Good time to read our Tweetorial/ X-planation of our https://t.co/sU6uF9rfGa paper now featured on the cover of @Nature!

Excellent talk @bergsa83 on the very important topic of upper tract urothelial cancer. Still need to find therapeutic strategies targeting the distinct biology in this disease #PrecisionMedicine one barrier is the lack of faithful UTUC animal models to test these strategies.

Teslas have the lowest maintenance & repair costs of any brand

📢 Excited to share the latest from our lab: we discovered a new synthetic-lethal vulnerability in cancer cells with APOBEC3A activity and its underlying mechanism 🔧🧩 -APOBEC3A induces DNA double-strand breaks🧬✂️🧬 - APOBEC3A shifts double-strand DNA break repair towards

This is the result of several years of dedicated work by many people. Spearheaded by @AbhishekBoseWCM @Weisi_liu in my lab. Important contributions from Paul yoo, Alina Sami @MichalBoniecki @madhuratweets @MHosmanMD @DuyDNguyen2 @UrkodC @GiannakakouEvi @BhavneetBhinder

@AbhishekBoseWCM

Full tweetorial below

Endlessly grateful to our collaborators and funders, this science is a team sport 🙌If you’re energized by APOBEC3 biology, DNA repair/TMEJ, replication stress, chromosomal instability, ecDNA, and precision oncology, come build with us: open postdoc → https://t.co/MldRB3s7Yt 🧬

Importantly, this therapeutic strategy is readily translatable to clinic. The clinical development of pol θ inhibitors such as ART6043 @artiospharma , GSK4524101 @GSK , and RP-3467 @RepareRx and novobiocin is already in Phase 1/2 trials for BRCA-deficient cancers. Our work

So this is our model: A3A → replication stress & DSBs → RPA displacement → TMEJ bias, TMEJ error-prone repair leaves behind microhomology-mediated deletions and chromosomal instability footprints; Polθ inhibition flips cells from damage tolerance to a targetable vulnerability.

We validated this in NSG #bladdercancer xenografts, dox-induced A3A + Polθ knockdown was synthetic lethality. This translates the mechanism into selective tumor control.

We tested dependency: Polθ knockdown reduced viability and increased apoptosis in A3A-high bladder cancer cell lines ; across cell lines, APOBEC3-induced mutations correlated with Polθ dependency (Chronos). ART558 synergized; novobiocin sensitivity scaled with A3 burden. 💊 These

So what is the mechanism? how does APOBEC3A shift DSB repair towards TMEJ. We investigated whether APOBEC3A competes with RPA to initiate TMEJ. By modifying an existing biochemical assay developed by @LChelico13828, we simulated the competitive binding between APOBEC3A and RPA on

We tested this hypothesis using HR/TMEJ repair fluorescent reporters in U2OS cells. APOBEC3A suppressed homologous recombination while promoting TMEJ repair.

Since APOBEC3A activity causes DSB formation and leads to S-phase arrest, either HR or TMEJ might serve as the primary repair pathways. Based on the prior data, we suspected it was TMEJ but we needed functional proof.

In our WCM cohort of urothelial cancers, we found that these micro-homology mediated deletions are significantly closer to APOBEC3-induced kataegis clusters than to clusters induced by other mutagens, such as chemotherapy. We see similar patterns in the TCGA datasets with

In several human cancers, including #bladdercancer we observe a significant correlation between APOBEC3-induced mutational signatures and these micro-homology mediated deletions.

Interestingly, using whole-exome sequencing of isogenic cells, following APOBEC3A expression, we observed an increase in a specific type of deletions associated with microhomology sequences that can be produced by a specific type of error-prone DNA repair called theta-mediated

We see a clear increase in γH2AX–RPA foci indicating DSBs and ssDNA presence following APOBEC3A expression.

To measure the impact on A3A on replication stresst, we worked with @Gerhardtlab to measured fork progression with DNA fiber assays. We found shorter nascent tracts with A3A; low-dose aphidicolin slowed them further, consistent with fork stalling. The cells also arrest in the

We modeled the episodic nature of APOBEC3A expression using a doxycycline-inducibleA3A system (with catalytic-dead control) and observed replication stress + double strand DNA breaks (DSBs). ↑pCHK1, ↑γH2AX, ↑RPA, ↑CHK2 in a deaminase-dependent manner. 🧬 A3A bursts triggered

So what about a different approach: can we identify synthetic-lethal vulnerabilities in APOBEC3-expressing cells that let us selectively eliminate them? This is where our most recent work comes in https://t.co/hEyJ7FIHtk