DNA methylation signature of human hippocampus in Alzheimer’s disease is linked to neurogenesis

Altuna, Miren; Urdánoz-Casado, Amaya; Sánchez-Ruiz de Gordoa, Javier; Zelaya, María V.; Labarga, Alberto; Lepesant, Julie M. J.; Roldán, Miren; Blanco-Luquin, Idoia; Perdones, Álvaro; Larumbe, Rosa; Jericó, Ivonne; Echavarri, Carmen; Méndez-López, Iván; Di Stefano, Luisa; Mendioroz, Maite

doi:10.1186/s13148-019-0672-7

Clinical Epigenetics

Table 1 Differentially methylated positions (DMPs) in AD hippocampus measured by 450K Illumina BeadChip array

From: DNA methylation signature of human hippocampus in Alzheimer’s disease is linked to neurogenesis

DMPs	Genomic coordinates		Beta. difference	FDR p value	GeneID1	GeneID2	Neurogenesis-related	Neurogenesis-related PMID
cg02091185	5	170288766	0.198	0.003	RANBP17		No
cg07333191	4	13526769	0.168	0.002	RAB28	NKX3-2	No
cg14780466	2	20870812	0.150	0.011	GDF7	APOB	Yes	17293457	22897442
cg04370442	16	58019866	0.147	0.013	TEPP	ZNF319	No
cg16867657	6	11044877	0.145	0.002	ELOVL2		No
cg04154027	5	78985588	0.144	0.002	CMYA5		No
cg19506623	2	161265259	0.143	0.036	RBMS1	ITGB6	No
cg04498198	17	27899966	0.140	0.002	TP53I13	GIT1	Yes		25792865
cg23077820	2	223154176	0.140	0.002	PAX3	EPHA4	Yes	26287727	25978062
cg11015251	7	27170554	0.138	0.005	HOXA4		No
cg16258854	2	20648194	0.138	0.005	RHOB	HS1BP3	Yes	15306568
cg01463828	8	22446721	0.137	0.007	PDLIM2		No
cg13935577	12	107974897	0.136	0.008	BTBD11	PWP1	No
cg12100751	1	109203672	0.134	0.002	HENMT1		No
cg19022697	1	55247140	0.133	0.004	PARS2	DHCR24	Yes	29410512	24842139
cg25840926	2	20647987	0.133	0.002	RHOB	HS1BP3	Yes	15306568
cg22962123	7	27153605	0.131	0.008	HOXA3	HOXA2	Yes	12954718	10230789
cg05637536	1	154475068	0.130	0.002	TDRD10		No
cg01331772	2	131094827	0.129	0.002	IMP4		No
cg23279355	5	78985592	0.128	0.002	CMYA5		No
cg01579024	5	170288757	0.127	0.013	RANBP17		No
cg15548613	22	38610795	0.127	0.002	MAFF	TMEM184B	No
cg13172549	7	27153636	0.125	0.019	HOXA3	HOXA2	Yes	12954718	10230789
cg02231404	20	62679635	0.124	0.008	SOX18		Yes	29666335
cg13327545	10	22623548	0.124	0.002	SPAG6	BMI1	Yes	29666335	19212323
cg18247055	10	22634226	0.122	0.003	SPAG6		Yes	26130477
cg00921266	7	27153663	0.122	0.039	HOXA3	HOXA2	Yes	12954718	10230789
cg09490371	2	233253024	0.120	0.011	ECEL1P2	ALPP	No
cg17448336	3	147141588	0.119	0.047	ZIC1		Yes	17507568
cg16127683	15	40268777	0.119	0.021	EIF2AK4	SRP14	No
cg25774643	11	627175	0.119	0.028	SCT	CDHR5	Yes	21159798
cg18121224	5	176559563	0.119	0.010	NSD1		No
