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Saha K, Sontheimer EJ, Brooks PJ, Dwinell MR, Gersbach CA, Liu DR, Murray SA, Tsai SQ, Wilson RC, Anderson DG, Asokan A, Banfield JF, Bankiewicz KS, Bao G, Bulte JWM, Bursac N, Campbell JM, Carlson DF, Chaikof EL, Chen ZY, Cheng RH, Clark KJ, Curiel DT, Dahlman JE, Deverman BE, Dickinson ME, Doudna JA, Ekker SC, Emborg ME, Feng G, Freedman BS, Gamm DM, Gao G, Ghiran IC, Glazer PM, Gong S, Heaney JD, Hennebold JD, Hinson JT, Khvorova A, Kiani S, Lagor WR, Lam KS, Leong KW, Levine JE, Lewis JA, Lutz CM, Ly DH, Maragh S, McCray PB, McDevitt TC, Mirochnitchenko O, Morizane R, Murthy N, Prather RS, Ronald JA, Roy S, Roy S, Sabbisetti V, Saltzman WM, Santangelo PJ, Segal DJ, Shimoyama M, Skala MC, Tarantal AF, Tilton JC, Truskey GA, Vandsburger M, Watts JK, Wells KD, Wolfe SA, Xu Q, Xue W, Yi G, Zhou J. The NIH Somatic Cell Genome Editing program. Nature 2021; 592:195-204. [PMID: 33828315 PMCID: PMC8026397 DOI: 10.1038/s41586-021-03191-1] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 01/05/2021] [Indexed: 12/14/2022]
Abstract
The move from reading to writing the human genome offers new opportunities to improve human health. The United States National Institutes of Health (NIH) Somatic Cell Genome Editing (SCGE) Consortium aims to accelerate the development of safer and more-effective methods to edit the genomes of disease-relevant somatic cells in patients, even in tissues that are difficult to reach. Here we discuss the consortium's plans to develop and benchmark approaches to induce and measure genome modifications, and to define downstream functional consequences of genome editing within human cells. Central to this effort is a rigorous and innovative approach that requires validation of the technology through third-party testing in small and large animals. New genome editors, delivery technologies and methods for tracking edited cells in vivo, as well as newly developed animal models and human biological systems, will be assembled-along with validated datasets-into an SCGE Toolkit, which will be disseminated widely to the biomedical research community. We visualize this toolkit-and the knowledge generated by its applications-as a means to accelerate the clinical development of new therapies for a wide range of conditions.
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Affiliation(s)
- Krishanu Saha
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Medical History & Bioethics, University of Wisconsin-Madison, Madison, WI, USA.
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA.
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, USA.
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.
| | - P J Brooks
- Office of Rare Diseases Research, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, MD, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - David R Liu
- Merkin Institute of Transformative Technologies, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | | | - Shengdar Q Tsai
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ross C Wilson
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Daniel G Anderson
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research at the Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Aravind Asokan
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA
| | | | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Jeff W M Bulte
- Russell H. Morgan Department of Radiology and Radiological Science, Division of MR Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Cellular Imaging Section and Vascular Biology Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nenad Bursac
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | | | - Elliot L Chaikof
- Department of Surgery, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Zheng-Yi Chen
- Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA, USA
- Program in Neuroscience, Harvard Medical School, Boston, MA, USA
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
| | - R Holland Cheng
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, USA
| | - Karl J Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic Rochester, Rochester, MN, USA
| | - David T Curiel
- Department of Radiation Oncology, Washington University in St Louis, St Louis, MO, USA
| | - James E Dahlman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Benjamin E Deverman
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
| | - Stephen C Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic Rochester, Rochester, MN, USA
| | - Marina E Emborg
- Department of Medical Physics, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Benjamin S Freedman
- Division of Nephrology, University of Washington, Seattle, WA, USA
- Kidney Research Institute, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - David M Gamm
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, USA
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ionita C Ghiran
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Shaoqin Gong
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jon D Hennebold
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - John T Hinson
- Pat and Jim Calhoun Cardiology Center, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Samira Kiani
- Pittsburgh Liver Research Center, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - William R Lagor
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Kit S Lam
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA
| | - Kam W Leong
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Jon E Levine
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Danith H Ly
