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Updated: Jul 17, 2025

Investigation of the Transcriptional Role of a RUNX1 Intronic Silencer by CRISPR/Cas9 Ribonucleoprotein in Acute Myeloid Leukemia Cells
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Datasets for the effects of RUNX2 silencing on transcriptomic and metabolomic profiles in SJSA-1 osteosarcoma cells

Mai Nhu Uyen Le1, Ruiqi Chen2, Liang-E Xia3

  • 1State Key Laboratory of Developmental Biology of Freshwater Fish & Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, China.

Data in Brief
|September 4, 2023
PubMed

Insights

RUNX2 gene silencing in osteosarcoma cells altered gene expression and metabolism. This study provides data to understand RUNX2

Area of Science:

  • Oncology
  • Molecular Biology
  • Metabolomics

Background:

  • Osteosarcoma is a prevalent primary bone cancer with significant metastatic and recurrent potential.
  • Metabolic reprogramming is a critical hallmark of cancer, including osteosarcoma, often driven by genetic and epigenetic changes.
  • RUNX2, a key transcription factor in osteoblastic differentiation, is implicated in osteosarcoma development and progression when aberrantly expressed.

Purpose of the Study:

  • To investigate the impact of RUNX2 gene silencing on the transcriptomic and metabolomic profiles of osteosarcoma cells.
  • To generate and analyze comprehensive datasets of gene expression and metabolite changes following RUNX2 knockdown.
  • To facilitate the identification of novel RUNX2 targets and elucidate its role in osteosarcoma pathogenesis and metabolic reprogramming.

Main Methods:

  • Generation of SJSA-1 osteosarcoma cell lines with stable RUNX2 shRNA expression and control scramble shRNA expression.
  • Transcriptome profiling using Illumina NovaSeq 6000 to analyze gene expression changes.
  • Metabolome profiling using ultrahigh-performance liquid chromatography coupled with time-of-flight mass spectrometry (UHPLC-TOF-MS) to analyze metabolite alterations.

Main Results:

  • Silencing of RUNX2 in osteosarcoma cells led to significant alterations in both transcriptome and metabolome profiles.
  • Comparative analysis revealed distinct gene expression patterns and metabolic signatures between RUNX2-silenced and control cells.
  • The generated datasets offer a valuable resource for identifying genes and metabolic pathways regulated by RUNX2.

Conclusions:

  • RUNX2 plays a crucial role in regulating gene expression and metabolic reprogramming in osteosarcoma.
  • Understanding RUNX2's function through transcriptomic and metabolomic analysis can reveal novel therapeutic targets.
  • The study provides foundational data for further research into the mechanisms underlying osteosarcoma development and progression.
Keywords:
Bone tumorMetabolic reprogrammingRNA interferenceRNA-seqRunt-related transcription factor

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