Quantitative differentiation of benign and misfolded glaucoma-causing myocilin variants on the basis of protein thermal stability

Scelsi, Hailee F.; Hill, Kamisha R.; Barlow, Brett M.; Martin, Mackenzie D.; Lieberman, Raquel L.

doi:10.1242/dmm.049816

Quantitative differentiation of benign and misfolded glaucoma-causing myocilin variants on the basis of protein thermal stability

Journal Article · Fri Jan 13 00:00:00 EST 2023 · Disease models & mechanisms

DOI:https://doi.org/10.1242/dmm.049816· OSTI ID:2470091

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Georgia Institute of Technology, Atlanta, GA (United States)

Accurate predictions of the pathogenicity of mutations associated with genetic diseases are key to the success of precision medicine. Inherited missense mutations in the myocilin (MYOC) gene, within its olfactomedin (OLF) domain, constitute the strongest genetic link to primary open-angle glaucoma via a toxic gain of function, and thus MYOC is an attractive precision-medicine target. However, not all mutations in MYOC cause glaucoma, and common variants are expected to be neutral polymorphisms. The Genome Aggregation Database (gnomAD) lists ~100 missense variants documented within OLF, all of which are relatively rare (allele frequency <0.001%) and nearly all are of unknown pathogenicity. To distinguish disease-causing OLF variants from benign OLF variants, we first characterized the most prevalent population-based variants using a suite of cellular and biophysical assays, and identified two variants with features of aggregation-prone familial disease variants. Next, we considered all available biochemical and clinical data to demonstrate that pathogenic and benign variants can be differentiated statistically based on a single metric: the thermal stability of OLF. Our results motivate genotyping MYOC in patients for clinical monitoring of this widespread, painless and irreversible ocular disease.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS)

Sponsoring Organization:: National Institute of General Medical Sciences (NIGMS); National Institutes of Health (NIH); USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC02-05CH11231; AC02-06CH11357; W-31109-ENG-38

OSTI ID:: 2470091

Journal Information:: Disease models & mechanisms, Journal Name: Disease models & mechanisms Journal Issue: 1 Vol. 16; ISSN 1754-8403

Publisher:: The Company of BiologistsCopyright Statement

Country of Publication:: United States

Language:: English

References (58)

