Ancient mitochondrial DNA pathogenic variants putatively associated with mitochondrial disease.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2020
2020
Historique:
received:
09
05
2020
accepted:
09
08
2020
entrez:
24
9
2020
pubmed:
25
9
2020
medline:
28
10
2020
Statut:
epublish
Résumé
Mitochondrial DNA variants associated with diseases are widely studied in contemporary populations, but their prevalence has not yet been investigated in ancient populations. The publicly available AmtDB database contains 1443 ancient mtDNA Eurasian genomes from different periods. The objective of this study was to use this data to establish the presence of pathogenic mtDNA variants putatively associated with mitochondrial diseases in ancient populations. The clinical significance, pathogenicity prediction and contemporary frequency of mtDNA variants were determined using online platforms. The analyzed ancient mtDNAs contain six variants designated as being "confirmed pathogenic" in modern patients. The oldest of these, m.7510T>C in the MT-TS1 gene, was found in a sample from the Neolithic period, dated 5800-5400 BCE. All six have well established clinical association, and their pathogenic effect is corroborated by very low population frequencies in contemporary populations. Analysis of the geographic location of the ancient samples, contemporary epidemiological trends and probable haplogroup association indicate diverse spatiotemporal dynamics of these variants. The dynamics in the prevalence and distribution is conceivably result of de novo mutations or human migrations and subsequent evolutionary processes. In addition, ten variants designated as possibly or likely pathogenic were found, but the clinical effect of these is not yet well established and further research is warranted. All detected mutations putatively associated with mitochondrial disease in ancient mtDNA samples are in tRNA coding genes. Most of these mutations are in a mt-tRNA type (Model 2) that is characterized by loss of D-loop/T-loop interaction. Exposing pathogenic variants in ancient human populations expands our understanding of their origin and prevalence dynamics.
Identifiants
pubmed: 32970680
doi: 10.1371/journal.pone.0233666
pii: PONE-D-20-13726
pmc: PMC7514063
doi:
Substances chimiques
DNA, Ancient
0
DNA, Mitochondrial
0
RNA, Transfer
9014-25-9
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0233666Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Nature. 1990 Dec 13;348(6302):651-3
pubmed: 2102678
Clin Genet. 2018 Apr;93(4):925-928
pubmed: 29266179
BMC Evol Biol. 2014 Oct 10;14:217
pubmed: 25301575
Br J Ophthalmol. 2017 Sep;101(9):1298-1302
pubmed: 28729369
Chin Med J (Engl). 2019 Apr 5;132(7):865-867
pubmed: 30897601
J Med Genet. 2006 Feb;43(2):175-9
pubmed: 15972314
Ann Clin Transl Neurol. 2018 Feb 07;5(3):333-345
pubmed: 29560378
Mitochondrion. 2017 Sep;36:130-137
pubmed: 28716668
Mitochondrion. 2019 May;46:69-72
pubmed: 29501485
Congenit Heart Dis. 2018 Sep;13(5):671-677
pubmed: 30133155
Sci Rep. 2018 Aug 8;8(1):11887
pubmed: 30089816
Neuromuscul Disord. 2008 Jan;18(1):63-7
pubmed: 17825557
Nature. 1981 Apr 9;290(5806):457-65
pubmed: 7219534
Headache. 1988 Aug;28(7):477-80
pubmed: 3243709
PLoS One. 2013 Jun 05;8(6):e64539
pubmed: 23755126
J Neurol Sci. 2012 Sep 15;320(1-2):131-5
pubmed: 22743145
Sci Rep. 2019 Apr 1;9(1):5412
pubmed: 30931994
Neuromuscul Disord. 2015 Jan;25(1):81-4
pubmed: 25447692
Am J Hum Genet. 2003 Sep;73(3):671-6
pubmed: 12870132
Clin Genet. 2008 Jan;73(1):50-4
pubmed: 18028453
Neurology. 2011 Nov 29;77(22):1965-71
pubmed: 22094475
J Clin Invest. 1993 Dec;92(6):2906-15
pubmed: 8254046
