The transcriptome of peripheral blood mononuclear cells in patients with clinical subtypes of late age-related macular degeneration

Subhi, Yousif; Nielsen, Marie Krogh; Molbech, Christopher Rue; Liisborg, Charlotte; Søndergaard, Helle Bach; Sellebjerg, Finn; Sørensen, Torben Lykke

doi:10.1186/s12979-019-0160-0

Table 2 Significantly differentially expressed genes in peripheral blood mononuclear cells of patients with different clinical subtypes of late AMD

From: The transcriptome of peripheral blood mononuclear cells in patients with clinical subtypes of late age-related macular degeneration

Gene name	Description	FC %	P-value
Patients with GA
SNORA14A	small nucleolar RNA, H/ACA box 14A	101	0.031
USP32P1	ubiquitin specific peptidase 32 pseudogene 1	67	< 0.001
SLC14A1	solute carrier family 14 (urea transporter), member 1 (Kidd blood group)	62	0.002
MIR4516	microRNA 4516	59	0.020
DDA1	DET1 and DDB1 associated 1	46	0.033
MIR3665	microRNA 3665	44	< 0.001
SNORA49	small nucleolar RNA, H/ACA box 49	43	0.025
MIR4509–1	microRNA 4509–1	39	0.024
TMEM120A	transmembrane protein 120A	38	0.004
LY6E	lymphocyte antigen 6 complex, locus E	35	0.021
IFITM1	interferon induced transmembrane protein 1	35	0.033
CSNK1G2	casein kinase 1, gamma 2	34	0.015
NINJ1	ninjurin 1	33	0.003
HSH2D	hematopoietic SH2 domain containing	33	0.009
GIMAP1-GIMAP5	GIMAP1-GIMAP5 readthrough	32	0.030
LINC01000	long intergenic non-protein coding RNA 1000	32	0.026
SNORD88A	small nucleolar RNA, C/D box 88A	32	0.014
CAMKK2	calcium/calmodulin-dependent protein kinase kinase 2, beta	32	0.049
KRT73	keratin 73, type II	32	0.034
SDF4	stromal cell derived factor 4	31	0.012
CD247	CD247 molecule	31	0.042
TMSB4XP4	thymosin beta 4, X-linked pseudogene 4	31	0.026
CD200R1	CD200 receptor 1	31	0.032
CISH	cytokine inducible SH2-containing protein	31	0.011
MX2	MX dynamin-like GTPase 2	30	0.035
MICALCL	MICAL C-terminal like	30	0.026
CD5	CD5 molecule	30	0.037
C15orf54	chromosome 15 open reading frame 54	− 108	0.008
RNU4ATAC	RNA, U4atac small nuclear (U12-dependent splicing)	− 91	0.031
LOC105370195	uncharacterized LOC105370195	− 89	0.012
MYCT1	myc target 1	−67	0.011
MS4A1	membrane-spanning 4-domains, subfamily A, member 1	−64	0.045
LOC105377384	uncharacterized LOC105377384	−56	0.034
OR2L1P	olfactory receptor, family 2, subfamily L, member 1 pseudogene	−55	0.006
LOC105379818	uncharacterized LOC105379818	−51	0.021
CD1C	CD1c molecule	−49	0.001
LOC105369884	uncharacterized LOC105369884	−49	0.002
LOC102724714	uncharacterized LOC102724714	−47	0.030
RSU1	Ras suppressor protein 1	−47	0.010
TNFSF4	tumor necrosis factor (ligand) superfamily, member 4	−46	0.028
SNORD42A	small nucleolar RNA, C/D box 42A	−45	0.026
WDR11-AS1	WDR11 antisense RNA 1	− 43	0.025
LINC00989	long intergenic non-protein coding RNA 989	−43	0.043
CRYZ	crystallin zeta	−43	0.016
DNM3	dynamin 3	−43	0.012
LINC00266–1	long intergenic non-protein coding RNA 266–1	−42	0.021
SLFN14	schlafen family member 14	−40	0.029
HIST1H2BC	histone cluster 1, H2bc	−38	0.016
GFI1B	growth factor independent 1B transcription repressor	−37	0.016
PF4	platelet factor 4	−37	0.015
PPIAL4A	peptidylprolyl isomerase A (cyclophilin A)-like 4A	−36	0.041
SENCR	smooth muscle and endothelial cell enriched migration/differentiation-associated lncRNA	−36	0.002
LOC101928979	uncharacterized LOC101928979	−35	0.023
MIR1321	microRNA 1321	−34	0.016
CTTN	cortactin	−33	0.033
GRB14	growth factor receptor bound protein 14	−32	0.008
PCYT1B	phosphate cytidylyltransferase 1, choline, beta	−32	0.028
P2RY1	purinergic receptor P2Y, G-protein coupled, 1	−32	0.011
KCNQ5-IT1	KCNQ5 intronic transcript 1	−32	0.037
FAM111B	family with sequence similarity 111, member B	−32	0.014
GUSBP1	glucuronidase, beta pseudogene 1	−31	0.033
LIMS1	LIM and senescent cell antigen-like domains 1	−31	0.016
Patients with nAMD
OSBP2	oxysterol binding protein 2	151	0.002
IGHV1OR21–1	immunoglobulin heavy variable 1/OR21–1 (non-functional)	106	0.013
ANK1	ankyrin 1, erythrocytic	83	0.002
PITHD1	PITH (C-Terminal Proteasome-Interacting Domain Of Thioredoxin-Like) Domain Containing 1	82	0.009
MIR4644	microRNA 4644	64	0.027
MARCH8	membrane associated ring finger 8	61	0.001
