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Yang X, Liu G, Feng G, Bu D, Wang P, Jiang J, Chen S, Yang Q, Miao H, Zhang Y, Man Z, Liang Z, Wang Z, Li Y, Li Z, Liu Y, Tian Y, Liu W, Li C, Li A, Dong J, Hu Z, Fang C, Cui L, Deng Z, Jiang H, Cui W, Zhang J, Yang Z, Li H, He X, Zhong L, Zhou J, Wang Z, Long Q, Xu P, Wang H, Meng Z, Wang X, Wang Y, Wang Y, Zhang S, Guo J, Zhao Y, Zhou Y, Li F, Liu J, Chen Y, Yang G, Li X. GeneCompass: deciphering universal gene regulatory mechanisms with a knowledge-informed cross-species foundation model. Cell Res 2024:10.1038/s41422-024-01034-y. [PMID: 39375485 DOI: 10.1038/s41422-024-01034-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 09/13/2024] [Indexed: 10/09/2024] Open
Abstract
Deciphering universal gene regulatory mechanisms in diverse organisms holds great potential for advancing our knowledge of fundamental life processes and facilitating clinical applications. However, the traditional research paradigm primarily focuses on individual model organisms and does not integrate various cell types across species. Recent breakthroughs in single-cell sequencing and deep learning techniques present an unprecedented opportunity to address this challenge. In this study, we built an extensive dataset of over 120 million human and mouse single-cell transcriptomes. After data preprocessing, we obtained 101,768,420 single-cell transcriptomes and developed a knowledge-informed cross-species foundation model, named GeneCompass. During pre-training, GeneCompass effectively integrated four types of prior biological knowledge to enhance our understanding of gene regulatory mechanisms in a self-supervised manner. By fine-tuning for multiple downstream tasks, GeneCompass outperformed state-of-the-art models in diverse applications for a single species and unlocked new realms of cross-species biological investigations. We also employed GeneCompass to search for key factors associated with cell fate transition and showed that the predicted candidate genes could successfully induce the differentiation of human embryonic stem cells into the gonadal fate. Overall, GeneCompass demonstrates the advantages of using artificial intelligence technology to decipher universal gene regulatory mechanisms and shows tremendous potential for accelerating the discovery of critical cell fate regulators and candidate drug targets.
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Affiliation(s)
- Xiaodong Yang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Key Laboratory of Mobile Computing and Pervasive Device, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guole Liu
- State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Guihai Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Dechao Bu
- Beijing Key Laboratory of Mobile Computing and Pervasive Device, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Pengfei Wang
- University of Chinese Academy of Sciences, Beijing, China
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Jie Jiang
- Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Shubai Chen
- Beijing Key Laboratory of Mobile Computing and Pervasive Device, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qinmeng Yang
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Hefan Miao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yiyang Zhang
- University of Chinese Academy of Sciences, Beijing, China
- CEMS, NCMIS, HCMS, MDIS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
| | - Zhenpeng Man
- University of Chinese Academy of Sciences, Beijing, China
- CEMS, NCMIS, HCMS, MDIS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
| | - Zhongming Liang
- University of Chinese Academy of Sciences, Beijing, China
- CEMS, NCMIS, HCMS, MDIS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
| | - Zichen Wang
- State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Yaning Li
- Beijing Key Laboratory of Mobile Computing and Pervasive Device, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zheng Li
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Yana Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yao Tian
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenhao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Cong Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ao Li
- State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Jingxi Dong
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhilong Hu
- University of Chinese Academy of Sciences, Beijing, China
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Chen Fang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lina Cui
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zixu Deng
- Beijing Key Laboratory of Mobile Computing and Pervasive Device, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haiping Jiang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wentao Cui
- University of Chinese Academy of Sciences, Beijing, China
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Jiahao Zhang
- University of Chinese Academy of Sciences, Beijing, China
- CEMS, NCMIS, HCMS, MDIS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
| | - Zhaohui Yang
- Beijing Key Laboratory of Mobile Computing and Pervasive Device, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Handong Li
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
- Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Xingjian He
- Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Liqun Zhong
- State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Jiaheng Zhou
- State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Zijian Wang
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Qingqing Long
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Ping Xu
- University of Chinese Academy of Sciences, Beijing, China
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Hongmei Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Zhen Meng
- University of Chinese Academy of Sciences, Beijing, China
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Xuezhi Wang
- University of Chinese Academy of Sciences, Beijing, China
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Yangang Wang
- University of Chinese Academy of Sciences, Beijing, China
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Yong Wang
- University of Chinese Academy of Sciences, Beijing, China
- CEMS, NCMIS, HCMS, MDIS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
| | - Shihua Zhang
- University of Chinese Academy of Sciences, Beijing, China
- CEMS, NCMIS, HCMS, MDIS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
| | - Jingtao Guo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Yi Zhao
- Beijing Key Laboratory of Mobile Computing and Pervasive Device, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.
