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Danaher P, Hasle N, Nguyen ED, Hayward K, Rosenwasser N, Alpers CE, Reed RC, Okamura DM, Baxter SK, Jackson SW. Single cell spatial transcriptomic profiling of childhood-onset lupus nephritis reveals complex interactions between kidney stroma and infiltrating immune cells. bioRxiv 2023:2023.11.09.566503. [PMID: 38014158 PMCID: PMC10680641 DOI: 10.1101/2023.11.09.566503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Children with systemic lupus erythematosus (SLE) are at increased risk of developing kidney disease, termed childhood-onset lupus nephritis (cLN). Single cell transcriptomics of dissociated kidney tissue has advanced our understanding of LN pathogenesis, but loss of spatial resolution prevents interrogation of in situ cellular interactions. Using a technical advance in spatial transcriptomics, we generated a spatially resolved, single cell resolution atlas of kidney tissue (>400,000 cells) from eight cLN patients and two controls. Annotated cells were assigned to 35 reference cell types, including major kidney subsets and infiltrating immune cells. Analysis of spatial distribution demonstrated that individual immune lineages localize to specific regions in cLN kidneys, including myeloid cells trafficking to inflamed glomeruli and B cells clustering within tubulointerstitial immune hotspots. Notably, gene expression varied as a function of tissue location, demonstrating how incorporation of spatial data can provide new insights into the immunopathogenesis of SLE. Alterations in immune phenotypes were accompanied by parallel changes in gene expression by resident kidney stromal cells. However, there was little correlation between histologic scoring of cLN disease activity and glomerular cell transcriptional signatures at the level of individual glomeruli. Finally, we identified modules of spatially-correlated gene expression with predicted roles in induction of inflammation and the development of tubulointerstitial fibrosis. In summary, single cell spatial transcriptomics allows unprecedented insights into the molecular heterogeneity of cLN, paving the way towards more targeted and personalized treatment approaches.
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McCabe MC, Okamura DM, Erickson CB, Perry BW, Brewer CM, Nguyen ED, Saviola AJ, Majesky MW, Hansen KC. ECM-Focused Proteomic Analysis of Ear Punch Regeneration in Acomys Cahirinus. bioRxiv 2023:2023.10.11.561940. [PMID: 37873317 PMCID: PMC10592745 DOI: 10.1101/2023.10.11.561940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
In mammals, significant injury is generally followed by the formation of a fibrotic scar which provides structural integrity but fails to functionally restore damaged tissue. Spiny mice of the genus Acomys represent the first example of full skin autotomy in mammals. Acomys cahirinus has evolved extremely weak skin as a strategy to avoid predation and is able to repeatedly regenerate healthy tissue without scar after severe skin injury or full-thickness ear punches. Extracellular matrix (ECM) composition is a critical regulator of wound repair and scar formation and previous studies have suggested that alterations in its expression may be responsible for the differences in regenerative capacity observed between Mus musculus and A. cahirinus , yet analysis of this critical tissue component has been limited in previous studies by its insolubility and resistance to extraction. Here, we utilize a 2-step ECM-optimized extraction to perform proteomic analysis of tissue composition during wound repair after full-thickness ear punches in A. cahirinus and M. musculus from weeks 1 to 4 post-injury. We observe changes in a wide range of ECM proteins which have been previously implicated in wound regeneration and scar formation, including collagens, coagulation and provisional matrix proteins, and matricryptic signaling peptides. We additionally report differences in crosslinking enzyme activity and ECM protein solubility between Mus and Acomys. Furthermore, we observed rapid and sustained increases in CD206, a marker of pro-regenerative M2 macrophages, in Acomys, whereas little or no increase in CD206 was detected in Mus. Together, these findings contribute to a comprehensive understanding of tissue cues which drive the regenerative capacity of Acomys and identify a number of potential targets for future pro-regenerative therapies.
