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Human mutation
04, 2019;40 (4): 458-471.

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

Brandon M D'Arcy, Jessa Blount, Aishwarya Prakash
Author Information
  1. Brandon M D'Arcy: Mitchell Cancer Institute, The University of South Alabama, Mobile, Alabama. ORCID
  2. Jessa Blount: Mitchell Cancer Institute, The University of South Alabama, Mobile, Alabama.
  3. Aishwarya Prakash: Mitchell Cancer Institute, The University of South Alabama, Mobile, Alabama. ORCID
PMID: 30653781 DOI: 10.1002/humu.23708

Abstract

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 the current study, 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.

Keywords

CMMRD DNA mismatch repair Lynch syndrome PMS2 structural analysis variants of uncertain significance

References

  1. Am J Surg Pathol. 2015 Aug;39(8):1114-20 [PMID: 25871621]
  2. Proc Natl Acad Sci U S A. 2017 Apr 4;114(14):3552-3554 [PMID: 28356513]
  3. J Appl Crystallogr. 2013 Feb 1;46(Pt 1):1-13 [PMID: 23396808]
  4. Biotechnol Annu Rev. 2004;10:31-50 [PMID: 15504702]
  5. Genes (Basel). 2014 Jun 27;5(3):497-507 [PMID: 24978665]
  6. Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):352-67 [PMID: 22505256]
  7. Curr Protoc Hum Genet. 2013 Jan;Chapter 7:Unit7.20 [PMID: 23315928]
  8. BMJ Open. 2016 Feb 19;6(2):e010293 [PMID: 26895986]
  9. J Biol Chem. 2000 Jun 16;275(24):18424-31 [PMID: 10747992]
  10. Hum Mutat. 2010 Mar;31(3):247-53 [PMID: 20020535]
  11. J Biol Chem. 2006 Oct 13;281(41):30305-9 [PMID: 16905530]
  12. J Appl Crystallogr. 2002 Dec;35(6):720-726 [PMID: 24899734]
  13. Curr Protoc Protein Sci. 2012 Nov;Chapter 17:Unit17.14 [PMID: 23151743]
  14. J Natl Cancer Inst. 2006 Mar 1;98(5):358-61 [PMID: 16507833]
  15. Nucleic Acids Res. 2003 Jul 1;31(13):3812-4 [PMID: 12824425]
  16. J Synchrotron Radiat. 2004 Sep 1;11(Pt 5):399-405 [PMID: 15310956]
  17. Prog Mol Biol Transl Sci. 2012;110:41-70 [PMID: 22749142]
  18. Genet Med. 2015 Aug;17(8):630-8 [PMID: 25503501]
  19. Methods Mol Biol. 1999;113:121-32 [PMID: 10443415]
  20. Angew Chem Int Ed Engl. 2016 Jul 18;55(30):8490-501 [PMID: 27198632]
  21. Gastroenterology. 2015 Sep;149(3):604-13.e20 [PMID: 25980754]
  22. Acta Crystallogr D Biol Crystallogr. 2010 Jan;66(Pt 1):12-21 [PMID: 20057044]
  23. Hum Mutat. 2013 Nov;34(11):1477-80 [PMID: 24027009]
  24. Proc Natl Acad Sci U S A. 2017 May 9;114(19):4930-4935 [PMID: 28439008]
  25. Annu Rev Genet. 2015;49:291-313 [PMID: 26436461]
  26. Hum Mutat. 2008 Nov;29(11):1282-91 [PMID: 18951446]
  27. Clin Genet. 2018 Jul;94(1):61-69 [PMID: 29286535]
  28. Nat Rev Cancer. 2015 Mar;15(3):181-94 [PMID: 25673086]
  29. J Clin Oncol. 2015 Feb 1;33(4):319-25 [PMID: 25512458]
  30. Hum Mutat. 2012 Dec;33(12):1617-25 [PMID: 22833534]
  31. Anal Biochem. 2011 Jun 15;413(2):179-84 [PMID: 21329650]
  32. J Synchrotron Radiat. 2002 Nov 1;9(Pt 6):401-6 [PMID: 12409628]
  33. J Med Genet. 2006 Apr;43(4):295-305 [PMID: 16014699]
  34. Hered Cancer Clin Pract. 2013 Aug 12;11(1):9 [PMID: 23938213]
  35. Mol Carcinog. 2017 Dec;56(12):2663-2668 [PMID: 28767177]
  36. Genet Med. 2015 May;17(5):405-24 [PMID: 25741868]
  37. Genet Med. 2018 Mar;20(3):346-350 [PMID: 29215655]
  38. Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501 [PMID: 20383002]
  39. Cold Spring Harb Perspect Biol. 2013 Apr 01;5(4):a012633 [PMID: 23545421]
  40. Genet Med. 2019 Jul;21(7):1486-1496 [PMID: 30504929]
  41. Int J Colorectal Dis. 2009 Aug;24(8):885-93 [PMID: 19479271]
  42. Hered Cancer Clin Pract. 2012 Jul 23;10(1):9 [PMID: 22824075]
  43. Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21 [PMID: 20124702]
  44. Gastroenterology. 2008 Aug;135(2):419-28 [PMID: 18602922]
  45. Proc Natl Acad Sci U S A. 1995 Mar 14;92(6):1950-4 [PMID: 7892206]
  46. Mol Genet Genomic Med. 2015 Jul;3(4):327-45 [PMID: 26247049]
  47. Nat Methods. 2009 Aug;6(8):606-12 [PMID: 19620974]
  48. Biopolymers. 2008 May;89(5):392-400 [PMID: 17896349]
  49. J Vis Exp. 2016 Aug 23;(114): [PMID: 27584824]
  50. J Appl Crystallogr. 2016 Feb 24;49(Pt 2):622-626 [PMID: 27047309]
  51. DNA Repair (Amst). 2016 Feb;38:127-134 [PMID: 26710976]
  52. Nat Protoc. 2006;1(6):2876-90 [PMID: 17406547]
  53. DNA Repair (Amst). 2006 Mar 7;5(3):347-61 [PMID: 16338176]
  54. J Clin Oncol. 2017 Aug 1;35(22):2568-2575 [PMID: 28514183]
  55. Indian J Hum Genet. 2014 Apr;20(2):192-4 [PMID: 25400351]
  56. Mol Biotechnol. 2000 Jun;15(2):97-104 [PMID: 10949822]
  57. EMBO J. 2001 Oct 1;20(19):5521-31 [PMID: 11574484]
  58. Hum Mutat. 2010 Aug;31(8):975-82 [PMID: 20533529]
  59. Anal Biochem. 2000 Dec 15;287(2):252-60 [PMID: 11112271]
  60. Carcinogenesis. 2015 Feb;36(2):202-11 [PMID: 25477341]
  61. J Law Biosci. 2018 Jan 22;4(3):648-657 [PMID: 29868193]
  62. BMC Genet. 2016 Jul 01;17(1):99 [PMID: 27363726]
  63. DNA Repair (Amst). 2016 Feb;38:42-49 [PMID: 26719141]

