Ubiquitous [Na+]i/[K+]i-sensitive transcriptome in mammalian cells: evidence for Ca(2+)i-independent excitation-transcription coupling.

Stimulus-dependent elevation of intracellular Ca(2+) ([Ca(2+)](i)) affects the expression of numerous genes--a phenomenon known as excitation-transcription coupling. Recently, we found that increases in [Na(+)](i) trigger c-Fos expression via a novel Ca(2+) (i)-independent pathway. In the present study, we identified ubiquitous and tissue-specific [Na(+)](i)/[K(+)](i)-sensitive transcriptomes by comparative analysis of differentially expressed genes in vascular smooth muscle cells from rat aorta (RVSMC), the human adenocarcinoma cell line HeLa, and human umbilical vein endothelial cells (HUVEC). To augment [Na(+)](i) and reduce [K(+)](i), cells were treated for 3 hrs with the Na(+),K(+)-ATPase inhibitor ouabain or placed for the same time in the K(+)-free medium. Employing Affymetrix-based technology, we detected changes in expression levels of 684, 737 and 1839 transcripts in HeLa, HUVEC and RVSMC, respectively, that were highly correlated between two treatments (p<0.0001; R(2)>0.62). Among these Na(+) (i)/K(+) (i)-sensitive genes, 80 transcripts were common for all three types of cells. To establish if changes in gene expression are dependent on increases in [Ca(2+)](i), we performed identical experiments in Ca(2+)-free media supplemented with extracellular and intracellular Ca(2+) chelators. Surprisingly, this procedure elevated rather than decreased the number of ubiquitous and cell-type specific Na(+) (i)/K(+) (i)-sensitive genes. Among the ubiquitous Na(+) (i)/K(+) (i)-sensitive genes whose expression was regulated independently of the presence of Ca(2+) chelators by more than 3-fold, we discovered several transcription factors (Fos, Jun, Hes1, Nfkbia), interleukin-6, protein phosphatase 1 regulatory subunit, dual specificity phosphatase (Dusp8), prostaglandin-endoperoxide synthase 2, cyclin L1, whereas expression of metallopeptidase Adamts1, adrenomedulin, Dups1, Dusp10 and Dusp16 was detected exclusively in Ca(2+)-depleted cells. Overall, our findings indicate that Ca(2+) (i)-independent mechanisms of excitation-transcription coupling are involved in transcriptomic alterations triggered by elevation of the [Na(+)](i)/[K(+)](i) ratio. There results likely have profound implications for normal and pathological regulation of mammalian cells, including sustained excitation of neuronal cells, intensive exercise and ischemia-triggered disorders.

Introduction

Gene expression is regulated by diverse stimuli to achieve tissue-specific functional responses via coordinate synthesis of the cell's macromolecular components [1]. Electrochemical gradients of monovalent cations across the plasma membrane (high intracellular potassium, [K+]i vs low intracellular sodium, [Na+]i) are created by the Na+,K+-pump and determine a large variety of physiologically important processes. These processes include maintenance of resting and action electrical membrane potentials, regulation of cell volume, secondary transport of mono- and divalent ions (such as chloride, calcium and phosphate), and accumulation of nutrients (glucose, amino acids, nucleotides) and other relevant molecules [2]. More recent studies demonstrated that side-by-side with the above-listed “classic” Na+ i,K+ i-dependent cellular processes, sustained elevation of the [Na+]i/[K+]i ratio in vascular smooth muscle cells, cardiomyocytes, hepatocytes, renal epithelial and neuronal cells causes differential expression of c-Fos and other immediate response genes (IRG), as well as cell type-specific late response genes, such as tumour growth factor-β, the α1- and β1-subunits of Na+,K+-ATPase, myosin light chain, skeletal muscle actin, atrial natriuretic factor and mortalin (for review see [3]–[5]).

According to the generally accepted paradigm Na+ i/K+ i-sensitive mechanism of excitation-transcription coupling is driven by changes in intracellular [Ca2+] and activation of several Ca2+-sensitive pathways – a phenomenon termed excitation-transcription coupling [6]–[8]. Indeed, it is well-documented that elevation of the [Na+]i/[K+]i ratio typically leads to increases in [Ca2+]i via activation of the Na+/Ca2+ exchanger [9] and/or voltage-gated Ca2+ channels [10]. It has also been shown that promoters of numerous genes including c-Fos contain serum response element (SRE) and Ca2++cAMP response element (CRE) activated by [Ca2+] increments in the cytoplasm and nucleus, respectively [11].

In contrast to the aforementioned mechanistic view, we found that in vascular smooth muscle cells from the rat aorta (RVSMC) and the human adenocarcinoma cell line (HeLa) the ouabain-induced changes in the c-Fos expression were preserved in the presence of Ca2+ channel blockers and extra- and intracellular Ca2+ chelators [12], [13]. These results made us conclude that along with canonical Ca2+ i-mediated signaling, sustained elevation of the [Na+]i/[K+]i ratio affects gene transcription via unknown Ca2+ i-independent mechanism(s) [4]. In the present study, we deployed Affymetrix technology to characterize the relative impact of Ca2+ i-mediated and -independent signaling on changes in gene expression triggered by sustained elevation of the [Na+]i/[K+]i ratio. To accomplish this goal, we compared transcriptomes in 3 different cell types treated with 2 distinct Na+,K+-ATPase inhibitors in the absence and presence of Ca2+ chelators. Our results strongly indicate that, in mammalian cells, Ca2+ i-independent pathways contribute to ubiquitous and cell type-specific transcriptomic alterations triggered by elevation of the [Na+]i/[K+]i ratio.

Results

Effect of ouabain and K+-free medium on the [Na+]i/[K+]i ratio and cell viability

Figure 1 illustrates that 3-hr inhibition of the Na+,K+-ATPase by ouabain in HeLa, human umbilical vein endothelial cells (HUVEC) and RVSMC increased Na+ i content from ∼50 to 400–600 nmol/mg protein and decreased K+ i from 600–800 to ∼100 nmol/mg protein. In RVSMC the action of K+-free medium on the [Na+]i/[K+]i ratio was similar, whereas in HUVEC and HeLa cells the gain of Na+ i and the loss of K+ i triggered by K+-free medium were higher compared to ouabain by ∼20% by ∼50%, respectively. Importantly, in all type of cells exposed to K+-free medium, the intracellular content of monovalent cations was not significantly affected by the addition of ouabain (Fig. 1). The control experiments demonstrated that 4 hr treatment with ouabain or K+-free medium as well as the addition of 50 µM EGTA and 10 µM BATPA-AM in Ca2+-free medium did not impact HeLa, HUVEC and RVSMC survival, as determined by lactate dehydrogenase (LDH) release, caspase-3 activity and chromatin cleavage assay (Table 1).

Figure 1

Effect of ouabain and K+-free medium on intracellular Na+ (a–c) and K+ (d–f) content in HeLa (a,d), HUVEC (b,e) and RVSMC (c,f).

Cells were incubated in control or K+-free medium during 3 hr and ouabain was added at a final concentration of 3 µM (HeLa and HUVEC) or 3 mM (RVSMC). Mean ± S.E. values of experiments performed in quadruplicate are shown.

Table 1

Lactate dehydrogenase release (LDH, %), caspase-3 activity (CAS, nmol per mg of protein per hr) and chromatin cleavage (CHR, %) in cells treated with ouabain, K+-free and Ca2+-free medium during 4 hr.

Incubation medium, additions	HeLa			HUVEC			RVSMC
	LDH	CAS	CHR	LDH	CAS	CHR	LDH	CAS	CHR
None (control)	5.3±1.6	0.36±0.05	3.3±0.9	7.0±2.1	0.26±0.07	4.4±0.7	3.0±0.6	0.46±0.04	5.1±1.2
Ouabain	6.3±0.6	0.44±0.07	2.9±1.6	7.3±1.6	0.41±0.08	6.9±1.8	4.3±1.1	0.37±0.03	3.9±2.6
K+-free medium	5.9±1.1	0.30±0.05	4.0±1.0	5.9±1.7	0.36±0.04	4.7±1.3	4.5±0.6	0.38±0.05	4.8±1.0
Ca2+-fre medium	6.9±1.2	0.46±0.09	4.9±1.6	8.5±3.0	0.53±0.07	7.1±1.7	5.5±1.1	0.57±0.08	6.9±2.2
Staurosporine	15.1±2.6*	1.33±0.25*	19.1±4.4*	35.3±3.9*	1.78±0.18*	32.1±6.4*	21.3±2.2*	2.91±0.30*	23.1±5.0*

To measure LDH release and chromatin cleavage, the total content of LDH and [3H]-labelled DNA were taken as 100%. Ouabain was added at final concentration of 3 µM (HeLa and HUVEC) or 3 mM (RVSMC). Ca2+-free medium contained 50 µM EGTA and 10 µM BAPTA-AM. Staurosporine, a potent trigger of apoptosis, was added as a positive control at concentration of 1 µM. Means ± S.E. from experiments performed with quadruplicate are given.

p<0.05 as compared to controls.

Effects of ouabain and K+-free medium on gene expression profile

Together with elevation of the [Na+]i/[K+]i ratio, ouabain and K+-free medium may affect cells independently of suppression of Na+,K+-ATPase-mediated ion fluxes. Thus, recent studies have revealed that ouabain triggered interaction of the Na+,K+-ATPase α-subunit with the membrane-associated nonreceptor tyrosine kinase Src, activation of Ras/Raf/ERK1,2, phosphatidyl inositol 3-kinase (PI(3)K), PI(3)K-dependent protein kinase B, phospholipase C, [Ca2+]i oscillations and augmented production of the reactive oxygen species (for review, see [14], [15]). On the other hand, the transfer of highly K+-permeable cells to K+-free medium results in transient membrane hyperpolarization, affecting the activity of diverse voltage-sensitive membrane-bound proteins [16], [17]. Considering this, we compared the actions of ouabain and K+-free medium on gene expression profiles in HUVEC, RVSMC and HeLa cells with a final goal of identifying ubiquitous and cell type-specific Na+ i,K+ i-sensitive transcriptomes.

The data obtained in 4 independent experiments were normalized and then analyzed by principal component analysis (PCA) [18]. Each point on the PCA represents the gene expression profile of an individual sample. Samples that are near each other in the resulting 3-dimensional plot have a similar transcriptome while those that are further apart have dissimilar transcriptional profiles. This approach identified treatments with ouabain and K+-free medium as major sources of variability within datasets (Fig. 2A).

Figure 2

Comparative analysis of the actions of Na+,K+-ATPase inhibition by ouabain and K+-free medium on HeLa, HUVEC and RVSMC transcriptomes.

A. Principal component analysis of the transcriptomes of HeLa, HUVEC and RVSMC. Cells were incubated for 3 hr in control Ca2+-containing media and processed for oligonucleotide microarray analysis as indicated in the Methods section. Ouabain was added at a final concentration of 3 µM (HeLa and HUVEC) or 3 mM (RVSMC). All experiments are repeated 4 times. Ellipsoids highlight portioning of samples based on the type of treatment. The principal components in 3-dimensional graphs (PC#1, PC#2 and PC#3) represent the variability of gene expression level within datasets. The total percentage of PCA mapping variability is shown on top. B. The total number of genes whose expression is altered by ouabain and K+-free medium by more than 1.2-fold with p<0.05 is indicated; numbers of genes affected by both stimuli appear in bold.

Figure 2B disclosed that the total numbers of differentially-expressed transcripts in HeLa, HUVEC and RVSMC treated for 3 hr with ouabain were 819, 886 and 3199, whereas inhibition of the Na+,K+-ATPase in K+-free medium altered the expression of 3078, 2858 and 3677 transcripts, respectively. In all types of cells, the number of up- and down regulated genes affected by these stimuli was about the same, whereas maximal fold of activation and suppression was 65 and 24, respectively (Table 2). The decreased number of differentially expressed transcripts detected in ouabain-treated HUVEC and HeLa cells, compared to RVSMC, can be explained by retarded kinetics of elevation of [Na+]i in ouabain-treated human cells compared to ouabain-treated RVSMC (Fig. 3A) and cells subjected to Na+,K+-ATPase inhibition in K+-free medium (Fig. 3B). This observation is consistent with the slow kinetics of ouabain interaction with the human house-keeping α1 Na+,K+-ATPase isoform demonstrated in early investigations [19].

Table 2

Total numbers of differentially expressed transcripts in HeLa, HUVEC and RVSMC in 3-hr of Na+,K+-ATPase inhibition in control (Ca2+ containing) medium.

	Ouabain-treated cells	Cells treated with K+-free medium	Transcripts affected by both stimuli
HeLa
Up-regulated transcripts
Number of transcripts	338	1371	278
Maximal fold of activation	13.78	46.86	N.A.
Down-regulated transcripts
Number of transcripts*	481	1707	406
Maximal fold of inhibition	2.85	7.96	N.A.
HUVEC
Up-regulated transcripts
Number of transcripts	400	1471	355
Maximal fold of activation	9.68	64.81	N.A.
Down-regulated transcripts
Number of transcripts*	486	1447	379
Maximal fold of inhibition	2.40	5.33	N.A.
RVSMC
Up-regulated transcripts
Number of transcripts	1288	1872	894
Maximal fold of activation	9.46	24.32	N.A.
Down-regulated transcripts
Number of transcripts*	1903	1805	945
Maximal fold of inhibition	4.15	7.50	N.A.

Transcripts whose expression was altered by more than 1.2-fold with p<0.05 were subjected to analysis. Ouabain was added at final concentration of 3 µM (HeLa and HUVEC) or 3 mM (RVSMC). N.A. – non-applicable.

Figure 3

Kinetics of elevation of intracellular Na+ in HeLa, HUVEC and RVSMC triggered by ouabain (A) or K+-free medium (B).

Ouabain was added at a final concentration of 3 µM (HeLa and HUVEC) or 3 mM (RVSMC). Intracellular Na+ content in the absence of Na+,K+-ATPase inhibitors was taken as 100%. Means obtained in experiments performed in triplicate are shown.

Further analysis determined that the expression of 684, 737 and 1839 transcripts in HeLa, HUVEC and RVSMC, respectively, was affected by both stimuli (Fig. 2B). Importantly, we observed highly significant (p<0.0003) and positive (R2>0.62) correlations between levels of differentially expressed transcripts identified in the presence of ouabain and K+-free medium (Fig. 4). Because the gain of Na+ i and loss of K+ i in cells treated with ouabain and K+-free medium are similar (Fig. 1), the results strongly suggest that the changes in gene expression evoked by both stimuli occur in response to elevation of the [Na+]i/[K+]i ratio rather than due to Na+ i,K+ i-independent events. Considering this, we classified Na+ i,K+ i-sensitive transcriptomes as sets of genes whose expression was impacted by both ouabain and K+-free medium.

