Open Access

Evaluation of suitable reference genes for normalization of real-time reverse transcription PCR analysis in colon cancer

  • Lise Aa Sørby1Email author,
  • Solveig N Andersen2, 3,
  • Ida RK Bukholm3, 4, 5 and
  • Morten B Jacobsen1, 3, 6
Journal of Experimental & Clinical Cancer Research201029:144

DOI: 10.1186/1756-9966-29-144

Received: 9 September 2010

Accepted: 8 November 2010

Published: 8 November 2010

Abstract

Background

Real-time reverse transcription PCR (qRT-PCR) is frequently used for gene expression quantification due to its methodological reproducibility and sensitivity. The gene expression is quantified by normalization to one or more reference genes which are presumed stably expressed throughout a given experiment. The aim of this study was to validate a standardized experimental setup to identifying reference genes for normalization of qRT-PCR in the metastatic and non-metastatic colon cancer.

Methods

In this study, expression of 16 commonly used reference genes was quantified in tumour tissue and individual-matched normal mucosa in 18 non-metastatic colon cancer patients and 20 colon cancer patients with distant metastases using TaqMan Low Density Array (TLDA). The expression stability was determined and compared by means of geNorm and NormFinder.

Results

Two pairs of genes, HPRT1/PPIA and IPO8/PPIA, were identified to be suitable to normalize gene expression data in metastatic and non-metastatic colon cancer patients, according to geNorm and NormFinder respectively.

Conclusion

We propose a standardized approach of finding the most suitable reference gene(s) in every qRT-PCR experiment using TLDA.

Background

qRT-PCR is one of the most sensitive methods for mRNA detection and quantification. The method has also become the preferred method for validating results obtained by other techniques, such as microarray [1]. There are differences among different qRT-PCR assays due to biological and technical variations [2, 3]. In order to identify truly gene specific variations it is important to use a suitable normalization method. One of the most commonly used approaches involves relative quantification of target genes against one or more reference genes which are thought to be stably expressed in the examined tissue [4]. There have been a number of reports that demonstrate that the expression levels of putative reference genes vary extensively in different tissues and diseases and thus are unsuitable for normalization purposes [515]. Consequently, each research group has to validate multiple reference genes in their own experimental setup and normalize qRT-PCR data against a few reference genes tested from independent pathways using at least one algorithm. It appears that improvements in methods of identifying reference genes are more important than the identification of the particular reference genes themselves [16].

It has been argued for use of multiple genes in the normalization of qRT-PCR analysis and several algorithms have been developed [1720]. Vandesompele et al., 2002, used the geometric mean of the most stable genes to improve the accuracy of the analysis in a method called geNorm [19]. This method relies on the principle that the expression ratio of two ideal reference genes is identical in all samples regardless of the experimental conditions. For every reference gene geNorm determine the pairwise variation with all other reference genes. The average pairwise variation of a particular gene is defined as the internal control stability measure; M. Genes with the lowest M values are the most stable ones. Another algorithm in which the expressional stability of genes is evaluated is NormFinder [17]. NormFinder estimates the intra-group and the inter-group expression variation. Both of these sources of variation are combined into a stability value. This method can account for heterogeneity of the tested tissue samples. Genes with the lowest stability value have the most stable expression.

