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Transcriptome profiles of carcinoma-in-situ and invasive non-small cell lung cancer as revealed by SAGE.

Lonergan KM, Chari R, Coe BP, Wilson IM, Tsao MS, Ng RT, Macaulay C, Lam S, Lam WL - PLoS ONE (2010)

Bottom Line: Expression of genes associated with epidermal development, and loss of expression of genes associated with mucociliary biology, are predominant features of CIS, largely shared with precancerous lesions.Additionally, expression of genes associated with xenobiotic metabolism/detoxification is a notable feature of CIS, and is largely maintained in invasive cancer.Additionally, up-regulated genes detected at extreme differences between CIS and invasive cancer may have potential to serve as biomarkers for early detection.

View Article: PubMed Central - PubMed

Affiliation: Genetics Unit, Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.

ABSTRACT

Background: Non-small cell lung cancer (NSCLC) presents as a progressive disease spanning precancerous, preinvasive, locally invasive, and metastatic lesions. Identification of biological pathways reflective of these progressive stages, and aberrantly expressed genes associated with these pathways, would conceivably enhance therapeutic approaches to this devastating disease.

Methodology/principal findings: Through the construction and analysis of SAGE libraries, we have determined transcriptome profiles for preinvasive carcinoma-in-situ (CIS) and invasive squamous cell carcinoma (SCC) of the lung, and compared these with expression profiles generated from both bronchial epithelium, and precancerous metaplastic and dysplastic lesions using Ingenuity Pathway Analysis. Expression of genes associated with epidermal development, and loss of expression of genes associated with mucociliary biology, are predominant features of CIS, largely shared with precancerous lesions. Additionally, expression of genes associated with xenobiotic metabolism/detoxification is a notable feature of CIS, and is largely maintained in invasive cancer. Genes related to tissue fibrosis and acute phase immune response are characteristic of the invasive SCC phenotype. Moreover, the data presented here suggests that tissue remodeling/fibrosis is initiated at the early stages of CIS. Additionally, this study indicates that alteration in copy-number status represents a plausible mechanism for differential gene expression in CIS and invasive SCC.

Conclusions/significance: This study is the first report of large-scale expression profiling of CIS of the lung. Unbiased expression profiling of these preinvasive and invasive lesions provides a platform for further investigations into the molecular genetic events relevant to early stages of squamous NSCLC development. Additionally, up-regulated genes detected at extreme differences between CIS and invasive cancer may have potential to serve as biomarkers for early detection.

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Genes up-regulated in the CIS and invasive SCC datasets relative to BE and PC.A. Venn diagram of up-regulated SAGE tags and corresponding IPA mapped IDs for the CIS and SCC datasets. (See Table S5 and Table S6 for description of up-regulated tags in the CIS and SCC datasets, respectively.) B. IPA pathway graphical representation for the CIS over BE_PC dataset (80 unique IDs displayed in green; 58 shared IDs displayed in gray), and the SCC over BE_PC dataset (112 unique IDs displayed in red; 58 shared IDs displayed in gray). Gene products are positioned according to subcellular localization. Only direct connections (i.e., direct physical contact between two molecules) among the individual gene products are shown for clarity of presentation; lines indicate protein-protein binding interactions, and arrows refer to “acts on” interactions such as proteolysis, expression, and protein-DNA/RNA interactions. Eleven genes were detected at levels 20-fold or greater in the CIS over BE_PC dataset relative to the invasive cancer dataset (indicated by dark green), and 10 genes were detected at levels 20-fold or greater in the SCC over BE_PC dataset relative to the CIS dataset (indicated by dark red).
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pone-0009162-g005: Genes up-regulated in the CIS and invasive SCC datasets relative to BE and PC.A. Venn diagram of up-regulated SAGE tags and corresponding IPA mapped IDs for the CIS and SCC datasets. (See Table S5 and Table S6 for description of up-regulated tags in the CIS and SCC datasets, respectively.) B. IPA pathway graphical representation for the CIS over BE_PC dataset (80 unique IDs displayed in green; 58 shared IDs displayed in gray), and the SCC over BE_PC dataset (112 unique IDs displayed in red; 58 shared IDs displayed in gray). Gene products are positioned according to subcellular localization. Only direct connections (i.e., direct physical contact between two molecules) among the individual gene products are shown for clarity of presentation; lines indicate protein-protein binding interactions, and arrows refer to “acts on” interactions such as proteolysis, expression, and protein-DNA/RNA interactions. Eleven genes were detected at levels 20-fold or greater in the CIS over BE_PC dataset relative to the invasive cancer dataset (indicated by dark green), and 10 genes were detected at levels 20-fold or greater in the SCC over BE_PC dataset relative to the CIS dataset (indicated by dark red).

