma Z. Recent advances in exploring transcriptional regulatory landscape of crops. FRONTIERS IN PLANT SCIENCE 2024; 15:1421503. [PMID: 38903438 PMCID: PMC11188431 DOI: 10.3389/fpls.2024.1421503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024]
Abstract
Crop breeding entails developing and selecting plant varieties with improved agronomic traits. Modern molecular techniques, such as genome editing, enable more efficient manipulation of plant phenotype by altering the expression of particular regulatory or functional genes. Hence, it is essential to thoroughly comprehend the transcriptional regulatory mechanisms that underpin these traits. In the multi-omics era, a large amount of omics data has been generated for diverse crop species, including genomics, epigenomics, transcriptomics, proteomics, and single-cell omics. The abundant data resources and the emergence of advanced computational tools offer unprecedented opportunities for obtaining a holistic view and profound understanding of the regulatory processes linked to desirable traits. This review focuses on integrated network approaches that utilize multi-omics data to investigate gene expression regulation. Various types of regulatory networks and their inference methods are discussed, focusing on recent advancements in crop plants. The integration of multi-omics data has been proven to be crucial for the construction of high-confidence regulatory networks. With the refinement of these methodologies, they will significantly enhance crop breeding efforts and contribute to global food security.
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Affiliation(s)
| | | | - Zeyang Ma
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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27
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Mok CH, Hu D, Losa M, Risolino M, Selleri L, Marcucio RS. PBX1 and PBX3 transcription factors regulate SHH expression in the Frontonasal Ectodermal Zone through complementary mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597450. [PMID: 38895322 PMCID: PMC11185640 DOI: 10.1101/2024.06.04.597450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Sonic hedgehog (SHH) signaling from the frontonasal ectodermal zone (FEZ) is a key regulator of craniofacial morphogenesis. Along with SHH, pre-B-cell leukemia homeobox (PBX) transcription factors regulate midfacial development. PBXs act in the epithelium during fusion of facial primordia, but their specific interactions with SHH have not been fully investigated. We hypothesized that PBX1/3 regulate SHH expression in the FEZ by activating or repressing transcription. The hypothesis was tested by manipulating PBX1/3 expression in chick embryos and profiling epigenomic landscapes at early developmental stages. PBX1/3 expression was perturbed in the chick face beginning at stage 10 (HH10) using RCAS viruses, and the resulting SHH expression was assessed at HH22. Overexpressing PBX1 expanded SHH expression, while overexpressing PBX3 decreased SHH expression. Conversely, reducing PBX1 expression decreased SHH expression, but reducing PBX3 induced ectopic SHH expression. We performed ATAC-seq and mapped binding of PBX1 and PBX3 with ChIP-seq on the FEZ at HH22 to assess direct interactions of PBX1/3 with the SHH locus. These multi-omics approaches uncovered a 400 bp PBX1-enriched element within intron 1 of SHH (chr2:8,173,222-8,173,621). Enhancer activity of this element was demonstrated by electroporation of reporter constructs in ovo and luciferase reporter assays in vitro . When bound by PBX1, this element upregulates transcription, while it downregulates transcription when bound by PBX3. The present study identifies a cis- regulatory element, named SFE1, that interacts with PBX1/3 to modulate SHH expression in the FEZ and establishes that PBX1 and PBX3 play complementary roles in SHH regulation during embryonic development.
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28
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Qiao X, van der Zanden SY, Li X, Tan M, Zhang Y, Song JY, van Gelder MA, Hamoen FL, Janssen L, Zuur CL, Pang B, van Tellingen O, Li J, Neefjes J. Diversifying the anthracycline class of anti-cancer drugs identifies aclarubicin for superior survival of acute myeloid leukemia patients. Mol Cancer 2024; 23:120. [PMID: 38831402 PMCID: PMC11149191 DOI: 10.1186/s12943-024-02034-7] [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: 11/22/2023] [Accepted: 05/28/2024] [Indexed: 06/05/2024] Open
Abstract
The efficacy of anthracycline-based chemotherapeutics, which include doxorubicin and its structural relatives daunorubicin and idarubicin, remains almost unmatched in oncology, despite a side effect profile including cumulative dose-dependent cardiotoxicity, therapy-related malignancies and infertility. Detoxifying anthracyclines while preserving their anti-neoplastic effects is arguably a major unmet need in modern oncology, as cardiovascular complications that limit anti-cancer treatment are a leading cause of morbidity and mortality among the 17 million cancer survivors in the U.S. In this study, we examined different clinically relevant anthracycline drugs for a series of features including mode of action (chromatin and DNA damage), bio-distribution, anti-tumor efficacy and cardiotoxicity in pre-clinical models and patients. The different anthracycline drugs have surprisingly individual efficacy and toxicity profiles. In particular, aclarubicin stands out in pre-clinical models and clinical studies, as it potently kills cancer cells, lacks cardiotoxicity, and can be safely administered even after the maximum cumulative dose of either doxorubicin or idarubicin has been reached. Retrospective analysis of aclarubicin used as second-line treatment for relapsed/refractory AML patients showed survival effects similar to its use in first line, leading to a notable 23% increase in 5-year overall survival compared to other intensive chemotherapies. Considering individual anthracyclines as distinct entities unveils new treatment options, such as the identification of aclarubicin, which significantly improves the survival outcomes of AML patients while mitigating the treatment-limiting side-effects. Building upon these findings, an international multicenter Phase III prospective study is prepared, to integrate aclarubicin into the treatment of relapsed/refractory AML patients.
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Affiliation(s)
- Xiaohang Qiao
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Department of Head and Neck Oncology and Surgery, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Sabina Y van der Zanden
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Xiaoyang Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minkang Tan
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Yunxiang Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ji-Ying Song
- Division of Experimental Animal Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Merle A van Gelder
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Feija L Hamoen
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Lennert Janssen
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Charlotte L Zuur
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Head and Neck Oncology and Surgery, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Baoxu Pang
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Olaf van Tellingen
- Division of Pharmacology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Junmin Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Wuxi Branch of Ruijin Hospital, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai , 200025, China.
| | - Jacques Neefjes
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center, Leiden, The Netherlands.
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29
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Loupe JM, Anderson AG, Rizzardi LF, Rodriguez-Nunez I, Moyers B, Trausch-Lowther K, Jain R, Bunney WE, Bunney BG, Cartagena P, Sequeira A, Watson SJ, Akil H, Cooper GM, Myers RM. Multiomic profiling of transcription factor binding and function in human brain. Nat Neurosci 2024:10.1038/s41593-024-01658-8. [PMID: 38831039 DOI: 10.1038/s41593-024-01658-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 04/19/2024] [Indexed: 06/05/2024]
Abstract
Transcription factors (TFs) orchestrate gene expression programs crucial for brain function, but we lack detailed information about TF binding in human brain tissue. We generated a multiomic resource (ChIP-seq, ATAC-seq, RNA-seq, DNA methylation) on bulk tissues and sorted nuclei from several postmortem brain regions, including binding maps for more than 100 TFs. We demonstrate improved measurements of TF activity, including motif recognition and gene expression modeling, upon identification and removal of high TF occupancy regions. Further, predictive TF binding models demonstrate a bias for these high-occupancy sites. Neuronal TFs SATB2 and TBR1 bind unique regions depleted for such sites and promote neuronal gene expression. Binding sites for TFs, including TBR1 and PKNOX1, are enriched for risk variants associated with neuropsychiatric disorders, predominantly in neurons. This work, titled BrainTF, is a powerful resource for future studies seeking to understand the roles of specific TFs in regulating gene expression in the human brain.
