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An integrated functional genomics and metabolomics approach for defining poor prognosis in human neuroendocrine cancers.

ABSTRACT: Human neuroendocrine (NE) cancers range from relatively indolent to highly aggressive. In this study, we combine functional genomics with metabolomics to identify features of NE cancers associated with a poor outcome. Analysis of GeneChip datasets of primary prostate tumors, as well as lymph node and liver metastases from transgenic mice with a NE cell cancer, plus derived NE cell lines yielded a signature of 446 genes whose expression is enriched in neoplastic mouse prostatic NE cells. This signature was used for in silico metabolic reconstructions of NE cell metabolism, directed liquid chromatography/tandem MS analysis of metabolites in prostatic NE tumors and cell lines, and analysis of GeneChip datasets of human NE tumors with good or poor prognoses. The results indicate that a distinguishing feature of poor-prognosis NE tumors is a glutamic acid decarboxylase-independent pathway for production of GABA and a pathway for production of imidazole-4-acetate that involves dopa decarboxylase and a membrane-associated amine oxidase, amiloride-binding protein 1. Electrophysiological studies disclosed that imidazole-4-acetate can bind and activate GABA(A) receptors expressed by transformed NE cells, thus providing a previously uncharacterized paradigm for NE tumor cell signaling. Transcriptional, metabolic, and electrophysiologic features of transformed mouse NE cells are also evident in neural progenitor cells.

SUBMITTER: Ippolito JE

PROVIDER: S-EPMC1169236 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Screening-based approach to discover effective platinum-based chemotherapies for cancers with poor prognosis.

Project description:Drug combinations are extensively used to treat cancer and are often selected according to complementary mechanisms. Here, we describe a cell-based high-throughput screening assay for identification of synergistic combinations between broadly applied platinum-based chemotherapeutics and drugs from a library composed of 1280 chemically and pharmacologically diverse (mostly FDA approved) compounds. The assay was performed on chemoresistant cell lines derived from lung (A549) and pancreatic (PANC-1) carcinoma, where platinum-based combination regimens are currently applied though with limited success. The synergistic combinations identified during the screening were validated by synergy quantification using the combination index method and via high content fluorescent microscopy analysis. New promising synergistic combinations discovered using this approach include compounds currently not used as anticancer drugs, such as cisplatin or carboplatin with hycanthone and cisplatin with spironolactone in pancreatic carcinoma, and carboplatin and deferoxamine in non-small cell lung cancer. Strong synergy between cisplatin or carboplatin and topotecan in PANC-1 cells, compared to A549 cells, suggests that this combination, currently used in lung cancer treatment regimens, could be applied to pancreatic carcinoma as well. Several drugs used to treat diseases other than cancer, including pyrvinium pamoate, auranofin, terfenadine and haloprogin, showed strong cytotoxicity on their own and synergistic interactions with platinum drugs. This study demonstrates that non-obvious drug combinations that would not be selected based on complementary mechanisms can be identified via high-throughput screening.

| S-EPMC6350982 | biostudies-literature

An integrated functional genomics approach identifies the regulatory network directed by brachyury in chordoma

Project description:shRNA-mediated brachyury knockdown was performed on the chordoma cell line U-CH1 as replicates. RNA was extracted, labelled and hybridised to Human Gene 1.0ST chips followed by gene expression microarray analysis.This was followed by a ChIP-seq experiment using a specific brachyury antibody, the data for which are stored in Raw ChIP-seq reads are stored under: European Nucleotide Archive accession ERP000953 and Array Express accession E-ERAD-23.

2012-10-08 | E-MEXP-3716 | biostudies-arrayexpress

An integrated functional and clinical genomics approach reveal genes driving aggressive metastatic prostate cancer

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-06-17 | GSE178330 | GEO

An integrated functional and clinical genomics approach reveals genes driving aggressive metastatic prostate cancer.