Grants

  1. R00 ES024417/NIEHS NIH HHS
  2. S10 OD018090/NIH HHS
  3. 5R00ES024417-04/NIEHS NIH HHS
  4. P41 GM103393/NIGMS NIH HHS
  5. P30 GM124169/NIGMS NIH HHS
  6. P41 GM103622/NIGMS NIH HHS

MeSH Term

Alleles
Amino Acid Substitution
Biomarkers
Cell Line
Colorectal Neoplasms, Hereditary Nonpolyposis
DNA Mismatch Repair
Gene Frequency
Genetic Association Studies
Genetic Predisposition to Disease
Genetic Variation
Humans
Mismatch Repair Endonuclease PMS2
Mutation
Pedigree
Protein Conformation
Risk Assessment
Structure-Activity Relationship

Chemicals

Biomarkers
PMS2 protein, human
Mismatch Repair Endonuclease PMS2
Journal Article Research Support, N.I.H., Extramural

Word Cloud

Created with Highcharts 10.0.0PMS2pvariantsmutationsuncertainsignificanceVUSsGly207GluLeu42_Glu44delLynchsyndromeLSDNAmismatchrepairMMRdiagnosismissensefunctionaltwocvariantcharacterizationX-raystructuralautosomaldominantinheriteddisorderassociatedincreasedpredispositioncertaincancerscausedloss-of-functiononefourgenesMLH1MSH2MSH6oftenchallengedidentificationeffectsknowntermedaccount20%-30%noncodingcauseambiguityclinicalhinderimplementationappropriatemedicalmanagementcurrentstudyfocusbiologicalconsequencesnonsynonymous620G>A123_131delGTTAGTAGAresultalterationglycine207glutamatedeletionaminoacidresidues42-44respectivelyretainsvitroATPaseactivitiesappearslackcapabilitiesStructuralbiophysicalusingcirculardichroismsmall-anglescatteringcrystallographyN-terminaldomainindicateproperlyfoldedsimilarwild-typeenzymewhereasdisorderedproneaggregationBiochemicalgeneCMMRDanalysis

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