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Affiliation(s)
- Jacob M Loupe
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Lindsay F Rizzardi
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Biochemistry and Molecular Biology, The University of Alabama in Birmingham, Birmingham, AL, USA
| | | | - Belle Moyers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Rashmi Jain
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - William E Bunney
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA, USA
| | - Blynn G Bunney
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA, USA
| | - Preston Cartagena
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA, USA
| | - Adolfo Sequeira
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA, USA
| | - Stanley J Watson
- The Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Huda Akil
- The Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | | | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
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30
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Gonzalez-Avalos E, Onodera A, Samaniego-Castruita D, Rao A, Ay F. Predicting gene expression state and prioritizing putative enhancers using 5hmC signal. Genome Biol 2024; 25:142. [PMID: 38825692 PMCID: PMC11145787 DOI: 10.1186/s13059-024-03273-z] [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: 04/03/2023] [Accepted: 05/11/2024] [Indexed: 06/04/2024] Open
Abstract
BACKGROUND Like its parent base 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) is a direct epigenetic modification of cytosines in the context of CpG dinucleotides. 5hmC is the most abundant oxidized form of 5mC, generated through the action of TET dioxygenases at gene bodies of actively-transcribed genes and at active or lineage-specific enhancers. Although such enrichments are reported for 5hmC, to date, predictive models of gene expression state or putative regulatory regions for genes using 5hmC have not been developed. RESULTS Here, by using only 5hmC enrichment in genic regions and their vicinity, we develop neural network models that predict gene expression state across 49 cell types. We show that our deep neural network models distinguish high vs low expression state utilizing only 5hmC levels and these predictive models generalize to unseen cell types. Further, in order to leverage 5hmC signal in distal enhancers for expression prediction, we employ an Activity-by-Contact model and also develop a graph convolutional neural network model with both utilizing Hi-C data and 5hmC enrichment to prioritize enhancer-promoter links. These approaches identify known and novel putative enhancers for key genes in multiple immune cell subsets. CONCLUSIONS Our work highlights the importance of 5hmC in gene regulation through proximal and distal mechanisms and provides a framework to link it to genome function. With the recent advances in 6-letter DNA sequencing by short and long-read techniques, profiling of 5mC and 5hmC may be done routinely in the near future, hence, providing a broad range of applications for the methods developed here.
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Affiliation(s)
- Edahi Gonzalez-Avalos
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Atsushi Onodera
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Daniela Samaniego-Castruita
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Biological Sciences Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Anjana Rao
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA.
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92093, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Ferhat Ay
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.
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31
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Peng D, Cahan P. OneSC: A computational platform for recapitulating cell state transitions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596831. [PMID: 38895453 PMCID: PMC11185539 DOI: 10.1101/2024.05.31.596831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Computational modelling of cell state transitions has been a great interest of many in the field of developmental biology, cancer biology and cell fate engineering because it enables performing perturbation experiments in silico more rapidly and cheaply than could be achieved in a wet lab. Recent advancements in single-cell RNA sequencing (scRNA-seq) allow the capture of high- resolution snapshots of cell states as they transition along temporal trajectories. Using these high-throughput datasets, we can train computational models to generate in silico 'synthetic' cells that faithfully mimic the temporal trajectories. Here we present OneSC, a platform that can simulate synthetic cells across developmental trajectories using systems of stochastic differential equations govern by a core transcription factors (TFs) regulatory network. Different from the current network inference methods, OneSC prioritizes on generating Boolean network that produces faithful cell state transitions and steady cell states that mimic real biological systems. Applying OneSC to real data, we inferred a core TF network using a mouse myeloid progenitor scRNA-seq dataset and showed that the dynamical simulations of that network generate synthetic single-cell expression profiles that faithfully recapitulate the four myeloid differentiation trajectories going into differentiated cell states (erythrocytes, megakaryocytes, granulocytes and monocytes). Finally, through the in-silico perturbations of the mouse myeloid progenitor core network, we showed that OneSC can accurately predict cell fate decision biases of TF perturbations that closely match with previous experimental observations.
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De Sá Fernandes C, Novoszel P, Gastaldi T, Krauß D, Lang M, Rica R, Kutschat AP, Holcmann M, Ellmeier W, Seruggia D, Strobl H, Sibilia M. The histone deacetylase HDAC1 controls dendritic cell development and anti-tumor immunity. Cell Rep 2024; 43:114308. [PMID: 38829740 DOI: 10.1016/j.celrep.2024.114308] [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: 10/23/2023] [Revised: 03/17/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024] Open
Abstract
Dendritic cell (DC) progenitors adapt their transcriptional program during development, generating different subsets. How chromatin modifications modulate these processes is unclear. Here, we investigate the impact of histone deacetylation on DCs by genetically deleting histone deacetylase 1 (HDAC1) or HDAC2 in hematopoietic progenitors and CD11c-expressing cells. While HDAC2 is not critical for DC development, HDAC1 deletion impairs pro-pDC and mature pDC generation and affects ESAM+cDC2 differentiation from tDCs and pre-cDC2s, whereas cDC1s are unchanged. HDAC1 knockdown in human hematopoietic cells also impairs cDC2 development, highlighting its crucial role across species. Multi-omics analyses reveal that HDAC1 controls expression, chromatin accessibility, and histone acetylation of the transcription factors IRF4, IRF8, and SPIB required for efficient development of cDC2 subsets. Without HDAC1, DCs switch immunologically, enhancing tumor surveillance through increased cDC1 maturation and interleukin-12 production, driving T helper 1-mediated immunity and CD8+ T cell recruitment. Our study reveals the importance of histone acetylation in DC development and anti-tumor immunity, suggesting DC-targeted therapeutic strategies for immuno-oncology.
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Affiliation(s)
- Cristiano De Sá Fernandes
- Center for Cancer Research, Medical University of Vienna, Comprehensive Cancer Center, Vienna, Austria
| | - Philipp Novoszel
- Center for Cancer Research, Medical University of Vienna, Comprehensive Cancer Center, Vienna, Austria
| | - Tommaso Gastaldi
- Center for Cancer Research, Medical University of Vienna, Comprehensive Cancer Center, Vienna, Austria
| | - Dana Krauß
- Center for Cancer Research, Medical University of Vienna, Comprehensive Cancer Center, Vienna, Austria
| | - Magdalena Lang
- Division of Immunology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Ramona Rica
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Ana P Kutschat
- St. Anna Children's Cancer Research Institute, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Martin Holcmann
- Center for Cancer Research, Medical University of Vienna, Comprehensive Cancer Center, Vienna, Austria
| | - Wilfried Ellmeier
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Davide Seruggia
- St. Anna Children's Cancer Research Institute, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Herbert Strobl
- Division of Immunology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Maria Sibilia
- Center for Cancer Research, Medical University of Vienna, Comprehensive Cancer Center, Vienna, Austria.
