Search results for the GEO ID: GSE16424  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM412716 | GPL96 |
|
0 hours with HGF n4 h0hgf1n4 experiment TR5
|
SK-OV-3 ovarian carcinoma cells
|
cell line: SK-OV-3
|
Advanced ovarian cancers are initially responsive to
chemotherapy with platinum drugs but develop drug
resistance in most cases. We showed recently that
hepatocyte growth factor (HGF) enhances death of human
ovarian cancer cell lines treated with cisplatin (CDDP) and
that this effect is mediated by the p38 mitogen-activated
protein kinase. In this work, we integrated genome-wide
expression profiling, in silico data survey, and functional
assays to identify transcripts regulated in SK-OV-3 ovarian
cancer cells made more responsive to CDDP by HGF.
Using oligonucleotide microarrays, we found that HGF
pretreatment changes the transcriptional response to
CDDP. Quantitative reverse transcription-PCR not only
validated all the 15 most differentially expressed genes
but also confirmed that they were primarily modulated by
the combined treatment with HGF and CDDP and reversed
by suppressing p38 mitogen-activated protein kinase
activity. Among the differentially expressed genes, we
focused functional analysis on two regulatory subunits of
the protein phosphatase 2A, which were down-modulated
by HGF plus CDDP. Decrease of each subunit by RNA
interference made ovarian cancer cells more responsive to
CDDP, mimicking the effect of HGF. In conclusion, we
show that HGF and CDDP modulate transcription in
ovarian cancer cells and that this transcriptional response
is involved in apoptosis regulation. We also provide the
proof-of-concept that the identified genes might be
targeted to either increase the efficacy of chemotherapeutics
or revert chemotherapy resistance.
|
| Sample_geo_accession | GSM412716
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 04 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Exponentially growing cells were cultured for 48 hours in
| | Sample_treatment_protocol_ch1 | the presence of pure recombinant HGF (R&D Systems,
| | Sample_treatment_protocol_ch1 | Minneapolis, MN) at the concentration of 50 ng/mL or
| | Sample_treatment_protocol_ch1 | control medium. Apoptosis was then induced by adding
| | Sample_treatment_protocol_ch1 | fresh medium, with or without HGF, supplemented with
| | Sample_treatment_protocol_ch1 | 10 Amol/L CDDP.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified from SK-OV-3 cell
| | Sample_extract_protocol_ch1 | lines at each time point using the Concert Cytoplasmic
| | Sample_extract_protocol_ch1 | RNA Purification Reagent (Invitrogen, Carlsbad, CA) as
| | Sample_extract_protocol_ch1 | suggested by the manufacturer
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated as suggested by Affymetrix
| | Sample_hyb_protocol | arrays were hybridized as suggested by manufacturer
| | Sample_scan_protocol | arrays were scanned as suggested by manufacturer
| | Sample_data_processing | Two of the time-course experiments, done independently, were analyzed. From digitized image data
| | Sample_data_processing | files of raw data, background-normalized image data (CEL
| | Sample_data_processing | files) were generated. Microarray quality control and
| | Sample_data_processing | statistical validation was done using Bioconductor.
| | Sample_data_processing | The presence of hybridization/construction artifacts was
| | Sample_data_processing | evaluated with the fitPLM function (Bioconductor package
| | Sample_data_processing | affyPLM). The probes (PM) intensity distribution was
| | Sample_data_processing | evaluated using hist function (Bioconductor package affy).
| | Sample_data_processing | Only two arrays, CDDP 6 hours and CDDP/HGF 6 hours
| | Sample_data_processing | in TR7 experiment were discarded due to low quality. TR5
| | Sample_data_processing | and TR7 experiments were then analyzed separately. Probe
| | Sample_data_processing | set intensities were obtained by robust multiarray average (RMA), and normalization was done according to quantiles
| | Sample_data_processing | method. Probe sets in TR5 and
| | Sample_data_processing | TR7 were filtered separately to have an interquantile range
| | Sample_data_processing | for each probe set greater than 0.4.
| | Sample_data_processing | TR5 and TR7, represented as ratio with
| | Sample_data_processing | respect to probe sets mean across the experiments, were
| | Sample_data_processing | combined in a unique exprSet object. The identification of
| | Sample_data_processing | differentially expressed genes associated to the HGF effect
| | Sample_data_processing | was addressed using linear modeling approach. For
| | Sample_data_processing | assessing differential expression, an empirical Bayes
| | Sample_data_processing | method was used to moderate the SE of the estimated
| | Sample_data_processing | log-fold changes together with the BH correction of the
| | Sample_data_processing | false discovery rate.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412716/suppl/GSM412716.CEL.gz
| | Sample_series_id | GSE16424
| | Sample_data_row_count | 22215
| | |
|
GSM412717 | GPL96 |
|
0 hours with HGF n5 h0hgf1n5 experiment TR5
|
SK-OV-3 ovarian carcinoma cells
|
cell line: SK-OV-3
|
Advanced ovarian cancers are initially responsive to
chemotherapy with platinum drugs but develop drug
resistance in most cases. We showed recently that
hepatocyte growth factor (HGF) enhances death of human
ovarian cancer cell lines treated with cisplatin (CDDP) and
that this effect is mediated by the p38 mitogen-activated
protein kinase. In this work, we integrated genome-wide
expression profiling, in silico data survey, and functional
assays to identify transcripts regulated in SK-OV-3 ovarian
cancer cells made more responsive to CDDP by HGF.
Using oligonucleotide microarrays, we found that HGF
pretreatment changes the transcriptional response to
CDDP. Quantitative reverse transcription-PCR not only
validated all the 15 most differentially expressed genes
but also confirmed that they were primarily modulated by
the combined treatment with HGF and CDDP and reversed
by suppressing p38 mitogen-activated protein kinase
activity. Among the differentially expressed genes, we
focused functional analysis on two regulatory subunits of
the protein phosphatase 2A, which were down-modulated
by HGF plus CDDP. Decrease of each subunit by RNA
interference made ovarian cancer cells more responsive to
CDDP, mimicking the effect of HGF. In conclusion, we
show that HGF and CDDP modulate transcription in
ovarian cancer cells and that this transcriptional response
is involved in apoptosis regulation. We also provide the
proof-of-concept that the identified genes might be
targeted to either increase the efficacy of chemotherapeutics
or revert chemotherapy resistance.
|
| Sample_geo_accession | GSM412717
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 04 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Exponentially growing cells were cultured for 48 hours in
| | Sample_treatment_protocol_ch1 | the presence of pure recombinant HGF (R&D Systems,
| | Sample_treatment_protocol_ch1 | Minneapolis, MN) at the concentration of 50 ng/mL or
| | Sample_treatment_protocol_ch1 | control medium. Apoptosis was then induced by adding
| | Sample_treatment_protocol_ch1 | fresh medium, with or without HGF, supplemented with
| | Sample_treatment_protocol_ch1 | 10 Amol/L CDDP.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified from SK-OV-3 cell
| | Sample_extract_protocol_ch1 | lines at each time point using the Concert Cytoplasmic
| | Sample_extract_protocol_ch1 | RNA Purification Reagent (Invitrogen, Carlsbad, CA) as
| | Sample_extract_protocol_ch1 | suggested by the manufacturer
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated as suggested by Affymetrix
| | Sample_hyb_protocol | arrays were hybridized as suggested by manufacturer
| | Sample_scan_protocol | arrays were scanned as suggested by manufacturer
| | Sample_data_processing | Two of the time-course experiments, done independently, were analyzed. From digitized image data
| | Sample_data_processing | files of raw data, background-normalized image data (CEL
| | Sample_data_processing | files) were generated. Microarray quality control and
| | Sample_data_processing | statistical validation was done using Bioconductor.
| | Sample_data_processing | The presence of hybridization/construction artifacts was
| | Sample_data_processing | evaluated with the fitPLM function (Bioconductor package
| | Sample_data_processing | affyPLM). The probes (PM) intensity distribution was
| | Sample_data_processing | evaluated using hist function (Bioconductor package affy).
| | Sample_data_processing | Only two arrays, CDDP 6 hours and CDDP/HGF 6 hours
| | Sample_data_processing | in TR7 experiment were discarded due to low quality. TR5
| | Sample_data_processing | and TR7 experiments were then analyzed separately. Probe
| | Sample_data_processing | set intensities were obtained by robust multiarray average (RMA), and normalization was done according to quantiles
| | Sample_data_processing | method. Probe sets in TR5 and
| | Sample_data_processing | TR7 were filtered separately to have an interquantile range
| | Sample_data_processing | for each probe set greater than 0.4.
| | Sample_data_processing | TR5 and TR7, represented as ratio with
| | Sample_data_processing | respect to probe sets mean across the experiments, were
| | Sample_data_processing | combined in a unique exprSet object. The identification of
| | Sample_data_processing | differentially expressed genes associated to the HGF effect
| | Sample_data_processing | was addressed using linear modeling approach. For
| | Sample_data_processing | assessing differential expression, an empirical Bayes
| | Sample_data_processing | method was used to moderate the SE of the estimated
| | Sample_data_processing | log-fold changes together with the BH correction of the
| | Sample_data_processing | false discovery rate.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412717/suppl/GSM412717.CEL.gz
| | Sample_series_id | GSE16424
| | Sample_data_row_count | 22215
| | |
|
GSM412718 | GPL96 |
|
0 hours with HGF n6bis h0hgf1n6bis experiment TR7
|
SK-OV-3 ovarian carcinoma cells
|
cell line: SK-OV-3
|
Advanced ovarian cancers are initially responsive to
chemotherapy with platinum drugs but develop drug
resistance in most cases. We showed recently that
hepatocyte growth factor (HGF) enhances death of human
ovarian cancer cell lines treated with cisplatin (CDDP) and
that this effect is mediated by the p38 mitogen-activated
protein kinase. In this work, we integrated genome-wide
expression profiling, in silico data survey, and functional
assays to identify transcripts regulated in SK-OV-3 ovarian
cancer cells made more responsive to CDDP by HGF.