Mentions: We identified 225 SAGE tags to be over-expressed in CIS relative to both BE and PC (Table S5), and 232 tags to be over-expressed in invasive SCC relative to both BE and PC (Table S6). It is noted that greater than 35% of the over-expressed tags within the CIS dataset (85 tags) were commonly up-regulated in SCC (Figure 3B), suggesting that significant expression changes relating to advanced cancer have already occurred by the time a diagnosis of CIS has been made, in accordance with irreversibility of CIS lesions. Discrepancy between the number of up-regulated tags and the number of IPA mapped IDs within each dataset, indicates that a significant proportion of potentially up-regulated genes in early-stage lung cancer remain to be identified (Figure 5A). IPA pathway graphical representation for up-regulated tags with mapped IDs for the two cancer datasets, is presented in Figure 5B. A higher proportion of up-regulated gene products are localized to the extracellular space in the SCC dataset relative to the CIS dataset. Considering the molecular interactions identified by IPA, functional networks involving the cell surface/extracellular matrix adhesion protein FN1, and transcriptional/cell cycle regulator CDKN2A, highlight the SCC dataset. Up-regulation of FN1-interacting proteins associated with tissue remodeling/fibrosis, and FN1-interacting proteins associated with acute phase response, suggests a link between these processes in SCC. A link between acute phase response and tissue repair has been previously proposed [68]. Activation of a CDKN2A functional network associated with cellular senescence, may reflect a protective response of the involved organ to acute tissue injury [69]. No outstanding molecular interactions were apparent for the CIS up-regulated dataset. Differential expression for a subset of the up-regulated genes in Figure 5B was validated by real-time quantitative RT-PCR (Table S7).


Transcriptome profiles of carcinoma-in-situ and invasive non-small cell lung cancer as revealed by SAGE.

Lonergan KM, Chari R, Coe BP, Wilson IM, Tsao MS, Ng RT, Macaulay C, Lam S, Lam WL - PLoS ONE (2010)

Genes up-regulated in the CIS and invasive SCC datasets relative to BE and PC.A. Venn diagram of up-regulated SAGE tags and corresponding IPA mapped IDs for the CIS and SCC datasets. (See Table S5 and Table S6 for description of up-regulated tags in the CIS and SCC datasets, respectively.) B. IPA pathway graphical representation for the CIS over BE_PC dataset (80 unique IDs displayed in green; 58 shared IDs displayed in gray), and the SCC over BE_PC dataset (112 unique IDs displayed in red; 58 shared IDs displayed in gray). Gene products are positioned according to subcellular localization. Only direct connections (i.e., direct physical contact between two molecules) among the individual gene products are shown for clarity of presentation; lines indicate protein-protein binding interactions, and arrows refer to “acts on” interactions such as proteolysis, expression, and protein-DNA/RNA interactions. Eleven genes were detected at levels 20-fold or greater in the CIS over BE_PC dataset relative to the invasive cancer dataset (indicated by dark green), and 10 genes were detected at levels 20-fold or greater in the SCC over BE_PC dataset relative to the CIS dataset (indicated by dark red).
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2820080&req=5