| | - Yuanchun Zhou
- University of Chinese Academy of Sciences, Beijing, China.
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.
| | - Fei Li
- University of Chinese Academy of Sciences, Beijing, China.
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.
| | - Jing Liu
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China.
- Institute of Automation, Chinese Academy of Sciences, Beijing, China.
| | - Yiqiang Chen
- Beijing Key Laboratory of Mobile Computing and Pervasive Device, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Ge Yang
- State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China.
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China.
| | - Xin Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
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2
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Ortigoza-Escobar JD, Zamani M, Dorison N, Sadeghian S, Azizimalamiri R, Alvi JR, Sultan T, Galehdari H, Shariati G, Saberi A, Leeuwen L, Zifarelli G, Bauer P, d'Hardemare V, Doummar D, Roze E, Travaglini L, Nicita F, Ojea Ponce N, Zahraei SM, Alabdi L, Tamim A, Hashem MO, Ababneh F, Morrow MM, Curry C, Tam A, Ruedy J, Bhambhani V, Veith R, Strømme P, Efthymiou S, Alkuraya FS, Moreno-De-Luca A, Burglen L, Houlden H, Maroofian R. Biallelic ZBTB11 Variants: A Neurodevelopmental Condition with Progressive Complex Movement Disorders. Mov Disord 2024. [PMID: 38899514 DOI: 10.1002/mds.29883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 05/08/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Biallelic ZBTB11 variants have previously been associated with an ultrarare subtype of autosomal recessive intellectual developmental disorder (MRT69). OBJECTIVE The aim was to provide insights into the clinical and genetic characteristics of ZBTB11-related disorders (ZBTB11-RD), with a particular emphasis on progressive complex movement abnormalities. METHODS Thirteen new and 16 previously reported affected individuals, ranging in age from 2 to 50 years, with biallelic ZBTB11 variants underwent clinical and genetic characterization. RESULTS All patients exhibited a range of neurodevelopmental phenotypes with varying severity, encompassing ocular and neurological features. Eleven new patients presented with complex abnormal movements, including ataxia, dystonia, myoclonus, stereotypies, and tremor, and 7 new patients exhibited cataracts. Deep brain stimulation was successful in treating 1 patient with generalized progressive dystonia. Our analysis revealed 13 novel variants. CONCLUSIONS This study provides additional insights into the clinical features and spectrum of ZBTB11-RD, highlighting the progressive nature of movement abnormalities in the background of neurodevelopmental phenotype. © 2024 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Juan Darío Ortigoza-Escobar
- Movement Disorders Unit, Pediatric Neurology Department, Institut de Recerca, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
- U-703 Centre for Biomedical Research on Rare Diseases (CIBER-ER), Instituto de Salud Carlos III, Barcelona, Spain
- European Reference Network for Rare Neurological Diseases (ERN-RND), Barcelona, Spain
| | - Mina Zamani
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran
| | - Nathalie Dorison
- Unité Dyspa, Neurochirurgie Pédiatrique, Hôpital Fondation Rothschild, Paris, France
| | - Saeid Sadeghian
- Department of Pediatric Neurology, Golestan Medical, Educational, and Research Centre, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Reza Azizimalamiri
- Department of Pediatric Neurology, Golestan Medical, Educational, and Research Centre, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Javeria Raza Alvi
- Department of Pediatric Neurology, The Children's Hospital and the University of Child Health Sciences, Lahore, Pakistan
| | - Tipu Sultan
- Department of Pediatric Neurology, The Children's Hospital and the University of Child Health Sciences, Lahore, Pakistan
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Gholamreza Shariati
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran
- Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Alihossein Saberi
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran
- Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Lisette Leeuwen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | | | - Vincent d'Hardemare
- Unité Dyspa, Neurochirurgie Pédiatrique, Hôpital Fondation Rothschild, Paris, France
| | - Diane Doummar
- AP-HP. Sorbonne Université, Service de Neuropédiatrie et Centre de Référence Neurogénétique, Hôpital Armand Trousseau, FHU I2D2, Paris, France
| | - Emmanuel Roze
- Assistance Publique-Hôpitaux de Paris CHU Pitié-Salpêtrière DMU Neurosciences et Sorbonne Université, INSERM, CNRS, Institut du Cerveau, Paris, France
| | - Lorena Travaglini
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, IRCCS, Bambino Gesù Children's Hospital, Rome, Italy
| | - Francesco Nicita
- Unit of Neuromuscular and Neurodegenerative Disorders, IRCCS, Bambino Gesù Children's Hospital of Rome, Rome, Italy
| | - Núria Ojea Ponce
- Department of Statistics, Institut de Recerca Sant Joan de Déu Barcelona, Barcelona, Spain
| | | | - Lama Alabdi
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Abdullah Tamim
- Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Mais O Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Faroug Ababneh
- Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | | | - Cynthia Curry
- Department of Pediatrics, Genetic Medicine, UCSF/Fresno, Fresno, California, USA
| | - Allison Tam
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Jessica Ruedy
- Genetics Clinic, Children's MN, Minneapolis, Minnesota, USA
| | | | - Regan Veith
- Genetics Clinic, Children's MN, Minneapolis, Minnesota, USA
| | - Petter Strømme
- Division of Pediatrics and Adolescent Medicine, Oslo, University Hospital and Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Andres Moreno-De-Luca
- Department of Radiology, Neuroradiology Section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences, Kingston, Ontario, Canada
| | - Lydie Burglen
- Centre de Référence Maladies Rares "Malformations et Maladies Congénitales du Cervelet," Hôpital Trousseau, APHP, Sorbonne University, Paris, France
- Département de Génétique, APHP, Sorbonne University, Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR, Paris, France
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
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3
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Ee LS, Medina-Cano D, Uyehara CM, Schwarz C, Goetzler E, Salataj E, Polyzos A, Madhuranath S, Evans T, Hadjantonakis AK, Apostolou E, Vierbuchen T, Stadtfeld M. Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596630. [PMID: 38854146 PMCID: PMC11160813 DOI: 10.1101/2024.05.30.596630] [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
The molecular mechanisms that drive essential developmental patterning events in the mammalian embryo remain poorly understood. To generate a conceptual framework for gene regulatory processes during germ layer specification, we analyzed transcription factor (TF) expression kinetics around gastrulation and during in vitro differentiation. This approach identified Otx2 as a candidate regulator of definitive endoderm (DE), the precursor of all gut- derived tissues. Analysis of multipurpose degron alleles in gastruloid and directed differentiation models revealed that loss of OTX2 before or after DE specification alters the expression of core components and targets of specific cellular signaling pathways, perturbs adhesion and migration programs as well as de-represses regulators of other lineages, resulting in impaired foregut specification. Key targets of OTX2 are conserved in human DE. Mechanistically, OTX2 is required to establish chromatin accessibility at candidate enhancers, which regulate genes critical to establishing an anterior cell identity in the developing gut. Our results provide a working model for the progressive establishment of spatiotemporal cell identity by developmental TFs across germ layers and species, which may facilitate the generation of gut cell types for regenerative medicine applications.
