1. Chromosomal instability and chromothripsis as a prognostic factor for metastatic colorectal cancer
Elina Skuja, Dagnija Kalniete, Miki Nakazawa-Miklasevica, Zanda Daneberga, Arnis Abolins, Gunta Purkalne, Edvins Miklasevics
Pauls Stradins Clinical University Hospital, Riga, Latvia
Riga Stradins University, Riga, Latvia
Pauls Stradins
Clinical University Hospital
Background
Materials and Methods
In 10 tumor samples (52.6%) we found multiple chromosomal fragmentations (>100 breakpoints detected at one chromosome) – chromothripsis. The most affected chromosomes were chromosome 1, chromosome 2 and chromosome 6 (52.6% of patient). The maximal count of chromosomes affected with chromothripsis in one tumor sample was 20; this was seen in one patient. Survival data. Progression free survival (PFS) and overall survival were measured for all patients in study. The patient had 3 to 48 months of follow up.
We observe:
slight correlation between high BPI and longer PFS. mPFS for BPI ≥1400 was 14 months, mPFS for <1400 was 8 months (95%CI , p=0.03).
Chromothripsis was associated with better survival. mPFS in patient with chromothripsis was 14 months, but in patient without detectable chromothripsis – 8 months ( HR 3.92, 95%CI , p=0.02).
We didn't observe statistically significant impact of any clinical or biological factor on overall survival in our study, which could be explained with small patient number and different second and third line chemotherapy and selvage treatment strategies.
Impacts of chromosomal rearrangements, mutations on pathogenesis, prognosis and treatment resistance, are widely described in metastatic colorectal cancer. Chromothripsis is massive chromosome fragmentation occurred in one catastrophic cell crisis observed in 2-3% cancer samples (1). Such genomic rearrangements can drive the development of cancer through several mechanisms including deletion of tumor suppressor genes and increased copy number of oncogenes. Chromothripsis has been associated with poor patient survival in several cancers (2,3), indicating it’s potential relevance as a prognostic marker, and suggesting chromothripsis as a feature of some particularly aggressive forms of cancer. Chromothripsis incidence and impact on survival in colorectal cancer is unclear, but this could be prevalent genomic rearrangement (4).
DNA was extracted from the formalin-fixed paraffin-embedded (FFPE) samples with QIAamp DNA Mini Kit (Qiagen) according to the instruction of the manufacturer. DNA quality was evaluated with Illumina FFPE QC Kit (Illumina) using RT-PCR. DNA was restored using Illumina DNA restoration Kit (Illumina). Microarray analysis was performed using Infinium HumanOmniExpress-12 v1.0 FFPE BeadChip Kit. BeadChip was imagen on HiScan (Illumina). Data was visualized and analyzed by GenomeStudio (Illumina) software.  Analyses were performed using R version Copy number variation and break points on the chromosomes were analyzed by using "DNAcopy" package.
Overall survival and progression free survival rates were estimated using the Kaplan-Meier method. The log-rank test was used to calculate any significant difference between the subgroups by univariate analysis. Significance levels were set at p< All statistical analyses were performed by using MedCalc.
Results
The highest number of breakpoint was seen in chromosome 1 ( breakpoints), followed by chromosome 2 (25-315), suggesting importance of these chromosomes in colorectal cancer genesis.
The lowest density of breaks occurred at chromosome 21 (7-99breakpoints).
Total number of breakpoints per genome in cancer sample – breakpoint instability index (BPI) – was
Conclusion
In our study, we found a correlation between DNA massive fragmentation – chromothripsis and PFS in metastatic colorectal cancer. As opposed recent studies suggested chromothripsis associated with worse prognosis, we find chromothripsis as positive predictive factor to chemotherapy.
Chromothripsis and breakpoint instability index per se did not show better OS in all cases, we suggest it is one of multiple factors predicting treatment response and prognosis.
Age
63.15 (38-78)
Gender:
Male
Female
11 (57.89%)
8 (42.11%)
Tumor localization:
Left part – sigmoid colon cancer, rectal cancer
Right part - Colon cancer
Grade:
Unknown G2 G3
1 (5.26%)
13 (68.42%)
5 (26.32%)
Metastases:
Synchronous
Metachronous
Median time to metastases moths (9-18)
Stage II – 3 patients
Stage III – 1 patient
15 (78.95%)
4 (21.05%)
Liver only
other
10(52.63%)
9(47.37%)
KRAS status in primary tumor:
Wild type
Mutation in 12 codon
Mutation in 13 codon
Not known
10 (52.64%)
7 (36.84%)
Serum CEA before chemotherapy:
CEA ≤5.5 ng/ml
CEA >5.5 ng/ml
Level of CEA, ng/ml
12 (63.16%)
232.1 (7.1 – 959.8)
Median follow up (months)
25.5 (3 – 48)
mPFS
1year PFS
2 year PFS
8 months
33.3%
5.6%
mOS
1 year OS
2 year OS
3 yearOS
21months
78.9%
42.1%
21.1%
Materials and methods
19 metastatic colorectal cancer patients who received FOLFOX type first line chemotherapy in Clinic of Oncology of Pauls Stradins Clinical University Hospital in Latvia in 2011 – 2012 where selected for this study.
The study was performed with approval from the ethics committee of Riga Stradin’s University
Written informed consent was taken from each patient who underwent study.
Tissue samples were previously acquired as part of series of routine diagnostic and pathological analyses in our hospital.
Acknowledgements
References:
Stephens PJ, Greenman CD, Fu B, et al. Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development. Cell. 2011;144(1):27-40.
Magrangeas F, Avet-Loiseau H, Munshi NC, Minvielle S. Chromothripsis identifies a rare and aggressive entity among newly diagnosed multiple myeloma patients. Blood. 2011;118(3):
Rausch T, Jones DTW, Zapatka M, et al. Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53Mutations. Cell. 2012;148(1-2):59-71.
Kloosterman WP, Hoogstraat M, Paling O, et al. Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer. Genome Biology. 2011;12(10):R103. .
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