1
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Jankowski MS, Griffith D, Shastry DG, Pelham JF, Ginell GM, Thomas J, Karande P, Holehouse AS, Hurley JM. Disordered clock protein interactions and charge blocks turn an hourglass into a persistent circadian oscillator. Nat Commun 2024; 15:3523. [PMID: 38664421 PMCID: PMC11045787 DOI: 10.1038/s41467-024-47761-z] [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] [Received: 09/07/2023] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Organismal physiology is widely regulated by the molecular circadian clock, a feedback loop composed of protein complexes whose members are enriched in intrinsically disordered regions. These regions can mediate protein-protein interactions via SLiMs, but the contribution of these disordered regions to clock protein interactions had not been elucidated. To determine the functionality of these disordered regions, we applied a synthetic peptide microarray approach to the disordered clock protein FRQ in Neurospora crassa. We identified residues required for FRQ's interaction with its partner protein FRH, the mutation of which demonstrated FRH is necessary for persistent clock oscillations but not repression of transcriptional activity. Additionally, the microarray demonstrated an enrichment of FRH binding to FRQ peptides with a net positive charge. We found that positively charged residues occurred in significant "blocks" within the amino acid sequence of FRQ and that ablation of one of these blocks affected both core clock timing and physiological clock output. Finally, we found positive charge clusters were a commonly shared molecular feature in repressive circadian clock proteins. Overall, our study suggests a mechanistic purpose for positive charge blocks and yielded insights into repressive arm protein roles in clock function.
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Affiliation(s)
- Meaghan S Jankowski
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Daniel Griffith
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Divya G Shastry
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Jacqueline F Pelham
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Garrett M Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Joshua Thomas
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Pankaj Karande
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Jennifer M Hurley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
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2
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Boo A, Toth T, Yu Q, Pfotenhauer A, Fields BD, Lenaghan SC, Stewart CN, Voigt CA. Synthetic microbe-to-plant communication channels. Nat Commun 2024; 15:1817. [PMID: 38418817 PMCID: PMC10901793 DOI: 10.1038/s41467-024-45897-6] [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] [Received: 02/10/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
Plants and microbes communicate to collaborate to stop pests, scavenge nutrients, and react to environmental change. Microbiota consisting of thousands of species interact with each other and plants using a large chemical language that is interpreted by complex regulatory networks. In this work, we develop modular interkingdom communication channels, enabling bacteria to convey environmental stimuli to plants. We introduce a "sender device" in Pseudomonas putida and Klebsiella pneumoniae, that produces the small molecule p-coumaroyl-homoserine lactone (pC-HSL) when the output of a sensor or circuit turns on. This molecule triggers a "receiver device" in the plant to activate gene expression. We validate this system in Arabidopsis thaliana and Solanum tuberosum (potato) grown hydroponically and in soil, demonstrating its modularity by swapping bacteria that process different stimuli, including IPTG, aTc and arsenic. Programmable communication channels between bacteria and plants will enable microbial sentinels to transmit information to crops and provide the building blocks for designing artificial consortia.
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Affiliation(s)
- Alice Boo
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tyler Toth
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Qiguo Yu
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alexander Pfotenhauer
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Brandon D Fields
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Scott C Lenaghan
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - C Neal Stewart
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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3
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Johnson ZV, Hegarty BE, Gruenhagen GW, Lancaster TJ, McGrath PT, Streelman JT. Cellular profiling of a recently-evolved social behavior in cichlid fishes. Nat Commun 2023; 14:4891. [PMID: 37580322 PMCID: PMC10425353 DOI: 10.1038/s41467-023-40331-9] [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] [Received: 01/24/2023] [Accepted: 07/21/2023] [Indexed: 08/16/2023] Open
Abstract
Social behaviors are diverse in nature, but it is unclear how conserved genes, brain regions, and cell populations generate this diversity. Here we investigate bower-building, a recently-evolved social behavior in cichlid fishes. We use single nucleus RNA-sequencing in 38 individuals to show signatures of recent behavior in specific neuronal populations, and building-associated rebalancing of neuronal proportions in the putative homolog of the hippocampal formation. Using comparative genomics across 27 species, we trace bower-associated genome evolution to a subpopulation of glia lining the dorsal telencephalon. We show evidence that building-associated neural activity and a departure from quiescence in this glial subpopulation together regulate hippocampal-like neuronal rebalancing. Our work links behavior-associated genomic variation to specific brain cell types and their functions, and suggests a social behavior has evolved through changes in glia.