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Affiliation(s)
- LS Ee
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - D Medina-Cano
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - CM Uyehara
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - C Schwarz
- Emerald Cloud Lab, Austin, TX 78728 USA
| | - E Goetzler
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - E Salataj
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - A Polyzos
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - S Madhuranath
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - T Evans
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, New York, NY 10065, USA
| | - AK Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - E Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - T Vierbuchen
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - M Stadtfeld
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
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4
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Tiniakou I, Hsu PF, Lopez-Zepeda LS, Garipler G, Esteva E, Adams NM, Jang G, Soni C, Lau CM, Liu F, Khodadadi-Jamayran A, Rodrick TC, Jones D, Tsirigos A, Ohler U, Bedford MT, Nimer SD, Kaartinen V, Mazzoni EO, Reizis B. Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation. Sci Immunol 2024; 9:eadi1023. [PMID: 38608038 PMCID: PMC11182672 DOI: 10.1126/sciimmunol.adi1023] [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: 04/05/2023] [Accepted: 03/21/2024] [Indexed: 04/14/2024]
Abstract
The development of dendritic cells (DCs), including antigen-presenting conventional DCs (cDCs) and cytokine-producing plasmacytoid DCs (pDCs), is controlled by the growth factor Flt3 ligand (Flt3L) and its receptor Flt3. We genetically dissected Flt3L-driven DC differentiation using CRISPR-Cas9-based screening. Genome-wide screening identified multiple regulators of DC differentiation including subunits of TSC and GATOR1 complexes, which restricted progenitor growth but enabled DC differentiation by inhibiting mTOR signaling. An orthogonal screen identified the transcriptional repressor Trim33 (TIF-1γ) as a regulator of DC differentiation. Conditional targeting in vivo revealed an essential role of Trim33 in the development of all DCs, but not of monocytes or granulocytes. In particular, deletion of Trim33 caused rapid loss of DC progenitors, pDCs, and the cross-presenting cDC1 subset. Trim33-deficient Flt3+ progenitors up-regulated pro-inflammatory and macrophage-specific genes but failed to induce the DC differentiation program. Collectively, these data elucidate mechanisms that control Flt3L-driven differentiation of the entire DC lineage and identify Trim33 as its essential regulator.
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Affiliation(s)
- Ioanna Tiniakou
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
| | - Pei-Feng Hsu
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
| | - Lorena S. Lopez-Zepeda
- Department of Biology, Humboldt Universität zu Berlin; Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine; Berlin, Germany
| | - Görkem Garipler
- Department of Biology, New York University; New York, NY, USA
| | - Eduardo Esteva
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
| | - Nicholas M. Adams
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
| | - Geunhyo Jang
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
| | - Chetna Soni
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
| | - Colleen M. Lau
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine; Ithaca, NY, USA
| | - Fan Liu
- Department of Biochemistry and Molecular Biology, Department of Medicine and Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine; Miami, FL, USA
| | - Alireza Khodadadi-Jamayran
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine; New York, NY, USA
| | - Tori C. Rodrick
- Metabolomics Laboratory, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine; New York, NY, USA
| | - Drew Jones
- Metabolomics Laboratory, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine; New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine; New York, NY, USA
| | - Uwe Ohler
- Department of Biology, Humboldt Universität zu Berlin; Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine; Berlin, Germany
| | - Mark T. Bedford
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center; Houston, TX, USA
| | - Stephen D. Nimer
- Department of Biochemistry and Molecular Biology, Department of Medicine and Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine; Miami, FL, USA
