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SOX2 is an oncogene activated by recurrent 3q26.3 amplifications in human lung squamous cell carcinomas.

Hussenet T, Dali S, Exinger J, Monga B, Jost B, Dembelé D, Martinet N, Thibault C, Huelsken J, Brambilla E, du Manoir S - PLoS ONE (2010)

Bottom Line: Intense SOX2 immunostaining is frequent in nuclei of lung SCC, indicating potential active transcriptional regulation by SOX2.In cell culture experiments, overexpression of SOX2 stimulates cellular migration and anchorage-independent growth while SOX2 knockdown impairs cell growth.These results indicate that the SOX2 transcription factor, a major regulator of stem cell function, is also an oncogene and a driver gene for the recurrent 3q26.33 amplifications in lung SCC.

View Article: PubMed Central - PubMed

Affiliation: Département Biologie du Cancer, Institut National de la Santé et de la Recherche Médicale, Institut de Génétique et de Biologie Moléculaire et Cellulaire, U964 Illkirch, France. hussenet@igbmc.fr

ABSTRACT
Squamous cell carcinoma (SCC) of the lung is a frequent and aggressive cancer type. Gene amplifications, a known activating mechanism of oncogenes, target the 3q26-qter region as one of the most frequently gained/amplified genomic sites in SCC of various types. Here, we used array comparative genomic hybridization to delineate the consensus region of 3q26.3 amplifications in lung SCC. Recurrent amplifications occur in 20% of lung SCC (136 tumors in total) and map to a core region of 2 Mb (Megabases) that encompasses SOX2, a transcription factor gene. Intense SOX2 immunostaining is frequent in nuclei of lung SCC, indicating potential active transcriptional regulation by SOX2. Analyses of the transcriptome of lung SCC, SOX2-overexpressing lung epithelial cells and embryonic stem cells (ESCs) reveal that SOX2 contributes to activate ESC-like phenotypes and provide clues pertaining to the deregulated genes involved in the malignant phenotype. In cell culture experiments, overexpression of SOX2 stimulates cellular migration and anchorage-independent growth while SOX2 knockdown impairs cell growth. Finally, SOX2 over-expression in non-tumorigenic human lung bronchial epithelial cells is tumorigenic in immunocompromised mice. These results indicate that the SOX2 transcription factor, a major regulator of stem cell function, is also an oncogene and a driver gene for the recurrent 3q26.33 amplifications in lung SCC.