Figure 4

Correlation analysis of transcripts whose expression is altered by ouabain and K+-free medium in HeLa, HUVEC and RVSMC by more than by 1.2-fold with p<0.05.

Cells were incubated during 3 hr; ouabain was added at a final concentration of 3 µM (HeLa and HUVEC) or 3 mM (RVSMC). Incubation medium contains 1.8 mM CaCl2. The total number of transcripts subjected to analysis is shown in Figure 2B. Transcript expression in control cells was taken as 1.00.

To confirm the ability of microarrays to resolve the differences in expression levels, we selected several Na+ i/K+ i-sensitive genes (Egr1, Ptgs2 and Ppp1r15a) for additional validation by quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis. These experiments revealed highly significant correlations between the RT-PCR results and the validated microarray data (R2 = 0.94, p<0.0000002; Fig. 5).

Figure 5

Verification of microarray results by quantitative RT-PCR.

Gene expression was quantified for 3 hr incubation of control and Ca2+-depleted HUVEC in the presence of 3 µM ouabain or in K+-free medium. Mean values obtained in 4 independent experiments are shown. Egr1 - early growth response protein 1, Ptgs2 - prostaglandin-endoperoxide synthase 2, Ppp1r15a - protein phosphatase 1, regulatory (inhibitor) subunit 15A.

Ubiquitous Na+ i,K+ i-sensitive transcriptome

Among the Na+ i,K+ i-sensitive genes detected in HeLa, HUVEC and RVSMC, we identified 80 common genes, i.e. genes whose differential expression was increased or decreased by both ouabain and K+-free medium by at least 1.2-fold (p<0.05) in all 3 cell types (Fig. 6A). We noted that the list of ubiquitous Na+ i,K+ i-sensitive transcriptome was enriched with genes involved in the regulation of transcription/translation (49%), cell cycle, adhesion and migration (24%), and inflammatory and immune responses (6%) (Table 3, Fig. 6B).

Figure 6

Na+ i,K+ i-sensitive transcriptomes identified in control Ca2+-containing media.

A. Pie-chart showing the numbers of Na+ i,K+ i-sensitive genes detected in HeLa, HUVEC and RVSMC and ubiquitous Na+ i,K+ i-sensitive genes found in all 3 cell types. B. Distribution of ubiquitous Na+ i,K+ i-sensitive genes among major functional groups. Digitals shown in correspond to gene numbers for each functional group.

Table 3

Ubiquitous Na+ i/K+ i-sensitive genes whose expression was up- and down-regulated by more than 1.2-fold (p≤0.05) in control (Ca2+-containing) medium.

No.	Gene symbol, title	RVSMC		HUVEC		HeLa
		Fold of activation/inhibition		Fold of activation/inhibition		Fold of activation/inhibition
		ouabain	K+-free medium	ouabain	K+-free medium	ouabain	K+-free medium
	Up-regulated genes
1t	Egr1 //early growth response 1	4.80±0.18	6.97±0.18	9.69±0.15	64.81±0.12	13.78±0.15	46.85±0.09
2t	Fos//FBJ osteosarcoma oncogene	3.17±0.08	8.76±0.08	2.60±0.09	15.97±0.11	5.88±0.13	41.93±0.09
3t	Fosb//FBJ osteosarcoma oncogene B	5.91±0.11	15.22±0.12	1.99±0.08	5.82±0.10	3.12±0.16	23.85±0.11
4t	Atf3 //activating transcription factor 3	4.72±0.03	20.63±0.08	1.86±0.05	7.50±0.05	2.28±0.10	11.29±0.05
5t	Zfp36//zinc finger protein 36	3.52±0.10	5.95±0.09	2.36±0.10	12.07±0.11	2.27±0.04	10.30±0.10
6t	Jun//Jun oncogene	1.28±0.06	1.62±0.07	1.94±0.06	5.11±0.05	1.91±0.11	8.03±0.04
7i	Il6//interleukin 6	3.40±0.14	4.76±0.15	1.44±0.09	2.12±0.08	2.01±0.11	8.01±0.08
8d	Ppp1r15a//protein phosphatase 1, regulatory (inhibitor) subunit 1	2.59±0.12	3.57±0.09	2.54±0.10	4.08±0.10	2.98±0.16	7.73±0.14
9d	Dusp8//dual specificity phosphatase 8	1.55±0.11	3.09±0.12	1.54±0.08	3.35±0.06	1.83±0.11	6.25±0.10
10t	Ddit3 //DNA-damage inducible transcript 3	2.15±0.03	4.26±0.03	1.35±0.09	4.91±0.09	1.52±0.13	5.46±0.10
11t	Junb //jun B proto-oncogene	4.03±0.08	4.24±0.07	1.85±0.09	7.32±0.07	2.20±0.09	5.40±0.08
12i	Ptgs2//prostaglandin-endoperoxide synthase 2	9.46±0.10	9.95±0.11	3.73±0.03	7.84±0.04	2.39±0.13	5.15±0.10
13t	Cyr61 //cysteine-rich, angiogenic inducer, 61	1.71±0.09	2.00±0.10	1.34±0.04	2.11±0.04	2.02±0.09	5.11±0.08
14t	Nr4a2 //nuclear receptor subfamily 4, group A, member 2	5.19±0.07	8.65±0.12	2.03±0.09	3.94±0.10	2.39±0.07	4.76±0.05
15i	Nfkbiz//nuclear factor of kappa light polypeptide gene enhance	3.24±0.09	4.47±0.08	2.44±0.06	5.15±0.02	2.11±0.07	4.66±0.07
16t	Hes1//hairy and enhancer of split 1 (Drosophila)	3.00±0.06	6.15±0.09	2.07±0.09	5.86±0.08	1.71±0.10	4.62±0.11
17d	Spry4 //sprouty homolog 4 (Drosophila)	1.84±0.06	1.40±0.09	3.27±0.12	4.91±0.12	2.12±0.17	4.26±0.17
18o	Txnip//thioredoxin interacting protein	3.85±0.10	5.84±0.10	2.62±0.09	6.99±0.12	3.07±0.10	4.18±0.09
19d	Areg //amphiregulin	1.90±0.04	1.75±0.06	1.36±0.11	1.39±0.07	1.93±0.13	4.13±0.14
20i	Nfkbia//nuclear factor of kappa light polypeptide gene	2.46±0.03	5.80±0.05	1.39±0.09	2.68±0.08	1.54±0.10	3.63±0.10
21t	Klf10 //Kruppel-like factor 10	2.80±0.05	3.66±0.06	1.83±0.07	4.53±0.05	1.74±0.06	3.57±0.05
22d	Plk3//polo-like kinase 3 (Drosophila)	3.29±0.12	3.64±0.12	1.22±0.06	2.15±0.06	1.41±0.05	2.83±0.07
23d	Ccnl1//cyclin L1	2.10±0.06	3.82±0.08	1.62±0.05	2.73±0.04	1.33±0.09	2.72±0.08
24d	Abl2//v-abl Abelson murine leukemia viral oncogene homolog 2	1.96±0.11	2.02±0.08	1.44±0.06	2.04±0.05	1.74±0.07	2.62±0.05
25d	Pmaip1 //phorbol-12-myristate-13-acetate-induced protein 1	1.46±0.06	1.64±0.05	1.51±0.11	2.30±0.11	1.71±0.08	2.55±0.06
26t	Bcl6 //B-cell CLL/lymphoma 6	1.64±0.10	1.88±0.09	1.89±0.07	3.78±0.07	1.32±0.10	2.53±0.10
27t	Mafk //v-maf musculoaponeurotic fibrosarcoma oncogene homolog K	2.94±0.08	3.19±0.11	1.37±0.08	1.23±0.08	1.59±0.07	2.50±0.07
28d	Errfi1 //ERBB receptor feedback inhibitor 1	3.14±0.07	2.59±0.10	1.75±0.07	3.06±0.07	1.45±0.05	2.42±0.06
29o	Dusp16//dual specificity phosphatase 16	2.33±0.08	2.47±0.09	1.62±0.09	3.49±0.08	1.46±0.11	2.38±0.11
30t	Maff//v-maf musculoaponeurotic fibrosarcoma oncogene homolog F	2.47±0.07	3.11±0.09	1.27±0.09	2.25±0.04	1.42±0.10	2.35±0.10
31t	Tsc22d2 //TSC22 domain family, member 2	1.21±0.04	1.76±0.06	1.80±0.05	3.80±0.03	1.41±0.05	2.24±0.05
32o	Slc25a25 //solute carrier family 25	2.18±0.03	3.56±0.05	1.77±0.06	2.97±0.05	1.49±0.05	2.23±0.07
33o	Insig1//insulin induced gene 1	1.93±0.08	1.96±0.09	1.36±0.04	1.86±0.03	1.67±0.06	2.23±0.05
34t	Mxd1 //max dimerization protein 1	1.83±0.06	3.21±0.05	1.49±0.07	2.42±0.06	1.66±0.08	2.19±0.08
35t	Fosl1 //fos-like antigen 1	1.92±0.07	2.17±0.07	1.29±0.04	2.35±0.04	1.20±0.04	2.17±0.06
36d	Hbegf //heparin-binding EGF-like growth factor	4.44±0.14	4.10±0.18	1.52±0.06	2.25±0.03	1.35±0.07	2.13±0.08
37d	Epha2 //Eph receptor A2	3.61±0.08	2.98±0.12	1.31±0.07	1.41±0.06	1.39±0.11	2.11±0.08
38d	Birc3 //baculoviral IAP repeat-containing 3	3.30±0.03	7.47±0.03	1.69±0.09	4.58±0.12	1.29/±0.09	2.04±0.09
39d	Efna1 //ephrin A1	1.82±0.04	1.26±0.03	1.48±0.04	1.83±0.05	1.34±0.09	2.02±0.09
40t	Zc3h12c //zinc finger CCCH type containing 12C	1.39±0.06	1.70±0.02	1.76±0.09	1.62±0.09	1.68±0.08	2.01±0.07
41o	Ldlr //low density lipoprotein receptor	1.50±0.04	1.51±0.04	1.48±0.05	1.86±0.05	1.75±0.03	1.95±0.04
42t	Sertad2 //SERTA domain containing 2	1.74±0.06	1.60±0.07	1.36±0.08	1.79±0.07	1.29±0.09	1.93±0.07
43t	Zc3h12a //zinc finger CCCH type containing 12A	2.14±0.06	2.25±0.08	1.35±0.06	2.68±0.07	1.25±0.05	1.92±0.03
44t	Cpeb4 //cytoplasmic polyadenylation element binding protein 4	2.46±0.04	2.59±0.05	1.26±0.06	1.74±0.07	1.31±0.06	1.87±0.05
45i	Il1rap //interleukin 1 receptor accessory protein	1.32±0.09	1.21±0.06	1.33±0.10	1.99±0.10	1.42±0.09	1.71±0.07
46f	Dnajb9 //DnaJ (Hsp40) homolog, subfamily B, member 9	1.33±0.03	1.30±0.03	1.63±0.05	2.20±0.06	1.46±0.07	1.67±0.10
47t	Ppp1r15b //protein phosphatase 1	1.72±0.02	1.77±0.02	1.30±0.05	1.63±0.03	1.35±0.04	1.66±0.03
48d	Dusp6 //dual specificity phosphatase 6	3.36±0.10	1.73±0.11	1.47±0.12	1.81±0.09	1.48±0.07	1.64±0.07
49d	Zswim6 //zinc finger, SWIM-type containing 6	1.44±0.03	1.70±0.04	1.22±0.03	1.64±0.03	1.35±0.02	1.62±0.03
50t	Zbtb43 //zinc finger and BTB domain containing 43	1.34±0.05	2.14±0.05	1.24±0.06	1.76±0.08	1.39±0.05	1.59±0.05
51o	Slc20a1 //solute carrier family 20 (phosphate transporter)	1.56±0.04	1.29±0.04	1.30±0.03	1.43±0.04	1.29±0.04	1.56±0.04
52o	Hmgcs1 //3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1	1.80±0.03	2.01±0.03	1.24±0.02	1.56±0.01	1.38±0.04	1.44±0.03
53f	Coq10b //coenzyme Q10 homolog B (S. cerevisiae)	1.71±0.03	1.47±0.03	1.22±0.04	1.47±0.05	1.41±0.05	1.43±0.06
54t	Clk1 //CDC-like kinase 1	1.37±0.07	2.14±0.07	1.40±0.07	1.66±0.07	1.41±0.06	1.40±0.07
55t	Zbtb11 //zinc finger and BTB domain containing 11	2.16±0.05	2.00±0.08	1.42±0.05	1.51±0.05	1.31±0.04	1.36±0.05
56t	Nr1d1 //nuclear receptor subfamily 1, group D, member 1	1.57±0.05	1.74±0.08	1.43±0.10	1.48±0.07	1.50±0.07	1.31±0.09
57o	Stard4 //StAR-related lipid transfer (START) domain	1.30±0.05	1.51±0.05	1.32±0.06	1.46±0.03	1.39±0.07	1.30±0.05
58t	Nfya//nuclear transcription factor-Y alpha	1.52±0.06	1.45±0.09	1.49±0.04	1.48±0.04	1.41±0.05	1.30±0.04
59t	Jmjd1c //jumonji domain containing 1C	1.49±0.03	1.59±0.05	1.39±0.03	1.52±0.05	1.28±0.04	1.29±0.05
60t	Dcp1a //DCP1 decapping enzyme homolog A (S. cerevisiae)	1.66±0.02	1.65±0.06	1.24±0.03	1.26±0.03	1.27±0.06	1.28±0.04
61t	E2f3 //E2F transcription factor 3	1.26±0.06	1.43±0.05	1.41±0.08	1.73±0.08	1.22±0.06	1.27±0.04
	Down-regulated genes
1o	Gabre //gamma-aminobutyric acid (GABA) A receptor, epsilon	−1.21±0.08	−1.45±0.06	−1.33±0.06	−1.48±0.03	−2.01±0.09	−3.15±0.14
2t	Hoxb5//homeo box B5	−2.25±0.12	−2.82±0.13	−1.75±0.06	−3.00±0.08	−1.49±0.08	−2.35±0.09
3t	Znf250 //zinc finger protein 250	−1.26±0.07	−1.20±0.08	−1.62±0.06	−1.90±0.05	−1.72±0.07	−2.08±0.06
4t	Rpp40//ribonuclease P 40 subunit (human)	−1.70±0.08	−1.84±0.05	−1.41±0.03	−1.79±0.06	−1.27±0.05	−2.03±0.06
5t	Rbm45 //RNA binding motif protein 45	−1.33±0.05	−1.37±0.05	−1.41±0.06	−1.67±0.05	−1.48±0.11	−1.89±0.08
6d	Aggf1 //angiogenic factor with G patch and FHA domains 1	−1.54±0.04	−1.24±0.06	−1.30±0.08	−1.29±0.08	−1.54±0.07	−1.83±0.06
7d	Fancf //Fanconi anemia, complementation group F	−1.51±0.07	−1.30±0.06	−1.85±0.08	−1.71±0.07	−1.48±0.10	−1.83±0.09
8o	Rhobtb1 //Rho-related BTB domain containing 1	−1.98±0.06	−1.35±0.06	−1.41±0.08	−1.48±0.08	−1.34±0.11	−1.80±0.07
9t	Znf691 //zinc finger protein 691	−1.42±0.09	−1.33±0.07	−1.28±0.08	−1.23±0.07	−1.46±0.11	−1.67±0.06
10o	Rrs1 //RRS1 ribosome biogenesis regulator homolog (S. cerevisiae)	−1.26±0.07	−1.39±0.10	−1.31±0.08	−1.33±0.07	−1.29±0.03	−1.59±0.03
11t	Mrpl46//mitochondrial ribosomal protein L46	−1.34±0.04	−1.24±0.05	−1.21±0.04	−1.34±0.03	−1.24±0.05	−1.58±0.07
12o	Golga5 //golgi autoantigen, golgin subfamily a	−1.65±0.04	−1.21±0.06	−1.38±0.05	−1.48±0.05	−1.29±0.05	−1.56±0.04
13d	Psrc1 //proline/serine-rich coiled-coil 1	−1.65±0.08	−1.80±0.07	−1.25±0.08	−1.44±0.05	−1.23±0.04	−1.53±0.05
14o	Spata7 //spermatogenesis associated 7/	−1.55±0.07	−1.32±0.06	−1.29±0.06	−1.31±0.06	−1.38±0.08	−1.49±0.08
15d	Tgfbrap1 //transforming growth factor, beta receptor	−1.49±0.06	−1.22±0.05	−1.36±0.05	−1.55±0.03	−1.29±0.06	−1.47±0.05
16o	Hps6 //Hermansky-Pudlak syndrome 6	−2.15±0.07	−1.69±0.10	−1.39±0.09	−1.31±0.10	−1.48±0.08	−1.46±0.06
17t	Znf18 4//zinc finger protein 184	−1.78±0.06	−1.55±0.08	−1.71±0.10	−2.01±0.08	−1.28±0.07	−1.44±0.06
18t	Pars2 //prolyl-tRNA synthetase (mitochondrial)(putative)	−1.61±0.04	−1.20±0.05	−1.28±0.05	−1.28±0.06	−1.38±0.05	−1.34±0.04
19o	Sh3bp5l //SH3 binding domain protein 5 like	−1.82±0.04	−1.54±0.03	−1.46±0.07	−1.40±0.09	−1.35±0.07	−1.27±0.07

