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Zhang P, Ye X, Wang JCK, Smith CL, Sousa S, Loas A, Eaton DL, Preciado López M, Pentelute BL. Development of an α-Klotho Recognizing High-Affinity Peptide Probe from In-Solution Enrichment. JACS Au 2024; 4:1334-1344. [PMID: 38665650 PMCID: PMC11040699 DOI: 10.1021/jacsau.3c00650] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 04/28/2024]
Abstract
The kidney, parathyroid gland, and choroid plexus express the aging-related transmembrane protein α-Klotho, a coreceptor of the fibroblast growth factor 23 (FGF23) receptor complex. Reduced α-Klotho levels are correlated with chronic kidney disease and other age-related diseases, wherein they are released from membranes into circulation. Klotho's potential physiological action as a hormone is of current scientific interest. Part of the challenges associated with advancing these studies, however, has been the long-standing difficulty in detecting soluble α-Klotho in biofluids. Here, we describe the discovery of peptides that recognize α-Klotho with high affinity and selectivity by applying in-solution size-exclusion-based affinity selection-mass spectrometry (AS-MS). After two rounds of AS-MS and subsequent N-terminal modifications, the peptides improved their binding affinity to α-Klotho by approximately 2300-fold compared to the reported starting peptide Pep-10, previously designed based on the C-terminal region of FGF23. The lead peptide binders were shown to enrich α-Klotho from cell lysates and to label α-Klotho in kidney cells. Our results further support the utility of in-solution, label-free AS-MS protocols to discover peptide-based binders to target proteins of interest with high affinity and selectivity, resulting in functional probes for biological studies.
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Affiliation(s)
- Peiyuan Zhang
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Xiyun Ye
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - John C. K. Wang
- Calico
Life Sciences LLC, 1170 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Corey L. Smith
- AbbVie
Bioresearch Center, 100 Research Drive, Worcester, Massachusetts 01605, United States
| | - Silvino Sousa
- AbbVie
Bioresearch Center, 100 Research Drive, Worcester, Massachusetts 01605, United States
| | - Andrei Loas
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Dan L. Eaton
- Calico
Life Sciences LLC, 1170 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Magdalena Preciado López
- Calico
Life Sciences LLC, 1170 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Bradley L. Pentelute
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02142, United States
- Center
for Environmental Health Sciences, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Broad Institute
of MIT and Harvard, 415
Main Street, Cambridge, Massachusetts 02142, United States
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2
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Basty N, Sorokin EP, Thanaj M, Srinivasan R, Whitcher B, Bell JD, Cule M, Thomas EL. Abdominal imaging associates body composition with COVID-19 severity. PLoS One 2023; 18:e0283506. [PMID: 37053189 PMCID: PMC10101472 DOI: 10.1371/journal.pone.0283506] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 02/28/2022] [Accepted: 03/10/2023] [Indexed: 04/14/2023] Open
Abstract
The main drivers of COVID-19 disease severity and the impact of COVID-19 on long-term health after recovery are yet to be fully understood. Medical imaging studies investigating COVID-19 to date have mostly been limited to small datasets and post-hoc analyses of severe cases. The UK Biobank recruited recovered SARS-CoV-2 positive individuals (n = 967) and matched controls (n = 913) who were extensively imaged prior to the pandemic and underwent follow-up scanning. In this study, we investigated longitudinal changes in body composition, as well as the associations of pre-pandemic image-derived phenotypes with COVID-19 severity. Our longitudinal analysis, in a population of mostly mild cases, associated a decrease in lung volume with SARS-CoV-2 positivity. We also observed that increased visceral adipose tissue and liver fat, and reduced muscle volume, prior to COVID-19, were associated with COVID-19 disease severity. Finally, we trained a machine classifier with demographic, anthropometric and imaging traits, and showed that visceral fat, liver fat and muscle volume have prognostic value for COVID-19 disease severity beyond the standard demographic and anthropometric measurements. This combination of image-derived phenotypes from abdominal MRI scans and ensemble learning to predict risk may have future clinical utility in identifying populations at-risk for a severe COVID-19 outcome.