Using oligonucleotide microarrays, we found that HGF
pretreatment changes the transcriptional response to
CDDP. Quantitative reverse transcription-PCR not only
validated all the 15 most differentially expressed genes
but also confirmed that they were primarily modulated by
the combined treatment with HGF and CDDP and reversed
by suppressing p38 mitogen-activated protein kinase
activity. Among the differentially expressed genes, we
focused functional analysis on two regulatory subunits of
the protein phosphatase 2A, which were down-modulated
by HGF plus CDDP. Decrease of each subunit by RNA
interference made ovarian cancer cells more responsive to
CDDP, mimicking the effect of HGF. In conclusion, we
show that HGF and CDDP modulate transcription in
ovarian cancer cells and that this transcriptional response
is involved in apoptosis regulation. We also provide the
proof-of-concept that the identified genes might be
targeted to either increase the efficacy of chemotherapeutics
or revert chemotherapy resistance.
|
| Sample_geo_accession | GSM412718
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 04 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Exponentially growing cells were cultured for 48 hours in
| | Sample_treatment_protocol_ch1 | the presence of pure recombinant HGF (R&D Systems,
| | Sample_treatment_protocol_ch1 | Minneapolis, MN) at the concentration of 50 ng/mL or
| | Sample_treatment_protocol_ch1 | control medium. Apoptosis was then induced by adding
| | Sample_treatment_protocol_ch1 | fresh medium, with or without HGF, supplemented with
| | Sample_treatment_protocol_ch1 | 10 Amol/L CDDP.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified from SK-OV-3 cell
| | Sample_extract_protocol_ch1 | lines at each time point using the Concert Cytoplasmic
| | Sample_extract_protocol_ch1 | RNA Purification Reagent (Invitrogen, Carlsbad, CA) as
| | Sample_extract_protocol_ch1 | suggested by the manufacturer
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated as suggested by Affymetrix
| | Sample_hyb_protocol | arrays were hybridized as suggested by manufacturer
| | Sample_scan_protocol | arrays were scanned as suggested by manufacturer
| | Sample_data_processing | Two of the time-course experiments, done independently, were analyzed. From digitized image data
| | Sample_data_processing | files of raw data, background-normalized image data (CEL
| | Sample_data_processing | files) were generated. Microarray quality control and
| | Sample_data_processing | statistical validation was done using Bioconductor.
| | Sample_data_processing | The presence of hybridization/construction artifacts was
| | Sample_data_processing | evaluated with the fitPLM function (Bioconductor package
| | Sample_data_processing | affyPLM). The probes (PM) intensity distribution was
| | Sample_data_processing | evaluated using hist function (Bioconductor package affy).
| | Sample_data_processing | Only two arrays, CDDP 6 hours and CDDP/HGF 6 hours
| | Sample_data_processing | in TR7 experiment were discarded due to low quality. TR5
| | Sample_data_processing | and TR7 experiments were then analyzed separately. Probe
| | Sample_data_processing | set intensities were obtained by robust multiarray average (RMA), and normalization was done according to quantiles
| | Sample_data_processing | method. Probe sets in TR5 and
| | Sample_data_processing | TR7 were filtered separately to have an interquantile range
| | Sample_data_processing | for each probe set greater than 0.4.
| | Sample_data_processing | TR5 and TR7, represented as ratio with
| | Sample_data_processing | respect to probe sets mean across the experiments, were
| | Sample_data_processing | combined in a unique exprSet object. The identification of
| | Sample_data_processing | differentially expressed genes associated to the HGF effect
| | Sample_data_processing | was addressed using linear modeling approach. For
| | Sample_data_processing | assessing differential expression, an empirical Bayes
| | Sample_data_processing | method was used to moderate the SE of the estimated
| | Sample_data_processing | log-fold changes together with the BH correction of the
| | Sample_data_processing | false discovery rate.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412718/suppl/GSM412718.CEL.gz
| | Sample_series_id | GSE16424
| | Sample_data_row_count | 22215
| | |
|
GSM412719 | GPL96 |
|
0 hours no HGF n1 h0hgf0n1 experiment TR5
|
SK-OV-3 ovarian carcinoma cells
|
cell line: SK-OV-3
|
Advanced ovarian cancers are initially responsive to
chemotherapy with platinum drugs but develop drug
resistance in most cases. We showed recently that
hepatocyte growth factor (HGF) enhances death of human
ovarian cancer cell lines treated with cisplatin (CDDP) and
that this effect is mediated by the p38 mitogen-activated
protein kinase. In this work, we integrated genome-wide
expression profiling, in silico data survey, and functional
assays to identify transcripts regulated in SK-OV-3 ovarian
cancer cells made more responsive to CDDP by HGF.
Using oligonucleotide microarrays, we found that HGF
pretreatment changes the transcriptional response to
CDDP. Quantitative reverse transcription-PCR not only
validated all the 15 most differentially expressed genes
but also confirmed that they were primarily modulated by
the combined treatment with HGF and CDDP and reversed
by suppressing p38 mitogen-activated protein kinase
activity. Among the differentially expressed genes, we
focused functional analysis on two regulatory subunits of
the protein phosphatase 2A, which were down-modulated
by HGF plus CDDP. Decrease of each subunit by RNA
interference made ovarian cancer cells more responsive to
CDDP, mimicking the effect of HGF. In conclusion, we
show that HGF and CDDP modulate transcription in
ovarian cancer cells and that this transcriptional response
is involved in apoptosis regulation. We also provide the
proof-of-concept that the identified genes might be
targeted to either increase the efficacy of chemotherapeutics
or revert chemotherapy resistance.
|
| Sample_geo_accession | GSM412719
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 04 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Exponentially growing cells were cultured for 48 hours in
| | Sample_treatment_protocol_ch1 | the presence of pure recombinant HGF (R&D Systems,
| | Sample_treatment_protocol_ch1 | Minneapolis, MN) at the concentration of 50 ng/mL or
| | Sample_treatment_protocol_ch1 | control medium. Apoptosis was then induced by adding
| | Sample_treatment_protocol_ch1 | fresh medium, with or without HGF, supplemented with
| | Sample_treatment_protocol_ch1 | 10 Amol/L CDDP.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified from SK-OV-3 cell
| | Sample_extract_protocol_ch1 | lines at each time point using the Concert Cytoplasmic
| | Sample_extract_protocol_ch1 | RNA Purification Reagent (Invitrogen, Carlsbad, CA) as
| | Sample_extract_protocol_ch1 | suggested by the manufacturer
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated as suggested by Affymetrix
| | Sample_hyb_protocol | arrays were hybridized as suggested by manufacturer
| | Sample_scan_protocol | arrays were scanned as suggested by manufacturer
| | Sample_data_processing | Two of the time-course experiments, done independently, were analyzed. From digitized image data
| | Sample_data_processing | files of raw data, background-normalized image data (CEL
| | Sample_data_processing | files) were generated. Microarray quality control and
| | Sample_data_processing | statistical validation was done using Bioconductor.
| | Sample_data_processing | The presence of hybridization/construction artifacts was
| | Sample_data_processing | evaluated with the fitPLM function (Bioconductor package
| | Sample_data_processing | affyPLM). The probes (PM) intensity distribution was
| | Sample_data_processing | evaluated using hist function (Bioconductor package affy).
| | Sample_data_processing | Only two arrays, CDDP 6 hours and CDDP/HGF 6 hours
| | Sample_data_processing | in TR7 experiment were discarded due to low quality. TR5
| | Sample_data_processing | and TR7 experiments were then analyzed separately. Probe
| | Sample_data_processing | set intensities were obtained by robust multiarray average (RMA), and normalization was done according to quantiles
| | Sample_data_processing | method. Probe sets in TR5 and
| | Sample_data_processing | TR7 were filtered separately to have an interquantile range
| | Sample_data_processing | for each probe set greater than 0.4.
| | Sample_data_processing | TR5 and TR7, represented as ratio with
| | Sample_data_processing | respect to probe sets mean across the experiments, were
| | Sample_data_processing | combined in a unique exprSet object. The identification of
| | Sample_data_processing | differentially expressed genes associated to the HGF effect
| | Sample_data_processing | was addressed using linear modeling approach. For
| | Sample_data_processing | assessing differential expression, an empirical Bayes
| | Sample_data_processing | method was used to moderate the SE of the estimated
| | Sample_data_processing | log-fold changes together with the BH correction of the
| | Sample_data_processing | false discovery rate.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412719/suppl/GSM412719.CEL.gz
| | Sample_series_id | GSE16424
| | Sample_data_row_count | 22215
| | |
|
GSM412720 | GPL96 |
|
0 hours no HGF n2 h0hgf0n2 experiment TR5
|
SK-OV-3 ovarian carcinoma cells
|
cell line: SK-OV-3
|
Advanced ovarian cancers are initially responsive to
chemotherapy with platinum drugs but develop drug
resistance in most cases. We showed recently that
hepatocyte growth factor (HGF) enhances death of human
ovarian cancer cell lines treated with cisplatin (CDDP) and
that this effect is mediated by the p38 mitogen-activated
protein kinase. In this work, we integrated genome-wide
expression profiling, in silico data survey, and functional
assays to identify transcripts regulated in SK-OV-3 ovarian
cancer cells made more responsive to CDDP by HGF.
Using oligonucleotide microarrays, we found that HGF
pretreatment changes the transcriptional response to
CDDP. Quantitative reverse transcription-PCR not only
validated all the 15 most differentially expressed genes
but also confirmed that they were primarily modulated by
the combined treatment with HGF and CDDP and reversed
by suppressing p38 mitogen-activated protein kinase
activity. Among the differentially expressed genes, we
focused functional analysis on two regulatory subunits of
the protein phosphatase 2A, which were down-modulated
by HGF plus CDDP. Decrease of each subunit by RNA
interference made ovarian cancer cells more responsive to
CDDP, mimicking the effect of HGF. In conclusion, we
show that HGF and CDDP modulate transcription in
ovarian cancer cells and that this transcriptional response
is involved in apoptosis regulation. We also provide the
proof-of-concept that the identified genes might be
targeted to either increase the efficacy of chemotherapeutics
or revert chemotherapy resistance.
|
| Sample_geo_accession | GSM412720
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 04 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Exponentially growing cells were cultured for 48 hours in
| | Sample_treatment_protocol_ch1 | the presence of pure recombinant HGF (R&D Systems,
| | Sample_treatment_protocol_ch1 | Minneapolis, MN) at the concentration of 50 ng/mL or
| | Sample_treatment_protocol_ch1 | control medium. Apoptosis was then induced by adding
| | Sample_treatment_protocol_ch1 | fresh medium, with or without HGF, supplemented with
| | Sample_treatment_protocol_ch1 | 10 Amol/L CDDP.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified from SK-OV-3 cell
| | Sample_extract_protocol_ch1 | lines at each time point using the Concert Cytoplasmic
| | Sample_extract_protocol_ch1 | RNA Purification Reagent (Invitrogen, Carlsbad, CA) as
| | Sample_extract_protocol_ch1 | suggested by the manufacturer
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated as suggested by Affymetrix
| | Sample_hyb_protocol | arrays were hybridized as suggested by manufacturer
| | Sample_scan_protocol | arrays were scanned as suggested by manufacturer
| | Sample_data_processing | Two of the time-course experiments, done independently, were analyzed. From digitized image data
| | Sample_data_processing | files of raw data, background-normalized image data (CEL
| | Sample_data_processing | files) were generated. Microarray quality control and
| | Sample_data_processing | statistical validation was done using Bioconductor.