HeLa, HUVEC and RVSMC were treated with ouabain or K+-free medium for 3 hr. Genes whose expression is not affected by Na+,K+-ATPase inhibition at least in one type of Ca2+-depleted cells are shown in . Genes whose expression is not affected by Na+,K+-ATPase inhibition in all 3 types of cells are shown in . Functional categories are indicated in the left column as: t – regulators of transcription/translation, RNA processing and degradation; d – regulators of cell adhesion, migration, proliferation, differentiation and death; f - protein folding and ubiquitination; i – inflammation and immune response; o – other functional categories and genes with unknown function.

Ubiquitous Na+ i/K+ i-sensitive genes, whose expression was increased by more than 3-fold, included the transcriptional regulator of C2H2-type zinc-finger protein Egr-1, members of the superfamily of b-zip transcriptional factors possessing basic DNA-binding domain and leucine-zipper dimerization motif and forming heterodimeric activating protein-1 (AP-1) (Fos, FosB, Jun, JunB, Atf3), transcription factor of the steroid-thyroid hormone-retinoid receptor superfamily Nr4a2 and the basic helix-loop-helix transcription regulator Hes1. Nfkbiz and Nfkbia are transcriptional regulators of genes encoding intermediates of inflammation whereas interleukin 6 (Il6) is a potent controller of the acute inflammatory response phase. Prostaglandin-endoperoxide synthase 2 (Ptgs2) also known as cyclooxygenase-2 is a key enzyme in the biosynthesis of prostaglandins implicated in inflammatory responses and mitogenesis. Na+ i/K+ i-sensitive regulators of cell proliferation, differentiation and death whose expression is sharply increased are represented by dual specificity protein phosphatase Dusp8, inhibitor of the receptor-transduced mitogen-activated protein kinase signaling pathway Spry4, the protein phosphatase 1 regulatory subunit Ppp1r15a, the cytokine inducible kinase Plk3, a member of the epidermal growth factor (EGF) family amphiregulin (Areg), and heparin-binding EGF-like growth factor Hbegf.

Among ubiquitous Na+ i,K+ i-sensitive genes from other functional categories, we noted augmented expression of oxidative stress mediator Txnip, the low-density lipoprotein receptor Ldlr, the regulator of cholesterol synthesis Insig1 and 2 carriers involved in intracellular phosphate handling, i.e. the Ca2+-dependent mitochondrial solute carrier Slc25a25 mediating ATP-Mg/Pi exchange and the sodium-phosphate symporter Slc20a1 (Table 3). In contrast to substantial number of ubiquitous Na+ i/K+ i-sensitive genes that were strongly up-regulated, we identified only one transcript – the epsilon subunit of GABA-activated Cl− channel (Gabre) – whose expression was decreased by more than 3-fold (Table 3).

Cell type-specific Na+ i,K+ i-sensitive transcriptomes

Because the number of cell-type specific Na+ i,K+ i-sensitive transcripts is very large (Fig. 2B, Table 2), we restricted their functional characterization to genes whose expression was altered by more than 4-fold. The relevant analysis led us to several conclusions. , ubiquitous genes comprised up to ∼50% of Na+ i,K+ i-sensitive genes whose expression was increased in HeLa, HUVEC and RVSMC by more than 4-fold (Tables 4,5,6). , strongly up-regulated Na+ i,K+ i-sensitive genes are abundant with the transcripts that were detected in 2 cell types. These transcripts (underlined and ) accounted for 37%, 18% and 16% of the total numbers of genes that manifested up- and down-regulation in HeLa, HUVEC and RVSMC, respectively. , similar to ubiquitously regulated genes (Table 3), the list of cell type-specific Na+ i,K+ i-sensitive genes that were strongly up- and down-regulated was enriched with the transcriptional regulators and regulators of immune responses and inflammation. Examples included nuclear receptor subfamily 4 group A Nr4a1 and Nr4a3 in HeLa and RVSMC, early growth response 2 Egr2 in HeLa and RVSMC, immediate early response 2 Ier2 in RVSMC, interleukin 8 IL8 in HeLa and HUVEC, tumour necrosis factor α-induced protein 3 TNFAIP3 in HeLa and HUVEC. From other functional categories, we observed substantial cell type-specific elevation of colony stimulating factor 3 Csf3 in RVSMC, metallopeptidase ADAMTS1 and vasoactive intestinal peptide VIP in HUVEC, the regulator of G-protein signalling Rgs2 in RVSMC, endothelin 1 EDN1 and the inhibitor of DNA binding-2 ID2 in HeLa cells (Tables 4,5,6).

Table 4

: the list of genes whose expression was changed by more than 4-fold in 3 hr of Na+,K+-ATPase inhibition in control (Ca2+ containing) medium.

Gene symbol, title	Affymetrix ID	Fold of activation or inhibition (-) by ouabain/p value	Fold of activation or inhibition (-) by K+-free medium/p value	Fold of activation by ouabain/K+-free medium in HUVEC or RVSMC
EGR1//early growth response 1	8108370	13.78/7.27E-08	46.85/8.18E-05
FOS//FBJ murine osteosarcoma viral oncogene	7975779	5.88/7.27E-08	41.93/8.56E-06
FOSB//FBJ murine osteosarcoma viral oncogene	8029693	3.12/2.78E-07	23.85/1.51E-05
NR4A1//nuclear receptor subfamily 4, group A,	7955589	2.63/1.39E-07	11.79/8.56E-06	3.52/10.73 (HUVEC)
TNFAIP3//tumor necrosis factor, alpha-induced protein 3	8122265	1.90/2.27E-07	11.77/8.56E-06	3.34/15.71 (HUVEC)
ATF3//activating transcription factor 3	7909610	2.28/9.86E-08	11.29/8.56E-06
EDN1//endothelin 1	8116921	2.31/2.55E-06	11.15/1.10E-04
NR4A3//nuclear receptor subfamily 4, group A	8156848	2.77/8.28E-08	11.06/8.56E-06	4.16/4.68 (HUVEC)
ZFP36//zinc finger protein 36, C3H type, homolog (mouse)	8028652	2.27/9.86E-08	10.30/8.56E-06
IL8//interleukin 8	8095680	2.93/5.07E-06	10.00/5.31E-04	1.96/4.45 (HUVEC)
JUN//jun oncogene	7916609	1.91/1.68E-07	8.03/8.56E-06
IL6//interleukin 6 (interferon, beta 2)	8131803	2.01/3.12E-07	8.01/1.51E-05
PPP1R15A//protein phosphatase 1, regulatory (inhibitor) subunit 15A	8030128	2.98/2.08E-06	7.73/5.19E-04
DUSP8//dual specificity phosphatase 8	7945641	1.83/4.85E-07	6.25/2.05E-05
EGR2//early growth response 2	7933872	1.85/1.39E-06	5.79/6.41E-05	2.87/9.08 (RVSMC)
DDIT3//DNA-damage-inducible transcript 3	7964460	1.52/2.19E-06	5.46/4.39E-05
JUNB//jun B proto-oncogene	8026047	2.20/5.35E-07	5.40/7.13E-05
PTGS2//prostaglandin-endoperoxide synthase 2	7922976	2.39/4.30E-06	5.15/9.30E-04
CYR61//cysteine-rich, angiogenic inducer, 61	7902687	2.02/2.78E-07	5.11/2.71E-05
CSRNP1//cysteine-serine-rich nuclear protein 1	8086330	2.32/2.88E-06	4.80/7.31E-04
HIST1H3J//histone cluster 1, H3j	8124537	1.69/2.25E-05	4.77/6.25E-04	1.40/1.62 (HUVEC)
NR4A2//nuclear receptor subfamily 4, group A,	8055952	2.39/1.39E-07	4.76/4.04E-05
NFKBIZ//nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta	8081386	2.11/3.12E-07	4.66/5.06E-05
AREG//amphiregulin	8095744	2.10/2.01E-05	4.64/2.04E-03
DUSP1//dual specificity phosphatase 1	8115831	2.24/1.60E-07	4.64/4.09E-05	1.59/3.81 (HUVEC)
HES1//hairy and enhancer of split 1, (Drosophila)	8084880	1.71/1.05E-06	4.62/4.57E-05
SPRY4//sprouty homolog 4 (Drosophila)	8114797	2.12/3.80E-05	4.26/5.65E-03
TXNIP//thioredoxin interacting protein	7904726	3.07/6.87E-07	4.18/1.03E-02
DUSP10//dual specificity phosphatase 10	7924450	1.88/3.99E-07	4.04/4.71E-05	1.32/3.02 (HUVEC)
CDKN2AIP//CDKN2A interacting protein	8098500	1.84/2.19E-06	4.01/2.10E-04	1.26/2.05 (HUVEC)
ID2//inhibitor of DNA binding 2, dominant negative helix-loop-helix protein	8040103	1.64/2.91E-06	4.01/1.25E-04
LOC100287934//similar to hCG2042721	7909990	−2.41/2.12E-03	−4.01/3.18E-05	−1.96/−4.68 (HUVEC)
LOC100131860//hypothetical protein	7991047	−2.47/3.26E-03	−4.73/3.32E-05
TRIM52//tripartite motif-containing 52	8110666	−1.57/6.01E-03	−5.03/8.88E-07	−1.64/−3.85 (HUVEC)
C9orf3//chromosome 9 open reading frame 3	8156571	−2.85/4.40E-05	−7.96/1.39E-07	−1.71/−2.24 (HUVEC)

Genes whose differential expression is limited to HeLa cells are shown in bold. Genes whose differential expression were also detected in HUVEC or RVSMC are shown in . All transcripts listed in this table were also differentially expressed in Ca2+-depleted cells.

Table 5

the list of genes whose expression was changed in by more than 4-fold in 3 hr of Na+,K+-ATPase inhibition in control (Ca2+ containing) medium.

