Methylomes in Vegans versus Pescatarians and Nonvegetarians
Abstract
:1. Introduction
2. Materials and Methods
2.1. Subjects and Study Design
2.2. Dietary Assessment
2.3. Anthropometric and Lifestyle Measures
2.4. Blood Collection
2.5. DNA Isolation and DNA Methylation Analysis
2.6. Methylation Data Analysis
2.7. Biological Pathway Analyses
3. Results
3.1. Characterization of Study Subjects
3.2. Identification of Differential Methylation Sites
3.3. Pathway Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Demographic and Lifestyle | n = 38 | n = 41 | n = 68 | Vegan vs. Omni | Pesco vs. Omni | Vegan vs. Pesco | |||
---|---|---|---|---|---|---|---|---|---|
Males (%) | |||||||||
Age at collection, mean ± SD (years) | 52.63 | 48.78 | 47.06 | 0.58 | 0.86 | 0.73 | |||
BMI at collection, mean ± SD | 67.78 (8.50) | 69.93 (7.87) | 66.42 (6.73) | 0.37 | 0.02 | 0.25 | |||
Exercise, mean ± SD (min/week) | 23.62 (4.23) | 25.36 (3.63) | 27.07 (3.69) | <0.0001 | 0.02 | 0.05 | |||
Sleep hours, mean ± SD (hrs/day) | 152.93 (109.59) | 76.68 (86.64) | 69.23 (95.72) | 0.0001 | 0.58 | 0.002 | |||
Perception of one’s own health (%) | 7.30 (0.81) | 7.03 (0.95) | 6.94 (0.93) | 0.05 | 0.65 | 0.18 | |||
Excellent | 0.07 | 0.82 | 0.22 | ||||||
Good | 25.71 | 22.50 | 17.65 | ||||||
Fair | 54.29 | 70.00 | 75.00 | ||||||
Prevalent cancer (%) | 20.00 | 7.50 | 7.35 | ||||||
Yes | 0.57 | 0.66 | 0.91 | ||||||
No | 10.53 | 9.76 | 7.35 | ||||||
CVD comorbidities (%) | 89.47 | 90.24 | 92.65 | ||||||
None | 0.35 | 0.74 | 0.57 | ||||||
1 or more | 76.32 | 70.73 | 67.65 | ||||||
Cigarette smoke (%) | 23.68 | 29.27 | 32.35 | ||||||
Never | 0.05 | 0.51 | 0.02 | ||||||
Ever | 97.37 | 80.49 | 85.29 | ||||||
2.63 | 19.51 | 14.71 | |||||||
Dietary intake, mean ± SD | |||||||||
Energy (kcal/d) | |||||||||
Carbohydrate (% of kcal) | 1769.82 (585.13) | 2029.3 (609.7) | 1927.77 (667.22) | 0.23 | 0.43 | 0.06 | |||
Fat (% of kcal) | 57.58 (6.96) | 52.83 (7.17) | 49.74 (8.13) | <0.0001 | 0.05 | 0.004 | |||
Protein (% of kcal) | 28.72 (6.92) | 33.20 (7.29) | 35.66 (7.85) | <0.0001 | 0.11 | 0.007 | |||
Vegetable protein (% of protein) | 13.70 (2.80) | 13.97 (2.42) | 14.61 (2.21) | 0.071 | 0.07 | 0.65 | |||
Animal protein (% of protein) | 96.87 (2.57) | 80.39 (12.56) | 60.63 (14.82) | <0.0001 | <0.0001 | <0.0001 | |||
Essential amino acids | 3.89 (2.33) | 19.92 (12.41) | 39.41 (14.75) | <0.0001 | <0.0001 | <0.0001 | |||
Leucine (% of protein) | |||||||||
Valine (% of protein) | 6.98 (0.48) | 7.40 (0.35) | 7.61 (0.36) | <0.0001 | 0.003 | <0.0001 | |||
Isoleucine (% of protein) | 4.66 (0.25) | 4.89 (0.21) | 4.98 (0.21) | <0.0001 | 0.03 | <0.0001 | |||