Project description:Genomic sequencing of thousands of tumors has revealed many genes associated with specific types of cancer. Similarly, large scale CRISPR functional genomics efforts have mapped genes required for cancer cell proliferation or survival in hundreds of cell lines. Despite this, for specific disease subtypes, such as metastatic prostate cancer, there are likely a number of undiscovered tumor specific driver genes that may represent potential drug targets. To identify such genetic dependencies, we performed genome-scale CRISPRi screens in metastatic prostate cancer models. We then created a pipeline in which we integrated pan-cancer functional genomics data with our metastatic prostate cancer functional and clinical genomics data to identify genes that can drive aggressive prostate cancer phenotypes. Our integrative analysis of these data reveals known prostate cancer specific driver genes, such as AR and HOXB13, as well as a number of top hits that are poorly characterized. In this study we highlight the strength of an integrated clinical and functional genomics pipeline and focus on two top hit genes, KIF4A and WDR62. We demonstrate that both KIF4A and WDR62 drive aggressive prostate cancer phenotypes in vitro and in vivo in multiple models, irrespective of AR-status, and are also associated with poor patient outcome.

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An integrated functional genomics approach identifies the regulatory network directed by brachyury (T) in chordoma.

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| S-EPMC6089345 | biostudies-literature

Orchidstra: an integrated orchid functional genomics database.

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Functional genomics atlas of synovial fibroblasts defining rheumatoid arthritis heritability.

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| S-EPMC8385949 | biostudies-literature

An integrated functional and clinical genomics approach reveal genes driving aggressive metastatic prostate cancer [RNA-Seq]

Project description:Genomic sequencing of many thousands of tumors has revealed many genes associated with specific types of cancer. Similarly, large scale CRISPR functional genomics efforts have mapped genes required for proliferation or survival in hundreds of cancer cell lines. Despite this, for specific disease subtypes, such as metastatic prostate cancer, it is likely that there exist many undiscovered tumor specific genetic dependencies, such as prostate cancer specific drivers, that represent drug targets. To identify such genetic dependencies, we performed genome-scale CRISPRi screens in metastatic prostate cancer models. We then created a pipeline in which we integrated publicly available pan-cancer functional genomics data with our metastatic prostate cancer functional and clinical genomics data to identify genes that can drive aggressive prostate cancer phenotypes. Our integrative analysis of these data revealed two known prostate cancer specific driver genes, AR and HOXB13, as the top two hits and also nominated a number of unexpected genes. In this study we highlight the strength of an integrated clinical and functional genomics pipeline and focus on two hit genes, KIF4A and WDR62. We demonstrate that both KIF4A and WDR62 drive aggressive prostate cancer phenotypes in vitro and in vivo in multiple models, irrespective of AR-status, and are also associated with poor patient outcome.

2021-06-17 | GSE178300 | GEO

An integrated functional and clinical genomics approach reveal genes driving aggressive metastatic prostate cancer [ATAC-Seq]

2021-06-17 | GSE178329 | GEO

Suppression of ABHD2, identified through a functional genomics screen, causes anoikis resistance, chemoresistance and poor prognosis in ovarian cancer.

Project description:Anoikis resistance is a hallmark of cancer, and relates to malignant phenotypes, including chemoresistance, cancer stem like phenotypes and dissemination. The aim of this study was to identify key factors contributing to anoikis resistance in ovarian cancer using a functional genomics screen. A library of 81 000 shRNAs targeting 15 000 genes was transduced into OVCA420 cells, followed by incubation in soft agar and colony selection. We found shRNAs directed to ABHD2, ELAC2 and CYB5R3 caused reproducible anoikis resistance. These three genes are deleted in many serous ovarian cancers according to The Cancer Genome Atlas data. Suppression of ABHD2 in OVCA420 cells increased phosphorylated p38 and ERK, platinum resistance, and side population cells (p<0.01, respectively). Conversely, overexpression of ABHD2 decreased resistance to anoikis (p<0.05) and the amount of phosphorylated p38 and ERK in OVCA420 and SKOV3 cells. In clinical serous ovarian cancer specimens, low expression of ABHD2 was associated with platinum resistance and poor prognosis (p<0.05, respectively). In conclusion, we found three novel genes relevant to anoikis resistance in ovarian cancer using a functional genomics screen. Suppression of ABHD2 may promote a malignant phenotype and poor prognosis for women with serous ovarian cancer.

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