Gene symbol, title	Affymetrix ID	Fold of activation or inhibition (-) by ouabain/p value	Fold of activation or inhibition (-) by K+-free medium/p value	Fold of modulation by ouabain/K+-free medium in HeLa or RVSMC
EGR1//early growth response 1	8108370	9.69/1.10E-05	64.81/1.98E-08
FOS//FBJ murine osteosarcoma viral oncogene	7975779	2.60/2.41E-04	15.97/7.24E-08
TNFAIP3//tumor necrosis factor, alpha-induced protein 3	8122265	3.34/7.23E-05	15.71/7.53E-08	1.90/11.77 (HeLa)
ZFP36//zinc finger protein 36, C3H type,	8028652	2.36/5.36E-04	12.07/1.99E-07
NUAK2//NUAK family, SNF1-like kinase, 2	7923753	2.22/3.28E-04	9.97/9.48E-08
IL1A//interleukin 1, alpha	8054712	3.30/5.79E-05	8.88/2.11E-07
CD274//CD274 molecule	8154233	3.71/1.71E-05	7.96/8.93E-08	1.42/2.31(HeLa)
PTGS2//prostaglandin-endoperoxide synthase 2	7922976	3.73/6.24E-08	7.84/1.12E-09
ATF3//activating transcription factor 3	7909610	1.86/7.23E-05	7.50/1.46E-08
JUNB//jun B proto-oncogene	8026047	1.85/6.08E-04	7.32/1.26E-07
TXNIP//thioredoxin interacting protein	7904726	2.62/3.51E-04	6.99/7.32E-07
ADAMTS1//ADAM metallopeptidase with thrombospondin type 1 motif, 1	8069676	2.42/2.49E-04	6.31/4.46E-07
est (ncrna:misc_RNA)	7919749	2.20/4.60E-03	6.23/7.44E-06
HES1//hairy and enhancer of split 1, (Drosophila)	8084880	2.07/2.77E-04	5.86/2.11E-07
KITLG//KIT ligand	7965322	1.85/4.92E-05	5.85/1.70E-08
FOSB//FBJ murine osteosarcoma viral oncogene	8029693	1.99/6.50E-04	5.82/4.46E-07
Novel scRNA pseudogene	8160086	1.47/2.70E-02	5.64/1.49E-06
SNAPC1//small nuclear RNA activating complex, polypeptide 1, 43 kD	7974870	2.17/2.13E-05	5.48/1.98E-08
NFKBIZ//nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta	8081386	2.44/1.10E-05	5.15/2.16E-08
JUN//jun oncogene	7916609	1.94/3.43E-05	5.11/1.98E-08
FAM148B//family with sequence similarity 148, member B	7989473	2.28/4.60E-03	5.09/2.05E-05
CXCL1//chemokine (C-X-C motif) ligand 1	8095697	2.03/2.26E-03	5.02/3.75E-06	2.97/4.02 (RVSMC)
SPRY4//sprouty homolog 4 (Drosophila)	8114797	3.27/5.05E-05	4.91/9.53E-07
DDIT3//DNA-damage-inducible transcript 3	7964460	1.35/1.12E-02	4.91/2.20E-07
HSPA1B//heat shock 70 kDa protein 1B	8178086	1.81/1.22E-02	4.78/1.22E-05
BIRC3//baculoviral IAP repeat-containing 3	7943413	1.69/5.91E-03	4.58/2.71E-06
KLF10//Kruppel-like factor 10	8152215	1.83/2.41E-04	4.53/1.34E-07
IL8//interleukin 8	8095680	1.96/2.61E-03	4.45/4.97E-06	2.93/10.00 (HeLa)
est (ncrna:snoRNA)	8126093	1.88/4.07E-04	4.41/4.46E-07
HSPA1A//heat shock 70 kDa protein 1A	8118310	1.85/7.33E-03	4.39/1.10E-05
SNORD3A//small nucleolar RNA, C/D box 3A	8005547	1.29/2.70E-02	4.31/4.46E-07
est (ncrna:misc_RNA)	8122816	1.52/8.96E-03	4.30/1.59E-06
PPP1R15A//protein phosphatase 1, regulatory (inhibitor) subunit 15A	8030128	2.54/1.58E-04	4.08/1.26E-06
VIP//vasoactive intestinal peptide	8122865	1.53/4.54E-02	4.02/1.97E-05
KDM6B//lysine (K)-specific demethylase 6B	8004671	1.63/5.12E-03	4.01/2.53E-06	1.73/2.83 (HeLa)
SNORD52//small nucleolar RNA, C/D box 52	8118322	−2.12/5.04E-03	−4.14/2.96E-05
est (ncrna:snoRNA)	8012906	−1.94/5.91E-04	−4.39/8.68E-07
LOC100287934//similar to hCG2042721	7896754	−1.93/2.58E-03	−4.46/4.31E-06	−2.41/−4.01 (HeLa)
est (ncrna:misc_RNA)	8007990	−1.37/4.92E-02	−5.03/1.59E-06

Genes whose differential expression is limited to HUVEC are shown in bold. Genes whose expression were also detected in HeLa or RVSMC are shown in . Genes whose expression was not affected by Na+,K+-ATPase inhibition in Ca2+-depleted cells are shown in italics.

Table 6

the list of genes whose expression was changed by more than 4-fold in 3 hr of Na+,K+-ATPase inhibition in control (Ca2+ containing) medium.

Gene symbol, title	Affymetrix ID	Fold of activation or inhibition (-) by ouabain/p value	Fold of activation or inhibition (-) by K+-free medium/p value	Fold of modulation by ouabain/K+-free medium in HUVEC or HeLa
Cxcl2//chemokine (C-X-C motif) ligand 2	10775896	3.44/7.21E-07	24.32/1.69E-09	1.38/2.58 (HUVEC)
Atf3//activating transcription factor 3	10770710	4.72/ 2.24E-07	20.63/ 2.72E-09
Fosb//FBJ osteosarcoma oncogene B	10719432	5.91/1.15E-06	15.22/4.45E-08
Btg2//B-cell translocation gene 2, anti-proliferative	10767767	5.28/1.08E-05	12.02/6.67E-07
Nr4a1//nuclear receptor subfamily 4, group A	10899387	3.52/2.89E-05	10.73/4.79E-07	2.63/11.79 (HeLa)
Csf2//colony stimulating factor 2	10742663	2.26/ 2.74E-05	10.35/ 4.23E-08
cDNA:known	10708091	3.89/1.50E-07	10.31/3.10E-09
Ptgs2//prostaglandin-endoperoxide synthase 2	10764551	9.46/1.08E-07	9.95/3.97E-08
Egr2 //early growth response 2	10832802	2.87/ 2.64E-06	9.08/ 2.01E-08	1.85/5.79 (HeLa)
Fos//FBJ osteosarcoma oncogene	10886031	3.17/3.92E-06	8.76/5.28E-08
Lif //leukemia inhibitory factor	10773853	6.68/ 7.21E-07	8.68/ 1.47E-07
Nr4a2//nuclear receptor subfamily 4, group A	10845384	5.19/1.51E-06	8.65/1.47E-07
Axud1//AXIN1 up-regulated 1	10920967	5.10/7.51E-08	8.22/4.42E-09
Rgs2//regulator of G-protein signaling 2	10768332	2.41/6.15E-04	7.67/3.13E-06	1.31/2.65 (HUVEC)
Snf1lk//SNF1-like kinase	10832197	3.80/4.77E-06	7.55/2.42E-07
Birc3//baculoviral IAP repeat-containing 3	10914799	3.30/2.04E-08	7.47/3.66E-10
Egr1//early growth response 1	10800919	4.80/ 8.98E-06	6.97/ 1.76E-06
Plk2//polo-like kinase 2 (Drosophila)	10812954	2.14/ 1.27E-06	6.77 3.10E-09
Irf1//interferon regulatory factor 1	10733553	1.51/1.47E-04	6.33/1.70E-08
Hes1//hairy and enhancer of split 1	10754943	3.00/2.07E-06	6.15/5.28E-08
Egr3//early growth response 3	10781337	3.87/4.79E-07	6.00/4.45E-08
Zfp36//zinc finger protein 36	10720215	3.52/1.19E-06	5.95/7.06E-08
Txnip//thioredoxin interacting protein	10817552	3.85/1.47E-06	5.84/1.46E-07
Nfkbia//nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha	10890024	2.46/3.55E-07	5.80/3.36E-09
Cish//cytokine inducible SH2-containing protein	10912908	3.59/8.97E-08	5.76/4.42E-09
Ier2//immediate early response 2	10806685	3.88/1.82E-06	5.26/2.80E-07
Hand1//heart and neural crest derivatives	10719358	1.86/7.51E-03	5.16/1.95E-05
Il6//interleukin 6	10859799	3.40/1.21E-05	4.76/2.03E-06
Nr4a3//nuclear receptor subfamily 4, group A	10868940	4.16/1.99E-05	4.68/9.44E-06	2.77/11.06 (HeLa)
Nfkbiz//nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta	10750848	3.24/8.70E-07	4.47/9.70E-08
Csf3//colony stimulating factor 3 (granulocyte)	10738051	7.04/2.47E-06	4.34/7.97E-06
Arrdc4//arrestin domain containing 4	10722720	2.39/2.99E-05	4.32/9.50E-07
Ddit3//DNA-damage inducible transcript 3	10895861	2.15/ 1.08E-07	4.26/ 1.52E-09
Junb//jun B proto-oncogene	10806585	4.03/ 2.54E-07	4.24/ 8.44E-08
Tiparp//TCDD-inducible poly(ADP-ribose) polymerase	10815763	2.64/1.51E-06	4.20/7.06E-08
Hbegf//heparin-binding EGF-like growth factor	10803947	4.44/1.55E-05	4.10/1.63E-05
Cxcl1//chemokine (C-X-C motif) ligand 1	10775900	2.97/3.28E-07	4.02/3.72E-08	2/03/5.02 (HUVEC)
Ttc30b//tetratricopeptide repeat domain 30B	10846293	−4.13/3.19E-05	−1.44/4.97E-02	−1.38/−1.54 (HUVEC)
Gemin4 //gem (nuclear organelle) associated protein	10745022	−4.08/ 2.21E-06	−2.10/ 6.59E-05
RGD1566325 //similar to regulator of sex-limitation candidate 16	10796900	−4.15/ 4.85E-06	−2.16/ 1.38E-04
est (ncrna: snoRNA)	10765034	−1.99/1.58E-06	−5.01/4.91E-09
est (ncrna: snoRNA)	10713606	−3.21/2.51E-06	−5.56/1.42E-07
est (ncrna: snoRNA)	10713604	−3.37/7.17E-06	−7.34/2.44E-07

Genes whose differential expression is limited to RVSMC are shown in bold. Genes whose expression were also detected in HeLa or HUVEC are shown in . Genes whose expression was not affected by Na+,K+-ATPase inhibition in Ca2+-depleted cells are shown in italics.

Effects of Ca2+-free medium and intracellular Ca2+ chelation on gene expression

To trigger Ca2+-depletion, we incubated cells in Ca2+-free medium containing extra- and intracellular Ca2+ chelators (50 µM EGTA and 10 µM BAPTA-AM, respectively). Figure 7A displays that in HeLa cells this procedure almost completely abolished sharp elevation of [Ca2+]i evoked by activation of purinergic receptors by ATP. We did not reveal any significant elevation of [Ca2+]i in Ca2+-depleted, ATP-treated HUVEC and RVSMC (Fig. 7B).

Figure 7

Effect of EGTA and BAPTA on Ca2+ signalling triggered by activation of purinergic receptors.

A. Representative records showing kinetics of elevation of intracellular Ca2+-concentration (F340/F360 ratio) in HeLa cells triggered by addition of 100 µM ATP. 1 – Control (Ca2+-containing medium); 2 – cells were preincubated for 10 min in Ca2+-free medium containing 50 µM EGTA and 10 µM BAPTA-AM. B. Baseline and maximal values of [Ca2+]i in ATP-treated HeLa, HUVEC and RVSMC in control and Ca2+-free medium containing 50 µM EGTA and 10 µM BAPTA-AM. Mean ± S.E. values obtained in 4 experiments are shown.

Similarly to the results obtained in Ca2+-containing media, PCA found that treatments with ouabain and K+-free medium produced dramatic changes in gene expression in Ca2+-depleted HUVEC, RVSMC and HeLa cells (Fig. 8A). Figures 8B and Table 7 show that in all types of Ca2+-depleted cells, the numbers of differentially expressed genes were increased in comparison to cells incubated in Ca2+-containing media (Fig. 3B, Table 2). As in Ca2+-containing media, we ascertained significant positive correlations between the differential expression of transcripts triggered by ouabain and K+-free medium in Ca2+-depleted RVSMC (R2 = 0.98; p<0.03), HUVEC (R2 = 0.96; p<3×10−7) and HeLa cells (R2 = 0.93; p<2×10−20) (Fig. 9). Importantly, the number of Na+ i,K+ i-sensitive transcripts, i.e. transcripts whose expression is affected by both ouabain and K+-free medium, was also increased in the presence of extra- and intracellular Ca2+ chelators by ∼3 fold in HeLa and HUVEC and by 2-fold in RVSMC (Fig. 10A, compare to Fig. 6A).

Figure 8

Comparative analysis of the actions of Na+,K+-ATPase inhibition by ouabain and K+-free medium on the transcriptome of Ca2+-depleted HeLa, HUVEC and RVSMC.

A. Principal component analysis of HeLa, HUVEC and RVSMC transcriptomes. Cells were incubated for 3 hr in Ca2+-free medium containing 50 µM EGTA and 10 µM BAPTA-AM and processed for oligonucleotide microarray analysis as indicated in the Methods section. Ouabain was added at a final concentration of 3 µM (HeLa and HUVEC) or 3 mM (RVSMC). Ellipsoids highlight portioning of samples based on the type of cell treatment. The principal components in 3-dimensional graphs (PC#1, PC#2 and PC#3) represent the variability in gene expression level within datasets. The total percentage of PCA mapping variability is shown on top. B. Total numbers of genes whose expression is altered by ouabain and K+-free medium by more than 1.2-fold with p<0.05 are indicated; numbers of genes affected by both stimuli appears in bold.

Table 7

Total numbers of differentially expressed transcripts in HeLa, HUVEC and RVSMC in 3-hr of Na+,K+-ATPase inhibition in Ca2+-free medium containing extra- and intracellular Ca2+ chelators.

	Ouabain-treated cells	Cells treated with K+-free medium	Transcripts affected by both stimuli
HeLa
Up-regulated transcripts
Number of transcripts	1007	1633	755
Maximal fold of activation	13.52	28.33	N.A.
Down-regulated transcripts
Number of transcripts*	1204	1868	996
Maximal fold of inhibition	5.18	9.31	N.A.
HUVEC
Up-regulated transcripts
Number of transcripts	1521	1696	1177
Maximal fold of activation	12.58	19.96	N.A.
Down-regulated transcripts
Number of transcripts*	1631	1813	1329
Maximal fold of inhibition	8.19	10.91	N.A.
RVSMC
Up-regulated transcripts
Number of transcripts	2342	3107	1911
Maximal fold of activation	7.60	10.17	N.A.
Down-regulated transcripts
Number of transcripts*	1835	2400	1543
Maximal fold of inhibition	13.49	12.91	N.A.

Transcripts whose expression was altered by more than 1.2-fold with p<0.05 were subjected to analysis. EGTA and BAPTA-AM were added at concentrations of 50 and 10 µM, respectively. Ouabain was added at final concentration of 3 µM (HeLa and HUVEC) or 3 mM (RVSMC). N.A. – non-applicable.

Figure 9

Correlation analysis of transcripts whose expression is altered by ouabain and K+-free medium in Ca2+-depleted HeLa, HUVEC and RVSMC more than by 1.2-fold with p<0.05.

Cells were incubated during 3 hr in Ca2+-free medium containing 50 µM EGTA and 10 µM BAPTA-AM. Ouabain was added at a final concentration of 3 µM (HeLa and HUVEC) or 3 mM (RVSMC). The total number of transcripts subjected to analysis is shown in Figure 8B. Transcript expression in control cells was taken as 1.00.

Figure 10

Na+ i,K+ i-sensitive transcriptomes identified in Ca2+-depleted cells.

A. Pie-chart showing the numbers of and cell type-specific, Na+ i,K+ i-sensitive genes detected in HeLa, HUVEC and RVSMC and ubiquitous Na+ i,K+ i-sensitive genes found in all 3 types of cells. Experiments were performed in Ca2+-free medium containing 50 µM EGTA and 10 µM BAPTA-AM. B. The distribution of ubiquitous and cell type-specific Na+ i,K+ i-sensitive among major functional groups. Digitals shown in correspond to gene numbers in each functional group.