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Affiliation(s)
- Nicolas Basty
- Research Centre for Optimal Health, School of Life Sciences, University of Westminster, London, United Kingdom
| | - Elena P. Sorokin
- Calico Life Sciences LLC, South San Francisco, California, United States of America
| | - Marjola Thanaj
- Research Centre for Optimal Health, School of Life Sciences, University of Westminster, London, United Kingdom
| | | | - Brandon Whitcher
- Research Centre for Optimal Health, School of Life Sciences, University of Westminster, London, United Kingdom
| | - Jimmy D. Bell
- Research Centre for Optimal Health, School of Life Sciences, University of Westminster, London, United Kingdom
| | - Madeleine Cule
- Calico Life Sciences LLC, South San Francisco, California, United States of America
| | - E. Louise Thomas
- Research Centre for Optimal Health, School of Life Sciences, University of Westminster, London, United Kingdom
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3
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Basty N, Thanaj M, Cule M, Sorokin EP, Liu Y, Thomas EL, Bell JD, Whitcher B. Artifact-free fat-water separation in Dixon MRI using deep learning. J Big Data 2023; 10:4. [PMID: 36686622 PMCID: PMC9835035 DOI: 10.1186/s40537-022-00677-1] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 12/25/2022] [Indexed: 06/17/2023]
Abstract
Chemical-shift encoded MRI (CSE-MRI) is a widely used technique for the study of body composition and metabolic disorders, where derived fat and water signals enable the quantification of adipose tissue and muscle. The UK Biobank is acquiring whole-body Dixon MRI (a specific implementation of CSE-MRI) for over 100,000 participants. Current processing methods associated with large whole-body volumes are time intensive and prone to artifacts during fat-water separation performed by the scanner, making quantitative analysis challenging. The most common artifacts are fat-water swaps, where the labels are inverted at the voxel level. It is common for researchers to discard swapped data (generally around 10%), which is wasteful and may lead to unintended biases. Given the large number of whole-body Dixon MRI acquisitions in the UK Biobank, thousands of swaps are expected to be present in the fat and water volumes from image reconstruction performed on the scanner. If they go undetected, errors will propagate into processes such as organ segmentation, and dilute the results in population-based analyses. There is a clear need for a robust method to accurately separate fat and water volumes in big data collections like the UK Biobank. We formulate fat-water separation as a style transfer problem, where swap-free fat and water volumes are predicted from the acquired Dixon MRI data using a conditional generative adversarial network, and introduce a new loss function for the generator model. Our method is able to predict highly accurate fat and water volumes free from artifacts in the UK Biobank. We show that our model separates fat and water volumes using either single input (in-phase only) or dual input (in-phase and opposed-phase) data, with the latter producing superior results. Our proposed method enables faster and more accurate downstream analysis of body composition from Dixon MRI in population studies by eliminating the need for visual inspection or discarding data due to fat-water swaps. Supplementary Information The online version contains supplementary material available at 10.1186/s40537-022-00677-1.
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Affiliation(s)
- Nicolas Basty
- Research Centre for Optimal Health, University of Westminster, London, UK
| | - Marjola Thanaj
- Research Centre for Optimal Health, University of Westminster, London, UK
| | | | | | - Yi Liu
- Calico Life Sciences LLC, South San Francisco, USA
| | - E. Louise Thomas
- Research Centre for Optimal Health, University of Westminster, London, UK
| | - Jimmy D. Bell
- Research Centre for Optimal Health, University of Westminster, London, UK
| | - Brandon Whitcher
- Research Centre for Optimal Health, University of Westminster, London, UK
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4
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Boone M, Wang L, Lawrence RE, Frost A, Walter P, Schoof M. A point mutation in the nucleotide exchange factor eIF2B constitutively activates the integrated stress response by allosteric modulation. eLife 2022; 11:e76171. [PMID: 35416150 PMCID: PMC9132573 DOI: 10.7554/elife.76171] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
In eukaryotic cells, stressors reprogram the cellular proteome by activating the integrated stress response (ISR). In its canonical form, stress-sensing kinases phosphorylate the eukaryotic translation initiation factor eIF2 (eIF2-P), which ultimately leads to reduced levels of ternary complex required for initiation of mRNA translation. Previously we showed that translational control is primarily exerted through a conformational switch in eIF2's nucleotide exchange factor, eIF2B, which shifts from its active A-State conformation to its inhibited I-State conformation upon eIF2-P binding, resulting in reduced nucleotide exchange on eIF2 (Schoof et al. 2021). Here, we show functionally and structurally how a single histidine to aspartate point mutation in eIF2B's β subunit (H160D) mimics the effects of eIF2-P binding by promoting an I-State like conformation, resulting in eIF2-P independent activation of the ISR. These findings corroborate our previously proposed A/I-State model of allosteric ISR regulation.