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Affiliation(s)
- Zachary V Johnson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA.
- Emory National Primate Research Center, Emory University, Atlanta, GA, USA.
| | - Brianna E Hegarty
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - George W Gruenhagen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Tucker J Lancaster
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Patrick T McGrath
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
| | - Jeffrey T Streelman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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4
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Champion KP, Gozel O, Lankow BS, Ermentrout GB, Goldman MS. An oscillatory mechanism for multi-level storage in short-term memory. Commun Biol 2023; 6:829. [PMID: 37563448 PMCID: PMC10415352 DOI: 10.1038/s42003-023-05200-7] [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] [Received: 04/01/2022] [Accepted: 08/01/2023] [Indexed: 08/12/2023] Open
Abstract
Oscillatory activity is commonly observed during the maintenance of information in short-term memory, but its role remains unclear. Non-oscillatory models of short-term memory storage are able to encode stimulus identity through their spatial patterns of activity, but are typically limited to either an all-or-none representation of stimulus amplitude or exhibit a biologically implausible exact-tuning condition. Here we demonstrate a simple mechanism by which oscillatory input enables a circuit to generate persistent or sequential activity that encodes information not only in the spatial pattern of activity, but also in the amplitude of activity. This is accomplished through a phase-locking phenomenon that permits many different amplitudes of persistent activity to be stored without requiring exact tuning of model parameters. Altogether, this work proposes a class of models for the storage of information in working memory, a potential role for brain oscillations, and a dynamical mechanism for maintaining multi-stable neural representations.
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Affiliation(s)
- Kathleen P Champion
- Department of Applied Mathematics, University of Washington, Seattle, WA, 98195, USA
| | - Olivia Gozel
- Departments of Neurobiology and Statistics, University of Chicago, Chicago, IL, 60637, USA
- Grossman Center for Quantitative Biology and Human Behavior, University of Chicago, Chicago, IL, 60637, USA
| | - Benjamin S Lankow
- Center for Neuroscience, University of California, Davis, Davis, CA, 95618, USA
| | - G Bard Ermentrout
- Department of Mathematics, University of Pittsburgh, Pittsburgh, PA, 15213, USA.
| | - Mark S Goldman
- Center for Neuroscience, University of California, Davis, Davis, CA, 95618, USA.
- Department of Neurobiology, Physiology, and Behavior, and Department of Ophthalmology and Vision Science, University of California, Davis, Davis, CA, 95618, USA.
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5
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Canty JT, Hensley A, Aslan M, Jack A, Yildiz A. TRAK adaptors regulate the recruitment and activation of dynein and kinesin in mitochondrial transport. Nat Commun 2023; 14:1376. [PMID: 36914620 PMCID: PMC10011603 DOI: 10.1038/s41467-023-36945-8] [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] [Received: 08/04/2021] [Accepted: 02/23/2023] [Indexed: 03/16/2023] Open
Abstract
Mitochondrial transport along microtubules is mediated by Miro1 and TRAK adaptors that recruit kinesin-1 and dynein-dynactin. To understand how these opposing motors are regulated during mitochondrial transport, we reconstitute the bidirectional transport of Miro1/TRAK along microtubules in vitro. We show that the coiled-coil domain of TRAK activates dynein-dynactin and enhances the motility of kinesin-1 activated by its cofactor MAP7. We find that TRAK adaptors that recruit both motors move towards kinesin-1's direction, whereas kinesin-1 is excluded from binding TRAK transported by dynein-dynactin, avoiding motor tug-of-war. We also test the predictions of the models that explain how mitochondrial transport stalls in regions with elevated Ca2+. Transport of Miro1/TRAK by kinesin-1 is not affected by Ca2+. Instead, we demonstrate that the microtubule docking protein syntaphilin induces resistive forces that stall kinesin-1 and dynein-driven motility. Our results suggest that mitochondrial transport stalls by Ca2+-mediated recruitment of syntaphilin to the mitochondrial membrane, not by disruption of the transport machinery.