Further analysis disclosed that () less than 25% of ubiquitous Na+ i,K+ i-sensitive genes were detected in the Ca2+-containing media only, () the expression of ∼15% of ubiquitous Na+ i,K+ i-sensitive genes was independent on the presence of extra- and intracellular Ca2+ chelators, and () more than 60% of ubiquitous and cell type-specific Na+ i,K+ i-sensitive genes were found exclusively in Ca2+-depleted cells (Fig. 11). In HeLa cells, among the Na+ i,K+ i-sensitive genes whose expression was changed by ouabain or K+-free medium by more than 4-fold, we did not observe any genes whose differential expression was abolished by Ca2+ depletion (Table 4). In HUVEC and RVSMC this procedure eliminated differential expression of ∼3 and 20% of transcripts, respectively (Tables 5,6).

Figure 11

Pie-chart showing the action of Ca2+ depletion on Na+ i,K+ i-sensitive transcriptomes.

Ca2+-depletion was triggered by omission of extracellular Ca2+ and addition of 50 µM EGTA and 10 µM BAPTA-AM. The numbers of ubiquitous Na+ i,K+ i-sensitive genes and Na+ i,K+ i-sensitive genes detected in HUVEC, HeLa and RVCSM are shown in .

To further verify the efficacy of Ca2+ depletion procedure employed in our study, we compared intracellular concentration of BAPTA, Ca2+ i and expression of 3 selected genes in HeLa cells incubated in the presence of 10 or 100 µM BAPTA-AM. In control Ca2+-containing medium, 3 hr incubation of HeLa cells with ouabain elevated [Ca2+]i by ∼35% and increased content of EGR1, PTGS2 and PPP1R15A RNAs by ∼56-, 6- and 9-fold, respectively (Table 8). Addition of 10 µM BAPTA-AM in Ca2+-free medium containing 50 µM EGTA completely abolished an increment of [Ca2+]i triggered by ouabain and increased the content of EGR1, PTGS2 and PPP1R15A RNAs by ∼6-, 2- and 1.3-fold, respectively. Elevation of BATPA-AM concentration in the incubation medium up to 100 µM increased intracellular [BAPTA] from 127 to 735 µM and augmented expression of EGR1, PTGS2 and PPP1R15A by ∼9-, 2,5- and 2.2-fold, respectively. This action of Ca2+-depletion procedure is probably caused by elevation of the passive permeability of the plasma membrane for Na+ and [Na+]i/[K+]i ratio detected in EGTA- and BAPTA-AM-treated RVSMC [20]. Importantly, elevation of intracellular [BAPTA] up to 735 µM did not abolished increments of gene expression evoked by 3 hr incubation with ouabain (Table 8).

Table 8

Intracellular concentration of BAPTA, Ca2+ and expression of EGR1, PTGS2 and PPP1R15A in HeLa cells.

Incubation medium	Ouabain, µM	Intracellular [BAPTA], µM	[Ca2+]i, nM	Gene expression, arbitrary units,
				EGR1	PTGS2	PPP1R15A
1. Control	0	ND	121±12	1.0	1.0	1.0
	3	ND	164±11*	56.4±2.3***	6.1±0.8***	9.3±1.1***
2. Ca2+-free+10 µM	0	127±33	97±8	6.0±0.6	1.9±0.3	1.3±0.2
BAPTA-AM	3	ND	92±14	59.9±1.7***	4.8±0.7**	5.1±0.7**
3. Ca2+-free+100 µM	0	735±101	91±15	9.3±0.8	2.5±0.3	2.2±0.4
BAPTA-AM	3	ND	104±9	55.2±3.4***	7.2±0.8**	6.4±0.5***

HeLa cells were incubated during 3 hrs with or without ouabain in control medium containing 1.8 mM CaCl2 (1) or in Ca2+-free medium containing 50 µM EGTA and 10 or 100 µM BAPTA-AM (2 and 3, respectively). Changes in the expression of of EGR1, PTGS2 and PPP1R15A were measured by qRT-PCR. For more details, see Methods section. Means ± S.E. obtained in experiments performed in quadruplicate are shown. ND – these values were not determined.

- p<0.05, 0.01 and 0.001 compared to values obtained in the absence of ouabain, respectively.

Table 9 lists the ubiquitous Na+ i,K+ i-sensitive genes, which were detected in Ca2+-depleted RVSMC, HUVEC and HeLa cells. Similarly to Ca2+-containing conditions, ubiquitous Na+ i,K+ i-sensitive transcriptomes in the Ca2+-depleted cells were abundant with regulators of transcription/translation, cell cycle control and inflammatory/immune responses (Fig. 10B). Importantly, the actions of elevated [Na+]i/[K+]i ratio on the differential expression of several genes shown in Table 8 in italics, such as nuclear receptor Nr4a1, anti-proliferative gene Btg2, angiogenic inducer Cyr61, adrenomedulin Adm and regulator of G-protein signaling Rgs2, were abolished in the presence of Ca2+. We also noted that in Ca2+-depleted cells 23 genes or 13% of ubiquitous Na+ i,K+ i-sensitive transcriptome were involved in protein folding and ubiquitination. This is in contrast to 2 genes in the same functional category that were detected in the presence of Ca2+ (Fig. 6B). These results are consistent with numerous observations that Ca2+-depletion causes endoplasmic reticulum stress and activates unfolded protein response (for review, see [21]).

Table 9

Genes whose expression was changed in HeLa, HUVEC and RVSMC by more than 1.2-fold (p≤0.05) in 3 hr of Na+,K+-ATPase inhibition in Ca2+-free medium containing extra- and intracellular Ca2+ chelators.

