# Stalled replication fork repair in cancer predisposition and cancertherapy

> **NIH NIH R35** · BETH ISRAEL DEACONESS MEDICAL CENTER · 2024 · $985,529

## Abstract

PROJECT SUMMARY
Error-free DNA repair initiated at the sites of replication fork stalling is critical for the prevention of genomic
instability in cycling cells. Defects in stalled fork repair have been directly implicated in cancer predisposition
and other human diseases. The clinical burden associated with failed stalled fork repair may include hereditary
breast and ovarian cancer (HBOC) predisposition, in light of the involvement of BRCA1 and BRCA2 in repair of
stalled replication forks, and Fanconi Anemia (FA)—a rare, autosomal recessive (or X-linked) disease caused
by inactivation of any one of several FA genes. Our work previously established roles for BRCA1 and BRCA2
in regulating HR at both double strand breaks (DSBs) and in stalled fork repair. We developed innovative tools
for quantifying homologous recombination (HR) and other repair outcomes at stalled mammalian replication
forks and, more recently, at broken replication forks. A major goal of this proposal is to define the fundamental
mechanisms of repair of stalled forks. We have developed an array of cutting-edge tools to support this study,
including unique, sophisticated HR reporters that can distinguish between error-free “short tract” HR and error-
prone “long tract” HR—a replicative response analogous to break-induced replication in yeast. One unusual
aberrant replicative response that we observe at stalled forks specifically in BRCA1 mutant cells is the
formation of <10 kb non-homologous tandem duplications (TDs). In a paradigm-shifting discovery, we found
that these highly specific forms of structural variation are also abundant in the human BRCA1-linked breast
and ovarian cancer genome. A major goal of this proposal is to define the genetic regulation and full
mechanism of TD formation at stalled forks in BRCA1 mutant cells. Success in this project will reveal in
unprecedented detail the mechanisms that regulate mammalian stalled (or broken) fork repair and their
relationship to cancer predisposition. In support of this, we will develop new techniques for analyzing DNA
structural intermediates, chromatin responses to fork stalling and protein composition of the stalled mammalian
replication fork. These analytical studies may also identify new molecular targets for therapy of breast and
ovarian cancer. Indeed, our recent work on the mechanisms underlying formation of BRCA1-linked TDs led us
to discover a synthetic lethal interaction between BRCA1 and FANCM loss-of-function mutations. FANCM is a
motor protein and, hence, an ATPase. We find that ablation of FANCM ATPase activity alone (leaving the rest
of the protein intact and stable within the cell) is sufficient to confer lethality on BRCA1 mutant cells. Thus,
FANCM may be a “druggable” target for therapy in BRCA1-linked cancer. In work proposed herein, we will
define the therapeutic potential of this discovery. During the funding period, we expect to make important
discoveries in this field and to open the door to new ther...

## Key facts

- **NIH application ID:** 10875613
- **Project number:** 5R35CA263813-03
- **Recipient organization:** BETH ISRAEL DEACONESS MEDICAL CENTER
- **Principal Investigator:** Ralph Scully
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $985,529
- **Award type:** 5
- **Project period:** 2022-08-10 → 2029-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10875613

## Citation

> US National Institutes of Health, RePORTER application 10875613, Stalled replication fork repair in cancer predisposition and cancertherapy (5R35CA263813-03). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10875613. Licensed CC0.

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