Advanced Genetic and Molecular Analysis of Solid Tumors
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ABSTRACT:
PROVIDER: PRJNA615693 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16987689_1.fastq.gz | Fastqsanger.gz | |||
| SRR16987689_2.fastq.gz | Fastqsanger.gz | |||
| SRR16987690_1.fastq.gz | Fastqsanger.gz | |||
| SRR16987690_2.fastq.gz | Fastqsanger.gz |
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Project description:Advanced Genetic and Molecular Analysis of Solid Tumors
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Project description:Background: Fatal cancer is often the result of spread, or metastasis, of a cancer cell from the site of its origin to a distant anatomic site. While the metastatic process and the foreign environment of the metastatic site impact a tumorâ??s biology, we continue to determine therapy for patients based upon their cancerâ??s site of origin. We have performed an unbiased analysis across metastatic solid tumors from common primary sites to determine the molecular impact of the metastatic process on site-specific biology and to identify novel therapeutic strategies. Methods: Global gene expression was used as a biological phenotype to perform a top-down analysis of 96 metastatic human tumors. Laser capture microdissection, RNA amplification, and microarray analysis were used to measure the transcription patterns of malignant epithelial cells. Genes, multi-gene expression â??signaturesâ??, and pathways associated with site of origin (SOO) and site of metastases (SOM) were identified using established computational approaches. SOO and SOM expression signatures were validated on multiple, independent datasets comprising 1217 samples (1104 samples from GSE2109 (Expression Project for Oncology) and 113 samples from GSE12630 (Monzon FA, Lyons-Weiler M, Buturovic LJ, Rigl CT et al. Multicenter validation of a 1,550-gene expression profile for identification of tumor tissue of origin. J Clin Oncol 2009 May 20;27(15):2503-8. PMID: 19332734). Reverse phase proteomics and in vitro tissue culture were used to validate associations between biological pathways, site of primary, and implicated therapeutic combinations. Findings: SOO has the dominant influence on solid tumor biology as samples segregate based upon their primary site during unsupervised hierarchical clustering. In addition, statistically significant associations are identified between single genes and pathways and each primary site investigated and SOO signatures for colon, breast, ovary, lung, and prostate cancers accurately identify primary site for independent samples of both local and metastatic tumors independent of degree of histological differentiation. The impact of SOM on tumor biology is evident as genes and pathways are significantly associated with metastatic site and SOM signatures can be generated but they are not strongly predictive when applied to localized tumors. Pathway analysis identified relatively increased expression of MYC, beta-catenin, and SRC gene sets in metastatic colorectal cancers which was confirmed with proteomic analysis of a sub-set of the original tumors. Within colorectal cancers, high SRC expression also correlates with predicted oxaliplatin sensitivity and the combination of an SRC inhibitor with oxaliplatin demonstrated synergy in three independent colorectal cancer cell lines. Interpretation: Our findings suggest that the complex alterations required for metastasis do not obscure the impact of a cancer cellâ??s origin. SOO signatures have the potential to be highly accurate diagnostic tools and the underlying site-specific biology can be used to identify novel therapeutic targets for advanced cancers. Keywords: Gene expression analysis Ninety-six laser capture microdissected adenocarcinoma patient tumor samples of various primary and metastatic sites were processed for Total RNA. Our 96-sample datatset was enriched by inclusion of previously deposited microarray data in GEO (reprocessed for this study): A total of 1217 samples (1104 samples from GSE2109, 113 samples from GSE12630) were reprocessed from the CEL files using RMA. Supplementary files: The reprocessed data matrices. A list of the 1217 Samples' GSM accession numbers and the corresponding reprocessed sample IDs.
2016-02-13 | E-GEOD-18549 | biostudies-arrayexpress
Project description:Background: Fatal cancer is often the result of spread, or metastasis, of a cancer cell from the site of its origin to a distant anatomic site. While the metastatic process and the foreign environment of the metastatic site impact a tumor’s biology, we continue to determine therapy for patients based upon their cancer’s site of origin. We have performed an unbiased analysis across metastatic solid tumors from common primary sites to determine the molecular impact of the metastatic process on site-specific biology and to identify novel therapeutic strategies. Methods: Global gene expression was used as a biological phenotype to perform a top-down analysis of 96 metastatic human tumors. Laser capture microdissection, RNA amplification, and microarray analysis were used to measure the transcription patterns of malignant epithelial cells. Genes, multi-gene expression “signatures”, and pathways associated with site of origin (SOO) and site of metastases (SOM) were identified using established computational approaches. SOO and SOM expression signatures were validated on multiple, independent datasets comprising 1217 samples (1104 samples from GSE2109 (Expression Project for Oncology) and 113 samples from GSE12630 (Monzon FA, Lyons-Weiler M, Buturovic LJ, Rigl CT et al. Multicenter validation of a 1,550-gene expression profile for identification of tumor tissue of origin. J Clin Oncol 2009 May 20;27(15):2503-8. PMID: 19332734). Reverse phase proteomics and in vitro tissue culture were used to validate associations between biological pathways, site of primary, and implicated therapeutic combinations. Findings: SOO has the dominant influence on solid tumor biology as samples segregate based upon their primary site during unsupervised hierarchical clustering. In addition, statistically significant associations