Transcriptome and chromatin landscape changes associated with trastuzumab resistance in HER2+ breast cancer cells
Rabi Murad1, Arabo Avanes2, Xinyi Ma1
1Department of Developmental & Cell Biology, University of California Irvine, Irvine, CA 92617, USA.
Abstract:
We set out to uncover transcriptome and chromatin landscape changes that occur in HER2 + breast cancer (BC) cells upon acquiring resistance to trastuzumab. RNA-seq analysis was applied to two independently-derived BC cell lines with acquired resistance to trastuzumab (SKBr3.HerR and BT-474HerR) and their parental drug-sensitive cell lines (SKBr3 and BT-474). Chromatin landscape analysis indicated that the most significant increase in accessibility in resistant cells occurs in PPP1R1B within a segment spanning introns 1b through intron 3. Footprint analysis of this segment revealed that FoxJ3 (within intron 2) and Pou5A1/Sox2 (within inton 3) transcription factor motifs are protected in resistant cells. Overall, 344 shared genes were upregulated in both resistant cell lines relative to their parental counterparts and 453 shared genes were downregulated in both resistant cell lines relative to their parental counterparts. In resistant cells, genes associated with autophagy and mitochondria organization are upregulated and genes associated with ribosome assembly and cell cycle are downregulated relative to parental cells. The five top upregulated genes in drug-resistant breast cancer cells are APOD, AZGP1, ETV5, ALPP, and PPP1R1B. This is the first report of increased chromatin accessibility within PPP1R1B associated with its t-Darpp transcript increase, and points to a possible mechanism for its activation in trastuzumab-resistant cells.
Insights
Trastuzumab-resistant HER2+ breast cancer cells show altered gene expression and chromatin accessibility. Key changes include upregulated autophagy and mitochondrial genes, and downregulated ribosome and cell cycle genes, revealing resistance mechanisms.
Area of Science:
- Oncology
- Genomics
- Molecular Biology
Background:
- HER2-positive breast cancer (BC) is a subtype often treated with trastuzumab.
- Acquired resistance to trastuzumab remains a significant clinical challenge.
- Understanding the molecular mechanisms of resistance is crucial for developing new therapies.
Purpose of the Study:
- To investigate transcriptome and chromatin landscape alterations in HER2+ BC cells developing resistance to trastuzumab.
- To identify specific genes and regulatory elements involved in trastuzumab resistance.
Main Methods:
- RNA-sequencing (RNA-seq) to analyze gene expression profiles.
- Chromatin accessibility and footprinting analyses to map regulatory regions.
- Comparison of resistant cell lines (SKBr3.HerR, BT-474HerR) with parental sensitive lines (SKBr3, BT-474).
Main Results:
- Significant increase in chromatin accessibility in resistant cells within the PPP1R1B gene locus.
- Protected transcription factor motifs (FoxJ3, Pou5A1/Sox2) identified in resistant cells.
- Shared upregulation of 344 genes and downregulation of 453 genes in both resistant cell lines.
- Upregulation of autophagy and mitochondria genes; downregulation of ribosome and cell cycle genes in resistant cells.
- Top upregulated genes include APOD, AZGP1, ETV5, ALPP, and PPP1R1B.
Conclusions:
- This study is the first to report increased chromatin accessibility in PPP1R1B linked to its transcript increase in trastuzumab-resistant cells.
- Identified molecular changes provide insights into trastuzumab resistance mechanisms in HER2+ breast cancer.
- The findings suggest potential therapeutic targets for overcoming trastuzumab resistance.
