BioMed Research International

Research Article

Cross-Omics Comparison of Stress Responses in Mesothelial Cells Exposed to Heat- versus Filter-Sterilized Peritoneal Dialysis Fluids

Table 1

Proteins and transcripts analyzed by 2D-DIGE and mRNA expression microarrays.


Gene name	Gene ID	Protein name	Transcriptomics data					Proteomics data
			RefSeq	Heat/filter				SwissProt entry name	Heat		Filter		Heat/filter
			RefSeq	Mean ratio	SD	CV	Chip CV	SwissProt entry name	Mean spot volume	SD	Mean spot volume	SD	Ratio	value

Increased protein abundance (proteomics ratio > 1)

Increased gene expression (transcriptomics ratio > 1)
HSPA8	3312	Heat shock cognate 71 kDa protein	NM_006597 NM_153201	1.60	0.02	3%	4%	HSP7C_HUMAN	132.893	9.736	112.899	11.838	1.177	0.203
HSPB1	3315	Heat shock protein beta-1	NM_001540	1.32	0.13	17%	4%	HSPB1_HUMAN	207.830	35.162	71.975	17.335	2.888	0.061
GSTP1	2950	Glutathione S-transferase P	NM_000852	1.16	0.04	5%	4%	GSTP1_HUMAN	88.029	66.625	61.654	10.343	1.428	0.562
GSR	2936	Glutathione reductase, mitochondrial	NM_000637	1.19	0.07	9%	0%	GSHR_HUMAN	140.743	12.299	129.512	4.931	1.087	0.438
PDIA3	2923	Protein disulfide-isomerase A3	NM_005313	1.07	0.14	14%	14%	PDIA3_HUMAN	185.997	3.950	125.444	20.051	1.483	0.031
PDIA3	2923	Protein disulfide-isomerase A3	NM_005313	1.07	0.14	14%	14%	PDIA3_HUMAN	147.417	4.727	115.852	16.524	1.272	0.094

Decreased gene expression (transcriptomics ratio < 1)
CCT5	22948	T-complex protein 1 subunit epsilon	NM_012073	0.82	0.09	7%	9%	TCPE_HUMAN	177.988	10.033	122.697	8.415	1.451	0.019
PSMB2	5690	Proteasome subunit beta type-2	NM_002794	0.87	0.09	7%	18%	PSB2_HUMAN	100.167	7.492	83.670	13.559	1.197	0.161
HSPA5	3309	78 kDa glucose-regulated protein	NM_005347	0.81	0.14	11%	4%	GRP78_HUMAN	254.121	5.404	106.676	15.450	2.382	0.001
P4HB	5034	Protein disulfide-isomerase	NM_000918	0.56	0.35	20%	7%	PDIA1_HUMAN	192.710	6.746	112.938	26.334	1.706	0.025
PDIA6	10130	Protein disulfide-isomerase A6	NM_005742	0.65	0.04	2%	4%	PDIA6_HUMAN	125.940	2.434	106.148	11.478	1.186	0.090
COPS4	51138	COP9 signalosome complex subunit 4	NM_016129	0.77	0.11	8%	7%	CSN4_HUMAN	151.484	17.903	108.440	17.368	1.397	0.139
HSPD1	3329	60 kDa heat shock protein, mitochondrial	NM_002156 NM_199440	0.82	0.06	5%	3%	CH60_HUMAN	275.662	1.224	155.233	8.962	1.776	0.001
RPSA	3921	40S ribosomal protein SA	NM_002295	0.75	0.24	18%	0.05	RSSA_HUMAN	111.019	23.693	110.845	9.474	1.002	0.993

Decreased protein abundance (proteomics ratio < 1)

