Biochemical and structural characterization of two variants of uncertain significance in the PMS2 gene

D'Arcy, Brandon M.; Blount, Jessa; Prakash, Aishwarya

doi:10.1002/humu.23708

Biochemical and structural characterization of two variants of uncertain significance in the PMS2 gene

Journal Article · Thu Jan 17 00:00:00 EST 2019 · Human Mutation

DOI:https://doi.org/10.1002/humu.23708· OSTI ID:1512992

^[1]; Blount, Jessa ^[1]; ^[1]

Univ. of South Alabama, Mobile, AL (United States). Mitchell Cancer Inst.

Lynch syndrome (LS) is an autosomal dominant inherited disorder that is associated with an increased predisposition to certain cancers caused by loss-of-function mutations in one of four DNA mismatch repair (MMR) genes (MLH1, MSH2, MSH6, or PMS2). The diagnosis of LS is often challenged by the identification of missense mutations where the functional effects are not known. These are termed variants of uncertain significance (VUSs) and account for 20%–30% of noncoding and missense mutations. VUSs cause ambiguity during clinical diagnosis and hinder implementation of appropriate medical management. In this work, we focus on the functional and biological consequences of two nonsynonymous VUSs in PMS2. These variants, c.620G>A and c.123_131delGTTAGTAGA, result in the alteration of glycine 207 to glutamate (p.Gly207Glu) and the deletion of amino acid residues 42–44 (p.Leu42_Glu44del), respectively. While the PMS2 p.Gly207Glu variant retains in vitro MMR and ATPase activities, PMS2 p.Leu42_Glu44del appears to lack such capabilities. Structural and biophysical characterization using circular dichroism, small-angle X-ray scattering, and X-ray crystallography of the N-terminal domain of the PMS2 variants indicate that the p.Gly207Glu variant is properly folded similar to the wild-type enzyme, whereas p.Leu42_Glu44del is disordered and prone to aggregation.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS); SLAC National Accelerator Laboratory, Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)

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

Grant/Contract Number:: AC02-06CH11357; AC02-76SF00515

OSTI ID:: 1512992

Journal Information:: Human Mutation, Journal Name: Human Mutation Journal Issue: 4 Vol. 40; ISSN 1059-7794

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

References (70)

