Table 3. Second-Generation Epigenetic Clocks
Reference:
1. Jones PA. Functions of DNA
methylation: islands, start sites, gene bodies and beyond. Nature
Reviews Genetics. 2012;13(7):484-492.
2. Jones MJ, Goodman SJ, Kobor MS. DNA
methylation and healthy human aging. Aging cell.2015;14(6):924-932.
3. Zeilinger S, Kühnel B, Klopp N, et
al. Tobacco smoking leads to extensive genome-wide changes in DNA
methylation. PloS one. 2013;8(5):e63812.
4. de Prado-Bert P, Ruiz-Arenas C,
Vives-Usano M, et al. The early-life exposome and epigenetic age
acceleration in children. Environment International.2021;155:106683.
5. Legaki E, Arsenis C, Taka S,
Papadopoulos NG. DNA methylation biomarkers in asthma and rhinitis: Are
we there yet? Clinical and translational allergy.2022;12(3):e12131.
6. Titus AJ, Gallimore RM, Salas LA,
Christensen BC. Cell-type deconvolution from DNA methylation: a review
of recent applications. Hum Mol Genet. 2017;26(R2):R216-r224.
7. Grant OA, Wang Y, Kumari M, Zabet
NR, Schalkwyk L. Characterising sex differences of autosomal DNA
methylation in whole blood using the Illumina EPIC array. Clin
Epigenetics. 2022;14(1):62.
8. Bjornsson HT, Sigurdsson MI, Fallin
MD, et al. Intra-individual change over time in DNA methylation with
familial clustering. Jama. 2008;299(24):2877-2883.
9. Rakyan VK, Down TA, Maslau S, et
al. Human aging-associated DNA hypermethylation occurs preferentially at
bivalent chromatin domains. Genome Res. 2010;20(4):434-439.
10. Martino DJ, Tulic MK, Gordon L,
et al. Evidence for age-related and individual-specific changes in DNA
methylation profile of mononuclear cells during early immune development
in humans. Epigenetics. 2011;6(9):1085-1094.
11. Florath I, Butterbach K, Müller
H, Bewerunge-Hudler M, Brenner H. Cross-sectional and longitudinal
changes in DNA methylation with age: an epigenome-wide analysis
revealing over 60 novel age-associated CpG sites. Hum Mol Genet.2014;23(5):1186-1201.
h12. Bell CG, Lowe R, Adams PD, et
al. DNA methylation aging clocks: challenges and recommendations.Genome biology. 2019;20(1):249.
13. Horvath S, Raj K. DNA
methylation-based biomarkers and the epigenetic clock theory of ageing.Nature Reviews Genetics. 2018;19(6):371-384.
14. Fransquet PD, Wrigglesworth J,
Woods RL, Ernst ME, Ryan J. The epigenetic clock as a predictor of
disease and mortality risk: a systematic review and meta-analysis.Clin Epigenetics. 2019;11(1):62.
15. Dugué PA, Bassett JK, Joo JE, et
al. DNA methylation-based biological aging and cancer risk and survival:
Pooled analysis of seven prospective studies. International
journal of cancer. 2018;142(8):1611-1619.
16. Chen BH, Marioni RE, Colicino E,
et al. DNA methylation-based measures of biological age: meta-analysis
predicting time to death. Aging. 2016;8(9):1844-1865.
17. Verschoor CP, Lin DTS, Kobor MS,
et al. Epigenetic age is associated with baseline and 3-year change in
frailty in the Canadian Longitudinal Study on Aging. Clin
Epigenetics. 2021;13(1):163-163.
18. Grodstein F, Lemos B, Yu L, et
al. The association of epigenetic clocks in brain tissue with brain
pathologies and common aging phenotypes. Neurobiology of disease.2021;157:105428.
19. Peng C, Cardenas A, Rifas-Shiman
SL, et al. Epigenetic age acceleration is associated with allergy and
asthma in children in Project Viva. J Allergy Clin Immunol.2019;143(6):2263-2270.e2214.
20. Cardenas A, Sordillo JE,
Rifas-Shiman SL, et al. The nasal methylome as a biomarker of asthma and
airway inflammation in children. Nature Communications.2019;10(1):3095.
21. Barker DJ. The origins of the
developmental origins theory. Journal of internal medicine.2007;261(5):412-417.
22. Ghildayal N, Fore R, Lutz SM, et
al. Early-pregnancy maternal body mass index is associated with common
DNA methylation markers in cord blood and placenta: a paired-tissue
epigenome-wide association study. Epigenetics.2022;17(7):808-818.
23. Park J, Kim WJ, Kim J, et al.
Prenatal Exposure to Traffic-Related Air Pollution and the DNA
Methylation in Cord Blood Cells: MOCEH Study. International
journal of environmental research and public health. 2022;19(6).