cg07816556	6	26017280	0.119	0.004	HIST1H4A	HIST1H3A	No
cg16308533	17	40838983	0.118	0.004	CNTNAP1	EZH1	Yes	26740489	23932971
cg04533276	22	19709548	0.117	0.007	SEPT5	GP1BB	Yes	17935997
cg22900415	13	20736075	0.117	0.010	GJA3		No
cg22385702	2	45175881	0.116	0.025	SIX3	SIX2	Yes	17576749	11401394
cg09655403	5	78985495	0.116	0.004	CMYA5		No
cg22507154	1	91185233	0.116	0.016	BARHL2		Yes	22307612
cg24369989	15	78933807	0.115	0.002	CHRNB4		No
cg16404157	14	38724648	0.115	0.010	CLEC14A		No
cg03146625	12	54448729	0.115	0.018	HOXC4	SMUG1	No
cg04027736	7	27143403	0.115	0.011	HOXA2		Yes	10230789
cg12024906	19	37825679	0.115	0.005	HKR1		No
cg00303378	1	159825552	0.115	0.002	VSIG8	C1orf204	No
cg17508941	7	19183280	0.114	0.002	TWIST1	FERD3L	Yes	23555309	23254923
cg24079702	2	106015771	0.114	0.005	FHL2		No
cg15084543	1	79472408	0.113	0.006	ELTD1		No
cg25738176	17	3848506	0.113	0.033	ATP2A3	P2RX1	No
cg20864214	11	73054121	0.113	0.018	RELT	ARHGEF17	No
cg06452665	13	43148436	0.113	0.010	TNFSF11		Yes	24087792
cg21572722	6	11044894	0.113	0.003	ELOVL2		No
cg26092675	6	26225258	0.112	0.002	HIST1H3E		No
cg07336350	16	54322127	0.111	0.013	IRX3		Yes	10704856
cg07809484	19	51231968	0.111	0.002	GPR32	CLEC11A	No
cg16651126	7	27170552	0.111	0.007	HOXA4		No
cg05726109	22	19709755	0.111	0.007	SEPT5	GP1BB	Yes	17935997
cg07584855	1	221055545	0.110	0.007	HLX	DUSP10	Yes	7907015	19139271
cg14566959	5	140772681	0.110	0.006	PCDHGA4		No
cg02798280	19	39087135	0.110	0.007	MAP4K1	RYR1	No		17767953
cg24756378	14	33401638	0.110	0.027	NPAS3	AKAP6	Yes	21709683
cg11864574	10	22635028	0.110	0.015	SPAG6		Yes	29666335
cg06555959	8	61835620	0.110	0.050	CLVS1	CHD7	Yes		23827709
cg12253175	12	58132093	0.110	0.029	AGAP2		No
cg15834355	12	54442075	0.110	0.014	HOXC4	HOXC5	Yes		23103965
cg09596958	12	58132105	0.109	0.031	AGAP2		No
cg02267270	6	37616410	0.109	0.047	MDGA1	CCDC167	Yes	21104742
cg18181229	1	164545699	0.109	0.016	PBX1	LMX1A	Yes	27226325	24172139
cg01421119	1	211555733	0.109	0.019	TRAF5	RD3	No
cg03729251	4	151501035	0.108	0.012	LRBA	MAB21L2	Yes		11960703
cg22090150	17	4098227	0.107	0.002	ANKFY1	CYB5D2	No
cg05877788	17	27899874	0.107	0.003	TP53I13	GIT1	Yes		25792865
cg06396119	13	49792767	0.106	0.025	MLNR		No
cg22154659	7	27134369	0.106	0.015	HOXA1	SKAP2	Yes	14522873
cg14266527	4	151501298	0.106	0.004	LRBA	MAB21L2	Yes		11960703
cg24177393	5	43037517	0.105	0.033	SEPP1	ZNF131	No
cg07942135	7	27154262	0.105	0.022	HOXA3	HOXA2	Yes	12954718	10230789
cg22904711	19	44278628	0.105	0.041	KCNN4	SMG9	No
cg01566965	4	174447847	0.104	0.028	HAND2	SCRG1	Yes	22323723