Histidine (% of protein) | 3.95 (0.24) | 4.12 (0.20) | 4.29 (0.19) | <0.0001 | <0.0001 | 0.0007 | |||
Methionine (% of protein) | 2.42 (0.13) | 2.45 (0.08) | 2.54 (0.1) | <0.0001 | <0.0001 | 0.24 | |||
Tryptophan (% of protein) | 1.50 (0.12) | 1.73 (0.17) | 1.92 (0.16) | <0.0001 | <0.0001 | <0.0001 | |||
Threonine (% of protein) | 1.26 (0.07) | 1.23 (0.06) | 1.22 (0.06) | 0.002 | 0.16 | 0.1 | |||
Lysine (% of protein) | 3.5 (0.26) | 3.47 (0.20) | 3.55 (0.17) | 0.33 | 0.04 | 0.54 | |||
Phenylalanine (% of protein) | 4.47 (0.48) | 4.93 (0.48) | 5.55 (0.64) | <0.0001 | <0.0001 | <0.0001 | |||
Non-essential amino acids | 4.88 (0.24) | 4.88 (0.11) | 4.75 (0.16) | 0.005 | <0.0001 | 0.99 | |||
Glutamate (% of protein) | |||||||||
Aspartate (% of protein) | 23.07 (1.94) | 22.82 (1.58) | 22.18 (1.64) | 0.010 | 0.05 | 0.53 | |||
Alanine (% of protein) | 10.20 (1.33) | 9.50 (0.79) | 9.07 (0.71) | <0.0001 | 0.004 | 0.005 | |||
Cysteine (% of protein) | 4.40 (0.38) | 4.25 (0.27) | 4.29 (0.23) | 0.06 | 0.46 | 0.05 | |||
Arginine (% of protein) | 1.61 (0.14) | 1.65 (0.16) | 1.65 (0.16) | 0.21 | 0.95 | 0.28 | |||
Tyrosine (% of protein) | 6.79 (0.79) | 6.12 (0.73) | 5.61 (0.66) | <0.0001 | 0.0003 | 0.0002 | |||
Glycine (% of protein) | 3.04 (0.28) | 3.24 (0.25) | 3.38 (0.20) | <0.0001 | 0.002 | 0.001 | |||
Proline (% of protein) | 4.27 (0.31) | 3.92 (0.34) | 3.79 (0.32) | <0.0001 | 0.05 | <0.0001 | |||
Serine (% of protein) | 6.65 (0.92) | 7.24 (0.86) | 7.31 (0.73) | <0.0001 | 0.64 | 0.004 | |||
Micronutrients | 4.87 (0.29) | 4.95 (0.16) | 4.79 (0.19) | 0.10 | <0.0001 | 0.12 | |||
Vitamin B2, mg/1000 kcal | |||||||||
Vitamin B6, mg/1000 kcal | 2.85 (3.28) | 3.64 (5.18) | 2.78 (6.62) | 0.95 | 0.43 | 0.42 | |||
Vitamin B-12, mcg/1000 kcal | 3.56 (7.04) | 8.54 (15.42) | 5.14 (10.21) | 0.4 | 0.17 | 0.07 | |||
Folate, mcg/1000 kcal | 3.93 (4.43) | 7.64 (9.38) | 6.19 (11.23) | 0.24 | 0.49 | 0.03 | |||
Choline, mg/1000 kcal | 460.0 (387.8) | 440.1 (193.0) | 401.9 (214.1) | 0.19 | 0.35 | 0.67 | |||
Betaine, mg/1000 kcal | 117.0 (21.73) | 122.9 (29.40) | 136.9 (27.61) | 0.0002 | 0.01 | 0.32 | |||
0.91 | 0.6 |
Entrez Gene Name | Symbol | Fold Change | Location | Type(s) |
---|---|---|---|---|
mitochondrial ribosomal protein L19 | MRPL19 | 2.517 | Cytoplasm | other |
proline rich 7, synaptic | PRR7 | 2.071 | Other | other |
glutathione S-transferase C-terminal domain containing | GSTCD | 1.879 | Cytoplasm | enzyme |
chromosome 7 open reading frame 50 | C7orf50 | 1.743 | Other | other |
dynein axonemal heavy chain 10 | DNAH10 | 1.636 | Cytoplasm | other |
solute carrier family 38 member 6 | SLC38A6 | 1.619 | Plasma Membrane | transporter |
