Download Final Report - The Bowel Disease Research Foundation

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Bowel Disease Research Foundation £29 500 – prediction radiotherapy
response rectal cancer (2011).
Simon P Bach and Andrew Beggs
Overview: This BDRF award funded the start of a programme that has explored molecular
stratification of rectal cancer to determine tumour factors associated with pathological
complete response (pCR) to neo-adjuvant chemoradiation (nCRT). Approximately 10-15% of
patients undergoing treatment for locally advanced rectal cancer achieve complete
regression of their cancer following nCRT. The role of radiotherapy is now being evaluated in
early stage disease where pCR rates approaching 50% are described.
The molecular
mechanisms around this are not clear, but may involve failures in DNA repair and visibility of
the tumour to the immune system during treatment. Patients who obtain a pCR may avoid
standard surgery and its side effects. Unfortunately those patients with residual cancer still
require radical surgery. These patients suffer toxicity from both radiotherapy and surgery.
Developing greater understanding of the factors that lead to radiotherapy response may lead
to personalized treatment for patients.
Outputs: This work was performed by Mr Andrew Beggs (ACPGBI young
coloproctologist 2016). (1) BDRF funding helped him to secure a prestigious Wellcome
Trust post-doctoral Clinician Scientist award. (2) The data generated was also used to
support our £5M MRC/ CRUK Stratification in Colorectal Cancer (S-CORT) award in 2014.
Research:
Figure 1: Sampling protocol in pathological complete response study.
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Assembly of patient cohort: Using a locally collated radiotherapy database spanning 16 years,
I collected a cohort of patients undergoing pathological complete response (pathCR) to nCRT
(n=30) as well as patients with minimal residual disease (n=100) and those who progress with
no pathological response (n=100). The samples available for these patients were exclusively
FFPE blocks, and I therefore developed techniques to carry out next generation sequencing
assays on this tissue type. I focused on pre-treatment samples on patients with pathCR for this
study in order to study an extreme phenotype, with resection specimens as a control group.
These samples, by their nature, were biopsy samples and thus heterogeneity could be a
potential issue. However, because the tumours had undergone pathological complete
response, I assumed that the tumour was likely to be homogenous with a common driver
permitting radiosensitivity to occur.
FBWX7 and PIK3CA mutations are associated with radiosensitivity: Using PCR amplicon
resequencing of a 16 gene panel focused on colorectal cancer associated driver genes
based on the findings in TCGA (see appendix) I sequenced this cohort to very high read
depth (>15000x) in order to understand clonality events as well as rare subclones. I used
analysis of significantly mutated genes as compared to the background mutation rate
(MutSigCV, Genome MuSIC) to identify that the pathCR population seemed to be enriched
for mutations in FBXW7 (p=1.84x10-10,QFDR=1.74x10-6) and PIK3CA (p=7.89x1011,Q
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FDR=1.49x10 ). FBXW7 (F-Box And WD Repeat Domain Containing 7) has recently
been identified as a key facilitator of non-homologous end joining via ATM which
phosphorylates FBXW7 at serine 26 to recruit it to DNA double-strand break (DSB) sites.
Loss of normal FBXW7 has been shown to increase genomic instability and trigger
programmed cell death, thus make it an attractive target for pharmacological inhibition to
increase radiosensitivity. This cohort is currently undergoing high read depth (150x) exome
sequencing to identify other driver mutations that may be enriched in this cohort.
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