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GSE108297
Homo sapiens
39 Downloadable Samples
Illumina HumanHT-12 V4.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Time
View Samples- Homo sapiens
- 112 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Molecular subtypes of metastatic colorectal cancer are associated with patient response to irinotecan-based therapies.
Sample Metadata Fields
Sex, Age
View Samples- Rattus norvegicus
- 115 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Transcriptomic response of tumoral and normal brain tissue, treated with the MRT irradiation or the BB irradiation, after 6 h, 48 h, 8 days, 15 days, using Affymetrix GeneChip Rat 230_ 2.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Homo sapiens
- 112 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a), Affymetrix Human Genome U133B Array (hgu133b)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Gene expression signature in advanced colorectal cancer patients select drugs and response for the use of leucovorin, fluorouracil, and irinotecan.
Sample Metadata Fields
Sex, Age, Specimen part, Subject
View Samples- Homo sapiens
- 15 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Without treatment, HIV-1 infection is characterized in the majority of individuals by a detectable HIV replication and a rapid decline in CD4+ T lymphocytes leading to AIDS. However, a minority of patients, called HIV Controllers (HIC), maintains spontaneous control of HIV replication and for a large part, normal CD4+ T cell counts. The mechanisms leading to this spontaneous virus control are not fully known. We used gene expression and functional cellular analyses to compare EC and chronically HIV-1 infected individuals with controlled virus replication under combined antiretroviral therapy (cART). In the blood, EC individuals are characterized by a low inflammation, a down modulation of NK inhibitory cell signaling and an up regulation of T-cell activation gene expression profiles. Interestingly, in contrast to cART individuals, this balance persists following in vitro stimulation of cells from HIC with HIV antigens. This favourable genetic profile in HIC was also consistent with functional analyses showing a bias towards a Th1 and cytotoxic T cell profile and a lower production of inflammatory cytokines. Finally, taking advantage of the characterization of HIC based upon their in vitro CD8+ T lymphocyte capacity of killing HIV-infected cells, we show that unsupervised genetic analysis of differentially expressed genes fits clearly with this cytotoxic activity allowing the characterization of a specific signature of HIC individuals. Globally, these results reveal significant features of HIC making the bridge between cellular function and gene signatures and the regulation of inflammation and killing capacity of HIV-specific CD8+T cells. Moreover, these genetic profiles are consistent through analyses performed from whole blood to PBMC and at the T-cell population levels. Likely, these data help to define the goals of immunotherapeutic approaches in the perspective of HIV-1 functional cure. These strategies would need to induce both strong HIV-1-specific immune responses whereas minimizing inflammation.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Time
View Samples- Homo sapiens
- 22 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Without treatment, HIV-1 infection is characterized in the majority of individuals by a detectable HIV replication and a rapid decline in CD4+ T lymphocytes leading to AIDS. However, a minority of patients, called HIV Controllers (HIC), maintains spontaneous control of HIV replication and for a large part, normal CD4+ T cell counts. The mechanisms leading to this spontaneous virus control are not fully known. We used gene expression and functional cellular analyses to compare EC and chronically HIV-1 infected individuals with controlled virus replication under combined antiretroviral therapy (cART). In the blood, EC individuals are characterized by a low inflammation, a down modulation of NK inhibitory cell signaling and an up regulation of T-cell activation gene expression profiles. Interestingly, in contrast to cART individuals, this balance persists following in vitro stimulation of cells from HIC with HIV antigens. This favourable genetic profile in HIC was also consistent with functional analyses showing a bias towards a Th1 and cytotoxic T cell profile and a lower production of inflammatory cytokines. Finally, taking advantage of the characterization of HIC based upon their in vitro CD8+ T lymphocyte capacity of killing HIV-infected cells, we show that unsupervised genetic analysis of differentially expressed genes fits clearly with this cytotoxic activity allowing the characterization of a specific signature of HIC individuals. Globally, these results reveal significant features of HIC making the bridge between cellular function and gene signatures and the regulation of inflammation and killing capacity of HIV-specific CD8+T cells. Moreover, these genetic profiles are consistent through analyses performed from whole blood to PBMC and at the T-cell population levels. Likely, these data help to define the goals of immunotherapeutic approaches in the perspective of HIV-1 functional cure. These strategies would need to induce both strong HIV-1-specific immune responses whereas minimizing inflammation.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 61 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We report that previously described molecular subtypes of colorectal cancer are associated with the response to therapy in patients with metastatic disease. We also identified a patient population with high FOLFIRI sensitivity, as indicated by their 2.7-fold longer overall survival when treated with FOLFIRI, as first-line regimen, instead of FOLFOX. Our results demonstrate the interest of molecular classifications to develop tailored therapies for patients with metastatic colorectal cancer.
Publication Title
Molecular subtypes of metastatic colorectal cancer are associated with patient response to irinotecan-based therapies.
Sample Metadata Fields
Sex, Age
View Samples- Homo sapiens
- 26 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
The objective of the sudy is to evalute the effects of quantity and quality of protein intake on large intestine mucosa
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 56 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
To identify genes implicated in metastatic colonization of the liver in colorectal cancer, we collected pairs of primary tumors and hepatic metastases before chemotherapy in 13 patients. We compared mRNA expression in the pairs of patients to identify genes deregulated during metastatic evolution. We then validated the identified genes using data obtained by different groups. The 33-gene signature was able to classify 87% of hepatic metastases, 98% of primary tumors, 97% of normal colon mucosa, and 95% of normal liver tissues in six datasets obtained using five different microarray platforms. The identified genes are specific to colon cancer and hepatic metastases since other metastatic locations and hepatic metastases originating from breast cancer were not classified by the signature. Gene Ontology term analysis showed that 50% of the genes are implicated in extracellular matrix remodeling, and more precisely in cell adhesion, extracellular matrix organization and angiogenesis. Because of the high efficiency of the signature to classify colon hepatic metastases, the identified genes represent promising targets to develop new therapies that will specifically affect hepatic metastasis microenvironment.
Publication Title
Specific extracellular matrix remodeling signature of colon hepatic metastases.
Sample Metadata Fields
Sex, Age, Specimen part, Subject
View Samples- Homo sapiens
- 56 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a), Affymetrix Human Genome U133B Array (hgu133b)
Description
To identify genes implicated in metastatic colonization of the liver in colorectal cancer, we collected pairs of primary tumors and hepatic metastases before chemotherapy in 13 patients. We compared mRNA expression in the pairs of patients to identify genes deregulated during metastatic evolution. We then validated the identified genes using data obtained by different groups. The 33-gene signature was able to classify 87% of hepatic metastases, 98% of primary tumors, 97% of normal colon mucosa, and 95% of normal liver tissues in six datasets obtained using five different microarray platforms. The identified genes are specific to colon cancer and hepatic metastases since other metastatic locations and hepatic metastases originating from breast cancer were not classified by the signature. Gene Ontology term analysis showed that 50% of the genes are implicated in extracellular matrix remodeling, and more precisely in cell adhesion, extracellular matrix organization and angiogenesis. Because of the high efficiency of the signature to classify colon hepatic metastases, the identified genes represent promising targets to develop new therapies that will specifically affect hepatic metastasis microenvironment.
Publication Title
Gene expression signature in advanced colorectal cancer patients select drugs and response for the use of leucovorin, fluorouracil, and irinotecan.
Sample Metadata Fields
Sex, Age, Specimen part, Subject
View Samples