Functional characterization of specific non-coding transcripts involved in chemo-resistant triple negative breast cancer

Triple-negative breast cancer (TNBC) accounts for many new breast cancer cases, with poorer outcomes than other molecular subtypes. Compared to other subtypes of breast cancer, TNBC is typically associated with larger, higher-grade tumors and decreased overall and recurrence-free survival rates. Treatment for this type of cancer is often aggressive and includes chemotherapeutic agents like anthracyclines, such as doxorubicin. However, it is not always effective due to dose-limiting toxicity and the development of resistance to doxorubicin over time. There are many theories behind the mechanism of resistance, possibly due to changes at the genetic level, transcriptome, cellular pathways, or epigenetic modifications, warranting further investigation. To study the mechanism of resistance, we developed doxorubicin-resistant MDAMB231 and HCC1143 TNBC cell lines that were engineered using physiological or low-dose doxorubicin concentrations with gradual increments of doxorubicin. We performed integrated genomic analyses to identify transcripts that are potentially contributing to the resistance mechanisms and also drive cancer progression. These transcripts range from coding RNAs, microRNAs, pseudogenes, divergent transcripts, and long noncoding RNAs. We focused on the intergenic long noncoding RNAs that are differentially expressed compared to non-resistant TNBC cells. We analyzed these RNAs by interrogating their neighborhood based on their chromosomal location, revealing that they could be involved in cellular plasticity, which allows cancer cells to adjust to the presence of doxorubicin, possibly through transcriptional reprogramming. A subset of them are localized to chromatin and the nucleus, which have the potential to reprogram the epigenetic landscape and drive resistance-specific genes and cellular pathways, and currently we are studying them for their role in chromatin organization. Additionally, we are also assessing their clinical utility using in vivo xenograft mouse models with genetically engineered chemo-sensitive and chemo-resistant cells, linking outcomes to changes observed in patient samples and associated with clinical prognosis. Collectively, our studies provide insights into mechanisms driving doxorubicin resistance in TNBC, which may offer new avenues for the development of diagnostic markers and targeted therapies.