| | Sample_data_processing | The presence of hybridization/construction artifacts was
| | Sample_data_processing | evaluated with the fitPLM function (Bioconductor package
| | Sample_data_processing | affyPLM). The probes (PM) intensity distribution was
| | Sample_data_processing | evaluated using hist function (Bioconductor package affy).
| | Sample_data_processing | Only two arrays, CDDP 6 hours and CDDP/HGF 6 hours
| | Sample_data_processing | in TR7 experiment were discarded due to low quality. TR5
| | Sample_data_processing | and TR7 experiments were then analyzed separately. Probe
| | Sample_data_processing | set intensities were obtained by robust multiarray average (RMA), and normalization was done according to quantiles
| | Sample_data_processing | method. Probe sets in TR5 and
| | Sample_data_processing | TR7 were filtered separately to have an interquantile range
| | Sample_data_processing | for each probe set greater than 0.4.
| | Sample_data_processing | TR5 and TR7, represented as ratio with
| | Sample_data_processing | respect to probe sets mean across the experiments, were
| | Sample_data_processing | combined in a unique exprSet object. The identification of
| | Sample_data_processing | differentially expressed genes associated to the HGF effect
| | Sample_data_processing | was addressed using linear modeling approach. For
| | Sample_data_processing | assessing differential expression, an empirical Bayes
| | Sample_data_processing | method was used to moderate the SE of the estimated
| | Sample_data_processing | log-fold changes together with the BH correction of the
| | Sample_data_processing | false discovery rate.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412720/suppl/GSM412720.CEL.gz
| | Sample_series_id | GSE16424
| | Sample_data_row_count | 22215
| | |
|
GSM412721 | GPL96 |
|
0 hours no HGF n3 h0hgf0n3 TR7
|
SK-OV-3 ovarian carcinoma cells
|
cell line: SK-OV-3
|
Advanced ovarian cancers are initially responsive to
chemotherapy with platinum drugs but develop drug
resistance in most cases. We showed recently that
hepatocyte growth factor (HGF) enhances death of human
ovarian cancer cell lines treated with cisplatin (CDDP) and
that this effect is mediated by the p38 mitogen-activated
protein kinase. In this work, we integrated genome-wide
expression profiling, in silico data survey, and functional
assays to identify transcripts regulated in SK-OV-3 ovarian
cancer cells made more responsive to CDDP by HGF.
Using oligonucleotide microarrays, we found that HGF
pretreatment changes the transcriptional response to
CDDP. Quantitative reverse transcription-PCR not only
validated all the 15 most differentially expressed genes
but also confirmed that they were primarily modulated by
the combined treatment with HGF and CDDP and reversed
by suppressing p38 mitogen-activated protein kinase
activity. Among the differentially expressed genes, we
focused functional analysis on two regulatory subunits of
the protein phosphatase 2A, which were down-modulated
by HGF plus CDDP. Decrease of each subunit by RNA
interference made ovarian cancer cells more responsive to
CDDP, mimicking the effect of HGF. In conclusion, we
show that HGF and CDDP modulate transcription in
ovarian cancer cells and that this transcriptional response
is involved in apoptosis regulation. We also provide the
proof-of-concept that the identified genes might be
targeted to either increase the efficacy of chemotherapeutics
or revert chemotherapy resistance.
|
| Sample_geo_accession | GSM412721
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 04 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Exponentially growing cells were cultured for 48 hours in
| | Sample_treatment_protocol_ch1 | the presence of pure recombinant HGF (R&D Systems,
| | Sample_treatment_protocol_ch1 | Minneapolis, MN) at the concentration of 50 ng/mL or
| | Sample_treatment_protocol_ch1 | control medium. Apoptosis was then induced by adding
| | Sample_treatment_protocol_ch1 | fresh medium, with or without HGF, supplemented with
| | Sample_treatment_protocol_ch1 | 10 Amol/L CDDP.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified from SK-OV-3 cell
| | Sample_extract_protocol_ch1 | lines at each time point using the Concert Cytoplasmic
| | Sample_extract_protocol_ch1 | RNA Purification Reagent (Invitrogen, Carlsbad, CA) as
| | Sample_extract_protocol_ch1 | suggested by the manufacturer
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated as suggested by Affymetrix
| | Sample_hyb_protocol | arrays were hybridized as suggested by manufacturer
| | Sample_scan_protocol | arrays were scanned as suggested by manufacturer
| | Sample_data_processing | Two of the time-course experiments, done independently, were analyzed. From digitized image data
| | Sample_data_processing | files of raw data, background-normalized image data (CEL
| | Sample_data_processing | files) were generated. Microarray quality control and
| | Sample_data_processing | statistical validation was done using Bioconductor.
| | Sample_data_processing | The presence of hybridization/construction artifacts was
| | Sample_data_processing | evaluated with the fitPLM function (Bioconductor package
| | Sample_data_processing | affyPLM). The probes (PM) intensity distribution was
| | Sample_data_processing | evaluated using hist function (Bioconductor package affy).
| | Sample_data_processing | Only two arrays, CDDP 6 hours and CDDP/HGF 6 hours
| | Sample_data_processing | in TR7 experiment were discarded due to low quality. TR5
| | Sample_data_processing | and TR7 experiments were then analyzed separately. Probe
| | Sample_data_processing | set intensities were obtained by robust multiarray average (RMA), and normalization was done according to quantiles
| | Sample_data_processing | method. Probe sets in TR5 and
| | Sample_data_processing | TR7 were filtered separately to have an interquantile range
| | Sample_data_processing | for each probe set greater than 0.4.
| | Sample_data_processing | TR5 and TR7, represented as ratio with
| | Sample_data_processing | respect to probe sets mean across the experiments, were
| | Sample_data_processing | combined in a unique exprSet object. The identification of
| | Sample_data_processing | differentially expressed genes associated to the HGF effect
| | Sample_data_processing | was addressed using linear modeling approach. For
| | Sample_data_processing | assessing differential expression, an empirical Bayes
| | Sample_data_processing | method was used to moderate the SE of the estimated
| | Sample_data_processing | log-fold changes together with the BH correction of the
| | Sample_data_processing | false discovery rate.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412721/suppl/GSM412721.CEL.gz
| | Sample_series_id | GSE16424
| | Sample_data_row_count | 22215
| | |
|
GSM412722 | GPL96 |
|
12 hours with HGF n13 h12hgf1n13 experiment TR5
|
SK-OV-3 ovarian carcinoma cells
|
cell line: SK-OV-3
|
Advanced ovarian cancers are initially responsive to
chemotherapy with platinum drugs but develop drug
resistance in most cases. We showed recently that
hepatocyte growth factor (HGF) enhances death of human
ovarian cancer cell lines treated with cisplatin (CDDP) and
that this effect is mediated by the p38 mitogen-activated
protein kinase. In this work, we integrated genome-wide
expression profiling, in silico data survey, and functional
assays to identify transcripts regulated in SK-OV-3 ovarian
cancer cells made more responsive to CDDP by HGF.
Using oligonucleotide microarrays, we found that HGF
pretreatment changes the transcriptional response to
CDDP. Quantitative reverse transcription-PCR not only
validated all the 15 most differentially expressed genes
but also confirmed that they were primarily modulated by
the combined treatment with HGF and CDDP and reversed
by suppressing p38 mitogen-activated protein kinase
activity. Among the differentially expressed genes, we
focused functional analysis on two regulatory subunits of
the protein phosphatase 2A, which were down-modulated
by HGF plus CDDP. Decrease of each subunit by RNA
interference made ovarian cancer cells more responsive to
CDDP, mimicking the effect of HGF. In conclusion, we
show that HGF and CDDP modulate transcription in
ovarian cancer cells and that this transcriptional response
is involved in apoptosis regulation. We also provide the
proof-of-concept that the identified genes might be
targeted to either increase the efficacy of chemotherapeutics
or revert chemotherapy resistance.
|
| Sample_geo_accession | GSM412722
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 04 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Exponentially growing cells were cultured for 48 hours in
| | Sample_treatment_protocol_ch1 | the presence of pure recombinant HGF (R&D Systems,
| | Sample_treatment_protocol_ch1 | Minneapolis, MN) at the concentration of 50 ng/mL or
| | Sample_treatment_protocol_ch1 | control medium. Apoptosis was then induced by adding
| | Sample_treatment_protocol_ch1 | fresh medium, with or without HGF, supplemented with
| | Sample_treatment_protocol_ch1 | 10 Amol/L CDDP.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified from SK-OV-3 cell
| | Sample_extract_protocol_ch1 | lines at each time point using the Concert Cytoplasmic
| | Sample_extract_protocol_ch1 | RNA Purification Reagent (Invitrogen, Carlsbad, CA) as
| | Sample_extract_protocol_ch1 | suggested by the manufacturer
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated as suggested by Affymetrix
| | Sample_hyb_protocol | arrays were hybridized as suggested by manufacturer
| | Sample_scan_protocol | arrays were scanned as suggested by manufacturer
| | Sample_data_processing | Two of the time-course experiments, done independently, were analyzed. From digitized image data
| | Sample_data_processing | files of raw data, background-normalized image data (CEL
| | Sample_data_processing | files) were generated. Microarray quality control and
| | Sample_data_processing | statistical validation was done using Bioconductor.
| | Sample_data_processing | The presence of hybridization/construction artifacts was
| | Sample_data_processing | evaluated with the fitPLM function (Bioconductor package
| | Sample_data_processing | affyPLM). The probes (PM) intensity distribution was
| | Sample_data_processing | evaluated using hist function (Bioconductor package affy).