24. Akhabir L, Stringer R, Desai D,
et al. DNA methylation changes in cord blood and the developmental
origins of health and disease - a systematic review and replication
study. BMC genomics. 2022;23(1):221.
25. Chowdhury NU, Guntur VP, Newcomb
DC, Wechsler ME. Sex and gender in asthma. European Respiratory
Review. 2021;30(162):210067.
26. DeVries A, Vercelli D. Epigenetic
Mechanisms in Asthma. Annals of the American Thoracic Society.2016;13 Suppl 1(Suppl 1):S48-50.
27. Strichman-Almashanu LZ, Lee RS,
Onyango PO, et al. A genome-wide screen for normally methylated human
CpG islands that can identify novel imprinted genes. Genome Res.2002;12(4):543-554.
28. Gardiner-Garden M, Frommer M. CpG
islands in vertebrate genomes. Journal of molecular biology.1987;196(2):261-282.
29. Saxonov S, Berg P, Brutlag DL. A
genome-wide analysis of CpG dinucleotides in the human genome
distinguishes two distinct classes of promoters. Proceedings of
the National Academy of Sciences of the United States of America.2006;103(5):1412-1417.
30. Weber M, Hellmann I, Stadler MB,
et al. Distribution, silencing potential and evolutionary impact of
promoter DNA methylation in the human genome. Nature genetics.2007;39(4):457-466.
31. Bibikova M, Le J, Barnes B, et
al. Genome-wide DNA methylation profiling using Infinium® assay.Epigenomics. 2009;1(1):177-200.
32. Bibikova M, Barnes B, Tsan C, et
al. High density DNA methylation array with single CpG site resolution.Genomics. 2011;98(4):288-295.
33. Pidsley R, Zotenko E, Peters TJ,
et al. Critical evaluation of the Illumina MethylationEPIC BeadChip
microarray for whole-genome DNA methylation profiling. Genome
biology. 2016;17(1):208.
34. Bell JT, Tsai PC, Yang TP, et al.
Epigenome-wide scans identify differentially methylated regions for age
and age-related phenotypes in a healthy ageing population. PLoS
genetics. 2012;8(4):e1002629.
35. Day K, Waite LL, Thalacker-Mercer
A, et al. Differential DNA methylation with age displays both common and
dynamic features across human tissues that are influenced by CpG
landscape. Genome biology. 2013;14(9):R102.
36. Heyn H, Li N, Ferreira HJ, et al.
Distinct DNA methylomes of newborns and centenarians. Proceedings
of the National Academy of Sciences. 2012;109(26):10522-10527.
37. Talens RP, Christensen K, Putter
H, et al. Epigenetic variation during the adult lifespan:
cross-sectional and longitudinal data on monozygotic twin pairs.Aging cell. 2012;11(4):694-703.
38. Herbstman JB, Wang S, Perera FP,
et al. Predictors and consequences of global DNA methylation in cord
blood and at three years. PloS one. 2013;8(9):e72824.
39. Martino D, Loke YJ, Gordon L, et
al. Longitudinal, genome-scale analysis of DNA methylation in twins from
birth to 18 months of age reveals rapid epigenetic change in early life
and pair-specific effects of discordance. Genome biology.2013;14(5):R42.
40. Acevedo N, Reinius LE, Vitezic M,
et al. Age-associated DNA methylation changes in immune genes, histone
modifiers and chromatin remodeling factors within 5 years after birth in
human blood leukocytes. Clin Epigenetics. 2015;7(1):34.
41. Lasky-Su J, Himes BE, Raby BA, et
al. HLA-DQ strikes again: genome-wide association study further confirms
HLA-DQ in the diagnosis of asthma among adults. Clinical and
experimental allergy : journal of the British Society for Allergy and
Clinical Immunology. 2012;42(12):1724-1733.
42. Waage J, Standl M, Curtin JA, et
al. Genome-wide association and HLA fine-mapping studies identify risk
loci and genetic pathways underlying allergic rhinitis. Nature
genetics. 2018;50(8):1072-1080.
43. Daya M, Cox C, Acevedo N, et al.
Multiethnic genome-wide and HLA association study of total serum IgE
level. J Allergy Clin Immunol. 2021;148(6):1589-1595.
44. Ramasamy A, Kuokkanen M, Vedantam
S, et al. Genome-wide association studies of asthma in population-based
cohorts confirm known and suggested loci and identify an additional
association near HLA. PloS one. 2012;7(9):e44008.
45. Asai Y, Eslami A, van Ginkel CD,
et al. A Canadian genome-wide association study and meta-analysis
confirm HLA as a risk factor for peanut allergy independent of asthma.J Allergy Clin Immunol. 2018;141(4):1513-1516.