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Affiliation(s)
- John T Canty
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, 94720, USA.
- Department of Cancer Immunology, Genentech Inc., 1 DNA Way, 94080, South San Francisco, CA, USA.
| | - Andrew Hensley
- Physics Department, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Merve Aslan
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Amanda Jack
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Ahmet Yildiz
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, 94720, USA.
- Physics Department, University of California at Berkeley, Berkeley, CA, 94720, USA.
- Department of Molecular and Cellular Biology, University of California at Berkeley, Berkeley, CA, 94720, USA.
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6
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Momin N, Palmeri JR, Lutz EA, Jailkhani N, Mak H, Tabet A, Chinn MM, Kang BH, Spanoudaki V, Hynes RO, Wittrup KD. Maximizing response to intratumoral immunotherapy in mice by tuning local retention. Nat Commun 2022; 13:109. [PMID: 35013154 PMCID: PMC8748612 DOI: 10.1038/s41467-021-27390-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 11/17/2021] [Indexed: 01/08/2023] Open
Abstract
Direct injection of therapies into tumors has emerged as an administration route capable of achieving high local drug exposure and strong anti-tumor response. A diverse array of immune agonists ranging in size and target are under development as local immunotherapies. However, due to the relatively recent adoption of intratumoral administration, the pharmacokinetics of locally-injected biologics remains poorly defined, limiting rational design of tumor-localized immunotherapies. Here we define a pharmacokinetic framework for biologics injected intratumorally that can predict tumor exposure and effectiveness. We find empirically and computationally that extending the tumor exposure of locally-injected interleukin-2 by increasing molecular size and/or improving matrix-targeting affinity improves therapeutic efficacy in mice. By tracking the distribution of intratumorally-injected proteins using positron emission tomography, we observe size-dependent enhancement in tumor exposure occurs by slowing the rate of diffusive escape from the tumor and by increasing partitioning to an apparent viscous region of the tumor. In elucidating how molecular weight and matrix binding interplay to determine tumor exposure, our model can aid in the design of intratumoral therapies to exert maximal therapeutic effect.
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Affiliation(s)
- Noor Momin
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Joseph R Palmeri
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Emi A Lutz
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Noor Jailkhani
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Howard Mak
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Anthony Tabet
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Magnolia M Chinn
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Byong H Kang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Virginia Spanoudaki
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Richard O Hynes
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - K Dane Wittrup
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
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7
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Abstract
The neural circuitry mediating taste has been mapped out from the periphery to the cortex, but genetic identity of taste-responsive neurons has remained elusive. Here, we describe a population of neurons in the gustatory region of the parabrachial nucleus that express the transcription factor Satb2 and project to taste-associated regions, including the gustatory thalamus and insular cortex. Using calcium imaging in awake, freely licking mice, we show that Satb2 neurons respond to the five basic taste modalities. Optogenetic activation of these neurons enhances taste preferences, whereas chronic inactivation decreases the magnitude of taste preferences in both brief- and long-access taste tests. Simultaneous inactivation of Satb2 and calcitonin gene-related peptide neurons in the PBN abolishes responses to aversive tastes. These data suggest that taste information in the parabrachial nucleus is conveyed by multiple populations of neurons, including both Satb2 and calcitonin gene-related peptide neurons.