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Related in: MedlinePlus

Characterization of chromosome 3 aberrations in lung SCC using array-CGH.A. Frequency of chromosome 3 losses and gains in 26 advanced lung SCCs. For each 2 Mb interval along chromosome 3, frequencies were calculated by dividing the total number of occurrences of losses or gains observed in the series by the total number of possible occurrences, expressed as percentages and represented along the chromosomal order. Gaps are due to intervals with no coverage on the array. Frequent 3p losses seem to affect discontinuous zones. The most frequently lost region is the 8–10 Mb interval (around 60% of samples). Gains were more frequently detected on the 3q arm: 3q26-qter was gained in 50–60% of the samples with two discrete intervals (180–182 and 188–190 Mb, denoted by asterisks) gained in around 80% of tumors. B. High level chromosome 3 amplification frequency in 26 advanced lung SCCs. For a given clone, a ratio greater than 2 (1 in log2 scale) in a single experiment was considered to represent a high-level amplification. Frequencies were calculated for the series of 26 cases and plotted according to clone localization. High level amplifications cluster in the 3q26-qter region. A peak maxima is observed for BAC clone RP11-259I19; high level amplifications of this locus are found in 20% of cases (5/26 tumors). C. Whole genome high level amplification frequencies in 34 advanced lung SCCs (independent cohort). Chromosome numbers are indicated above the graph, and different chromosomes are separated by vertical gray lines. For a given clone, a ratio greater than 1.5 in log2 scale in a single experiment was considered to represent a high-level amplification. Frequencies were calculated for the series of 34 cases and plotted according to clone localization on the genome. Two genomic regions, on chromosomes 3 and 4 were amplified in >20% of the cases. D. High level chromosome 3 high level amplification frequency in 34 advanced lung SCCs (independent cohort). The graph corresponds to panel C restricted to chromosome 3. E. Individual array-CGH profiles obtained for the five tumors with high level 3q26.3 gene amplifications. High ratio deviations were observed for two tumors with straight amplicon boundaries (#15 and #35). The consensus region of 3q26.3 amplifications is a 2.7 Mb segment spanning the 181.9–184.6 Mb interval (denoted by a grey rectangle). F. UCSC genome browser map of the 3q26.33 consensus region of amplifications in lung SCCs. This fully sequenced and assembled genomic region (181.9–184.6 Mb, NCBI build 34) contains nine genes (Refseq), including DCUN1D1 and SOX2, and various Genbank mRNAs. This image was downloaded from the UCSC genome browser (http://genome.ucsc.edu/, [64], [65]). The green arrows in panels B and C/D point to BAC clones RPCI11-259I19 and RPCI11-701O19, respectively, corresponding to the maxima of chromosome 3 amplification in these lung SCC cohorts. RPCI11-259I19 and RPCI11-701O19 are mapped, respectively, between the SOX2 and DCUN1D1, and FXR1 and SOX2, genes. Two different clones were found due to the composition of the two arrays (RPCI11-259I19 in our Chr3 array and RPCI11-701O19 in the GSE12280 array). Mapping of the amplification by two independent clones suggest that it is not a clone-derived artifact.
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pone-0008960-g001: Characterization of chromosome 3 aberrations in lung SCC using array-CGH.A. Frequency of chromosome 3 losses and gains in 26 advanced lung SCCs. For each 2 Mb interval along chromosome 3, frequencies were calculated by dividing the total number of occurrences of losses or gains observed in the series by the total number of possible occurrences, expressed as percentages and represented along the chromosomal order. Gaps are due to intervals with no coverage on the array. Frequent 3p losses seem to affect discontinuous zones. The most frequently lost region is the 8–10 Mb interval (around 60% of samples). Gains were more frequently detected on the 3q arm: 3q26-qter was gained in 50–60% of the samples with two discrete intervals (180–182 and 188–190 Mb, denoted by asterisks) gained in around 80% of tumors. B. High level chromosome 3 amplification frequency in 26 advanced lung SCCs. For a given clone, a ratio greater than 2 (1 in log2 scale) in a single experiment was considered to represent a high-level amplification. Frequencies were calculated for the series of 26 cases and plotted according to clone localization. High level amplifications cluster in the 3q26-qter region. A peak maxima is observed for BAC clone RP11-259I19; high level amplifications of this locus are found in 20% of cases (5/26 tumors). C. Whole genome high level amplification frequencies in 34 advanced lung SCCs (independent cohort). Chromosome numbers are indicated above the graph, and different chromosomes are separated by vertical gray lines. For a given clone, a ratio greater than 1.5 in log2 scale in a single experiment was considered to represent a high-level amplification. Frequencies were calculated for the series of 34 cases and plotted according to clone localization on the genome. Two genomic regions, on chromosomes 3 and 4 were amplified in >20% of the cases. D. High level chromosome 3 high level amplification frequency in 34 advanced lung SCCs (independent cohort). The graph corresponds to panel C restricted to chromosome 3. E. Individual array-CGH profiles obtained for the five tumors with high level 3q26.3 gene amplifications. High ratio deviations were observed for two tumors with straight amplicon boundaries (#15 and #35). The consensus region of 3q26.3 amplifications is a 2.7 Mb segment spanning the 181.9–184.6 Mb interval (denoted by a grey rectangle). F. UCSC genome browser map of the 3q26.33 consensus region of amplifications in lung SCCs. This fully sequenced and assembled genomic region (181.9–184.6 Mb, NCBI build 34) contains nine genes (Refseq), including DCUN1D1 and SOX2, and various Genbank mRNAs. This image was downloaded from the UCSC genome browser (http://genome.ucsc.edu/, [64], [65]). The green arrows in panels B and C/D point to BAC clones RPCI11-259I19 and RPCI11-701O19, respectively, corresponding to the maxima of chromosome 3 amplification in these lung SCC cohorts. RPCI11-259I19 and RPCI11-701O19 are mapped, respectively, between the SOX2 and DCUN1D1, and FXR1 and SOX2, genes. Two different clones were found due to the composition of the two arrays (RPCI11-259I19 in our Chr3 array and RPCI11-701O19 in the GSE12280 array). Mapping of the amplification by two independent clones suggest that it is not a clone-derived artifact.

