Parallel mRNA, proteomics and miRNA expression analysis in cell line models of the intestine

Table 1 Twenty-seven downregulated proteins with no DE mRNA targeted by 19 upregulated miRNAs

Protein					microRNA
Uniprot	Symbol	Title	Linear FC	Adj. P value	miRBase ID	logFC	LinFC	AveExpr	P value	Adj. P value
Q09666	AHNAK	Neuroblast differentiation-associated protein AHNAK	1.66	0.02036	hsa-miR-30b	1.39	2.62	10.38	5.04E-04	0.011296975
					hsa-miR-30d	1.36	2.56	11.05	1.17E-04	0.003668745
					hsa-miR-372	12.21	4743.91	7.03	6.55E-11	2.27E-07
					hsa-miR-373	12.12	4451.32	7.23	2.25E-11	1.88E-07
P04075	ALDOA	Fructose-bisphosphate aldolase A	2.03	0.00001	hsa-miR-122	5.85	57.63	5.04	3.71E-05	0.001621788
P50995	ANXA11	Annexin A11	4.57	0.00012	hsa-miR-182	1.09	2.13	12.01	2.48E-04	0.006341084
Q14444	CAPRIN1	Caprin-1	1.42	0.00658	hsa-miR-28-5p	1.16	2.24	9.32	7.05E-05	0.002531521
					hsa-miR-320a	1.46	2.76	12.49	2.74E-05	0.001333363
					hsa-miR-320b	1.46	2.76	12.49	4.80E-05	0.001959043
					hsa-miR-320c	1.46	2.74	12.35	5.43E-05	0.002111768
					hsa-miR-371-5p	11.89	3799.61	7.79	1.04E-10	2.62E-07
P23528	CFL1	Cofilin-1	1.53	0.00962	hsa-miR-182	1.09	2.13	12.01	2.48E-04	0.006341084
P62633	CNBP	Cellular nucleic acid-binding protein	1.79	0.00064	hsa-miR-320a	1.46	2.76	12.49	2.74E-05	0.001333363
					hsa-miR-320b	1.46	2.76	12.49	4.80E-05	0.001959043
					hsa-miR-320c	1.46	2.74	12.35	5.43E-05	0.002111768
Q14247	CTTN	Src substrate cortactin	1.33	0.00716	hsa-miR-182	1.09	2.13	12.01	2.48E-04	0.006341084
P68104	EEF1A1	Elongation factor 1-alpha 1	1.46	0.01148	hsa-miR-371-5p	11.89	3799.61	7.79	1.04E-10	2.62E-07
P06733	ENO1	Alpha-enolase	2.06	0.00015	hsa-miR-22	1.96	3.9	10.84	1.01E-04	0.003309338
Q96AE4	FUBP1	Far upstream element-binding protein 1	2.17	0.00290	hsa-miR-155	1.85	3.61	9.51	5.54E-05	0.002127503
P22626	HNRNPA2B1	Heterogeneous nuclear ribonucleoproteins A2/B1	1.72	0.00053	hsa-miR-371-5p	11.89	3799.61	7.79	1.04E-10	2.62E-07
Q00839	HNRNPU	Heterogeneous nuclear ribonucleoprotein U	4.51	0.00152	hsa-miR-92b	1.22	2.33	6.95	4.51E-04	0.010275397
					hsa-miR-122	5.85	57.63	5.04	3.71E-05	0.001621788
P31153	MAT2A	S-adenosylmethionine synthase isoform type-2	1.92	0.00023	hsa-miR-30b	1.39	2.62	10.38	5.04E-04	0.011296975
					hsa-miR-30d	1.36	2.56	11.05	1.17E-04	0.003668745
Q15233	NONO	Non-POU domain-containing octamer-binding protein	2.74	0.00522	hsa-miR-320a	1.46	2.76	12.49	2.74E-05	0.001333363
					hsa-miR-320b	1.46	2.76	12.49	4.80E-05	0.001959043
					hsa-miR-320c	1.46	2.74	12.35	5.43E-05	0.002111768
P06748	NPM1	Nucleophosmin	1.51	0.01869	hsa-miR-182	1.09	2.13	12.01	2.48E-04	0.006341084
P30101	PDIA3	Protein disulfide-isomerase A3	1.84	0.00465	hsa-miR-155	1.85	3.61	9.51	5.54E-05	0.002127503