| | Sample_data_processing | Only two arrays, CDDP 6 hours and CDDP/HGF 6 hours
| | Sample_data_processing | in TR7 experiment were discarded due to low quality. TR5
| | Sample_data_processing | and TR7 experiments were then analyzed separately. Probe
| | Sample_data_processing | set intensities were obtained by robust multiarray average (RMA), and normalization was done according to quantiles
| | Sample_data_processing | method. Probe sets in TR5 and
| | Sample_data_processing | TR7 were filtered separately to have an interquantile range
| | Sample_data_processing | for each probe set greater than 0.4.
| | Sample_data_processing | TR5 and TR7, represented as ratio with
| | Sample_data_processing | respect to probe sets mean across the experiments, were
| | Sample_data_processing | combined in a unique exprSet object. The identification of
| | Sample_data_processing | differentially expressed genes associated to the HGF effect
| | Sample_data_processing | was addressed using linear modeling approach. For
| | Sample_data_processing | assessing differential expression, an empirical Bayes
| | Sample_data_processing | method was used to moderate the SE of the estimated
| | Sample_data_processing | log-fold changes together with the BH correction of the
| | Sample_data_processing | false discovery rate.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412722/suppl/GSM412722.CEL.gz
| | Sample_series_id | GSE16424
| | Sample_data_row_count | 22215
| | |
|
GSM412723 | GPL96 |
|
12 hours with HGF n14 h12hgf1n14 experiment TR7
|
SK-OV-3 ovarian carcinoma cells
|
cell line: SK-OV-3
|
Advanced ovarian cancers are initially responsive to
chemotherapy with platinum drugs but develop drug
resistance in most cases. We showed recently that
hepatocyte growth factor (HGF) enhances death of human
ovarian cancer cell lines treated with cisplatin (CDDP) and
that this effect is mediated by the p38 mitogen-activated
protein kinase. In this work, we integrated genome-wide
expression profiling, in silico data survey, and functional
assays to identify transcripts regulated in SK-OV-3 ovarian
cancer cells made more responsive to CDDP by HGF.
Using oligonucleotide microarrays, we found that HGF
pretreatment changes the transcriptional response to
CDDP. Quantitative reverse transcription-PCR not only
validated all the 15 most differentially expressed genes
but also confirmed that they were primarily modulated by
the combined treatment with HGF and CDDP and reversed
by suppressing p38 mitogen-activated protein kinase
activity. Among the differentially expressed genes, we
focused functional analysis on two regulatory subunits of
the protein phosphatase 2A, which were down-modulated
by HGF plus CDDP. Decrease of each subunit by RNA
interference made ovarian cancer cells more responsive to
CDDP, mimicking the effect of HGF. In conclusion, we
show that HGF and CDDP modulate transcription in
ovarian cancer cells and that this transcriptional response
is involved in apoptosis regulation. We also provide the
proof-of-concept that the identified genes might be
targeted to either increase the efficacy of chemotherapeutics
or revert chemotherapy resistance.
|
| Sample_geo_accession | GSM412723
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 04 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Exponentially growing cells were cultured for 48 hours in
| | Sample_treatment_protocol_ch1 | the presence of pure recombinant HGF (R&D Systems,
| | Sample_treatment_protocol_ch1 | Minneapolis, MN) at the concentration of 50 ng/mL or
| | Sample_treatment_protocol_ch1 | control medium. Apoptosis was then induced by adding
| | Sample_treatment_protocol_ch1 | fresh medium, with or without HGF, supplemented with
| | Sample_treatment_protocol_ch1 | 10 Amol/L CDDP.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified from SK-OV-3 cell
| | Sample_extract_protocol_ch1 | lines at each time point using the Concert Cytoplasmic
| | Sample_extract_protocol_ch1 | RNA Purification Reagent (Invitrogen, Carlsbad, CA) as
| | Sample_extract_protocol_ch1 | suggested by the manufacturer
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated as suggested by Affymetrix
| | Sample_hyb_protocol | arrays were hybridized as suggested by manufacturer
| | Sample_scan_protocol | arrays were scanned as suggested by manufacturer
| | Sample_data_processing | Two of the time-course experiments, done independently, were analyzed. From digitized image data
| | Sample_data_processing | files of raw data, background-normalized image data (CEL
| | Sample_data_processing | files) were generated. Microarray quality control and
| | Sample_data_processing | statistical validation was done using Bioconductor.
| | Sample_data_processing | The presence of hybridization/construction artifacts was
| | Sample_data_processing | evaluated with the fitPLM function (Bioconductor package
| | Sample_data_processing | affyPLM). The probes (PM) intensity distribution was
| | Sample_data_processing | evaluated using hist function (Bioconductor package affy).
| | Sample_data_processing | Only two arrays, CDDP 6 hours and CDDP/HGF 6 hours
| | Sample_data_processing | in TR7 experiment were discarded due to low quality. TR5
| | Sample_data_processing | and TR7 experiments were then analyzed separately. Probe
| | Sample_data_processing | set intensities were obtained by robust multiarray average (RMA), and normalization was done according to quantiles
| | Sample_data_processing | method. Probe sets in TR5 and
| | Sample_data_processing | TR7 were filtered separately to have an interquantile range
| | Sample_data_processing | for each probe set greater than 0.4.
| | Sample_data_processing | TR5 and TR7, represented as ratio with
| | Sample_data_processing | respect to probe sets mean across the experiments, were
| | Sample_data_processing | combined in a unique exprSet object. The identification of
| | Sample_data_processing | differentially expressed genes associated to the HGF effect
| | Sample_data_processing | was addressed using linear modeling approach. For
| | Sample_data_processing | assessing differential expression, an empirical Bayes
| | Sample_data_processing | method was used to moderate the SE of the estimated
| | Sample_data_processing | log-fold changes together with the BH correction of the
| | Sample_data_processing | false discovery rate.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412723/suppl/GSM412723.CEL.gz
| | Sample_series_id | GSE16424
| | Sample_data_row_count | 22215
| | |
|
GSM412724 | GPL96 |
|
12 hours no HGF n11 h12hgf0n11 experiment TR5
|
SK-OV-3 ovarian carcinoma cells
|
cell line: SK-OV-3
|
Advanced ovarian cancers are initially responsive to
chemotherapy with platinum drugs but develop drug
resistance in most cases. We showed recently that
hepatocyte growth factor (HGF) enhances death of human
ovarian cancer cell lines treated with cisplatin (CDDP) and
that this effect is mediated by the p38 mitogen-activated
protein kinase. In this work, we integrated genome-wide
expression profiling, in silico data survey, and functional
assays to identify transcripts regulated in SK-OV-3 ovarian
cancer cells made more responsive to CDDP by HGF.
Using oligonucleotide microarrays, we found that HGF
pretreatment changes the transcriptional response to
CDDP. Quantitative reverse transcription-PCR not only
validated all the 15 most differentially expressed genes
but also confirmed that they were primarily modulated by
the combined treatment with HGF and CDDP and reversed
by suppressing p38 mitogen-activated protein kinase
activity. Among the differentially expressed genes, we
focused functional analysis on two regulatory subunits of
the protein phosphatase 2A, which were down-modulated
by HGF plus CDDP. Decrease of each subunit by RNA
interference made ovarian cancer cells more responsive to
CDDP, mimicking the effect of HGF. In conclusion, we
show that HGF and CDDP modulate transcription in
ovarian cancer cells and that this transcriptional response
is involved in apoptosis regulation. We also provide the
proof-of-concept that the identified genes might be
targeted to either increase the efficacy of chemotherapeutics
or revert chemotherapy resistance.
|
| Sample_geo_accession | GSM412724
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 04 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Exponentially growing cells were cultured for 48 hours in
| | Sample_treatment_protocol_ch1 | the presence of pure recombinant HGF (R&D Systems,
| | Sample_treatment_protocol_ch1 | Minneapolis, MN) at the concentration of 50 ng/mL or
| | Sample_treatment_protocol_ch1 | control medium. Apoptosis was then induced by adding
| | Sample_treatment_protocol_ch1 | fresh medium, with or without HGF, supplemented with
| | Sample_treatment_protocol_ch1 | 10 Amol/L CDDP.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified from SK-OV-3 cell
| | Sample_extract_protocol_ch1 | lines at each time point using the Concert Cytoplasmic
| | Sample_extract_protocol_ch1 | RNA Purification Reagent (Invitrogen, Carlsbad, CA) as
| | Sample_extract_protocol_ch1 | suggested by the manufacturer
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated as suggested by Affymetrix
| | Sample_hyb_protocol | arrays were hybridized as suggested by manufacturer
| | Sample_scan_protocol | arrays were scanned as suggested by manufacturer
| | Sample_data_processing | Two of the time-course experiments, done independently, were analyzed. From digitized image data
| | Sample_data_processing | files of raw data, background-normalized image data (CEL
| | Sample_data_processing | files) were generated. Microarray quality control and
| | Sample_data_processing | statistical validation was done using Bioconductor.
| | Sample_data_processing | The presence of hybridization/construction artifacts was
| | Sample_data_processing | evaluated with the fitPLM function (Bioconductor package
| | Sample_data_processing | affyPLM). The probes (PM) intensity distribution was
| | Sample_data_processing | evaluated using hist function (Bioconductor package affy).
| | Sample_data_processing | Only two arrays, CDDP 6 hours and CDDP/HGF 6 hours
| | Sample_data_processing | in TR7 experiment were discarded due to low quality. TR5
| | Sample_data_processing | and TR7 experiments were then analyzed separately. Probe
| | Sample_data_processing | set intensities were obtained by robust multiarray average (RMA), and normalization was done according to quantiles
| | Sample_data_processing | method. Probe sets in TR5 and
| | Sample_data_processing | TR7 were filtered separately to have an interquantile range
| | Sample_data_processing | for each probe set greater than 0.4.
| | Sample_data_processing | TR5 and TR7, represented as ratio with
| | Sample_data_processing | respect to probe sets mean across the experiments, were
| | Sample_data_processing | combined in a unique exprSet object. The identification of
| | Sample_data_processing | differentially expressed genes associated to the HGF effect
| | Sample_data_processing | was addressed using linear modeling approach. For
| | Sample_data_processing | assessing differential expression, an empirical Bayes
| | Sample_data_processing | method was used to moderate the SE of the estimated
| | Sample_data_processing | log-fold changes together with the BH correction of the
| | Sample_data_processing | false discovery rate.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412724/suppl/GSM412724.CEL.gz
| | Sample_series_id | GSE16424
| | Sample_data_row_count | 22215
| | |
|
GSM412725 | GPL96 |
|
12 hours no HGF n12 h12hgf0n12 experiment TR7
|
SK-OV-3 ovarian carcinoma cells
|
cell line: SK-OV-3
|
Advanced ovarian cancers are initially responsive to
chemotherapy with platinum drugs but develop drug
resistance in most cases. We showed recently that
hepatocyte growth factor (HGF) enhances death of human
ovarian cancer cell lines treated with cisplatin (CDDP) and
that this effect is mediated by the p38 mitogen-activated
protein kinase. In this work, we integrated genome-wide
expression profiling, in silico data survey, and functional
assays to identify transcripts regulated in SK-OV-3 ovarian
cancer cells made more responsive to CDDP by HGF.