Mentions: To delineate chromosome 3 consensus regions of deletions and gains/amplifications, we analyzed 26 advanced stage lung SCCs using a chromosome 3-dedicated array composed of 214 genomic clones. All data are available in GEO (GSE15080). Losses on the 3p arm, gains of large 3q regions and high-level amplifications at 3q26-qter were found (Figure 1 panel A–B). Deletions mostly occurred on the 3p arm and seemed to affect several sites. Among genomic positions evaluated on the short arm, the interval from 8 to 10 Mb, (containing OGG1 and RAD18) was the most frequently lost (60% of tumors). Large gains often targeted the 3q arm, with a global gain of the 3q26-qter (176–196 Mb) region in 60% of tumors. Two interval regions, from 180 to 182 Mb (including the PIK3CA locus) and from 188 to 190 Mb (including the RFC4/SST locus) were gained in about 80% of tumors. Frequent high-level amplifications clustered in the 3q26-qter region (Figure 1 panel B), with a maximum for clone RPCI11-259I19 amplified in nearly 20% (5/26). This clone is located at 3q26.33, between SOX2 and DCUN1D1 (Figure 1 panel F). Whole genome surveys of the two tumors with the most accentuated amplifications revealed that the highest copy number levels across all chromosomes were located at 3q26.33 (Figure S1, panel A).


SOX2 is an oncogene activated by recurrent 3q26.3 amplifications in human lung squamous cell carcinomas.

Hussenet T, Dali S, Exinger J, Monga B, Jost B, Dembelé D, Martinet N, Thibault C, Huelsken J, Brambilla E, du Manoir S - PLoS ONE (2010)

Characterization of chromosome 3 aberrations in lung SCC using array-CGH.A. Frequency of chromosome 3 losses and gains in 26 advanced lung SCCs. For each 2 Mb interval along chromosome 3, frequencies were calculated by dividing the total number of occurrences of losses or gains observed in the series by the total number of possible occurrences, expressed as percentages and represented along the chromosomal order. Gaps are due to intervals with no coverage on the array. Frequent 3p losses seem to affect discontinuous zones. The most frequently lost region is the 8–10 Mb interval (around 60% of samples). Gains were more frequently detected on the 3q arm: 3q26-qter was gained in 50–60% of the samples with two discrete intervals (180–182 and 188–190 Mb, denoted by asterisks) gained in around 80% of tumors. B. High level chromosome 3 amplification frequency in 26 advanced lung SCCs. For a given clone, a ratio greater than 2 (1 in log2 scale) in a single experiment was considered to represent a high-level amplification. Frequencies were calculated for the series of 26 cases and plotted according to clone localization. High level amplifications cluster in the 3q26-qter region. A peak maxima is observed for BAC clone RP11-259I19; high level amplifications of this locus are found in 20% of cases (5/26 tumors). C. Whole genome high level amplification frequencies in 34 advanced lung SCCs (independent cohort). Chromosome numbers are indicated above the graph, and different chromosomes are separated by vertical gray lines. For a given clone, a ratio greater than 1.5 in log2 scale in a single experiment was considered to represent a high-level amplification. Frequencies were calculated for the series of 34 cases and plotted according to clone localization on the genome. Two genomic regions, on chromosomes 3 and 4 were amplified in >20% of the cases. D. High level chromosome 3 high level amplification frequency in 34 advanced lung SCCs (independent cohort). The graph corresponds to panel C restricted to chromosome 3. E. Individual array-CGH profiles obtained for the five tumors with high level 3q26.3 gene amplifications. High ratio deviations were observed for two tumors with straight amplicon boundaries (#15 and #35). The consensus region of 3q26.3 amplifications is a 2.7 Mb segment spanning the 181.9–184.6 Mb interval (denoted by a grey rectangle). F. UCSC genome browser map of the 3q26.33 consensus region of amplifications in lung SCCs. This fully sequenced and assembled genomic region (181.9–184.6 Mb, NCBI build 34) contains nine genes (Refseq), including DCUN1D1 and SOX2, and various Genbank mRNAs. This image was downloaded from the UCSC genome browser (http://genome.ucsc.edu/, [64], [65]). The green arrows in panels B and C/D point to BAC clones RPCI11-259I19 and RPCI11-701O19, respectively, corresponding to the maxima of chromosome 3 amplification in these lung SCC cohorts. RPCI11-259I19 and RPCI11-701O19 are mapped, respectively, between the SOX2 and DCUN1D1, and FXR1 and SOX2, genes. Two different clones were found due to the composition of the two arrays (RPCI11-259I19 in our Chr3 array and RPCI11-701O19 in the GSE12280 array). Mapping of the amplification by two independent clones suggest that it is not a clone-derived artifact.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2813300&req=5