| | - Vesa Kaartinen
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry; Ann Arbor, MI, USA
| | | | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine; New York, NY, USA
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5
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Barakat S, Ezen E, Devecioğlu İ, Gezen M, Piepoli S, Erman B. Dimerization choice and alternative functions of ZBTB transcription factors. FEBS J 2024; 291:237-255. [PMID: 37450366 DOI: 10.1111/febs.16905] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 06/09/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Zinc Finger DNA-binding domain-containing proteins are the most populous family among eukaryotic transcription factors. Among these, members of the BTB domain-containing ZBTB sub-family are mostly known for their transcriptional repressive functions. In this Viewpoint article, we explore molecular mechanisms that potentially diversify the function of ZBTB proteins based on their homo and heterodimerization, alternative splicing and post-translational modifications. We describe how the BTB domain is as much a scaffold for the assembly of co-repressors, as a domain that regulates protein stability. We highlight another mechanism that regulates ZBTB protein stability: phosphorylation in the zinc finger domain. We explore the non-transcriptional, structural roles of ZBTB proteins and highlight novel findings that describe the ability of ZBTB proteins to associate with poly adenosine ribose in the nucleus during the DNA damage response. Herein, we discuss the contribution of BTB domain scaffolds to the formation of transcriptional repressive complexes, to chromosome compartmentalization and their non-transcriptional, purely structural functions in the nucleus.
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Affiliation(s)
- Sarah Barakat
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Ege Ezen
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - İzem Devecioğlu
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Melike Gezen
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Sofia Piepoli
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Batu Erman
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
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6
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Cao H, Naik SH, Amann-Zalcenstein D, Hickey P, Salim A, Cao B, Nilsson SK, Keightley MC, Lieschke GJ. Late fetal hematopoietic failure results from ZBTB11 deficiency despite abundant HSC specification. Blood Adv 2023; 7:6506-6519. [PMID: 37567157 PMCID: PMC10632610 DOI: 10.1182/bloodadvances.2022009580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/13/2023] Open
Abstract
Hematopoiesis produces diverse blood cell lineages to meet the basal needs and sudden demands of injury or infection. A rapid response to such challenges requires the expansion of specific lineages and a prompt return to balanced steady-state levels, necessitating tightly coordinated regulation. Previously we identified a requirement for the zinc finger and broad complex, tramtrak, bric-a-brac domain-containing 11 (ZBTB11) transcription factor in definitive hematopoiesis using a forward genetic screen for zebrafish myeloid mutants. To understand its relevance to mammalian systems, we extended these studies to mice. When Zbtb11 was deleted in the hematopoietic compartment, embryos died at embryonic day (E) 18.5 with hematopoietic failure. Zbtb11 hematopoietic knockout (Zbtb11hKO) hematopoietic stem cells (HSCs) were overabundantly specified from E14.5 to E17.5 compared with those in controls. Overspecification was accompanied by loss of stemness, inability to differentiate into committed progenitors and mature lineages in the fetal liver, failure to seed fetal bone marrow, and total hematopoietic failure. The Zbtb11hKO HSCs did not proliferate in vitro and were constrained in cell cycle progression, demonstrating the cell-intrinsic role of Zbtb11 in proliferation and cell cycle regulation in mammalian HSCs. Single-cell RNA sequencing analysis identified that Zbtb11-deficient HSCs were underrepresented in an erythroid-primed subpopulation and showed downregulation of oxidative phosphorylation pathways and dysregulation of genes associated with the hematopoietic niche. We identified a cell-intrinsic requirement for Zbtb11-mediated gene regulatory networks in sustaining a pool of maturation-capable HSCs and progenitor cells.