Colorectal cancer is among the most frequent malignant diseases worldwide, and is one of the leading causes of cancer-related deaths [21]. The majority of colorectal tumours develop along a well-defined adenoma-carcinoma sequence in which oncogenes are activated and tumour suppressor genes lose their function [22]. Despite a high 5-year survival rate in early colorectal cancer, only 10% of the patients with distant metastases survive after five years [23]. Thus, it is important to elucidate the biology that contributes to this progression, especially those processes that facilitates the switch to invasive and metastatic disease. Biological changes are a result of partly differential gene expression, which can be confirmed by qRT-PCR. It is necessary to validate reference genes in the particular experimental system in order to trust the differential gene expressions which are detected. Previous studies have tried to find universally stable reference genes across several types of cancers, including colon cancer [2426]. Recent reports, however, claim that stably expressed genes in one tumour type may not predict stable expression in another tumour type [12, 27]. Moreover, results in one tumour type, like colorectal cancer, show stably expressed genes in one experimental in which are different from the stably expressed genes in another experimental setup [2830]. Hence, reference genes should be validated and selected in every experiment in any tissue type. Recently, it has been suggested that the focus should be on introducing and validating novel approach for reference gene identification and standardizing experimental setup rather than giving general suggestions for different tissues [16]. Applying TaqMan Low Density Array (TLDA) to examining reference genes is a step towards a more standardized experimental setup. TLDA was evaluated in colorectal cancer by Lü et al., 2008, as a roughly robust and labour-saving method for gene quantification compared with routine qRT-PCR [31]. Well-designed TaqMan probes require little optimization, and TLDA allows simultaneously real-time detection of many gene products in several samples offering higher through put than established single array method [31, 32]. Hence, in the present study we used TLDA to find potential reference genes for data normalization in qRT-PCR experiments in metastatic and non-metastatic colon cancer patients. The gene expression of 16 commonly used reference genes in tumour tissue and individual-matched normal mucosa of metastatic and non-metastatic colon cancer patients were analyzed and the expression stability was determined and compared using geNorm and NormFinder.

Methods

Patients and tissue specimens

RNAlater-stored tumour tissue samples and individual-matched normal mucosa were obtained from 38 patients with colonic adenocarcinoma who underwent resection at Akershus University Hospital Trust between 2004 and 2009. The dissected tissue samples were collected in the operating room and stored immediately in approximately five volumes of RNAlater (Ambion Inc., Austin TX, USA) and frozen at -80°C. Eighteen patients with non-metastatic disease, Dukes B (with a minimum of 12 negative lymph nodes) where no metastases occurred during 5 years follow up, and 20 patients originally staged as Duke C who displayed distant metastases during a 5 year follow-up (Duke C) or patients classified as Dukes D were included in the study. There were 22 women and 16 men with a mean age of 69 +/- 14 years (range 29-92) at surgery. Three sectioned pieces of the tumour samples were made. The central piece was further processed for RNA isolation, while the two end pieces were fixed in formalin and embedded in paraffin (FFPE). Four μm sections of FFPE samples were stained with Hagens Hematoxylin and examined by a pathologist for determination of percentage tumour cells. To avoid bias from necrosis or minimal tumour representation we included tumour tissue samples with more than 70% tumour cells.

mRNA isolation

Total RNA isolation was performed using the method of Wei and Khan, 2002, [33] modified according to T. Lüders (unpublished work) to also include miRNA for further analyses. Approximately 60 mg frozen tissue was homogenized in TriReagent (Ambion) using Mixer Mill MM301 (Retch) for 2 × 2 min at 30 Hz. After phase-separation with chloroform, the aqueous phase (containing RNA) was mixed with 1.5 volumes 100% ethanol and transferred to an RNeasy Mini spin column (Qiagen). Further processing was performed following the manufacturer's protocol. A DNase treatment was included in the procedure. RNA was eluted in 60 μl RNase-free water and stored at -80°C. The concentration of each RNA sample was obtained from A260 measurements using the NanoDrop 2000 (Thermo Fischer Scientific Inc.). The RNA integrity number (RIN) was tested by using the Agilent 2100 Bioanalyzer (Agilent Technologies).

cDNA synthesis

Complementary DNAs (cDNAs) were produced from 1 μg RNA of each sample using the High Capacity RNA-to-cDNA Master Mix (Applied Biosystems) according to the manufacturer's instructions. The following thermal cycler conditions were used: 5 min at 25°C, 30 min at 42°C and 5 min at 85°C. Three random RNA samples were additionally run in the absence of reverse transcriptase enzyme to assess the degree of contaminating genomic DNA. Real-time PCR with genomic DNA specific assay revealed that RNA was free of genomic DNA (data not shown).