Increased gene expression (transcriptomics ratio > 1)
HSPA9	3313	Stress-70 protein, mitochondrial	NM_004134	1.32	0.07	9%	4%	GRP75_HUMAN	108.049	9.256	123.253	5.843	0.877	0.156
HSPA1A	3303	Heat shock 70 kDa protein 1	NM_005345 NM_005346	2.59	0.07	17%	6%	HSP71_HUMAN	108.049	9.256	123.253	5.843	0.877	0.156
HSPA8	3312	Heat shock cognate 71 kDa protein	NM_006597 NM_153201	1.60	0.02	3%	4%	HSP7C_HUMAN	108.049	9.256	123.253	5.843	0.877	0.156
HSPA1A	3303	Heat shock 70 kDa protein 1	NM_005345 NM_005346	2.59	0.07	17%	6%	HSP71_HUMAN	104.254	14.587	130.041	4.812	0.802	0.091
HSPA8	3312	Heat shock cognate 71 kDa protein	NM_006597 NM_153201	1.60	0.02	3%	4%	HSP7C_HUMAN	106.853	10.219	123.120	6.412	0.868	0.163
HSPA1A	3303	Heat shock 70 kDa protein 1	NM_005345 NM_005346	2.59	0.07	17%	6%	HSP71_HUMAN	87.591	12.214	113.858	5.948	0.769	0.043
G6PD	2539	Glucose-6-phosphate 1-dehydrogenase	NM_000402	1.02	0.08	8%	6%	G6PD_HUMAN	80.836	16.641	121.330	10.229	0.666	0.035
GSTP1	2950	Glutathione S-transferase P	NM_000852	1.16	0.04	5%	4%	GSTP1_HUMAN	65.268	7.174	85.964	20.885	0.759	0.190
CCT2	10576	T-complex protein 1 subunit beta	NM_006431	1.19	0.03	3%	2%	TCPB_HUMAN	104.714	6.378	119.187	12.088	0.879	0.267
TXNRD1	7296	Thioredoxin reductase 1, cytoplasmic	NM_001093771 NM_003330 NM_182729 NM_182742 NM_182743	1.47	0.12	17%	6%	TRXR1_HUMAN	104.714	6.378	119.187	12.088	0.879	0.267
G6PD	2539	Glucose-6-phosphate 1-dehydrogenase	NM_000402	1.02	0.08	8%	6%	G6PD_HUMAN	85.848	8.356	124.140	5.506	0.692	0.005
HSPB1	3315	Heat shock protein beta-1	NM_001540	1.32	0.13	17%	4%	HSPB1_HUMAN	69.930	23.921	86.813	8.060	0.806	0.258
NME1	4830	Nucleoside diphosphate kinase A	NM_000269 NM_198175	1.14	0.08	9%	8%	NDKA_HUMAN	59.789	20.657	144.627	66.411	0.413	0.283

Decreased gene expression (transcriptomics ratio < 1)
CCT7	10574	T-complex protein 1 subunit eta	NM_006429	0.81	0.04	3%	2%	TCPH_HUMAN	95.381	7.459	95.731	10.280	0.996	0.969
PSMA2	5683	Proteasome subunit alpha type-2	NM_002787	0.69	0.15	10%	4%	PSA2_HUMAN	116.477	11.780	148.569	14.466	0.784	0.150
FKBP1A	2280	Peptidyl-prolyl cis-trans-isomerase FKBP1A	NM_054014	0.65	0.26	17%	15%	FKB1A_HUMAN	473.565	141.421	65245.936	99.946	0.007	0.275
PPIA	5478	Peptidyl-prolyl cis-trans-isomerase A	NM_021130	0.86	0.04	4%	6%	PPIA_HUMAN	60.340	16.561	121.603	9.785	0.496	0.005
PCNA	5111	Proliferating cell nuclear antigen	NM_002592 NM_182649	0.46	0.26	12%	7%	PCNA_HUMAN	87.296	8.040	123.909	6.426	0.705	0.008
HADHA	3030	Trifunctional enzyme subunit alpha, mitochondrial	NM_000182	0.85	0.05	4%	5%	ECHA_HUMAN	85.564	23.723	90.073	12.598	0.950	0.798
PPIA	5478	Peptidyl-prolyl cis-trans-isomerase A	NM_021130	0.86	0.04	4%	6%	PPIA_HUMAN	62.919	11.686	115.738	10.498	0.544	0.006
PSMD4	5710	26S proteasome non-ATPase regulatory subunit 4	NM_002810 NR_002319	0.74	0.09	7%	8%	PSMD4_HUMAN	85.455	14.214	148.812	10.063	0.574	0.010
HSPD1	3329	60 kDa heat shock protein, mitochondrial	NM_002156 NM_199440	0.82	0.06	5%	3%	CH60_HUMAN	101.423	11.218	170.552	7.472	0.595	0.005
HSP90B1	7184	Endoplasmin	NM_003299	0.59	0.19	11%	5%	ENPL_HUMAN	92.818	33.376	93.651	22.914	0.991	0.977
HSPA4	3308	Heat shock 70 kDa protein 4	NM_002154	0.68			4%	HSP74_HUMAN	123.829	30.682	141.986	16.324	0.872	0.595

Proteins and transcripts, which could be mapped and analyzed by both proteomics by 2D-DIGE combined with MS protein identification and topic defined mRNA expression microarray analysis (Miltenyi PIQOR toxicology array). Ratio: fold-change of mRNA expression of cells treated with H-PDF versus cells treated with F-PDF as obtained from the PIQOR microarray service. Standard deviation of mRNA expression ratios of cells treated with H-PDF versus cells treated with F-PDF. Coefficient variation: relative standard deviation in percent of mRNA expression ratios of cells treated with H-PDF versus cells treated with F-PDF. Chip CV: the column contains the relative standard deviation in percent for the respective rRNA by the number of multiple features on the microarray () as obtained from the PIQOR microarray service. Mean spot volume: mean of the spot quantification data over the biological replicates within the given groups. Standard deviation of the spot quantification data within the given groups. Ratio: fold-change of protein spot abundance in cells treated with H-PDF versus cells treated with F-PDF as obtained from 2D-DIGE analysis. The column contains the value of the -test comparing relative spot abundance of cells treated with H-PDF versus cells treated with F-PDF. Protein quantifications, reaching the according levels of statistical significance, are marked with asterisks (, , and ) after the protein name.