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Affiliation(s)
- Huimin Cao
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, VIC, Australia
| | - Shalin H. Naik
- Department of Immunology, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Single Cell Open Research Endeavour, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Daniela Amann-Zalcenstein
- Single Cell Open Research Endeavour, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Advanced Genomics Facility, Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Peter Hickey
- Single Cell Open Research Endeavour, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Advanced Genomics Facility, Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Agus Salim
- Mathematics and Statistics, La Trobe University, Bundoora, VIC, Australia
- Melbourne School of Population and Global Health, School of Mathematics and Statistics, University of Melbourne, Parkville, VIC, Australia
| | - Benjamin Cao
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, VIC, Australia
| | - Susan K. Nilsson
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, VIC, Australia
| | - M. Cristina Keightley
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
- Rural Clinical Sciences, La Trobe Rural Health School, Bendigo, VIC, Australia
| | - Graham J. Lieschke
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
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7
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Cheng R, Zhou S, K C R, Lizarazo S, Mouli L, Jayanth A, Liu Q, Van Bortle K. A Combinatorial Regulatory Platform Determines Expression of RNA Polymerase III Subunit RPC7α ( POLR3G) in Cancer. Cancers (Basel) 2023; 15:4995. [PMID: 37894362 PMCID: PMC10605170 DOI: 10.3390/cancers15204995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
RNA polymerase III (Pol III) subunit RPC7α, which is encoded by POLR3G in humans, has been linked to both tumor growth and metastasis. Accordantly, high POLR3G expression is a negative prognostic factor in multiple cancer subtypes. To date, the mechanisms underlying POLR3G upregulation have remained poorly defined. We performed a large-scale genomic survey of mRNA and chromatin signatures to predict drivers of POLR3G expression in cancer. Our survey uncovers positive determinants of POLR3G expression, including a gene-internal super-enhancer bound with multiple transcription factors (TFs) that promote POLR3G expression, as well as negative determinants that include gene-internal DNA methylation, retinoic-acid induced differentiation, and MXD4-mediated disruption of POLR3G expression. We show that novel TFs identified in our survey, including ZNF131 and ZNF207, functionally enhance POLR3G expression, whereas MXD4 likely obstructs MYC-driven expression of POLR3G and other growth-related genes. Integration of chromatin architecture and gene regulatory signatures identifies additional factors, including histone demethylase KDM5B, as likely influencers of POLR3G gene activity. Taken together, our findings support a model in which POLR3G expression is determined with multiple factors and dynamic regulatory programs, expanding our understanding of the circuitry underlying POLR3G upregulation and downstream consequences in cancer.
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Affiliation(s)
- Ruiying Cheng
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; (R.C.); (S.Z.)
| | - Sihang Zhou
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; (R.C.); (S.Z.)
| | - Rajendra K C
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA;
| | - Simon Lizarazo
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA;
| | - Leela Mouli
- School of Molecular and Cellular Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; (L.M.); (A.J.)
| | - Anshita Jayanth
- School of Molecular and Cellular Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; (L.M.); (A.J.)
| | - Qing Liu
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA;
- Center for Human Genetics, Clemson University, Greenwood, SC 29646, USA
| | - Kevin Van Bortle
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; (R.C.); (S.Z.)
- School of Molecular and Cellular Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; (L.M.); (A.J.)
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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8
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Wang R, Xu Q, Wang C, Tian K, Wang H, Ji X. Multiomic analysis of cohesin reveals that ZBTB transcription factors contribute to chromatin interactions. Nucleic Acids Res 2023; 51:6784-6805. [PMID: 37264934 PMCID: PMC10359638 DOI: 10.1093/nar/gkad401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/23/2023] [Indexed: 06/03/2023] Open
Abstract
One bottleneck in understanding the principles of 3D chromatin structures is caused by the paucity of known regulators. Cohesin is essential for 3D chromatin organization, and its interacting partners are candidate regulators. Here, we performed proteomic profiling of the cohesin in chromatin and identified transcription factors, RNA-binding proteins and chromatin regulators associated with cohesin. Acute protein degradation followed by time-series genomic binding quantitation and BAT Hi-C analysis were conducted, and the results showed that the transcription factor ZBTB21 contributes to cohesin chromatin binding, 3D chromatin interactions and transcriptional repression. Strikingly, multiomic analyses revealed that the other four ZBTB factors interacted with cohesin, and double degradation of ZBTB21 and ZBTB7B led to a further decrease in cohesin chromatin occupancy. We propose that multiple ZBTB transcription factors orchestrate the chromatin binding of cohesin to regulate chromatin interactions, and we provide a catalog of many additional proteins associated with cohesin that warrant further investigation.