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33
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Iurlaro M, Masoni F, Flyamer IM, Wirbelauer C, Iskar M, Burger L, Giorgetti L, Schübeler D. Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF. Nat Genet 2024; 56:1203-1212. [PMID: 38816647 PMCID: PMC11176080 DOI: 10.1038/s41588-024-01767-x] [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: 07/07/2023] [Accepted: 04/23/2024] [Indexed: 06/01/2024]
Abstract
Catalytic activity of the imitation switch (ISWI) family of remodelers is critical for nucleosomal organization and DNA binding of certain transcription factors, including the insulator protein CTCF. Here we define the contribution of individual subcomplexes by deriving a panel of isogenic mouse stem cell lines, each lacking one of six ISWI accessory subunits. Individual deletions of subunits of either CERF, RSF, ACF, WICH or NoRC subcomplexes only moderately affect the chromatin landscape, while removal of the NURF-specific subunit BPTF leads to a strong reduction in chromatin accessibility and SNF2H ATPase localization around CTCF sites. This affects adjacent nucleosome occupancy and CTCF binding. At a group of sites with reduced chromatin accessibility, CTCF binding persists but cohesin occupancy is reduced, resulting in decreased insulation. These results suggest that CTCF binding can be separated from its function as an insulator in nuclear organization and identify a specific role for NURF in mediating SNF2H localization and chromatin opening at bound CTCF sites.
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Affiliation(s)
- Mario Iurlaro
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Disease Area Oncology, Novartis Biomedical Research, Basel, Switzerland
| | - Francesca Masoni
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Ilya M Flyamer
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Murat Iskar
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Lukas Burger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
- Faculty of Science, University of Basel, Basel, Switzerland.
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Nanda AS, Wu K, Irkliyenko I, Woo B, Ostrowski MS, Clugston AS, Sayles LC, Xu L, Satpathy AT, Nguyen HG, Alejandro Sweet-Cordero E, Goodarzi H, Kasinathan S, Ramani V. Direct transposition of native DNA for sensitive multimodal single-molecule sequencing. Nat Genet 2024; 56:1300-1309. [PMID: 38724748 PMCID: PMC11176058 DOI: 10.1038/s41588-024-01748-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 04/08/2024] [Indexed: 05/23/2024]
Abstract
Concurrent readout of sequence and base modifications from long unamplified DNA templates by Pacific Biosciences of California (PacBio) single-molecule sequencing requires large amounts of input material. Here we adapt Tn5 transposition to introduce hairpin oligonucleotides and fragment (tagment) limiting quantities of DNA for generating PacBio-compatible circular molecules. We developed two methods that implement tagmentation and use 90-99% less input than current protocols: (1) single-molecule real-time sequencing by tagmentation (SMRT-Tag), which allows detection of genetic variation and CpG methylation; and (2) single-molecule adenine-methylated oligonucleosome sequencing assay by tagmentation (SAMOSA-Tag), which uses exogenous adenine methylation to add a third channel for probing chromatin accessibility. SMRT-Tag of 40 ng or more human DNA (approximately 7,000 cell equivalents) yielded data comparable to gold standard whole-genome and bisulfite sequencing. SAMOSA-Tag of 30,000-50,000 nuclei resolved single-fiber chromatin structure, CTCF binding and DNA methylation in patient-derived prostate cancer xenografts and uncovered metastasis-associated global epigenome disorganization. Tagmentation thus promises to enable sensitive, scalable and multimodal single-molecule genomics for diverse basic and clinical applications.
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Affiliation(s)
- Arjun S Nanda
- Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Ke Wu
- Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
| | - Iryna Irkliyenko
- Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
| | - Brian Woo
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Helen-Diller Cancer Center, San Francisco, CA, USA
| | - Megan S Ostrowski
- Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
| | - Andrew S Clugston
- Helen-Diller Cancer Center, San Francisco, CA, USA
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Leanne C Sayles
- Helen-Diller Cancer Center, San Francisco, CA, USA
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Lingru Xu
- Helen-Diller Cancer Center, San Francisco, CA, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Gladstone-University of California, San Francisco Institute for Genomic Immunology, Gladstone Institutes, San Francisco, CA, USA
| | - Hao G Nguyen
- Helen-Diller Cancer Center, San Francisco, CA, USA
| | - E Alejandro Sweet-Cordero
- Helen-Diller Cancer Center, San Francisco, CA, USA
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Helen-Diller Cancer Center, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, San Francisco, CA, USA
| | - Sivakanthan Kasinathan
- Gladstone-University of California, San Francisco Institute for Genomic Immunology, Gladstone Institutes, San Francisco, CA, USA.
- Division of Rheumatology, Department of Pediatrics, Stanford University, Stanford, CA, USA.
| | - Vijay Ramani
- Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
- Helen-Diller Cancer Center, San Francisco, CA, USA.
- Bakar Computational Health Sciences Institute, San Francisco, CA, USA.
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35
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Serra-Bardenys G, Blanco E, Escudero-Iriarte C, Serra-Camprubí Q, Querol J, Pascual-Reguant L, Morancho B, Escorihuela M, Tissera NS, Sabé A, Martín L, Segura-Bayona S, Verde G, Aiese Cigliano R, Millanes-Romero A, Jerónimo C, Cebrià-Costa JP, Nuciforo P, Simonetti S, Viaplana C, Dienstmann R, Oliveira M, Peg V, Stracker TH, Arribas J, Canals F, Villanueva J, Di Croce L, García de Herreros A, Tian TV, Peiró S. LOXL2-mediated chromatin compaction is required to maintain the oncogenic properties of triple-negative breast cancer cells. FEBS J 2024; 291:2423-2448. [PMID: 38451841 DOI: 10.1111/febs.17112] [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: 06/01/2023] [Revised: 01/02/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024]
Abstract
Oxidation of histone H3 at lysine 4 (H3K4ox) is catalyzed by lysyl oxidase homolog 2 (LOXL2). This histone modification is enriched in heterochromatin in triple-negative breast cancer (TNBC) cells and has been linked to the maintenance of compacted chromatin. However, the molecular mechanism underlying this maintenance is still unknown. Here, we show that LOXL2 interacts with RuvB-Like 1 (RUVBL1), RuvB-Like 2 (RUVBL2), Actin-like protein 6A (ACTL6A), and DNA methyltransferase 1associated protein 1 (DMAP1), a complex involved in the incorporation of the histone variant H2A.Z. Our experiments indicate that this interaction and the active form of RUVBL2 are required to maintain LOXL2-dependent chromatin compaction. Genome-wide experiments showed that H2A.Z, RUVBL2, and H3K4ox colocalize in heterochromatin regions. In the absence of LOXL2 or RUVBL2, global levels of the heterochromatin histone mark H3K9me3 were strongly reduced, and the ATAC-seq signal in the H3K9me3 regions was increased. Finally, we observed that the interplay between these series of events is required to maintain H3K4ox-enriched heterochromatin regions, which in turn is key for maintaining the oncogenic properties of the TNBC cell line tested (MDA-MB-231).