Using oligonucleotide microarrays, we found that HGF
pretreatment changes the transcriptional response to
CDDP. Quantitative reverse transcription-PCR not only
validated all the 15 most differentially expressed genes
but also confirmed that they were primarily modulated by
the combined treatment with HGF and CDDP and reversed
by suppressing p38 mitogen-activated protein kinase
activity. Among the differentially expressed genes, we
focused functional analysis on two regulatory subunits of
the protein phosphatase 2A, which were down-modulated
by HGF plus CDDP. Decrease of each subunit by RNA
interference made ovarian cancer cells more responsive to
CDDP, mimicking the effect of HGF. In conclusion, we
show that HGF and CDDP modulate transcription in
ovarian cancer cells and that this transcriptional response
is involved in apoptosis regulation. We also provide the
proof-of-concept that the identified genes might be
targeted to either increase the efficacy of chemotherapeutics
or revert chemotherapy resistance.
|
| Sample_geo_accession | GSM412725
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 04 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Exponentially growing cells were cultured for 48 hours in
| | Sample_treatment_protocol_ch1 | the presence of pure recombinant HGF (R&D Systems,
| | Sample_treatment_protocol_ch1 | Minneapolis, MN) at the concentration of 50 ng/mL or
| | Sample_treatment_protocol_ch1 | control medium. Apoptosis was then induced by adding
| | Sample_treatment_protocol_ch1 | fresh medium, with or without HGF, supplemented with
| | Sample_treatment_protocol_ch1 | 10 Amol/L CDDP.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified from SK-OV-3 cell
| | Sample_extract_protocol_ch1 | lines at each time point using the Concert Cytoplasmic
| | Sample_extract_protocol_ch1 | RNA Purification Reagent (Invitrogen, Carlsbad, CA) as
| | Sample_extract_protocol_ch1 | suggested by the manufacturer
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated as suggested by Affymetrix
| | Sample_hyb_protocol | arrays were hybridized as suggested by manufacturer
| | Sample_scan_protocol | arrays were scanned as suggested by manufacturer
| | Sample_data_processing | Two of the time-course experiments, done independently, were analyzed. From digitized image data
| | Sample_data_processing | files of raw data, background-normalized image data (CEL
| | Sample_data_processing | files) were generated. Microarray quality control and
| | Sample_data_processing | statistical validation was done using Bioconductor.
| | Sample_data_processing | The presence of hybridization/construction artifacts was
| | Sample_data_processing | evaluated with the fitPLM function (Bioconductor package
| | Sample_data_processing | affyPLM). The probes (PM) intensity distribution was
| | Sample_data_processing | evaluated using hist function (Bioconductor package affy).
| | Sample_data_processing | Only two arrays, CDDP 6 hours and CDDP/HGF 6 hours
| | Sample_data_processing | in TR7 experiment were discarded due to low quality. TR5
| | Sample_data_processing | and TR7 experiments were then analyzed separately. Probe
| | Sample_data_processing | set intensities were obtained by robust multiarray average (RMA), and normalization was done according to quantiles
| | Sample_data_processing | method. Probe sets in TR5 and
| | Sample_data_processing | TR7 were filtered separately to have an interquantile range
| | Sample_data_processing | for each probe set greater than 0.4.
| | Sample_data_processing | TR5 and TR7, represented as ratio with
| | Sample_data_processing | respect to probe sets mean across the experiments, were
| | Sample_data_processing | combined in a unique exprSet object. The identification of
| | Sample_data_processing | differentially expressed genes associated to the HGF effect
| | Sample_data_processing | was addressed using linear modeling approach. For
| | Sample_data_processing | assessing differential expression, an empirical Bayes
| | Sample_data_processing | method was used to moderate the SE of the estimated
| | Sample_data_processing | log-fold changes together with the BH correction of the
| | Sample_data_processing | false discovery rate.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412725/suppl/GSM412725.CEL.gz
| | Sample_series_id | GSE16424
| | Sample_data_row_count | 22215
| | |
|
GSM412726 | GPL96 |
|
24 hours with HGF n17 h24hgf1n17 experiment TR5
|
SK-OV-3 ovarian carcinoma cells
|
cell line: SK-OV-3
|
Advanced ovarian cancers are initially responsive to
chemotherapy with platinum drugs but develop drug
resistance in most cases. We showed recently that
hepatocyte growth factor (HGF) enhances death of human
ovarian cancer cell lines treated with cisplatin (CDDP) and
that this effect is mediated by the p38 mitogen-activated
protein kinase. In this work, we integrated genome-wide
expression profiling, in silico data survey, and functional
assays to identify transcripts regulated in SK-OV-3 ovarian
cancer cells made more responsive to CDDP by HGF.
Using oligonucleotide microarrays, we found that HGF
pretreatment changes the transcriptional response to
CDDP. Quantitative reverse transcription-PCR not only
validated all the 15 most differentially expressed genes
but also confirmed that they were primarily modulated by
the combined treatment with HGF and CDDP and reversed
by suppressing p38 mitogen-activated protein kinase
activity. Among the differentially expressed genes, we
focused functional analysis on two regulatory subunits of
the protein phosphatase 2A, which were down-modulated
by HGF plus CDDP. Decrease of each subunit by RNA
interference made ovarian cancer cells more responsive to
CDDP, mimicking the effect of HGF. In conclusion, we
show that HGF and CDDP modulate transcription in
ovarian cancer cells and that this transcriptional response
is involved in apoptosis regulation. We also provide the
proof-of-concept that the identified genes might be
targeted to either increase the efficacy of chemotherapeutics
or revert chemotherapy resistance.
|
| Sample_geo_accession | GSM412726
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 04 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Exponentially growing cells were cultured for 48 hours in
| | Sample_treatment_protocol_ch1 | the presence of pure recombinant HGF (R&D Systems,
| | Sample_treatment_protocol_ch1 | Minneapolis, MN) at the concentration of 50 ng/mL or
| | Sample_treatment_protocol_ch1 | control medium. Apoptosis was then induced by adding
| | Sample_treatment_protocol_ch1 | fresh medium, with or without HGF, supplemented with
| | Sample_treatment_protocol_ch1 | 10 Amol/L CDDP.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified from SK-OV-3 cell
| | Sample_extract_protocol_ch1 | lines at each time point using the Concert Cytoplasmic
| | Sample_extract_protocol_ch1 | RNA Purification Reagent (Invitrogen, Carlsbad, CA) as
| | Sample_extract_protocol_ch1 | suggested by the manufacturer
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated as suggested by Affymetrix
| | Sample_hyb_protocol | arrays were hybridized as suggested by manufacturer
| | Sample_scan_protocol | arrays were scanned as suggested by manufacturer
| | Sample_data_processing | Two of the time-course experiments, done independently, were analyzed. From digitized image data
| | Sample_data_processing | files of raw data, background-normalized image data (CEL
| | Sample_data_processing | files) were generated. Microarray quality control and
| | Sample_data_processing | statistical validation was done using Bioconductor.
| | Sample_data_processing | The presence of hybridization/construction artifacts was
| | Sample_data_processing | evaluated with the fitPLM function (Bioconductor package
| | Sample_data_processing | affyPLM). The probes (PM) intensity distribution was
| | Sample_data_processing | evaluated using hist function (Bioconductor package affy).
| | Sample_data_processing | Only two arrays, CDDP 6 hours and CDDP/HGF 6 hours
| | Sample_data_processing | in TR7 experiment were discarded due to low quality. TR5
| | Sample_data_processing | and TR7 experiments were then analyzed separately. Probe
| | Sample_data_processing | set intensities were obtained by robust multiarray average (RMA), and normalization was done according to quantiles
| | Sample_data_processing | method. Probe sets in TR5 and
| | Sample_data_processing | TR7 were filtered separately to have an interquantile range
| | Sample_data_processing | for each probe set greater than 0.4.
| | Sample_data_processing | TR5 and TR7, represented as ratio with
| | Sample_data_processing | respect to probe sets mean across the experiments, were
| | Sample_data_processing | combined in a unique exprSet object. The identification of
| | Sample_data_processing | differentially expressed genes associated to the HGF effect
| | Sample_data_processing | was addressed using linear modeling approach. For
| | Sample_data_processing | assessing differential expression, an empirical Bayes
| | Sample_data_processing | method was used to moderate the SE of the estimated
| | Sample_data_processing | log-fold changes together with the BH correction of the
| | Sample_data_processing | false discovery rate.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412726/suppl/GSM412726.CEL.gz
| | Sample_series_id | GSE16424
| | Sample_data_row_count | 22215
| | |
|
GSM412727 | GPL96 |
|
24 hours with HGF n18 h24hgf1n18 experiment TR7
|
SK-OV-3 ovarian carcinoma cells
|
cell line: SK-OV-3
|
Advanced ovarian cancers are initially responsive to
chemotherapy with platinum drugs but develop drug
resistance in most cases. We showed recently that
hepatocyte growth factor (HGF) enhances death of human
ovarian cancer cell lines treated with cisplatin (CDDP) and
that this effect is mediated by the p38 mitogen-activated
protein kinase. In this work, we integrated genome-wide
expression profiling, in silico data survey, and functional
assays to identify transcripts regulated in SK-OV-3 ovarian
cancer cells made more responsive to CDDP by HGF.