TLDA design and preparation

TaqMan Endogenous Control Assays (Applied Biosystems) are 384-well microfluidic cards containing 16 preoptimized human TaqMan Gene Expression Assays commonly used as endogenous controls and genes that exhibit minimal differential expression across different tissues (Table 1). The assay was performed in triplicates. 50 μl cDNA (1 μg mRNA) was used as a template. Matched samples from 4 patients where loaded on each card. NTC (no template control) was added in one loading port. PCR amplification was performed using the ABI Prism 7900 HT Real Time PCR System (Perkin-Elmer Applied Biosystems, Foster City, California, USA). Thermal cycling conditions were used as follows: 2 min at 50°C, 10 min at 94.5°C, 30 sec at 97°C, and 1 min at 59.7°C for 40 cycles.
Table 1

Candidate reference genes included in the TaqMan Endogenous Control Assay.

Gene name

Gene symbol

Assay ID

Size (bp)

Function

18S Ribosomal RNA

18S

Hs99999901_s1

187

Part of a ribosomal subunit

Phosphoglycerate kinase-1

PGK1

Hs99999906_m1

75

Key enzyme in glycolysis

Β-Actin

ACTB

Hs99999903_m1

171

Cytoskeletal structural protein

Polymerase (RNA) II polypeptide A

POLR2A

Hs00172187_m1

61

Catalyzes the RNA synthesis from DNA

Beta-2-microglobulin

B2M

Hs99999907_m1

75

Beta-chain of major histocompatibility complex class I molecules

Peptidyl-prolyl isomerase/cyclophilin A

PPIA

Hs99999904_m1

98

Catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides, accelerating folding

Glyceraldehyd-3-phosphate dehydrogenase

GAPDH

Hs99999905_m1

122

Dehydrogenase, oxidoreductase in glycolysis and gluconeogenesis

Acidic ribosomal phosphoprotein P0

RPLP0

Hs99999902_m1

105

Ribosome biogenesis and assembly

Β-Glucuronidase

GUSB

Hs99999908_m1

81

Glycoprotein, degradation of dermatan and keratin sulfates

Transcription factor IID, TATA box binding protein

TBP

Hs99999910_m1

127

TATA binding protein, general RNA polymerase II transcription factor

Hydromethylbilane synthase

HMBS

Hs00609297_m1

64

Heme synthesis, porphyrin metabolism

Transferrin receptor (p90, CD71)

TFRC

Hs99999911_m1

105

Cellular uptake of iron

Hypoxanthine-phosphoribosyl-transferase 1

HPRT1

Hs99999909_m1

100

Glycosyltransferase, purine synthesis in salvage pathway

Ubiquitin C

UBC

Hs00824723_m1

71

Protein degradation

Importin 8

IPO8

Hs00183533_m1

71

Function in nuclear protein import

Tyrosine 3 monooxygenase activation protein, zeta polypeptide

YWHAZ

Hs00237047_m1

70

Signal transduction by binding to phosphorylated serine residues on a variety of signalling molecules

TLDA analysis and Statistical analysis

RealTime Statminer 3.0 Software (Integromics, Madrid, Spain) was used for implementation of quality controls in addition to calculation of optimal endogenous controls. This program uses the comparative Ct method for relative quantification analysis, and the results are expressed as a fold change of expression levels (DDCt values). The mean value of triplicates was applied for all calculations. Medians were used to replace missing values that occurred due to inconsistencies between replicates rather than from low expression. The detectability threshold was set to 36, meaning failing detectors are those with a Ct greater than or equal to 36. To measure the expressional stability of the candidate endogenous control genes, two commonly used programs were employed: geNorm [19] and NormFinder [17], both of which available in RealTime Statminer. Ct coefficients of variations (CtCV%) were calculated for every reference gene across all samples. All data are expressed as means ± SD. Except from the analyses in RealTime Statminer, all other calculations were performed using SPSS (version 14.0; SPSS, Chicago, IL, USA).

Research Ethics

This project was approved by the Regional Committee for Medical Research Ethics, Eastern Norway. The Norwegian Social Science Data Service has approved the collection and analysis of data.