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Affiliation(s)
- Morgane Boone
- Howard Hughes Medical Institute, University of California at San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California at San FranciscoSan FranciscoUnited States
| | - Lan Wang
- Howard Hughes Medical Institute, University of California at San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California at San FranciscoSan FranciscoUnited States
| | - Rosalie E Lawrence
- Howard Hughes Medical Institute, University of California at San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California at San FranciscoSan FranciscoUnited States
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California at San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Peter Walter
- Howard Hughes Medical Institute, University of California at San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California at San FranciscoSan FranciscoUnited States
| | - Michael Schoof
- Howard Hughes Medical Institute, University of California at San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California at San FranciscoSan FranciscoUnited States
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5
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Samaddar M, Goudeau J, Sanchez M, Hall DH, Bohnert KA, Ingaramo M, Kenyon C. A genetic screen identifies new steps in oocyte maturation that enhance proteostasis in the immortal germ lineage. eLife 2021; 10:e62653. [PMID: 33848238 PMCID: PMC8043744 DOI: 10.7554/elife.62653] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 09/02/2020] [Accepted: 03/24/2021] [Indexed: 12/24/2022] Open
Abstract
Somatic cells age and die, but the germ-cell lineage is immortal. In Caenorhabditis elegans, germline immortality involves proteostasis renewal at the beginning of each new generation, when oocyte maturation signals from sperm trigger the clearance of carbonylated proteins and protein aggregates. Here, we explore the cell biology of this proteostasis renewal in the context of a whole-genome RNAi screen. Oocyte maturation signals are known to trigger protein-aggregate removal via lysosome acidification. Our findings suggest that lysosomes are acidified as a consequence of changes in endoplasmic reticulum activity that permit assembly of the lysosomal V-ATPase, which in turn allows lysosomes to clear the aggregates via microautophagy. We define two functions for mitochondria, both of which appear to be independent of ATP generation. Many genes from the screen also regulate lysosome acidification and age-dependent protein aggregation in the soma, suggesting a fundamental mechanistic link between proteostasis renewal in the germline and somatic longevity.
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Affiliation(s)
| | - Jérôme Goudeau
- Calico Life Sciences LLCSouth San FranciscoUnited States
| | - Melissa Sanchez
- Department of Molecular and Cellular Biology, University of California, BerkeleyBerkeleyUnited States
| | - David H Hall
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of MedicineNew YorkUnited States
| | - K Adam Bohnert
- Calico Life Sciences LLCSouth San FranciscoUnited States
| | - Maria Ingaramo
- Calico Life Sciences LLCSouth San FranciscoUnited States
| | - Cynthia Kenyon
- Calico Life Sciences LLCSouth San FranciscoUnited States
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6
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Gibney PA, Chen A, Schieler A, Chen JC, Xu Y, Hendrickson DG, McIsaac RS, Rabinowitz JD, Botstein D. A tps1Δ persister-like state in Saccharomyces cerevisiae is regulated by MKT1. PLoS One 2020; 15:e0233779. [PMID: 32470059 PMCID: PMC7259636 DOI: 10.1371/journal.pone.0233779] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/12/2020] [Indexed: 11/18/2022] Open
Abstract
Trehalose metabolism in yeast has been linked to a variety of phenotypes, including heat resistance, desiccation tolerance, carbon-source utilization, and sporulation. The relationships among the several phenotypes of mutants unable to synthesize trehalose are not understood, even though the pathway is highly conserved. One of these phenotypes is that tps1Δ strains cannot reportedly grow on media containing glucose or fructose, even when another carbon source they can use (e.g. galactose) is present. Here we corroborate the recent observation that a small fraction of yeast tps1Δ cells do grow on glucose, unlike the majority of the population. This is not due to a genetic alteration, but instead resembles the persister phenotype documented in many microorganisms and cancer cells undergoing lethal stress. We extend these observations to show that this phenomenon is glucose-specific, as it does not occur on another highly fermented carbon source, fructose. We further demonstrate that this phenomenon appears to be related to mitochondrial complex III function, but unrelated to inorganic phosphate levels in the cell, as had previously been suggested. Finally, we found that this phenomenon is specific to S288C-derived strains, and is the consequence of a variant in the MKT1 gene.
