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Updated: Feb 20, 2026
Studying Triple Negative Breast Cancer Using Orthotopic Breast Cancer Model
Published on: March 20, 2020
Integrative Computational and Transcriptional Analysis of NF-κB and HIF-1α Modulation Following Doxorubicin Treatment
Nurul Utami1,2, Arif Setiawansyah3, Muhammad Hasan Bashari4
1Doctoral Program in Medical Science, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia.
Purpose:
Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype with limited targeted treatment options. Doxorubicin remains a cornerstone of TNBC treatment; however, its molecular effects beyond canonical cytotoxic mechanisms are not fully characterized. This study aimed to explore NF-κB- and HIF-1α-related transcriptional responses associated with doxorubicin treatment in TNBC cells using an integrative computational and experimental approach, in line with global cancer research priorities supporting Sustainable Development Goal (SDG) 3: Good Health and Well-Being.
Methods:
Network pharmacology analysis, molecular docking, and molecular dynamics simulations were employed to explore potential pathway-level associations of doxorubicin with NF-κB and HIF-1α-related signaling. In vitro validation was performed using MTT cytotoxicity assays in MDA-MB-231 cells cultured in DMEM and RPMI-1640 media. Half-maximal inhibitory concentrations (IC5 0) were determined using four-parameter logistic regression. Transcriptional responses of NF-κB and HIF-1α were evaluated by RT-qPCR under normoxic conditions.
Results:
Computational analyses suggested potential associations between doxorubicin and components of NF-κB and HIF-1α-related signaling pathways. In vitro assays demonstrated concentration-dependent cytotoxicity, with IC5 0 values of 2.34 µM (95% CI: 2.11-2.74) in DMEM and 1.07 µM (95% CI: 0.92-1.32 µM) in RPMI-1640. RT-qPCR analysis revealed downregulation of NF-κB and HIF-1α mRNA expression following doxorubicin treatment. These findings indicate transcriptional modulation associated with doxorubicin exposure, without establishing functional pathway inhibition.
Conclusion:
This study provides transcriptional-level evidence suggesting the involvement of NF-κB- and HIF-1α-related pathways in the cellular response of TNBC cells to doxorubicin treatment. By integrating computational predictions with early experimental validation, the findings generate biologically plausible hypotheses for further mechanistic and functional investigations, contributing to foundational cancer research efforts aligned with SDG 3 (Good Health and Well-Being).
Insights
Triple-negative breast cancer (TNBC) cells treated with doxorubicin showed altered expression of NF-κB and HIF-1α pathways. This study integrates computational and experimental methods to explore doxorubicin
Area of Science:
- Molecular Biology
- Cancer Research
- Computational Biology
Background:
- Triple-negative breast cancer (TNBC) is an aggressive subtype with limited targeted therapies.
- Doxorubicin is a key treatment, but its non-cytotoxic molecular effects require further characterization.
- Understanding molecular responses is crucial for advancing TNBC treatment strategies and global health goals (SDG 3).
Purpose of the Study:
- To investigate the transcriptional responses related to NF-κB and HIF-1α signaling pathways in TNBC cells treated with doxorubicin.
- To integrate computational predictions with experimental validation for a comprehensive understanding of doxorubicin's molecular effects.
- To generate hypotheses for future mechanistic studies in TNBC.
Main Methods:
- Employed network pharmacology, molecular docking, and molecular dynamics simulations to predict pathway associations.
- Conducted in vitro cytotoxicity assays (MTT) to determine half-maximal inhibitory concentrations (IC50) in MDA-MB-231 cells.
- Utilized RT-qPCR to evaluate the mRNA expression levels of NF-κB and HIF-1α under normoxic conditions.
Main Results:
- Computational analyses indicated potential links between doxorubicin and NF-κB/HIF-1α signaling components.
- In vitro assays confirmed dose-dependent cytotoxicity, with varying IC50 values in different cell culture media.
- RT-qPCR revealed a significant downregulation of NF-κB and HIF-1α mRNA following doxorubicin treatment.
Conclusions:
- The study provides transcriptional evidence for the involvement of NF-κB and HIF-1α pathways in TNBC's response to doxorubicin.
- Integrated computational and experimental findings generate testable hypotheses for further research into doxorubicin's mechanisms.
- Contributes to foundational cancer research aligned with SDG 3, promoting good health and well-being.
