1
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Hernandez-Benitez R, Wang C, Shi L, Ouchi Y, Zhong C, Hishida T, Liao HK, Magill EA, Memczak S, Soligalla RD, Fresia C, Hatanaka F, Lamas V, Guillen I, Sahu S, Yamamoto M, Shao Y, Aguirre-Vazquez A, Nuñez Delicado E, Guillen P, Rodriguez Esteban C, Qu J, Reddy P, Horvath S, Liu GH, Magistretti P, Izpisua Belmonte JC. Intervention with metabolites emulating endogenous cell transitions accelerates muscle regeneration in young and aged mice. Cell Rep Med 2024; 5:101449. [PMID: 38508141 PMCID: PMC10983034 DOI: 10.1016/j.xcrm.2024.101449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/10/2023] [Accepted: 02/08/2024] [Indexed: 03/22/2024]
Abstract
Tissue regeneration following an injury requires dynamic cell-state transitions that allow for establishing the cell identities required for the restoration of tissue homeostasis and function. Here, we present a biochemical intervention that induces an intermediate cell state mirroring a transition identified during normal differentiation of myoblasts and other multipotent and pluripotent cells to mature cells. When applied in somatic differentiated cells, the intervention, composed of one-carbon metabolites, reduces some dedifferentiation markers without losing the lineage identity, thus inducing limited reprogramming into a more flexible cell state. Moreover, the intervention enabled accelerated repair after muscle injury in young and aged mice. Overall, our study uncovers a conserved biochemical transitional phase that enhances cellular plasticity in vivo and hints at potential and scalable biochemical interventions of use in regenerative medicine and rejuvenation interventions that may be more tractable than genetic ones.
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Affiliation(s)
- Reyna Hernandez-Benitez
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Altos Labs, Inc., San Diego, CA 92121, USA
| | - Chao Wang
- Altos Labs, Inc., San Diego, CA 92121, USA
| | - Lei Shi
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Yasuo Ouchi
- Altos Labs, Inc., San Diego, CA 92121, USA; Department of Regenerative Medicine, Chiba University Graduate School of Medicine, Chiba, Japan
| | | | - Tomoaki Hishida
- Laboratory of Biological Chemistry, School of Pharmaceutical Sciences, Wakayama Medical University, 25-1 Shichibancho, Wakayama 640-8156, Japan
| | - Hsin-Kai Liao
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Eric A Magill
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Rupa D Soligalla
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Chiara Fresia
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | | | | | | | | | | | | | - Estrella Nuñez Delicado
- Universidad Católica San Antonio de Murcia (UCAM), Campus de los Jerónimos, Nº 135 12, 30107 Guadalupe, Spain
| | | | | | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | | | | | - Guang-Hui Liu
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Pierre Magistretti
- King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Altos Labs, Inc., San Diego, CA 92121, USA.
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2
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Memczak S, Belmonte JC. Overcoming muscle stem cell aging. Curr Opin Genet Dev 2023; 83:102127. [PMID: 37839315 DOI: 10.1016/j.gde.2023.102127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/06/2023] [Accepted: 09/19/2023] [Indexed: 10/17/2023]
Abstract
Reduced muscle strength and mass is one of the hallmarks of physiological aging in humans and can result in severe impairment of the quality of life. In part this is caused by a functional loss of the highly specialized muscle stem cells (MuSCs), which in healthy conditions provide maintenance, growth, and regeneration. Recent progress in understanding of the stem cell niche and results from single cell technologies reveal exciting insights at unprecedented detail into MuSCs and muscle biology during aging. Here, we review this field and discuss the implications of current findings with a focus on cellular reprogramming approaches as a novel therapeutic avenue for age-related muscle decline.
