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Differential expression profiling of onco and tumor-suppressor genes from major-signaling pathways in Wilms' tumor

Dinesh Kumar Sahu1,2, Neetu Singh3, Mumani Das4

  • 1Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India. dinesh23biotech@gmail.com.

Pediatric Surgery International
|September 15, 2022
PubMed
Abstract

Insights

This study profiled oncogenes and tumor-suppressor genes in Wilms' tumor, revealing altered expression patterns. PBRM1, ERBB2, and EGFR show potential as diagnostic markers for this pediatric kidney cancer.

Area of Science:

  • Pediatric Oncology
  • Molecular Biology
  • Cancer Genomics

Background:

  • Wilms' tumor is a common pediatric kidney malignancy.
  • Genetic alterations in oncogenes (OG) and tumor-suppressor genes (TG) are implicated in its development.
  • While many genes are linked, WT1's role is established, but a broader genetic profile is needed.

Purpose of the Study:

  • To investigate the mRNA expression levels of 16 OGs and 20 TGs in Wilms' tumor.
  • To identify key signaling pathways affected by these genetic alterations.
  • To explore potential diagnostic markers for Wilms' tumor.

Main Methods:

  • Analyzed mRNA expression of 36 genes across 24 fresh Wilms' tumor samples.
  • Utilized capture-and-reporter probe Code-Sets chemistry.
  • Focused on genes in critical signaling pathways including chromatin modification, RAS, APC, Cell Cycle/Apoptosis, Transcriptional Regulation, PI3K, NOTCH, and HH.

Main Results:

  • Significant up-regulation of MEN1, MLL2, MLL3, PBRM1, PRDM1, SMARCB1, SETD2, WT1, PTPN11, KRAS, HRAS, NF1, APC, RB1, FUBP1, BCOR, U2AF1, PIK3CA, PTEN, EBXW7, SMO, ALK, CBL, EP300, and GATA1 observed in varying percentages of cases.
  • Significant down-regulation of BRAF, NF2, CDH1, BCL2, FGFR3, ERBB2, MET, RET, EGFR, and GATA2 noted in a majority of cases.
  • WT1 gene showed a five-fold down-regulation in 41.66% of cases.

Conclusions:

  • Extensive profiling of OG and TG associations in major signaling pathways can aid Wilms' tumor diagnosis.
  • PBRM1 (up-regulated in 91.67%), ERBB2, and EGFR (down-regulated in 91.66%) are potential marker genes.
  • Further validation in larger sample cohorts is necessary to confirm these findings.
Keywords:
Copy number variationsOncogenesTumor suppressor genesWilms’ tumor

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