# Extreme genomic instability at large transcribed genes: mechanisms and consequences for the cancer genome

> **NIH NIH R01** · UNIVERSITY OF MICHIGAN AT ANN ARBOR · 2020 · $485,226

## Abstract

PROJECT SUMMARY/ABSTRACT
Chromosomal rearrangements are a fundamental form of mutagenesis with a profound impact on human
health. Poorly understood processes of structural mutagenesis are active in somatic cells where they ultimately
lead to cancer. A flood of genomic data from The Cancer Genome Atlas (TCGA) and other projects is revealing
that intrachromosomal rearrangements are especially common and that certain genomic loci are highly prone
to their occurrence. The nature and mechanisms of unstable loci are thus of central importance to cancer
etiology. We are exploring these questions using models of acquired genomic copy number variants (CNVs), a
term encompassing interstitial deletions and duplications and representing the same mechanisms as copy-
number-neutral inversions and translocations. In these models, exogenous replication stress in the form of low-
dose aphidicolin or hydroxyurea is a potent inducer of new CNVs in cultured somatic cells. CNVs are
characterized by microhomologous junctions typical of pathogenic rearrangements that likely arise as
replication errors. Hotspots of induced CNV formation are the same loci as common fragile sites, and it is the
active transcription of large genes that leads to their extreme cell-type-specific instability. This project explores
the hypothesis that the same instability mechanism(s) observed in these models of exogenous somatic CNV
induction lead to recurrent genomic alterations in cancer as a result of endogenous replication stress. This idea
is tested in three aims that examine the mechanisms leading to the extreme locus instability at large
transcribed genes and the consequences of these mechanisms for the cancer genome. Aims 1 and 2 address
non-exclusive hypotheses for how transcription interacts with replication stress to confer locus instability. Aim 1
argues that large genes create a dynamic conflict in which transcription into S-phase removes late-firing
replication origins and creates large replicons highly sensitive to replication inhibition. Novel approaches will
test this hypothesis by determining the cell-cycle timing of replication, transcription, and origin presence and
firing. Aim 2 argues that transcription leads to persistent R-loops that cause fork stalling and thus precursor
lesions for CNV formation. Monitoring and manipulating R-loop formation in cell lines that variably express
specific large genes will test this hypothesis. Aim 3 addresses the consequences of these mechanisms on the
cancer genome first through bioinformatic explorations of TCGA cancer data sets to correlate deletion hotspots
with tumor- and cancer-type-specific transcription. Tissue-culture models of forced oncogene activation and
mouse models of colon cancer will relate de novo CNV formation with the endogenous replication stress
inherent to cancer.

## Key facts

- **NIH application ID:** 9993309
- **Project number:** 5R01CA200731-05
- **Recipient organization:** UNIVERSITY OF MICHIGAN AT ANN ARBOR
- **Principal Investigator:** THOMAS W GLOVER
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $485,226
- **Award type:** 5
- **Project period:** 2016-09-01 → 2022-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9993309

## Citation

> US National Institutes of Health, RePORTER application 9993309, Extreme genomic instability at large transcribed genes: mechanisms and consequences for the cancer genome (5R01CA200731-05). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/9993309. Licensed CC0.

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