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Pablo JLB, Cornett SL, Wang LA, Jo S, Brünger T, Budnik N, Hegde M, DeKeyser JM, Thompson CH, Doench JG, Lal D, George AL, Pan JQ. Scanning mutagenesis of the voltage-gated sodium channel Na V1.2 using base editing. Cell Rep 2023; 42:112563. [PMID: 37267104 PMCID: PMC10592450 DOI: 10.1016/j.celrep.2023.112563] [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: 08/09/2022] [Revised: 03/24/2023] [Accepted: 05/08/2023] [Indexed: 06/04/2023] Open
Abstract
It is challenging to apply traditional mutational scanning to voltage-gated sodium channels (NaVs) and functionally annotate the large number of coding variants in these genes. Using a cytosine base editor and a pooled viability assay, we screen a library of 368 guide RNAs (gRNAs) tiling NaV1.2 to identify more than 100 gRNAs that change NaV1.2 function. We sequence base edits made by a subset of these gRNAs to confirm specific variants that drive changes in channel function. Electrophysiological characterization of these channel variants validates the screen results and provides functional mechanisms of channel perturbation. Most of the changes caused by these gRNAs are classifiable as loss of function along with two missense mutations that lead to gain of function in NaV1.2 channels. This two-tiered strategy to functionally characterize ion channel protein variants at scale identifies a large set of loss-of-function mutations in NaV1.2.
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Affiliation(s)
- Juan Lorenzo B Pablo
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Savannah L Cornett
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lei A Wang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sooyeon Jo
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tobias Brünger
- Cologne Center for Genomics, University of Cologne, 51149 Cologne, Germany; Genomic Medicine Institute, Lerner Research Institute, Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Nikita Budnik
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mudra Hegde
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jean-Marc DeKeyser
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Christopher H Thompson
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dennis Lal
- Cologne Center for Genomics, University of Cologne, 51149 Cologne, Germany; Genomic Medicine Institute, Lerner Research Institute, Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Neurology, McGovern Medical School, UTHealth, Houston, TX 77030, USA
| | - Alfred L George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jen Q Pan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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Zhou Y, Kim C, Pablo JLB, Zhang F, Jung JY, Xiao L, Bazua-Valenti S, Emani M, Hopkins CR, Weins A, Greka A. TRPC5 Channel Inhibition Protects Podocytes in Puromycin-Aminonucleoside Induced Nephrosis Models. Front Med (Lausanne) 2021; 8:721865. [PMID: 34621762 PMCID: PMC8490698 DOI: 10.3389/fmed.2021.721865] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 06/07/2021] [Accepted: 08/04/2021] [Indexed: 02/05/2023] Open
Abstract
Podocyte injury and the appearance of proteinuria are key features of several progressive kidney diseases. Genetic deletion or selective inhibition of TRPC5 channels with small-molecule inhibitors protects podocytes in rodent models of kidney disease, but less is known about the human relevance and translatability of TRPC5 inhibition. Here, we investigate the effect of TRPC5 inhibition in puromycin aminonucleoside (PAN)-treated rats, human iPSC-derived podocytes, and kidney organoids. We first established that systemic administration of the TRPC5 inhibitor AC1903 was sufficient to protect podocyte cytoskeletal proteins and suppress proteinuria in PAN-induced nephrosis rats, an established model of podocyte injury. TRPC5 current was recorded in the human iPSC-derived podocytes and was blocked by AC1903. PAN treatment caused podocyte injury in human iPSC-derived podocytes and kidney organoids. Inhibition of TRPC5 channels reversed the effects of PAN-induced injury in human podocytes in both 2D and 3D culture systems. Taken together, these results revealed the relevance of TRPC5 channel inhibition in puromycin-aminonucleoside induced nephrosis models, highlighting the potential of this therapeutic strategy for patients.
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Affiliation(s)
- Yiming Zhou
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States.,Center for the Development of Therapeutics (CDoT), Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Choah Kim
- Center for the Development of Therapeutics (CDoT), Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Juan Lorenzo B Pablo
- Center for the Development of Therapeutics (CDoT), Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Fan Zhang
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - Ji Yong Jung
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States.,Department of Internal Medicine, Gachon University Gil Medical Center, College of Medicine, Incheon, South Korea
| | - Li Xiao
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - Silvana Bazua-Valenti
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States.,Center for the Development of Therapeutics (CDoT), Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Maheswarareddy Emani
- Center for the Development of Therapeutics (CDoT), Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Corey R Hopkins
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, United States
| | - Astrid Weins
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - Anna Greka
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States.,Center for the Development of Therapeutics (CDoT), Broad Institute of MIT and Harvard, Cambridge, MA, United States
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Narciso JET, Uy IDC, Cabang AB, Chavez JFC, Pablo JLB, Padilla-Concepcion GP, Padlan EA. Analysis of the antibody structure based on high-resolution crystallographic studies. N Biotechnol 2011; 28:435-47. [PMID: 21477671 DOI: 10.1016/j.nbt.2011.03.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
High-resolution structures of liganded and unliganded antibody molecules were analyzed in terms of the interaction between the antibody with ligand, between the residues in the contact between the variable domains, and between the framework and the complementarity-determining regions of the antibody. The solvent accessibilities of the residues in the variable domains were also analyzed. The structural information is useful in the engineering of antibodies for therapeutic and other purposes.
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Affiliation(s)
- Jo Erika T Narciso
- The Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines
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