P13667	PDIA4	Protein disulfide-isomerase A4	1.74	0.00006	hsa-miR-378	1.35	2.55	11.31	7.79E-05	0.002720502
					hsa-miR-378c	1.17	2.25	10.21	5.74E-04	0.012576882
					hsa-miR-378i	0.85	1.80	9.00	7.98E-04	0.01627753
O15212	PFDN6	Prefoldin subunit 6	2.26	0.02810	hsa-miR-22	1.96	3.90	10.84	1.01E-04	0.003309338
P14618	PKM	Pyruvate kinase PKM	1.91	0.00020	hsa-miR-122	5.85	57.63	5.04	3.71E-05	0.001621788
P62491	RAB11A	Ras-related protein Rab-11A	1.74	0.00318	hsa-miR-138	5.84	57.23	4.36	6.08E-08	2.62E-05
					hsa-miR-30b	1.39	2.62	10.38	5.04E-04	0.011296975
					hsa-miR-30d	1.36	2.56	11.05	1.17E-04	0.003668745
					hsa-miR-320a	1.46	2.76	12.49	2.74E-05	0.001333363
					hsa-miR-320b	1.46	2.76	12.49	4.80E-05	0.001959043
					hsa-miR-320c	1.46	2.74	12.35	5.43E-05	0.002111768
					hsa-miR-371-5p	11.89	3799.61	7.79	1.04E-10	2.62E-07
					hsa-miR-372	12.21	4743.91	7.03	6.55E-11	2.27E-07
					hsa-miR-373	12.12	4451.32	7.23	2.25E-11	1.88E-07
Q09028	RBBP4	Histone-binding protein RBBP4	1.76	0.00339	hsa-miR-138	5.84	57.23	4.36	6.08E-08	2.62E-05
					hsa-miR-138	5.84	57.23	4.36	6.08E-08	2.62E-05
					hsa-miR-182	1.09	2.13	12.01	2.48E-04	0.006341084
					hsa-miR-371-5p	11.89	3799.61	7.79	1.04E-10	2.62E-07
Q9UHD8	9-Sep	Septin-9	1.98	0.00016	hsa-miR-182	1.09	2.13	12.01	2.48E-04	0.006341084
Q8NC51	SERBP1	Plasminogen activator inhibitor 1 RNA-binding protein	2.35	0.00473	hsa-miR-130b	1.77	3.42	11.03	2.57E-05	0.00127274
					hsa-miR-155	1.85	3.61	9.51	5.54E-05	0.002127503
					hsa-miR-320a	1.46	2.76	12.49	2.74E-05	0.001333363
					hsa-miR-320b	1.46	2.76	12.49	4.80E-05	0.001959043
					hsa-miR-320c	1.46	2.74	12.35	5.43E-05	0.002111768
P29401	TKT	Transketolase	1.56	0.00000	hsa-miR-371-5p	11.89	3799.61	7.79	1.04E-10	2.62E-07
P31946	YWHAB	14-3-3 protein beta/alpha	1.35	0.01490	hsa-miR-155	1.85	3.61	9.51	5.54E-05	0.002127503
P61981	YWHAG	14-3-3 protein gamma	2.05	0.00007	hsa-miR-182	1.09	2.13	12.01	2.48E-04	0.006341084
					hsa-miR-320a	1.46	2.76	12.49	2.74E-05	0.001333363
					hsa-miR-320b	1.46	2.76	12.49	4.80E-05	0.001959043
					hsa-miR-320c	1.46	2.74	12.35	5.43E-05	0.002111768
P63104	YWHAZ	14-3-3 protein zeta/delta	2.52	0.00005	hsa-miR-155	1.85	3.61	9.51	5.54E-05	0.002127503
					hsa-miR-22	1.96	3.90	10.84	1.01E-04	0.003309338
					hsa-miR-28-5p	1.16	2.24	9.32	7.05E-05	0.002531521
					hsa-miR-30b	1.39	2.62	10.38	5.04E-04	0.011296975
					hsa-miR-30d	1.36	2.56	11.05	1.17E-04	0.003668745
					hsa-miR-320a	1.46	2.76	12.49	2.74E-05	0.001333363
					hsa-miR-320b	1.46	2.76	12.49	4.80E-05	0.001959043
					hsa-miR-320c	1.46	2.74	12.35	5.43E-05	0.002111768

Twenty-seven proteins found downregulated in the Caco-2 cell line relative to the HT-29 cell line and predicted to be targeted by 19 unique anti-correlated/upregulated microRNAs.