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Okamura DM, Nguyen ED, Collins SJ, Yoon K, Gere JB, Weiser-Evans MCM, Beier DR, Majesky MW. Mammalian organ regeneration in spiny mice. J Muscle Res Cell Motil 2023; 44:39-52. [PMID: 36131170 DOI: 10.1007/s10974-022-09631-3] [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: 04/07/2022] [Accepted: 08/30/2022] [Indexed: 11/26/2022]
Abstract
Fibrosis-driven solid organ failure is a major world-wide health burden with few therapeutic options. Spiny mice (genus: Acomys) are terrestrial mammals that regenerate severe skin wounds without fibrotic scars to evade predators. Recent studies have shown that spiny mice also regenerate acute ischemic and traumatic injuries to kidney, heart, spinal cord, and skeletal muscle. A common feature of this evolved wound healing response is a lack of formation of fibrotic scar tissue that degrades organ function, inhibits regeneration, and leads to organ failure. Complex tissue regeneration is an extremely rare property among mammalian species. In this article, we discuss the evidence that Acomys represents an emerging model organism that offers a unique opportunity for the biomedical community to investigate and clinically translate molecular mechanisms of scarless wound healing and regeneration of organ function in a mammalian species.
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Affiliation(s)
- Daryl M Okamura
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
| | - Elizabeth D Nguyen
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
| | - Sarah J Collins
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
| | - Kevin Yoon
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
| | - Joshua B Gere
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
| | - Mary C M Weiser-Evans
- Department of Medicine, Division of Renal Diseases & Hypertension, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - David R Beier
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
| | - Mark W Majesky
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA.
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA.
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, 98195, USA.
- Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, 98195, USA.
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4
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Okamura DM, Nguyen ED, Collins SJ, Yoon K, Gere JB, Beier DR, Majesky MW. Abstract 480: Mammalian Organ Regeneration In Spiny Mice. Arterioscler Thromb Vasc Biol 2022. [DOI: 10.1161/atvb.42.suppl_1.480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Fibrosis-driven solid organ failure is a major global health burden. Spiny mice (genus:
Acomys
) are terrestrial mammals that regenerate severe skin wounds without scars to avoid predation. To test whether spiny mice can also regenerate internal organ injuries, we performed acute obstructive or ischemic surgeries on adult kidneys of
Acomys cahirinus
compared to
Mus musculus.
Despite equivalent acute tissue damage,
Acomys
fully regenerate nephron structure, vascular & lymphatic networks, and organ function without fibrosis by 14d while
Mus
(CD1 or C57BL/6) develop extensive interstitial fibrosis and progress to organ failure and death. Comparative transcriptomic, epigenetic, and single-cell assays revealed that the
Acomys
genome appears poised to initiate a regenerative response at the time of injury. In addition, we found the Hippo pathway effector protein YAP localized to the nucleus in renal tubular epithelial cells (RTEs) undergoing scarless wound healing in
Acomys
while it was either cytoplasmic or not detectable in
Mus
RTEs. Experiments
in vitro
revealed an accelerated PP2A-dependent YAP phosphatase activity that maintained nuclear YAP in
Acomys
RTEs and was not detected in
Mus
or human cells. Treatment of
Acomys in vivo
with the nuclear YAP-TEAD inhibitor verteporfin converted tissue regeneration to fibrosis in the dermis and similar experiments for the kidney are in progress. These results suggest that the spiny mouse genome evolved both transcriptional and post-translational adaptations important for scar-free regenerative wound healing
in vivo
.
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Affiliation(s)
| | | | | | - Kevin Yoon
- SEATTLE CHILDRENS RESEARCH INSTITU, Seattle, WA
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Okamura DM, Nguyen ED, Beier DR, Majesky MW. Wound healing and regeneration in spiny mice (Acomys cahirinus). Curr Top Dev Biol 2022; 148:139-164. [DOI: 10.1016/bs.ctdb.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Okamura DM, Brewer CM, Wakenight P, Bahrami N, Bernardi K, Tran A, Olson J, Shi X, Yeh SY, Piliponsky A, Collins SJ, Nguyen ED, Timms AE, MacDonald JW, Bammler TK, Nelson BR, Millen KJ, Beier DR, Majesky MW. Spiny mice activate unique transcriptional programs after severe kidney injury regenerating organ function without fibrosis. iScience 2021; 24:103269. [PMID: 34849462 PMCID: PMC8609232 DOI: 10.1016/j.isci.2021.103269] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 09/02/2021] [Accepted: 10/12/2021] [Indexed: 12/13/2022] Open
Abstract
Fibrosis-driven solid organ failure is an enormous burden on global health. Spiny mice (Acomys) are terrestrial mammals that can regenerate severe skin wounds without scars to avoid predation. Whether spiny mice also regenerate internal organ injuries is unknown. Here, we show that despite equivalent acute obstructive or ischemic kidney injury, spiny mice fully regenerate nephron structure and organ function without fibrosis, whereas C57Bl/6 or CD1 mice progress to complete organ failure with extensive renal fibrosis. Two mechanisms for vertebrate regeneration have been proposed that emphasize either extrinsic (pro-regenerative macrophages) or intrinsic (surviving cells of the organ itself) controls. Comparative transcriptome analysis revealed that the Acomys genome appears poised at the time of injury to initiate regeneration by surviving kidney cells, whereas macrophage accumulation was not detected until about day 7. Thus, we provide evidence for rapid activation of a gene expression signature for regenerative wound healing in the spiny mouse kidney.