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3
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Memczak S, Izpisua Belmonte JC. Chemical fast track to induced pluripotency. Nat Cell Biol 2023; 25:1079-1080. [PMID: 37550514 DOI: 10.1038/s41556-023-01202-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
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4
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Hishida T, Yamamoto M, Hishida-Nozaki Y, Shao C, Huang L, Wang C, Shojima K, Xue Y, Hang Y, Shokhirev M, Memczak S, Sahu SK, Hatanaka F, Ros RR, Maxwell MB, Chavez J, Shao Y, Liao HK, Martinez-Redondo P, Guillen-Guillen I, Hernandez-Benitez R, Esteban CR, Qu J, Holmes MC, Yi F, Hickey RD, Garcia PG, Delicado EN, Castells A, Campistol JM, Yu Y, Hargreaves DC, Asai A, Reddy P, Liu GH, Belmonte JCI. In vivo partial cellular reprogramming enhances liver plasticity and regeneration. Cell Rep 2022; 39:110730. [PMID: 35476977 PMCID: PMC9807246 DOI: 10.1016/j.celrep.2022.110730] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 12/28/2021] [Accepted: 04/01/2022] [Indexed: 01/07/2023] Open
Abstract
Mammals have limited regenerative capacity, whereas some vertebrates, like fish and salamanders, are able to regenerate their organs efficiently. The regeneration in these species depends on cell dedifferentiation followed by proliferation. We generate a mouse model that enables the inducible expression of the four Yamanaka factors (Oct-3/4, Sox2, Klf4, and c-Myc, or 4F) specifically in hepatocytes. Transient in vivo 4F expression induces partial reprogramming of adult hepatocytes to a progenitor state and concomitantly increases cell proliferation. This is indicated by reduced expression of differentiated hepatic-lineage markers, an increase in markers of proliferation and chromatin modifiers, global changes in DNA accessibility, and an acquisition of liver stem and progenitor cell markers. Functionally, short-term expression of 4F enhances liver regenerative capacity through topoisomerase2-mediated partial reprogramming. Our results reveal that liver-specific 4F expression in vivo induces cellular plasticity and counteracts liver failure, suggesting that partial reprogramming may represent an avenue for enhancing tissue regeneration.
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Affiliation(s)
- Tomoaki Hishida
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA,Laboratory of Biological Chemistry, School of Pharmaceutical Sciences, Wakayama Medical University, 25-1 Shitibancho, Wakayama, Wakayama 640-8156, Japan,These authors contributed equally
| | - Mako Yamamoto
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA,These authors contributed equally
| | - Yuriko Hishida-Nozaki
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Changwei Shao
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ling Huang
- Razavi Newman Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Chao Wang
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA,Altos Labs, 5510 Morehouse Drive, San Diego, CA 92121, USA
| | - Kensaku Shojima
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yuan Xue
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yuqing Hang
- Razavi Newman Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Maxim Shokhirev
- Razavi Newman Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sebastian Memczak
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA,Altos Labs, 5510 Morehouse Drive, San Diego, CA 92121, USA
| | - Sanjeeb Kumar Sahu
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA,Altos Labs, 5510 Morehouse Drive, San Diego, CA 92121, USA
| | - Fumiyuki Hatanaka
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA,Altos Labs, 5510 Morehouse Drive, San Diego, CA 92121, USA
| | - Ruben Rabadan Ros
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA,Universidad Católica San Antonio de Murcia (UCAM), Campus de los Jerónimos, N° 135 12, 30107 Guadalupe, Spain
| | - Matthew B. Maxwell
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA,Division of Biological Sciences, UCSD, La Jolla, CA 92037, USA
| | - Jasmine Chavez
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yanjiao Shao
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA,Altos Labs, 5510 Morehouse Drive, San Diego, CA 92121, USA
| | - Hsin-Kai Liao
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Paloma Martinez-Redondo
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Isabel Guillen-Guillen
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA,Altos Labs, 5510 Morehouse Drive, San Diego, CA 92121, USA
| | - Reyna Hernandez-Benitez
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA,Altos Labs, 5510 Morehouse Drive, San Diego, CA 92121, USA
| | - Concepcion Rodriguez Esteban
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA,Altos Labs, 5510 Morehouse Drive, San Diego, CA 92121, USA
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Michael C. Holmes
- Ambys Medicines, 131 Oyster Point Boulevard, Suite 200, South San Francisco, CA 94080, USA
| | - Fei Yi
- Ambys Medicines, 131 Oyster Point Boulevard, Suite 200, South San Francisco, CA 94080, USA
| | - Raymond D. Hickey
- Ambys Medicines, 131 Oyster Point Boulevard, Suite 200, South San Francisco, CA 94080, USA
| | | | - Estrella Nuñez Delicado
- Universidad Católica San Antonio de Murcia (UCAM), Campus de los Jerónimos, N° 135 12, 30107 Guadalupe, Spain
| | - Antoni Castells
- Hospital Clinic of Barcelona, Carrer Villarroel, 170, 08036 Barcelona, Spain
| | - Josep M. Campistol
- Hospital Clinic of Barcelona, Carrer Villarroel, 170, 08036 Barcelona, Spain
| | - Yang Yu
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Diana C. Hargreaves
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Akihiro Asai
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA,Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Pradeep Reddy
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA,Altos Labs, 5510 Morehouse Drive, San Diego, CA 92121, USA,Lead contact,Correspondence:
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5
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Abstract
The regeneration potential of axons projecting from retinal ganglion cells (RGCs) is lost shortly after birth. In Nature, Lu et al. (2020) demonstrate that epigenetic reprogramming of RGCs by overexpression of Oct4, Sox2, and Klf4 leads to axon regeneration and restoration of vision in a glaucoma model and aged mice.