are identified between single genes and pathways and each primary site investigated and SOO signatures for colon, breast, ovary, lung, and prostate cancers accurately identify primary site for independent samples of both local and metastatic tumors independent of degree of histological differentiation. The impact of SOM on tumor biology is evident as genes and pathways are significantly associated with metastatic site and SOM signatures can be generated but they are not strongly predictive when applied to localized tumors. Pathway analysis identified relatively increased expression of MYC, beta-catenin, and SRC gene sets in metastatic colorectal cancers which was confirmed with proteomic analysis of a sub-set of the original tumors. Within colorectal cancers, high SRC expression also correlates with predicted oxaliplatin sensitivity and the combination of an SRC inhibitor with oxaliplatin demonstrated synergy in three independent colorectal cancer cell lines. Interpretation: Our findings suggest that the complex alterations required for metastasis do not obscure the impact of a cancer cell’s origin. SOO signatures have the potential to be highly accurate diagnostic tools and the underlying site-specific biology can be used to identify novel therapeutic targets for advanced cancers. Keywords: Gene expression analysis
2016-02-13 | GSE18549 | GEO
Project description:Immune checkpoint inhibitors such as anti-cytotoxic T-lymphocyte–associated antigen-4 and anti-programmed cell death-1 monoclonal antibodies (mAbs) agents or these combinations has improved outcomes of various cancers.However, still not a few patients fail to achieve clinical benefit, this highlights the importance of additional treatment to overcome its resistance. Previously, we showed that administration of the anti-CD4 mAb alone had strong anti-tumor effects that were superior to those elicited by CD25+ Treg depletion or other immune checkpoint mAbs in B16F10, Colon 26, or Lewis lung carcinoma subcutaneous tumor models. IT1208 (IDAC Theranostics, Tokyo, Japan) is a humanized anti-CD4 immunoglobulin G1 (IgG1) monoclonal antibody with a defucosylated Fc region, which markedly enhances antibody dependent cellular cytotoxicity. In a first-in-human, phase I, open-label, dose-escalation study, we performed transcriptomic analysis of tumors to clarify molecular responses against IT1208 monotherapy in patients with advanced solid tumors.
2019-08-06 | GSE120028 | GEO
Project description:Purpose: To evaluate whether administration of the oral DNA hypomethylating agent (HMA) CC-486 enhances the poor response rate of immunologically ‘cold’ solid tumors to immune checkpoint inhibitor durvalumab.
2020-07-26 | GSE147537 | GEO
Project description:BACKGROUND: Because of the distinct clinical presentation of early and advanced stage ovarian cancer, we aim to clarify whether these disease entities are solely separated by time of diagnosis or whether they arise from distinct molecular events. METHODS: Sixteen early and sixteen advanced stage ovarian carcinomas, matched for histological subtype and differentiation grade, were included. Genomic aberrations were compared for each early and advanced stage ovarian cancer by array comparative genomic hybridization. To study how the aberrations correlate to the clinical characteristics of the tumors we clustered tumors based on the genomic aberrations. RESULTS: The genomic aberration patterns in advanced stage cancer equalled those in early stage, but were more frequent in advanced stage (p?=?0.012). Unsupervised clustering based on genomic aberrations yielded two clusters that significantly discriminated early from advanced stage (p?=?0.001), and that did differ significantly in survival (p?=?0.002). These clusters however did give a more accurate prognosis than histological subtype or differentiation grade. CONCLUSION: This study indicates that advanced stage ovarian cancer either progresses from early stage or from a common precursor lesion but that they do not arise from distinct carcinogenic molecular events. Furthermore, we show that array comparative genomic hybridization has the potential to identify clinically distinct patients. Sixteen early and sixteen advanced stage ovarian carcinomas
2012-08-22 | E-GEOD-24418 | biostudies-arrayexpress
Project description:This phase II MATCH trial studies how well treatment that is directed by genetic testing works in patients with solid tumors or lymphomas that have progressed following at least one line of standard treatment or for which no agreed upon treatment approach exists. Genetic tests look at the unique genetic material (genes) of patients’ tumor cells. Patients with genetic abnormalities (such as mutations, amplifications, or translocations) may benefit more from treatment which targets their tumor’s particular genetic abnormality. Identifying these genetic abnormalities first may help doctors plan better treatment for patients with solid tumors, lymphomas, or multiple myeloma.
| 2191620 | ecrin-mdr-crc
Project description:Immune checkpoint inhibitors such as anti-cytotoxic T-lymphocyte–associated antigen-4 and anti-programmed cell death-1 monoclonal antibodies (mAbs) agents or these combinations has improved outcomes of various cancers.However, still not a few patients fail to achieve clinical benefit, this highlights the importance of additional treatment to overcome its resistance. Previously, we showed that administration of the anti-CD4 mAb alone had strong anti-tumor effects that were superior to those elicited by CD25+ Treg depletion or other immune checkpoint mAbs in B16F10, Colon 26, or Lewis lung carcinoma subcutaneous tumor models. IT1208 (IDAC Theranostics, Tokyo, Japan) is a humanized anti-CD4 immunoglobulin G1 (IgG1) monoclonal antibody with a defucosylated Fc region, which markedly enhances antibody dependent cellular cytotoxicity. In a first-in-human, phase I, open-label, dose-escalation study, we performed T cell repertoire analysis of T cell subsets in the tumors and peripheral blood mononuclear cells (PBMCs) to clarify T cell responses against IT1208 monotherapy in patients with advanced solid tumors.
2019-08-06 | GSE120101 | GEO