Limits...
Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues.

Grigoriadis A, Oliver GR, Tanney A, Kendrick H, Smalley MJ, Jat P, Neville AM - BMC Genomics (2009)

Bottom Line: Expression of 431 NATs were confirmed by either of the other two technologies.Expression of a proportion of these NATs has already been confirmed by other technologies while the true existence of the remaining ones has to be validated.Nevertheless, future studies will reveal whether the relative abundances of antisense and sense transcripts have regulatory influences on the translation of these mRNAs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Ludwig Institute for Cancer Research, 605 Third Avenue, New York, NY 10158, USA. anita.grigoriadis@kcl.ac.uk

ABSTRACT

Background: More than 20% of human transcripts have naturally occurring antisense products (or natural antisense transcripts--NATs), some of which may play a key role in a range of human diseases. To date, several databases of in silico defined human sense-antisense (SAS) pairs have appeared, however no study has focused on differential expression of SAS pairs in breast tissue. We therefore investigated the expression levels of sense and antisense transcripts in normal and malignant human breast epithelia using the Affymetrix HG-U133 Plus 2.0 and Almac Diagnostics Breast Cancer DSA microarray technologies as well as massively parallel signature sequencing (MPSS) data.

Results: The expression of more than 2500 antisense transcripts were detected in normal breast duct luminal cells and in primary breast tumors substantially enriched for their epithelial cell content by DSA microarray. Expression of 431 NATs were confirmed by either of the other two technologies. A corresponding sense transcript could be identified on DSA for 257 antisense transcripts. Of these SAS pairs, 163 have not been previously reported. A positive correlation of differential expression between normal and malignant breast samples was observed for most SAS pairs. Orientation specific RT-QPCR of selected SAS pairs validated their expression in several breast cancer cell lines and solid breast tumours.

Conclusion: Disease-focused and antisense enriched microarray platforms (such as Breast Cancer DSA) confirm the assumption that antisense transcription in the human breast is more prevalent than previously anticipated. Expression of a proportion of these NATs has already been confirmed by other technologies while the true existence of the remaining ones has to be validated. Nevertheless, future studies will reveal whether the relative abundances of antisense and sense transcripts have regulatory influences on the translation of these mRNAs.

Show MeSH

Related in: MedlinePlus

Overlay of expression detection between MPSS and microarray for sense and antisense transcripts malignant and normal breast epithelium. Human transcriptome clusters (HTR) were used to measure the concordance in detecting sense and antisense transcripts for the Breast Cancer DSA (green), Affymetrix HG U133 Plus 2.0 (blue) and MPSS (red) in both the malignant breast epithelium and normal luminal epithelium. The presence of a MPPS tag was determined if a MPSS tag had at least a count of 3 tpm in these samples. For the two microarray platforms, a HTR cluster was called present when its containing sense (top section) or antisense (bottom section) probe set obtained a present calls with the MAS5 algorithm.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2721853&req=5

Figure 1: Overlay of expression detection between MPSS and microarray for sense and antisense transcripts malignant and normal breast epithelium. Human transcriptome clusters (HTR) were used to measure the concordance in detecting sense and antisense transcripts for the Breast Cancer DSA (green), Affymetrix HG U133 Plus 2.0 (blue) and MPSS (red) in both the malignant breast epithelium and normal luminal epithelium. The presence of a MPPS tag was determined if a MPSS tag had at least a count of 3 tpm in these samples. For the two microarray platforms, a HTR cluster was called present when its containing sense (top section) or antisense (bottom section) probe set obtained a present calls with the MAS5 algorithm.

Mentions: As shown in Figure 1, the two microarray platforms had a concordance of ~9,000 transcripts in the normal setting, but nearly five times more transcripts were detected specifically on the breast tissue specific Breast Cancer DSA microarray platform in the normal and malignant epithelium (Figure 1). Furthermore, expression profiles obtained by the Breast Cancer DSA identified three times more transcripts found by MPSS than the Affymetrix platform. This difference between the generic Affymetrix Plus 2.0 and the tissue-specific Breast Cancer DSA became even more apparent when antisense-containing HTR clusters were compared. While 43% of all antisense-detecting probes sets obtained a present call, only 14% on the Plus 2.0 could be detected, corresponding to the unique detection of > 2,000 antisense-containing HTR clusters in the normal and the malignant breast epithelium by Breast Cancer DSA. For the DSA platform, 2452 antisense detecting probe sets were in common between the normal and the malignant epithelium, of which 868 showed more than two-fold difference in expression level with a pValue < 0.05. In contrast, 344 Affymetrix probe sets mapping to antisense transcripts were detectable in normal and malignant breast epithelium, of which 60 passed the same criteria, and only 48 MPSS tags showed different expression level.


Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues.

Grigoriadis A, Oliver GR, Tanney A, Kendrick H, Smalley MJ, Jat P, Neville AM - BMC Genomics (2009)

Overlay of expression detection between MPSS and microarray for sense and antisense transcripts malignant and normal breast epithelium. Human transcriptome clusters (HTR) were used to measure the concordance in detecting sense and antisense transcripts for the Breast Cancer DSA (green), Affymetrix HG U133 Plus 2.0 (blue) and MPSS (red) in both the malignant breast epithelium and normal luminal epithelium. The presence of a MPPS tag was determined if a MPSS tag had at least a count of 3 tpm in these samples. For the two microarray platforms, a HTR cluster was called present when its containing sense (top section) or antisense (bottom section) probe set obtained a present calls with the MAS5 algorithm.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2721853&req=5

Figure 1: Overlay of expression detection between MPSS and microarray for sense and antisense transcripts malignant and normal breast epithelium. Human transcriptome clusters (HTR) were used to measure the concordance in detecting sense and antisense transcripts for the Breast Cancer DSA (green), Affymetrix HG U133 Plus 2.0 (blue) and MPSS (red) in both the malignant breast epithelium and normal luminal epithelium. The presence of a MPPS tag was determined if a MPSS tag had at least a count of 3 tpm in these samples. For the two microarray platforms, a HTR cluster was called present when its containing sense (top section) or antisense (bottom section) probe set obtained a present calls with the MAS5 algorithm.
Mentions: As shown in Figure 1, the two microarray platforms had a concordance of ~9,000 transcripts in the normal setting, but nearly five times more transcripts were detected specifically on the breast tissue specific Breast Cancer DSA microarray platform in the normal and malignant epithelium (Figure 1). Furthermore, expression profiles obtained by the Breast Cancer DSA identified three times more transcripts found by MPSS than the Affymetrix platform. This difference between the generic Affymetrix Plus 2.0 and the tissue-specific Breast Cancer DSA became even more apparent when antisense-containing HTR clusters were compared. While 43% of all antisense-detecting probes sets obtained a present call, only 14% on the Plus 2.0 could be detected, corresponding to the unique detection of > 2,000 antisense-containing HTR clusters in the normal and the malignant breast epithelium by Breast Cancer DSA. For the DSA platform, 2452 antisense detecting probe sets were in common between the normal and the malignant epithelium, of which 868 showed more than two-fold difference in expression level with a pValue < 0.05. In contrast, 344 Affymetrix probe sets mapping to antisense transcripts were detectable in normal and malignant breast epithelium, of which 60 passed the same criteria, and only 48 MPSS tags showed different expression level.

Bottom Line: Expression of 431 NATs were confirmed by either of the other two technologies.Expression of a proportion of these NATs has already been confirmed by other technologies while the true existence of the remaining ones has to be validated.Nevertheless, future studies will reveal whether the relative abundances of antisense and sense transcripts have regulatory influences on the translation of these mRNAs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Ludwig Institute for Cancer Research, 605 Third Avenue, New York, NY 10158, USA. anita.grigoriadis@kcl.ac.uk

ABSTRACT

Background: More than 20% of human transcripts have naturally occurring antisense products (or natural antisense transcripts--NATs), some of which may play a key role in a range of human diseases. To date, several databases of in silico defined human sense-antisense (SAS) pairs have appeared, however no study has focused on differential expression of SAS pairs in breast tissue. We therefore investigated the expression levels of sense and antisense transcripts in normal and malignant human breast epithelia using the Affymetrix HG-U133 Plus 2.0 and Almac Diagnostics Breast Cancer DSA microarray technologies as well as massively parallel signature sequencing (MPSS) data.

Results: The expression of more than 2500 antisense transcripts were detected in normal breast duct luminal cells and in primary breast tumors substantially enriched for their epithelial cell content by DSA microarray. Expression of 431 NATs were confirmed by either of the other two technologies. A corresponding sense transcript could be identified on DSA for 257 antisense transcripts. Of these SAS pairs, 163 have not been previously reported. A positive correlation of differential expression between normal and malignant breast samples was observed for most SAS pairs. Orientation specific RT-QPCR of selected SAS pairs validated their expression in several breast cancer cell lines and solid breast tumours.

Conclusion: Disease-focused and antisense enriched microarray platforms (such as Breast Cancer DSA) confirm the assumption that antisense transcription in the human breast is more prevalent than previously anticipated. Expression of a proportion of these NATs has already been confirmed by other technologies while the true existence of the remaining ones has to be validated. Nevertheless, future studies will reveal whether the relative abundances of antisense and sense transcripts have regulatory influences on the translation of these mRNAs.

Show MeSH
Related in: MedlinePlus