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Affiliation(s)
- Gemma Serra-Bardenys
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Institut Bonanova FP Sanitaria, Consorci Mar Parc de Salut de Barcelona, Spain
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
| | | | | | - Jessica Querol
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Laura Pascual-Reguant
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
| | | | | | | | - Anna Sabé
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Luna Martín
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Gaetano Verde
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Alba Millanes-Romero
- Institute for Research in Biomedicine (IRB Barcelona) and Barcelona Institute of Science and Technology, Spain
| | - Celia Jerónimo
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
- Institut de Recherches Cliniques de Montréal, Canada
| | | | - Paolo Nuciforo
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Sara Simonetti
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | | | - Mafalda Oliveira
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Vicente Peg
- Medical Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncología (CIBERONC), Barcelona, Spain
- Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Travis H Stracker
- Radiation Oncology Branch, National Cancer Institute, Bethesda, MD, USA
| | - Joaquín Arribas
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Francesc Canals
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Antonio García de Herreros
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Tian V Tian
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Sandra Peiró
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
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36
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Gualdrini F, Rizzieri S, Polletti S, Pileri F, Zhan Y, Cuomo A, Natoli G. An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitors. Mol Syst Biol 2024; 20:626-650. [PMID: 38724853 PMCID: PMC11148061 DOI: 10.1038/s44320-024-00040-x] [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: 10/28/2023] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 06/05/2024] Open
Abstract
More than 500 kinases are implicated in the control of most cellular process in mammals, and deregulation of their activity is linked to cancer and inflammatory disorders. 80 clinical kinase inhibitors (CKIs) have been approved for clinical use and hundreds are in various stages of development. However, CKIs inhibit other kinases in addition to the intended target(s), causing both enhanced clinical effects and undesired side effects that are only partially predictable based on in vitro selectivity profiling. Here, we report an integrative approach grounded on the use of chromatin modifications as unbiased, information-rich readouts of the functional effects of CKIs on macrophage activation. This approach exceeded the performance of transcriptome-based approaches and allowed us to identify similarities and differences among CKIs with identical intended targets, to recognize novel CKI specificities and to pinpoint CKIs that may be repurposed to control inflammation, thus supporting the utility of this strategy to improve selection and use of CKIs in clinical settings.
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Affiliation(s)
- Francesco Gualdrini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, 20139, Italy.
| | - Stefano Rizzieri
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, 20139, Italy
| | - Sara Polletti
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, 20139, Italy
| | - Francesco Pileri
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, 20139, Italy
| | - Yinxiu Zhan
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, 20139, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, 20139, Italy
| | - Gioacchino Natoli
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, 20139, Italy.
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37
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Anderson CJ, Talmane L, Luft J, Connelly J, Nicholson MD, Verburg JC, Pich O, Campbell S, Giaisi M, Wei PC, Sundaram V, Connor F, Ginno PA, Sasaki T, Gilbert DM, López-Bigas N, Semple CA, Odom DT, Aitken SJ, Taylor MS. Strand-resolved mutagenicity of DNA damage and repair. Nature 2024; 630:744-751. [PMID: 38867042 PMCID: PMC11186772 DOI: 10.1038/s41586-024-07490-1] [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: 06/10/2022] [Accepted: 04/30/2024] [Indexed: 06/14/2024]
Abstract
DNA base damage is a major source of oncogenic mutations1. Such damage can produce strand-phased mutation patterns and multiallelic variation through the process of lesion segregation2. Here we exploited these properties to reveal how strand-asymmetric processes, such as replication and transcription, shape DNA damage and repair. Despite distinct mechanisms of leading and lagging strand replication3,4, we observe identical fidelity and damage tolerance for both strands. For small alkylation adducts of DNA, our results support a model in which the same translesion polymerase is recruited on-the-fly to both replication strands, starkly contrasting the strand asymmetric tolerance of bulky UV-induced adducts5. The accumulation of multiple distinct mutations at the site of persistent lesions provides the means to quantify the relative efficiency of repair processes genome wide and at single-base resolution. At multiple scales, we show DNA damage-induced mutations are largely shaped by the influence of DNA accessibility on repair efficiency, rather than gradients of DNA damage. Finally, we reveal specific genomic conditions that can actively drive oncogenic mutagenesis by corrupting the fidelity of nucleotide excision repair. These results provide insight into how strand-asymmetric mechanisms underlie the formation, tolerance and repair of DNA damage, thereby shaping cancer genome evolution.
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Affiliation(s)
- Craig J Anderson
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Lana Talmane
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Juliet Luft
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - John Connelly
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
- Edinburgh Pathology, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Laboratory Medicine, NHS Lothian, Edinburgh, UK
| | - Michael D Nicholson
- CRUK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Jan C Verburg
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Oriol Pich
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Susan Campbell
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Marco Giaisi
- Brain Mosaicism and Tumorigenesis (B400), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pei-Chi Wei
- Brain Mosaicism and Tumorigenesis (B400), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vasavi Sundaram
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Frances Connor
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Paul A Ginno
- Division of Regulatory Genomics and Cancer Evolution (B270), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Takayo Sasaki
- San Diego Biomedical Research Institute, San Diego, CA, USA
| | | | - Núria López-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Colin A Semple
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Duncan T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Division of Regulatory Genomics and Cancer Evolution (B270), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Sarah J Aitken
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
| | - Martin S Taylor
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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Guan X, Liu R, Wang B, Xiong R, Cui L, Liao Y, Ruan Y, Fang L, Lu X, Yu X, Su D, Ma Y, Dang T, Chen Z, Yao Y, Liu C, Zhang Y. Inhibition of HDAC2 sensitises antitumour therapy by promoting NLRP3/GSDMD-mediated pyroptosis in colorectal cancer. Clin Transl Med 2024; 14:e1692. [PMID: 38804602 PMCID: PMC11131357 DOI: 10.1002/ctm2.1692] [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: 12/26/2023] [Revised: 04/04/2024] [Accepted: 04/27/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Although numerous studies have indicated that activated pyroptosis can enhance the efficacy of antitumour therapy in several tumours, the precise mechanism of pyroptosis in colorectal cancer (CRC) remains unclear. METHODS Pyroptosis in CRC cells treated with antitumour agents was assessed using various techniques, including Western blotting, lactate dehydrogenase release assay and microscopy analysis. To uncover the epigenetic mechanisms that regulate NLRP3, chromatin changes and NLRP3 promoter histone modifications were assessed using Assay for Transposase-Accessible Chromatin using sequencing and RNA sequencing. Chromatin immunoprecipitation‒quantitative polymerase chain reaction was used to investigate the NLRP3 transcriptional regulatory mechanism. Additionally, xenograft and patient-derived xenograft models were constructed to validate the effects of the drug combinations. RESULTS As the core molecule of the inflammasome, NLRP3 expression was silenced in CRC, thereby limiting gasdermin D (GSDMD)-mediated pyroptosis. Supplementation with NLRP3 can rescue pyroptosis induced by antitumour therapy. Overexpression of HDAC2 in CRC silences NLRP3 via epigenetic regulation. Mechanistically, HDAC2 suppressed chromatin accessibility by eliminating H3K27 acetylation. HDAC2 knockout promotes H3K27ac-mediated recruitment of the BRD4-p-P65 complex to enhance NLRP3 transcription. Inhibiting HDAC2 by Santacruzamate A in combination with classic antitumour agents (5-fluorouracil or regorafenib) in CRC xenograft-bearing animals markedly activated pyroptosis and achieved a significant therapeutic effect. Clinically, HDAC2 is inversely correlated with H3K27ac/p-P65/NLRP3 and is a prognostic factor for CRC patients. CONCLUSION Collectively, our data revealed a crucial role for HDAC2 in inhibiting NLRP3/GSDMD-mediated pyroptosis in CRC cells and highlighted HDAC2 as a potential therapeutic target for antitumour therapy. HIGHLIGHTS Silencing of NLRP3 limits the GSDMD-dependent pyroptosis in colorectal cancer. HDAC2-mediated histone deacetylation leads to epigenetic silencing of NLRP3. HDAC2 suppresses the NLRP3 transcription by inhibiting the formation of H3K27ac/BRD4/p-P65 complex. Targeting HDAC2 activates pyroptosis and enhances therapeutic effect.