Using oligonucleotide microarrays, we found that HGF
pretreatment changes the transcriptional response to
CDDP. Quantitative reverse transcription-PCR not only
validated all the 15 most differentially expressed genes
but also confirmed that they were primarily modulated by
the combined treatment with HGF and CDDP and reversed
by suppressing p38 mitogen-activated protein kinase
activity. Among the differentially expressed genes, we
focused functional analysis on two regulatory subunits of
the protein phosphatase 2A, which were down-modulated
by HGF plus CDDP. Decrease of each subunit by RNA
interference made ovarian cancer cells more responsive to
CDDP, mimicking the effect of HGF. In conclusion, we
show that HGF and CDDP modulate transcription in
ovarian cancer cells and that this transcriptional response
is involved in apoptosis regulation. We also provide the
proof-of-concept that the identified genes might be
targeted to either increase the efficacy of chemotherapeutics
or revert chemotherapy resistance.
|
| Sample_geo_accession | GSM412727
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 04 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Exponentially growing cells were cultured for 48 hours in
| | Sample_treatment_protocol_ch1 | the presence of pure recombinant HGF (R&D Systems,
| | Sample_treatment_protocol_ch1 | Minneapolis, MN) at the concentration of 50 ng/mL or
| | Sample_treatment_protocol_ch1 | control medium. Apoptosis was then induced by adding
| | Sample_treatment_protocol_ch1 | fresh medium, with or without HGF, supplemented with
| | Sample_treatment_protocol_ch1 | 10 Amol/L CDDP.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified from SK-OV-3 cell
| | Sample_extract_protocol_ch1 | lines at each time point using the Concert Cytoplasmic
| | Sample_extract_protocol_ch1 | RNA Purification Reagent (Invitrogen, Carlsbad, CA) as
| | Sample_extract_protocol_ch1 | suggested by the manufacturer
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated as suggested by Affymetrix
| | Sample_hyb_protocol | arrays were hybridized as suggested by manufacturer
| | Sample_scan_protocol | arrays were scanned as suggested by manufacturer
| | Sample_data_processing | Two of the time-course experiments, done independently, were analyzed. From digitized image data
| | Sample_data_processing | files of raw data, background-normalized image data (CEL
| | Sample_data_processing | files) were generated. Microarray quality control and
| | Sample_data_processing | statistical validation was done using Bioconductor.
| | Sample_data_processing | The presence of hybridization/construction artifacts was
| | Sample_data_processing | evaluated with the fitPLM function (Bioconductor package
| | Sample_data_processing | affyPLM). The probes (PM) intensity distribution was
| | Sample_data_processing | evaluated using hist function (Bioconductor package affy).
| | Sample_data_processing | Only two arrays, CDDP 6 hours and CDDP/HGF 6 hours
| | Sample_data_processing | in TR7 experiment were discarded due to low quality. TR5
| | Sample_data_processing | and TR7 experiments were then analyzed separately. Probe
| | Sample_data_processing | set intensities were obtained by robust multiarray average (RMA), and normalization was done according to quantiles
| | Sample_data_processing | method. Probe sets in TR5 and
| | Sample_data_processing | TR7 were filtered separately to have an interquantile range
| | Sample_data_processing | for each probe set greater than 0.4.
| | Sample_data_processing | TR5 and TR7, represented as ratio with
| | Sample_data_processing | respect to probe sets mean across the experiments, were
| | Sample_data_processing | combined in a unique exprSet object. The identification of
| | Sample_data_processing | differentially expressed genes associated to the HGF effect
| | Sample_data_processing | was addressed using linear modeling approach. For
| | Sample_data_processing | assessing differential expression, an empirical Bayes
| | Sample_data_processing | method was used to moderate the SE of the estimated
| | Sample_data_processing | log-fold changes together with the BH correction of the
| | Sample_data_processing | false discovery rate.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412727/suppl/GSM412727.CEL.gz
| | Sample_series_id | GSE16424
| | Sample_data_row_count | 22215
| | |
|
GSM412728 | GPL96 |
|
24 hours no HGF n15 h24hgf0n15 experiment TR5
|
SK-OV-3 ovarian carcinoma cells
|
cell line: SK-OV-3
|
Advanced ovarian cancers are initially responsive to
chemotherapy with platinum drugs but develop drug
resistance in most cases. We showed recently that
hepatocyte growth factor (HGF) enhances death of human
ovarian cancer cell lines treated with cisplatin (CDDP) and
that this effect is mediated by the p38 mitogen-activated
protein kinase. In this work, we integrated genome-wide
expression profiling, in silico data survey, and functional
assays to identify transcripts regulated in SK-OV-3 ovarian
cancer cells made more responsive to CDDP by HGF.
Using oligonucleotide microarrays, we found that HGF
pretreatment changes the transcriptional response to
CDDP. Quantitative reverse transcription-PCR not only
validated all the 15 most differentially expressed genes
but also confirmed that they were primarily modulated by
the combined treatment with HGF and CDDP and reversed
by suppressing p38 mitogen-activated protein kinase
activity. Among the differentially expressed genes, we
focused functional analysis on two regulatory subunits of
the protein phosphatase 2A, which were down-modulated
by HGF plus CDDP. Decrease of each subunit by RNA
interference made ovarian cancer cells more responsive to
CDDP, mimicking the effect of HGF. In conclusion, we
show that HGF and CDDP modulate transcription in
ovarian cancer cells and that this transcriptional response
is involved in apoptosis regulation. We also provide the
proof-of-concept that the identified genes might be
targeted to either increase the efficacy of chemotherapeutics
or revert chemotherapy resistance.
|
| Sample_geo_accession | GSM412728
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 04 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Exponentially growing cells were cultured for 48 hours in
| | Sample_treatment_protocol_ch1 | the presence of pure recombinant HGF (R&D Systems,
| | Sample_treatment_protocol_ch1 | Minneapolis, MN) at the concentration of 50 ng/mL or
| | Sample_treatment_protocol_ch1 | control medium. Apoptosis was then induced by adding
| | Sample_treatment_protocol_ch1 | fresh medium, with or without HGF, supplemented with
| | Sample_treatment_protocol_ch1 | 10 Amol/L CDDP.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified from SK-OV-3 cell
| | Sample_extract_protocol_ch1 | lines at each time point using the Concert Cytoplasmic
| | Sample_extract_protocol_ch1 | RNA Purification Reagent (Invitrogen, Carlsbad, CA) as
| | Sample_extract_protocol_ch1 | suggested by the manufacturer
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated as suggested by Affymetrix
| | Sample_hyb_protocol | arrays were hybridized as suggested by manufacturer
| | Sample_scan_protocol | arrays were scanned as suggested by manufacturer
| | Sample_data_processing | Two of the time-course experiments, done independently, were analyzed. From digitized image data
| | Sample_data_processing | files of raw data, background-normalized image data (CEL
| | Sample_data_processing | files) were generated. Microarray quality control and
| | Sample_data_processing | statistical validation was done using Bioconductor.
| | Sample_data_processing | The presence of hybridization/construction artifacts was
| | Sample_data_processing | evaluated with the fitPLM function (Bioconductor package
| | Sample_data_processing | affyPLM). The probes (PM) intensity distribution was
| | Sample_data_processing | evaluated using hist function (Bioconductor package affy).
| | Sample_data_processing | Only two arrays, CDDP 6 hours and CDDP/HGF 6 hours
| | Sample_data_processing | in TR7 experiment were discarded due to low quality. TR5
| | Sample_data_processing | and TR7 experiments were then analyzed separately. Probe
| | Sample_data_processing | set intensities were obtained by robust multiarray average (RMA), and normalization was done according to quantiles
| | Sample_data_processing | method. Probe sets in TR5 and
| | Sample_data_processing | TR7 were filtered separately to have an interquantile range
| | Sample_data_processing | for each probe set greater than 0.4.
| | Sample_data_processing | TR5 and TR7, represented as ratio with
| | Sample_data_processing | respect to probe sets mean across the experiments, were
| | Sample_data_processing | combined in a unique exprSet object. The identification of
| | Sample_data_processing | differentially expressed genes associated to the HGF effect
| | Sample_data_processing | was addressed using linear modeling approach. For
| | Sample_data_processing | assessing differential expression, an empirical Bayes
| | Sample_data_processing | method was used to moderate the SE of the estimated
| | Sample_data_processing | log-fold changes together with the BH correction of the
| | Sample_data_processing | false discovery rate.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412728/suppl/GSM412728.CEL.gz
| | Sample_series_id | GSE16424
| | Sample_data_row_count | 22215
| | |
|
GSM412729 | GPL96 |
|
24 hours no HGF n16 h24hgf0n16 experiment TR7
|
SK-OV-3 ovarian carcinoma cells
|
cell line: SK-OV-3
|
Advanced ovarian cancers are initially responsive to
chemotherapy with platinum drugs but develop drug
resistance in most cases. We showed recently that
hepatocyte growth factor (HGF) enhances death of human
ovarian cancer cell lines treated with cisplatin (CDDP) and
that this effect is mediated by the p38 mitogen-activated
protein kinase. In this work, we integrated genome-wide
expression profiling, in silico data survey, and functional
assays to identify transcripts regulated in SK-OV-3 ovarian
cancer cells made more responsive to CDDP by HGF.
Using oligonucleotide microarrays, we found that HGF
pretreatment changes the transcriptional response to
CDDP. Quantitative reverse transcription-PCR not only
validated all the 15 most differentially expressed genes
but also confirmed that they were primarily modulated by
the combined treatment with HGF and CDDP and reversed
by suppressing p38 mitogen-activated protein kinase
activity. Among the differentially expressed genes, we
focused functional analysis on two regulatory subunits of
the protein phosphatase 2A, which were down-modulated
by HGF plus CDDP. Decrease of each subunit by RNA
interference made ovarian cancer cells more responsive to
CDDP, mimicking the effect of HGF. In conclusion, we
show that HGF and CDDP modulate transcription in
ovarian cancer cells and that this transcriptional response
is involved in apoptosis regulation. We also provide the
proof-of-concept that the identified genes might be
targeted to either increase the efficacy of chemotherapeutics
or revert chemotherapy resistance.
|
| Sample_geo_accession | GSM412729
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 04 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Exponentially growing cells were cultured for 48 hours in
| | Sample_treatment_protocol_ch1 | the presence of pure recombinant HGF (R&D Systems,
| | Sample_treatment_protocol_ch1 | Minneapolis, MN) at the concentration of 50 ng/mL or
| | Sample_treatment_protocol_ch1 | control medium. Apoptosis was then induced by adding
| | Sample_treatment_protocol_ch1 | fresh medium, with or without HGF, supplemented with
| | Sample_treatment_protocol_ch1 | 10 Amol/L CDDP.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified from SK-OV-3 cell
| | Sample_extract_protocol_ch1 | lines at each time point using the Concert Cytoplasmic
| | Sample_extract_protocol_ch1 | RNA Purification Reagent (Invitrogen, Carlsbad, CA) as
| | Sample_extract_protocol_ch1 | suggested by the manufacturer
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated as suggested by Affymetrix
| | Sample_hyb_protocol | arrays were hybridized as suggested by manufacturer
| | Sample_scan_protocol | arrays were scanned as suggested by manufacturer
| | Sample_data_processing | Two of the time-course experiments, done independently, were analyzed. From digitized image data
| | Sample_data_processing | files of raw data, background-normalized image data (CEL
| | Sample_data_processing | files) were generated. Microarray quality control and
| | Sample_data_processing | statistical validation was done using Bioconductor.