cg14557699	5	140254909	0.104	0.002	PCDHA12		No
cg26698460	19	58716004	0.104	0.010	ZNF274	ZNF544	No
cg02287710	14	102027660	0.103	0.004	DIO3		Yes	27707971
cg21415530	8	140715802	0.103	0.010	KCNK9		No
cg07589899	2	62020677	0.103	0.002	XPO1	FAM161A	No
cg20192747	18	44774846	0.103	0.003	SKOR2		Yes	24491816
cg17179862	17	46681362	0.103	0.003	HOXB6	LOC404266	Yes	10686603
cg26587870	6	27730563	0.103	0.010	ZNF184	HIST1H2BL	No
cg01089914	2	218843229	0.102	0.017	RUFY4	TNS1	No
cg14962509	1	36039655	0.102	0.004	TFAP2E		No
cg21869609	19	2291613	0.102	0.018	LINGO3		Yes	18297755
cg08865099	7	27281581	0.102	0.043	EVX1		Yes	10399918
cg13836098	6	26225268	0.102	0.002	HIST1H3E		No
cg00611789	5	78985432	0.102	0.011	CMYA5		No
cg13771313	11	72533295	0.102	0.017	ATG16L2	FCHSD2	No
cg21811021	4	6659346	0.101	0.015	S100P	MRFAP1	No
cg11254700	19	53561386	0.101	0.020	ERVV-2	ZNF160	No
cg14557202	12	54764371	0.101	0.028	ZNF385A	GPR84	No
cg03422911	1	237205295	0.101	0.004	RYR2		Yes	17767953
cg19153828	2	127782651	0.101	0.009	BIN1	GYPC	No
cg06867571	11	65306934	0.101	0.019	LTBP3	SCYL1	No
cg09317554	4	151505084	0.101	0.014	LRBA	MAB21L2	Yes		11960703
cg05404236	13	110437093	0.100	0.017	IRS2		Yes	28833887
cg02771117	8	11279352	− 0.100	0.022	FAM167A	BLK	No
cg10373891	13	52338758	− 0.101	0.017	DHRS12	WDFY2	No
cg24607755	11	36171375	− 0.102	0.010	LDLRAD3	PRR5L	No
cg20102280	13	47470793	− 0.102	0.004	HTR2A		No
cg21735068	8	97975467	− 0.104	0.015	PGCP	TSPYL5	Yes		26911678
cg23907053	12	70215816	− 0.107	0.015	RAB3IP	MYRFL	No
cg14701867	10	64193068	− 0.107	0.023	ZNF365	ADO	No
cg14830371	8	25991602	− 0.108	0.027	PPP2R2A	EBF2	Yes		25762221
cg16668651	15	81316319	− 0.110	0.035	IL16	MESDC2	No
cg06688910	8	122466955	− 0.110	0.027	SNTB1	HAS2	No
cg07463059	1	158979810	− 0.119	0.010	IFI16		No
cg05165025	14	74253312	− 0.119	0.046	PTGR2	ELMSAN1	No
cg07677157	12	66050928	− 0.133	0.026	HMGA2	MSRB3	Yes	18640244
cg11236550	1	167090757	− 0.138	0.012	DUSP27	POU2F1	No		18241856
cg20597486	1	158979841	− 0.151	0.002	IFI16		No
cg19987768	17	750306	− 0.162	0.043	NXN	GLOD4	Yes	29037191

The table shows 118 DMPs with β-difference > 0.100, prioritized by beta difference (delta) criteria. FDR false discovery rate, Adj. adjusted, ID identification, PMID PubMed identification. Each probe (CpG site) was annotated by UCSC hg19 build. The last two columns show the PMID of papers supporting the involvement of the genes into neurogenesis or neural development

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