Sample Preparation, Data Collection, and Preliminary Data Analysis in Biomolecular Solution X‐Ray Scattering Grishaev, Alexander Current Protocols in Protein Science, Vol. 70, Issue 1 https://doi.org/10.1002/0471140864.ps1714s70	journal	November 2012
Predicting Functional Effect of Human Missense Mutations Using PolyPhen-2 Adzhubei, Ivan; Jordan, Daniel M.; Sunyaev, Shamil R. Current Protocols in Human Genetics, Vol. 76, Issue 1 https://doi.org/10.1002/0471142905.hg0720s76	journal	January 2013
Mechanisms in E. coli and Human Mismatch Repair (Nobel Lecture) Modrich, Paul Angewandte Chemie International Edition, Vol. 55, Issue 30 https://doi.org/10.1002/anie.201601412	journal	May 2016
Protein secondary structure analyses from circular dichroism spectroscopy: Methods and reference databases Whitmore, Lee; Wallace, B. A. Biopolymers, Vol. 89, Issue 5, p. 392-400 https://doi.org/10.1002/bip.20853	journal	May 2008
Sequence variant classification and reporting: recommendations for improving the interpretation of cancer susceptibility genetic test results Plon, Sharon E.; Eccles, Diana M.; Easton, Douglas Human Mutation, Vol. 29, Issue 11 https://doi.org/10.1002/humu.20880	journal	November 2008
A cell-free assay for the functional analysis of variants of the mismatch repair protein MLH1 Drost, Mark; Zonneveld, Jos é B. M.; van Dijk, Linda Human Mutation, Vol. 31, Issue 3 https://doi.org/10.1002/humu.21180	journal	March 2010
Identification of Lynch syndrome mutations in the MLH1-PMS2 interface that disturb dimerization and mismatch repair Kosinski, Jan; Hinrichsen, Inga; Bujnicki, Janusz M. Human Mutation, Vol. 31, Issue 8 https://doi.org/10.1002/humu.21301	journal	May 2010
Pathological assessment of mismatch repair gene variants in Lynch syndrome: Past, present, and future Rasmussen, Lene Juel; Heinen, Christopher D.; Royer-Pokora, Brigitte Human Mutation, Vol. 33, Issue 12 https://doi.org/10.1002/humu.22168	journal	August 2012
Inactivation of DNA Mismatch Repair by Variants of Uncertain Significance in the PMS2 Gene Drost, Mark; Koppejan, Hester; de Wind, Niels Human Mutation, Vol. 34, Issue 11 https://doi.org/10.1002/humu.22426	journal	September 2013
Phosphorylation-dependent signaling controls degradation of DNA mismatch repair protein PMS2 Hinrichsen, Inga; Weßbecher, Isabel M.; Huhn, Meik Molecular Carcinogenesis, Vol. 56, Issue 12 https://doi.org/10.1002/mc.22709	journal	September 2017
Splicing analysis for exonic and intronic mismatch repair gene variants associated with Lynch syndrome confirms high concordance between minigene assays and patient RNA analyses van der Klift, Heleen M.; Jansen, Anne M. L.; van der Steenstraten, Niki Molecular Genetics & Genomic Medicine, Vol. 3, Issue 4 https://doi.org/10.1002/mgg3.145	journal	April 2015
Estimation of Protein Secondary Structure from Circular Dichroism Spectra: Comparison of CONTIN, SELCON, and CDSSTR Methods with an Expanded Reference Set Sreerama, Narasimha; Woody, Robert W. Analytical Biochemistry, Vol. 287, Issue 2, p. 252-260 https://doi.org/10.1006/abio.2000.4880	journal	December 2000
Four novel germline mutations in the MLH1 and PMS2 mismatch repair genes in patients with hereditary nonpolyposis colorectal cancer Montazer Haghighi, Mahdi; Radpour, Ramin; Aghajani, Katayoun International Journal of Colorectal Disease, Vol. 24, Issue 8 https://doi.org/10.1007/s00384-009-0731-1	journal	May 2009
Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen Zacarias, Sónia; Temporão, Adriana; Carpentier, Philippe JBIC Journal of Biological Inorganic Chemistry, Vol. 25, Issue 6 https://doi.org/10.1007/s00775-020-01814-y	journal	August 2020
In vitro studies of DNA mismatch repair proteins Geng, Hui; Du, Chunwei; Chen, Siying Analytical Biochemistry, Vol. 413, Issue 2 https://doi.org/10.1016/j.ab.2011.02.017	journal	June 2011
Truncation of the C-terminus of human MLH1 blocks intracellular stabilization of PMS2 and disrupts DNA mismatch repair Mohd, Azizah B.; Palama, Brett; Nelson, Scott E. DNA Repair, Vol. 5, Issue 3 https://doi.org/10.1016/j.dnarep.2005.11.001	journal	March 2006
