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A rare subpopulation of melanoma cells with low expression of metastasis suppressor NME1 has a neural crest-like phenotype and is highly metastatic in vivo

ABSTRACT: A rare subpopulation of melanoma cells with low expression of metastasis suppressor NME1 has a neural crest-like phenotype and is highly metastatic in vivo

PROVIDER: PRJNA588431 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10423267_1.fastq.gz	Fastqsanger.gz
	SRR10423267_2.fastq.gz	Fastqsanger.gz
	SRR10423268_1.fastq.gz	Fastqsanger.gz
	SRR10423268_2.fastq.gz	Fastqsanger.gz
	SRR10423269_1.fastq.gz	Fastqsanger.gz

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A rare subpopulation of melanoma cells with low expression of metastasis suppressor NME1 has a neural crest-like phenotype and is highly metastatic in vivo

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Project description:Transciptome analysis using a panel of WM793 melanoma cell lines following stable overexpression of wild-type or mutant forms of human NME1 NME1 is well known for its ability to suppress melanoma metastasis, however the means by which NME1 accomplishes this remains controversial. Herein, we utilized a bioinformatics approach to systematically identify effector genes of NME1’s metastasis suppressor function by tracking genes regulated by wild-type NME1 but not by metastasis suppressor deficient mutants of NME1. This approach identified a number of novel genes, such as ALDOC, CXCL11, LRP1b and XAGE1 as well as known targets of NME1 such as NETO2. Our NME1-mediated Metastasis Suppressor Signature (MSS) was capable of identifying subpopulations of metastatic melanoma patients with prolonged progression free survival. Interestingly, when patients were clustered by an extension of the MSS, two populations of metastatic melanoma patients were identified with significantly lowered overall and progression free survival times. Together, these data demonstrate that NMEl is a powerful tool for identifying genes that both promote and inhibit melanoma metastasis.

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Project description:Metastasis suppressor genes (MSGs) have contributed to an understanding of regulatory pathways unique to the lethal metastatic process. When re-expressed in experimental models, MSGs block cancer spread to, and colonization of distant sites without affecting primary tumor formation. On a single MSG basis, genes have been identified with expression patterns inverse to a MSG, and found to encode functional, druggable signaling pathways. We now hypothesize that common signaling pathways mediate the effects of many MSGs. By gene expression profiling of human MCF7 breast carcinoma cells expressing a scrambled siRNA or siRNAs to each of 19 validated MSGs (NME1, BRMS1, CD82, CDH1, CDH2, CDH11, CASP8, MAP2K4, MAP2K6, MAP2K7, MAPK14, GSN, ARHGDIB, AKAP12, DRG1, CD44, PEBP1, RRM1, KISS1), we identified genes whose expression was significantly opposite to at least five MSGs. We used microarrays to evaluate the modification in gene expression profile after donregulation of multiple metastasis suppressors (NME1, BRMS1, CD82, CDH1, CDH2, CDH11, CASP8, MAP2K4, MAP2K6, MAP2K7, MAPK14, GSN, ARHGDIB, AKAP12, DRG1, CD44, PEBP1, RRM1, KISS1) in the breast cancer cell line, MCF7. MCF7 cell line was transfected with siRNA targeting each of 19 metastasis suppressors (NME1, BRMS1, CD82, CDH1, CDH2, CDH11, CASP8, MAP2K4, MAP2K6, MAP2K7, MAPK14, GSN, ARHGDIB, AKAP12, DRG1, CD44, PEBP1, RRM1, KISS1). Two siRNA sequences (siRNA1 and siRNA2) were used for each metastasis suppressor. Two time points (48hr and 96hr) were considered as end of transfection in order to measure early and late effects of the metastasis suppressors downregulation.

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A rare subpopulation of melanoma cells with low expression of metastasis suppressor NME1 is highly metastatic in vivo.

Project description:Despite recent advances in melanoma treatment, metastasis and resistance to therapy remain serious clinical challenges. NME1 is a metastasis suppressor, a class of proteins which inhibits metastatic spread of cancer cells without impact on growth of the primary tumor. We have identified a rare subpopulation of cells with markedly reduced expression of NME1 (NME1LOW) in human melanoma cell lines. To enable isolation of viable NME1LOW cells for phenotypic analysis by fluorescence-activated cell sorting (FACS), a CRISPR-Cas9-mediated approach was used to attach an EGFP coding module to the C-terminus of the endogenous NME1 gene in melanoma cell lines. NME1LOW cells displayed enhanced collective invasion in vitro when implanted as 3D aggregates in Matrigel. NME1LOW cells were also highly metastatic to lung and liver when xenografted subcutaneously in immune-deficient NSG mice. RNA-seq analysis revealed that NME1LOW cells express elevated levels of genes associated with tumor aggressiveness, as well as with morphogenesis of tissues of neural crest-like origin (melanocytes and neurons, bone and heart tissues; GO: 0009653). The highly malignant NME1LOW variant of melanoma cells has potential to provide novel therapeutic targets and molecular markers for improved clinical management of patients with advanced melanoma.

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Project description:Metastatic potential in clonal melanomal cells is driven by a rare, early-invading subpopulation

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Project description:Metastatic potential in clonal melanomal cells is driven by a rare, early-invading subpopulation [RNA-Seq]

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Metastatic potential in clonal melanomal cells is driven by a rare, early-invading subpopulation [ATAC-Seq]

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