| | Sample_data_processing | The presence of hybridization/construction artifacts was
| | Sample_data_processing | evaluated with the fitPLM function (Bioconductor package
| | Sample_data_processing | affyPLM). The probes (PM) intensity distribution was
| | Sample_data_processing | evaluated using hist function (Bioconductor package affy).
| | Sample_data_processing | Only two arrays, CDDP 6 hours and CDDP/HGF 6 hours
| | Sample_data_processing | in TR7 experiment were discarded due to low quality. TR5
| | Sample_data_processing | and TR7 experiments were then analyzed separately. Probe
| | Sample_data_processing | set intensities were obtained by robust multiarray average (RMA), and normalization was done according to quantiles
| | Sample_data_processing | method. Probe sets in TR5 and
| | Sample_data_processing | TR7 were filtered separately to have an interquantile range
| | Sample_data_processing | for each probe set greater than 0.4.
| | Sample_data_processing | TR5 and TR7, represented as ratio with
| | Sample_data_processing | respect to probe sets mean across the experiments, were
| | Sample_data_processing | combined in a unique exprSet object. The identification of
| | Sample_data_processing | differentially expressed genes associated to the HGF effect
| | Sample_data_processing | was addressed using linear modeling approach. For
| | Sample_data_processing | assessing differential expression, an empirical Bayes
| | Sample_data_processing | method was used to moderate the SE of the estimated
| | Sample_data_processing | log-fold changes together with the BH correction of the
| | Sample_data_processing | false discovery rate.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412729/suppl/GSM412729.CEL.gz
| | Sample_series_id | GSE16424
| | Sample_data_row_count | 22215
| | |
|
GSM412730 | GPL96 |
|
6 hours with HGF n10 h6hgf1n10 experiment TR7
|
SK-OV-3 ovarian carcinoma cells
|
cell line: SK-OV-3
|
Advanced ovarian cancers are initially responsive to
chemotherapy with platinum drugs but develop drug
resistance in most cases. We showed recently that
hepatocyte growth factor (HGF) enhances death of human
ovarian cancer cell lines treated with cisplatin (CDDP) and
that this effect is mediated by the p38 mitogen-activated
protein kinase. In this work, we integrated genome-wide
expression profiling, in silico data survey, and functional
assays to identify transcripts regulated in SK-OV-3 ovarian
cancer cells made more responsive to CDDP by HGF.
Using oligonucleotide microarrays, we found that HGF
pretreatment changes the transcriptional response to
CDDP. Quantitative reverse transcription-PCR not only
validated all the 15 most differentially expressed genes
but also confirmed that they were primarily modulated by
the combined treatment with HGF and CDDP and reversed
by suppressing p38 mitogen-activated protein kinase
activity. Among the differentially expressed genes, we
focused functional analysis on two regulatory subunits of
the protein phosphatase 2A, which were down-modulated
by HGF plus CDDP. Decrease of each subunit by RNA
interference made ovarian cancer cells more responsive to
CDDP, mimicking the effect of HGF. In conclusion, we
show that HGF and CDDP modulate transcription in
ovarian cancer cells and that this transcriptional response
is involved in apoptosis regulation. We also provide the
proof-of-concept that the identified genes might be
targeted to either increase the efficacy of chemotherapeutics
or revert chemotherapy resistance.
|
| Sample_geo_accession | GSM412730
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 04 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Exponentially growing cells were cultured for 48 hours in
| | Sample_treatment_protocol_ch1 | the presence of pure recombinant HGF (R&D Systems,
| | Sample_treatment_protocol_ch1 | Minneapolis, MN) at the concentration of 50 ng/mL or
| | Sample_treatment_protocol_ch1 | control medium. Apoptosis was then induced by adding
| | Sample_treatment_protocol_ch1 | fresh medium, with or without HGF, supplemented with
| | Sample_treatment_protocol_ch1 | 10 Amol/L CDDP.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified from SK-OV-3 cell
| | Sample_extract_protocol_ch1 | lines at each time point using the Concert Cytoplasmic
| | Sample_extract_protocol_ch1 | RNA Purification Reagent (Invitrogen, Carlsbad, CA) as
| | Sample_extract_protocol_ch1 | suggested by the manufacturer
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated as suggested by Affymetrix
| | Sample_hyb_protocol | arrays were hybridized as suggested by manufacturer
| | Sample_scan_protocol | arrays were scanned as suggested by manufacturer
| | Sample_data_processing | Two of the time-course experiments, done independently, were analyzed. From digitized image data
| | Sample_data_processing | files of raw data, background-normalized image data (CEL
| | Sample_data_processing | files) were generated. Microarray quality control and
| | Sample_data_processing | statistical validation was done using Bioconductor.
| | Sample_data_processing | The presence of hybridization/construction artifacts was
| | Sample_data_processing | evaluated with the fitPLM function (Bioconductor package
| | Sample_data_processing | affyPLM). The probes (PM) intensity distribution was
| | Sample_data_processing | evaluated using hist function (Bioconductor package affy).
| | Sample_data_processing | Only two arrays, CDDP 6 hours and CDDP/HGF 6 hours
| | Sample_data_processing | in TR7 experiment were discarded due to low quality. TR5
| | Sample_data_processing | and TR7 experiments were then analyzed separately. Probe
| | Sample_data_processing | set intensities were obtained by robust multiarray average (RMA), and normalization was done according to quantiles
| | Sample_data_processing | method. Probe sets in TR5 and
| | Sample_data_processing | TR7 were filtered separately to have an interquantile range
| | Sample_data_processing | for each probe set greater than 0.4.
| | Sample_data_processing | TR5 and TR7, represented as ratio with
| | Sample_data_processing | respect to probe sets mean across the experiments, were
| | Sample_data_processing | combined in a unique exprSet object. The identification of
| | Sample_data_processing | differentially expressed genes associated to the HGF effect
| | Sample_data_processing | was addressed using linear modeling approach. For
| | Sample_data_processing | assessing differential expression, an empirical Bayes
| | Sample_data_processing | method was used to moderate the SE of the estimated
| | Sample_data_processing | log-fold changes together with the BH correction of the
| | Sample_data_processing | false discovery rate.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412730/suppl/GSM412730.CEL.gz
| | Sample_series_id | GSE16424
| | Sample_data_row_count | 22215
| | |
|
GSM412731 | GPL96 |
|
6 hours with HGF n9 h6hgf1n9 experiment TR5
|
SK-OV-3 ovarian carcinoma cells
|
cell line: SK-OV-3
|
Advanced ovarian cancers are initially responsive to
chemotherapy with platinum drugs but develop drug
resistance in most cases. We showed recently that
hepatocyte growth factor (HGF) enhances death of human
ovarian cancer cell lines treated with cisplatin (CDDP) and
that this effect is mediated by the p38 mitogen-activated
protein kinase. In this work, we integrated genome-wide
expression profiling, in silico data survey, and functional
assays to identify transcripts regulated in SK-OV-3 ovarian
cancer cells made more responsive to CDDP by HGF.
Using oligonucleotide microarrays, we found that HGF
pretreatment changes the transcriptional response to
CDDP. Quantitative reverse transcription-PCR not only
validated all the 15 most differentially expressed genes
but also confirmed that they were primarily modulated by
the combined treatment with HGF and CDDP and reversed
by suppressing p38 mitogen-activated protein kinase
activity. Among the differentially expressed genes, we
focused functional analysis on two regulatory subunits of
the protein phosphatase 2A, which were down-modulated
by HGF plus CDDP. Decrease of each subunit by RNA
interference made ovarian cancer cells more responsive to
CDDP, mimicking the effect of HGF. In conclusion, we
show that HGF and CDDP modulate transcription in
ovarian cancer cells and that this transcriptional response
is involved in apoptosis regulation. We also provide the
proof-of-concept that the identified genes might be
targeted to either increase the efficacy of chemotherapeutics
or revert chemotherapy resistance.
|
| Sample_geo_accession | GSM412731
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 04 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Exponentially growing cells were cultured for 48 hours in
| | Sample_treatment_protocol_ch1 | the presence of pure recombinant HGF (R&D Systems,
| | Sample_treatment_protocol_ch1 | Minneapolis, MN) at the concentration of 50 ng/mL or
| | Sample_treatment_protocol_ch1 | control medium. Apoptosis was then induced by adding
| | Sample_treatment_protocol_ch1 | fresh medium, with or without HGF, supplemented with
| | Sample_treatment_protocol_ch1 | 10 Amol/L CDDP.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified from SK-OV-3 cell
| | Sample_extract_protocol_ch1 | lines at each time point using the Concert Cytoplasmic
| | Sample_extract_protocol_ch1 | RNA Purification Reagent (Invitrogen, Carlsbad, CA) as
| | Sample_extract_protocol_ch1 | suggested by the manufacturer
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated as suggested by Affymetrix
| | Sample_hyb_protocol | arrays were hybridized as suggested by manufacturer
| | Sample_scan_protocol | arrays were scanned as suggested by manufacturer
| | Sample_data_processing | Two of the time-course experiments, done independently, were analyzed. From digitized image data
| | Sample_data_processing | files of raw data, background-normalized image data (CEL
| | Sample_data_processing | files) were generated. Microarray quality control and
| | Sample_data_processing | statistical validation was done using Bioconductor.
| | Sample_data_processing | The presence of hybridization/construction artifacts was
| | Sample_data_processing | evaluated with the fitPLM function (Bioconductor package
| | Sample_data_processing | affyPLM). The probes (PM) intensity distribution was
| | Sample_data_processing | evaluated using hist function (Bioconductor package affy).