pone-0008960-g001: Characterization of chromosome 3 aberrations in lung SCC using array-CGH.A. Frequency of chromosome 3 losses and gains in 26 advanced lung SCCs. For each 2 Mb interval along chromosome 3, frequencies were calculated by dividing the total number of occurrences of losses or gains observed in the series by the total number of possible occurrences, expressed as percentages and represented along the chromosomal order. Gaps are due to intervals with no coverage on the array. Frequent 3p losses seem to affect discontinuous zones. The most frequently lost region is the 8–10 Mb interval (around 60% of samples). Gains were more frequently detected on the 3q arm: 3q26-qter was gained in 50–60% of the samples with two discrete intervals (180–182 and 188–190 Mb, denoted by asterisks) gained in around 80% of tumors. B. High level chromosome 3 amplification frequency in 26 advanced lung SCCs. For a given clone, a ratio greater than 2 (1 in log2 scale) in a single experiment was considered to represent a high-level amplification. Frequencies were calculated for the series of 26 cases and plotted according to clone localization. High level amplifications cluster in the 3q26-qter region. A peak maxima is observed for BAC clone RP11-259I19; high level amplifications of this locus are found in 20% of cases (5/26 tumors). C. Whole genome high level amplification frequencies in 34 advanced lung SCCs (independent cohort). Chromosome numbers are indicated above the graph, and different chromosomes are separated by vertical gray lines. For a given clone, a ratio greater than 1.5 in log2 scale in a single experiment was considered to represent a high-level amplification. Frequencies were calculated for the series of 34 cases and plotted according to clone localization on the genome. Two genomic regions, on chromosomes 3 and 4 were amplified in >20% of the cases. D. High level chromosome 3 high level amplification frequency in 34 advanced lung SCCs (independent cohort). The graph corresponds to panel C restricted to chromosome 3. E. Individual array-CGH profiles obtained for the five tumors with high level 3q26.3 gene amplifications. High ratio deviations were observed for two tumors with straight amplicon boundaries (#15 and #35). The consensus region of 3q26.3 amplifications is a 2.7 Mb segment spanning the 181.9–184.6 Mb interval (denoted by a grey rectangle). F. UCSC genome browser map of the 3q26.33 consensus region of amplifications in lung SCCs. This fully sequenced and assembled genomic region (181.9–184.6 Mb, NCBI build 34) contains nine genes (Refseq), including DCUN1D1 and SOX2, and various Genbank mRNAs. This image was downloaded from the UCSC genome browser (http://genome.ucsc.edu/, [64], [65]). The green arrows in panels B and C/D point to BAC clones RPCI11-259I19 and RPCI11-701O19, respectively, corresponding to the maxima of chromosome 3 amplification in these lung SCC cohorts. RPCI11-259I19 and RPCI11-701O19 are mapped, respectively, between the SOX2 and DCUN1D1, and FXR1 and SOX2, genes. Two different clones were found due to the composition of the two arrays (RPCI11-259I19 in our Chr3 array and RPCI11-701O19 in the GSE12280 array). Mapping of the amplification by two independent clones suggest that it is not a clone-derived artifact.
Mentions: To delineate chromosome 3 consensus regions of deletions and gains/amplifications, we analyzed 26 advanced stage lung SCCs using a chromosome 3-dedicated array composed of 214 genomic clones. All data are available in GEO (GSE15080). Losses on the 3p arm, gains of large 3q regions and high-level amplifications at 3q26-qter were found (Figure 1 panel A–B). Deletions mostly occurred on the 3p arm and seemed to affect several sites. Among genomic positions evaluated on the short arm, the interval from 8 to 10 Mb, (containing OGG1 and RAD18) was the most frequently lost (60% of tumors). Large gains often targeted the 3q arm, with a global gain of the 3q26-qter (176–196 Mb) region in 60% of tumors. Two interval regions, from 180 to 182 Mb (including the PIK3CA locus) and from 188 to 190 Mb (including the RFC4/SST locus) were gained in about 80% of tumors. Frequent high-level amplifications clustered in the 3q26-qter region (Figure 1 panel B), with a maximum for clone RPCI11-259I19 amplified in nearly 20% (5/26). This clone is located at 3q26.33, between SOX2 and DCUN1D1 (Figure 1 panel F). Whole genome surveys of the two tumors with the most accentuated amplifications revealed that the highest copy number levels across all chromosomes were located at 3q26.33 (Figure S1, panel A).