glutathione S-transferase theta 1 | GSTT1 | 1.594 | Cytoplasm | enzyme |
calcium voltage-gated channel auxiliary subunit beta 2 | CACNB2 | 1.541 | Plasma Membrane | ion channel |
family with sequence similarity 19 member A5, C-C motif chemokine like | FAM19A5 | 1.524 | Extracellular Space | other |
transmembrane protein 229A | TMEM229A | 1.523 | Other | other |
Entrez Gene Name | Symbol | Fold Change | Location | Type(s) |
---|---|---|---|---|
purine rich element binding protein G | PURG | 2.488 | Other | other |
proline rich 7, synaptic | PRR7 | 2.421 | Plasma Membrane | other |
mitochondrial ribosomal protein L19 | MRPL19 | 2.067 | Cytoplasm | other |
catalase | CAT | 1.864 | Cytoplasm | enzyme |
kinesin family member 15 | KIF15 | 1.523 | Nucleus | other |
solute carrier family 38 member 6 | SLC38A6 | 1.507 | Plasma Membrane | transporter |
proteasome 26S subunit, non-ATPase 5 | PSMD5 | 1.478 | Other | other |
Rap associating with DIL domain | RADIL | 1.433 | Cytoplasm | other |
amyloid beta precursor protein binding family B member 2 | APBB2 | 1.431 | Cytoplasm | other |
Annotation Cluster 1 | Enrichment Score: 5.206834531318599 | ||||||||
---|---|---|---|---|---|---|---|---|---|
Category | Term | Count | % | p Value | List Total | Fold Enrichment | Bonferroni | Benjamini | FDR |
INTERPRO | IPR017970:Homeobox, conserved site | 16 | 4.98 | 4.5 × 10−7 | 299 | 5.23 | 2.9 × 10−4 | 2.9 × 10−4 | 6.7 × 10−4 |
UP_KEYWORDS | Homeobox | 17 | 5.30 | 3.2 × 10−6 | 317 | 4.21 | 9.5 × 10−4 | 4.7 × 10−4 | 0.004 |
INTERPRO | IPR001356:Homeodomain | 17 | 5.30 | 4.1 × 10−6 | 299 | 4.12 | 0.003 | 0.001 | 0.006 |
UP_SEQ_FEATURE | DNA-binding region:Homeobox | 14 | 4.36 | 9.7 × 10−6 | 313 | 4.70 | 0.011 | 0.011 | 0.016 |
SMART | SM00389:HOX | 17 | 5.30 | 2.9 × 10−6 | 197 | 3.47 | 0.005 | 0.005 | 0.036 |
INTERPRO | IPR009057:Homeodomain-like | 18 | 5.61 | 3.3 × 10−5 | 299 | 3.33 | 0.022 | 0.007 | 0.049 |
Annotation Cluster 1 | Enrichment Score: 1.945388640497003 | ||||||||
---|---|---|---|---|---|---|---|---|---|
Category | Term | Count | % | p Value | List Total | Fold Enrichment | Bonferroni | Benjamini | FDR |
UP_SEQ_FEATURE | DNA-binding region:Homeobox | 8 | 3.76 | 0.0033 | 203 | 4.14 | 0.88 | 0.88 | 4.79 |
INTERPRO | IPR020479:Homeodomain, metazoa | 6 | 2.82 | 0.0035 | 205 | 5.90 | 0.81 | 0.81 | 4.85 |
INTERPRO | IPR017970:Homeobox, conserved site | 8 | 3.76 | 0.0051 | 205 | 3.81 | 0.91 | 0.71 | 7.05 |
UP_KEYWORDS | Homeobox | 8 | 3.76 | 0.0171 | 208 | 3.02 | 0.99 | 0.52 | 20.09 |
INTERPRO | IPR001356:Homeodomain | 8 | 3.76 | 0.0230 | 205 | 2.83 | 1.00 | 0.89 | 28.36 |
SMART | SM00389:HOX | 8 | 3.76 | 0.0323 | 123 | 2.62 | 0.98 | 0.86 | 31.44 |