Endonuclease activities of MutLα and its homologs in DNA mismatch repair Kadyrova, Lyudmila Y.; Kadyrov, Farid A. DNA Repair, Vol. 38 https://doi.org/10.1016/j.dnarep.2015.11.023	journal	February 2016
Mismatch repair defects and Lynch syndrome: The role of the basic scientist in the battle against cancer Heinen, Christopher D. DNA Repair, Vol. 38 https://doi.org/10.1016/j.dnarep.2015.11.025	journal	February 2016
Prevalence of mutations in a panel of breast cancer susceptibility genes in BRCA1/2-negative patients with early-onset breast cancer Maxwell, Kara N.; Wubbenhorst, Bradley; D’Andrea, Kurt Genetics in Medicine, Vol. 17, Issue 8 https://doi.org/10.1038/gim.2014.176	journal	December 2014
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology Richards, Sue; Aziz, Nazneen; Bale, Sherri Genetics in Medicine, Vol. 17, Issue 5 https://doi.org/10.1038/gim.2015.30	journal	March 2015
Observed frequency and challenges of variant reclassification in a hereditary cancer clinic Macklin, Sarah; Durand, Nisha; Atwal, Paldeep Genetics in Medicine, Vol. 20, Issue 3 https://doi.org/10.1038/gim.2017.207	journal	December 2017
Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS) Hura, Greg L.; Menon, Angeli L.; Hammel, Michal Nature Methods, Vol. 6, Issue 8 https://doi.org/10.1038/nmeth.1353	journal	July 2009
Using circular dichroism spectra to estimate protein secondary structure Greenfield, Norma J Nature Protocols, Vol. 1, Issue 6, p. 2876-2890 https://doi.org/10.1038/nprot.2006.202	journal	January 2007
Milestones of Lynch syndrome: 1895–2015 Lynch, Henry T.; Snyder, Carrie L.; Shaw, Trudy G. Nature Reviews Cancer, Vol. 15, Issue 3 https://doi.org/10.1038/nrc3878	journal	February 2015
IDDCA syndrome in a Chinese infant due to GNB5 biallelic mutations Tang, Mingxing; Wang, Yajian; Xu, Yuanyuan Journal of Human Genetics, Vol. 65, Issue 7 https://doi.org/10.1038/s10038-020-0742-x	journal	March 2020
A functional assay–based procedure to classify mismatch repair gene variants in Lynch syndrome Drost, Mark; Tiersma, Yvonne; Thompson, Bryony A. Genetics in Medicine, Vol. 21, Issue 7 https://doi.org/10.1038/s41436-018-0372-2	journal	December 2018
PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome Sharma, Deepti; De Falco, Louis; Padavattan, Sivaraman Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13641-0	journal	December 2019
Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation Tillu, Vikas A.; Rae, James; Gao, Ya Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-21035-4	journal	February 2021
The Clinical Phenotype of Lynch Syndrome Due to Germ-Line PMS2 Mutations Senter, Leigha; Clendenning, Mark; Sotamaa, Kaisa Gastroenterology, Vol. 135, Issue 2 https://doi.org/10.1053/j.gastro.2008.04.026	journal	August 2008
Identification of a Variety of Mutations in Cancer Predisposition Genes in Patients With Suspected Lynch Syndrome Yurgelun, Matthew B.; Allen, Brian; Kaldate, Rajesh R. Gastroenterology, Vol. 149, Issue 3 https://doi.org/10.1053/j.gastro.2015.05.006	journal	September 2015
Interaction of proliferating cell nuclear antigen with PMS2 is required for MutLα activation and function in mismatch repair Genschel, Jochen; Kadyrova, Lyudmila Y.; Iyer, Ravi R. Proceedings of the National Academy of Sciences, Vol. 114, Issue 19 https://doi.org/10.1073/pnas.1702561114	journal	April 2017
The Devil is in the details for DNA mismatch repair Hsieh, Peggy; Zhang, Yongliang Proceedings of the National Academy of Sciences, Vol. 114, Issue 14 https://doi.org/10.1073/pnas.1702747114	journal	March 2017
Restoration of mismatch repair to nuclear extracts of H6 colorectal tumor cells by a heterodimer of human MutL homologs. Li, G. M.; Modrich, P. Proceedings of the National Academy of Sciences, Vol. 92, Issue 6 https://doi.org/10.1073/pnas.92.6.1950	journal	March 1995
Steady-state Regulation of the Human DNA Mismatch Repair System Chang, Dong Kyung; Ricciardiello, Luigi; Goel, Ajay Journal of Biological Chemistry, Vol. 275, Issue 24 https://doi.org/10.1074/jbc.M001140200	journal	March 2000
Mechanisms in Eukaryotic Mismatch Repair Modrich, Paul Journal of Biological Chemistry, Vol. 281, Issue 41 https://doi.org/10.1074/jbc.R600022200	journal	August 2006
