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Zhu D, Brookes DH, Busia A, Carneiro A, Fannjiang C, Popova G, Shin D, Donohue KC, Lin LF, Miller ZM, Williams ER, Chang EF, Nowakowski TJ, Listgarten J, Schaffer DV. Optimal trade-off control in machine learning-based library design, with application to adeno-associated virus (AAV) for gene therapy. Sci Adv 2024; 10:eadj3786. [PMID: 38266077 PMCID: PMC10807795 DOI: 10.1126/sciadv.adj3786] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
Adeno-associated viruses (AAVs) hold tremendous promise as delivery vectors for gene therapies. AAVs have been successfully engineered-for instance, for more efficient and/or cell-specific delivery to numerous tissues-by creating large, diverse starting libraries and selecting for desired properties. However, these starting libraries often contain a high proportion of variants unable to assemble or package their genomes, a prerequisite for any gene delivery goal. Here, we present and showcase a machine learning (ML) method for designing AAV peptide insertion libraries that achieve fivefold higher packaging fitness than the standard NNK library with negligible reduction in diversity. To demonstrate our ML-designed library's utility for downstream engineering goals, we show that it yields approximately 10-fold more successful variants than the NNK library after selection for infection of human brain tissue, leading to a promising glial-specific variant. Moreover, our design approach can be applied to other types of libraries for AAV and beyond.
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Affiliation(s)
- Danqing Zhu
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - David H. Brookes
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Akosua Busia
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ana Carneiro
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Galina Popova
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Psychiatry and Behavioural Sciences, University of California San Francisco, San Francisco, CA 94143, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA
| | - David Shin
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Psychiatry and Behavioural Sciences, University of California San Francisco, San Francisco, CA 94143, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA
| | - Kevin C. Donohue
- Department of Psychiatry and Behavioural Sciences, University of California San Francisco, San Francisco, CA 94143, USA
- School of Medicine, University of California San Francisco, San Francisco, CA, USA. 94143
- Kavli Institute of Fundamental Neuroscience, University of California San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Li F. Lin
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Zachary M. Miller
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Edward F. Chang
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Tomasz J. Nowakowski
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Psychiatry and Behavioural Sciences, University of California San Francisco, San Francisco, CA 94143, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Jennifer Listgarten
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - David V. Schaffer
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Institute (IGI), University of California, Berkeley, Berkeley, CA 94720, USA
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Bashkirova EV, Klimpert N, Monahan K, Campbell CE, Osinski J, Tan L, Schieren I, Pourmorady A, Stecky B, Barnea G, Xie XS, Abdus-Saboor I, Shykind BM, Marlin BJ, Gronostajski RM, Fleischmann A, Lomvardas S. Opposing, spatially-determined epigenetic forces impose restrictions on stochastic olfactory receptor choice. eLife 2023; 12:RP87445. [PMID: 38108811 PMCID: PMC10727497 DOI: 10.7554/elife.87445] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023] Open
Abstract
Olfactory receptor (OR) choice represents an example of genetically hardwired stochasticity, where every olfactory neuron expresses one out of ~2000 OR alleles in the mouse genome in a probabilistic, yet stereotypic fashion. Here, we propose that topographic restrictions in OR expression are established in neuronal progenitors by two opposing forces: polygenic transcription and genomic silencing, both of which are influenced by dorsoventral gradients of transcription factors NFIA, B, and X. Polygenic transcription of OR genes may define spatially constrained OR repertoires, among which one OR allele is selected for singular expression later in development. Heterochromatin assembly and genomic compartmentalization of OR alleles also vary across the axes of the olfactory epithelium and may preferentially eliminate ectopically expressed ORs with more dorsal expression destinations from this 'privileged' repertoire. Our experiments identify early transcription as a potential 'epigenetic' contributor to future developmental patterning and reveal how two spatially responsive probabilistic processes may act in concert to establish deterministic, precise, and reproducible territories of stochastic gene expression.
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Affiliation(s)
- Elizaveta V Bashkirova
- Integrated Program in Cellular, Molecular and Biomedical Studies, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, Columbia UniversityNew YorkUnited States
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Nell Klimpert
- Department of Neuroscience, Division of Biology and Medicine and Robert J. and Nancy D. Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Kevin Monahan
- Department of Biochemistry and Molecular Biology, Rutgers UniversityNewarkUnited States
| | - Christine E Campbell
- Department of Biochemistry, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
- Genetics, Genomics, and Bioinformatics Graduate Program, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
| | - Jason Osinski
- Department of Biochemistry, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
- Genetics, Genomics, and Bioinformatics Graduate Program, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
| | - Longzhi Tan
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Ira Schieren
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Ariel Pourmorady
- Integrated Program in Cellular, Molecular and Biomedical Studies, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, Columbia UniversityNew YorkUnited States
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Beka Stecky
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Gilad Barnea
- Department of Neuroscience, Division of Biology and Medicine and Robert J. and Nancy D. Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Xiaoliang Sunney Xie
- Beijing Innovation Center for Genomics, Peking UniversityBeijingChina
- Biomedical Pioneering Innovation Center, Peking UniversityBeijingChina
| | - Ishmail Abdus-Saboor
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Benjamin M Shykind
- Prevail Therapeutics- a wholly-owned subsidiary of Eli Lilly and CompanyNew YorkUnited States
| | - Bianca J Marlin
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Richard M Gronostajski
- Department of Biochemistry, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
- Genetics, Genomics, and Bioinformatics Graduate Program, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
| | - Alexander Fleischmann
- Department of Neuroscience, Division of Biology and Medicine and Robert J. and Nancy D. Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Stavros Lomvardas
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
- Department of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, Columbia UniversityNew YorkUnited States
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