pone-0009162-g005: Genes up-regulated in the CIS and invasive SCC datasets relative to BE and PC.A. Venn diagram of up-regulated SAGE tags and corresponding IPA mapped IDs for the CIS and SCC datasets. (See Table S5 and Table S6 for description of up-regulated tags in the CIS and SCC datasets, respectively.) B. IPA pathway graphical representation for the CIS over BE_PC dataset (80 unique IDs displayed in green; 58 shared IDs displayed in gray), and the SCC over BE_PC dataset (112 unique IDs displayed in red; 58 shared IDs displayed in gray). Gene products are positioned according to subcellular localization. Only direct connections (i.e., direct physical contact between two molecules) among the individual gene products are shown for clarity of presentation; lines indicate protein-protein binding interactions, and arrows refer to “acts on” interactions such as proteolysis, expression, and protein-DNA/RNA interactions. Eleven genes were detected at levels 20-fold or greater in the CIS over BE_PC dataset relative to the invasive cancer dataset (indicated by dark green), and 10 genes were detected at levels 20-fold or greater in the SCC over BE_PC dataset relative to the CIS dataset (indicated by dark red).
Mentions: We identified 225 SAGE tags to be over-expressed in CIS relative to both BE and PC (Table S5), and 232 tags to be over-expressed in invasive SCC relative to both BE and PC (Table S6). It is noted that greater than 35% of the over-expressed tags within the CIS dataset (85 tags) were commonly up-regulated in SCC (Figure 3B), suggesting that significant expression changes relating to advanced cancer have already occurred by the time a diagnosis of CIS has been made, in accordance with irreversibility of CIS lesions. Discrepancy between the number of up-regulated tags and the number of IPA mapped IDs within each dataset, indicates that a significant proportion of potentially up-regulated genes in early-stage lung cancer remain to be identified (Figure 5A). IPA pathway graphical representation for up-regulated tags with mapped IDs for the two cancer datasets, is presented in Figure 5B. A higher proportion of up-regulated gene products are localized to the extracellular space in the SCC dataset relative to the CIS dataset. Considering the molecular interactions identified by IPA, functional networks involving the cell surface/extracellular matrix adhesion protein FN1, and transcriptional/cell cycle regulator CDKN2A, highlight the SCC dataset. Up-regulation of FN1-interacting proteins associated with tissue remodeling/fibrosis, and FN1-interacting proteins associated with acute phase response, suggests a link between these processes in SCC. A link between acute phase response and tissue repair has been previously proposed [68]. Activation of a CDKN2A functional network associated with cellular senescence, may reflect a protective response of the involved organ to acute tissue injury [69]. No outstanding molecular interactions were apparent for the CIS up-regulated dataset. Differential expression for a subset of the up-regulated genes in Figure 5B was validated by real-time quantitative RT-PCR (Table S7).

Bottom Line: Expression of genes associated with epidermal development, and loss of expression of genes associated with mucociliary biology, are predominant features of CIS, largely shared with precancerous lesions.Additionally, expression of genes associated with xenobiotic metabolism/detoxification is a notable feature of CIS, and is largely maintained in invasive cancer.Additionally, up-regulated genes detected at extreme differences between CIS and invasive cancer may have potential to serve as biomarkers for early detection.

View Article: PubMed Central - PubMed

Affiliation: Genetics Unit, Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.

ABSTRACT

Background: Non-small cell lung cancer (NSCLC) presents as a progressive disease spanning precancerous, preinvasive, locally invasive, and metastatic lesions. Identification of biological pathways reflective of these progressive stages, and aberrantly expressed genes associated with these pathways, would conceivably enhance therapeutic approaches to this devastating disease.

Methodology/principal findings: Through the construction and analysis of SAGE libraries, we have determined transcriptome profiles for preinvasive carcinoma-in-situ (CIS) and invasive squamous cell carcinoma (SCC) of the lung, and compared these with expression profiles generated from both bronchial epithelium, and precancerous metaplastic and dysplastic lesions using Ingenuity Pathway Analysis. Expression of genes associated with epidermal development, and loss of expression of genes associated with mucociliary biology, are predominant features of CIS, largely shared with precancerous lesions. Additionally, expression of genes associated with xenobiotic metabolism/detoxification is a notable feature of CIS, and is largely maintained in invasive cancer. Genes related to tissue fibrosis and acute phase immune response are characteristic of the invasive SCC phenotype. Moreover, the data presented here suggests that tissue remodeling/fibrosis is initiated at the early stages of CIS. Additionally, this study indicates that alteration in copy-number status represents a plausible mechanism for differential gene expression in CIS and invasive SCC.

Conclusions/significance: This study is the first report of large-scale expression profiling of CIS of the lung. Unbiased expression profiling of these preinvasive and invasive lesions provides a platform for further investigations into the molecular genetic events relevant to early stages of squamous NSCLC development. Additionally, up-regulated genes detected at extreme differences between CIS and invasive cancer may have potential to serve as biomarkers for early detection.

Show MeSH
Related in: MedlinePlus