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Affiliation(s)
- Pradeep Reddy
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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6
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Dan J, Memczak S, Izpisua Belmonte JC. Expanding the Toolbox and Targets for Gene Editing. Trends Mol Med 2021; 27:203-206. [PMID: 33487569 DOI: 10.1016/j.molmed.2020.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/08/2020] [Accepted: 12/08/2020] [Indexed: 12/26/2022]
Abstract
Genome editing holds great promise for treating a range of human genetic diseases. While emerging clustered regularly interspaced short-palindromic repeats (CRISPR) technologies allow editing of the nuclear genome, it is still not possible to precisely manipulate mitochondrial DNA (mtDNA). Here, we summarize past developments and recent advances in nuclear and mitochondrial genome editing.
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Affiliation(s)
- Jiameng Dan
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Sebastian Memczak
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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7
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Abstract
Organismal ageing results from interlinked molecular changes in multiple organs over time. The study of ageing at the molecular level is complicated by varying decay characteristics and kinetics-both between and within organs-driven by intrinsic and extracellular factors. Emerging single-cell omics methods allow for molecular and spatial profiling of cells, and probing of regulatory states and cell-fate determination, thus providing promising tools for unravelling the heterogeneous process of ageing and making it amenable to intervention. These new strategies are enabled by advances in genomic, epigenomic and transcriptomic technologies. Combined with methods for proteome and metabolome analysis, single-cell techniques provide multidimensional, integrated data with unprecedented detail and throughput. Here, we provide an overview of the current state, and perspectives on the future, of this emerging field. We discuss how single-cell approaches can advance understanding of mechanisms underlying organismal ageing and aid in the development of interventions for ageing and ageing-associated diseases.
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Affiliation(s)
- Xiaojuan He
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Sebastian Memczak
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jing Qu
- 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 of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, China.
| | | | - Guang-Hui Liu
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, China.
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8
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Maass PG, Glažar P, Memczak S, Dittmar G, Hollfinger I, Schreyer L, Sauer AV, Toka O, Aiuti A, Luft FC, Rajewsky N. A map of human circular RNAs in clinically relevant tissues. J Mol Med (Berl) 2017; 95:1179-1189. [PMID: 28842720 PMCID: PMC5660143 DOI: 10.1007/s00109-017-1582-9] [Citation(s) in RCA: 248] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 08/03/2017] [Accepted: 08/18/2017] [Indexed: 01/09/2023]
Abstract
Abstract Cellular circular RNAs (circRNAs) are generated by head-to-tail splicing and are present in all multicellular organisms studied so far. Recently, circRNAs have emerged as a large class of RNA which can function as post-transcriptional regulators. It has also been shown that many circRNAs are tissue- and stage-specifically expressed. Moreover, the unusual stability and expression specificity make circRNAs important candidates for clinical biomarker research. Here, we present a circRNA expression resource of 20 human tissues highly relevant to disease-related research: vascular smooth muscle cells (VSMCs), human umbilical vein cells (HUVECs), artery endothelial cells (HUAECs), atrium, vena cava, neutrophils, platelets, cerebral cortex, placenta, and samples from mesenchymal stem cell differentiation. In eight different samples from a single donor, we found highly tissue-specific circRNA expression. Circular-to-linear RNA ratios revealed that many circRNAs were expressed higher than their linear host transcripts. Among the 71 validated circRNAs, we noticed potential biomarkers. In adenosine deaminase-deficient, severe combined immunodeficiency (ADA-SCID) patients and in Wiskott-Aldrich-Syndrome (WAS) patients’ samples, we found evidence for differential circRNA expression of genes that are involved in the molecular pathogenesis of both phenotypes. Our findings underscore the need to assess circRNAs in mechanisms of human disease. Key messages circRNA resource catalog of 20 clinically relevant tissues. circRNA expression is highly tissue-specific. circRNA transcripts are often more abundant than their linear host RNAs. circRNAs can be differentially expressed in disease-associated genes.
