Periodic Reporting for period 2 - EpigeneticScars (Understanding DSB repair from pathway choice to long term effects and their consequences.)
Reporting period: 2022-02-01 to 2023-07-31
DNA double-strand breaks (DSB) are critical genomic lesions, and reduced DSB repair efficiency is associated with age-related disease development, like cancer, immunodeficiencies Alzheimer’s and Parkinson´s. Once DSB occurs, the DNA Damage Response (DDR) is initiated by binding of DSB sensor to the damaged DNA. During this response, there is massive recruitment of signaling proteins, chromatin remodelers, and effector molecules that will cope with the lesion and will decide cell’s fate. However, this network is complicated and many of the proteins involved haven’t been identified, particularly in the initial response as well as the resolution of the damage. This may be influences by the sensor arriving to the site of damage and the pathway choice.
Cells have two main DSB-repair pathways, an error-free repair known as homology recombination (HR) and non-homologous end joining (NHEJ), which usually generates mutations. Both mechanisms are selectively used, and the activity of the sensor proteins arriving at the DSB site has a major role in the repair outcome.
We investigated the sensor-dependent interaction networks of three sensors in a time-dependent manner (Sirt6, Ku80, and NBS1). This could lead to important proteins to resolve DNA damage and prevent age-related diseases Using a proximity-labeling assay (BioID) and IP-mass spec, we identified chromatin networks for each sensor during different DDR time points. Our results showed that after DSB induction, the basal interactome of each sensor protein changes, progressively incorporating new proteins and approaching a similar state that requires functions like Nucleolar metabolism, RNA processing and degradation, and chromatin remodeling. Each sensor has its independent interactome and the shared interactome of DDR repair proteins. These interactome network will help us understand the DDR in a sensor dependent manner, to identify new relevant pathways and proteins involved that could be relevant for age-related diseases. In the following months we will focus on these novel proteins and pathways to understand their roles in DDR.
Cells have two main DSB-repair pathways, an error-free repair known as homology recombination (HR) and non-homologous end joining (NHEJ), which usually generates mutations. Both mechanisms are selectively used, and the activity of the sensor proteins arriving at the DSB site has a major role in the repair outcome.
We investigated the sensor-dependent interaction networks of three sensors in a time-dependent manner (Sirt6, Ku80, and NBS1). This could lead to important proteins to resolve DNA damage and prevent age-related diseases Using a proximity-labeling assay (BioID) and IP-mass spec, we identified chromatin networks for each sensor during different DDR time points. Our results showed that after DSB induction, the basal interactome of each sensor protein changes, progressively incorporating new proteins and approaching a similar state that requires functions like Nucleolar metabolism, RNA processing and degradation, and chromatin remodeling. Each sensor has its independent interactome and the shared interactome of DDR repair proteins. These interactome network will help us understand the DDR in a sensor dependent manner, to identify new relevant pathways and proteins involved that could be relevant for age-related diseases. In the following months we will focus on these novel proteins and pathways to understand their roles in DDR.
In our proposed plan, we dedicated the first year to generating the system vector and cell lines and identifying the Epigenetic landscape and proteins involved. We have generated two out of the three cell lines proposed, the SIRT6-BioID and the KU80-BioID. We have identified the proteins arriving at the sites of damage for the early time points. Ranging from 5min 30 min, 2hr 8hrs and 24 hours.
The last vector and cell line with MRE11-BioID resulted in cell death due to the expression of this protein. MRE11 is in a complex with the protein NBS1 to form the MRN complex, which serves as a DNA-damage sensor. Therefore we decided to use NBS1 protein instead. NBS1 expressing cells are tolerating the expression of the protein. We are obtaining the protein interactome in a kinetic manner as we did for the other two DNA-damage sensors.
Regarding the Epigenetic signature, the material obtained in mass spectrometry was insufficient. Therefore, we are changing our protocol from acid to High salt extraction to obtain better histone purification. Last, we performed ChIP analysis on SIRT6 and Ku80 cell lines with and without damage. The data is being analyzed, but it is possible that this method will not be sensitive enough from our preliminary analysis, and we would need to implement an improved sequencing method.
Regarding the Epigenetic signature, the material obtained in mass spectrometry was insufficient. Therefore, we are changing our protocol from acid to High salt extraction to obtain better histone purification. Last, we performed ChIP analysis on SIRT6 and Ku80 cell lines with and without damage. The data is being analyzed, but it is possible that this method will not be sensitive enough from our preliminary analysis, and we would need to implement an improved sequencing method.