- Department of Chemistry, Carnegie-Mellon University, Pittsburgh, PA, USA
| | - Samantha Maragh
- Biomarker and Genomic Sciences Group, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Paul B McCray
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Todd C McDevitt
- Gladstone Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Oleg Mirochnitchenko
- Office of Research Infrastructure Programs, Division of Program Coordination, Planning, and Strategic Initiatives, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Ryuji Morizane
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Niren Murthy
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Randall S Prather
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - John A Ronald
- Robarts Research Institute and Department of Medical Biophysics, The University of Western Ontario, London, Ontario, Canada
| | - Subhojit Roy
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Sushmita Roy
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | | | - W Mark Saltzman
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Philip J Santangelo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - David J Segal
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA
| | - Mary Shimoyama
- Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, WI, USA
| | - Melissa C Skala
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
| | - Alice F Tarantal
- Department of Pediatrics, University of California, Davis, Davis, CA, USA
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, USA
- School of Medicine, University of California, Davis, Davis, CA, USA
- California National Primate Research Center, University of California, Davis, Davis, CA, USA
| | - John C Tilton
- Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA
| | - George A Truskey
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Moriel Vandsburger
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Kevin D Wells
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Worcester, MA, USA
| | - Qiaobing Xu
- Department of Biomedical Engineering, Tufts University, Medford, MA, USA
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Guohua Yi
- Department of Pulmonary Immunology, University of Texas Health Sciences Center at Tyler, Tyler, TX, USA
| | - Jiangbing Zhou
- Department of Neurosurgery, Yale University, New Haven, CT, USA
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12
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Ariyasinghe NR, Santoso JW, Gupta D, Pincus MJ, August PR, McCain ML. Optical Clearing of Skeletal Muscle Bundles Engineered in 3-D Printed Templates. Ann Biomed Eng 2020; 49:523-535. [PMID: 32748107 DOI: 10.1007/s10439-020-02583-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 07/22/2020] [Indexed: 01/23/2023]
Abstract
Many techniques for engineering and interrogating three-dimensional (3-D) muscle bundles from animal- or patient-derived myoblasts have recently been developed to overcome the limitations of existing in vitro and in vivo model systems. However, many approaches for engineering 3-D muscle bundles rely on specialized and time-consuming techniques, such as photolithography for fabrication and cryosectioning for histology. Cryosectioning also limits visualization to a single plane instead of the entire 3-D structure. To address these challenges, we first implemented a consumer-grade 3-D-printer to rapidly prototype multiple templates for engineering muscle bundles. We then employed our templates to engineer 3D muscle bundles and identify template geometries that promoted bundle survival over three weeks. Subsequently, we implemented tissue clearing, immunostaining, and confocal imaging to acquire z-stacks of intact muscle bundles labelled for myogenic markers. With this approach, we could select the imaging plane on-demand and visualize the intact 3-D structure of bundles. However, tissue clearing did cause some tissue degradation that should be considered. Together, these advances in muscle tissue engineering and imaging will accelerate the use of these 3-D tissue platforms for disease modeling and therapeutic discovery.
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Affiliation(s)
- Nethika R Ariyasinghe
- Smidt Heart Institute, Cedars-Sinai Medical Center, 127 San Vicente Blvd, AHSP A9228, Los Angeles, CA, 90048, USA.,Laboratory for Living Systems Engineering, Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, 1042 Downey Way, DRB 140, Los Angeles, CA, 90089, USA.,Icagen, 2090 E. Innovation Park Dr, Oro Valley, AZ, 85755, USA
| | - Jeffrey W Santoso
- Laboratory for Living Systems Engineering, Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, 1042 Downey Way, DRB 140, Los Angeles, CA, 90089, USA
| | - Divya Gupta
- Laboratory for Living Systems Engineering, Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, 1042 Downey Way, DRB 140, Los Angeles, CA, 90089, USA
| | - Mark J Pincus
- Icagen, 2090 E. Innovation Park Dr, Oro Valley, AZ, 85755, USA.,Department of Science & CTE, Ironwood Ridge High School, 2475 W Naranja Dr, Oro Valley, AZ, 85742, USA
| | - Paul R August
- Icagen, 2090 E. Innovation Park Dr, Oro Valley, AZ, 85755, USA.,Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA, 02139, USA
| | - Megan L McCain
- Laboratory for Living Systems Engineering, Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, 1042 Downey Way, DRB 140, Los Angeles, CA, 90089, USA. .,Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of USC, University of Southern California, 1975 Zonal Ave, Los Angeles, CA, 90033, USA.
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