title: The Primary Effect on the Proteome of ARID1A-mutated Ovarian Clear Cell Carcinoma is Downregulation of the Mevalonate Pathway at the Post-transcriptional Level.
abstract: Inactivating mutations in ARID1A, which encodes a subunit of the SWI/SNF chromatin-remodeling complex, are found in over half of ovarian clear cell carcinoma cases and more broadly across most types of cancers. To identify ARID1A-dependent changes in intracellular signaling pathways, we performed proteome analyses of isogenic ovarian clear cell carcinoma cell lines with or without ARID1A expression. Knockout of ARID1A in an ovarian clear cell carcinoma cell line with wild-type ARID1A, OVCA429, primarily resulted in downregulation of the mevalonate pathway, an important metabolic pathway involved in isoprenoid synthesis, cholesterol synthesis, and other downstream pathways. In a complementary experiment, expression of wild-type ARID1A in an ovarian clear cell carcinoma cell line containing mutated ARID1A, OVISE, affected the mevalonate pathway in a reciprocal manner. A striking aspect of these analyses was that, although only 5% of the detected proteome showed significant abundance changes, most proteins in the mevalonate pathway were coordinately affected by ARID1A status. There were generally corresponding changes when comparing the proteomics data to our previously published microarray data for ectopic expression of ARID1A in the OVISE cell line. However, ARID1A-dependent changes were not detected for genes within the mevalonate pathway. This discrepancy suggests that the mevalonate pathway is not regulated directly by ARID1A-mediated transcription and may be regulated post-transcriptionally. We conclude that ARID1A status indirectly influences the mevalonate pathway and probably influences other processes including glycogen metabolism and 14-3-3-mediated signaling. Further, our findings demonstrate that changes in mRNA levels are sometimes poor indicators of signaling pathways affected by gene manipulations in cancer cells.
authors.affiliation: From the ‡Molecular and Cellular Oncogenesis Program, The Wistar Institute, 3601 Spruce St., Philadelphia, Pennsylvania 19104.
authors.forename: Aaron R
authors.initials: AR
authors.lastname: Goldman
authors.affiliation: §Gene Expression and Regulation Program, The Wistar Institute, 3601 Spruce St., Philadelphia, Pennsylvania 19104.
authors.forename: Benjamin G
authors.initials: BG
authors.lastname: Bitler
authors.affiliation: From the ‡Molecular and Cellular Oncogenesis Program, The Wistar Institute, 3601 Spruce St., Philadelphia, Pennsylvania 19104.
authors.forename: Zachary
authors.initials: Z
authors.lastname: Schug
authors.affiliation: ¶Tumor Microenvironment and Metastasis Program, The Wistar Institute, 3601 Spruce St., Philadelphia, Pennsylvania 19104.
authors.forename: Jose R
authors.initials: JR
authors.lastname: Conejo-Garcia
authors.affiliation: §Gene Expression and Regulation Program, The Wistar Institute, 3601 Spruce St., Philadelphia, Pennsylvania 19104.
authors.forename: Rugang
authors.initials: R
authors.lastname: Zhang
authors.affiliation: From the ‡Molecular and Cellular Oncogenesis Program, The Wistar Institute, 3601 Spruce St., Philadelphia, Pennsylvania 19104; speicher@wistar.org.|‖The Center for Systems and Computational Biology, The Wistar Institute, 3601 Spruce St., Philadelphia, Pennsylvania 19104.
authors.forename: David W
authors.initials: DW
authors.lastname: Speicher
mesh_terms: D018262:Adenocarcinoma, Clear Cell / Q000235:genetics / Q000378:metabolism*; D045744:Cell Line, Tumor; D002853:Chromatography, Liquid; D004268:DNA-Binding Proteins; D015536:Down-Regulation; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D055786:Gene Knockout Techniques; D006801:Humans; D053858:Metabolic Networks and Pathways; D008798:Mevalonic Acid / Q000378:metabolism*; D009154:Mutation; D009687:Nuclear Proteins / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D010051:Ovarian Neoplasms / Q000235:genetics / Q000378:metabolism*; D020543:Proteome / Q000235:genetics / Q000378:metabolism*; D053719:Tandem Mass Spectrometry; D014157:Transcription Factors / Q000235:genetics*
chemical_list: C112476:ARID1A protein, human; D004268:DNA-Binding Proteins; D009687:Nuclear Proteins; D020543:Proteome; D014157:Transcription Factors; D008798:Mevalonic Acid