No.	Gene symbol, title	WKY-7		HUVEC		HeLA
		Fold of activation by		Fold of activation by		Fold of activation by
		ouabain	K+-free medium	Ouabain	K+-free medium	ouabain	K+-free medium
	Up-regulated genes
1t	Fos//FBJ osteosarcoma oncogene	6.11±0.12	6.97±0.10	11.05±0.14	19.68±0.13	13.52±0,10	28.33±0,08
2t	Zfp36//zinc finger protein 36	2.77±0.06	3.42±0.06	12.58±0.06	15.10±0.09	8.34±0,11	13.83±0,10
3t	Fosb//FBJ osteosarcoma oncogene B	4.07±0.11	5.60±0.11	2.70±0.11	4.30±0.07	3.73±0,12	11.09±0,06
4t	Nr4a1 //nuclear receptor subfamily 4, group A, member 1	1.36±0.06	1.83±0.07	1.31±0.03	1.77±0.04	4.23±0,09	8.75±0,09
5t	Jun//Jun oncogene	1.75±0.04	2.16±0.03	3.46±0.06	4.76±0.06	3.81±0,10	8.18±0,08
6d	Dusp8//dual specificity phosphatase 8	2.34±0.05	2.07±0.05	3.59±0.11	4,73±0.07	3.26±0,10	6.31±0,12
7d	Btg2 //B-cell translocation gene 2, anti-proliferative	3.68±0.07	4.44±0.08	1.42±0.11	1.59±0.11	2.51±0,11	5.36±0,06
8d	Cyr61 //cysteine-rich, angiogenic inducer, 61	1.58±0.04	1.61±0.04	2.16±0.05	2.43±0.05	3.04±0,09	4.94±0,09
9d	Ppp1r15a//protein phosphatase 1, regulatory (inhibitor) subunit 1	1.33±0.08	1.59±0.07	1.48±0.07	1.63±0.07	2.59±0,11	3.92±0,10
10d	Nuak2 //NUAK family, SNF1-like kinase, 2	1.44±0.09	1.95±0.07	2.91±0.12	4.18±0.14	1.78±0,10	3.85±0,09
11t	Hes1//hairy and enhancer of split 1 (Drosophila)	3.56±0.05	4.07±0.05	2.69±0.02	2.96±0.02	2.75±0,04	3.77±0,05
12i	Adamts1 //ADAM metallopeptidase with thrombospondin type 1 motif	2.06±0.07	2.77±0.07	1.60±0.07	2.54±0.09	2.62±0,07	3.56±0,08
13d	Rhob //ras homolog gene family, member B	1.72±0.09	1.74±0.10	1.33±0.03	1.52±0.04	2.10±0,08	3.31±0,07
14t	Id2 //inhibitor of DNA binding 2	1.29±0.08	1.31±0.07	1.93±0.08	2.71±0.11	1.77±0,09	3.29±0,06
15o	Adm //adrenomedullin	3.28±0.10	4.25±0.09	3.07±0.05	3.76±0.07	2.01±0,09	3.21±0,06
16d	Dusp1 //dual specificity phosphatase 1	5.45±0.10	6.90±0.10	2.71±0.06	3.29±0.06	2.34±0,05	3.13±0,04
17i	Nfkbia//nuclear factor of kappa light polypeptide gene	2.53±0.03	3.25±0.04	1.77±0.04	2.18±0.09	1.83±0,08	3.07±0,08
18t	Ier2 //immediate early response 2	1.30±0.02	1.48±0.06	1.82±0.05	2.05±0.06	2.03±0,07	2.86±0,06
19i	Nfkbiz//nuclear factor of kappa light polypeptide gene	1.29±0.06	1.51±0.07	2.44±0.05	3.19±0.05	2.18±0,04	2.64±0,04
20d	Dusp10 //dual specificity phosphatase 10	1.58±0.04	2.08±0.03	1.56±0.06	2.14±0.04	1.99±0,09	2.59±0,06
21o	Tiparp //TCDD-inducible poly(ADP-ribose) polymerase	1.92±0.04	2.01±0.04	2.01±0.04	2.31±0.04	1.89±0,04	2.57±0,04
22d	Plk3//polo-like kinase 3 (Drosophila)	1.48±0.04	1.51±0.04	1.52±0.06	1.79±0.09	1.79±0,06	2.52±0,06
23o	Il6//interleukin 6	1.84±0.11	2.00±0.11	1.42±0.03	1.27±0.07	1.39±0,13	2.45±0,14
24t	Maff//v-maf musculoaponeurotic fibrosarcoma oncogene homolog F	2.45±0.12	2.64±0.11	2.21±0.05	2.27±0.05	1.78±0,07	2.24±0,08
25o	Ptgs2//prostaglandin-endoperoxide synthase 2	1.78±0.04	2.11±0.03	1.83±0.06	2.12±0.06	1.82±0,09	2.23±0,06
26t	Jund //Jun D proto-oncogene	1.38±0.04	1.52±0.04	1.73±0.05	1.96±0.07	1.47±0,10	2.16±0,11
27t	Rgs2 //regulator of G-protein signaling 2	1.35±0.07	1.72±0.08	2.31±0.07	2.99±0.07	1.33±0,08	2.14±0,09
28d	Ccnl1//cyclin L1	1.76±0.04	1.72±0.04	1.89±0.06	2.11±0.04	1.52±0,05	2.10±0,03
29o	Dusp16 //dual specificity phosphatase 16	1.38±0.04	1.28±0.03	2.34±0.07	3.43±0.09	1.43±0,07	2.02±0,11
30d	Lats2 //large tumor suppressor 2	1.46±0.06	1.39±0.06	1.43±0.03	1.51±0.03	1.55±0,06	1.94±0,07
31o	Insig1//insulin induced gene 1	1.31±0.03	1.42±0.03	1.81±0.03	2.06±0.03	1.50±0,03	1.89±0,03
32d	Gadd45b //growth arrest and DNA-damage-inducible, beta	1.44±0.08	1.71±0.06	1.68±0.06	1.72±0.08	1.23±0,09	1.87±0,07
33d	Abl2//v-abl Abelson murine leukemia viral oncogene homolog 2	2.21±0.06	1.86±0.06	1.38±0.03	1.52±0.03	1.51±0,07	1.84±0,09
34o	Cd68 //Cd68 molecule	2.52±0.17	1.52±0.16	1.31±0.09	1.22±0.10	1.38±0,07	1.83±0,05
35d	Skil //SKI-like oncogene	1.44±0.04	1.45±0.05	1.36±0.05	1.52±0.05	1.40±0,07	1.78±0,05
36t	Crem //cAMP responsive element modulator	1.32±0.06	1.65±0.05	1.51±0.03	1.64±0.05	1.45±0,04	1.68±0,05
37d	Wee1 //wee 1 homolog (S. pombe)	1.48±0.06	1.30±0.07	1.52±0.04	1.68±0.05	1.48±0,03	1.63±0,04
38f	Yod1 //YOD1 OTU deubiquinating enzyme 1 homolog (S. cerevisiae)	1.32±0.06	1.31±0.04	1.37±0.04	1.22±0.04	1.55±0,07	1.63±0,07
39d	Cd274 //CD274 molecule	1.31±0.06	1.30±0.06	4.60±0.10	6.81±0.10	1.54±0,05	1.61±0,09
40d	Hspg2 //heparan sulfate proteoglycan 2	1.87±0.03	1.99±0.04	1.36±0.04	1.35±0.04	1.48±0,05	1.58±0,05
41o	Slc19a2 //solute carrier family 19 (thiamine transporter)	1.29±0.02	1.38±0.06	1.60±0.06	1.56±0.06	1.62±0,07	1.55±0,07
42o	Zswim6 //zinc finger, SWIM-type containing 6	1.26±0.05	1.33±0.05	1.47±0.02	1.56±0.03	1.37±0,02	1.49±0,02
43o	Agrn //agrin	1.89±0.04	1.92±0.03	1.73±0.06	1.63±0.08	1.34±0,05	1.49±0,05
44o	Neu1 //sialidase 1 (lysosomal sialidase)	1.28±0.07	1.49±0.07	1.29±0.09	1.26±0.12	1.38±0,07	1.48±0,05
45d	Ptprj //protein tyrosine phosphatase, receptor type	1.79±0.05	1.81±0.06	1.53±0.06	1.47±0.06	1.39±0,03	1.47±0,03
46o	Pfkfb4 //6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4	1.23±0.04	1.26±0.04	1.29±0.07	1.30±0.07	1.27±0,08	1.46±0,05
47o	Lama5 //laminin, alpha 5	1.37±0.03	1.45±0.03	1.55±0.04	1.55±0.06	1.24±0,04	1.46±0,06
48d	Cdc26 //cell division cycle 26	2.10±0.09	2.12±0.08	1.56±0.05	1.62±0.09	1.47±0,05	1.46±0,06
49t	Cbx6 //chromobox homolog 6	1.60±0.03	1.74±0.04	1.59±0.04	1.49±0.04	1.38±0,03	1.42±0,04
50d	Cnnm4 //cyclin M4	1.27±0.08	1.37±0.06	1.31±0.03	1.37±0.07	1.21±0,09	1.42±0,09
51o	Txnip//thioredoxin interacting protein	3.81±0.07	3.72±0.07	3.23±0.05	2.40±0.08	1.31±0,06	1.40±0,04
52f	Skp1 //S-phase kinase-associated protein 1	1.30±0.04	1.30±0.03	1.41±0.08	1.52±0.09	1.30±0,05	1.38±0,05
53d	Ltbp2 //latent transforming growth factor beta binding protein 2	1.27±0.03	1.32±0.04	1.24±0.04	1.21±0.04	1.27±0,04	1.37±0,04
54o	B4galt5 //UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase	1.60±0.03	1.79±0.03	1.28±0.02	1.20±0.02	1.42±0,02	1.36±0,03
55i	Relt //RELT tumor necrosis factor receptor	1.51±0.05	1.31±0.05	1.33±0.05	1.25±0.07	1.39±0,03	1.36±0,07
56t	Rfx1 //regulatory factor X, 1 (influences HLA class II expression)	1.29±0.07	1.23±0.07	1.36±0.11	1.27±0.10	1.31±0,04	1.34±0,08
57o	Pip5k1c //phosphatidylinositol-4-phosphate 5-kinase, type I	1.26±0.05	1.29±0.05	1.25±0.06	1.23±0.06	1.23±0,02	1.33±0,06
58d	Efhd2 //EF-hand domain family, member D2	1.23±0.04	1.36±0.04	1.53±0.09	1.52±0.11	1.23±0,04	1.32±0,07
59o	Slc16a3 //solute carrier family 16, member 3	2.17±0.11	2.30±0.11	1.36±0.07	1.30±0.07	1.26±0,04	1.32±0,06
60d	Ccnd1 //cyclin D1	1.25±0.03	1.33±0.03	1.42±0.04	1.35±0.03	1.25±0,03	1.32±0,04
61o	Gla //galactosidase, alpha	1.72±0.03	1.61±0.06	1.34±0.09	1.50±0.07	1.31±0,06	1.30±0,08
62o	Abca2 //ATP-binding cassette, sub-family A (ABC1), member 2	1.48±0.04	1.45±0.05	1.37±0.05	1.28±0.07	1.22±0,04	1.27±0,04
63o	Epha4 //Eph receptor A4	2.03±0.08	2.28±0.09	1.67±0.06	1.83±0.06	1.28±0,06	1.27±0,08
64t	Nfya//nuclear transcription factor-Y alpha	1.40±0.06	1.27±0.05	1.35±0.02	1.30±0.07	1.47±0,06	1.26±0,05
65o	Megf9 //multiple EGF-like-domains 9	1.40±0.05	1.55±0.05	1.27±0.07	1.29±0.07	1.26±0,04	1.26±0,08
66t	Arid3b //AT rich interactive domain 3B (Bright like)	1.46±0.05	1.24±0.05	1.57±0.07	1.51±0.07	1.29±0,11	1.26±0,10
67o	Pnkd //paroxysmal nonkinesiogenic dyskinesia	1.55±0.08	1.71±0.08	1.42±0.05	1.27±0.07	1.28±0,04	1.26±0,05
68t	Sart3 //squamous cell carcinoma antigen recognized by T-cells 3	1.34±0.05	1.28±0.05	1.53±0.04	1.49±0.04	1.23±0,08	1.24±0,05
69o	Myl6 //myosin, light chain 6, alkali, smooth muscle and non-muscle	1.22±0.01	1.24±0.01	1.22±0.04	1.22±0.04	1.30±0,04	1.23±0,04
70o	Slc2a12 //solute carrier family 2 (facilitated glucose transport)	1.45±0.07	1.58±0.06	1.34±0.09	1.45±0.10	1.34±0,08	1.22±0,05
	Down-regulated genes
1d	Chac1 //ChaC, cation transport regulator homolog 1 (E. coli)	−1.80±0.07	−2.21±0.10	−4.07±0.12	−5.17±0.20	−5.18±0,09	−9.31±0,11
2f	Herpud1 //homocysteine-inducible, endoplasmic reticulum stress-ind	−2.66±0.06	−3.03±0.05	−2.30±0.06	−3.12±0.05	−1.95±0,07	−2.64±0,07
3t	Sdf2l1 //stromal cell-derived factor 2-like 1	−1.82±0.07	−1.63±0.07	−3.03±0.04	−3.67±0.03	−1.80±0,08	−2.36±0,05
4t	Hoxb5//homeo box B5	−1.57±0.11	−1.53±0.11	−1.96±0.06	−2.19±0.08	−1.92±0,06	−2.33±0,04
5o	Asns //asparagine synthetase	−1.34±0.05	−1.43±0.04	−1.67±0.06	−1.67±0.09	−1.64±0,07	−1.96±0,04
6t	Trnt1 //tRNA nucleotidyl transferase, CCA-adding, 1	−1.37±0.14	−1.69±0.08	−1.20±0.06	−1.25±0.07	−1.51±0,10	−1.94±0,07
7f	Dnajc3 //DnaJ (Hsp40) homolog, subfamily C, member 3	−2.12±0.06	−2.17±0.05	−2.25±0.04	−2.51±0.03	−1.72±0,06	−1.91±0,06
8t	Cebpg //CCAAT/enhancer binding protein (C/EBP), gamma	−1.30±0.04	−1.45±0.03	−1.81±0.06	−1.91±0.05	−1.47±0,07	−1.91±0,08
9o	Riok2 //RIO kinase 2 (yeast)	−1.68±0.05	−1.60±0.05	−1.59±0.06	−1.53±0.06	−1.61±0,06	−1.89±0,08
10o	Ficd //FIC domain containing	−4.62±0.09	−4.59±0.08	−3.75±0.15	−3.79±0.17	−1.71±0,09	−1.87±0,09
11o	Pdia4 //protein disulfide isomerase family A, member 4	−1.82±0.05	−1.70±0.05	−1.58±0.04	−1.67±0.04	−1.64±0,07	−1.86±0,07
12o	Pck2 //phosphoenolpyruvate carboxykinase 2 (mitochondrial)	−1.50±0.05	−1.49±0.05	−1.95±0.05	−2.06±0.08	−1.79±0,05	−1.86±0,06
13t	Cars //cysteinyl-tRNA synthetase	−1.41±0.04	−1.97±0.04	−1.67±0.05	−1.89±0.06	−1.51±0,10	−1.85±0,09
14d	Dnajb9 //DnaJ (Hsp40) homolog, subfamily B, member 9	−1.91±0.05	−2.09±0.06	−4.30±0.11	−4.87±0.07	−1.73±0,10	−1.80±0,08
15o	Stc2 //stanniocalcin 2	−1.99±0.03	−2.03±0.05	−3.35±0.07	−3.40±0.09	−2.17±0,10	−1.79±0,11
16o	Zbed3 //zinc finger, BED-type containing 3	−1.52±0.11	−1.33±0.10	−1.65±0.08	−1.88±0.07	−1.56±0,09	−1.76±0,12
17o	Rpp40//ribonuclease P 40 subunit (human)	−1.35±0.08	−1.40±0.09	−1.46±0.04	−1.24±0.05	−1.31±0,07	−1.74±0,07
18t	Trim27 //tripartite motif-containing 27	−1.87±0.07	−1.84±0.06	−1.45±0.03	−1.30±0.03	−1.59±0,05	−1.72±0,07
19f	Hyou1 //hypoxia up-regulated 1	−2.24±0.08	−2.25±0.08	−1.71±0.05	−1.87±0.05	−1.42±0,04	−1.71±0,04
20t	Mrpl46//mitochondrial ribosomal protein L46	−1.34±0.05	−1.35±0.06	−1.36±0.04	−1.60±0.05	−1.33±0,04	−1.70±0,09
21t	Xbp1 //X-box binding protein 1	−1.67±0.04	−1.86±0.03	−1.46±0.07	−1.61±0.07	−1.30±0,05	−1.70±0,04
22f	Sel1l //sel-1 suppressor of lin-12-like (C. elegans)	−1.58±0.07	−1.74±0.07	−2.20±0.01	−2.37±0.02	−1.57±0,06	−1.68±0,07
23o	Ankrd49 //ankyrin repeat domain 49	−1.43±0.04	−1.33±0.06	−1.50±0.11	−1.49±0.08	−1.51±0,10	−1.66±0,08
24o	Lin37 //lin-37 homolog (C. elegans)	−1.40±0.06	−1.34±0.04	−1.45±0.06	−1.62±0.05	−1.46±0,06	−1.64±0,07
25t	Alkbh8 //alkB, alkylation repair homolog 8 (E. coli)	−1.92±0.05	−1.92±0.07	−1.37±0.07	−1.26±0.05	−1.37±0,10	−1.64±0,08
26o	Gpt2 //glutamic pyruvate transaminase	−1.35±0.07	−1.38±0.08	−1.64±0.06	−1.58±0.05	−1.70±0,08	−1.63±0,04
27o	Kctd6 //potassium channel tetramerisation domain containing 6	−1.80±0.10	−1.65±0.09	−1.51±0.07	−1.69±0.13	−1.41±0,08	−1.62±0,08
28t	Hoxb6 //homeo box B6	−1.60±0.08	−1.58±0.08	−1.38±0.10	−1.33±0.08	−1.38±0,07	−1.58±0,08
29d	Ddit4 //DNA-damage-inducible transcript 4	−2.29±0.02	−1.97±0.05	−5.09±0.10	−3.69±0.13	−1.84±0,05	−1.58±0,06
30o	Slc25a28 //solute carrier family 25, member 28	−1.85±0.05	−1.83±0.04	−1.41±0.07	−1.53±0.07	−1.28±0,06	−1.57±0,05
31o	Cth //cystathionase (cystathionine gamma-lyase)	−2.51±0.05	−2.62±0.06	−2.22±0.09	−2.20±0.12	−1.89±0,09	−1.54±0,09
32f	Rnf217 //ring finger protein 217	−1.31±0.09	−1.33±0.09	−2.73±0.08	−2.86±0.05	−1.28±0,09	−1.53±0,10
33f	Rnf146 //ring finger protein 146	−1.30±0.02	−1.21±0.03	−1.43±0.03	−1.59±0.06	−1.35±0,05	−1.50±0,07
34f	Fbxo42 //F-box protein 42	−1.42±0.05	−1.41±0.05	−1.38±0.04	−1.41±0.05	−1.43±0,04	−1.50±0,06
35o	Creld2 //cysteine-rich with EGF-like domains 2	−3.27±0.09	−2.99±0.08	−1.55±0.05	−1.51±0.05	−1.50±0,06	−1.49±0,07
36f	Hspa5 //heat shock protein 5	−1.28±0.03	−1.23±0.03	−1.57±0.03	−1.72±0.01	−1.42±0,04	−1.48±0,07
37o	Ttc14 //tetratricopeptide repeat domain 14	−1.23±0.08	−1.41±0.06	−1.42±0.04	−1.69±0.06	−1.27±0,06	−1.48±0,08
38d	Trib3 //tribbles homolog 3 (Drosophila)	−2.60±0.03	−3.86±0.06	−1.26±0.05	−1.41±0.07	−1.26±0,07	−1.46±0,07
39d	Jag1 //jagged 1	−1.45±0.04	−1.76±0.02	−1.36±0.04	−1.33±0.05	−1.39±0,04	−1.45±0,05
40d	Esco1 //establishment of cohesion 1 homolog 1 (S. cerevisiae)	−1.40±0.04	−1.43±0.04	−1.36±0.09	−1.21±0.08	−1.66±0,12	−1.45±0,10
41t	Exosc3 //exosome component 3	−1.29±0.06	−1.25±0.06	−1.46±0.06	−1.33±0.06	−1.27±0,10	−1.44±0,12
42o	Slc33a1 //solute carrier family 33 (acetyl-CoA transporter)	−1.88±0.10	−2.21±0.09	−1.92±0.08	−1.89±0.06	−1.41±0,05	−1.44±0,06
43d	Tbccd1 //TBCC domain containing 1	−1.35±0.06	−1.28±0.04	−1.38±0.04	−1.40±0.08	−1.41±0,06	−1.44±0,03
44o	Znf509 //zinc finger protein 509	−1.39±0.04	−1.26±0.04	−1.42±0.12	−1.29±0.10	−1.41±0,02	−1.43±0,07
45o	Slc25a37 //solute carrier family 25, member 37	−2.17±0.05	−1.89±0.07	−1.25±0.05	−1.20±0.06	−1.33±0,06	−1.42±0,06
46f	Dnajb11 //DnaJ (Hsp40) homolog, subfamily B, member 11	−1.33±0.05	−1.25±0.03	−1.62±0.06	−1.80±0.04	−1.28±0,05	−1.42±0,06
47f	Fem1b //feminization 1 homolog b (C. elegans)	−1.71±0.03	−1.60±0.03	−1.37±0.05	−1.39±0.05	−1.31±0,04	−1.39±0,04
48f	Trim23 //tripartite motif-containing 23	−1.37±0.05	−1.28±0.05	−1.57±0.08	−1.63±0.09	−1.40±0,09	−1.39±0,09
49t	Snapc3 //small nuclear RNA activating complex, polypeptide 3	−1.36±0.05	−1.40±0.05	−1.35±0.05	−1.41±0.04	−1.24±0,07	−1.37±0,06
50t	Gars //glycyl-tRNA synthetase	−1.31±0.02	−1.33±0.02	−1.24±0.02	−1.25±0.03	−1.25±0,03	−1.36±0,03
51o	Cyp2r1 //cytochrome P450, family 2, subfamily r, polypeptide 1	−1.37±0.07	−1.63±0.08	−1.31±0.07	−1.34±0.07	−1.31±0,09	−1.36±0,06
52o	Napb //N-ethylmaleimide-sensitive factor attachment prote	−1.31±0.10	−1.27±0.11	−1.32±0.12	−1.43±0.10	−1.36±0,07	−1.35±0,10
53o	Oraov1 //oral cancer overexpressed 1	−1.29±0.04	−1.42±0.08	−1.27±0.09	−1.30±0.09	−1.22±0,08	−1.34±0,07
54o	Piga //phosphatidylinositol glycan anchor biosynthesis, class A	−2.27±0.07	−2.92±0.06	−2.29±0.04	−2.56±0.03	−1.33±0,06	−1.34±0,06
55f	Dnajb5 //DnaJ (Hsp40) homolog, subfamily B, member 5	−1.24±0.04	−1.22±0.05	−1.76±0.06	−1.70±0.06	−1.46±0,09	−1.33±0,07
56f	Siah2 //seven in absentia 2	−1.34±0.02	−1.29±0.06	−1.47±0.09	−1.50±0.12	−1.27±0,10	−1.33±0,07
57t	Ccdc101 //coiled-coil domain containing 101	−1.22±0.06	−1.32±0.06	−1.63±0.10	−1.52±0.08	−1.30±0,04	−1.33±0,08
58t	Ccdc76 //coiled-coil domain containing 76	−1.23±0.05	−1.53±0.06	−1.26±0.05	−1.26±0.05	−1.35±0,06	−1.33±0,05
59d	Rad17 //RAD17 homolog (S. pombe)	−1.22±0.10	−1.42±0.05	−1.30±0.08	−1.32±0.07	−1.29±0,09	−1.32±0,07
60t	Lrrfip1 //leucine rich repeat (in FLII) interacting protein 1	−1.49±0.08	−1.52±0.07	−2.92±0.16	−3.62±0.21	−1.30±0,09	−1.32±0,10
61t	Zxdc //ZXD family zinc finger C	−1.31±0.06	−1.27±0.06	−1.39±0.11	−1.31±0.09	−1.27±0,11	−1.28±0,10
62t	Zrsr2 //zinc finger (CCCH type), RNA binding motif and serine/a	−1.40±0.07	−1.68±0.09	−1.31±0.06	−1.24±0.07	−1.23±0,07	−1.28±0,07
63f	Txndc11 //thioredoxin domain containing 11	−1.31±0.05	−1.32±0.04	−1.26±0.02	−1.34±0.04	−1.22±0,03	−1.24±0,06
64o	Ibtk //inhibitor of Bruton agammaglobulinemia tyrosine kinase	−1.37±0.07	−1.38±0.06	−1.41±0.03	−1.37±0.04	−1.24±0,06	−1.23±0,07
65f	Gopc //golgi associated PDZ and coiled-coil motif containing	−1.21±0.07	−1.28±0.06	−1.40±0.05	−1.39±0.07	−1.24±0,06	−1.23±0,04

Genes whose expression was not affected by ouabain or K+-free medium in the presence of Ca2+ in at least one of cell types are shown in . Genes whose expression was not affected by ouabain or K+-free medium in the presence of Ca2+ in all 3 types of cells shown in . Gene functions are indicated in the left column as: t – regulators of transcription/translation, RNA processing and degradation; d – regulators of cell adhesion, migration, proliferation, differentiation and death; f - protein folding and ubiquitination; i – inflammation and immune response; o – other functional categories and genes withy unknown function.