Molecular and Clinical Evaluation of a Patient Hemizygous for TIGR/MYOC Wiggs, Janey L. Archives of Ophthalmology, Vol. 119, Issue 11 https://doi.org/10.1001/archopht.119.11.1674	journal	November 2001
Association of a Primary Open-Angle Glaucoma Genetic Risk Score With Earlier Age at Diagnosis Fan, Bao Jian; Bailey, Jessica Cooke; Igo, Rob P. JAMA Ophthalmology, Vol. 137, Issue 10 https://doi.org/10.1001/jamaophthalmol.2019.3109	journal	October 2019
Myocilin allele-specific glaucoma phenotype database Hewitt, Alex W.; Mackey, David A.; Craig, Jamie E. Human Mutation, Vol. 29, Issue 2 https://doi.org/10.1002/humu.20634	journal	February 2008
Common and rare myocilin variants: Predicting glaucoma pathogenicity based on genetics, clinical, and laboratory misfolding data Scelsi, Hailee F.; Barlow, Brett M.; Saccuzzo, Emily G. Human Mutation, Vol. 42, Issue 8 https://doi.org/10.1002/humu.24238	journal	June 2021
Novel Cell- and Tissue-Based Assays for Detecting Misfolded and Aggregated Protein Accumulation Within Aggresomes and Inclusion Bodies Shen, Dee; Coleman, Jack; Chan, Eric Cell Biochemistry and Biophysics, Vol. 60, Issue 3 https://doi.org/10.1007/s12013-010-9138-4	journal	December 2010
Age-dependent prevalence of mutations at the GLC1A locus in primary open-angle glaucoma Shimizu, Satoko; Lichter, Paul R.; Johnson, A. Tim American Journal of Ophthalmology, Vol. 130, Issue 2 https://doi.org/10.1016/S0002-9394(00)00536-5	journal	August 2000
The genetic aspects of adult-onset glaucoma: a perspective from the Greater Toronto area Williams-Lyn, Donna; Flanagan, John; Buys, Yvonne Canadian Journal of Ophthalmology, Vol. 35, Issue 1 https://doi.org/10.1016/S0008-4182(00)80103-9	journal	February 2000
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
Accumulation of mutant myocilins in ER leads to ER stress and potential cytotoxicity in human trabecular meshwork cells Joe, Myung Kuk; Sohn, Seongsoo; Hur, Wonhee Biochemical and Biophysical Research Communications, Vol. 312, Issue 3 https://doi.org/10.1016/j.bbrc.2003.10.162	journal	December 2003
Temperature sensitive secretion of mutant myocilins Vollrath, Douglas; Liu, Yuhui Experimental Eye Research, Vol. 82, Issue 6 https://doi.org/10.1016/j.exer.2005.10.007	journal	June 2006
Functional analysis of the glaucoma-causing TIGR/myocilin protein: Integrity of amino-terminal coiled-coil regions and olfactomedin homology domain is essential for extracellular adhesion and secretion Gobeil, Stéphane; Letartre, Laurence; Raymond, Vincent Experimental Eye Research, Vol. 82, Issue 6 https://doi.org/10.1016/j.exer.2005.11.002	journal	June 2006
Glaucoma-associated myocilin: A better understanding but much more to learn Resch, Zachary T.; Fautsch, Michael P. Experimental Eye Research, Vol. 88, Issue 4 https://doi.org/10.1016/j.exer.2008.08.011	journal	April 2009
Molecular architecture and modifications of full-length myocilin Martin, Mackenzie D.; Huard, Dustin J. E.; Guerrero-Ferreira, Ricardo C. Experimental Eye Research, Vol. 211 https://doi.org/10.1016/j.exer.2021.108729	journal	October 2021
Amyloid Fibril Formation by the Glaucoma-Associated Olfactomedin Domain of Myocilin Orwig, Susan D.; Perry, Christopher W.; Kim, Laura Y. Journal of Molecular Biology, Vol. 421, Issue 2-3 https://doi.org/10.1016/j.jmb.2011.12.016	journal	August 2012
The Glaucoma-Associated Olfactomedin Domain of Myocilin Forms Polymorphic Fibrils That Are Constrained by Partial Unfolding and Peptide Sequence Hill, Shannon E.; Donegan, Rebecca K.; Lieberman, Raquel L. Journal of Molecular Biology, Vol. 426, Issue 4 https://doi.org/10.1016/j.jmb.2013.12.002	journal	February 2014
Glaucoma – risk factors and current challenges in the diagnosis of a leading cause of visual impairment Lee, Samantha Sze-Yee; Mackey, David A. Maturitas, Vol. 163 https://doi.org/10.1016/j.maturitas.2022.05.002	journal	September 2022
Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability Goldenzweig, Adi; Goldsmith, Moshe; Hill, Shannon E. Molecular Cell, Vol. 63, Issue 2 https://doi.org/10.1016/j.molcel.2016.06.012	journal	July 2016
Structure and Misfolding of the Flexible Tripartite Coiled-Coil Domain of Glaucoma-Associated Myocilin Hill, Shannon E.; Nguyen, Elaine; Donegan, Rebecca K. Structure, Vol. 25, Issue 11 https://doi.org/10.1016/j.str.2017.09.008	journal	November 2017
Molecular Insights into Myocilin and Its Glaucoma-Causing Misfolded Olfactomedin Domain Variants Lieberman, Raquel L.; Ma, Minh Thu Accounts of Chemical Research, Vol. 54, Issue 9 https://doi.org/10.1021/acs.accounts.1c00060	journal	April 2021