INTERPRO | IPR009057:Homeodomain-like | 9 | 4.23 | 0.0327 | 205 | 2.42 | 1.00 | 0.90 | 37.89 |
ID | Gene Name | FC in Omnivores | FC in Piscvores |
---|---|---|---|
BARHL1 | BarH like homeobox 1(BARHL1) | −1.23555 | |
ISL1 | ISL LIM homeobox 1(ISL1) | 1.23352 | 1.2188 |
NKX3-2 | NK3 homeobox 2(NKX3-2) | 1.25585 | 1.26999 |
NKX6-1 | NK6 homeobox 1(NKX6-1) | −1.32335 | |
EVX1 | even-skipped homeobox 1(EVX1) | 1.27498 | |
HOXA2 | homeobox A2(HOXA2) | 1.24374 | |
HOXC9 | homeobox C9(HOXC9) | 1.29757 | |
RAX | retina and anterior neural fold homeobox(RAX) | 1.27834 | 1.24775 |
Term | Count | % | p Value | Fold Enrichment | Bonferroni | Benjamini | FDR |
---|---|---|---|---|---|---|---|
hsa04390:Hippo signaling pathway | 7 | 3.29 | 0.0031 | 4.76 | 0.34 | 0.34 | 3.58 |
hsa05014:Amyotrophic lateral sclerosis (ALS) | 4 | 1.88 | 0.0120 | 8.21 | 0.80 | 0.55 | 13.16 |
hsa04724:Glutamatergic synapse | 5 | 2.35 | 0.0235 | 4.50 | 0.96 | 0.65 | 24.25 |
Term | Count | % | p Value | Fold Enrichment | Bonferroni | Benjamini | FDR |
---|---|---|---|---|---|---|---|
hsa05033:Nicotine addiction | 5 | 1.56 | 0.0032 | 8.04 | 0.42 | 0.42 | 3.82 |
hsa04723:Retrograde endocannabinoid signaling | 6 | 1.87 | 0.0195 | 3.82 | 0.97 | 0.82 | 21.38 |
hsa04921:Oxytocin signaling pathway | 7 | 2.18 | 0.0279 | 3.00 | 0.99 | 0.80 | 29.23 |
hsa04390:Hippo signaling pathway | 7 | 2.18 | 0.0287 | 2.98 | 0.99 | 0.71 | 29.94 |
hsa04727:GABAergic synapse | 5 | 1.56 | 0.0417 | 3.78 | 1.00 | 0.77 | 40.59 |
hsa04810:Regulation of actin cytoskeleton | 8 | 2.49 | 0.0429 | 2.45 | 1.00 | 0.72 | 41.46 |
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Filippov, V.; Jaceldo-Siegl, K.; Eroshkin, A.; Loskutov, V.; Chen, X.; Wang, C.; Duerksen-Hughes, P.J. Methylomes in Vegans versus Pescatarians and Nonvegetarians. Epigenomes 2020, 4, 28. https://doi.org/10.3390/epigenomes4040028
Filippov V, Jaceldo-Siegl K, Eroshkin A, Loskutov V, Chen X, Wang C, Duerksen-Hughes PJ. Methylomes in Vegans versus Pescatarians and Nonvegetarians. Epigenomes. 2020; 4(4):28. https://doi.org/10.3390/epigenomes4040028
Chicago/Turabian StyleFilippov, Valery, Karen Jaceldo-Siegl, Alexey Eroshkin, Vasiliy Loskutov, Xin Chen, Charles Wang, and Penelope J. Duerksen-Hughes. 2020. "Methylomes in Vegans versus Pescatarians and Nonvegetarians" Epigenomes 4, no. 4: 28. https://doi.org/10.3390/epigenomes4040028
APA StyleFilippov, V., Jaceldo-Siegl, K., Eroshkin, A., Loskutov, V., Chen, X., Wang, C., & Duerksen-Hughes, P. J. (2020). Methylomes in Vegans versus Pescatarians and Nonvegetarians. Epigenomes, 4(4), 28. https://doi.org/10.3390/epigenomes4040028