Mapping the Subtype-Specific PARP1 ADP-ribosylated Proteome in Breast Cancer Cells

Area of Science:

• Molecular Biology
• Genomics
• Cancer Research

Background:

• Breast cancers exhibit molecular heterogeneity, impacting treatment outcomes.
• Poly (ADP-ribose) polymerase 1 (PARP1) is known for DNA repair but also regulates gene expression.
• Understanding PARP1's role in different breast cancer subtypes is crucial.

Purpose of the Study:

• To map Poly (ADP-ribose) polymerase 1 (PARP1) substrates and ADP-ribosylation sites across breast cancer subtypes.
• To investigate subtype-specific differences in PARP1 activity and its substrates.
• To explore the broader role of PARP1 in gene regulation beyond DNA repair.

Main Methods:

• Utilized an NAD+ analog-sensitive PARP1 (asPARP1) chemical genetics approach.
• Employed mass spectrometry to identify ADP-ribosylated proteins (proteome mapping).
• Analyzed six human breast cancer cell lines representing luminal and basal/triple-negative subtypes.

Main Results:

• Identified thousands of PARP1 substrates and hundreds of ADP-ribosylation sites.
• Discovered shared and subtype-specific modifications.
• Luminal-specific substrates included chromatin and transcriptional regulators; basal-specific substrates were linked to translation and RNA processing.
• Transcription factors, like TFAP2A, were major substrates, with subtype-specific modification and promoter occupancy changes.

Conclusions:

• PARP1-driven ADP-ribosylation encodes subtype-specific transcriptional programs in breast cancer.
• PARP1 has a broader role in gene regulation than previously understood.
• Findings offer mechanistic insights into subtype-specific gene regulation and potential determinants of PARP inhibitor sensitivity.