Bottom Line: Intense SOX2 immunostaining is frequent in nuclei of lung SCC, indicating potential active transcriptional regulation by SOX2.In cell culture experiments, overexpression of SOX2 stimulates cellular migration and anchorage-independent growth while SOX2 knockdown impairs cell growth.These results indicate that the SOX2 transcription factor, a major regulator of stem cell function, is also an oncogene and a driver gene for the recurrent 3q26.33 amplifications in lung SCC.

View Article: PubMed Central - PubMed

Affiliation: Département Biologie du Cancer, Institut National de la Santé et de la Recherche Médicale, Institut de Génétique et de Biologie Moléculaire et Cellulaire, U964 Illkirch, France. hussenet@igbmc.fr

ABSTRACT
Squamous cell carcinoma (SCC) of the lung is a frequent and aggressive cancer type. Gene amplifications, a known activating mechanism of oncogenes, target the 3q26-qter region as one of the most frequently gained/amplified genomic sites in SCC of various types. Here, we used array comparative genomic hybridization to delineate the consensus region of 3q26.3 amplifications in lung SCC. Recurrent amplifications occur in 20% of lung SCC (136 tumors in total) and map to a core region of 2 Mb (Megabases) that encompasses SOX2, a transcription factor gene. Intense SOX2 immunostaining is frequent in nuclei of lung SCC, indicating potential active transcriptional regulation by SOX2. Analyses of the transcriptome of lung SCC, SOX2-overexpressing lung epithelial cells and embryonic stem cells (ESCs) reveal that SOX2 contributes to activate ESC-like phenotypes and provide clues pertaining to the deregulated genes involved in the malignant phenotype. In cell culture experiments, overexpression of SOX2 stimulates cellular migration and anchorage-independent growth while SOX2 knockdown impairs cell growth. Finally, SOX2 over-expression in non-tumorigenic human lung bronchial epithelial cells is tumorigenic in immunocompromised mice. These results indicate that the SOX2 transcription factor, a major regulator of stem cell function, is also an oncogene and a driver gene for the recurrent 3q26.33 amplifications in lung SCC.

Show MeSH
Related in: MedlinePlus