Results

RNA quality control

mRNAs of 16 potential reference genes were quantified by qRT-PCR using equal amounts of RNA templates from every tissue samples. The integrity of RNA (RIN) was ranged from 7.2 to 10.0, with a mean value of 8.9, which indicates good preservation of the RNA; thus suitable for RNA studies.

Range of expression of candidate endogenous control genes

Table 2 presents the mean Ct and SD values obtained across the candidate endogenous control genes in normal and tumour tissue separated into the two groups of patients; non-metastatic and metastatic colon cancer patients. Additional calculations across all patients are shown in Table 3. Mean Ct values ranged from 8.71 (± 1.31 SD) (18S) across all samples to 26.70 (± 1.69 SD) (TBP). The gene with the lowest standard deviation across all samples was IPO8 which showed an overall SD of 1.28, while the gene with the highest standard deviation across the samples was PGK1 with an overall SD of 2.49. The reference genes displayed a relatively broad range of expression. PGK1 had the widest range of Ct values between 8.35 and 29.83 (mean 21.03 ± 2.49 SD, range of 21.47), while B2M had the narrowest range of Ct values between 15.25 and 23.59 (mean 17.10 ± 1.31 SD, range of 8.34). During the subsequent analyses using Statminer Ct values above 36 are excluded and imputed, because Ct values above this level are not reliable. This quality control will thus influence the Ct ranges.
Table 2

Cycle threshold (Ct) values of candidate reference genes divided in the four tissue groups.

Gene symbol

Non-metastatic colon cancer

Metastatic colon cancer

 

Tumour

Normal

Tumour

Normal

 

Mean

SD

N

Mean

SD

N

Mean

SD

N

Mean

SD

N

18S

8,095

0,546

18

8,440

1,066

18

8,800

1.066

20

9,408

2,035

20

ACTB

20,003

0,765

18

19,949

1,209

18

20,363

1.209

20

20,578

2,673

20

B2M

17,050

0,996

18

17,041

1,002

18

17,217

1.002

20

17,085

1,632

20

GAPDH

18,503

0,722

18

19,502

1,044

18

19,211

1.044

20

20,145

2,541

20

GUSB

23,274

0,375

18

24,081

0,865

18

23,564

0.865

20

24,060

1,981

20

HMBS

25,328

0,736

18

26,577

0,974

18

25,963

0.974

20

27,030

2,436

20

HPRT1

22,795

0,814

18

24,183

0,750

18

23,320

0.750

20

24,264

1,849

20

IPO8

24,575

0,469

18

25,084

0,780

18

25,099

0.780

20

25,529

2,108

20

PGK1

20,322

1,054

18

21,151

1,012

18

20,996

1.011

20

21,573

3,257

20

POLR2A

24,007

0,634

18

24,508

1,061

18

24,933

1.061

20

25,330

2,590

20

PPIA

17,081

0,485

18

18,241

0,906

18

17,506

0.906

20

18,335

1,724

20

RPLP0

19,706

0,637

18

20,647

0,952

18

20,319

0.952

20

21,081

2,002

20

TBP

26,157

0,577

18

26,860

1,035

18

26,649

1.035

20

27,110

2,797

20

TFRC

21,774

0,926

18

23,334

1,030

18

22,679

1.030

20

23,663

2,303

20

UBC

21,285

0,675

18

21,771

1,046

18

21,532

1.046

20

22,044

2,180

20

YWHAZ

23,933

0,723

18

25,041

1,275

18

24,457

1.275

20

25,401

2,174

20

Table 3

Cycle threshold (Ct) values of candidate endogenous control genes across all tissue samples.