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Affiliation(s)
- Daryl M. Okamura
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Chris M. Brewer
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Paul Wakenight
- Center for Integrated Brain Research, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Nadia Bahrami
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Kristina Bernardi
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Amy Tran
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Jill Olson
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Xiaogang Shi
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Szu-Ying Yeh
- Center for Integrated Brain Research, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Adrian Piliponsky
- Center for Immunity & Immunotherapies, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Sarah J. Collins
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Elizabeth D. Nguyen
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Andrew E. Timms
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - James W. MacDonald
- Department of Environmental & Occupational Health, University of Washington, Seattle, WA 98195, USA
| | - Theo K. Bammler
- Department of Environmental & Occupational Health, University of Washington, Seattle, WA 98195, USA
| | - Branden R. Nelson
- Center for Integrated Brain Research, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Kathleen J. Millen
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Center for Integrated Brain Research, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - David R. Beier
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Mark W. Majesky
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA 98195, USA
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Abstract
With the advent of the electronic medical record, automated alerts have allowed for improved recognition of patients with acute kidney injury (AKI). Pediatric patients have the opportunity to benefit from such alerts, as those with a diagnosis of AKI are at risk of developing long-term consequences including reduced renal function and hypertension. Despite extensive studies on the implementation of electronic alerts, their overall impact on clinical outcomes have been unclear. Understanding the results of these studies have helped define best practices in developing electronic alerts with the aim of improving their impact on patient care. As electronic alerts for AKI are applied to pediatric patients, identifying their strengths and limitations will allow for continued improvement in its use and efficacy.
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Affiliation(s)
- Elizabeth D Nguyen
- Division of Pediatric Nephrology, Department of Pediatrics, Seattle Children's Hospital, University of Washington School of Medicine, Seattle, WA, United States
| | - Shina Menon
- Division of Pediatric Nephrology, Department of Pediatrics, Seattle Children's Hospital, University of Washington School of Medicine, Seattle, WA, United States
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Gregory KJ, Nguyen ED, Malosh C, Mendenhall JL, Zic JZ, Bates BS, Noetzel MJ, Squire EF, Turner EM, Rook JM, Emmitte KA, Stauffer SR, Lindsley CW, Meiler J, Conn PJ. Identification of specific ligand-receptor interactions that govern binding and cooperativity of diverse modulators to a common metabotropic glutamate receptor 5 allosteric site. ACS Chem Neurosci 2014; 5:282-95. [PMID: 24528109 DOI: 10.1021/cn400225x] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A common metabotropic glutamate receptor 5 (mGlu5) allosteric site is known to accommodate diverse chemotypes. However, the structural relationship between compounds from different scaffolds and mGlu5 is not well understood. In an effort to better understand the molecular determinants that govern allosteric modulator interactions with mGlu5, we employed a combination of site-directed mutagenesis and computational modeling. With few exceptions, six residues (P654, Y658, T780, W784, S808, and A809) were identified as key affinity determinants across all seven allosteric modulator scaffolds. To improve our interpretation of how diverse allosteric modulators occupy the common allosteric site, we sampled the wealth of mGlu5 structure-activity relationship (SAR) data available by docking 60 ligands (actives and inactives) representing seven chemical scaffolds into our mGlu5 comparative model. To spatially and chemically compare binding modes of ligands from diverse scaffolds, the ChargeRMSD measure was developed. We found a common binding mode for the modulators that placed the long axes of the ligands parallel to the transmembrane helices 3 and 7. W784 in TM6 not only was identified as a key NAM cooperativity determinant across multiple scaffolds, but also caused a NAM to PAM switch for two different scaffolds. Moreover, a single point mutation in TM5, G747V, altered the architecture of the common allosteric site such that 4-nitro-N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamide (VU29) was noncompetitive with the common allosteric site. Our findings highlight the subtleties of allosteric modulator binding to mGlu5 and demonstrate the utility in incorporating SAR information to strengthen the interpretation and analyses of docking and mutational data.
