Weight loss after Roux-En-Y gastric bypass surgery reveals skeletal muscle DNA methylation changes

Garcia, Luis A.; Day, Samantha E.; Coletta, Richard L.; Campos, Baltazar; Benjamin, Tonya R.; De Filippis, Eleanna; Madura, James A.; Mandarino, Lawrence J.; Roust, Lori R.; Coletta, Dawn K.

doi:10.1186/s13148-021-01086-6

Clinical Epigenetics

Table 2 Differentially methylated cytosines (DMCs; q < 0.05) decreased post-surgery versus pre-surgery

From: Weight loss after Roux-En-Y gastric bypass surgery reveals skeletal muscle DNA methylation changes

Chr	Position	Gene	Pre-surgery methylation %	Post-surgery methylation %	P value	q value	Genic region	CpG region
chr19	9,271,227	ZNF317	99.54 ± 0.46	88.87 ± 2.27	8.86E−09	0.0020	Exon	CpG_Island
chrX	41,782,532	CASK	36.44 ± 4.47	7.49 ± 1.49	1.61E−08	0.0028	Promoter	CpG_Island
chr9	134,346,329	PRRC2B	99.15 ± 0.57	86.92 ± 2.80	1.69E−08	0.0028	Exon	InterCpgi
chr15	101,420,903	ALDH1A3	81.98 ± 2.87	58.77 ± 5.28	3.90E−08	0.0050	Intron	CpG_Island
chr3	13,696,951	LOC285375	9.02 ± 2.58	0 ± 0	3.63E−08	0.0050	Intergenic	CpG_Island
chr11	70,008,217	ANO1	99.47 ± 0.53	82.21 ± 2.68	6.57E−08	0.0079	Intron	InterCpgi
chr5	9,509,512	SEMA5A	100 ± 0	91.29 ± 2.45	8.58E−08	0.0091	utr5	InterCpgi
chr19	48,824,452 ≠	CCDC114	79.96 ± 2.47	52.67 ± 3.92	1.11E−07	0.0105	Promoter	North_shore
chr19	48,824,452 ≠	EMP3	79.96 ± 2.47	52.67 ± 3.92	1.11E−07	0.0105	Promoter	North_shore
chr15	76,634,525	ISL2	6.79 ± 1.30	0 ± 0	1.09E−07	0.0105	utr3	CpG_Island
chr16	1,774,262	MAPK8IP3	96.07 ± 0.89	86.94 ± 2.61	1.36E−07	0.0116	Intron	InterCpgi
chr15	62,457,572	C2CD4B	52.02 ± 4.77	15.90 ± 4.03	1.48E−07	0.0122	Promoter	CpG_Island
chr16	89,687,436	DPEP1	74.63 ± 2.21	46.44 ± 4.95	1.80E−07	0.0135	utr5	InterCpgi
chr17	45,330,989	ITGB3	13.64 ± 2.74	0.51 ± 0.51	1.96E−07	0.0135	Promoter	CpG_Island
chr9	104,075,142	LPPR1	100 ± 0	82.89 ± 5.22	2.13E−07	0.0135	Exon	InterCpgi
chr16	30,990,627	SETD1A	86.89 ± 3.56	57.56 ± 5.29	1.84E−07	0.0135	Exon	North_shore
chr12	54,345,965	HOXC12	15.68 ± 1.11	3.11 ± 1.14	2.69E−07	0.0159	Intergenic	South_shore
chr19	619,189	POLRMT	99.40 ± 0.6	91.17 ± 1.00	3.34E−07	0.0188	Intron	CpG_Island
chr11	628,172^‡	CDHR5	100 ± 0	89.48 ± 2.13	3.74E−07	0.0192	Promoter	South_shore
chr11	628,172^‡	SCT	100 ± 0	89.48 ± 2.13	3.74E−07	0.0192	Promoter	South_shore
chr10	88,269,670	WAPAL	99.68 ± 0.32	91.58 ± 1.90	3.76E−07	0.0192	Intron	InterCpgi
chr1	235,979,239	LYST	42.96 ± 5.36	15.09 ± 3.25	3.94E−07	0.0197	Intron	InterCpgi
chr19	50,098,039	PRR12	87.92 ± 1.83	67.43 ± 3.66	4.39E−07	0.0216	Exon	CpG_Island