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Affiliation(s)
- Rui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Qiqin Xu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Chenlu Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Kai Tian
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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9
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Lobanova Y, Filonova G, Kaplun D, Zhigalova N, Prokhortchouk E, Zhenilo S. TRIM28 regulates transcriptional activity of methyl-DNA binding protein Kaiso by SUMOylation. Biochimie 2023; 206:73-80. [PMID: 36252888 DOI: 10.1016/j.biochi.2022.10.006] [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: 06/27/2022] [Revised: 09/12/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022]
Abstract
Kaiso is a methyl DNA binding transcriptional factor involved in cell cycle control, WNT signaling, colon inflammation, and cancer progression. Recently, it was shown that SUMOylation dynamically modulates the transcriptional activity of Kaiso. However, factors involved in SUMOylation of Kaiso are unknown. Here we show that TRIM28 enhances SUMOylation of Kaiso leading to a decreased methyl-dependent repression ability. TRIM28 is a scaffold protein that regulates transcription and posttranslational modifications of factors involved in cell cycle progression, DNA damage, and viral gene expression. It has SUMO and ubiquitin E3 ligase activity. Here, we defined the domains involved in Kaiso-TRIM28 interaction. The RBCC domain of TRIM28 interacts with the BTB/POZ domain and the zinc fingers of Kaiso. The PHD-bromodomain of TRIM28 is sufficient for the interaction with zinc fingers of Kaiso. Additionally, we found that Kaiso enhances SUMOylation of TRIM28. Altogether our data suggest self-enhancement of SUMOylation of both Kaiso and TRIM28 that affects transcriptional activity of Kaiso.
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Affiliation(s)
- Y Lobanova
- Sckryabin Institute of Bioengineering, Federal Research Centre «Fundamentals of Biotechnology» RAS, pr. 60 let Oktyabrya, 7-1, 117312, Moscow, Russia
| | - G Filonova
- Sckryabin Institute of Bioengineering, Federal Research Centre «Fundamentals of Biotechnology» RAS, pr. 60 let Oktyabrya, 7-1, 117312, Moscow, Russia
| | - D Kaplun
- Sckryabin Institute of Bioengineering, Federal Research Centre «Fundamentals of Biotechnology» RAS, pr. 60 let Oktyabrya, 7-1, 117312, Moscow, Russia; Institute of Gene Biology RAS, 34/5 Vavilova Street, 119334 Moscow, Russia
| | - N Zhigalova
- Sckryabin Institute of Bioengineering, Federal Research Centre «Fundamentals of Biotechnology» RAS, pr. 60 let Oktyabrya, 7-1, 117312, Moscow, Russia
| | - E Prokhortchouk
- Sckryabin Institute of Bioengineering, Federal Research Centre «Fundamentals of Biotechnology» RAS, pr. 60 let Oktyabrya, 7-1, 117312, Moscow, Russia; Institute of Gene Biology RAS, 34/5 Vavilova Street, 119334 Moscow, Russia
| | - S Zhenilo
- Sckryabin Institute of Bioengineering, Federal Research Centre «Fundamentals of Biotechnology» RAS, pr. 60 let Oktyabrya, 7-1, 117312, Moscow, Russia; Institute of Gene Biology RAS, 34/5 Vavilova Street, 119334 Moscow, Russia.