Table 2 Seven upregulated proteins with no DE mRNA targeted by 15 downregulated miRNAs

Protein					microRNA
Uniprot	Symbol	Title	Linear FC	Adj. P value	miRBase ID	logFC	LinFC	AveExpr	P Value	Adj. P value
O43852	CALU	Calumenin	1.86	0.0162	hsa-let-7a	-1.44	-2.72	12.58	1.30E-04	0.00396
					hsa-let-7b	-2.61	-6.11	12.84	1.71E-06	0.00017
					hsa-let-7c	-3.45	-10.94	11.26	2.39E-06	0.00021
					hsa-let-7d	-2.66	-6.34	12.12	2.20E-06	0.00020
					hsa-let-7e	-1.40	-2.65	12.39	6.41E-05	0.00236
					hsa-let-7f	-2.85	-7.20	8.75	5.04E-06	0.00034
					hsa-let-7g	-1.06	-2.08	8.90	2.99E-04	0.00737
					hsa-let-7i	-2.31	-4.95	10.22	2.35E-06	0.00021
					hsa-miR-29a	-1.63	-3.09	9.69	1.14E-04	0.00361
					hsa-miR-200a	-2.68	-6.43	9.16	4.14E-04	0.00965
					hsa-miR-200b	-2.54	-5.81	10.40	2.63E-05	0.00129
P20810	CAST	Calpastatin	2.39	0.00011	hsa-miR-125a-3p	-3.14	-8.83	5.84	3.26E-05	0.00150
					hsa-miR-224	-2.44	-5.42	7.35	8.21E-04	0.01667
					hsa-miR-375	-4.06	-16.67	8.29	1.50E-05	0.00083
P21333	FLNA	Filamin-A	3.59	0.00048	hsa-miR-125a-3p	-3.14	-8.83	5.84	3.26E-05	0.00150
P13797	PLS3	Plastin-3	5.88	0.00006	hsa-miR-200b	-2.54	-5.81	10.40	2.63E-05	0.00129
P78330	PSPH	Phosphoserine phosphatase	2.22	0.0004	hsa-miR-200b	-2.54	-5.81	10.40	2.63E-05	0.00129
P35241	RDX	Radixin	5.57	0.00012	hsa-let-7a	-1.44	-2.72	12.58	1.30E-04	0.00396
					hsa-let-7b	-2.61	-6.11	12.84	1.71E-06	0.00017
					hsa-let-7c	-3.45	-10.94	11.26	2.39E-06	0.00021
					hsa-let-7d	-2.66	-6.34	12.12	2.20E-06	0.00020
					hsa-let-7e	-1.40	-2.65	12.39	6.41E-05	0.00236
					hsa-let-7f	-2.85	-7.20	8.75	5.04E-06	0.00034
					hsa-let-7g	-1.06	-2.08	8.90	2.99E-04	0.00737
					hsa-let-7i	-2.31	-4.95	10.22	2.35E-06	0.00021
					hsa-miR-31	-1.94	-3.83	12.79	7.91E-05	0.00274
Q13885	TUBB2A	Tubulin beta-2A chain	1.46	0.00388	hsa-miR-29a	-1.63	-3.09	9.69	1.14E-04	0.00361

Seven proteins found upregulated in the Caco-2 cell line relative to the HT-29 cell line and predicted to be targeted by 15 unique anti-correlated/downregulated microRNAs.

Table 3 Overlap of DE genes, proteins, microRNAs with other HT-29/Caco-2 profiling studies