46. Madore AM, Vaillancourt VT, Asai
Y, et al. HLA-DQB1*02 and DQB1*06:03P are associated with peanut
allergy. Eur J Hum Genet. 2013;21(10):1181-1184.
47. Wieczorek M, Abualrous ET, Sticht
J, et al. Major Histocompatibility Complex (MHC) Class I and MHC Class
II Proteins: Conformational Plasticity in Antigen Presentation.Frontiers in immunology. 2017;8:292.
48. Simon AK, Hollander GA, McMichael
A. Evolution of the immune system in humans from infancy to old age.Proceedings Biological sciences. 2015;282(1821):20143085.
49. Berger A. Th1 and Th2 responses:
what are they? BMJ (Clinical research ed). 2000;321(7258):424.
50. Holgate ST. Innate and adaptive
immune responses in asthma. Nature medicine. 2012;18(5):673-683.
51. Zhang H, Tong X, Holloway JW, et
al. The interplay of DNA methylation over time with Th2 pathway genetic
variants on asthma risk and temporal asthma transition. Clin
Epigenetics. 2014;6(1):8.
52. Alisch RS, Barwick BG, Chopra P,
et al. Age-associated DNA methylation in pediatric populations.Genome Res. 2012;22(4):623-632.
53. Horvath S. DNA methylation age of
human tissues and cell types. Genome biology. 2013;14(10):R115.
54. Snir S, Farrell C, Pellegrini M.
Human epigenetic ageing is logarithmic with time across the entire
lifespan. Epigenetics. 2019;14(9):912-926.
55. Fraga MF, Ballestar E, Paz MF, et
al. Epigenetic differences arise during the lifetime of monozygotic
twins. Proceedings of the National Academy of Sciences.2005;102(30):10604-10609.
56. Poulsen P, Esteller M, Vaag A,
Fraga MF. The Epigenetic Basis of Twin Discordance in Age-Related
Diseases. Pediatric Research. 2007;61(7):38-42.
57. Bocklandt S, Lin W, Sehl ME, et
al. Epigenetic predictor of age. PloS one. 2011;6(6):e14821.
58. Vaiserman A. Developmental Tuning
of Epigenetic Clock. Front Genet. 2018;9.
59. Perna L, Zhang Y, Mons U,
Holleczek B, Saum K-U, Brenner H. Epigenetic age acceleration predicts
cancer, cardiovascular, and all-cause mortality in a German case cohort.Clin Epigenetics. 2016;8(1):64.
60. de Prado-Bert P, Ruiz-Arenas C,
Vives-Usano M, et al. The early-life exposome and epigenetic age
acceleration in children. Environ Int. 2021;155:106683.
61. Simpkin AJ, Hemani G, Suderman M,
et al. Prenatal and early life influences on epigenetic age in children:
a study of mother-offspring pairs from two cohort studies. Hum Mol
Genet. 2016;25(1):191-201.
62. Quach A, Levine ME, Tanaka T, et
al. Epigenetic clock analysis of diet, exercise, education, and
lifestyle factors. Aging. 2017;9(2):419-446.
63. Song AY, Feinberg JI, Bakulski
KM, et al. Prenatal Exposure to Ambient Air Pollution and Epigenetic
Aging at Birth in Newborns. Front Genet. 2022;13:929416.
64. Zou H, Hastie T. Regularization
and Variable Selection via the Elastic Net. Journal of the Royal
Statistical Society Series B (Statistical Methodology).2005;67(2):301-320.
65. Field AE, Robertson NA, Wang T,
Havas A, Ideker T, Adams PD. DNA Methylation Clocks in Aging:
Categories, Causes, and Consequences. Molecular cell.2018;71(6):882-895.
66. Levine ME, Lu AT, Quach A, et al.
An epigenetic biomarker of aging for lifespan and healthspan.Aging. 2018;10(4):573-591.
67. Hannum G, Guinney J, Zhao L, et
al. Genome-wide methylation profiles reveal quantitative views of human
aging rates. Molecular cell. 2013;49(2):359-367.
68. Horvath S, Oshima J, Martin GM,
et al. Epigenetic clock for skin and blood cells applied to Hutchinson
Gilford Progeria Syndrome and ex vivo studies. Aging.2018;10(7):1758-1775.
69. McEwen LM, O’Donnell KJ, McGill
MG, et al. The PedBE clock accurately estimates DNA methylation age in
pediatric buccal cells. Proceedings of the National Academy of
Sciences. 2020;117(38):23329-23335.
70. Teschendorff AE, Menon U,
Gentry-Maharaj A, et al. Age-dependent DNA methylation of genes that are
suppressed in stem cells is a hallmark of cancer. Genome Res.2010;20(4):440-446.
71. Koch CM, Wagner W.
Epigenetic-aging-signature to determine age in different tissues.Aging. 2011;3(10):1018-1027.