Based on this work we selected 8 ubiquitous Na+ i,K+ i-sensitive genes whose expression was increased by more than 5-fold in Ca2+-containing media, and whose augmented expression was preserved in the presence of extra- and intracellular Ca2+ chelators. As seen in Figure 12, Ca2+-depletion strongly attenuated (but did not completely abolish) Na+ i/K+ i-dependent changes in gene expression for FosB, Il6, Pppr1r15a and Ptgs2 in all cell types. In contrast, Ca2+-depletion slightly decreased, did not affect, or increased expression of Fos, Zfp36, Jun and Dusp8 in a cell type-specific manner. These results further illustrate that () [Ca2+]i elevation is not obligatory for changes in gene expression, and () Ca2+ i-dependent signaling may have complex effects on ubiquitous and cell type specific Na+ i,K+ i-sensitive transcriptomes.

Figure 12

Effect of Ca2+-depletion on expression of ubiquitous Na+ i,K+ i-sensitive genes in HeLa, HUVEC and RVSMC.

Cells were incubated during 3 hrs in control medium containing 1.8 mM CaCl2 or in Ca2+-containing K+-free medium. To trigger Ca2+-depletion, CaCl2 was omitted and 50 µM EGTA and 10 µM BAPTA-AM were added. Increments of gene expression triggered by Na+,K+-ATPase inhibition in Ca2+-containing medium were taken as 100%. For absolute values of gene expression, see Tables 3 and 8.

Discussion

In the present study we utilized genome-wide Affymetrix arrays to identify [Na+]i/[K+]i-sensitive transcriptomes in 3 diverse cell lines. Based on the results presented here we can conclude that elevation of the [Na+]i/[K+]i-ratio causes robust changes in gene expression in both ubiquitous and cell type-dependent manners. The number of regulated transcripts was high and represented more than 2% of the total genome. Surprisingly, Ca2+-depletion increased rather than decreased number of the [Na+]i/[K+]i-sensitive genes. These findings point to the existence of novel, yet unidentified Ca2+ i-independent mechanisms of transcriptional regulation, which are determined by the intracellular concentration of monovalent cations.

Characterization of ubiquitous Na+ i,K+ i-sensitive transcriptome

We observed that sustained Na+,K+-ATPase inhibition by ouabain led to the differential expression of 886 transcripts in primary cultured human endothelial cells, 819 transcripts in human epitheloid carcinoma cell line and 3191 transcripts in smooth muscle cells obtained from the rat aorta (Fig. 2). Differentially regulated genes represent ∼3 and ∼10% of genes in human and rat genome, respectively. Keeping in mind that ouabain may affect signaling pathways independently of inhibition of Na+,K+-ATPase [14], [15], we tested K+-free medium as an alternative approach to elevation of the [Na+]i/[K+]i ratio. Three hour incubation of cells in K+-free medium resulted in gain of Na+ i and loss of K+ i that were quantitatively similar to those triggered by ouabain (Fig. 1). We found highly significant positive correlations between the levels of transcripts impacted by both stimuli (Fig. 4). These data strongly indicate that differential gene expression is evoked by elevation of the [Na+]i/[K+]i ratio rather than by Na+ i,K+ i-independent mechanisms.

Among 684, 737 and 1839 Na+ i,K+ i-sensitive transcripts detected in HeLa, HUVEC and RVSMC, we discerned 80 genes whose expression was increased up to 60-fold or decreased up to ∼3-fold independently of the origin of cultured cells (Table 3). It should be noted that because of the retarded kinetics of elevation of the [Na+]i/[K+]i ratio in human cells (Fig. 3), the number of Na+ i,K+ i-sensitive genes in HeLa and HUVEC as well as the number of ubiquitous Na+ i,K+ i-sensitive genes is probably underestimated.

Functional analysis demonstrated that almost the half of the ubiquitous Na+ i,K+ i-sensitive genes belonged to transcription and translation regulators (Fig. 6). Important examples include Egr1, Fos, Fosb, Atf3, Jun, Ddit3, Junb, Cyr61. Although functional characterization is somewhat artificial – because genes are usually multifunctional and fall into several categories – the relative content of transcriptional regulators identified in the ubiquitous Na+ i,K+ i-sensitive transcriptome was ∼7-fold higher than in total human genome [22]. These findings strongly suggest that heightened expression of ubiquitous Na+ i,K+ i-sensitive regulators of transcription underlie ubiquitous and cell-type specific transcriptomic modifications triggered by elevation of the [Na+]i/[K+]i. This conclusion is supported by analysis of the top gene expression network revealed using the IPA Knowledge Base software. Indeed, Figure 13 illustrates the central role of ubiquitous Na+ i/K+ i-sensitive regulators of gene expression such as Fos, FosB, Jun, JunB, Atf3, Cyr61 in the triggering of diverse cellular signals.

Figure 13

The signaling network possessing the highest score of 48 for association with differential expression of ubiquitous Na+ i,K+ i-sensitive genes.

The p-value and geometric fold change for each gene listed in Table 3 were overlaid onto a global molecular network developed from information within the IPA Knowledge Base. Genes are represented as nodes of various shapes to represent the functional category of gene product as shown in the top corner, and the biological relationship between two nodes is represented as a line. The up-regulated Na+ i,K+ i-sensitive genes are shown in pink. Note that network's Score of 48 is equal to -log(Fisher's Exact test result). It means that there is a 1 in 1048 chance of getting a network from Ingenuity Knowledge Base containing at least the same number of eligible molecules by chance when randomly picking molecules derived form 80 ubiquitous Na+ i,K+ i-sensitive genes listed in Table 3.

Figure 14 shows that cellular development, gene expression, cell death, immunological and inflammatory responses are among top altered biological functions controlled by ubiquitous Na+ i/K+ i-sensitive transcriptome and mapped in this software with p<10−5. Importantly, cellular responses triggered by differential expression of Na+ i,K+ i-sensitive genes might be cell type-specific. Thus, for example 24 hr incubation with ouabain resulted in death of renal epithelial cells [23] but rescued RVSMC from apoptosis triggered by serum deprivation [24].

Figure 14

Top significantly altered biological functions associated with differential expression of ubiquitous Na+ i,K+ i-sensitive genes.

The p-value and geometric fold change for each gene listed in Table 3 were imported into Ingenuity Pathway Analysis. The significance criteria with a threshold of p = 0.05 (or 1.3 when expressed as -log(p-value) is shown by line.

Ca2+-depletion increases the number of [Na+]i/[K+]i-sensitive genes

Numerous studies have demonstrated that elevation of the [Na+]i/[K+]i ratio heightens [Ca2+]i via activation of Na+ i/Ca2+ o exchanger as well as via depolarization and activation of voltage-gated Ca2+ channels (for review, see [9], [10]). It has also been well-documented that elevation of [Ca2+]i affects gene expression by activation of SRE via Ras-Raf-Erk-Elk1-mediated signaling, CRE via phosphorylation of CRE binding protein and nuclear factor AT (NFAT) binding sites via NFAT dephosphorylation by calcineurin [7], [25]–[27]. Unexpectedly, we found that in the presence of extra- and intracellular Ca2+ chelators (EGTA and BAPTA, respectively) the number of cell type-specific and ubiquitous Na+ i,K+ i-sensitive genes was increased rather than decreased. Importantly, differential expression of more than 50% of ubiquitous and cell type-specific Na+ i,K+ i-sensitive genes was detected in Ca2+-depleted cells only (Fig. 11). Furthermore, the expression of several genes such as Fos, Zfp36, Jun and Dusp8 was not affected or even activated in the presence of extra- and intracellular Ca2+ chelators (Fig. 12).

Recently, Akita and Okada reported that activation of volume-sensitive anion channels in astrocytes by bradykinin was suppressed by addition of BAPTA-AM at concentration higher than 100 µM [28]. Thus, it may be proposed that at concentration 10 µM used in our study BAPTA-AM was unable completely abolish elevation of [Ca2+]i triggered by sustained inhibition of the Na+/K+-ATPase. However, data listed below did not support this assumption. , 30 min incubation in Ca2+-free medium containing 10 µM BAPTA-AM and 50 µM EGTA sharply suppressed or completely abolished an increment of [Ca2+]i triggered by activation of purinergic receptors (Fig. 7). , in contrast to overwhelming number of electrically excitable cells, 2 hr exposure of RVSMC to ouabain did not affect [Ca2+]i but sharply increased expression of Fos and Jun superfamily IRG [12]. Here, we demonstrated that addition of 50 µM EGTA and 10 µM BAPTA-AM completely abolished a modest increment of [Ca2+]i triggered by 3 hr incubation of HeLa cells with ouabain whereas augmented expression of EGR1, PTGS2 and PPP1R15A was preserved (Table 8). , in the presence of 10 µM BAPTA-AM, intracellular concentration BAPTA in HeLa cells reached a value of ∼130 µM (Table 8). Based on the volume of intracellular water (∼2 µl/mg of protein), the intracellular BAPTA content on these cells (∼260 pmol/mg protein) was sufficient to bind the total pool of intracellular exchangeable calcium (∼200 pmol/mg protein) [13]. , elevation of intracellular [BAPTA] up to ∼700 µM did not abolished increments of gene expression evoked by ouabain (Table 8). It is important to note that long-term exposure of cells to Ca2+ chelators at higher concentrations causes diverse side-effects including elevated permeability of the plasma membrane for Na+ [20]. Moreover, because of the high affinity to other di- and trivalent cations [29], Ca2+ chelators can affect transcriptome via irreversible conformational transition and inactivation of transcriptional adaptor Zn2+-binding domain [30]. Viewed collectively, these data strongly indicate that besides canonical Ca2+-mediated signalling, gain of [Na+]i and/or loss of [K+]i influence gene expression via Ca2+ i-independent mechanism.

Physiological and pathophysiological implications

The Na+ i/K+ i-dependent regulation of gene expression may have numerous physiological and pathological implications (Fig. 15). Here, we discuss a few of tissue-specific examples.

Figure 15

Mechanisms underlying transcriptomic alterations in normal and pathophysiological conditions: a working hypothesis.

Activation of Na+-permeable channels such as NMDA receptors (1), Na+/H+ exchanger (2), voltage-gated K+ channels (6) and inhibition of Na+,K+-ATPase (4) lead to elevation of the [Na+]i/[K+]i ratio. In cells abundant with Na+/Ca2+ exchanger (3), the dissipation of transmembrane gradients of monovalent cations is accompanied by elevation of [Ca2+]i. Elevation of the [Na+]i/[K+]i ratio affects the expression of X and Z genes via activation of unknown Na/K sensor(s) and Na/K response elements (Na/KRE). Expression of Z genes is also subjected to regulation by elevated [Ca2+]i via its interaction with calmodulin (CaM) and other Ca2+ i sensors and diverse Ca2+-response elements (CaRE), whereas Y genes lacking Na/KRE are controlled by [Ca2+]i only. The set of Na+ i,K+ i-sensitive transcription regulators shown as X, Y and Z contributes to overall transcriptomic changes via activation of canonical response elements (RE) within V genes. Autocrine pathways triggered by the release of interleukin 6 and other [Na+]i/[K+]i-sensitive regulators of gene expression (Z) may also contribute to overall transcriptomic changes via activation of their receptors (7).

Excitation of neuronal cells

Almost 30 years ago, several research teams reported that expression of Erg1 and other Na+ i,K+ i-sensitive IGR listed in Table 2 is strongly increased in neuronal cell subjected to excitation by diverse stimuli including neurotransmitters, depolarization and light [31]–[33]. The mechanisms of this phenomenon, widely employed for the identification of excited brain areas, remain largely unknown. It has been shown that activation of N-methyl-D-aspartate (NMDA) receptor contributes to elevation of Egr1 mRNA content in excited neuronal cells. This link is so prominent that monitoring Egr1 expression has been proposed as a biological assay for NMDA receptor activity. Given a key role of NMDA receptor activation in regulating synaptic strength, Egr1 accumulation has also been connected with learning and memory (for review, see [34]). Indeed, experiments performed on Egr1 deficient mice showed that their inability to form long-term memory in a variety of behavioural tasks [35]. It is generally accepted that Egr1 expression in neuronal cells is triggered by [Ca2+]i elevation [25]. However, ion currents through NMDA channels are mainly mediated by monovalent cations (PNa∼PK≫PCa), and short periods of synaptic activity in apical dendrites and dendritic spines produce increases in [Na+]i, from ∼10 to 30 and 100 mM, respectively [36]. Recently, sharp elevation of [Na+]i in response to local application of glutamate was demonstrated in neocortical neurons loaded with sodium-sensitive nanoprobe [37]. Here, we report that elevation of the [Na+]i/[K+]i ratio in Ca2+-depleted HUVEC and HeLa cells augmented Egr1 expression by ∼10-fold, which is comparable to increments detected in Ca2+-containing medium (Tables 4,5). In contrast, in RVSMC, Egr1 up regulation was exclusively detected in the presence of Ca2+ (Table 6). Therefore, the relative impact of Ca2+ i- mediated and Ca2+ i -independent mechanisms on Egr1 expression triggered by elevation of the [Na+]i/[K+]i ratio in neuronal cells and their roles in memory formation and storage should be further examined in light of the data presented here.