| | Sample_data_processing | Only two arrays, CDDP 6 hours and CDDP/HGF 6 hours
| | Sample_data_processing | in TR7 experiment were discarded due to low quality. TR5
| | Sample_data_processing | and TR7 experiments were then analyzed separately. Probe
| | Sample_data_processing | set intensities were obtained by robust multiarray average (RMA), and normalization was done according to quantiles
| | Sample_data_processing | method. Probe sets in TR5 and
| | Sample_data_processing | TR7 were filtered separately to have an interquantile range
| | Sample_data_processing | for each probe set greater than 0.4.
| | Sample_data_processing | TR5 and TR7, represented as ratio with
| | Sample_data_processing | respect to probe sets mean across the experiments, were
| | Sample_data_processing | combined in a unique exprSet object. The identification of
| | Sample_data_processing | differentially expressed genes associated to the HGF effect
| | Sample_data_processing | was addressed using linear modeling approach. For
| | Sample_data_processing | assessing differential expression, an empirical Bayes
| | Sample_data_processing | method was used to moderate the SE of the estimated
| | Sample_data_processing | log-fold changes together with the BH correction of the
| | Sample_data_processing | false discovery rate.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412731/suppl/GSM412731.CEL.gz
| | Sample_series_id | GSE16424
| | Sample_data_row_count | 22215
| | |
|
GSM412735 | GPL96 |
|
6 hours no HGF n7 h6hgf0n7 experiment TR5
|
SK-OV-3 ovarian carcinoma cells
|
cell line: SK-OV-3
|
Advanced ovarian cancers are initially responsive to
chemotherapy with platinum drugs but develop drug
resistance in most cases. We showed recently that
hepatocyte growth factor (HGF) enhances death of human
ovarian cancer cell lines treated with cisplatin (CDDP) and
that this effect is mediated by the p38 mitogen-activated
protein kinase. In this work, we integrated genome-wide
expression profiling, in silico data survey, and functional
assays to identify transcripts regulated in SK-OV-3 ovarian
cancer cells made more responsive to CDDP by HGF.
Using oligonucleotide microarrays, we found that HGF
pretreatment changes the transcriptional response to
CDDP. Quantitative reverse transcription-PCR not only
validated all the 15 most differentially expressed genes
but also confirmed that they were primarily modulated by
the combined treatment with HGF and CDDP and reversed
by suppressing p38 mitogen-activated protein kinase
activity. Among the differentially expressed genes, we
focused functional analysis on two regulatory subunits of
the protein phosphatase 2A, which were down-modulated
by HGF plus CDDP. Decrease of each subunit by RNA
interference made ovarian cancer cells more responsive to
CDDP, mimicking the effect of HGF. In conclusion, we
show that HGF and CDDP modulate transcription in
ovarian cancer cells and that this transcriptional response
is involved in apoptosis regulation. We also provide the
proof-of-concept that the identified genes might be
targeted to either increase the efficacy of chemotherapeutics
or revert chemotherapy resistance.
|
| Sample_geo_accession | GSM412735
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 04 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Exponentially growing cells were cultured for 48 hours in
| | Sample_treatment_protocol_ch1 | the presence of pure recombinant HGF (R&D Systems,
| | Sample_treatment_protocol_ch1 | Minneapolis, MN) at the concentration of 50 ng/mL or
| | Sample_treatment_protocol_ch1 | control medium. Apoptosis was then induced by adding
| | Sample_treatment_protocol_ch1 | fresh medium, with or without HGF, supplemented with
| | Sample_treatment_protocol_ch1 | 10 Amol/L CDDP.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified from SK-OV-3 cell
| | Sample_extract_protocol_ch1 | lines at each time point using the Concert Cytoplasmic
| | Sample_extract_protocol_ch1 | RNA Purification Reagent (Invitrogen, Carlsbad, CA) as
| | Sample_extract_protocol_ch1 | suggested by the manufacturer
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated as suggested by Affymetrix
| | Sample_hyb_protocol | arrays were hybridized as suggested by manufacturer
| | Sample_scan_protocol | arrays were scanned as suggested by manufacturer
| | Sample_data_processing | Two of the time-course experiments, done independently, were analyzed. From digitized image data
| | Sample_data_processing | files of raw data, background-normalized image data (CEL
| | Sample_data_processing | files) were generated. Microarray quality control and
| | Sample_data_processing | statistical validation was done using Bioconductor.
| | Sample_data_processing | The presence of hybridization/construction artifacts was
| | Sample_data_processing | evaluated with the fitPLM function (Bioconductor package
| | Sample_data_processing | affyPLM). The probes (PM) intensity distribution was
| | Sample_data_processing | evaluated using hist function (Bioconductor package affy).
| | Sample_data_processing | Only two arrays, CDDP 6 hours and CDDP/HGF 6 hours
| | Sample_data_processing | in TR7 experiment were discarded due to low quality. TR5
| | Sample_data_processing | and TR7 experiments were then analyzed separately. Probe
| | Sample_data_processing | set intensities were obtained by robust multiarray average (RMA), and normalization was done according to quantiles
| | Sample_data_processing | method. Probe sets in TR5 and
| | Sample_data_processing | TR7 were filtered separately to have an interquantile range
| | Sample_data_processing | for each probe set greater than 0.4.
| | Sample_data_processing | TR5 and TR7, represented as ratio with
| | Sample_data_processing | respect to probe sets mean across the experiments, were
| | Sample_data_processing | combined in a unique exprSet object. The identification of
| | Sample_data_processing | differentially expressed genes associated to the HGF effect
| | Sample_data_processing | was addressed using linear modeling approach. For
| | Sample_data_processing | assessing differential expression, an empirical Bayes
| | Sample_data_processing | method was used to moderate the SE of the estimated
| | Sample_data_processing | log-fold changes together with the BH correction of the
| | Sample_data_processing | false discovery rate.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412735/suppl/GSM412735.CEL.gz
| | Sample_series_id | GSE16424
| | Sample_data_row_count | 22215
| | |
|
GSM412737 | GPL96 |
|
6 hours no HGF n8bis h6hgf0n8bis experiment TR7
|
SK-OV-3 ovarian carcinoma cells
|
cell line: SK-OV-3
|
Advanced ovarian cancers are initially responsive to
chemotherapy with platinum drugs but develop drug
resistance in most cases. We showed recently that
hepatocyte growth factor (HGF) enhances death of human
ovarian cancer cell lines treated with cisplatin (CDDP) and
that this effect is mediated by the p38 mitogen-activated
protein kinase. In this work, we integrated genome-wide
expression profiling, in silico data survey, and functional
assays to identify transcripts regulated in SK-OV-3 ovarian
cancer cells made more responsive to CDDP by HGF.
Using oligonucleotide microarrays, we found that HGF
pretreatment changes the transcriptional response to
CDDP. Quantitative reverse transcription-PCR not only
validated all the 15 most differentially expressed genes
but also confirmed that they were primarily modulated by
the combined treatment with HGF and CDDP and reversed
by suppressing p38 mitogen-activated protein kinase
activity. Among the differentially expressed genes, we
focused functional analysis on two regulatory subunits of
the protein phosphatase 2A, which were down-modulated
by HGF plus CDDP. Decrease of each subunit by RNA
interference made ovarian cancer cells more responsive to
CDDP, mimicking the effect of HGF. In conclusion, we
show that HGF and CDDP modulate transcription in
ovarian cancer cells and that this transcriptional response
is involved in apoptosis regulation. We also provide the
proof-of-concept that the identified genes might be
targeted to either increase the efficacy of chemotherapeutics
or revert chemotherapy resistance.
|
| Sample_geo_accession | GSM412737
| | Sample_status | Public on Jun 10 2009
| | Sample_submission_date | Jun 04 2009
| | Sample_last_update_date | Jun 09 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Exponentially growing cells were cultured for 48 hours in
| | Sample_treatment_protocol_ch1 | the presence of pure recombinant HGF (R&D Systems,
| | Sample_treatment_protocol_ch1 | Minneapolis, MN) at the concentration of 50 ng/mL or
| | Sample_treatment_protocol_ch1 | control medium. Apoptosis was then induced by adding
| | Sample_treatment_protocol_ch1 | fresh medium, with or without HGF, supplemented with
| | Sample_treatment_protocol_ch1 | 10 Amol/L CDDP.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified from SK-OV-3 cell
| | Sample_extract_protocol_ch1 | lines at each time point using the Concert Cytoplasmic
| | Sample_extract_protocol_ch1 | RNA Purification Reagent (Invitrogen, Carlsbad, CA) as
| | Sample_extract_protocol_ch1 | suggested by the manufacturer
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNAs were generated as suggested by Affymetrix
| | Sample_hyb_protocol | arrays were hybridized as suggested by manufacturer
| | Sample_scan_protocol | arrays were scanned as suggested by manufacturer
| | Sample_data_processing | Two of the time-course experiments, done independently, were analyzed. From digitized image data
| | Sample_data_processing | files of raw data, background-normalized image data (CEL
| | Sample_data_processing | files) were generated. Microarray quality control and
| | Sample_data_processing | statistical validation was done using Bioconductor.
| | Sample_data_processing | The presence of hybridization/construction artifacts was
| | Sample_data_processing | evaluated with the fitPLM function (Bioconductor package
| | Sample_data_processing | affyPLM). The probes (PM) intensity distribution was
| | Sample_data_processing | evaluated using hist function (Bioconductor package affy).
| | Sample_data_processing | Only two arrays, CDDP 6 hours and CDDP/HGF 6 hours
| | Sample_data_processing | in TR7 experiment were discarded due to low quality. TR5
| | Sample_data_processing | and TR7 experiments were then analyzed separately. Probe
| | Sample_data_processing | set intensities were obtained by robust multiarray average (RMA), and normalization was done according to quantiles
| | Sample_data_processing | method. Probe sets in TR5 and
| | Sample_data_processing | TR7 were filtered separately to have an interquantile range
| | Sample_data_processing | for each probe set greater than 0.4.
| | Sample_data_processing | TR5 and TR7, represented as ratio with
| | Sample_data_processing | respect to probe sets mean across the experiments, were
| | Sample_data_processing | combined in a unique exprSet object. The identification of
| | Sample_data_processing | differentially expressed genes associated to the HGF effect
| | Sample_data_processing | was addressed using linear modeling approach. For
| | Sample_data_processing | assessing differential expression, an empirical Bayes
| | Sample_data_processing | method was used to moderate the SE of the estimated
| | Sample_data_processing | log-fold changes together with the BH correction of the
| | Sample_data_processing | false discovery rate.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412737/suppl/GSM412737.CEL.gz
| | Sample_series_id | GSE16424
| | Sample_data_row_count | 22215
| | |
|
| |
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