72. McEwen LM, Jones MJ, Lin DTS, et
al. Systematic evaluation of DNA methylation age estimation with common
preprocessing methods and the Infinium MethylationEPIC BeadChip array.Clin Epigenetics. 2018;10(1):123.
73. El Khoury LY, Gorrie-Stone T,
Smart M, et al. Systematic underestimation of the epigenetic clock and
age acceleration in older subjects. Genome biology.2019;20(1):283-283.
74. Knight AK, Craig JM, Theda C, et
al. An epigenetic clock for gestational age at birth based on blood
methylation data. Genome biology. 2016;17(1):206.
75. Horvath S. DNA methylation age of
human tissues and cell types. Genome Biology. 2013;14(10):3156.
76. Lu AT, Quach A, Wilson JG, et al.
DNA methylation GrimAge strongly predicts lifespan and healthspan.Aging. 2019;11(2):303-327.
77. Horvath S, Gurven M, Levine ME,
et al. An epigenetic clock analysis of race/ethnicity, sex, and coronary
heart disease. Genome biology. 2016;17(1):171.
78. Bantz SK, Zhu Z, Zheng T. The
Atopic March: Progression from Atopic Dermatitis to Allergic Rhinitis
and Asthma. J Clin Cell Immunol. 2014;5(2):202.
79. McGeachie MJ, Stahl EA, Himes BE,
et al. Polygenic heritability estimates in pharmacogenetics: focus on
asthma and related phenotypes. Pharmacogenetics and genomics.2013;23(6):324-328.
80. Thomsen SF. Genetics of asthma:
an introduction for the clinician. European clinical respiratory
journal. 2015;2.
81. Xu CJ, Söderhäll C, Bustamante M,
et al. DNA methylation in childhood asthma: an epigenome-wide
meta-analysis. The Lancet Respiratory medicine.2018;6(5):379-388.
82. Forno E, Wang T, Qi C, et al. DNA
methylation in nasal epithelium, atopy, and atopic asthma in children: a
genome-wide study. The Lancet Respiratory medicine.2019;7(4):336-346.
83. Paller AS, Spergel JM,
Mina-Osorio P, Irvine AD. The atopic march and atopic multimorbidity:
Many trajectories, many pathways. J Allergy Clin Immunol.2019;143(1):46-55.
84. Daley D. The evolution of the
hygiene hypothesis: the role of early-life exposures to viruses and
microbes and their relationship to asthma and allergic diseases.Curr Opin Allergy Clin Immunol. 2014;14(5):390-396.
85. Pischedda S, Rivero-Calle I,
Gómez-Carballa A, et al. Role and Diagnostic Performance of Host
Epigenome in Respiratory Morbidity after RSV Infection: The EPIRESVi
Study. Frontiers in immunology. 2022;13:875691.
86. Chlamydas S, Markouli M, Strepkos
D, Piperi C. Epigenetic mechanisms regulate sex-specific bias in disease
manifestations. Journal of molecular medicine (Berlin, Germany).2022;100(8):1111-1123.
87. Taneja V. Sex Hormones Determine
Immune Response. Frontiers in immunology. 2018;9:1931.
88. Patel R, Solatikia F, Zhang H, et
al. Sex-specific associations of asthma acquisition with changes in DNA
methylation during adolescence. Clinical and experimental allergy
: journal of the British Society for Allergy and Clinical Immunology.2021;51(2):318-328.
89. Han L, Zhang H, Kaushal A, et al.
Changes in DNA methylation from pre- to post-adolescence are associated
with pubertal exposures. Clinical Epigenetics. 2019;11(1):176.
90. Kananen L, Marttila S, Nevalainen
T, et al. The trajectory of the blood DNA methylome ageing rate is
largely set before adulthood: evidence from two longitudinal studies.AGE. 2016;38(3):65.
91. Fuseini H, Newcomb DC. Mechanisms
Driving Gender Differences in Asthma. Curr Allergy Asthma Rep.2017;17(3):19.
92. Shah R, Newcomb DC. Sex Bias in
Asthma Prevalence and Pathogenesis. Frontiers in immunology.2018;9:2997.
93. Weidner CI, Lin Q, Koch CM, et
al. Aging of blood can be tracked by DNA methylation changes at just
three CpG sites. Genome biology. 2014;15(2):R24.
94. Castle JR, Lin N, Liu J, et al.
Estimating breast tissue-specific DNA methylation age using
next-generation sequencing data. Clin Epigenetics. 2020;12(1):45.
95. Haftorn KL, Lee Y, Denault WRP,
et al. An EPIC predictor of gestational age and its application to
newborns conceived by assisted reproductive technologies. Clin
Epigenetics. 2021;13(1):82.