Electronic supplementary material The online version of this article (10.1007/s00109-017-1582-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Philipp G Maass
- Experimental and Clinical Research Center (ECRC), a joint cooperation between the Charité Medical Faculty and the Max Delbrück Center for Molecular Medicine (MDC), Lindenberger Weg 80, 13125, Berlin, Germany. .,Max Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Strasse 10, 13125, Berlin, Germany. .,Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave, Cambridge, MA, 02138, USA.
| | - Petar Glažar
- Max Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Sebastian Memczak
- Experimental and Clinical Research Center (ECRC), a joint cooperation between the Charité Medical Faculty and the Max Delbrück Center for Molecular Medicine (MDC), Lindenberger Weg 80, 13125, Berlin, Germany.,Max Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Gunnar Dittmar
- Max Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Irene Hollfinger
- Experimental and Clinical Research Center (ECRC), a joint cooperation between the Charité Medical Faculty and the Max Delbrück Center for Molecular Medicine (MDC), Lindenberger Weg 80, 13125, Berlin, Germany.,Max Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Luisa Schreyer
- Max Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Aisha V Sauer
- Scientific Institute HS Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), 20132, Milan, Italy
| | - Okan Toka
- Department of Pediatric Cardiology, Children's Hospital, Friedrich-Alexander University Erlangen, Loschge Strasse 15, 91054, Erlangen, Germany.,The German Registry for Congenital Heart Defects, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Alessandro Aiuti
- Scientific Institute HS Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), 20132, Milan, Italy.,Vita Salute San Raffaele University, Milan, Italy
| | - Friedrich C Luft
- Experimental and Clinical Research Center (ECRC), a joint cooperation between the Charité Medical Faculty and the Max Delbrück Center for Molecular Medicine (MDC), Lindenberger Weg 80, 13125, Berlin, Germany.,Max Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Strasse 10, 13125, Berlin, Germany.,Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA
| | - Nikolaus Rajewsky
- Max Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Strasse 10, 13125, Berlin, Germany.
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Piwecka M, Glažar P, Hernandez-Miranda LR, Memczak S, Wolf SA, Rybak-Wolf A, Filipchyk A, Klironomos F, Cerda Jara CA, Fenske P, Trimbuch T, Zywitza V, Plass M, Schreyer L, Ayoub S, Kocks C, Kühn R, Rosenmund C, Birchmeier C, Rajewsky N. Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function. Science 2017; 357:science.aam8526. [DOI: 10.1126/science.aam8526] [Citation(s) in RCA: 713] [Impact Index Per Article: 101.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/26/2017] [Indexed: 12/29/2022]
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10
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Memczak S, Papavasileiou P, Peters O, Rajewsky N. Identification and Characterization of Circular RNAs As a New Class of Putative Biomarkers in Human Blood. PLoS One 2015; 10:e0141214. [PMID: 26485708 PMCID: PMC4617279 DOI: 10.1371/journal.pone.0141214] [Citation(s) in RCA: 486] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/05/2015] [Indexed: 12/25/2022] Open
Abstract
Covalently closed circular RNA molecules (circRNAs) have recently emerged as a class of RNA isoforms with widespread and tissue specific expression across animals, oftentimes independent of the corresponding linear mRNAs. circRNAs are remarkably stable and sometimes highly expressed molecules. Here, we sequenced RNA in human peripheral whole blood to determine the potential of circRNAs as biomarkers in an easily accessible body fluid. We report the reproducible detection of thousands of circRNAs. Importantly, we observed that hundreds of circRNAs are much higher expressed than corresponding linear mRNAs. Thus, circRNA expression in human blood reveals and quantifies the activity of hundreds of coding genes not accessible by classical mRNA specific assays. Our findings suggest that circRNAs could be used as biomarker molecules in standard clinical blood samples.
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Affiliation(s)
- Sebastian Memczak
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Robert Rössle Straße 10, D-13125 Berlin, Germany
| | - Panagiotis Papavasileiou
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Robert Rössle Straße 10, D-13125 Berlin, Germany
| | - Oliver Peters
- Department of Psychiatry, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, D-12203 Berlin, Germany
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Robert Rössle Straße 10, D-13125 Berlin, Germany
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11
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Ivanov A, Memczak S, Wyler E, Torti F, Porath H, Orejuela M, Piechotta M, Levanon E, Landthaler M, Dieterich C, Rajewsky N. Analysis of Intron Sequences Reveals Hallmarks of Circular RNA Biogenesis in Animals. Cell Rep 2015; 10:170-7. [DOI: 10.1016/j.celrep.2014.12.019] [Citation(s) in RCA: 601] [Impact Index Per Article: 66.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/25/2014] [Accepted: 12/09/2014] [Indexed: 01/24/2023] Open
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12
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Ashwal-Fluss R, Meyer M, Pamudurti N, Ivanov A, Bartok O, Hanan M, Evantal N, Memczak S, Rajewsky N, Kadener S. circRNA Biogenesis Competes with Pre-mRNA Splicing. Mol Cell 2014; 56:55-66. [DOI: 10.1016/j.molcel.2014.08.019] [Citation(s) in RCA: 1632] [Impact Index Per Article: 163.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/11/2014] [Accepted: 08/14/2014] [Indexed: 02/08/2023]
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