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Affiliation(s)
- Brooke C Jarvie
- Departments of Biochemistry and Genome Sciences, University of Washington, Seattle, WA, 98195, USA
- Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA
| | - Jane Y Chen
- Departments of Biochemistry and Genome Sciences, University of Washington, Seattle, WA, 98195, USA
- Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA
| | - Hunter O King
- Departments of Biochemistry and Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Richard D Palmiter
- Departments of Biochemistry and Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
- Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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8
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Li P, Jeong H. The social brain of language: grounding second language learning in social interaction. NPJ Sci Learn 2020; 5:8. [PMID: 32595983 PMCID: PMC7305321 DOI: 10.1038/s41539-020-0068-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/29/2020] [Indexed: 05/13/2023]
Abstract
For centuries, adults may have relied on pedagogies that promote rote memory for the learning of foreign languages through word associations and grammar rules. This contrasts sharply with child language learning which unfolds in socially interactive contexts. In this paper, we advocate an approach to study the social brain of language by grounding second language learning in social interaction. Evidence has accumulated from research in child language, education, and cognitive science pointing to the efficacy and significance of social learning. Work from several recent L2 studies also suggests positive brain changes along with enhanced behavioral outcomes as a result of social learning. Here we provide a blueprint for the brain network underlying social L2 learning, enabling the integration of neurocognitive bases with social cognition of second language while combining theories of language and memory with practical implications for the learning and teaching of a new language in adulthood.
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Affiliation(s)
- Ping Li
- Department of Chinese and Bilingual Studies, Faculty of Humanities, The Hong Kong Polytechnic University, Kowloon, Hong Kong China
| | - Hyeonjeong Jeong
- Graduate School of International Cultural Studies & Department of Human Brain Science, Institute of Development, Aging, and Cancer, Tohoku University, Aoba-ku, Sendai Japan
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9
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Moss EL, Maghini DG, Bhatt AS. Complete, closed bacterial genomes from microbiomes using nanopore sequencing. Nat Biotechnol 2020; 38:701-707. [PMID: 32042169 PMCID: PMC7283042 DOI: 10.1038/s41587-020-0422-6] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 12/12/2019] [Accepted: 01/10/2020] [Indexed: 02/07/2023]
Abstract
Microbial genomes can be assembled from short-read sequencing data, but the assembly contiguity of these metagenome-assembled genomes is constrained by repeat elements. Correct assignment of genomic positions of repeats is crucial for understanding the effect of genome structure on genome function. We applied nanopore sequencing and our workflow, named Lathe, which incorporates long-read assembly and short-read error correction, to assemble closed bacterial genomes from complex microbiomes. We validated our approach with a synthetic mixture of 12 bacterial species. Seven genomes were completely assembled into single contigs and three genomes were assembled into four or fewer contigs. Next, we used our methods to analyze metagenomics data from 13 human stool samples. We assembled 20 circular genomes, including genomes of Prevotella copri and a candidate Cibiobacter sp. Despite the decreased nucleotide accuracy compared with alternative sequencing and assembly approaches, our methods improved assembly contiguity, allowing for investigation of the role of repeat elements in microbial function and adaptation.
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Affiliation(s)
- Eli L Moss
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Dylan G Maghini
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA.
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10
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Wang J, Agarwal D, Huang M, Hu G, Zhou Z, Ye C, Zhang NR. Data denoising with transfer learning in single-cell transcriptomics. Nat Methods 2019; 16:875-878. [PMID: 31471617 PMCID: PMC7781045 DOI: 10.1038/s41592-019-0537-1] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 07/23/2019] [Indexed: 02/06/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) data are noisy and sparse. Here, we show that transfer learning across datasets remarkably improves data quality. By coupling a deep autoencoder with a Bayesian model, SAVER-X extracts transferable gene-gene relationships across data from different labs, varying conditions and divergent species, to denoise new target datasets.
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Affiliation(s)
- Jingshu Wang
- Department of Statistics, University of Pennsylvania, Philadelphia, PA, USA
| | - Divyansh Agarwal
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Mo Huang
- Department of Statistics, University of Pennsylvania, Philadelphia, PA, USA
| | - Gang Hu
- School of Mathematical Sciences, Nankai University, Tianjin, China
| | - Zilu Zhou
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Chengzhong Ye
- School of Medicine, Tsinghua University, Beijing, China
| | - Nancy R Zhang
- Department of Statistics, University of Pennsylvania, Philadelphia, PA, USA.
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