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Balard A, Baltazar-Soares M, Eizaguirre C, Heckwolf MJ. An epigenetic toolbox for conservation biologists. Evol Appl 2024; 17:e13699. [PMID: 38832081 PMCID: PMC11146150 DOI: 10.1111/eva.13699] [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: 11/10/2023] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 06/05/2024] Open
Abstract
Ongoing climatic shifts and increasing anthropogenic pressures demand an efficient delineation of conservation units and accurate predictions of populations' resilience and adaptive potential. Molecular tools involving DNA sequencing are nowadays routinely used for these purposes. Yet, most of the existing tools focusing on sequence-level information have shortcomings in detecting signals of short-term ecological relevance. Epigenetic modifications carry valuable information to better link individuals, populations, and species to their environment. Here, we discuss a series of epigenetic monitoring tools that can be directly applied to various conservation contexts, complementing already existing molecular monitoring frameworks. Focusing on DNA sequence-based methods (e.g. DNA methylation, for which the applications are readily available), we demonstrate how (a) the identification of epi-biomarkers associated with age or infection can facilitate the determination of an individual's health status in wild populations; (b) whole epigenome analyses can identify signatures of selection linked to environmental conditions and facilitate estimating the adaptive potential of populations; and (c) epi-eDNA (epigenetic environmental DNA), an epigenetic-based conservation tool, presents a non-invasive sampling method to monitor biological information beyond the mere presence of individuals. Overall, our framework refines conservation strategies, ensuring a comprehensive understanding of species' adaptive potential and persistence on ecologically relevant timescales.
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Affiliation(s)
- Alice Balard
- School of Biological and Behavioural Sciences Queen Mary University of London London UK
| | | | - Christophe Eizaguirre
- School of Biological and Behavioural Sciences Queen Mary University of London London UK
| | - Melanie J Heckwolf
- Department of Ecology Leibniz Centre for Tropical Marine Research Bremen Germany
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40
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Malone CF, Mabe NW, Forman AB, Alexe G, Engel KL, Chen YJC, Soeung M, Salhotra S, Basanthakumar A, Liu B, Dent SYR, Stegmaier K. The KAT module of the SAGA complex maintains the oncogenic gene expression program in MYCN-amplified neuroblastoma. SCIENCE ADVANCES 2024; 10:eadm9449. [PMID: 38820154 PMCID: PMC11141635 DOI: 10.1126/sciadv.adm9449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/29/2024] [Indexed: 06/02/2024]
Abstract
Pediatric cancers are frequently driven by genomic alterations that result in aberrant transcription factor activity. Here, we used functional genomic screens to identify multiple genes within the transcriptional coactivator Spt-Ada-Gcn5-acetyltransferase (SAGA) complex as selective dependencies for MYCN-amplified neuroblastoma, a disease of dysregulated development driven by an aberrant oncogenic transcriptional program. We characterized the DNA recruitment sites of the SAGA complex in neuroblastoma and the consequences of loss of SAGA complex lysine acetyltransferase (KAT) activity on histone acetylation and gene expression. We demonstrate that loss of SAGA complex KAT activity is associated with reduced MYCN binding on chromatin, suppression of MYC/MYCN gene expression programs, and impaired cell cycle progression. Further, we showed that the SAGA complex is pharmacologically targetable in vitro and in vivo with a KAT2A/KAT2B proteolysis targeting chimeric. Our findings expand our understanding of the histone-modifying complexes that maintain the oncogenic transcriptional state in this disease and suggest therapeutic potential for inhibitors of SAGA KAT activity in MYCN-amplified neuroblastoma.
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Affiliation(s)
- Clare F Malone
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Nathaniel W Mabe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Alexandra B Forman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kathleen L Engel
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ying-Jiun C Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Melinda Soeung
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Silvi Salhotra
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Allen Basanthakumar
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sharon Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
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41
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Fang J, Singh S, Wells B, Wu Q, Jin H, Janke LJ, Wan S, Steele JA, Connelly JP, Murphy AJ, Wang R, Davidoff AM, Ashcroft M, Pruett-Miller SM, Yang J. The context-dependent epigenetic and organogenesis programs determine 3D vs. 2D cellular fitness of MYC-driven cancer. RESEARCH SQUARE 2024:rs.3.rs-4390765. [PMID: 38853928 PMCID: PMC11160912 DOI: 10.21203/rs.3.rs-4390765/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
3D cellular-specific epigenetic and transcriptomic reprogramming is critical to organogenesis and tumorigenesis. Here we dissect the distinct cell fitness in 2D (normoxia vs. chronic hypoxia) vs 3D (normoxia) culture conditions. We identify over 600 shared essential genes and additional context-specific fitness genes and pathways. Knockout of the VHL-HIF1 pathway results in incompatible fitness defects under normoxia vs. 1% oxygen or 3D culture conditions. Moreover, deletion of each of the mitochondrial respiratory electron transport chain complex has distinct fitness outcomes. Notably, multicellular organogenesis signaling pathways including TGFβ-SMAD specifically constrict the uncontrolled cell proliferation in 3D while inactivation of epigenetic modifiers (Bcor, Kmt2d, Mettl3 and Mettl14) has opposite outcomes in 2D vs. 3D. We further identify a 3D-dependent synthetic lethality with partial loss of Prmt5 due to a reduction of Mtap expression resulting from 3D-specific epigenetic reprogramming. Our study highlights unique epigenetic, metabolic and organogenesis signaling dependencies under different cellular settings.