Intensive exercise

Numerous studies demonstrated that the plasma concentration of IL6 increases up to 100-fold during muscular exercise. This increase is followed by the expression of the IL1 receptor agonist (Il1ra) and the anti-inflammatory cytokine IL10. Importantly, contracting skeletal muscle rather than the immune cells is the only source of the IL6 in circulation in response to exercise. The mechanism of this phenomenon, which plays a key role in the energy supply via elevation of glucose uptake in hepatocytes and lipolysis in adipose tissue, remains poorly understood (for comprehensive review, see [38]). It is known, however, that in both humans and experimental animals, intensive exercise increases [Na+]i in skeletal muscles by 3–4-fold and decreases [K+]i by 15–25% via activation of voltage-gated K+ and Na+ channels and partial inactivation of Na+,K+-ATPase [39], [40]. Here, we demonstrated that Il6 is among the ubiquitous genes whose expression is strongly increased by elevation of the [Na+]i/[K+]i ratio (Table 3). Therefore, our data allow us hypothesize that elevation of plasma level of IL6 during intensive exercise is caused by elevation of the [Na+]i/[K+]i ratio in skeletal muscle that, in turn, increases expression of the [Na+]i/[K+]i-sensitive genes, including Il6.

Ischemia

To date, transcriptomic alterations in response to oxygen deprivation, such as modest hypoxia in solid tumours or in the adipose tissue of obese patients, have been largely ascribed to the overexpression of hypoxia-inducible factor 1 (HIF-1) known to be the molecular pO2 sensor that affects gene expression via its binding to cis-acting hypoxic-response elements (HRE) [41]. It should be noted, however, that the overwhelming number of genes, such as Egr1, Atf3, Ptgs2, Il6, Ppp1r5, Hes1, Nfkbiz, Txnip, Adamts1, Egr 3, Cxcl2, Hsp70, whose expression is strongly increased in cells subjected to ischemia/reperfusion both in vivo and in vitro [42]–[52], lack HRE. Significantly, we detected the above-listed genes among ubiquitous (Egr1, Atf3, Ptgs2, Il6, Ppp1r5, Hes1, Nfkbiz, Txnip, Tables 3 and 9) or cell-type specific (Adamts1, Egr 3, Cxcl2, Hsp70, Table 4,5,6) [Na+]i/[K+]i-sensitive genes. Since even transient ischemia increases [Na+]i from 5–8 to 25–40 mM and causes reciprocal changes in [K+]i [53], it can be hypothesized that inversion of the [Na+]i/[K+]i ratio contributes to transcriptomic changes triggered by ischemia, with pathways that are complementary to those previously associated with activation of HIF-1. This conclusion is consistent with IPA Knowledge Base data showing abnormalities of gene expression revealed in ischemic liver, heart and kidney among disorders linked with ubiquitous Na+ i/K+ i-sensitive transcriptome (Fig. 16).

Figure 16

Disorders significantly associated with differential expression of ubiquitous Na+ i,K+ i-sensitive genes.

The p-value and geometric fold change for each genes listed in Table 3 were imported into Ingenuity Pathway Analysis. The criteria with a threshold for significance of p = 0.05 (or 1.3 when expressed as -log(p-value) is shown by line.

In conclusion, we report here that elevation of the [Na+]i/[K+]i ratio affects expression of hundreds of genes via the activation of Ca2+-mediated and most importantly Ca2+-independent signaling pathways. The proposed hypothetical hierarchy of these pathways is depicted in Figure 15. Previously, we demonstrated that gain of Na+ i rather than loss of K+ i triggers augmented c-Fos expression in RVSMC [12]. We also reported that c-Fos expression triggered by [Na+]i elevation occurs via Ca2+ i-independent signaling mechanism that is not mediated by any known transcriptional elements in 5′-promoter [13]. We firmly believe that the newly gained knowledge of the Na+ i/K+ i-sensitive transcripts (genes X1,2,3…, Fig. 15) will allow researchers to take powerful bioinformatics approaches to identify previously-unfamiliar Ca2+ i-independent mechanism of the excitation-transcription coupling as well as its involvement in cellular responses triggered by sustained elevation of the [Na+]i/[K+]i ratio.

Methods

Cell cultures

We studied three cell types in the experiments reported here. RVSMC cells were isolated from rat aortae according to the procedures outlined in the Guide for the Care and Use of Experimental Animals endorsed by the Canadian Institutes of Health Research and accepted by the Institutional Animal Protection Committee of the CRCHUM. These cells maintain a number of characteristics of primary cultured RVSMC including high expression of smooth muscle-specific α-actin, SM22 protein and myosin light chain kinase [54]. The human cervical adenocarcinoma cell line HeLa was purchased from the American Type Culture Collection (Rockville, MA, USA). The human umbilical vein endothelial cells (HUVEC) were purchased from Lonza (Walkersville, MD, USA) and passaged 4–12 times. RVSMC and HeLa were maintained in Dulbecco's Modified Eagle Medium (DMEM, Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS) and 100 U/ml penicillin and 100 µg/ml streptomycin. HUVEC were cultured in complete endothelial cell growth medium-2 (EGM-2 BulletKit, CC3162, Lonza). All cell cultures were maintained in a humidified atmosphere with 5% CO2/balance air at 37°C. To establish quiescence, cells were incubated for 24 hr in the media in which concentration of FBS was reduced to 0.2%. The possible impact of Na+,K+-ATPase inhibition and Ca2+-depletion on cell viability and apoptosis was studied by lactate dehydrogenase (LDH) release and measurement of caspase-3 activity and chromatin cleavage, as described in details elsewhere [23], [24], [55].

Elevation of the [Na+]i/[K+]i ratio

Quiescent cells were washed with Ca2+- and K+-free DMEM (Sp-DMEM; Invitrogen, Carlsbad, CA) and incubated for 3 hr in either control medium containing 1.8 mM CaCl2 and 5 mM KCl (Sp-DMEM+Ca,K) or in Ca2+-free medium (Sp-DMEM+K) containing 50 µM EGTA and 10 µM BAPTA-AM. To increase the [Na+]i/[K+]i ratio, the Na+,K+-ATPase activity was inhibited by the addition of ouabain or the omission of extracellular K+ (K+-free medium, Sp-DMEM+Ca). Because the affinity of the ubiquitous α1-Na+,K+-ATPase for ouabain and other cardiotonic steroids (CTS) in rodents is ∼1000-fold lower than in other mammalian species [56], ouabain was added to the media with human and rat cells at the concentrations of 3 and 3,000 µM, respectively.

Intracellular content of exchangeable K+ and Na+

Intracellular content of exchangeable K+ and Na+ was measured as the steady-state distribution of extra- and intracellular 86Rb and 22Na, respectively. To establish isotope equilibrium, cells growing in 12-well plates were preincubated for 3 hr in control or K+-free medium (Sp-DMEM+Ca) containing 0.5 µCi/ml 86RbCl or 3 µCi/ml 22NaCl and ouabain was added for the next 3 hr. To test the action of K+-free medium, cells were washed twice with ice-cold Sp-DMEM+Ca. Then, cells loaded with 22Na were transferred to Sp-DMEM+Ca, containing 3 µCi/ml 22NaCl, whereas cells loaded with 86Rb were transferred to isotope-free Sp-DMEM+Ca. After 3 hr, the cells were transferred onto ice, washed 4 times with 2 ml of ice-cold medium W containing 100 mM MgCl2 and 10 mM HEPES-tris buffer (pH 7.4). The washing medium was aspirated and cells were lysed with 1% SDS and 4 mM EDTA solution. Radioactivity of incubation media and cell lysates was quantified, and intracellular cation content was calculated as A/am, where A was the radioactivity of the samples (cpm), a was the specific radioactivity of 86Rb (K+) and 22Na in the medium (cpm/nmol), and m was protein content. For more details, see [57].

Measurement of intracellular Ca2+

Cells grown on glass cover slips were incubated for 30–40 min in medium containing 5 µM fura 2-AM, washed twice and kept for up to 30 min at room temperature before the experiments. Then, the cover slips treated as indicated in figure and table legends were mounted in a diagonal position in a 1×1 cm cuvette, and fluorescence was determined under permanent stirring at 37°C (λex = 340 and 380 nm, slit 4 nm; λem = 510 nm, slit 12 nm), using a SPEX FluoroMax spectrofluorimeter (Edison, NJ). Free [Ca2+]i was quantified as [Ca2+]i = Kd (R−Rmin)x(Rmax−R)−1, where Kd is the dissociation constant of the Ca2+-fura 2 complex (224 nM at 37°C), and R = F340/F380 is the ratio of fluorescence at λex = 340 and 380 nm. To determine Fmax, the cells were treated with 0.5 µM ionomycin in the presence of 1 mM CaCl2. To determine Fmin, MnCl2 was added at a final concentration of 2 mM.

Measurement if intracellular BAPTA

HeLa cells seeded in 12-well plates were incubated for 3 hr in control or Ca2+-free media containing 2 µCi/ml [14C]-urea. Then, the cells were washed with 4×3 ml of ice-cold medium W and lysed for BAPTA measurement by addition of 200 µl of 10% trichloroacetic acid containing 1 mM CaCl2 or for radioactivity measurement as described above. The content of BAPTA in cell lysates was estimated by the increment of absorbance at 255 nm triggered by addition of 10 mM EGTA (ΔA). Intracellular concentration of BAPTA (µmol/L) was calculated as ΔA, where ΔA is the Ca2+-dependent increment of A255 in the presence of 0.001 µmol BAPTA (internal standard) and V is the volume of intracellular water (µl/mg protein). V was calculated as the volume of [14C]-urea available space V, where A and A are the radioactivity of [14C]-urea in the cell lysate and incubation medium, respectively (dpm), m is protein content in the cell lysate (mg), and V is the volume of incubation medium (L) used for Ao determination.

RNA isolation

Total RNA was extracted from cells grown in 6-well plates using TRIzol® reagent (Invitrogen, Carlsbad, CA and purified with the RNeasy® MinElute cleanup kit (Qiagen, Valencia, CA) following the manufacturers' protocols. Only the RNA samples that had more than 7.0 RNA integrity number (RIN) and no detectable genomic DNA contamination were used for the subsequent gene array analyses. RNA quality was assessed by 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Microarray experiments were performed with GeneChip® Human Gene 1.0 ST array (which detects 28,869 gene products) and GeneChip® Rat Gene 1.0 ST array (detects 27 342 gene products). On both arrays, each gene was represented by approximately 26 probes along the entire length of the transcript (Affymetrix, Santa Clara, CA). 100 ng of total RNA for each sample was processed with Ambion® WT Expression Kit (Invitrogen). This kit uses a reverse transcription priming method that specifically primes non-ribosomal RNA, including both poly(A) and non-poly(A) mRNA, and generates sense-strand cDNA as the final product. 5.5 µg of the single-stranded cDNA was fragmented and labeled using the Affymetrix GeneChip® WT Terminal Labeling Kit and 2.0 µg of the resulting cDNA was hybridized on the chip.

GeneChip expression analysis

The whole hybridization procedure was conducted with the Affymetrix GeneChip® system according to the protocol recommended by the manufacturer. The hybridization results were evaluated with Affymetrix GeneChip® Command Console Software (AGCC). Quality of the chips was determined using Affymetrix Expression Console. Data analysis was performed within Partek Genomics Suite (Partek, St. Louis, Missouri). The data were initially normalized by Robust Multichip Average (RMA) algorithm, which uses background adjustment, quantile normalization and summarization. Then, normalized data were analyzed by principal component analysis (PCA) [18] to identify patterns in the dataset and high-light similarities and differences among the samples. Major sources of variability identified within the dataset by PCA were used as grouping variabilities for analysis of variance (ANOVA) with n = 4 for each group of samples. The ensuing data were filtered to identify transcripts with statistically significant variation of expression among the groups that are modulated by at least 20%, with multiple testing correction by the false discovery rate (FDR). The calculated p-value and geometric fold change for each probe set identifier were imported into Ingenuity Pathway Analysis (IPA, Ingenuity Systems, http://www.ingenuity.com) to ascertain networks, biological functions and their pathophysiological implications. Functional information on regulated gene was also obtained using PubMed and cited publications.

Real-time quantitative RT-PCR

To validate data obtained by genome-wide Affymetric gene arrays, we estimated changes in the gene expression for several selected transcripts by qRT-PCR, which was performed using Express SYBR GreenER qPCR Supermix kit (Invitrogen, Carlsbad, CA, USA) according to the manufacture's instructions. The reaction was carried out with a 7900 HT Fast RT – PCR system (Applied Biosystems, Foster City, CA, USA). Primers for Egr1, Ptgs2 and Ppp1r15a were designed using Primer3Plus online software from consensus sequences provided by Affymetrix for each gene of interest. The relevant primer sequences were: Egr1-sens (5′-TGACCGCAGAGTCTTTTCCT-3′), Egr1-anti-sense (5′-AGCGGCCAGTATAGGTGATG-3′), Ptgs2-sens (5′-TGTGTTGACATCCAGATCACAT-3′), Prgs2-anti-sense (5′-GCTGCTTTTTACCTTTGACACC-3′), Ppp1r15a-sens (5′-GGCCATCTATGTACCTGGAGA-3′) and Ppp1r15a-anti-sense (5′ GAGAAGCGCACCTTTCTGG-3′). All experiments were analyzed in duplicate. β2 microglobulin mRNA expression was used to normalize and compare the expression values of genes of interest. The results were quantified by the ΔΔCt method with Excel Microsoft software.

Chemicals

Methyl-[3H]-thymidine was purchased from ICN Biomedicals, Inc. (Irvine, CA); 22NaCl and 86Rb were obtained from PerkinElmer (Waltham, MA); [14C]-urea was provided by Amersham (Montreal, PQ). DEVD-AMC, DEVD-CHO and z-VAD.fmk were procured from BIOMOL Research Laboratories (Plymouth Meeting, PA). The remaining chemicals were supplied by Gibco BRL (Gaithersburg, MO), Calbiochem (La Jolla, CA), Sigma (St. Louis, MO) and Anachemia (Montreal, QC).