chr8	101,723,031	PABPC1	83.96 ± 3.70	42.12 ± 5.68	4.62E−07	0.0219	Intron	InterCpgi
chr15	23,932,055	NDN	39.77 ± 5.54	14.89 ± 3.47	4.81E−07	0.0222	Exon	CpG_Island
chr5	1,491,652	LPCAT1	98.22 ± 1.19	79.85 ± 3.10	5.04E−07	0.0226	Intron	South_shore
chr11	61,486,429	DAGLA	58.08 ± 3.83	34.62 ± 3.51	5.53E−07	0.0241	utr5	North_shore
chr3	126,746,778	PLXNA1	100 ± 0	87.57 ± 1.95	5.87E−07	0.0251	Intron	North_shore
chr15	23,892,609	MAGEL2	54.77 ± 8.17	19.70 ± 3.99	6.66E−07	0.0276	Exon	InterCpgi
chr4	111,553,834	PITX2	88.67 ± 3.28	55.56 ± 9.64	7.47E−07	0.0297	Intron	CpG_Island
chr17	79,497,291	FSCN2	57.24 ± 5.14	29.65 ± 3.61	8.94E−07	0.0308	Intron	South_shore
chr14	24,666,733	TM9SF1	93.83 ± 2.06	71.93 ± 3.85	8.75E−07	0.0308	Promoter	South_shore
chr21	43,859,102	UBASH3A	86.97 ± 2.24	68.44 ± 4.45	8.62E−07	0.0308	Intron	InterCpgi
chrX	152,600,028	ZNF275	48.08 ± 2.35	25.34 ± 3.90	8.31E−07	0.0308	utr5	CpG_Island
chr4	3,678,810	LOC100133461	93.87 ± 2.40	63.82 ± 6.14	9.43E−07	0.0317	Intergenic	InterCpgi
chr13	67,135,465	PCDH9	98.97 ± 0.50	89.39 ± 1.64	1.14E−06	0.0370	Intron	InterCpgi
chrX	10,188,915	CLCN4	100 ± 0	91.75 ± 2.13	1.42E−06	0.0419	Exon	InterCpgi
chr18	34,274,365	FHOD3	59.66 ± 4.19	34.53 ± 3.20	1.51E−06	0.0429	Intron	InterCpgi
chr20	62,329,849	TNFRSF6B	76.74 ± 2.63	57.78 ± 4.65	1.62E−06	0.0448	Exon	South_shore
chr15	101,421,027	ALDH1A3	79.81 ± 3.85	54.34 ± 5.33	2.04E−06	0.0479	Intron	CpG_Island
chr20	3,778,167	CDC25B	95.43 ± 1.99	75.05 ± 3.37	1.90E−06	0.0479	utr5	South_shore
chr7	27169037^{^}	HOXA3	94.58 ± 1.54	78.97 ± 4.24	1.96E−06	0.0479	Exon	North_shore
chr7	27169037^{^}	HOXA4	94.58 ± 1.54	78.97 ± 4.24	1.96E−06	0.0479	Exon	north_shore
chr6	100,906,424	SIM1	49.04 ± 2.93	18.82 ± 4.42	2.00E−06	0.0479	Intron	CpG_Island
chr22	19,747,159	TBX1	44.30 ± 4.95	22.56 ± 2.96	2.14E−06	0.0498	utr5	South_shore

Data are mean ± SEM. The P value is calculated from the MethylSig analysis. The q value is generated by Benjamini–Hochberg multiple testing correction
^‡Two genes [SCT and CDHR5] are associated with the same differentially methylated cytosine [Chr11:628172]; ≠ Two genes [EMP3 and CCDC114] are associated with the same differentially methylated cytosine [Chr19: 48824452]
^≠ Two genes [EMP3 and CCDC114] are associated with the same differentially methylated cytosine [Chr19: 48824452]
^{^}Two genes [HOXA3 and HOXA4] are associated with the same differentially methylated cytosine [Chr7: 27169037]

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ISSN: 1868-7083

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