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Affiliation(s)
- Karen J. Gregory
- Drug Discovery
Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
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9
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Turlington M, Noetzel MJ, Chun A, Zhou Y, Gogliotti RD, Nguyen ED, Gregory KJ, Vinson PN, Rook JM, Gogi KK, Xiang Z, Bridges TM, Daniels JS, Jones C, Niswender CM, Meiler J, Conn PJ, Lindsley CW, Stauffer SR. Exploration of allosteric agonism structure-activity relationships within an acetylene series of metabotropic glutamate receptor 5 (mGlu5) positive allosteric modulators (PAMs): discovery of 5-((3-fluorophenyl)ethynyl)-N-(3-methyloxetan-3-yl)picolinamide (ML254). J Med Chem 2013; 56:7976-96. [PMID: 24050755 PMCID: PMC3908770 DOI: 10.1021/jm401028t] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [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] [Indexed: 01/22/2023]
Abstract
Positive allosteric modulators (PAMs) of metabotropic glutamate receptor 5 (mGlu5) represent a promising therapeutic strategy for the treatment of schizophrenia. Both allosteric agonism and high glutamate fold-shift have been implicated in the neurotoxic profile of some mGlu5 PAMs; however, these hypotheses remain to be adequately addressed. To develop tool compounds to probe these hypotheses, the structure-activity relationship of allosteric agonism was examined within an acetylenic series of mGlu5 PAMs exhibiting allosteric agonism in addition to positive allosteric modulation (ago-PAMs). PAM 38t, a low glutamate fold-shift allosteric ligand (maximum fold-shift ~ 3.0), was selected as a potent PAM with no agonism in the in vitro system used for compound characterization and in two native electrophysiological systems using rat hippocampal slices. PAM 38t (ML254) will be useful to probe the relative contribution of cooperativity and allosteric agonism to the adverse effect liability and neurotoxicity associated with this class of mGlu5 PAMs.
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Affiliation(s)
- Mark Turlington
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Specialized Chemistry Center for Probe Development (MLPCN), Nashville, TN 37232, USA
| | - Meredith J. Noetzel
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Aspen Chun
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Specialized Chemistry Center for Probe Development (MLPCN), Nashville, TN 37232, USA
| | - Ya Zhou
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Specialized Chemistry Center for Probe Development (MLPCN), Nashville, TN 37232, USA
| | - Rocco D. Gogliotti
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Specialized Chemistry Center for Probe Development (MLPCN), Nashville, TN 37232, USA
| | - Elizabeth D. Nguyen
- Center for Structural Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Karen J. Gregory
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052
| | - Paige N. Vinson
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jerri M. Rook
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kiran K. Gogi
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Zixiu Xiang
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Thomas M. Bridges
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Specialized Chemistry Center for Probe Development (MLPCN), Nashville, TN 37232, USA
| | - J. Scott Daniels
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Specialized Chemistry Center for Probe Development (MLPCN), Nashville, TN 37232, USA
| | - Carrie Jones
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Specialized Chemistry Center for Probe Development (MLPCN), Nashville, TN 37232, USA
| | - Colleen M. Niswender
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Specialized Chemistry Center for Probe Development (MLPCN), Nashville, TN 37232, USA
| | - Jens Meiler
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Institute for Chemical Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - P. Jeffrey Conn
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Specialized Chemistry Center for Probe Development (MLPCN), Nashville, TN 37232, USA
| | - Craig W. Lindsley
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Specialized Chemistry Center for Probe Development (MLPCN), Nashville, TN 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Shaun R. Stauffer
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Specialized Chemistry Center for Probe Development (MLPCN), Nashville, TN 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
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Combs SA, Deluca SL, Deluca SH, Lemmon GH, Nannemann DP, Nguyen ED, Willis JR, Sheehan JH, Meiler J. Small-molecule ligand docking into comparative models with Rosetta. Nat Protoc 2013; 8:1277-98. [PMID: 23744289 DOI: 10.1038/nprot.2013.074] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Structure-based drug design is frequently used to accelerate the development of small-molecule therapeutics. Although substantial progress has been made in X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, the availability of high-resolution structures is limited owing to the frequent inability to crystallize or obtain sufficient NMR restraints for large or flexible proteins. Computational methods can be used to both predict unknown protein structures and model ligand interactions when experimental data are unavailable. This paper describes a comprehensive and detailed protocol using the Rosetta modeling suite to dock small-molecule ligands into comparative models. In the protocol presented here, we review the comparative modeling process, including sequence alignment, threading and loop building. Next, we cover docking a small-molecule ligand into the protein comparative model. In addition, we discuss criteria that can improve ligand docking into comparative models. Finally, and importantly, we present a strategy for assessing model quality. The entire protocol is presented on a single example selected solely for didactic purposes. The results are therefore not representative and do not replace benchmarks published elsewhere. We also provide an additional tutorial so that the user can gain hands-on experience in using Rosetta. The protocol should take 5-7 h, with additional time allocated for computer generation of models.
