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| Status |
Public on May 01, 2023 |
| Title |
Differential gene expression profile analysis of parental, Cas9-p15 control, and MELK knockout cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Triple-negative breast cancer (TNBC) has high relapse and metastasis rates and a high proportion of cancer stem-like cells (CSCs), which possess self-renewal and tumor initiation capacity. MELK (maternal embryonic leucine zipper kinase), a protein kinase of the Snf1/AMPK kinase family, is known to promote CSC maintenance and malignant transformation. Our study showed that MELK knockdown using siRNA or MELK inhibition using the MELK inhibitor MELK-In-17 significantly reduced invasiveness, reversed epithelial-to-mesenchymal transition (EMT), and reduced CSC self-renewal and maintenance in TNBC cells. Nude mice injected with CRISPR MELK-knockout MDA-MB-231 cells exhibited suppression of lung metastasis and improved overall survival compared with mice injected with control cells. Furthermore, MELK-In-17 suppressed 4T1 tumor growth in syngeneic BALB/c mice. Our findings indicate that MELK supports metastasis by promoting EMT and the CSC phenotype in TNBC. In our microarray analysis, we identified potential downstream targets of MELK, including STAT5 and NF-kB target genes, as well as genes involved in tumor progression and metastasis (i.e., EMT, angiogenesis, hypoxia, and apical junction). EMT was the most strongly enriched hallmark among genes highly expressed in Cas9-p15 control cells, further confirming that EMT is a major factor contributing to MELK-induced metastasis in TNBC. We also identified a direct physical interaction partner (PRKAB2) of MELK and a set of intermediate proteins (CDC25B, EZH2, FOXM1, JUN, MAP3K5, PRKAB1, PRKAB2, and SMAD2), suggesting that these proteins are key components of MELK-induced signal transduction.
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| Overall design |
RNA was extracted from parental, Cas9-p15 control, and MELK KO MDA-MB-231 cells. RNA was hybridized onto Affymetrix Human Transcriptome Arrays (version 2.0). Raw gene expression data were read into R using the BioC-package affy, normalized using the Robust MultiArray (RMA) algorithm, and log2-transformed. Probes with normalized expression values exceeding log2(100) in at least 25% of the arrays were filtered for further analysis. In addition, redundancy in probes mapping to the same gene was removed by retaining only the probe with the largest reported variation in gene expression measured by standard deviation. In total, 10,059 unique genes were included for final analysis.
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| Contributor(s) |
Bartholomeusz C |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Mar 20, 2023 |
| Last update date |
May 03, 2023 |
| Contact name |
Chandra Bartholomeusz |
| E-mail(s) |
chbartho@mdanderson.org
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| Phone |
713-745-1086
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| Organization name |
The University of Texas MD Anderson Cancer Center
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| Street address |
1515 Holcombe Blvd
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| City |
HOUSTON |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platforms (1) |
| GPL17586 |
[HTA-2_0] Affymetrix Human Transcriptome Array 2.0 [transcript (gene) version] |
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| Samples (12)
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| GSM7107998 |
MDA-MB-231 Cas9-P15 control, biological rep 1 |
| GSM7107999 |
MDA-MB-231 Cas9-P15 control, biological rep 2 |
| GSM7108000 |
MDA-MB-231 Cas9-P15 control, biological rep 3 |
| GSM7108001 |
MDA-MB-231 MELK KO clone C3, biological rep 1 |
| GSM7108002 |
MDA-MB-231 MELK KO clone C3, biological rep 2 |
| GSM7108003 |
MDA-MB-231 MELK KO clone C3, biological rep 3 |
| GSM7108004 |
MDA-MB-231 MELK KO clone C28, biological rep 1 |
| GSM7108005 |
MDA-MB-231 MELK KO clone C28, biological rep 2 |
| GSM7108006 |
MDA-MB-231 MELK KO clone C28, biological rep 3 |
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| Relations |
| BioProject |
PRJNA946793 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE227774_Master_regulators_of_gene_expression_20221021_ORAPaths.xlsx |
20.2 Kb |
(ftp)(http) |
XLSX |
| GSE227774_RAW.tar |
285.7 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
| Processed data are available on Series record |
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