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Affiliation(s)
- Jie Fang
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shivendra Singh
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Brennan Wells
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Qiong Wu
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Laura J. Janke
- Department of Pathology and Division of Comparative Pathology, St. Jude Children’s Research Hospital, TN 38105, USA
| | - Shibiao Wan
- Bioinformatics and Systems Biology Core and Department of Genetics, Cell Biology and Anatomy University of Nebraska Medical Center, Omaha, NE 68198-5805, USA
| | - Jacob A. Steele
- Department of Cell and Molecular Biology, Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jon P. Connelly
- Department of Cell and Molecular Biology, Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Andrew J. Murphy
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ruoning Wang
- Center for Childhood Cancer Research, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Department of Pediatrics at The Ohio State University, Columbus, OH 43025, USA
| | - Andrew M. Davidoff
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
- St Jude Graduate School of Biomedical Sciences, St Jude Children’s Research Hospital, TN 38105
- Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science Center, 930 Madison Ave, Suite 500, Memphis, TN 38163, USA
| | - Margaret Ashcroft
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, United Kingdom
| | - Shondra M. Pruett-Miller
- Department of Cell and Molecular Biology, Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jun Yang
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
- St Jude Graduate School of Biomedical Sciences, St Jude Children’s Research Hospital, TN 38105
- Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science Center, 930 Madison Ave, Suite 500, Memphis, TN 38163, USA
- College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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Zhao Z, Guo D, Wei Y, Li J, Jia X, Niu Y, Liu Z, Bai Y, Chen Z, Shi B, Zhang X, Hu J, Wang J, Liu X, Li S. Integrative ATAC-seq and RNA-seq Analysis of the Longissimus Dorsi Muscle of Gannan Yak and Jeryak. Int J Mol Sci 2024; 25:6029. [PMID: 38892214 PMCID: PMC11172533 DOI: 10.3390/ijms25116029] [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: 04/29/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Jeryak is the F1 generation of the cross between Gannan yak and Jersey cattle, which has the advantages of fast growth and high adaptability. The growth and development of skeletal muscle is closely linked to meat production and the quality of meat. However, the molecular regulatory mechanisms of muscle growth differences between Gannan yak and Jeryak analyzed from the perspective of chromatin opening have not been reported. In this study, ATAC-seq was used to analyze the difference of chromatin openness in longissimus muscle of Gannan yak and Jeryak. It was found that chromatin accessibility was more enriched in Jeryak compared to Gannan yak, especially in the range of the transcription start site (TSS) ± 2 kb. GO and KEGG enrichment analysis indicate that differential peak-associated genes are involved in the negative regulation of muscle adaptation and the Hippo signaling pathway. Integration analysis of ATAC-seq and RNA-seq revealed overlapping genes were significantly enriched during skeletal muscle cell differentiation and muscle organ morphogenesis. At the same time, we screened FOXO1, ZBED6, CRY2 and CFL2 for possible involvement in skeletal muscle development, constructed a genes and transcription factors network map, and found that some transcription factors (TFs), including YY1, KLF4, KLF5 and Bach1, were involved in skeletal muscle development. Overall, we have gained a comprehensive understanding of the key factors that impact skeletal muscle development in various breeds of cattle, providing new insights for future analysis of the molecular regulatory mechanisms involved in muscle growth and development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730000, China; (Z.Z.); (D.G.); (Y.W.); (J.L.); (X.J.); (Y.N.); (Z.L.); (Y.B.); (Z.C.); (B.S.); (X.Z.); (J.W.); (X.L.); (S.L.)
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Chen D, Fan X, Wang K, Gong L, Melero-Martin JM, Pu WT. Pioneer factor ETV2 safeguards endothelial cell specification by recruiting the repressor REST to restrict alternative lineage commitment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.595971. [PMID: 38853821 PMCID: PMC11160620 DOI: 10.1101/2024.05.28.595971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Mechanisms of cell fate specification remain a central question for developmental biology and regenerative medicine. The pioneer factor ETV2 is a master regulator for the endothelial cell (EC) lineage specification. Here, we studied mechanisms of ETV2-driven fate specification using a highly efficient system in which ETV2 directs human induced pluripotent stem cell-derived mesodermal progenitors to form ECs over two days. By applying CUT&RUN, single-cell RNA-sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) analyses, we characterized the transcriptomic profiles, chromatin landscapes, dynamic cis-regulatory elements (CREs), and molecular features of EC cell differentiation mediated by ETV2. This defined the scope of ETV2 pioneering activity and identified its direct downstream target genes. Induced ETV2 expression both directed specification of endothelial progenitors and suppressed acquisition of alternative fates. Functional screening and candidate validation revealed cofactors essential for efficient EC specification, including the transcriptional activator GABPA. Surprisingly, the transcriptional repressor REST was also necessary for efficient EC specification. ETV2 recruited REST to occupy and repress non-EC lineage genes. Collectively, our study provides an unparalleled molecular analysis of EC specification at single-cell resolution and identifies the important role of pioneer factors to recruit repressors that suppress commitment to alternative lineages.
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44
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Gahan JM, Helfrich LW, Wetzel LA, Bhanu NV, Yuan ZF, Garcia BA, Klose R, Booth DS. Chromatin profiling identifies putative dual roles for H3K27me3 in regulating transposons and cell type-specific genes in choanoflagellates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596151. [PMID: 38854040 PMCID: PMC11160669 DOI: 10.1101/2024.05.28.596151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Gene expression is tightly controlled during animal development to allow the formation of specialized cell types. Our understanding of how animals evolved this exquisite regulatory control remains elusive, but evidence suggests that changes in chromatin-based mechanisms may have contributed. To investigate this possibility, here we examine chromatin-based gene regulatory features in the closest relatives of animals, choanoflagellates. Using Salpingoeca rosetta as a model system, we examined chromatin accessibility and histone modifications at the genome scale and compared these features to gene expression. We first observed that accessible regions of chromatin are primarily associated with gene promoters and found no evidence of distal gene regulatory elements resembling the enhancers that animals deploy to regulate developmental gene expression. Remarkably, a histone modification deposited by polycomb repressive complex 2, histone H3 lysine 27 trimethylation (H3K27me3), appeared to function similarly in S. rosetta to its role in animals, because this modification decorated genes with cell type-specific expression. Additionally, H3K27me3 marked transposons, retaining what appears to be an ancestral role in regulating these elements. We further uncovered a putative new bivalent chromatin state at cell type-specific genes that consists of H3K27me3 and histone H3 lysine 4 mono-methylation (H3K4me1). Together, our discoveries support the scenario that gene-associated histone modification states that underpin development emerged before the evolution of animal multicellularity.