Gene

Mean

± s.e.m

Standard deviation (SD)

Ct min

Ct max

Ct Range

CtCV%

18S

8.708

0.151

1.314

6.858

16.932

10.073

14,99

ACTB

20.236

0.187

1.630

17.979

31.018

13.039

8,10

B2M

17.101

0.150

1.306

15.251

23.587

8.336

7,69

GAPDH

19.358

0.191

1.661

17.382

30.403

17.382

8,63

GUSB

23.748

0.150

1.309

21.719

32.338

10.619

5,55

HMBS

26.239

0.186

1.625

24.315

36.823

12.508

6,23

HPRT1

23.649

0.164

1.429

21.852

31.617

9.765

6,04

IPO8

25.085

0.146

1.276

23.749

33.903

10.154

5,12

PGK1

21.025

0.285

2.487

8.354

29.829

21.474

10,35

POLR2A

24.717

0.184

1.606

20.827

34.874

14.047

6,54

PPIA

17.978

0.150

1.305

15.980

25.150

9.170

7,34

RPLP0

20.452

0.162

1.413

18.682

29.171

10.489

6,93

TBP

26.704

0.194

1.692

24.858

38.656

13.799

6,38

TFRC

22.878

0.196

1.711

19.907

32.261

12.354

7,53

UBC

21.665

0.163

1.422

19.475

30.387

10.912

6,60

YWHAZ

24.720

0.193

1.685

22.733

32.853

10.120

6,86

Note. S.e.m, standard error of mean; CtCV%, Coefficients of variations of candidate reference genes.

Results of validation programs

In order to determine the stability of genes and thus find the best endogenous controls, the data were analysed by geNorm and NormFinder. In these analyses, medians were used to replace missing values because they occurred due to inconsistencies between replicates rather than from low expression. The ranking of the gene expression stability values (M) of the tested endogenous control genes using geNorm is illustrated in Figure 1.A. The genes with the highest M, i.e. the least stable genes, gets stepwise excluded until the most stable genes remain. The best two genes are ranked without distinguishing between them. HPRT1 and PPIA were identified as the most stable pair of genes, followed by PGK1 as the third most stable gene. Furthermore, pairwise variation were also calculated using geNorm in order to determine the optimal number of genes required for normalization, Figure 1.B. The analysis showed that HPRT1 and PPIA may be sufficient for calculation of the normalization factor and normalization to genes of interest, since the V2/3 value is in this analysis equal to the cut-off value of 0.15 [19]. However, there is a gradual decrease in the pairwise variability plot and thereby an improvement to the normalization factor by adding additional genes to the calculation. Nevertheless, two or three genes would be satisfactory for normalization according to the cut-off value of 0.15. While geNorm uses a pairwise comparison approach, NormFinder first estimates the intra-group and then the inter-group variability of expression of a control gene [17]. In contrast to the geNorm results, NormFinder ranked RPLP0 as the most stable gene, with TBP and GUSB closely behind as second and third, respectively (Figure 2). However, using this algorithm the combination of IPO8 and PPIA turned out to have a lower stability score than the most stable single gene. Thus this combination is more suitable for normalizing qPCR. There was considerably closer agreement between the geNorm and Normfinder results on the least stable genes, with the order of 4 out of 5 worst ranking genes being identical; ACTB, 18S, B2M and TFRC. These genes had a stability value more than twice so high (geNorm) and more than 3 times so high (NormFinder) as the best ranking genes.
https://static-content.springer.com/image/art%3A10.1186%2F1756-9966-29-144/MediaObjects/13046_2010_Article_391_Fig1_HTML.jpg
Figure 1

GeNorm analysis of the candidate reference genes. (A) Average expression stability values of reference genes. Genes are presented in an increasing order of stability from left to right with ACTB being the least stable gene and HPRT1 and PPIA the most stable genes. (B) Determination of optimal number of control genes for normalization. Every bar represents change in normalization accuracy when stepwise adding more reference genes according to ranking in Figure 1. A. To meet the recommended cut-off value of 0.15 two pr three genes would be satisfactory for normalization.

https://static-content.springer.com/image/art%3A10.1186%2F1756-9966-29-144/MediaObjects/13046_2010_Article_391_Fig2_HTML.jpg
Figure 2

NormFinder analysis of the candidate reference genes. Genes are presented in an increasing order of stability from left to right with B2M as the least stable gene and RPLP0 as the most stable gene.

