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Updated: Mar 23, 2026
Utilizing Functional Genomics Screening to Identify Potentially Novel Drug Targets in Cancer Cell Spheroid Cultures
Published on: December 26, 2016
MiRNA Transcriptome Profiling of Spheroid-Enriched Cells with Cancer Stem Cell Properties in Human Breast MCF-7 Cell
Lily Boo1, Wan Yong Ho2, Norlaily Mohd Ali1
11. Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, 43000 Cheras, Malaysia;
Abstract:
Breast cancer is the second leading cause of cancer-related mortality worldwide as most patients often suffer cancer relapse. The reason is often attributed to the presence of cancer stem cells (CSCs). Recent studies revealed that dysregulation of microRNA (miRNA) are closely linked to breast cancer recurrence and metastasis. However, no specific study has comprehensively characterised the CSC characteristic and miRNA transcriptome in spheroid-enriched breast cells. This study described the generation of spheroid MCF-7 cell in serum-free condition and the comprehensive characterisation for their CSC properties. Subsequently, miRNA expression differences between the spheroid-enriched CSC cells and their parental cells were evaluated using next generation sequencing (NGS). Our results showed that the MCF-7 spheroid cells were enriched with CSCs properties, indicated by the ability to self-renew, increased expression of CSCs markers, and increased resistance to chemotherapeutic drugs. Additionally, spheroid-enriched CSCs possessed greater cell proliferation, migration, invasion, and wound healing ability. A total of 134 significantly (p<0.05) differentially expressed miRNAs were identified between spheroids and parental cells using miRNA-NGS. MiRNA-NGS analysis revealed 25 up-regulated and 109 down-regulated miRNAs which includes some miRNAs previously reported in the regulation of breast CSCs. A number of miRNAs (miR-4492, miR-4532, miR-381, miR-4508, miR-4448, miR-1296, and miR-365a) which have not been previously reported in breast cancer were found to show potential association with breast cancer chemoresistance and self-renewal capability. The gene ontology (GO) analysis showed that the predicted genes were enriched in the regulation of metabolic processes, gene expression, DNA binding, and hormone receptor binding. The corresponding pathway analyses inferred from the GO results were closely related to the function of signalling pathway, self-renewability, chemoresistance, tumorigenesis, cytoskeletal proteins, and metastasis in breast cancer. Based on these results, we proposed that certain miRNAs identified in this study could be used as new potential biomarkers for breast cancer stem cell diagnosis and targeted therapy.
Insights
This study characterized breast cancer stem cells (CSCs) in spheroids, revealing enriched CSC properties and identifying 134 differentially expressed microRNAs (miRNAs). These findings suggest potential new biomarkers for breast cancer diagnosis and therapy.
Area of Science:
- Oncology
- Molecular Biology
- Genetics
Background:
- Breast cancer is a leading cause of mortality, with relapse often linked to cancer stem cells (CSCs).
- Dysregulation of microRNAs (miRNAs) is implicated in breast cancer recurrence and metastasis.
- Comprehensive characterization of CSCs and miRNA profiles in enriched breast cancer cells is lacking.
Purpose of the Study:
- To generate and characterize spheroid-enriched breast cancer cells for CSC properties.
- To comprehensively analyze the miRNA transcriptome in these enriched CSCs.
- To identify potential novel miRNA biomarkers for breast cancer stem cell diagnosis and targeted therapy.
Main Methods:
- Generation of spheroid MCF-7 cells in serum-free conditions.
- Characterization of CSC properties including self-renewal, marker expression, and drug resistance.
- Next-generation sequencing (NGS) for miRNA expression profiling and differential analysis.
Main Results:
- Spheroid-enriched cells exhibited enhanced CSC properties, including self-renewal, increased CSC marker expression, and chemoresistance.
- These cells also showed increased proliferation, migration, invasion, and wound healing capabilities.
- 134 significantly differentially expressed miRNAs were identified, including 25 up-regulated and 109 down-regulated, with several novel miRNAs linked to chemoresistance and self-renewal.
Conclusions:
- Spheroid formation enriches breast cancer cells with CSC properties.
- A distinct miRNA signature is associated with these CSC-enriched cells.
- Novel miRNAs identified may serve as potential biomarkers for breast cancer stem cell diagnosis and targeted therapeutic strategies.