Differential Misfolding Properties of Glaucoma-Associated Olfactomedin Domains from Humans and Mice Patterson-Orazem, Athéna C.; Hill, Shannon E.; Wang, Yiming Biochemistry, Vol. 58, Issue 13 https://doi.org/10.1021/acs.biochem.8b01309	journal	February 2019
Dominant forces in protein folding Dill, Ken A. Biochemistry, Vol. 29, Issue 31 https://doi.org/10.1021/bi00483a001	journal	August 1990
The Stability of Myocilin Olfactomedin Domain Variants Provides New Insight into Glaucoma as a Protein Misfolding Disorder Burns, J. Nicole; Turnage, Katherine C.; Walker, Chandler A. Biochemistry, Vol. 50, Issue 26 https://doi.org/10.1021/bi200231x	journal	July 2011
Rescue of Glaucoma-Causing Mutant Myocilin Thermal Stability by Chemical Chaperones Burns, J. Nicole; Orwig, Susan D.; Harris, Julia L. ACS Chemical Biology, Vol. 5, Issue 5 https://doi.org/10.1021/cb900282e	journal	March 2010
A method and server for predicting damaging missense mutations Adzhubei, Ivan A.; Schmidt, Steffen; Peshkin, Leonid Nature Methods, Vol. 7, Issue 4 https://doi.org/10.1038/nmeth0410-248	journal	April 2010
SIFT missense predictions for genomes Vaser, Robert; Adusumalli, Swarnaseetha; Leng, Sim Ngak Nature Protocols, Vol. 11, Issue 1 https://doi.org/10.1038/nprot.2015.123	journal	December 2015
Towards precision medicine Ashley, Euan A. Nature Reviews Genetics, Vol. 17, Issue 9 https://doi.org/10.1038/nrg.2016.86	journal	August 2016
The mutational constraint spectrum quantified from variation in 141,456 humans Karczewski, Konrad J.; Francioli, Laurent C.; Tiao, Grace Nature, Vol. 581, Issue 7809 https://doi.org/10.1038/s41586-020-2308-7	journal	May 2020
Multitrait analysis of glaucoma identifies new risk loci and enables polygenic prediction of disease susceptibility and progression Craig, Jamie E.; Han, Xikun; Qassim, Ayub Nature Genetics, Vol. 52, Issue 2 https://doi.org/10.1038/s41588-019-0556-y	journal	January 2020
Clinical Features Associated with Mutations in the Chromosome 1 Open-Angle Glaucoma Gene ( GLC1A ) Alward, Wallace L. M.; Fingert, John H.; Coote, Michael A. New England Journal of Medicine, Vol. 338, Issue 15 https://doi.org/10.1056/NEJM199804093381503	journal	April 1998
Autosomal dominant myopathy: Missense mutation (Glu-706 → Lys) in the myosin heavy chain IIa gene Martinsson, Tommy; Oldfors, Anders; Darin, Niklas Proceedings of the National Academy of Sciences, Vol. 97, Issue 26 https://doi.org/10.1073/pnas.250289597	journal	December 2000
The Glaucoma-associated Olfactomedin Domain of Myocilin Is a Novel Calcium Binding Protein Donegan, Rebecca K.; Hill, Shannon E.; Turnage, Katherine C. Journal of Biological Chemistry, Vol. 287, Issue 52 https://doi.org/10.1074/jbc.M112.408906	journal	November 2012
Stable calcium-free myocilin olfactomedin domain variants reveal challenges in differentiating between benign and glaucoma-causing mutations Hill, Shannon E.; Kwon, Michelle S.; Martin, Mackenzie D. Journal of Biological Chemistry, Vol. 294, Issue 34 https://doi.org/10.1074/jbc.RA119.009419	journal	July 2019
Occurrence of MYOC and CYP1B1 variants in juvenile open angle glaucoma Brazilian patients Svidnicki, Paulo Vinicius; Braghini, Carolina Ayumi; Costa, Vital Paulino Ophthalmic Genetics, Vol. 39, Issue 6 https://doi.org/10.1080/13816810.2018.1546405	journal	November 2018
Using SIFT and PolyPhen to Predict Loss-of-Function and Gain-of-Function Mutations Flanagan, Sarah E.; Patch, Ann-Marie; Ellard, Sian Genetic Testing and Molecular Biomarkers, Vol. 14, Issue 4 https://doi.org/10.1089/gtmb.2010.0036	journal	August 2010
The disease-linked Glu-26-Lys mutant version of Coronin 1A exhibits pleiotropic and pathway-specific signaling defects Ojeda, Virginia; Robles-Valero, Javier; Barreira, María Molecular Biology of the Cell, Vol. 26, Issue 16 https://doi.org/10.1091/mbc.E15-01-0052	journal	August 2015
Non-secretion of mutant proteins of the glaucoma gene myocilin in cultured trabecular meshwork cells and in aqueous humor Jacobson, N. Human Molecular Genetics, Vol. 10, Issue 2 https://doi.org/10.1093/hmg/10.2.117	journal	January 2001
Founder TIGR/myocilin mutations for glaucoma in the Quebec population Faucher, M. Human Molecular Genetics, Vol. 11, Issue 18 https://doi.org/10.1093/hmg/11.18.2077	journal	September 2002
A Cellular Assay Distinguishes Normal and Mutant TIGR/Myocilin Protein Zhou, Z.; Vollrath, D. Human Molecular Genetics, Vol. 8, Issue 12 https://doi.org/10.1093/hmg/8.12.2221	journal	November 1999
Analysis of Myocilin Mutations in 1703 Glaucoma Patients From Five Different Populations Fingert, J. H.; Heon, E.; Liebmann, J. M. Human Molecular Genetics, Vol. 8, Issue 5 https://doi.org/10.1093/hmg/8.5.899	journal	May 1999
Reversal of mutant myocilin non-secretion and cell killing: implications for glaucoma Liu, Yuhui; Vollrath, Douglas Human Molecular Genetics, Vol. 13, Issue 11 https://doi.org/10.1093/hmg/ddh128	journal	April 2004