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Affiliation(s)
- Steven A Combs
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
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11
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Gregory KJ, Nguyen ED, Reiff SD, Squire EF, Stauffer SR, Lindsley CW, Meiler J, Conn PJ. Probing the metabotropic glutamate receptor 5 (mGlu₅) positive allosteric modulator (PAM) binding pocket: discovery of point mutations that engender a "molecular switch" in PAM pharmacology. Mol Pharmacol 2013; 83:991-1006. [PMID: 23444015 DOI: 10.1124/mol.112.083949] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Positive allosteric modulation of metabotropic glutamate receptor subtype 5 (mGlu₅) is a promising novel approach for the treatment of schizophrenia and cognitive disorders. Allosteric binding sites are topographically distinct from the endogenous ligand (orthosteric) binding site, allowing for co-occupation of a single receptor with the endogenous ligand and an allosteric modulator. Negative allosteric modulators (NAMs) inhibit and positive allosteric modulators (PAMs) enhance the affinity and/or efficacy of the orthosteric agonist. The molecular determinants that govern mGlu₅ modulator affinity versus cooperativity are not well understood. Focusing on the modulators based on the acetylene scaffold, we sought to determine the molecular interactions that contribute to PAM versus NAM pharmacology. Generation of a comparative model of the transmembrane-spanning region of mGlu₅ served as a tool to predict and interpret the impact of mutations in this region. Application of an operational model of allosterism allowed for determination of PAM and NAM affinity estimates at receptor constructs that possessed no detectable radioligand binding as well as delineation of effects on affinity versus cooperativity. Novel mutations within the transmembrane domain (TM) regions were identified that had differential effects on acetylene PAMs versus 2-methyl-6-(phenylethynyl)-pyridine, a prototypical NAM. Three conserved amino acids (Y658, T780, and S808) and two nonconserved residues (P654 and A809) were identified as key determinants of PAM activity. Interestingly, we identified two point mutations in TMs 6 and 7 that, when mutated, engender a mode switch in the pharmacology of certain PAMs.
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Affiliation(s)
- Karen J Gregory
- Department of Pharmacology and Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, TN 37232-0697, USA
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Hui H, Khoury N, Zhao X, Balkir L, D'Amico E, Bullotta A, Nguyen ED, Gambotto A, Perfetti R. Adenovirus-mediated XIAP gene transfer reverses the negative effects of immunosuppressive drugs on insulin secretion and cell viability of isolated human islets. Diabetes 2005; 54:424-33. [PMID: 15677500 DOI: 10.2337/diabetes.54.2.424] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Immunosuppressive drugs are routinely used to provide tolerance after whole pancreas and islet cell transplantations. While they are essential in inhibiting graft rejection, little is known about their effect on islet function and beta-cell viability. In this study, we report that tacrolimus, sirolimus, and mycophenolic acid, when added to cultures of freshly isolated human islets, induce a downregulation of the synthesis and secretion of insulin. These functional changes are associated with decreased islet cell viability. All three agents induce a decrease of intracellular levels of Bcl-2 and Bcl-xL, with an increased level of Smac, indicating that they are capable of promoting a downregulation of anti-apoptotic factors and an accumulation of pro-apoptotic mediators. Transduction of islet cells with the anti-apoptotic gene XIAP prevents the negative effects of these drugs on the function and viability of islets. XIAP-infected cells show a higher expression of phospho-CREB (cAMP-responsive element binding protein) and a reduced level of Smac, resulting in a significant reduction of apoptotic cells and a preservation of the glucose-dependent secretion of insulin. In conclusion, the present study demonstrates that genetically modified human islets expressing XIAP are resistant to the negative effects of immunosuppressive drugs on insulin secretion and cell viability.
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Affiliation(s)
- Hongxiang Hui
- Division of Endocrinology & Diabetes and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, 8723 Alden Dr., SSB #290, Los Angeles, CA 90048, USA
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