A CRISPR based approach to identifying target genes and causal variants at breast cancer risk loci
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Embargo End Date
2026-06-17
ICR Authors
Authors
Sevgi, S
Document Type
Thesis or Dissertation
Date
2025-12-17
Date Accepted
Abstract
Genome wide association studies (GWAS) and fine mapping analysis have identified 196
independent signals associated with breast cancer risk. Deciphering the functional basis
of these associations has the potential to further our understanding of the biology of breast
cancer risk and inform future prevention strategies. Most GWAS variants map to noncoding
regions which makes identifying causal (as opposed to correlated) variants and
their target genes challenging. As a result, causal variants and target genes at most of
these regions remain unknown. Transcription of genes and activity of regulatory elements
can be perturbed without making permanent changes to the genome using a catalytically
inactive dCas9 fused to a transcriptional activator (CRISPRa) or repressor (CRISPRi). This
project uses these techniques to evaluate the probability that one or more credible causal
variants (CCVs), defined as variants that cannot be excluded as causal on statistical
grounds alone, is truly functional and to identify the gene(s) that the functional variant
impacts. sgRNAs targeting each CCV at each of two loci mapping to gene-rich regions at
19q13.3 were transduced into CRISPRa/CRISPRi modified normal breast epithelial cells
(MCF-10A) and changes in gene expression were measured using NanoString nCounter.
This identified rs1685191 and rs4399645 as potentially causal variants with KCNN4 and
GIPR as their target genes respectively. KCNN4 and GIPR show cell type-specific
expression in normal breast and breast cancer, with KCNN4 preferentially expressed in
basal-like breast cancer cells and estrogen receptor-negative breast cancers and GIPR in
luminal breast cancer cells and estrogen receptor-positive breast cancers. Follow-up
experiments demonstrate that GIPR expressed on normal breast and breast cancer cells
can signal in response to both the GIPR ligand (GIP) and agonist (tirzepatide) to regulate
cellular functional responses. These findings demonstrate that GWAS have the potential
to identify genes that may be new targets for breast cancer prevention
Citation
2025
DOI
Source Title
Publisher
Institute of Cancer Research (University Of London)
ISSN
eISSN
Collections
Research Team
Functional Genetic Epi