Functional testing strategy for coding genetic variants of unclear significance in MLH1 in Lynch syndrome diagnosis Hinrichsen, I.; Schafer, D.; Langer, D. Carcinogenesis, Vol. 36, Issue 2 https://doi.org/10.1093/carcin/bgu239	journal	December 2014
Structure and function of the N-terminal 40 kDa fragment of human PMS2: a monomeric GHL ATPase Guarne, A. The EMBO Journal, Vol. 20, Issue 19 https://doi.org/10.1093/emboj/20.19.5521	journal	October 2001
The known unknown: the challenges of genetic variants of uncertain significance in clinical practice Hoffman-Andrews, Lily Journal of Law and the Biosciences, Vol. 4, Issue 3 https://doi.org/10.1093/jlb/lsx038	journal	December 2017
PMS2 Mutations in Childhood Cancer De Vos, Michel; Hayward, Bruce E.; Charlton, Ruth JNCI: Journal of the National Cancer Institute, Vol. 98, Issue 5 https://doi.org/10.1093/jnci/djj073	journal	March 2006
SIFT: predicting amino acid changes that affect protein function Ng, P. C. Nucleic Acids Research, Vol. 31, Issue 13 https://doi.org/10.1093/nar/gkg509	journal	July 2003
Germline MLH1 Mutations Are Frequently Identified in Lynch Syndrome Patients With Colorectal and Endometrial Carcinoma Demonstrating Isolated Loss of PMS2 Immunohistochemical Expression Dudley, Beth; Brand, Randall E.; Thull, Darcy The American Journal of Surgical Pathology, Vol. 39, Issue 8 https://doi.org/10.1097/PAS.0000000000000425	journal	January 2015
Postreplicative Mismatch Repair Jiricny, J. Cold Spring Harbor Perspectives in Biology, Vol. 5, Issue 4 https://doi.org/10.1101/cshperspect.a012633	journal	April 2013
An automated system to mount cryo-cooled protein crystals on a synchrotron beamline, using compact sample cassettes and a small-scale robot Cohen, Aina E.; Ellis, Paul J.; Miller, Mitchell D. Journal of Applied Crystallography, Vol. 35, Issue 6 https://doi.org/10.1107/S0021889802016709	journal	November 2002
PRIMUS: a Windows PC-based system for small-angle scattering data analysis Konarev, Petr V.; Volkov, Vladimir V.; Sokolova, Anna V. Journal of Applied Crystallography, Vol. 36, Issue 5, p. 1277-1282 https://doi.org/10.1107/S0021889803012779	journal	September 2003
Web-Ice : integrated data collection and analysis for macromolecular crystallography González, A.; Moorhead, P.; McPhillips, S. E. Journal of Applied Crystallography, Vol. 41, Issue 1 https://doi.org/10.1107/S0021889807057822	journal	January 2008
Scatter : software for the analysis of nano- and mesoscale small-angle scattering Förster, S.; Apostol, L.; Bras, W. Journal of Applied Crystallography, Vol. 43, Issue 3 https://doi.org/10.1107/S0021889810008289	journal	April 2010
Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source Classen, Scott; Hura, Greg L.; Holton, James M. Journal of Applied Crystallography, Vol. 46, Issue 1 https://doi.org/10.1107/S0021889812048698	journal	January 2013
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
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
Blu-Ice and the Distributed Control System : software for data acquisition and instrument control at macromolecular crystallography beamlines McPhillips, Timothy M.; McPhillips, Scott E.; Chiu, Hsiu-Ju Journal of Synchrotron Radiation, Vol. 9, Issue 6 https://doi.org/10.1107/S0909049502015170	journal	November 2002
The BioCAT undulator beamline 18ID: a facility for biological non-crystalline diffraction and X-ray absorption spectroscopy at the Advanced Photon Source Fischetti, R.; Stepanov, S.; Rosenbaum, G. Journal of Synchrotron Radiation, Vol. 11, Issue 5 https://doi.org/10.1107/S0909049504016760	journal	August 2004
The Stanford Automated Mounter: pushing the limits of sample exchange at the SSRL macromolecular crystallography beamlines Russi, Silvia; Song, Jinhu; McPhillips, Scott E. Journal of Applied Crystallography, Vol. 49, Issue 2 https://doi.org/10.1107/S1600576716000649	journal	February 2016
The changing landscape of Lynch syndrome due to PMS2 mutations Blount, J.; Prakash, A. Clinical Genetics, Vol. 94, Issue 1 https://doi.org/10.1111/cge.13205	journal	March 2018
