Abstract
BackgroundOur understanding of the molecular pathways that underlie melanoma remains incomplete. Although several published microarray studies of clinical melanomas have provided valuable information, we found only limited concordance between these studies. Therefore, we took an in vitro functional genomics approach to understand melanoma molecular pathways.Methodology/Principal FindingsAffymetrix microarray data were generated from A375 melanoma cells treated in vitro with siRNAs against 45 transcription factors and signaling molecules. Analysis of this data using unsupervised hierarchical clustering and Bayesian gene networks identified proliferation-association RNA clusters, which were co-ordinately expressed across the A375 cells and also across melanomas from patients. The abundance in metastatic melanomas of these cellular proliferation clusters and their putative upstream regulators was significantly associated with patient prognosis. An 8-gene classifier derived from gene network hub genes correctly classified the prognosis of 23/26 metastatic melanoma patients in a cross-validation study. Unlike the RNA clusters associated with cellular proliferation described above, co-ordinately expressed RNA clusters associated with immune response were clearly identified across melanoma tumours from patients but not across the siRNA-treated A375 cells, in which immune responses are not active. Three uncharacterised genes, which the gene networks predicted to be upstream of apoptosis- or cellular proliferation-associated RNAs, were found to significantly alter apoptosis and cell number when over-expressed in vitro.Conclusions/SignificanceThis analysis identified co-expression of RNAs that encode functionally-related proteins, in particular, proliferation-associated RNA clusters that are linked to melanoma patient prognosis. Our analysis suggests that A375 cells in vitro may be valid models in which to study the gene expression modules that underlie some melanoma biological processes (e.g., proliferation) but not others (e.g., immune response). The gene expression modules identified here, and the RNAs predicted by Bayesian network inference to be upstream of these modules, are potential prognostic biomarkers and drug targets.
Highlights
Clinical aspects of melanoma Malignant melanoma is a devastating form of cancer with a high incidence in New Zealand (NZ) and Australia [1]
We generate microarray data from the melanoma cell line A375 exposed to a set of targeted siRNA disruptions, and used these data to identify co-expressed clusters of genes that are strongly conserved between siRNA-treated A375 cells and melanomas from patients. Several of these individual clusters encode proteins with shared cellular functions; we show that those clusters related predominantly to cellular proliferation are significantly associated with the prognosis of metastatic melanoma patients
Published melanoma studies fail to identify consistent gene or molecular pathway signatures In several individual published microarray studies of melanomas from patients, sets of genes appear to be differentially expressed in association with three aspects of tumour biology: progression, metastasis and prognosis
Summary
Clinical aspects of melanoma Malignant melanoma is a devastating form of cancer with a high incidence in New Zealand (NZ) and Australia [1]. For disseminated melanoma there are currently only a small number of chemotherapeutic agents in general use (e.g. temozolomide and dacarbazine), which are not effective in all patients [2]. Emerging approaches such as BRAF inhibition (PLX4032, [3]) and immune-based therapies ([4,5,6,7,8]) hold great promise, but are unlikely to be effective for all melanoma patients. Our understanding of the molecular pathways that underlie melanoma remains incomplete. We took an in vitro functional genomics approach to understand melanoma molecular pathways
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.