HAL Id: hal-01120049
https://hal.archives-ouvertes.fr/hal-01120049
Submitted on 24 Feb 2015
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Bioinformatics methods for analyzing anti-hormonal treatment resistance in breast cancer
Justine Rudewicz, Hayssam Soueidan, Audrey Gros, Gaetan Macgrogan, Hervé Bonnefoi, Macha Nikolski, Richard Iggo
To cite this version:
Justine Rudewicz, Hayssam Soueidan, Audrey Gros, Gaetan Macgrogan, Hervé Bonnefoi, et al.. Bioin-formatics methods for analyzing anti-hormonal treatment resistance in breast cancer. BCBB 2014 (Bordeaux Computational Biology and Bioinformatics), Nov 2014, Bordeaux, France. �hal-01120049�
Bioinformatics methods for analyzing
anti-hormonal treatment resistance
in breast cancer
One in eight women are affected by breast cancer. Most of them receive hormonal therapy. Neoadjuvant hormonal therapy is a form of hormonal therapy given before surgery. Treatment for 6 months causes tumours to shrink, after which residual tumour is removed by surgery. Unfortunately, in some cases, the tumour cells are resistant to hormonal therapy and the patients relapse. This can be caused by intra-tumour heterogeneity: hormonal therapy eliminates drug-sensitive clones, leaving behind resistant clones. Understanding why some clones are resistant and what their characteristics are may lead to the development of alternative therapies.
We compare DNA copy number profiles before and after treatment in
the case of ER+ breast cancers. Very low depth sequencing was performed (Illumina GAIIx technology) on biopsies from breast tumours, before and after treatment. Reads were aligned to the human genome hg19 (bwa). CNAnorm was used to partition reference genome in intervals G = (i1, ...,in)
of non-overlapping sliding windows. Number of reads was converted to a count vector C = (c1, ...,cn) and then to a ratio vector with respect to a pool
of normal female DNA.
Hormonal therapy
Treatment
resistant clone
Residual tumour
Clone as a part of
numerous tumour
sub-‐popula9ons
Bam files available in the NCBI Sequence Read Archive under accession number SRP035504
C1 C2 . . . Cn
i
n> A T C G A T C A T G A C T A C A G A T A >GATCATGACTATCATGATCATG > A T G C A C A C G T T C A G G A T C A T > A C G A T A A T G A C T A C A G A T A > T G A C T A C C A T A T A T A C A G A T A >TCTAATAGCCATAGTAATAAGT >GCTTATAGCTAATCGTACATAT > T A T C G A T C A T G A C T A C A G A T A >GATCATGACTATCATGATCATG > A T G C A C A C G T T C A G G A T C A T > A C G A T A A T G A C T A C A G A T A > T G A C T A C C A T A T A T A C A G A T A >TCTAATAGCCATAGTAATAAGT >GCTTATAGCTAATCGTACATATT >CTATTGAACATAGCATGACATGA
Mapping Binning Segmentation
C’1 C’2 . . . C’n Before After ●●●●●●● ● ● ●● ● ● ● ● ● ● ● ● H09 ● ●●●●●●● ● ● ●● ● ● ● ● ● ● ● ● 0.5 1 2 4 8 0.5 1 2 4 8 Before treatment After treatment ESR1
Tumour DNA
Before treatment
Cons9tu9ve DNA
ADer treatment
Tumour DNA
WHOLE GENOME SEQUENCING AND ANALYSES
Reference genome ...AGTCATTAGGACATGCCTAGCTGAATGA… > CCATTAG >ACGGGCCTC >GAATTGG >TGCACCTAG >… > GCCATTAG >ACGGGCCT >GAATTGGCT >TGCATATAG >… >AGCCATTAG >ACATGCCTCT >GAATTGGCT >TGCATA >… Tumour DNA Before treatment Tumour DNA A5er treatment Cons7tu7ve DNA
=
>AGTCATTAGG+
>ACATGCCTCT >GAATTGGCTA >TGCATATAG >… >AGTCATTAGG >ACATGCCTCT >GAATTGGCTA >TGCATATAG >…=
>AGTCATTAGG+
>ACATGCCTCT >GAATTGGCTA >TGCATATAG >… >AGTCATTAGG >ACATGCCTCT >GAATTGGCTA >TGCACCTAG >…+
>AGTCATTAGG >ACATGCCTCT >GAATTGGCTA >TGCATATAG >…tumour
=
heterogeneous
popula9on
Varia9on
iden9fica9on
Genomic
varia9on
comparison
Future work: We will reconstruct tumour from point mutations, copy number
aberrations and their distribution in the clones. This analyses allow the identification of different cell populations present in the tumour, their proportions and genomic variations but also the phylogenetic links between them to understand mechanisms of clone resistance and characteristics of resistant clones
Justine Rudewicz
12345, Hayssam Soueidan
14, Audrey Gros
123, Gaetan MacGrogan
123, Hervé Bonnefoi
123, Macha Nikolski
345and Richard D Iggo
1231. Institut Bergonié Comprehensive Cancer Centre, 2. INSERM U916, 3. University of Bordeaux, 4. Bordeaux Bioinformatics Center, 5. CNRS UMR5800, Bordeaux Computer Science Lab
Sample H09: new amplicons appeared in the copy number
profile after treatment, including an amplicon on chromosome 6q containing the ER gene (ESR1). In the same way, the normalized segmented copy number ratio of the individual ESR1 gene before and after treatment shows this amplification. FISH confirmed that the amplicon was present after treatment.
r
1r
2.
.
.
r
ni
nBefore treatment ● ● ● ● 1 2 3 4 0.0 0.2 0.4 0.6 0.8 1.0 Ploidy Relative density
Ra9
os
re
la9
ve
d
en
si
ty
Copy number
Density of ratios was used to identify different ploidy levels and to assign it to overall intervals G.
Green: ESR1 probe ; Red: Chr 6 centromere probe
Very low depth sequencing indicates that there is a clonal selection under anti-hormonal treatment. To confirm our finding and better characterise clonal evolution during estrogen deprivation, we will perform deep sequencing of constitutive and tumour DNA before and after treatment.
