Functional annotation of the human retinal pigment epithelium transcriptome

Booij, Judith C; van Soest, Simone; Swagemakers, Sigrid MA; Essing, Anke HW; Verkerk, Annemieke JMH; van der Spek, Peter J; Gorgels, Theo GMF; Bergen, Arthur AB

doi:10.1186/1471-2164-10-164

BMC Genomics

Table 2 The thirty most highly expressed genes in macular RPE identified in six different human donors, sorted by intensity in descending order.

From: Functional annotation of the human retinal pigment epithelium transcriptome

gene symbol	Genbank ID	mean intensity μ_int perc	CV perc	gene name	relevant function
KIAA0241	AA205569	99	98	KIAA0241
AI003379	AI003379	99	98	Transcribed locus
ACN9	NM_020186	99	98	ACN9 homolog	gluconeogenesis [25]
MT1A	BG191659	99	98	Metallothionein 1A	protection against reactive oxygen species[22]
SLC17A7	NM_020309	99	98	Solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 7	glutamate transporter, expressed in RPE[14, 15]
TP53	NM_000546	99	98	Tumor protein p53	protection against reactive oxygen species[23]
ELF2	NM_006874	99	98	E74-like factor 2 (ets domain transcription factor)
AI272368	AI272368	99	95	cDNA clone
AA807363	AA807363	99	79	cDNA clone
SERPINB5	NM_002639	99	98	Serpin peptidase inhibitor, clade B, member 5
MCM7	NM_005916	99	97	minichromosome maintenance deficient 7
SLC1A2	NM_004171	99	96	Solute carrier family 1 member 2	glutamate transporter[1]
HBB	NM_000518	99	99	Hemoglobin, beta
PTGDS	NM_000954	99	94	Prostaglandin D2 synthase 21 kDa	released from RPE during rod phagocytosis [17, 19]
T26536	T26536	99	75	cDNA clone
EEF1A1	NM_001402	99	80	Eukaryotic translation elongation factor 1 alpha 1
TTR	NM_000371	99	80	Transthyretin (prealbumin, amyloidosis type I)	maintains normal levels of retinol and retinol binding proteins in plasma [14, 20]
BE260168	BE260168	99	90	cDNA clone
CST3	NM_000099	99	92	Cystatin C	associated with AMD[16, 18]
ZNF503	NM_032772	99	95	Zinc finger protein 503
BG190000	BG190000	99	94	cDNA clone
BE262306	BE262306	99	80	cDNA clone
HSP90B1	NM_003299	99	94	Heat shock protein 90 kDa beta (Grp94), member 1	[21]
GNGT1	NM_021955	99	90	Guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1
RPL3	NM_000967	99	20	Ribosomal protein L3
RPL41	NM_021104	99	23	Ribosomal protein L41
AI857840	AI857840	99	77	cDNA clone
PCSK7	NM_004716	99	90	Proprotein convertase subtilisin/kexin type 7
AL521537	AL521537	99	75	cDNA clone
CLU	NM_001831	99	42	Clusterin	member of complement system [24]

Among these genes we identified five genes with known expression in the RPE (SLC17A7[14], CST3[18], TTR[14], HSP90B1[21] and PTGDS[17]). The SLC17A7 gene is a glutamate transporter, like the SLC1A2 gene which is also in the top 30 highly expressed genes. The CST3 gene was previously suggested to have an association with AMD[16, 17]. The list also contains two genes with a role in the protection against oxidative stress (MT1A[22], TP53[23]). The GNGT1 gene, expressed in photoreceptors[30], suggests the inevitable presence of photoreceptor contamination. Perc: percentile.

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ISSN: 1471-2164

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