Due to different ranking by geNorm and NormFinder of the most stable genes, cycle threshold coefficient of variation (CtCV%) was calculated for each of them. This calculation was recommended by Caradec et al., 2010, in order to validate the NormFinder and geNorm results [12]. According to the CtCV% calculation, one of the NormFinder pairing genes, IPO8, was ranked as the most stable gene with a CtCV% of 5.12%, which supports the NormFinder result. GUSB (5.5%) and HPRT1 (6.04%) are ranked as the second and third respectively, which do not give identical ranking of results obtain using geNorm and NormFinder. The least stable gene using CtCV% was 18S (14.99%), which was according to geNorm and NormFinder ranked as the second and fifth least stable gene, respectively. The summary of the best ranking genes as determined by each of these calculations is illustrated in Table 4.
Table 4

Ranking and best combination of reference genes determined by geNorm, NormFinder and CtCV%.

Rank

GeNorm

NormFinder

CtCV%

1

HPRT1

RPLP0

IPO8 (5.12)

2

PPIA

TBP

GUSB (5.55)

3

PGK1

GUSB

HPRT1 (6.04)

4

RPLP0

POLR2A

HMBS (6.23)

5

HMBS

IPO8

TBP (6.38)

6

GAPDH

GAPDH

POLR2A (6.54)

7

GUSB

PPIA

UBC (6.60)

8

IPO8

HPRT1

YWHAZ (6.86)

Best gene/combination

HPRT1/PP1A

IPO8/PPIA

IPO8

Discussion

qRT-PCR has been a breakthrough for the quantification of gene expression in many biological systems. In this study we assume that no single gene stays unaffected under malignant development in colon cancer and therefore identify genes with least variation. We identified two pairs of genes, HPRT1/PPIA and IPO8/PPIA, which may be suitable to normalize gene expression data in studies conducted in metastatic and non-metastatic colon cancer patients. In addition, we found that B2M, ACTB and 18S were unstable in the tissue examined. We propose a standardized approach of finding the most suitable reference gene(s) in every qRT-PCR experiment using TLDA.

Complex signalling pathways have been related to the metastatic progression of colon cancer, hence pathway based gene expression assays, often revealed by qRT-PCR, are significant in cancer biology. Publications dealing with colon cancer have reported gene expression studies in metastatic diseases [34, 35]. However, the stability of the reference gene expression in metastatic and non-metastatic primary tumours remains crucial. Ramaswamy et al., 2003, described a gene expression signature that distinguished primary and metastatic adenocarcinomas, indicating that the metastatic potential of human tumours is encoded in the bulk of the primary tumour [36], fully in accordance with modern clonal stem cell theories [37]. Hence, one may presume that the metastatic capacity of the primary tumour will influence commonly chosen reference genes.

The most recent study of reference genes in colon cancer was reported by Kheirelseid et al., 2010, where 64 colorectal tumours and tumour associated normal specimens were examined using qRT-PCR followed by three different statistical algorithms, geNorm, NormFinder and qBaseplus [30]. Kheirelseid et al., 2010, found that the combination of two reference genes, B2M and PPIA, more accurately normalized qRT-PCR data in colorectal cancer. This is in concordance with our findings, where PPIA was one of the two genes identified as the most stable pair. In contrast, B2M was identified as one of the most variable genes in the tissue examined. This disparity may be explained by the difference in patient material since Kheirelseid et al., 2010, included all stages of colon cancer and even included rectum tumour samples. Furthermore the percentage of tumour cells in the samples was not addressed. In the study of Kheirelseid et al., 2010, all three algorithms confirmed the selection of the B2M and PPIA pairing as the best combination of reference genes. In the present study however, the geNorm algorithm differs from the results obtained by NormFinder. According to geNorm HPRT1 and PPIA were the most suitable genes for normalization, but NormFinder suggested IPO8 and PPIA. This discrepancy confirms previous results reported by Caradec et al., 2010, concluding that the evaluation of suitable reference genes dramatically differs according to the statistical method used [12]. Caradec et al., 2010, investigated reference genes in four cell lines treated with four different oxygen concentrations, and observed large variations in gene expression results depending of statistical method used. Thus Caradec et al., 2010, recommended Ct coefficients of variation (CtCV%) calculation for each reference gene for validation of the statistical methods. It is defined as the ratio of the standard deviation to the mean. Genes with low CtCV% value indicate more stable expression of those genes. In the present study, IPO8 was the most stable gene on the basis of CtCV% (5.12%), followed by GUSB (5.55%) and HPRT1 (6.04%) as the second and third most stable gene. Using NormFinder IPO8 was one of the genes which were identified as the most stable pair of genes, which may indicate that the CtCV% verifies the NormFinder results. Nevertheless, PPIA, which was suggested by both geNorm and NormFinder as one of the stable pair of genes, was ranked as the tenth most stable gene with a CtCV% of 7.34%. This may be explained by the low Ct mean of this particular gene (18.0), resulting in a relatively high CtCV% despite a low standard deviation. Another aspect which strengthens the results achieved by NormFinder compared with geNorm is the argument that geNorm lacks robustness compared with NormFinder [32]. Reports show that exclusion of one sample in a specific tissue collection led geNorm to change a suggested reference gene (18S) from being an unstable gene to one of the top ranking stable genes [32]. NormFinder also enables estimation of the variation between sample subgroups, like tumour and normal tissue, thus this algorithm can account for heterogeneity in the tested samples, which may be important considering the heterogeneity of the samples studied.