Structural basis for misfolding in myocilin-associated glaucoma Donegan, Rebecca K.; Hill, Shannon E.; Freeman, Dana M. Human Molecular Genetics, Vol. 24, Issue 8 https://doi.org/10.1093/hmg/ddu730	journal	December 2014
Solving structures of protein complexes by molecular replacement with Phaser McCoy, Airlie J. Acta Crystallographica Section D Biological Crystallography, Vol. 63, Issue 1 https://doi.org/10.1107/S0907444906045975	journal	December 2006
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Towards automated crystallographic structure refinement with phenix.refine Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4 https://doi.org/10.1107/S0907444912001308	journal	March 2012
Calcium-ligand variants of the myocilin olfactomedin propeller selected from invertebrate phyla reveal cross-talk with N-terminal blade and surface helices Hill, Shannon E.; Cho, Hayeon; Raut, Priyam Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 9 https://doi.org/10.1107/S205979831901074X	journal	August 2019
A guided tour into subcellular colocalization analysis in light microscopy Bolte, S.; CordeliÈRes, F. P. Journal of Microscopy, Vol. 224, Issue 3 https://doi.org/10.1111/j.1365-2818.2006.01706.x	journal	December 2006
Identification of a Gene That Causes Primary Open Angle Glaucoma Stone, E. M. Science, Vol. 275, Issue 5300 https://doi.org/10.1126/science.275.5300.668	journal	January 1997
Mutant Myocilin Nonsecretion In Vivo Is Not Sufficient To Cause Glaucoma Gould, Douglas B.; Reedy, Mark; Wilson, Lawriston A. Molecular and Cellular Biology, Vol. 26, Issue 22 https://doi.org/10.1128/MCB.01127-06	journal	November 2006
Targeted Disruption of the Myocilin Gene (Myoc) Suggests that Human Glaucoma-Causing Mutations Are Gain of Function Kim, B. S.; Savinova, O. V.; Reedy, M. V. Molecular and Cellular Biology, Vol. 21, Issue 22 https://doi.org/10.1128/MCB.21.22.7707-7713.2001	journal	November 2001
Global variations and time trends in the prevalence of primary open angle glaucoma (POAG): a systematic review and meta-analysis Kapetanakis, Venediktos V.; Chan, Michelle P. Y.; Foster, Paul J. British Journal of Ophthalmology, Vol. 100, Issue 1 https://doi.org/10.1136/bjophthalmol-2015-307223	journal	August 2015
Variations in Primary Open-Angle Glaucoma Prevalence by Age, Gender, and Race: A Bayesian Meta-Analysis Rudnicka, Alicja R.; Mt-Isa, Shahrul; Owen, Christopher G. Investigative Opthalmology & Visual Science, Vol. 47, Issue 10 https://doi.org/10.1167/iovs.06-0299	journal	October 2006
A Novel Luciferase Assay For Sensitively Monitoring Myocilin Variants in Cell Culture Zadoo, Serena; Nguyen, Annie; Zode, Gulab Investigative Opthalmology & Visual Science, Vol. 57, Issue 4 https://doi.org/10.1167/iovs.15-18789	journal	April 2016
Screening for Primary Open-Angle Glaucoma in the Primary Care Setting: An Update for the US Preventive Services Task Force Fleming, C. The Annals of Family Medicine, Vol. 3, Issue 2 https://doi.org/10.1370/afm.293	journal	March 2005
Prominent features of the amino acid mutation landscape in cancer Szpiech, Zachary A.; Strauli, Nicolas B.; White, Katharine A. PLOS ONE, Vol. 12, Issue 8 https://doi.org/10.1371/journal.pone.0183273	journal	August 2017
The Use of Circular Dichroism in the Investigation of Protein Structure and Function Kelly, Sharon; Price, Nicholas Current Protein & Peptide Science, Vol. 1, Issue 4, p. 349-384 https://doi.org/10.2174/1389203003381315	journal	December 2000
Aggregated Myocilin Induces Russell Bodies and Causes Apoptosis Yam, Gary Hin-Fai; Gaplovska-Kysela, Katarina; Zuber, Christian The American Journal of Pathology, Vol. 170, Issue 1 https://doi.org/10.2353/ajpath.2007.060806	journal	January 2007
Age at Glaucoma Diagnosis in Germline Myocilin Mutation Patients: Associations with Polymorphisms in Protein Stabilities Tanji, Tarin; Cohen, Emily; Shen, Darrick Genes, Vol. 12, Issue 11 https://doi.org/10.3390/genes12111802	journal	November 2021
Epidemiology of Glaucoma: The Past, Present, and Predictions for the Future Allison, Karen; Patel, Deepkumar; Alabi, Omobolanle Cureus https://doi.org/10.7759/cureus.11686	journal	November 2020

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59 BASIC BIOLOGICAL SCIENCES
Genetic mutation
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Misfolding
Protein homeostasis
Thermal stability

Quantitative differentiation of benign and misfolded glaucoma-causing myocilin variants on the basis of protein thermal stability

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References (58)

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