Identifier	Symbol	Description/Family	LinFC	P value	Overlapping study	Dataset
hsa-miR-196a_st	hsa-miR-196a	miR-196abc	-5.06	8.53E-05	88	microRNA
hsa-let-7a_st	hsa-let-7a	let-7/98/4458/4500	-2.72	6.34E-04	57
hsa-miR-10a_st	hsa-miR-10a	miR-10abc/10a-5p	-46.76	7.40E-06	57
hsa-miR-98_st	hsa-miR-98_st	miR-98	-11.90	4.50E-06	57
P17931	LGALS3	Galectin-3	2.09	1.10E-03	89; 90	Protein
P06576	ATP5B	ATP synthase subunit beta, mitochondrial	2.07	1.20E-03	89
P27797	CALR	Calreticulin	1.62	3.35E-02	89
P23528	CFL1	Cofilin-1	1.53	5.94E-03	89
P07858	CTSB	Cathepsin B	5.15	5.36E-05	89
P06733	ENO1	Alpha-enolase	2.06	4.65E-03	89
P22626	HNRNPA2B1	Heterogeneous nuclear ribonucleoproteins A2/B1	1.72	9.62E-03	89
P61978	HNRNPK	Heterogeneous nuclear ribonucleoprotein K	1.38	4.38E-04	89
P14866	HNRNPL	Heterogeneous nuclear ribonucleoprotein L	1.69	4.02E-03	89
P05787	KRT8	Keratin, type II cytoskeletal 8	2.21	1.81E-03	89
P07237	P4HB	Protein disulfide-isomerase	1.41	3.49E-03	89
P30101	PDIA3	Protein disulfide-isomerase A3	1.84	7.49E-05	89
P18669	PGAM1	Phosphoglycerate mutase 1	1.93	1.42E-04	89
P12429	ANXA3	Annexin A3	2.53	1.55E-06	90
P19338	NCL	Nucleolin	2.74	4.80E-03	90
P06748	NPM1	Nucleophosmin	1.51	1.15E-02	90
Q00796	SORD	Sorbitol dehydrogenase	4.21	7.73E-05	90
16779311	ATP7B	ATPase, Cu++ transporting, beta polypeptide	3.60	1.57E-05	91; 92	Gene
16823109	ABCA3	ATP-binding cassette, sub-family A (ABC1), member 3	10.07	1.75E-05	91
17059491	ABCB1	ATP-binding cassette, sub-family B (MDR/TAP), member 1	36.64	2.14E-06
16701957	AKR1E2	aldo-keto reductase family 1, member E2	4.56	1.09E-05
17005368	ALDH5A1	aldehyde dehydrogenase 5 family, member A1	3.38	4.08E-06
16794632	ALDH6A1	aldehyde dehydrogenase 6 family, member A1	2.27	7.54E-05
17067102	CDCA2	carboxylesterase 1	2.32	2.28E-03
16889762	CYP20A1	cytochrome P450, family 20, subfamily A, polypeptide 1	2.78	8.71E-04
16891082	CYP27A1	cytochrome P450, family 27, subfamily A, polypeptide 1	20.68	2.05E-06
17067284	EPHX2	epoxide hydrolase 2, cytoplasmic	6.51	3.62E-06
17020103	GSTA4	glutathione S-transferase alpha 4	2.25	4.04E-04
16877728	NCOA1	nuclear receptor coactivator 1	2.99	7.90E-04
16675638	NR5A2	nuclear receptor subfamily 5, group A, member 2	2.33	1.73E-03
16959797	RBP2	retinol binding protein 2, cellular	27.20	2.06E-06
16780481	SLC15A1	solute carrier family 15 (oligopeptide transporter), member 1	20.05	1.95E-06
16909257	SLC19A3	solute carrier family 19 (thiamine transporter), member 3	35.13	6.97E-08
16984056	SLC1A3	solute carrier family 1 (glial high affinity glutamate transporter), member 3	50.97	1.62E-07
16989018	SLC22A5	solute carrier family 22 (organic cation/carnitine transporter), member 5	2.21	5.49E-04
16843078	SLC6A4	solute carrier family 6 (neurotransmitter transporter), member 4	9.33	1.33E-06
16820398	SLC7A6	solute carrier family 7 (amino acid transporter light chain, y+L system), member 6	4.71	5.00E-06
16790744	SLC7A8	solute carrier family 7 (amino acid transporter light chain, L system), member 8	11.99	4.99E-06
16729064	SLCO2B1	solute carrier organic anion transporter family, member 2B1	10.15	8.38E-06
16998551	SLCO4C1	solute carrier organic anion transporter family, member 4C1	11.95	2.59E-03
16884050	SULT1C4	sulfotransferase family, cytosolic, 1C, member 4	15.89	2.49E-07
16951567	THRB	thyroid hormone receptor, beta	4.38	1.90E-04
17068541	VDAC3	voltage-dependent anion channel 3	2.28	3.11E-04

List of 49 gene, protein and miRNA annotated candidates (6 microRNAs, 17 proteins, 26 genes) which are differentially expressed between the HT-29 and Caco-2 cell lines in this and other published profiling studies that combine both cell lines.