Proc Natl Acad Sci U S A. 2017 Sep 19;114(38):10083-10088
pubmed: 28874531
Ann Neurol. 2015 May;77(5):753-9
pubmed: 25652200
Diabetologia. 1998 May;41(5):584-8
pubmed: 9628277
Biochem Biophys Res Commun. 1996 Aug 5;225(1):180-5
pubmed: 8769114
PLoS One. 2013 Jul 31;8(7):e70492
pubmed: 23936216
Mitochondrion. 2007 May;7(3):230-3
pubmed: 17300999
Muscle Nerve. 2010 May;41(5):607-13
pubmed: 19941338
Ann Neurol. 2008 Jan;63(1):35-9
pubmed: 17886296
PLoS Comput Biol. 2017 Dec 11;13(12):e1005867
pubmed: 29227991
Brain Behav. 2017 Nov 19;7(12):e00859
pubmed: 29299381
Nature. 2018 May;557(7705):369-374
pubmed: 29743675
Hand Clin. 2011 Feb;27(1):1-10
pubmed: 21176794
Hum Mutat. 2011 Nov;32(11):1319-25
pubmed: 21882289
Neuromuscul Disord. 2001 Jul;11(5):481-4
pubmed: 11404121
BMC Bioinformatics. 2016 Nov 8;17(Suppl 12):338
pubmed: 28185569
PLoS One. 2009 Nov 19;4(11):e7922
pubmed: 19936068
Biochem Biophys Res Commun. 1998 Apr 17;245(2):523-7
pubmed: 9571188
Nucleic Acids Res. 2019 Jan 8;47(D1):D29-D32
pubmed: 30247677
Hum Mol Genet. 2008 Jun 15;17(12):1814-20
pubmed: 18337306
Ann Neurol. 2003 Jul;54(1):86-92
pubmed: 12838523
J Med Genet. 2003 Oct;40(10):752-7
pubmed: 14569122
Mitochondrion. 2012 Nov;12(6):617-22
pubmed: 23063709
JIMD Rep. 2013;9:105-111
pubmed: 23430555
Neuromuscul Disord. 1999 Mar;9(2):66-71
pubmed: 10220860
J Inherit Metab Dis. 2003;26(5):507-8
pubmed: 14518831
Eur J Hum Genet. 2015 Dec;23(12):1735-8
pubmed: 25873012
Sci Rep. 2017 Mar 07;7:43950
pubmed: 28266657
Proc Natl Acad Sci U S A. 2019 May 28;116(22):10705-10710
pubmed: 31061125
Muscle Nerve. 2007 Sep;36(3):279-93
pubmed: 17503499
Nature. 2018 Mar 8;555(7695):197-203
pubmed: 29466330
Neuromuscul Disord. 2018 Feb;28(2):137-143
pubmed: 29174468
Hum Biol. 2017 Jan;89(1):7-19
pubmed: 29285967
J Neurol. 2014 Mar;261(3):504-10
pubmed: 24375076
PLoS One. 2014 Mar 17;9(3):e90924
pubmed: 24637948
J Med Genet. 2000 Sep;37(9):692-4
pubmed: 10978361
Mitochondrion. 2012 Mar;12(2):288-93
pubmed: 22094595
Neuromuscul Disord. 1993 Jan;3(1):43-50
pubmed: 8392410
Mol Genet Genomic Med. 2014 Mar;2(2):107-14
pubmed: 24689073
J Child Neurol. 1999 Sep;14(9):610-3
pubmed: 10488907
J Med Genet. 2002 Dec;39(12):e82
pubmed: 12471220
Chin Med J (Engl). 2019 Jul 20;132(14):1752
pubmed: 31268906
Radiology. 2003 Mar;226(3):614-29
pubmed: 12601185
J Med Genet. 2011 Oct;48(10):660-668
pubmed: 21931168
Am J Hum Genet. 2012 Apr 6;90(4):675-84
pubmed: 22482806
Am J Hum Genet. 2012 May 4;90(5):915-24
pubmed: 22560092
Neuromuscul Disord. 2014 Feb;24(2):162-6
pubmed: 24161205
Nucleic Acids Res. 2019 Jan 8;47(D1):D1202-D1210
pubmed: 30371888
Nucleic Acids Res. 2016 Jan 4;44(D1):D67-72
pubmed: 26590407
Nucleic Acids Res. 2014 Jan;42(Database issue):D980-5
pubmed: 24234437
Hum Mutat. 2013 Sep;34(9):1260-8
pubmed: 23696415
Sci Rep. 2018 Feb 6;8(1):2455
pubmed: 29410482
PLoS Genet. 2017 Dec 18;13(12):e1007126
pubmed: 29253894
Environ Mol Mutagen. 2010 Jun;51(5):440-50
pubmed: 20544884
J Neurol. 2007 Sep;254(9):1283-5
pubmed: 17410322
Science. 1988 Dec 9;242(4884):1427-30
pubmed: 3201231
Science. 2016 Jul 29;353(6298):499-503
pubmed: 27417496
Brain. 2009 Nov;132(Pt 11):3165-74
pubmed: 19720722
Ann Neurol. 2010 Dec;68(6):845-54
pubmed: 21194154
J Med Genet. 1995 Aug;32(8):654-6
pubmed: 7473662
Diabetes. 1994 Jun;43(6):746-51
pubmed: 7910800
Hum Mutat. 2009 Jan;30(1):1-6
pubmed: 18566966
J Mol Med (Berl). 2001 Nov;79(11):641-7
pubmed: 11715067
Curr Protoc Bioinformatics. 2013 Dec;44:1.23.1-26
pubmed: 25489354
J Neurol Sci. 2011 Jan 15;300(1-2):187-90
pubmed: 20884012
Am J Hum Genet. 1998 Aug;63(2):447-54
pubmed: 9683591
BBA Clin. 2016 Apr 29;6:19-24
pubmed: 27331024