PAGE2B	P antigen family, member 2B	60	0.009
TMOD1	tropomodulin 1	60	0.013
HBD	hemoglobin, delta	56	0.003
LOC401127	WD repeat domain 5 pseudogene	51	0.018
RHD	Rh blood group, D antigen	48	0.036
TRBV7–4	T cell receptor beta variable 7–4 (gene/pseudogene)	48	0.001
USP32P1	ubiquitin specific peptidase 32 pseudogene 1	47	0.038
FAM210B	family with sequence similarity 210, member B	47	0.027
BPGM	2,3-bisphosphoglycerate mutase	47	0.040
FECH	ferrochelatase	45	0.009
LINC01291	long intergenic non-protein coding RNA 1291	44	< 0.001
HBM	hemoglobin, mu	43	0.015
MMP8	matrix metallopeptidase 8	43	0.004
DCAF12	DDB1 and CUL4 associated factor 12	41	0.044
FAM46C	family with sequence similarity 46, member C	40	0.043
LTF	lactotransferrin	39	0.001
PGLYRP1	peptidoglycan recognition protein 1	37	0.007
CAMP	cathelicidin antimicrobial peptide	35	0.010
SLC25A39	solute carrier family 25, member 39	34	0.010
SLC14A1	solute carrier family 14 (urea transporter), member 1 (Kidd blood group)	34	0.013
SLC25A37	solute carrier family 25 (mitochondrial iron transporter), member 37	32	0.009
SLC4A1	solute carrier family 4 (anion exchanger), member 1 (Diego blood group)	31	0.001
IFIT1B	interferon-induced protein with tetratricopeptide repeats 1B	31	0.002
AHSP	alpha hemoglobin stabilizing protein	31	0.015
ALAS2	5-aminolevulinate synthase 2	30	0.001
RNU4ATAC	RNA, U4atac small nuclear (U12-dependent splicing)	− 125	0.002
SNORD3C	small nucleolar RNA, C/D box 3C	−66	0.028
ADAM28	ADAM metallopeptidase domain 28	− 48	0.017
RNU5E-1	RNA, U5E small nuclear 1	−42	0.044
SNORD12C	small nucleolar RNA, C/D box 12C	−41	0.026
FRG1JP	FSHD region gene 1 family member J, pseudogene	−37	0.005
MIR1537	microRNA 1537	−36	0.025
CD1C	CD1c molecule	−34	0.004
SNAR-G2	small ILF3/NF90-associated RNA G2	− 34	0.018
LOC105374775	uncharacterized LOC105374775	−31	0.033
Patients with PCV
TRIM48	tripartite motif containing 48	146	0.040
LOC105373103	uncharacterized LOC105373103	54	0.026
TRAJ13	T cell receptor alpha joining 13	45	0.046
SLC14A1	solute carrier family 14 (urea transporter), member 1 (Kidd blood group)	44	0.040
IGKV1–12	immunoglobulin kappa variable 1–12	42	0.024
LTF	lactotransferrin	41	0.050
TRAV8–4	T cell receptor alpha variable 8–4	40	0.041
IGHG4	immunoglobulin heavy constant gamma 4 (G4 m marker)	37	0.021
IGKV2D-24	immunoglobulin kappa variable 2D-24 (non-functional)	34	0.024
SNORA71D	small nucleolar RNA, H/ACA box 71D	34	0.013
FAR2P3	fatty acyl-CoA reductase 2 pseudogene 3	30	0.011
LOC101928215	uncharacterized LOC101928215	−81	0.001
SNORD117	small nucleolar RNA, C/D box 117	− 76	0.017
SNORD63	small nucleolar RNA, C/D box 63	−73	0.017
SCARNA9L	small Cajal body-specific RNA 9-like	−63	0.028
SNORD14E	small nucleolar RNA, C/D box 14E	−62	0.004
SNORD59B	small nucleolar RNA, C/D box 59B	−61	0.032
ZEB2	zinc finger E-box binding homeobox 2	−58	0.044
LOC105370515	uncharacterized LOC105370515	−48	0.017
H1F0	H1 histone family, member 0	−47	0.017
USP12-AS1	USP12 antisense RNA 1	−47	0.023
TRAJ56	T cell receptor alpha joining 56	−46	0.001
CD1C	CD1c molecule	−42	0.001
RNVU1–15	RNA, variant U1 small nuclear 15	−42	0.008
LOC728093	putative POM121-like protein 1-like	−41	0.045
LOC105374775	uncharacterized LOC105374775	−40	0.010
LOC105375566	uncharacterized LOC105375566	−39	0.035
LOC101927770	uncharacterized LOC101927770	−36	0.030
FLT3	fms-related tyrosine kinase 3	−35	0.011
OR2L1P	olfactory receptor, family 2, subfamily L, member 1 pseudogene	−34	0.030
LOC100272216	uncharacterized LOC100272216	−34	0.028
MERTK	MER proto-oncogene, tyrosine kinase	−34	0.023
MIR486–2	microRNA 486–2	−33	0.029
NFKBIZ	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta	−33	0.046
LOC105378488	uncharacterized LOC105378488	−33	0.017
MIR3160–1	microRNA 3160–1	−32	0.004
YPEL5	yippee like 5	−32	0.002
NLRP3	NLR family, pyrin domain containing 3	−31	0.035
SNORA7B	small nucleolar RNA, H/ACA box 7B	−31	0.045
HIST1H2BN	histone cluster 1, H2bn	−31	0.018
LOC101929516	uncharacterized LOC101929516	−30	0.049

Abbreviations: FC Fold change, GA Geographic atrophy, nAMD Neovascular age-related macular degeneration, PCV Polypoidal choroidal vasculopathy

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