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Affiliation(s)
- Patrick A. Gibney
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Calico Life Sciences LLC, South San Francisco, California, United States of America
- Department of Food Science, Cornell University, Ithaca, New York, United States of America
| | - Anqi Chen
- Department of Food Science, Cornell University, Ithaca, New York, United States of America
| | - Ariel Schieler
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Jonathan C. Chen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Chemistry, Princeton University, Princeton, New Jersey, United States of America
| | - Yifan Xu
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Chemistry, Princeton University, Princeton, New Jersey, United States of America
| | - David G. Hendrickson
- Calico Life Sciences LLC, South San Francisco, California, United States of America
| | - R. Scott McIsaac
- Calico Life Sciences LLC, South San Francisco, California, United States of America
| | - Joshua D. Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Chemistry, Princeton University, Princeton, New Jersey, United States of America
| | - David Botstein
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Calico Life Sciences LLC, South San Francisco, California, United States of America
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7
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LoCoco PM, Risinger AL, Smith HR, Chavera TS, Berg KA, Clarke WP. Pharmacological augmentation of nicotinamide phosphoribosyltransferase (NAMPT) protects against paclitaxel-induced peripheral neuropathy. eLife 2017; 6:e29626. [PMID: 29125463 PMCID: PMC5701795 DOI: 10.7554/elife.29626] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [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: 06/14/2017] [Accepted: 11/03/2017] [Indexed: 01/03/2023] Open
Abstract
Chemotherapy-induced peripheral neuropathy (CIPN) arises from collateral damage to peripheral afferent sensory neurons by anticancer pharmacotherapy, leading to debilitating neuropathic pain. No effective treatment for CIPN exists, short of dose-reduction which worsens cancer prognosis. Here, we report that stimulation of nicotinamide phosphoribosyltransferase (NAMPT) produced robust neuroprotection in an aggressive CIPN model utilizing the frontline anticancer drug, paclitaxel (PTX). Daily treatment of rats with the first-in-class NAMPT stimulator, P7C3-A20, prevented behavioral and histologic indicators of peripheral neuropathy, stimulated tissue NAD recovery, improved general health, and abolished attrition produced by a near maximum-tolerated dose of PTX. Inhibition of NAMPT blocked P7C3-A20-mediated neuroprotection, whereas supplementation with the NAMPT substrate, nicotinamide, potentiated a subthreshold dose of P7C3-A20 to full efficacy. Importantly, P7C3-A20 blocked PTX-induced allodynia in tumored mice without reducing antitumoral efficacy. These findings identify enhancement of NAMPT activity as a promising new therapeutic strategy to protect against anticancer drug-induced peripheral neurotoxicity.
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Affiliation(s)
- Peter M LoCoco
- Department of PharmacologyUniversity of Texas Health Science Center at San AntonioSan AntonioUnited States
| | - April L Risinger
- Department of PharmacologyUniversity of Texas Health Science Center at San AntonioSan AntonioUnited States
| | - Hudson R Smith
- Department of PharmacologyUniversity of Texas Health Science Center at San AntonioSan AntonioUnited States
| | - Teresa S Chavera
- Department of PharmacologyUniversity of Texas Health Science Center at San AntonioSan AntonioUnited States
| | - Kelly A Berg
- Department of PharmacologyUniversity of Texas Health Science Center at San AntonioSan AntonioUnited States
| | - William P Clarke
- Department of PharmacologyUniversity of Texas Health Science Center at San AntonioSan AntonioUnited States
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