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Affiliation(s)
- James M. Gahan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Biochemistry, University of Oxford, Oxford, UK
- Present Address: Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Lily W. Helfrich
- Howard Hughes Medical Institute / University of California, Berkeley, Department of Molecular and Cell Biology, Berkeley, CA 94720
- Present Address: Benchling
| | - Laura A. Wetzel
- Howard Hughes Medical Institute / University of California, Berkeley, Department of Molecular and Cell Biology, Berkeley, CA 94720
- Present Address: BioMarin Pharmaceutical Inc
| | - Natarajan V. Bhanu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Zuo-Fei Yuan
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Rob Klose
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - David S. Booth
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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45
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Balan D, Kampan NC, Plebanski M, Abd Aziz NH. Unlocking ovarian cancer heterogeneity: advancing immunotherapy through single-cell transcriptomics. Front Oncol 2024; 14:1388663. [PMID: 38873253 PMCID: PMC11169633 DOI: 10.3389/fonc.2024.1388663] [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: 02/20/2024] [Accepted: 05/15/2024] [Indexed: 06/15/2024] Open
Abstract
Ovarian cancer, a highly fatal gynecological cancer, warrants the need for understanding its heterogeneity. The disease's prevalence and impact are underscored with statistics on mortality rates. Ovarian cancer is categorized into distinct morphological groups, each with its characteristics and prognosis. Despite standard treatments, survival rates remain low due to relapses and chemoresistance. Immune system involvement is evident in ovarian cancer's progression, although the tumor employs immune evasion mechanisms. Immunotherapy, particularly immune checkpoint blockade therapy, is promising, but ovarian cancer's heterogeneity limits its efficacy. Single-cell sequencing technology could be explored as a solution to dissect the heterogeneity within tumor-associated immune cell populations and tumor microenvironments. This cutting-edge technology has the potential to enhance diagnosis, prognosis, and personalized immunotherapy in ovarian cancer, reflecting its broader application in cancer research. The present review focuses on recent advancements and the challenges in applying single-cell transcriptomics to ovarian cancer.
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Affiliation(s)
- Dharvind Balan
- Department of Obstetrics and Gynaecology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nirmala Chandralega Kampan
- Department of Obstetrics and Gynaecology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Magdalena Plebanski
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Nor Haslinda Abd Aziz
- Department of Obstetrics and Gynaecology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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Lin P, Gan YB, He J, Lin SE, Xu JK, Chang L, Zhao LM, Zhu J, Zhang L, Huang S, Hu O, Wang YB, Jin HJ, Li YY, Yan PL, Chen L, Jiang JX, Liu P. Advancing skeletal health and disease research with single-cell RNA sequencing. Mil Med Res 2024; 11:33. [PMID: 38816888 PMCID: PMC11138034 DOI: 10.1186/s40779-024-00538-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 05/15/2024] [Indexed: 06/01/2024] Open
Abstract
Orthopedic conditions have emerged as global health concerns, impacting approximately 1.7 billion individuals worldwide. However, the limited understanding of the underlying pathological processes at the cellular and molecular level has hindered the development of comprehensive treatment options for these disorders. The advent of single-cell RNA sequencing (scRNA-seq) technology has revolutionized biomedical research by enabling detailed examination of cellular and molecular diversity. Nevertheless, investigating mechanisms at the single-cell level in highly mineralized skeletal tissue poses technical challenges. In this comprehensive review, we present a streamlined approach to obtaining high-quality single cells from skeletal tissue and provide an overview of existing scRNA-seq technologies employed in skeletal studies along with practical bioinformatic analysis pipelines. By utilizing these methodologies, crucial insights into the developmental dynamics, maintenance of homeostasis, and pathological processes involved in spine, joint, bone, muscle, and tendon disorders have been uncovered. Specifically focusing on the joint diseases of degenerative disc disease, osteoarthritis, and rheumatoid arthritis using scRNA-seq has provided novel insights and a more nuanced comprehension. These findings have paved the way for discovering novel therapeutic targets that offer potential benefits to patients suffering from diverse skeletal disorders.
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Grants
- 2022YFA1103202 National Key Research and Development Program of China
- 82272507 National Natural Science Foundation of China
- 32270887 National Natural Science Foundation of China
- 32200654 National Natural Science Foundation of China
- CSTB2023NSCQ-ZDJO008 Natural Science Foundation of Chongqing
- BX20220397 Postdoctoral Innovative Talent Support Program
- SFLKF202201 Independent Research Project of State Key Laboratory of Trauma and Chemical Poisoning
- 2021-XZYG-B10 General Hospital of Western Theater Command Research Project
- 14113723 University Grants Committee, Research Grants Council of Hong Kong, China
- N_CUHK472/22 University Grants Committee, Research Grants Council of Hong Kong, China
- C7030-18G University Grants Committee, Research Grants Council of Hong Kong, China
- T13-402/17-N University Grants Committee, Research Grants Council of Hong Kong, China
- AoE/M-402/20 University Grants Committee, Research Grants Council of Hong Kong, China
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Affiliation(s)
- Peng Lin
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Yi-Bo Gan
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Jian He
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
- Pancreatic Injury and Repair Key Laboratory of Sichuan Province, the General Hospital of Western Theater Command, Chengdu, 610031, China
| | - Si-En Lin
- Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, Faculty of Medicine, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, 999077, China
| | - Jian-Kun Xu
- Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, Faculty of Medicine, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, 999077, China
| | - Liang Chang
- Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, Faculty of Medicine, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, 999077, China
| | - Li-Ming Zhao
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Sacramento, CA, 94305, USA
| | - Jun Zhu
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Liang Zhang
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Sha Huang
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Ou Hu
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Ying-Bo Wang
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Huai-Jian Jin
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Yang-Yang Li
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Pu-Lin Yan
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Lin Chen
- Center of Bone Metabolism and Repair, State Key Laboratory of Trauma and Chemical Poisoning, Trauma Center, Research Institute of Surgery, Laboratory for the Prevention and Rehabilitation of Military Training Related Injuries, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Jian-Xin Jiang
- Wound Trauma Medical Center, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China.
| | - Peng Liu
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China.
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47
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Hsieh JWA, Lin PY, Wang CT, Lee YJ, Chang P, Lu RJH, Chen PY, Wang CJR. Establishing an optimized ATAC-seq protocol for the maize. FRONTIERS IN PLANT SCIENCE 2024; 15:1370618. [PMID: 38863553 PMCID: PMC11165127 DOI: 10.3389/fpls.2024.1370618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/07/2024] [Indexed: 06/13/2024]
Abstract
The advent of next-generation sequencing in crop improvement offers unprecedented insights into the chromatin landscape closely linked to gene activity governing key traits in plant development and adaptation. Particularly in maize, its dynamic chromatin structure is found to collaborate with massive transcriptional variations across tissues and developmental stages, implying intricate regulatory mechanisms, which highlights the importance of integrating chromatin information into breeding strategies for precise gene controls. The depiction of maize chromatin architecture using Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) provides great opportunities to investigate cis-regulatory elements, which is crucial for crop improvement. In this context, we developed an easy-to-implement ATAC-seq protocol for maize with fewer nuclei and simple equipment. We demonstrate a streamlined ATAC-seq protocol with four key steps for maize in which nuclei purification can be achieved without cell sorting and using only a standard bench-top centrifuge. Our protocol, coupled with the bioinformatic analysis, including validation by read length periodicity, key metrics, and correlation with transcript abundance, provides a precise and efficient assessment of the maize chromatin landscape. Beyond its application to maize, our testing design holds the potential to be applied to other crops or other tissues, especially for those with limited size and amount, establishing a robust foundation for chromatin structure studies in diverse crop species.