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10
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Chen L, Liu Z, Tang H, Zhou Z, Chen J, Ma Z, Deng M, Li X, Wu Y, Zheng L, Zhou L, Zheng X, Liu Z. Knockdown of ZBTB11 impedes R‐loop elimination and increases the sensitivity to cisplatin by inhibiting DDX1 transcription in bladder cancer. Cell Prolif 2022; 55:e13325. [DOI: 10.1111/cpr.13325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/28/2022] [Accepted: 07/26/2022] [Indexed: 11/26/2022] Open
Affiliation(s)
- Lei Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
- Department of Urology Sun Yat‐sen University Cancer Center Guangzhou China
| | - Zefu Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
- Department of Urology Sun Yat‐sen University Cancer Center Guangzhou China
| | - Huancheng Tang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
- Department of Urology Sun Yat‐sen University Cancer Center Guangzhou China
| | - Zhaohui Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
- Department of Urology Sun Yat‐sen University Cancer Center Guangzhou China
| | - Jiawei Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
- Department of Urology Sun Yat‐sen University Cancer Center Guangzhou China
| | - Zikun Ma
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
- Department of Urology Sun Yat‐sen University Cancer Center Guangzhou China
| | - Minhua Deng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
- Department of Urology Sun Yat‐sen University Cancer Center Guangzhou China
| | - Xiangdong Li
- Department of Urology Sun Yat‐sen University Cancer Center Guangzhou China
| | - Yuanzhong Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
| | - Lisi Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
| | - Liwen Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
| | - Xianchong Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
- Department of Urology Sun Yat‐sen University Cancer Center Guangzhou China
| | - Zhuowei Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine Sun Yat‐sen University Cancer Center Guangzhou China
- Department of Urology Sun Yat‐sen University Cancer Center Guangzhou China
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11
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Amweg A, Tusup M, Cheng P, Picardi E, Dummer R, Levesque MP, French LE, Guenova E, Läuchli S, Kundig T, Mellett M, Pascolo S. The A to I editing landscape in melanoma and its relation to clinical outcome. RNA Biol 2022; 19:996-1006. [PMID: 35993275 PMCID: PMC9415457 DOI: 10.1080/15476286.2022.2110390] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
RNA editing refers to non-transient RNA modifications that occur after transcription and prior to translation by the ribosomes. RNA editing is more widespread in cancer cells than in non-transformed cells and is associated with tumorigenesis of various cancer tissues. However, RNA editing can also generate neo-antigens that expose tumour cells to host immunosurveillance. Global RNA editing in melanoma and its relevance to clinical outcome currently remain poorly characterized. The present study compared RNA editing as well as gene expression in tumour cell lines from melanoma patients of short or long metastasis-free survival, patients relapsing or not after immuno- and targeted therapy and tumours harbouring BRAF or NRAS mutations. Overall, our results showed that NTRK gene expression can be a marker of resistance to BRAF and MEK inhibition and gives some insights of candidate genes as potential biomarkers. In addition, this study revealed an increase in Adenosine-to-Inosine editing in Alu regions and in non-repetitive regions, including the hyperediting of the MOK and DZIP3 genes in relapsed tumour samples during targeted therapy and of the ZBTB11 gene in NRAS mutated melanoma cells. Therefore, RNA editing could be a promising tool for identifying predictive markers, tumour neoantigens and targetable pathways that could help in preventing relapses during immuno- or targeted therapies.
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Affiliation(s)
- Austeja Amweg
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Marina Tusup
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Phil Cheng
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Bari, Italy
| | - Reinhard Dummer
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Lars E French
- Department of Dermatology and Allergy, University Hospital, LMU Munich, Munich, Germany.,Dr. Philip Frost, Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Emmanuella Guenova
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland.,Department of Dermatology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Severin Läuchli
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Thomas Kundig
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Mark Mellett
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Steve Pascolo
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
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