Germline mutations in PMS2 and MLH1 in individuals with solitary loss of PMS2 expression in colorectal carcinomas from the Colon Cancer Family Registry Cohort Rosty, Christophe; Clendenning, Mark; Walsh, Michael D. BMJ Open, Vol. 6, Issue 2 https://doi.org/10.1136/bmjopen-2015-010293	journal	February 2016
Comprehensive statistical study of 452 BRCA1 missense substitutions with classification of eight recurrent substitutions as neutral Tavtigian, S. V. Journal of Medical Genetics, Vol. 43, Issue 4 https://doi.org/10.1136/jmg.2005.033878	journal	September 2005
Eukaryotic Mismatch Repair in Relation to DNA Replication Kunkel, Thomas A.; Erie, Dorothy A. Annual Review of Genetics, Vol. 49, Issue 1 https://doi.org/10.1146/annurev-genet-112414-054722	journal	November 2015
Determining the functional significance of mismatch repair gene missense variants using biochemical and cellular assays Heinen, Christopher D.; Rasmussen, Lj Hereditary Cancer in Clinical Practice, Vol. 10, Issue 1 https://doi.org/10.1186/1897-4287-10-9	journal	July 2012
Germline deletions in the EPCAM gene as a cause of Lynch syndrome – literature review Tutlewska, Katarzyna; Lubinski, Jan; Kurzawski, Grzegorz Hereditary Cancer in Clinical Practice, Vol. 11, Issue 1 https://doi.org/10.1186/1897-4287-11-9	journal	August 2013
Lynch Syndrome Caused by Germline PMS2 Mutations: Delineating the Cancer Risk ten Broeke, Sanne W.; Brohet, Richard M.; Tops, Carli M. Journal of Clinical Oncology, Vol. 33, Issue 4 https://doi.org/10.1200/JCO.2014.57.8088	journal	February 2015
Multigene Panel Testing Provides a New Perspective on Lynch Syndrome Espenschied, Carin R.; LaDuca, Holly; Li, Shuwei Journal of Clinical Oncology, Vol. 35, Issue 22 https://doi.org/10.1200/JCO.2016.71.9260	journal	August 2017
Preparation of DNA Substrates for In Vitro Mismatch Repair Wang, Huixian; Hays, John B. Molecular Biotechnology, Vol. 15, Issue 2 https://doi.org/10.1385/MB:15:2:97	journal	January 2000
Germline mutations in PMS2 and MLH1 in individuals with solitary loss of PMS2 expression in colorectal carcinomas from the Colon Cancer Family Registry Cohort A., Baron, John; P., Young, Joanne; M., Lindor, Noralane The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/2awh-0725	text	January 2016
Eukaryotic Mismatch Repair in Relation to DNA Replication A., Kunkel, Thomas; A., Erie, Dorothy The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/r98e-vh63	text	January 2015
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.45787	text	January 2010
Lynch Syndrome: An Updated Review Sehgal, Rishabh; Sheahan, Kieran; O'Connell, Patrick Genes, Vol. 5, Issue 3 https://doi.org/10.3390/genes5030497	journal	June 2014
Measuring In Vitro ATPase Activity for Enzymatic Characterization Rule, Chelsea S.; Patrick, Marcella; Sandkvist, Maria Journal of Visualized Experiments, Issue 114 https://doi.org/10.3791/54305	journal	January 2016
Constitutional mismatch repair deficiency syndrome: Do we know it? Ramachandra, C.; Challa, VasuReddy; Shetty, Rachan Indian Journal of Human Genetics, Vol. 20, Issue 2 https://doi.org/10.4103/0971-6866.142902	journal	January 2014
Postreplicative mismatch repair Jiricny, Josef Cold Spring Harbor Laboratory Press https://doi.org/10.5167/uzh-77249	text	January 2013

Similar Records

Structure of the human MLH1 N-terminus: implications for predisposition to Lynch syndrome

Journal Article · Fri Jul 31 20:00:00 EDT 2015 · Acta Crystallographica. Section F, Structural Biology Communications · OSTI ID:1208676

Structure of the human MLH1 N-terminus: implications for predisposition to Lynch syndrome

Journal Article · Tue Jul 28 00:00:00 EDT 2015 · Acta crystallographica. Section F, Structural biology communications · OSTI ID:22389087

Deficiency of mismatch repair genes is less frequently observed in signet ring cell compared with non-signet ring cell gastric cancer

Journal Article · Fri Mar 15 00:00:00 EDT 2019 · Medical Oncology (Online) · OSTI ID:22938441

Related Subjects

60 APPLIED LIFE SCIENCES
CMMRD
DNA mismatch repair
Lynch syndrome
PMS2
structural analysis
variants of uncertain significance

Biochemical and structural characterization of two variants of uncertain significance in the PMS2 gene

Citation Formats

References (70)

Similar Records

Related Subjects