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Affiliation(s)
- Jo-Wei Allison Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
| | - Pei-Yu Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chi-Ting Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Jing Lee
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pearl Chang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Tropical Agriculture and International Cooperation/Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Rita Jui-Hsien Lu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
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48
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Liu W, Kurkewich JL, Stoddart A, Khan S, Anandan D, Gaubil AN, Wolfgeher DJ, Jueng L, Kron SJ, McNerney ME. CUX1 regulates human hematopoietic stem cell chromatin accessibility via the BAF complex. Cell Rep 2024; 43:114227. [PMID: 38735044 PMCID: PMC11163479 DOI: 10.1016/j.celrep.2024.114227] [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: 07/27/2023] [Revised: 03/16/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024] Open
Abstract
CUX1 is a homeodomain-containing transcription factor that is essential for the development and differentiation of multiple tissues. CUX1 is recurrently mutated or deleted in cancer, particularly in myeloid malignancies. However, the mechanism by which CUX1 regulates gene expression and differentiation remains poorly understood, creating a barrier to understanding the tumor-suppressive functions of CUX1. Here, we demonstrate that CUX1 directs the BAF chromatin remodeling complex to DNA to increase chromatin accessibility in hematopoietic cells. CUX1 preferentially regulates lineage-specific enhancers, and CUX1 target genes are predictive of cell fate in vivo. These data indicate that CUX1 regulates hematopoietic lineage commitment and homeostasis via pioneer factor activity, and CUX1 deficiency disrupts these processes in stem and progenitor cells, facilitating transformation.
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Affiliation(s)
- Weihan Liu
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA; Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA
| | | | - Angela Stoddart
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Saira Khan
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Dhivyaa Anandan
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Alexandre N Gaubil
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Donald J Wolfgeher
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Lia Jueng
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Stephen J Kron
- The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA; Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Megan E McNerney
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA; The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA; Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago, Chicago, IL 60637, USA.
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49
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Bujosa P, Reina O, Caballé A, Casas-Lamesa A, Torras-Llort M, Pérez-Roldán J, Nacht AS, Vicent GP, Bernués J, Azorín F. Linker histone H1 regulates homeostasis of heterochromatin-associated cRNAs. Cell Rep 2024; 43:114137. [PMID: 38662543 DOI: 10.1016/j.celrep.2024.114137] [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: 04/14/2023] [Revised: 12/23/2023] [Accepted: 04/08/2024] [Indexed: 06/01/2024] Open
Abstract
Chromatin-associated RNAs (cRNAs) are a poorly characterized fraction of cellular RNAs that co-purify with chromatin. Their full complexity and the mechanisms regulating their packaging and chromatin association remain poorly understood. Here, we address these questions in Drosophila. We find that cRNAs constitute a heterogeneous group of RNA species that is abundant in heterochromatic transcripts. We show that heterochromatic cRNAs interact with the heterogeneous nuclear ribonucleoproteins (hnRNP) hrp36/hrp48 and that depletion of linker histone dH1 impairs this interaction. dH1 depletion induces the accumulation of RNA::DNA hybrids (R-loops) in heterochromatin and, as a consequence, increases retention of heterochromatic cRNAs. These effects correlate with increased RNA polymerase II (RNAPII) occupancy at heterochromatin. Notably, impairing cRNA assembly by depletion of hrp36/hrp48 mimics heterochromatic R-loop accumulation induced by dH1 depletion. We also show that dH1 depletion alters nucleosome organization, increasing accessibility of heterochromatin. Altogether, these perturbations facilitate annealing of cRNAs to the DNA template, enhancing R-loop formation and cRNA retention at heterochromatin.
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Affiliation(s)
- Paula Bujosa
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Oscar Reina
- Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Adrià Caballé
- Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Anna Casas-Lamesa
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Mònica Torras-Llort
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Juan Pérez-Roldán
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Ana Silvina Nacht
- Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Guillermo P Vicent
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jordi Bernués
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.
| | - Fernando Azorín
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.
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50
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Agoro R, Myslinski J, Marambio YG, Janosevic D, Jennings KN, Liu S, Hibbard LM, Fang F, Ni P, Noonan ML, Solis E, Chu X, Wang Y, Dagher PC, Liu Y, Wan J, Hato T, White KE. Dynamic Single Cell Transcriptomics Defines Kidney FGF23/KL Bioactivity and Novel Segment-Specific Inflammatory Targets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595014. [PMID: 38853876 PMCID: PMC11160572 DOI: 10.1101/2024.05.24.595014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
FGF23 via its coreceptor αKlotho (KL) provides critical control of phosphate metabolism, which is altered in rare and very common syndromes, however the spatial-temporal mechanisms dictating renal FGF23 functions remain poorly understood. Thus, developing approaches to modify specific FGF23-dictated pathways has proven problematic. Herein, wild type mice were injected with rFGF23 for 1, 4 and 12h and renal FGF23 bioactivity was determined at single cell resolution. Computational analysis identified distinct epithelial, endothelial, stromal, and immune cell clusters, with differential expressional analysis uniquely tracking FGF23 bioactivity at each time point. FGF23 actions were sex independent but critically relied upon constitutive KL expression mapped within proximal tubule (S1-S3) and distal tubule (DCT/CNT) cell sub-populations. Temporal KL-dependent FGF23 responses drove unique and transient cellular identities, including genes in key MAPK- and vitamin D-metabolic pathways via early- (AP-1-related) and late-phase (EIF2 signaling) transcriptional regulons. Combining ATACseq/RNAseq data from a cell line stably expressing KL with the in vivo scRNAseq pinpointed genomic accessibility changes in MAPK-dependent genes, including the identification of FGF23-dependent EGR1 distal enhancers. Finally, we isolated unexpected crosstalk between FGF23-mediated MAPK signaling and pro-inflammatory TNF receptor activation via NF-κB, which blocked FGF23 bioactivity in vitro and in vivo . Collectively, our findings have uncovered novel pathways at the single cell level that likely influence FGF23-dependent disease mechanisms. Translational statement Inflammation and elevated FGF23 in chronic kidney disease (CKD) are both associated with poor patient outcomes and mortality. However, the links between these manifestations and the effects of inflammation on FGF23-mediated mineral metabolism within specific nephron segments remain unclear. Herein, we isolated an inflammatory pathway driven by TNF/NF-κB associated with regulating FGF23 bioactivity. The findings from this study could be important in designing future therapeutic approaches for chronic mineral diseases, including potential combination therapies or early intervention strategies. We also suggest that further studies could explore these pathways at the single cell level in CKD models, as well as test translation of our findings to interactions of chronic inflammation and elevated FGF23 in human CKD kidney datasets.
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