The optimal normalization will vary with study design. The most suitable reference gene in one medical condition may be regulated in other tissues or diseases. Blanquicett et al., 2002, found that 18S, S9 and GUS were the least regulated genes among 15 putative reference genes when examining tumour and normal colorectal and liver tissues [28]. Furthermore, Dydensborg et al., 2006, identified B2M as the most appropriate gene for normalizing colon carcinomas comparing to normal mucosa when they investigated seven colon adenocarcinomas containing both epithelial and stromal cells [29]. B2M was in this study identified as the least stable gene using NormFinder, and the third most variable gene using geNorm. In the present study where the tumour tissue samples consisted of more than 70% tumour cells some of the stromal cells are excluded. This might explain the discrepancies in the ranking of B2M since tumour tissue is heterogeneous and the fraction of different cells may influence the gene expression results. Moreover, different patient groups, including age and clinical background, may also give dissimilarities across studies. Experimental variations may also influence the gene expression results, though using triplicates in the qRT-PCR analysis as used in this study will diminish this variation.

Single assays qRT-PCR are time- and labour-intensive, and require relatively large amounts of cDNA and PCR reagents in multivariate gene expression studies. TLDA overcome these drawbacks since this technique allows for simultaneously detection of expression of up to 384 genes and requires less template cDNA and PCR reagents than routine qRT-PCR [1, 31, 3840].

Conclusions

In this study we applied TaqMan Low Density Array in order to identify reference genes in metastatic and non-metastatic colon cancer. The genes often used for normalization of gene expression data may be unstable and thus not suited for use, and therefore identifying stable reference genes in the specific experiment is vital for the results. The approach described herein can serve as a template to identify valid reference genes in any disease state. However, the optimal statistical approach to identify the best reference gene(s) remains to be determined. In the present study NormFinder and geNorm identified two different pairs of the most stable genes. The use of CTCV% might be a good validation of the two results. Nevertheless, the expression of target genes should be evaluated and a comparison of the effect of each pair of reference genes should be determined.

Declarations

Acknowledgements

We thank Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, Norway, for laboratory facilities, and Randi Bjørseth at Department of Pathology, Akershus University Hospital, Norway, for guidance and technical assistance. The authors declare that they have no conflicts of interest. This study was supported by grants from South Eastern Norway Regional Health Authority, Norway.

Authors’ Affiliations

(1)
Quality and Research Department, Ostfold Hospital Trust
(2)
Dep. of Pathology, Akershus University Hospital
(3)
Institute of Clinical Medicine, University of Oslo
(4)
Dep. of Surgery, Akershus University Hospital
(5)
Dep. of Health Promotion, Akershus University Hospital
(6)
Dep. of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences

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This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://​creativecommons.​org/​licenses/​by/​2.​0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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